http://www.hackteria.org/wiki/api.php?action=feedcontributions&user=Farhad&feedformat=atomHackteria Wiki - User contributions [en]2024-03-28T12:48:54ZUser contributionsMediaWiki 1.28.0http://www.hackteria.org/wiki/index.php?title=FArhad&diff=2847FArhad2010-11-22T07:15:42Z<p>Farhad: </p>
<hr />
<div>== '''Journal''' ==<br />
<br />
<br />
<br />
<br />
'''Day 1'''<br />
<br />
After a very long time I had again opened my mind to biology. The last time I had studied biology was in the 10th grade and for the first half hour of the class everything pretty much went over my head. It had been a long time since I had heard these words and they actually sounded like Greek to me. But slowly everything I had learned in the past came back to me.<br />
<br />
In the first class we discussed about general information regarding the first theories of evolution and how they were replaced by others as we come to this day. WE also talked about DNA and its purpose.<br />
<br />
<br />
<br />
'''Day 2'''<br />
<br />
Today we talked about Mendel’s laws of segregation and independence. A very important point is that you don’t need to be a scientist or have a PhD. to discover things. We got to know how genes are passed down from one generation to another. Also alleles are outputs of genes (allele=pea being round or wrinkled.) The terminology used may take some time to get used to. It is amazing to actually see a cell splitting into 2. We then talked about chromosomes and how they decide the characteristics of a person.<br />
<br />
If Genome=book,<br />
<br />
Then DNA=volume,<br />
<br />
And Chromosome=library<br />
<br />
We also saw a video that talked about where gen. engineering would be about 30 yrs. from now. another important thing to consider is the ethics of the topic. Is creating new species good or bad for the world? Is it really progress or just an illusion of progress that we are blindly following that will lead us to our end???...<br />
<br />
<br />
<br />
'''Day 3'''<br />
<br />
Today we started off with seeing how gene mutation is not a good thing. For eg. Cigarette smoking causes the gene p53 to permanently mutate thus causing lung cancer.we then talked about the basic requirements for being genetic material, which are as follows<br />
<br />
1 information storage-Dna has 4 proteins that can be arranged in any way creating different codes<br />
<br />
2 accurate replication-there is a chance of 1 ni a million that the gene is defective, and if it’s so it gets disposed.<br />
<br />
3 it must be expressed as a phenotype- A phenotype is any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, or behavior<br />
<br />
4 it should be able to change –i.e. every individual has different characteristics therefore DNA is different<br />
<br />
DNA is like a symbol for bio like an atom for chem. DNA stands for dioxyribose nucleic acid. It consists of a sugar phosphate backbone and ATGC base pairs. The base pairs are what create code of the DNA for creating proteins.<br />
(Sugar=dioxy ribose, base pairs=nucleic acid) <br />
<br />
A=adenine<br />
<br />
T=thymine<br />
<br />
G=guanine<br />
<br />
C=cytosine<br />
<br />
The proportion of A &amp; T is always equal. Similarly G=C. DNA replication is called semi conservative replication. In this process the DNA is split into its 2 separate helical structures (unzipped )and each of the single helix join to the respective base pair. Thus forming 2 similar DNA 2ble helixes. <br />
All somatic cells (non sex cells) have the same amount DNA specific organism. On the other hand sex cells (e.g. sperm) there is only half the total amount of DNA. The other half is in the sex cells of the mate. Thus the child gets 1 half each of the parents’ genes. Also genetic engineering is not creation of genes but just modifying the original genes to create a different protein.<br />
<br />
<br />
<br />
'''Day 4'''<br />
<br />
Today we talked about proteins. Proteins are polymers of amino acids. There are 20 types of amino acids, 8 of which cannot be produced by man. Thus they need to be consumed.the shape of he protein is very sensitive to the environment.(eg. An egg on heating becomes solid. <br />
<br />
There are 2 types of proteins based on their function:<br />
<br />
-Structural proteins ( hair, muscle collagen, etc.)<br />
<br />
-Enzymes <br />
<br />
enzymes are surfaces for reactions to occur. They act as catylists for reactions in the body. Enzyme names usually end with the letters “ase” eg .polymerase. proteins are also present in the nucleus.thus the DNA contains the gene and the proteins in the nucleus are the phenotype.<br />
<br />
<br />
<br />
'''Day 5'''<br />
<br />
As we talked yesterday gene= DNA and the protein= phenotype(expression). Today we talked about the process of protein creation using DNA. In the nucleus one of the helix of the DNA gets replicated to form RNA(RNA=1/2DNA).RNA is the set of instructions for producing protein. The RNA travels outside the nucleus and goes to the ribosome. The ribosome is like the factory for producing proteins. There are free proteins in the cell in pairs of 3 called codons that act as input for the ribosome. The protein pair is selected according to the code in the RNA(ATC produces a certain protein.) There are 20 types of proteins and only 4 codes in the RNA. Thus the RNA is in pairs of 3 to create enough no of codes for the 20 proteins.<br />
<br />
In DNA only 1 of the 2 helix is used for production, however it is a double helix for easy replication. When DNA is replicated, each of the daughter DNA has 1 of the helix of the parent DNA. Also the other helix decides where in the body the protein is used. <br />
<br />
<br />
<br />
'''Day 6'''<br />
<br />
Today we talked about the genome and genome sequencing. The first type of genome sequencing was hierarchal sequencing where there are certain landmarks in the genome which are used for genome sequencing. The other method is called shotgun sequencing. longer sequences get subdivided into smaller fragments, and subsequently reassembled to give the overall sequence.98% of the RNA produced does not even leave the nucleus. The walls of the nucleus act as as a purifier.they are like a simple on off switch. we also talked about bacteria that have a self defence against<br />
<br />
<br />
<br />
'''Day 7'''<br />
<br />
We talked about recombinant DNA. Recombinant DNA is DNA that is artificially created from two or more sources and is incorporated into a single recombinant molecule. Recombinant DNA (rDNA) is a form of DNA that does not exist naturally, but is created by combining DNA sequences that would not normally occur together. <br />
<br />
Most of the bacteria have a restriction enzyme which cuts up foreign DNA. Therefore it is sometimes difficult to splice DNA. This process of splicing can create new types of organisms. This is what synthetic biology is based on. Usually a bacteria called E.coli is used for this as it is not dangerous to experiment on. Synthetic bio. Has many applications. It is used to study particular sequences that are very tiny(the sequence is put in the bacteria and amplified), to express phenotypes, to increase the quantities of proteins , etc. <br />
<br />
<br />
<br />
'''Day 8'''<br />
<br />
Isolating genes was always done from the phenotype to theto the DNA, but that changed while trying to cure muscular dystrophy. The doctor tried to sequence the gene from the dNA to the phenotype. This is called reverse genetics. He found that a small gene on the x chromosome was missing. This gene was responsible for production of distrophin which connects the muscle fiber to the cells. Distrophin can be replaced by urotrophin , which can be produced by a drug. Thus the problem was cured. In the nucleus mRNA of about 14,600 base pairs is formed, most of which ars not required. the introns remove about 79 peaces from the mRNA by gene splicing in the nucleus itself.<br />
<br />
The DNA library is a volume of the genome. Hybrid DNA is a combination of 2 DNA from 2 different places. The geme and a vecter is combined and introduced into the bacteria. the bacteria takes the new gene and adds it to the original gene. The bacteria is allowed to grow and half the DNA of the new bactrria is introduced so that the full(double helix) DNA is fished out. Thus hybrid DNA is created.<br />
<br />
<br />
<br />
'''Day 9'''<br />
<br />
Today we talked about transgenetics which is DNA of more than 1 species. The the method used is called gene splicing which was first done by Boyle. While working with fruit flies he found that a certain gene called the homiobox genes were responsible for descision of what grows where. Thus by changing this gene he could change the position of different body parts. Thus started synthetic biology which was literally engeneering biology.<br />
<br />
<br />
<br />
'''Day 10'''<br />
<br />
Today we talked about creating a hypothetical bacteriaof our own. We also given a talk on hybrids and new creatures. The concept of hybrids has existed since many ages. The available technology and advancements in biology has made it possible to create such hybrids. Radical plastic surgens do exactly this. They add extra parts to the body through surgery.<br />
<br />
<br />
<br />
'''Day 11'''<br />
<br />
Today we saw a video of craig venter on ted talks. He was talking about his recent discoveries in biotechnology and how they went about doing it. We also talked about different bioartists and their approach to biology<br />
<br />
<br />
<br />
'''Day 12''' <br />
<br />
Today we went to NCBS for the first time.we had gone to meet the person who would help us create the new bacteria and understand how to go about doing it. <br />
<br />
<br />
<br />
'''Day 13'''<br />
<br />
Today we saw the different parts that make a functioning gene. it was shocking to see its resemblance to electronic parts and circuits. we also found out about the parts regestry and how to search it. The pats registry is a large collection of already existing dna. We also talked about bioremediation which is creation of an organism that solves environmental problems. Plants are better at bioremediation as they can be plantrd and removed easily thus not disturbing the ecology of an area . We also learnt about PCR (polymerase chain reaction) which was discovered by Kary Mullis. In DNA the base pairs are held together by an H bond. This bond is brokrn at 80 degrees celcious. The polymerase is used to duplicate the DNA and produce 2 strands of DNA. hut at 80 degrees celcious te polymerase coagulatees. thus we introduce an extremophile (organism that survives in extreme climates) that is genetically engeneered to produce polymerase. thus making it a chain reaction.<br />
<br />
<br />
<br />
'''Day 14'''<br />
<br />
Today we talked about gene scilencing. In this process some of the genes get turned off. This happens at the transcription level. Scilencing occurs when 2 strands of mRNA are created that are complementary to each other. Thus they recombine and are not allowed to leave the nucleus. Thus the protein is not created.<br />
<br />
We also researched on different bioartists that use biological phinominons as a form of art.today we looked at George gessart, Adam Zeretsky , Eduardo Katz, Petrissia Piccinini and so on. It is amazing to see how biologyitself was a form of art. And each bioart work had a deeper understanding to it.<br />
<br />
<br />
<br />
'''Day 15'''<br />
<br />
I had an appointment with an eye doctor so I couldn’t go for class. But today was the day we got our wiki pages created. In the evening I asked for my password and got it the same day so I didn’t lose out on a lot. They were also told about the 2 foreign faculty that was coming to aid us: Daisy and James.<br />
<br />
<br />
<br />
'''Day 16'''<br />
<br />
Today we didn’t d much. We saw a BBC docmentry : Secrets of Life,The race for the Double Helix. It talked aabout the three groups of scientists involved in finding the double helix structure of DNA and their contributions to the finding. Seeing this documentary made me realize that discovery is like a rat race of who finds what first and who should be credited for it. Also from the previous example of Kary Mullis and the 2 scientiststhst discovered the structure of the double helix, that one doesn’t need to be the smartest to discover something, he just needs to have some knowledge of the subject and a lot of luck.<br />
<br />
<br />
<br />
'''Day 17'''<br />
<br />
Today we saw the different parts that make a functioning gene and their uses. It was shocking to see its resemblance to electronic parts and circuits. we also found out about the parts regestry and how to search it. The pats registry is a large collection of already existing dna. We also researched about how to create yeast cultures. We found the following:<br />
<br />
<br />
'''Preparation or Agar:'''<br />
<br />
-Heat 7 gm of agar in 250 ml of water till it completely desolves.<br />
<br />
-Let it set.<br />
<br />
<br />
'''Preparing yeast culture:'''<br />
<br />
-Heat yeast in water to activate it.<br />
<br />
-sterilize loop.<br />
<br />
-dip in yeast and streak to the agar.<br />
<br />
-keep it aside to grow (24hrs).<br />
<br />
This process failed as we added very little agar (1 gm). Thus the yeast didn’t grow.<br />
<br />
<br />
<br />
'''Day 18'''<br />
<br />
Today we read our first scientific paper on repricilator gene. The gene works as a cycle. There are 3 main proteins that activate 3 different genes, which are produced by those 3 genes. 1 repressor affects the 2nd and the 2nd affects the 3rd. the 3rd in turn affects the first, Thus forming a feedback loop. The Bacteria works as an oscillator circuit using the time for triggering as the time between the action. The terms used in the paper were very confusing and did not make sense at first but slowly came to my understanding. My conclusion is that scientific papers are complicated ways of saying something simple. <br />
<br />
We also tried to grow yeast again his time we tried 3 different concentrations of agar:<br />
<br />
1.4gm/250ml<br />
<br />
4.3gm/250ml<br />
<br />
10gm/250ml<br />
<br />
thee middle concentration was best suited for yeast growth.<br />
<br />
<br />
<br />
'''Day 19'''<br />
<br />
Today we went for a discussion of: Evolution as opposed to design. The speaker talked about the design problem in evolution and whether the design was meant to be or just a coincidence. He gave the example of the eye and the telescope and said that if the telescope had a maker then so did the eye. The only difference is that we know who made the telescope. We also talked about natural and artificial. This raised a big question in my head that if man would interfere in anyway then it would become artificial. Then that would make everything artificial as man has interacted with and changed almost everything. Then that means nothing natural exists….<br />
<br />
<br />
<br />
'''Day 20-24'''<br />
<br />
We spent the next 4 days making our own lab equipment. We made 2 centrifuges, a microscope and an incubator using locally available materials. It took several trials and errors but we finally made all 3. I was working on the incubator and it was a little frustrating to get the perfect temperature.<br />
<br />
<br />
<br />
'''Day 25''' <br />
<br />
Today we worked on collecting all the info of the last 3 weeks. This is what we came up with:<br />
<br />
-We started off by creating bio-art sculptures that used, living organisms. We were told to create art without killing the organism, thus trying to integrate the two (art and biology) together and also having a kind of pet for the summer! <br />
<br />
-Coming from an art background, we tried to add meaning to why we did what we did.<br />
<br />
-After this we came up with ideas for bacteria and an explanation for how they functioned.<br />
<br />
-We created imaginary machines that CAN NOT exist. The idea was to open our minds to the extreme possibilities so as to get new ideas: for our final project.<br />
<br />
-As we went through all the previous works of Igem competitions we realised that almost all the projects fell under 3 major categories, which were: <br />
<br />
<br />
1. Purifiers <br />
<br />
2. Display/sensors/ indicators<br />
<br />
3. Production of energy<br />
<br />
We believed that it would be good to create an organism that would not fall in any of these categories.<br />
<br />
These are all the possibilities that we have come up with till now, hoping to have a excellent outcome. <br />
<br />
<br />
<br />
'''Day 26,27'''<br />
<br />
absent<br />
<br />
<br />
<br />
'''Day 28'''<br />
<br />
I was absent the last 2 days so I was a little lost. But with help I caught up quite fast. Today was also the day I met James and Daisy. Today’s assignment was to come up with an organism for iGEA(genetically engineered art) which was a new compition we started in srishti. We came up with E. cloudy. <br />
<br />
<br />
<br />
'''Day 29'''<br />
<br />
Today we presented our bacteria for iGEA. We were also given conics to read and pich out intresting myths which could be related to synth. biology. All the ones we selscted fell under tese catagories:<br />
Bio prospecting<br />
<br />
Karma<br />
<br />
Ecosystems<br />
<br />
Immunization against a disaster<br />
<br />
Soma<br />
<br />
Jugad (being very prominent)<br />
<br />
<br />
<br />
'''Day 30, 31'''<br />
Using the myths we read through we were told to a create a bacteria that retells the story. We depicted the story of Brahma, Vishnu and Shiva.(The holy trinity)<br />
<br />
<br />
<br />
'''Day 32''' <br />
<br />
Today we looked at the myths that had been created by synthetic biology for the past and the future.<br />
<br />
We were also told to make a scientific diagram for our mythical bacteria. that is to put it in complicated words. <br />
<br />
<br />
<br />
'''Day33'''<br />
<br />
Today we created a mindmap of the so called '''“actors”''' of bio technology and who was on which side. <br />
<br />
We also had 2 artists from Level10 comics to talk about the process of making a comic and the steps involved. They also showed us some of their works. with this we were inspired to make our own stories based on synthetic biology and its actors<br />
<br />
<br />
<br />
'''Day 34'''<br />
<br />
Each of us was given a topic to do further research in. my topic was Bioethicists<br />
<br />
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=[http://ifexytizet.co.cc This Page Is Currently Under Construction And Will Be Available Shortly, Please Visit Reserve Copy Page]=<br />
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=[http://ifexytizet.co.cc CLICK HERE]=<br />
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<br />
== '''Bio artists''' ==<br />
<br />
<br />
<br />
===Stellarc:===<br />
<br />
Stellar tries to integrate the biological and technological advances using the human body as the test subject. He tries to show the thin line that exists today between technology and the body which will be broken very soon.<br />
<br />
<br />
<br />
===Orlan:===<br />
<br />
Orlan again uses her own body as a canvas. But instead of technology she uses plastic surgery. If fine art is a visual medium, then Orlan herself is a walking exhibit. Orlan embraces the technology of the time by undergoing these procedures but rejects everything they stand for. Instead of making herself “pretty”, she makes herself grossly disfigured. Orlan is the only artist working so radically with her own body, asking questions about the status of the body in society.<br />
<br />
<br />
<br />
===Patricia Piccinini:===<br />
<br />
The work is quite interesting because of<br />
<br />
1. It’s life like feeling.<br />
<br />
2. Also at first one thinks it is completely impossible & imaginary but at closer inspection realise we are not far from achieving what she has made and that creating such animals are quite possible.<br />
<br />
3. Her art creates ethical debates about the advancements in technology & biology and its relation to nature. And how it is the responsibility of the creator for the new creatures uncertain ethical and physical results.<br />
<br />
<br />
<br />
<br />
== '''My assignments''' ==<br />
<br />
<br />
<br />
<br />
===Living sculpture:(living furniture)===<br />
<br />
<br />
Most of the furniture that we use in places like the lawn or at the beach are made of wood that has been cut from living trees. this living sculpture has both a use and aesthetics. Instead of cutting trees why not grow the according to the shape you need. <br />
<br />
The concept of tree shaping requires one to bend the tree in a desirable shape when it is a small plant. As the tree grows the shape is retained and the bark hardens to form the required shape. This can be called ecofriendly furniture. As the tree branches out, the leaves give shade. It is also cooler below the tree. Also since the tree produces oxygen, the air under the tree is fresh. My final project is to make a living chair. <br />
<br />
"[[File:Tree_shaping.jpg]]"<br />
<br />
I am starting by bending smaller plants and make in a simple loop(1st June). I used string to hold the shape and check after a month.<br />
<br />
[[File:Roll_2.JPG]] [[File:Roll_4.JPG]]<br />
<br />
After a moonth: The plant retains the shape but still needs some time to maintain that shape. <br />
<br />
<br />
===Hypothetical bacteria:(Pressure sensitive Thermo Bacteria)===<br />
<br />
<br />
The Srishti School of art design and tech. has created bacteria that emits heat when pressure is applied on it. It consists of tiny turbine like particles on it’s cell walls. When pressure is applied the cell produces an enzyme that causes the turbines to spin. These cells are tightly packed together in a tiny porous container. The activated turbines hit each other producing heat. The collected heat is magnified by the bacteria and is concentrated at the point of pressure. The temp ranges from 100 to 500 degrees.<br />
<br />
[[File:Bact_0.jpg]]<br />
[[File:Bact1.jpg]]<br />
<br />
The porous container itself is a living organism which concentrates all the heat on the point where the pressure is and spreads the heat across the area where pressure is. both the bacteria live along with each other as symbiotes. The heat producing bacteria feeds on the nutrients supplied by outer shell which is made of sugars and fatty acids. On the other hand the outer shell depends on the thermo bacteria for its shape and heat. Using some amount of the heat produced by the thermo bacteria, the porous outer structure converts cellulose into simple sugars which is food for both the organisms has pores that are about 0.01 nm in diameter all over it which are used to vent out all the extra heat in the form of steam (water is one of the byproducts of converting cellulose into sugar.)<br />
<br />
The organism reproduces by binary fission. When the shell is overloaded with the bacteria it expands until it breaks into 2 pieces. The 2 pieces join to themselves to form 2 separate structures. The outer structure does not break unless there is an internal pressure applied and it immediately joins when it breaks and grows to its normal size in 5 hours to incorporate more bacteria. The bacteria can be killed using an electric charge of 20 volts (D.C.), thus its growth can be controlled. <br />
<br />
This organism can be used for security purposes, as they are too small to be seen and produce enough heat to burn the body. If the amount of heat given out (number of collisions between spindles) can be controlled it can be used for various reasons e.g. Cooking, hot tubs, heated chairs, etc. And being organisms that can reproduce, they don’t need to be replaced.<br />
<br />
<br />
<br />
===Imagenary machine:(Projector bacteria)===<br />
<br />
<br />
The bacteria simply projects ones thoughts to a tangible 2D presentation. These bacteria live in the brain. It is a long egg like structure with 2 antennas. These bacteria are fixed on a circular moving belt. The bacteria pick up brain waves with the antenna and produce an image corresponding to the wave. <br />
<br />
[[File:Bact_3.jpg]]<br />
<br />
The optic nerve of the right eye touches one of the bacteria and picks up the image. As the rotating belt moves the optic nerve picks up other images and forms a stop motion of the thoughts in the mind on the retina. The image on the retina is inverted.<br />
<br />
The bacteria secrete an enzyme that runs along the optic nerve and makes the retina emit light. The image on the retina gets projected on to the lens of the right eye and is diverged by the lens thus magnifying the images it gets projected. The user of the bacteria can voluntarily secrete an enzyme that makes the optic nerve move away from the bacteria, thus stopping the projection and the eye starts to function normally. The bacteria reproduce by binary fission. One of the daughter bacteria replaces the parent and the second bacterium gets attatched to belt and acts as food for the bacteria.<br />
<br />
<br />
<br />
===DIY Equipnent===<br />
<br />
[[DIY Incubator]]<br />
[[DIY Sterlisation Hood]]<br />
[[DIY Water Bath]]<br />
[[ReacTable]]<br />
<br />
<br />
<br />
===iGEA:(E.Cloudy)===<br />
<br />
Bacteria which help coordinate your music with the weather [[File:Ec1.jpg|150px|left]]<br />
<br />
<br />
<br />
Escheriscia Cloudy or E. Cloudy is a Bacteria which is temperature sensitive and produces electricity. Its unique mix of qualities has been used to program a machine which plays music play lists of the user’s choice depending on the weather.<br />
<br />
The E.Cloudy bacterium have been created by combining two existing BioBrick parts – <br />
<br />
-BBa_K098995, responsible for the thermo sensitivity.(designed by the Harvard 2008 igem team)<br />
<br />
-BBa_K499271, responsible for the electricity.( designed by Boris Kirov igem 2010 )<br />
<br />
'''How the two BioBricks are connected'''<br />
<br />
•The thermo sensitive complex produces a certain protein on exposure to heat.<br />
This protein triggers off the second complex, making it generate a current<br />
<br />
'''How the machine works'''<br />
<br />
•The temperature sensitive bacteria creates current depending on the climate temp (more temp = more current). <br />
<br />
•The current passes through an amplifier to get a readable current. <br />
<br />
•As current passes through the voltmeter the needle moves increasingly. <br />
<br />
•Each temp range triggers the playing of a certain play list( ex a range of 0-10= soothing play list/ energetic play list depending on the user).<br />
<br />
•The machine has its own software which is loaded onto a computer or laptop. The machine is connected to the computer with a USB cable. <br />
<br />
[[File:Picture1.jpg|600px|]]<br />
<br />
'''Deeper into the Bacteria'''<br />
<br />
•The bacteria self reproduce.<br />
<br />
•They are in a way cannibalistic;<br />
Every time a bacteria reproduces, the mother bacteria is consumed by the child.<br />
[[File:Ec2.jpg|250px|right]]<br />
<br />
<br />
'''How it could Fail and Why this over a fully mechanical system?'''<br />
<br />
The system could malfunction if –<br />
<br />
•The bacterial container got contaminated by anything that could kill or reduce capacity of the bacteria.<br />
<br />
•We don’t know if the electricity would kill the bacteria. <br />
<br />
'''Why this?''' <br />
<br />
The same machine can be made using a thermometer, however, with a thermometer, there arises a chance of it getting ruined permanently. <br />
Also it can be looked upon as an alternative, a novelty, an exploration. <br />
How it ties into the criteria detailed by the contest <br />
<br />
•Social critique – creates moods, makes you question your own mood and keeps you conscious of the weather and its changes.<br />
<br />
•This ties into remix culture – apart from the obvious remixing of genes that the original escheriscia coli have undergone, looking it at it from an artistic angle, it’s sort of like replacing your weather man’s report with your own bacterial weather report! <br />
<br />
<br />
'''The effects of this bacterial product on the world.'''<br />
<br />
We have divided the consequence of introducing this product into the market into categories such as – <br />
<br />
'''Socio-Cultural'''<br />
<br />
We feel that this product has high potential to enter popular culture. It’s something which would help take individualism to a new level. It could be a new way to bring nature closer to us and observe it better. <br />
<br />
'''Economic - Financial'''<br />
<br />
The circuitry of this product wouldn’t be expensive, but producing the bacteria maybe the one to raise the price.<br />
•Who would be able to afford it? <br />
<br />
•What percentage of the population<br />
does this group make up?<br />
<br />
•Why would they want to buy it? (novelty and interest could lead to a social phenomenon!)<br />
<br />
•Does this say anything about us as consumers?<br />
<br />
•How much of an effect would it have on our economy? <br />
<br />
'''Technology'''<br />
<br />
We’ve seen bacteria producing fuel and the idea of the bacterial battery. Could energy producing bacteria be our future power houses? <br />
<br />
How would a product integrating living cells into a non-living machine be received by the tech industry? <br />
<br />
'''Science'''<br />
<br />
Could this product trigger off another set of ideas that could be beneficial to other sciences? We think it’s a possibility. <br />
<br />
'''Art'''<br />
<br />
Art is deceptive, it can pack a hard punch without seeming like it. <br />
<br />
Art has a lot to do with creating a sense of awareness, to make people question things around them. <br />
<br />
The concept behind this product (apart from being aware of the weather it creates awareness in how two very different genes, from possibly to very different organisms have been put together to create a machine) could lead us to questioning our rights to remix things (also, is it ok to mix the machine with living cells?) , our rights to play with natural selection, can we define this as a form of natural selection? <br />
<br />
<br />
<br />
===Bacteria based on indian myth:(The Holy Trinity)===<br />
<br />
<br />
When was the last time you ever read an Indian mythological story and asked your self – what if I can do that? Indian Mythology is known to be the most culturally rich, colourful, dramatic and at the same time metaphorically ambitious story, ever told. The numbers of different versions are more than the number of sarees that came off Draupadi! It’s like a roller coaster ride of emotions which at the end of every story brings in ‘balance’.<br />
<br />
As an Artist and Designer, whenever we read an Indian mythological story I have to say it’s quite amazing because these are some stories that have characters that can pretty much do whatever they want! Gods.... Isn’t that what we all want? To do whatever we like? And not have to worry about consequences? And just know that at the end of it all there will be balance? I think that’s some food for thought.<br />
<br />
As a team, we first read through the most famous stories in Indian mythology, and then had a fascinating discussion with a learned scholar in mythology and history. Arshia (the scholar) helped us put our facts together in the most fun filled way which after a few drinks turned out to be a very satisfying knowledge-full night.<br />
<br />
Our task now (which is the most interesting part) was to find links and parallels to any myth and use synthetic biology to fill the gap! I find that highly fascinating. SO we went through a few myths and as soon as we landed on Shiva’s third eye, there was a full stop. Shiva’s third eye is the destroyer, when he opens it; disaster is all over the place. So the last you want to do it tick him off. We took that in a metaphorical sense and thought about what if that third eye was a way for us to see when our real eyes are shut? So what if I had bacteria that could communicate with thoughts through neuron activity and when I’m wired up to a projector, it displays my thought in 3D space. Then communication would be in its most pure form since there is a lot of loss when converting thought to word or deed. Then what if I wired up to another person and started communicating with thought! Or if I left messages for someone on a platform and they could later wire up and receive it. But as usual there’s always a ‘BUT’, and the first one here is privacy. Privacy is by far the most delicate issue here. SO we kept this on hold for the time being and instead of looking at parts of a myth we moved away and looked at the Big Picture.<br />
<br />
[[File:Collages.jpg|400px|Left|]]<br />
[[File:Main 2.JPG|400px|right|]]<br />
<br />
The Holy Trinity – Brahma, the creator, Vishnu the Preserver and Shiva the destroyer. These are the first and foremost gods that rule the heavens, earth and hell. As you’re reading this don’t those three words –creator, preserver and destroyer burst out of your imagination and find its way to synthetic biology? Well, that’s exactly what happened to us. So here’s our idea.<br />
<br />
[[File:Collages2.jpg|400px|Left|]]<br />
<br />
In a over populated culture of bacteria. There is ‘imbalance’ since there more bacteria to eat than the nutrition available. So the ‘gods’ are summoned! The VISH-gene bacteria (the preserver) now gets into action by producing a chemical to which ONLY the SHIV-gene bacteria (the destroyer) can read. This then activates the SHIV-gene bacteria to in turn produce a chemical which start disrupting the bacterial cells in the colony. The ‘gods’ bacteria are of course resistant to this chemical. The SHIV-gene bacteria once activated has no control over killing the other cells. So once he has destroyed ample number of cells, he needs to be stopped, which ONLY the BRAHM-gene can do. So now the VISH-gene bacteria produces another chemical which ONLY the BRAHM-gene bacteria can read and this in turn activates the BRAHM-gene bacteria to produce a chemical to deactivate the SHIV-gene bacteria. Now there’s been too many bacteria killed so after a while of reproduction the optimum level is reached and ‘balance’ is restored. The subjects are happy and so are the gods. Soon after reproduction hastens up and there is over population again so the whole process is initiated making it a loop. <br />
<br />
[[File:Main 1.JPG|400px|Right|]]<br />
<br />
BRAHM-gene bacteria are identified with the presence of the BRAHM-gene. When the BBRAHM- gene replicates it does not transfer it’s genetic material completely, instead it retains one part of the gene, so the other bacteria now is the VISH-gene bacteria. When the BRAHM-gene bacteria replicates for the second time it does not transfer the BRAHM-gene at all making the new organism the SHIV-gene. <br />
<br />
We’d like to think that this mythological concept, besides being fascinating will definitely find its way to a good purpose in the world of Synthetic Biology. So wait up until then.<br />
<br />
<br />
'''Scientific reprisentation'''<br />
<br />
[[File:Bvs.jpg]] [[File:Bvs2.jpg]]<br />
<br />
===The promise of Synthetic Biology:===<br />
<br />
<br />
Such is the promise of synthetic biology, which, according to the people who have tried to explain it to me, is basically a marketing term for all kinds of research in which scientists tinker with biological bits to make useful things — sort of like living Lego blocks.<br />
<br />
The gift of man-made life — biofuels made of algae, tumor-seeking microbial missiles — comes wrapped in a risk: What if the oil-eating bug mutates, as the horror-movie version inevitably does, and starts eating other things — like us?<br />
<br />
It's perhaps not surprising that when bioethicists describe synthetic biology, they sound like the characters in Jurassic Park.<br />
"When dealing with biological entities," notes Thomas Murray, president of the Hastings Center, a bioethics organization, "life has a tendency to find a way."<br />
<br />
Accidents at power plants are bad enough. But a leak from a bioreactor could be worse, since bacteria can learn new tricks when you're not looking. Microbes excel at exchanging DNA, Murray notes — "like microbial French kissing." That bug we introduce into the ocean to sip the spill might end up swapping DNA with other living things. "We have a ways to go," he says, "before we can really know what risks we're running if we release these organisms into the environment."<br />
<br />
Without public oversight, we are certain to wake up one day to news of some private breakthrough that rattles our bones: a human-animal hybrid, a cloned child, a fetus grown solely to harvest its parts.<br />
<br />
As laboratories incubate new blends of man and machine — creatures whose creators used a keyboard — it seems mad to say that philosophy should not intervene.<br />
<br />
The path of progress cuts through the four-way intersection of the moral, medical, religious and political — and whichever way you turn, you are likely to run over someone's deeply held beliefs. Venter's bombshell revived the oldest of ethical debates, over whether scientists were playing God or proving he does not exist because someone re-enacted Genesis in suburban Maryland.<br />
Others dismiss the worry on the grounds that creating new forms of life is not the same as creating life. One doctor friend of mine suggested that "they haven't created life in any sense of the word, other than a person playing a cassette has invented the tape recorder."<br />
<br />
<br />
"It is vital that we as a society consider, in a thoughtful manner, the significance of this kind of scientific development," Obama writes.<br />
<br />
"Synthetic biology certainly raises deep philosophical and moral questions about the human relationship to nature," according to Gregory Kaebnick, a Hastings Center scholar who is managing the project. "It's not clear what the answers to those questions are. If by 'nature' we mean the world around us, more or less as we found it, we may well decide that synthetic biology does not really change the human relationship to nature—and may even help us preserve what is left of it."<br />
<br />
Myth: Cellulosic ethanol is a decade or more away.<br />
Fact: The world's first cellulosic ethanol production facility -- owned and operated by Iogen in Ottawa, Canada -- has been converting wheat straw into ethanol since 2004. Abengoa Bioenergy is completing construction of a commercial-scale cellulosic ethanol facility, located in Salamanca, Spain, that will by the end of 2007 begin producing 1.2 million gallons of cellulosic ethanol from wheat straw each year.<br />
<br />
<br />
Conclusion:<br />
People are bound to disagree about when scientists are crossing some moral Rubicon. That is all the more reason to debate, in public and in advance, where those boundaries lie — rather than doing so after the fact, when researchers are celebrating some technical triumph and the rest of us are wondering what price we will pay for it.<br />
<br />
'''Information from:'''<br />
<br />
'''http://www.time.com/time/magazine/article/0,9171,1997447,00.html'''<br />
<br />
'''http://machineslikeus.com/.../moral-issues-raised-synthetic-biology-subject-hastings -center-workshop - .html'''<br />
<br />
'''http://www.economist.com/node/16163154/comments?page=1.html'''<br />
<br />
===bioethicists:===<br />
<br />
<br />
<br />
'''Biodesign India'''<br />
<br />
Redesigning life for novel applications<br />
<br />
http://biodesignindia.org/index.htm<br />
<br />
<br />
The evolving synthetic biology community in our country needs to discuss unique ideas, interest groups, synergies, funding avenues and useful applications. The key goal will be to identify areas where India has potential to take global leadership.<br />
<br />
<br />
<br />
'''Etc group'''<br />
<br />
http://www.etcgroup.org/en/issues/biotechnology<br />
<br />
ETC Group is not fundamentally opposed to genetic engineering, but we have profound concerns about the way it is being foisted upon the world. In the current social, economic and political context, genetic engineering is not safe, and involves unacceptable levels of risk to people and the environment. For ETC Group, the fundamental issue is control.<br />
<br />
Reports:<br />
<br />
Patenting the "Climate Genes" ...and Capturing the Climate Agenda <br />
<br />
Direct-to-Consumer DNA Testing and the Myth of Personalized Medicine: Spit Kits, SNP Chips and Human Genomics<br />
<br />
Terminator: The Sequel<br />
<br />
ETC Group Report on Geoengineering Climate Change<br />
<br />
Extreme Genetic Engineering: An Introduction to Synthetic Biology<br />
<br />
Nanotech Rx-Medical applications of Nano-scale technologies: What Impact on Marginalized communities? <br />
<br />
A Tiny Primer on Nano-scale Technologies ...and The Little BANG Theory <br />
<br />
Down on the Farm: The Impact of Nano-scale Technologies on Food and Agriculture <br />
<br />
Report Prepared for the South Centre - The Potential Impacts of Nano-Scale Technologies on Commodity Markets: The Implications for Commodity Dependent Developing Countries<br />
<br />
<br />
<br />
'''Johns Hopkins (Berman Institute)''' <br />
<br />
http://www.lse.ac.uk/collections/humanRights/research/groups/Bioethics.htm<br />
<br />
Berman Institute scholar calls for a new legal, ethical framework for research with human tissue specimens<br />
What’s known on the subject: There is growing concern and confusion about the use of “banked” human tissue and cells for research. Several court cases involving the use of human tissue specimens, recent stories in the news, as well as the popularity of a book, The Immortal Life of Henrietta Lacks, all reflect a growing interest in the rights and expectations of the people who provide tissue samples and DNA for research.<br />
What this article adds: This review contends that the current legal and ethical framework for the use of human tissue specimens in research fails to consider the role or preferences of the tissue contributors, and argues that courts have failed to apply a consistent legal framework in addressing disputes between contributors and recipients of the biological samples used in research. <br />
This paper proposes a framework that acknowledges the separate contexts and relationships inherent in that distinction, and sets out the social, legal and ethical perils of ignoring the role that tissue sample providers play in the research enterprise.<br />
<br />
<br />
<br />
'''LSE BIOS''' <br />
<br />
http://www.lse.ac.uk/collections/humanRights/research/groups/Bioethics.htm<br />
<br />
The Bioethics, Rights and Human Rights group is led by Dr Alasdair Cochrane.<br />
<br />
Members:<br />
<br />
Btihaj Ajana (BIOS)<br />
<br />
Perveen Ali (Department of Law)<br />
<br />
Rachel Bell (BIOS)<br />
<br />
Meg Clinch (BIOS)<br />
<br />
Caitlin Connors (BIOS)<br />
<br />
Dr Carrie Friese (BIOS)<br />
<br />
Dr Roberto Fumagalli (Department of Philosophy, Logic and Scientific Method)<br />
<br />
Professor Conor Gearty (Department of Law)<br />
<br />
Amy Hinterberger (BIOS)<br />
<br />
Professor Emily Jackson (Department of Law) <br />
<br />
Kerstin Klein (BIOS)<br />
<br />
Dean Peters (Department of Philosophy, Logic and Scientific Method)<br />
<br />
Dr Joelle Abi Rached (BIOS)<br />
<br />
Dr David Reubi (Public & Environmental Health Research Unit, London School of Hygiene and Tropical Medicine)<br />
<br />
Professor Nikolas Rose (BIOS)<br />
<br />
Dr Igor Stramignoni (Department of Law)<br />
<br />
Dr Sivaramjani Thambisetty (Department of Law)<br />
<br />
Dr Scott Vrecko (BIOS)<br />
<br />
Dr Ayo Wahlberg (BIOS)<br />
<br />
Jeremy Williams (Department of Government)<br />
<br />
Alasdair Cochrane joined the Centre for the Study of Human Rights in 2007. He teaches on the core course for the MSc Human Rights ‘Approaches to Human Rights’, as well as on an undergraduate option in Sociology, ‘Environmentalism: Theory Politics and Practice’. Prior to joining the Centre, Alasdair taught in the Department of Government at the LSE, where he completed his PhD. He holds a 1st Class BA in Politics from the University of Sheffield, an MSc in Political Theory, and a PGCHE, both from the LSE.<br />
Alasdair Cochrane’s research interests include the philosophical justification of rights, contemporary political theory, environmentalism, animal ethics and bioethics. <br />
<br />
Selected publications include: <br />
<br />
-“Ownership and Justice for Animals”, Utilitas, Vol. 21, No. 4 (Dec, 2009). <br />
<br />
-“Do Animals Have an Interest in Liberty?”, Political Studies Vol. 57, No. 3 (Oct, 2009). <br />
<br />
-“Animal Rights and Animal Experiments: An Interest-Based Approach”, Res Publica, Vol. 3, No. 3 (Sep. <br />
2007). <br />
<br />
-“Environmental Ethics”, Internet Encyclopedia of Philosophy, (www.iep.utm.edu). <br />
<br />
-Selected research projects under review and in preparation include:<br />
<br />
-“Undignified Bioethics” (paper)<br />
<br />
-“Evaluating the Political Conception of Human Rights” (paper)<br />
<br />
-“Are Human Rights Speciesist and Does it Matter?” (paper)<br />
<br />
-Animal Rights without Liberation (book)<br />
<br />
-An Introduction to Animals and Political Theory (book)<br />
<br />
<br />
<br />
'''The Hastings Center''' <br />
<br />
http://www.thehastingscenter.org/Publications/BriefingBook/Default.aspx<br />
<br />
The Hastings Center, founded in 1969, is an independent, non-partisan, non-profit bioethics research institute based in the United States. It is dedicated to the examination of essential questions in health care, biotechnology, and the environment. The center has over 200 fellows, including many physicians, attorneys, PhDs and bioethicists.<br />
<br />
Bioethics Briefing Book<br />
<br />
From Birth to Death and Bench to Clinic: The Hastings Center Bioethics Briefing Book for Journalists, Policymakers, and Campaigns contains 36 overviews of issues in bioethics of high public interest, such as abortion, health care reform, human and sports enhancement, organ transplantation, personalized medicine, medical error, and stem cells. The chapters, written by leading ethicists, are nonpartisan, presenting reasonable considerations from various perspectives that are grounded in good scientific and ethical facts. They each include recent news stories, clickable experts to contact, linked resources, and (where available) recent legislation and campaign positions. Greater detail on how to use the book is in the introduction. The three framing essays offer valuable insights into the historical and increasing relevance of bioethics to public policy.<br />
<br />
<br />
<br />
'''Biotechnology Regulatory Bill of India – Five Fallacies'''<br />
<br />
Find out the loopholes in the bill which can have disastrous effect not to India alone bu to whole world at: <br />
<br />
http://scienceray.com/technology/biotechnology-regulatory-bill-of-india-five-fallacies/<br />
<br />
<br />
Mind map<br />
<br />
[[File:Bioethisists_mindmap.jpg]]</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=Ideas_for_Bacteria.&diff=2846Ideas for Bacteria.2010-11-22T07:02:43Z<p>Farhad: </p>
<hr />
<div>-bacteria that prevents corrosion <br />
<br />
-Time keeper or clock<br />
<br />
-Combustible bacteria<br />
<br />
-Related to weather - smell of rain<br />
<br />
-Bacteria that is resistant to Scientific Probing/Instruments<br />
<br />
-Mirror of bacteria<br />
<br />
-Buoyant bacteria<br />
<br />
-Interactive bacteria(painting)<br />
<br />
-Another creature made from bacteria<br />
<br />
-Bacteria and sound<br />
<br />
-Bacteria visualizations. (Both colour changes and 'choreographed' movement)<br />
<br />
-Neuro transmitters- bacteria as sensors for emotions<br />
<br />
-Glue<br />
<br />
-Bacteria that detects cravings<br />
<br />
-Magnetic bacteria<br />
<br />
-Self mutating Bacteria<br />
<br />
-Lie detector<br />
<br />
-Bacteria creates an identity<br />
<br />
-Bacteria becoming material on death<br />
<br />
-Constructing a 'Bacterial Ecology'<br />
<br />
-Bacteria that acts like oil<br />
- A lubricant<br />
- A liquid that can withstand high temperatures</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=FArhad&diff=2812FArhad2010-10-27T04:32:33Z<p>Farhad: </p>
<hr />
<div>== '''Journal''' ==<br />
<br />
<br />
<br />
<br />
'''Day 1'''<br />
<br />
After a very long time I had again opened my mind to biology. The last time I had studied biology was in the 10th grade and for the first half hour of the class everything pretty much went over my head. It had been a long time since I had heard these words and they actually sounded like Greek to me. But slowly everything I had learned in the past came back to me.<br />
<br />
In the first class we discussed about general information regarding the first theories of evolution and how they were replaced by others as we come to this day. WE also talked about DNA and its purpose.<br />
<br />
<br />
<br />
'''Day 2'''<br />
<br />
Today we talked about Mendel’s laws of segregation and independence. A very important point is that you don’t need to be a scientist or have a PhD. to discover things. We got to know how genes are passed down from one generation to another. Also alleles are outputs of genes (allele=pea being round or wrinkled.) The terminology used may take some time to get used to. It is amazing to actually see a cell splitting into 2. We then talked about chromosomes and how they decide the characteristics of a person.<br />
<br />
If Genome=book,<br />
<br />
Then DNA=volume,<br />
<br />
And Chromosome=library<br />
<br />
We also saw a video that talked about where gen. engineering would be about 30 yrs. from now. another important thing to consider is the ethics of the topic. Is creating new species good or bad for the world? Is it really progress or just an illusion of progress that we are blindly following that will lead us to our end???...<br />
<br />
<br />
<br />
'''Day 3'''<br />
<br />
Today we started off with seeing how gene mutation is not a good thing. For eg. Cigarette smoking causes the gene p53 to permanently mutate thus causing lung cancer.we then talked about the basic requirements for being genetic material, which are as follows<br />
<br />
1 information storage-Dna has 4 proteins that can be arranged in any way creating different codes<br />
<br />
2 accurate replication-there is a chance of 1 ni a million that the gene is defective, and if it’s so it gets disposed.<br />
<br />
3 it must be expressed as a phenotype- A phenotype is any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, or behavior<br />
<br />
4 it should be able to change –i.e. every individual has different characteristics therefore DNA is different<br />
<br />
DNA is like a symbol for bio like an atom for chem. DNA stands for dioxyribose nucleic acid. It consists of a sugar phosphate backbone and ATGC base pairs. The base pairs are what create code of the DNA for creating proteins.<br />
(Sugar=dioxy ribose, base pairs=nucleic acid) <br />
<br />
A=adenine<br />
<br />
T=thymine<br />
<br />
G=guanine<br />
<br />
C=cytosine<br />
<br />
The proportion of A & T is always equal. Similarly G=C. DNA replication is called semi conservative replication. In this process the DNA is split into its 2 separate helical structures (unzipped )and each of the single helix join to the respective base pair. Thus forming 2 similar DNA 2ble helixes. <br />
All somatic cells (non sex cells) have the same amount DNA specific organism. On the other hand sex cells (e.g. sperm) there is only half the total amount of DNA. The other half is in the sex cells of the mate. Thus the child gets 1 half each of the parents’ genes. Also genetic engineering is not creation of genes but just modifying the original genes to create a different protein.<br />
<br />
<br />
<br />
'''Day 4'''<br />
<br />
Today we talked about proteins. Proteins are polymers of amino acids. There are 20 types of amino acids, 8 of which cannot be produced by man. Thus they need to be consumed.the shape of he protein is very sensitive to the environment.(eg. An egg on heating becomes solid. <br />
<br />
There are 2 types of proteins based on their function:<br />
<br />
-Structural proteins ( hair, muscle collagen, etc.)<br />
<br />
-Enzymes <br />
<br />
enzymes are surfaces for reactions to occur. They act as catylists for reactions in the body. Enzyme names usually end with the letters “ase” eg .polymerase. proteins are also present in the nucleus.thus the DNA contains the gene and the proteins in the nucleus are the phenotype.<br />
<br />
<br />
<br />
'''Day 5'''<br />
<br />
As we talked yesterday gene= DNA and the protein= phenotype(expression). Today we talked about the process of protein creation using DNA. In the nucleus one of the helix of the DNA gets replicated to form RNA(RNA=1/2DNA).RNA is the set of instructions for producing protein. The RNA travels outside the nucleus and goes to the ribosome. The ribosome is like the factory for producing proteins. There are free proteins in the cell in pairs of 3 called codons that act as input for the ribosome. The protein pair is selected according to the code in the RNA(ATC produces a certain protein.) There are 20 types of proteins and only 4 codes in the RNA. Thus the RNA is in pairs of 3 to create enough no of codes for the 20 proteins.<br />
<br />
In DNA only 1 of the 2 helix is used for production, however it is a double helix for easy replication. When DNA is replicated, each of the daughter DNA has 1 of the helix of the parent DNA. Also the other helix decides where in the body the protein is used. <br />
<br />
<br />
<br />
'''Day 6'''<br />
<br />
Today we talked about the genome and genome sequencing. The first type of genome sequencing was hierarchal sequencing where there are certain landmarks in the genome which are used for genome sequencing. The other method is called shotgun sequencing. longer sequences get subdivided into smaller fragments, and subsequently reassembled to give the overall sequence.98% of the RNA produced does not even leave the nucleus. The walls of the nucleus act as as a purifier.they are like a simple on off switch. we also talked about bacteria that have a self defence against<br />
<br />
<br />
<br />
'''Day 7'''<br />
<br />
We talked about recombinant DNA. Recombinant DNA is DNA that is artificially created from two or more sources and is incorporated into a single recombinant molecule. Recombinant DNA (rDNA) is a form of DNA that does not exist naturally, but is created by combining DNA sequences that would not normally occur together. <br />
<br />
Most of the bacteria have a restriction enzyme which cuts up foreign DNA. Therefore it is sometimes difficult to splice DNA. This process of splicing can create new types of organisms. This is what synthetic biology is based on. Usually a bacteria called E.coli is used for this as it is not dangerous to experiment on. Synthetic bio. Has many applications. It is used to study particular sequences that are very tiny(the sequence is put in the bacteria and amplified), to express phenotypes, to increase the quantities of proteins , etc. <br />
<br />
<br />
<br />
'''Day 8'''<br />
<br />
Isolating genes was always done from the phenotype to theto the DNA, but that changed while trying to cure muscular dystrophy. The doctor tried to sequence the gene from the dNA to the phenotype. This is called reverse genetics. He found that a small gene on the x chromosome was missing. This gene was responsible for production of distrophin which connects the muscle fiber to the cells. Distrophin can be replaced by urotrophin , which can be produced by a drug. Thus the problem was cured. In the nucleus mRNA of about 14,600 base pairs is formed, most of which ars not required. the introns remove about 79 peaces from the mRNA by gene splicing in the nucleus itself.<br />
<br />
The DNA library is a volume of the genome. Hybrid DNA is a combination of 2 DNA from 2 different places. The geme and a vecter is combined and introduced into the bacteria. the bacteria takes the new gene and adds it to the original gene. The bacteria is allowed to grow and half the DNA of the new bactrria is introduced so that the full(double helix) DNA is fished out. Thus hybrid DNA is created.<br />
<br />
<br />
<br />
'''Day 9'''<br />
<br />
Today we talked about transgenetics which is DNA of more than 1 species. The the method used is called gene splicing which was first done by Boyle. While working with fruit flies he found that a certain gene called the homiobox genes were responsible for descision of what grows where. Thus by changing this gene he could change the position of different body parts. Thus started synthetic biology which was literally engeneering biology.<br />
<br />
<br />
<br />
'''Day 10'''<br />
<br />
Today we talked about creating a hypothetical bacteriaof our own. We also given a talk on hybrids and new creatures. The concept of hybrids has existed since many ages. The available technology and advancements in biology has made it possible to create such hybrids. Radical plastic surgens do exactly this. They add extra parts to the body through surgery.<br />
<br />
<br />
<br />
'''Day 11'''<br />
<br />
Today we saw a video of craig venter on ted talks. He was talking about his recent discoveries in biotechnology and how they went about doing it. We also talked about different bioartists and their approach to biology<br />
<br />
<br />
<br />
'''Day 12''' <br />
<br />
Today we went to NCBS for the first time.we had gone to meet the person who would help us create the new bacteria and understand how to go about doing it. <br />
<br />
<br />
<br />
'''Day 13'''<br />
<br />
Today we saw the different parts that make a functioning gene. it was shocking to see its resemblance to electronic parts and circuits. we also found out about the parts regestry and how to search it. The pats registry is a large collection of already existing dna. We also talked about bioremediation which is creation of an organism that solves environmental problems. Plants are better at bioremediation as they can be plantrd and removed easily thus not disturbing the ecology of an area . We also learnt about PCR (polymerase chain reaction) which was discovered by Kary Mullis. In DNA the base pairs are held together by an H bond. This bond is brokrn at 80 degrees celcious. The polymerase is used to duplicate the DNA and produce 2 strands of DNA. hut at 80 degrees celcious te polymerase coagulatees. thus we introduce an extremophile (organism that survives in extreme climates) that is genetically engeneered to produce polymerase. thus making it a chain reaction.<br />
<br />
<br />
<br />
'''Day 14'''<br />
<br />
Today we talked about gene scilencing. In this process some of the genes get turned off. This happens at the transcription level. Scilencing occurs when 2 strands of mRNA are created that are complementary to each other. Thus they recombine and are not allowed to leave the nucleus. Thus the protein is not created.<br />
<br />
We also researched on different bioartists that use biological phinominons as a form of art.today we looked at George gessart, Adam Zeretsky , Eduardo Katz, Petrissia Piccinini and so on. It is amazing to see how biologyitself was a form of art. And each bioart work had a deeper understanding to it.<br />
<br />
<br />
<br />
'''Day 15'''<br />
<br />
I had an appointment with an eye doctor so I couldn’t go for class. But today was the day we got our wiki pages created. In the evening I asked for my password and got it the same day so I didn’t lose out on a lot. They were also told about the 2 foreign faculty that was coming to aid us: Daisy and James.<br />
<br />
<br />
<br />
'''Day 16'''<br />
<br />
Today we didn’t d much. We saw a BBC docmentry : Secrets of Life,The race for the Double Helix. It talked aabout the three groups of scientists involved in finding the double helix structure of DNA and their contributions to the finding. Seeing this documentary made me realize that discovery is like a rat race of who finds what first and who should be credited for it. Also from the previous example of Kary Mullis and the 2 scientiststhst discovered the structure of the double helix, that one doesn’t need to be the smartest to discover something, he just needs to have some knowledge of the subject and a lot of luck.<br />
<br />
<br />
<br />
'''Day 17'''<br />
<br />
Today we saw the different parts that make a functioning gene and their uses. It was shocking to see its resemblance to electronic parts and circuits. we also found out about the parts regestry and how to search it. The pats registry is a large collection of already existing dna. We also researched about how to create yeast cultures. We found the following:<br />
<br />
<br />
'''Preparation or Agar:'''<br />
<br />
-Heat 7 gm of agar in 250 ml of water till it completely desolves.<br />
<br />
-Let it set.<br />
<br />
<br />
'''Preparing yeast culture:'''<br />
<br />
-Heat yeast in water to activate it.<br />
<br />
-sterilize loop.<br />
<br />
-dip in yeast and streak to the agar.<br />
<br />
-keep it aside to grow (24hrs).<br />
<br />
This process failed as we added very little agar (1 gm). Thus the yeast didn’t grow.<br />
<br />
<br />
<br />
'''Day 18'''<br />
<br />
Today we read our first scientific paper on repricilator gene. The gene works as a cycle. There are 3 main proteins that activate 3 different genes, which are produced by those 3 genes. 1 repressor affects the 2nd and the 2nd affects the 3rd. the 3rd in turn affects the first, Thus forming a feedback loop. The Bacteria works as an oscillator circuit using the time for triggering as the time between the action. The terms used in the paper were very confusing and did not make sense at first but slowly came to my understanding. My conclusion is that scientific papers are complicated ways of saying something simple. <br />
<br />
We also tried to grow yeast again his time we tried 3 different concentrations of agar:<br />
<br />
1.4gm/250ml<br />
<br />
4.3gm/250ml<br />
<br />
10gm/250ml<br />
<br />
thee middle concentration was best suited for yeast growth.<br />
<br />
<br />
<br />
'''Day 19'''<br />
<br />
Today we went for a discussion of: Evolution as opposed to design. The speaker talked about the design problem in evolution and whether the design was meant to be or just a coincidence. He gave the example of the eye and the telescope and said that if the telescope had a maker then so did the eye. The only difference is that we know who made the telescope. We also talked about natural and artificial. This raised a big question in my head that if man would interfere in anyway then it would become artificial. Then that would make everything artificial as man has interacted with and changed almost everything. Then that means nothing natural exists….<br />
<br />
<br />
<br />
'''Day 20-24'''<br />
<br />
We spent the next 4 days making our own lab equipment. We made 2 centrifuges, a microscope and an incubator using locally available materials. It took several trials and errors but we finally made all 3. I was working on the incubator and it was a little frustrating to get the perfect temperature.<br />
<br />
<br />
<br />
'''Day 25''' <br />
<br />
Today we worked on collecting all the info of the last 3 weeks. This is what we came up with:<br />
<br />
-We started off by creating bio-art sculptures that used, living organisms. We were told to create art without killing the organism, thus trying to integrate the two (art and biology) together and also having a kind of pet for the summer! <br />
<br />
-Coming from an art background, we tried to add meaning to why we did what we did.<br />
<br />
-After this we came up with ideas for bacteria and an explanation for how they functioned.<br />
<br />
-We created imaginary machines that CAN NOT exist. The idea was to open our minds to the extreme possibilities so as to get new ideas: for our final project.<br />
<br />
-As we went through all the previous works of Igem competitions we realised that almost all the projects fell under 3 major categories, which were: <br />
<br />
<br />
1. Purifiers <br />
<br />
2. Display/sensors/ indicators<br />
<br />
3. Production of energy<br />
<br />
We believed that it would be good to create an organism that would not fall in any of these categories.<br />
<br />
These are all the possibilities that we have come up with till now, hoping to have a excellent outcome. <br />
<br />
<br />
<br />
'''Day 26,27'''<br />
<br />
absent<br />
<br />
<br />
<br />
'''Day 28'''<br />
<br />
I was absent the last 2 days so I was a little lost. But with help I caught up quite fast. Today was also the day I met James and Daisy. Today’s assignment was to come up with an organism for iGEA(genetically engineered art) which was a new compition we started in srishti. We came up with E. cloudy. <br />
<br />
<br />
<br />
'''Day 29'''<br />
<br />
Today we presented our bacteria for iGEA. We were also given conics to read and pich out intresting myths which could be related to synth. biology. All the ones we selscted fell under tese catagories:<br />
Bio prospecting<br />
<br />
Karma<br />
<br />
Ecosystems<br />
<br />
Immunization against a disaster<br />
<br />
Soma<br />
<br />
Jugad (being very prominent)<br />
<br />
<br />
<br />
'''Day 30, 31'''<br />
Using the myths we read through we were told to a create a bacteria that retells the story. We depicted the story of Brahma, Vishnu and Shiva.(The holy trinity)<br />
<br />
<br />
<br />
'''Day 32''' <br />
<br />
Today we looked at the myths that had been created by synthetic biology for the past and the future.<br />
<br />
We were also told to make a scientific diagram for our mythical bacteria. that is to put it in complicated words. <br />
<br />
<br />
<br />
'''Day33'''<br />
<br />
Today we created a mindmap of the so called “actors” of bio technology and who was on which side. <br />
<br />
We also had 2 artists from Level10 comics to talk about the process of making a comic and the steps involved. They also showed us some of their works.<br />
<br />
<br />
<br />
'''Day 34'''<br />
<br />
Each of us was given a topic to do further research in. my topic was Bioethicists<br />
<br />
<br />
<br />
<br />
== '''Bio artists''' ==<br />
<br />
<br />
<br />
===Stellarc:===<br />
<br />
Stellar tries to integrate the biological and technological advances using the human body as the test subject. He tries to show the thin line that exists today between technology and the body which will be broken very soon.<br />
<br />
<br />
<br />
===Orlan:===<br />
<br />
Orlan again uses her own body as a canvas. But instead of technology she uses plastic surgery. If fine art is a visual medium, then Orlan herself is a walking exhibit. Orlan embraces the technology of the time by undergoing these procedures but rejects everything they stand for. Instead of making herself “pretty”, she makes herself grossly disfigured. Orlan is the only artist working so radically with her own body, asking questions about the status of the body in society.<br />
<br />
<br />
<br />
===Patricia Piccinini:===<br />
<br />
The work is quite interesting because of<br />
<br />
1. It’s life like feeling.<br />
<br />
2. Also at first one thinks it is completely impossible & imaginary but at closer inspection realise we are not far from achieving what she has made and that creating such animals are quite possible.<br />
<br />
3. Her art creates ethical debates about the advancements in technology & biology and its relation to nature. And how it is the responsibility of the creator for the new creatures uncertain ethical and physical results.<br />
<br />
<br />
<br />
<br />
== '''My assignments''' ==<br />
<br />
<br />
<br />
<br />
===Living sculpture:(living furniture)===<br />
<br />
<br />
Most of the furniture that we use in places like the lawn or at the beach are made of wood that has been cut from living trees. this living sculpture has both a use and aesthetics. Instead of cutting trees why not grow the according to the shape you need. <br />
<br />
The concept of tree shaping requires one to bend the tree in a desirable shape when it is a small plant. As the tree grows the shape is retained and the bark hardens to form the required shape. This can be called ecofriendly furniture. As the tree branches out, the leaves give shade. It is also cooler below the tree. Also since the tree produces oxygen, the air under the tree is fresh. My final project is to make a living chair. <br />
<br />
"[[File:Tree_shaping.jpg]]"<br />
<br />
I am starting by bending smaller plants and make in a simple loop(1st June). I used string to hold the shape and check after a month.<br />
<br />
[[File:Roll_2.JPG]] [[File:Roll_4.JPG]]<br />
<br />
After a moonth: The plant retains the shape but still needs some time to maintain that shape. <br />
<br />
<br />
===Hypothetical bacteria:(Pressure sensitive Thermo Bacteria)===<br />
<br />
<br />
The Srishti School of art design and tech. has created bacteria that emits heat when pressure is applied on it. It consists of tiny turbine like particles on it’s cell walls. When pressure is applied the cell produces an enzyme that causes the turbines to spin. These cells are tightly packed together in a tiny porous container. The activated turbines hit each other producing heat. The collected heat is magnified by the bacteria and is concentrated at the point of pressure. The temp ranges from 100 to 500 degrees.<br />
<br />
[[File:Bact_0.jpg]]<br />
[[File:Bact1.jpg]]<br />
<br />
The porous container itself is a living organism which concentrates all the heat on the point where the pressure is and spreads the heat across the area where pressure is. both the bacteria live along with each other as symbiotes. The heat producing bacteria feeds on the nutrients supplied by outer shell which is made of sugars and fatty acids. On the other hand the outer shell depends on the thermo bacteria for its shape and heat. Using some amount of the heat produced by the thermo bacteria, the porous outer structure converts cellulose into simple sugars which is food for both the organisms has pores that are about 0.01 nm in diameter all over it which are used to vent out all the extra heat in the form of steam (water is one of the byproducts of converting cellulose into sugar.)<br />
<br />
The organism reproduces by binary fission. When the shell is overloaded with the bacteria it expands until it breaks into 2 pieces. The 2 pieces join to themselves to form 2 separate structures. The outer structure does not break unless there is an internal pressure applied and it immediately joins when it breaks and grows to its normal size in 5 hours to incorporate more bacteria. The bacteria can be killed using an electric charge of 20 volts (D.C.), thus its growth can be controlled. <br />
<br />
This organism can be used for security purposes, as they are too small to be seen and produce enough heat to burn the body. If the amount of heat given out (number of collisions between spindles) can be controlled it can be used for various reasons e.g. Cooking, hot tubs, heated chairs, etc. And being organisms that can reproduce, they don’t need to be replaced.<br />
<br />
<br />
<br />
===Imagenary machine:(Projector bacteria)===<br />
<br />
<br />
The bacteria simply projects ones thoughts to a tangible 2D presentation. These bacteria live in the brain. It is a long egg like structure with 2 antennas. These bacteria are fixed on a circular moving belt. The bacteria pick up brain waves with the antenna and produce an image corresponding to the wave. <br />
<br />
[[File:Bact_3.jpg]]<br />
<br />
The optic nerve of the right eye touches one of the bacteria and picks up the image. As the rotating belt moves the optic nerve picks up other images and forms a stop motion of the thoughts in the mind on the retina. The image on the retina is inverted.<br />
<br />
The bacteria secrete an enzyme that runs along the optic nerve and makes the retina emit light. The image on the retina gets projected on to the lens of the right eye and is diverged by the lens thus magnifying the images it gets projected. The user of the bacteria can voluntarily secrete an enzyme that makes the optic nerve move away from the bacteria, thus stopping the projection and the eye starts to function normally. The bacteria reproduce by binary fission. One of the daughter bacteria replaces the parent and the second bacterium gets attatched to belt and acts as food for the bacteria.<br />
<br />
<br />
<br />
===DIY Equipnent===<br />
<br />
[[DIY Incubator]]<br />
[[DIY Sterlisation Hood]]<br />
[[DIY Water Bath]]<br />
[[ReacTable]]<br />
<br />
<br />
<br />
===iGEA:(E.Cloudy)===<br />
<br />
Bacteria which help coordinate your music with the weather [[File:Ec1.jpg|150px|left]]<br />
<br />
<br />
<br />
Escheriscia Cloudy or E. Cloudy is a Bacteria which is temperature sensitive and produces electricity. Its unique mix of qualities has been used to program a machine which plays music play lists of the user’s choice depending on the weather.<br />
<br />
The E.Cloudy bacterium have been created by combining two existing BioBrick parts – <br />
<br />
-BBa_K098995, responsible for the thermo sensitivity.(designed by the Harvard 2008 igem team)<br />
<br />
-BBa_K499271, responsible for the electricity.( designed by Boris Kirov igem 2010 )<br />
<br />
'''How the two BioBricks are connected'''<br />
<br />
•The thermo sensitive complex produces a certain protein on exposure to heat.<br />
This protein triggers off the second complex, making it generate a current<br />
<br />
'''How the machine works'''<br />
<br />
•The temperature sensitive bacteria creates current depending on the climate temp (more temp = more current). <br />
<br />
•The current passes through an amplifier to get a readable current. <br />
<br />
•As current passes through the voltmeter the needle moves increasingly. <br />
<br />
•Each temp range triggers the playing of a certain play list( ex a range of 0-10= soothing play list/ energetic play list depending on the user).<br />
<br />
•The machine has its own software which is loaded onto a computer or laptop. The machine is connected to the computer with a USB cable. <br />
<br />
[[File:Picture1.jpg|600px|]]<br />
<br />
'''Deeper into the Bacteria'''<br />
<br />
•The bacteria self reproduce.<br />
<br />
•They are in a way cannibalistic;<br />
Every time a bacteria reproduces, the mother bacteria is consumed by the child.<br />
[[File:Ec2.jpg|250px|right]]<br />
<br />
<br />
'''How it could Fail and Why this over a fully mechanical system?'''<br />
<br />
The system could malfunction if –<br />
<br />
•The bacterial container got contaminated by anything that could kill or reduce capacity of the bacteria.<br />
<br />
•We don’t know if the electricity would kill the bacteria. <br />
<br />
'''Why this?''' <br />
<br />
The same machine can be made using a thermometer, however, with a thermometer, there arises a chance of it getting ruined permanently. <br />
Also it can be looked upon as an alternative, a novelty, an exploration. <br />
How it ties into the criteria detailed by the contest <br />
<br />
•Social critique – creates moods, makes you question your own mood and keeps you conscious of the weather and its changes.<br />
<br />
•This ties into remix culture – apart from the obvious remixing of genes that the original escheriscia coli have undergone, looking it at it from an artistic angle, it’s sort of like replacing your weather man’s report with your own bacterial weather report! <br />
<br />
<br />
'''The effects of this bacterial product on the world.'''<br />
<br />
We have divided the consequence of introducing this product into the market into categories such as – <br />
<br />
'''Socio-Cultural'''<br />
<br />
We feel that this product has high potential to enter popular culture. It’s something which would help take individualism to a new level. It could be a new way to bring nature closer to us and observe it better. <br />
<br />
'''Economic - Financial'''<br />
<br />
The circuitry of this product wouldn’t be expensive, but producing the bacteria maybe the one to raise the price.<br />
•Who would be able to afford it? <br />
<br />
•What percentage of the population<br />
does this group make up?<br />
<br />
•Why would they want to buy it? (novelty and interest could lead to a social phenomenon!)<br />
<br />
•Does this say anything about us as consumers?<br />
<br />
•How much of an effect would it have on our economy? <br />
<br />
'''Technology'''<br />
<br />
We’ve seen bacteria producing fuel and the idea of the bacterial battery. Could energy producing bacteria be our future power houses? <br />
<br />
How would a product integrating living cells into a non-living machine be received by the tech industry? <br />
<br />
'''Science'''<br />
<br />
Could this product trigger off another set of ideas that could be beneficial to other sciences? We think it’s a possibility. <br />
<br />
'''Art'''<br />
<br />
Art is deceptive, it can pack a hard punch without seeming like it. <br />
<br />
Art has a lot to do with creating a sense of awareness, to make people question things around them. <br />
<br />
The concept behind this product (apart from being aware of the weather it creates awareness in how two very different genes, from possibly to very different organisms have been put together to create a machine) could lead us to questioning our rights to remix things (also, is it ok to mix the machine with living cells?) , our rights to play with natural selection, can we define this as a form of natural selection? <br />
<br />
<br />
<br />
===Bacteria based on indian myth:(The Holy Trinity)===<br />
<br />
<br />
When was the last time you ever read an Indian mythological story and asked your self – what if I can do that? Indian Mythology is known to be the most culturally rich, colourful, dramatic and at the same time metaphorically ambitious story, ever told. The numbers of different versions are more than the number of sarees that came off Draupadi! It’s like a roller coaster ride of emotions which at the end of every story brings in ‘balance’.<br />
<br />
As an Artist and Designer, whenever we read an Indian mythological story I have to say it’s quite amazing because these are some stories that have characters that can pretty much do whatever they want! Gods.... Isn’t that what we all want? To do whatever we like? And not have to worry about consequences? And just know that at the end of it all there will be balance? I think that’s some food for thought.<br />
<br />
As a team, we first read through the most famous stories in Indian mythology, and then had a fascinating discussion with a learned scholar in mythology and history. Arshia (the scholar) helped us put our facts together in the most fun filled way which after a few drinks turned out to be a very satisfying knowledge-full night.<br />
<br />
Our task now (which is the most interesting part) was to find links and parallels to any myth and use synthetic biology to fill the gap! I find that highly fascinating. SO we went through a few myths and as soon as we landed on Shiva’s third eye, there was a full stop. Shiva’s third eye is the destroyer, when he opens it; disaster is all over the place. So the last you want to do it tick him off. We took that in a metaphorical sense and thought about what if that third eye was a way for us to see when our real eyes are shut? So what if I had bacteria that could communicate with thoughts through neuron activity and when I’m wired up to a projector, it displays my thought in 3D space. Then communication would be in its most pure form since there is a lot of loss when converting thought to word or deed. Then what if I wired up to another person and started communicating with thought! Or if I left messages for someone on a platform and they could later wire up and receive it. But as usual there’s always a ‘BUT’, and the first one here is privacy. Privacy is by far the most delicate issue here. SO we kept this on hold for the time being and instead of looking at parts of a myth we moved away and looked at the Big Picture.<br />
<br />
[[File:Collages.jpg|400px|Left|]]<br />
[[File:Main 2.JPG|400px|right|]]<br />
<br />
The Holy Trinity – Brahma, the creator, Vishnu the Preserver and Shiva the destroyer. These are the first and foremost gods that rule the heavens, earth and hell. As you’re reading this don’t those three words –creator, preserver and destroyer burst out of your imagination and find its way to synthetic biology? Well, that’s exactly what happened to us. So here’s our idea.<br />
<br />
[[File:Collages2.jpg|400px|Left|]]<br />
<br />
In a over populated culture of bacteria. There is ‘imbalance’ since there more bacteria to eat than the nutrition available. So the ‘gods’ are summoned! The VISH-gene bacteria (the preserver) now gets into action by producing a chemical to which ONLY the SHIV-gene bacteria (the destroyer) can read. This then activates the SHIV-gene bacteria to in turn produce a chemical which start disrupting the bacterial cells in the colony. The ‘gods’ bacteria are of course resistant to this chemical. The SHIV-gene bacteria once activated has no control over killing the other cells. So once he has destroyed ample number of cells, he needs to be stopped, which ONLY the BRAHM-gene can do. So now the VISH-gene bacteria produces another chemical which ONLY the BRAHM-gene bacteria can read and this in turn activates the BRAHM-gene bacteria to produce a chemical to deactivate the SHIV-gene bacteria. Now there’s been too many bacteria killed so after a while of reproduction the optimum level is reached and ‘balance’ is restored. The subjects are happy and so are the gods. Soon after reproduction hastens up and there is over population again so the whole process is initiated making it a loop. <br />
<br />
[[File:Main 1.JPG|400px|Right|]]<br />
<br />
BRAHM-gene bacteria are identified with the presence of the BRAHM-gene. When the BBRAHM- gene replicates it does not transfer it’s genetic material completely, instead it retains one part of the gene, so the other bacteria now is the VISH-gene bacteria. When the BRAHM-gene bacteria replicates for the second time it does not transfer the BRAHM-gene at all making the new organism the SHIV-gene. <br />
<br />
We’d like to think that this mythological concept, besides being fascinating will definitely find its way to a good purpose in the world of Synthetic Biology. So wait up until then.<br />
<br />
<br />
'''Scientific reprisentation'''<br />
<br />
[[File:Bvs.jpg]] [[File:Bvs2.jpg]]<br />
<br />
===The promise of Synthetic Biology:===<br />
<br />
<br />
Such is the promise of synthetic biology, which, according to the people who have tried to explain it to me, is basically a marketing term for all kinds of research in which scientists tinker with biological bits to make useful things — sort of like living Lego blocks.<br />
<br />
The gift of man-made life — biofuels made of algae, tumor-seeking microbial missiles — comes wrapped in a risk: What if the oil-eating bug mutates, as the horror-movie version inevitably does, and starts eating other things — like us?<br />
<br />
It's perhaps not surprising that when bioethicists describe synthetic biology, they sound like the characters in Jurassic Park.<br />
"When dealing with biological entities," notes Thomas Murray, president of the Hastings Center, a bioethics organization, "life has a tendency to find a way."<br />
<br />
Accidents at power plants are bad enough. But a leak from a bioreactor could be worse, since bacteria can learn new tricks when you're not looking. Microbes excel at exchanging DNA, Murray notes — "like microbial French kissing." That bug we introduce into the ocean to sip the spill might end up swapping DNA with other living things. "We have a ways to go," he says, "before we can really know what risks we're running if we release these organisms into the environment."<br />
<br />
Without public oversight, we are certain to wake up one day to news of some private breakthrough that rattles our bones: a human-animal hybrid, a cloned child, a fetus grown solely to harvest its parts.<br />
<br />
As laboratories incubate new blends of man and machine — creatures whose creators used a keyboard — it seems mad to say that philosophy should not intervene.<br />
<br />
The path of progress cuts through the four-way intersection of the moral, medical, religious and political — and whichever way you turn, you are likely to run over someone's deeply held beliefs. Venter's bombshell revived the oldest of ethical debates, over whether scientists were playing God or proving he does not exist because someone re-enacted Genesis in suburban Maryland.<br />
Others dismiss the worry on the grounds that creating new forms of life is not the same as creating life. One doctor friend of mine suggested that "they haven't created life in any sense of the word, other than a person playing a cassette has invented the tape recorder."<br />
<br />
<br />
"It is vital that we as a society consider, in a thoughtful manner, the significance of this kind of scientific development," Obama writes.<br />
<br />
"Synthetic biology certainly raises deep philosophical and moral questions about the human relationship to nature," according to Gregory Kaebnick, a Hastings Center scholar who is managing the project. "It's not clear what the answers to those questions are. If by 'nature' we mean the world around us, more or less as we found it, we may well decide that synthetic biology does not really change the human relationship to nature—and may even help us preserve what is left of it."<br />
<br />
Myth: Cellulosic ethanol is a decade or more away.<br />
Fact: The world's first cellulosic ethanol production facility -- owned and operated by Iogen in Ottawa, Canada -- has been converting wheat straw into ethanol since 2004. Abengoa Bioenergy is completing construction of a commercial-scale cellulosic ethanol facility, located in Salamanca, Spain, that will by the end of 2007 begin producing 1.2 million gallons of cellulosic ethanol from wheat straw each year.<br />
<br />
<br />
Conclusion:<br />
People are bound to disagree about when scientists are crossing some moral Rubicon. That is all the more reason to debate, in public and in advance, where those boundaries lie — rather than doing so after the fact, when researchers are celebrating some technical triumph and the rest of us are wondering what price we will pay for it.<br />
<br />
'''Information from:'''<br />
<br />
'''http://www.time.com/time/magazine/article/0,9171,1997447,00.html'''<br />
<br />
'''http://machineslikeus.com/.../moral-issues-raised-synthetic-biology-subject-hastings -center-workshop - .html'''<br />
<br />
'''http://www.economist.com/node/16163154/comments?page=1.html'''<br />
<br />
===bioethicists:===<br />
<br />
<br />
<br />
'''Biodesign India'''<br />
<br />
Redesigning life for novel applications<br />
<br />
http://biodesignindia.org/index.htm<br />
<br />
<br />
The evolving synthetic biology community in our country needs to discuss unique ideas, interest groups, synergies, funding avenues and useful applications. The key goal will be to identify areas where India has potential to take global leadership.<br />
<br />
<br />
<br />
'''Etc group'''<br />
<br />
http://www.etcgroup.org/en/issues/biotechnology<br />
<br />
ETC Group is not fundamentally opposed to genetic engineering, but we have profound concerns about the way it is being foisted upon the world. In the current social, economic and political context, genetic engineering is not safe, and involves unacceptable levels of risk to people and the environment. For ETC Group, the fundamental issue is control.<br />
<br />
Reports:<br />
<br />
Patenting the "Climate Genes" ...and Capturing the Climate Agenda <br />
<br />
Direct-to-Consumer DNA Testing and the Myth of Personalized Medicine: Spit Kits, SNP Chips and Human Genomics<br />
<br />
Terminator: The Sequel<br />
<br />
ETC Group Report on Geoengineering Climate Change<br />
<br />
Extreme Genetic Engineering: An Introduction to Synthetic Biology<br />
<br />
Nanotech Rx-Medical applications of Nano-scale technologies: What Impact on Marginalized communities? <br />
<br />
A Tiny Primer on Nano-scale Technologies ...and The Little BANG Theory <br />
<br />
Down on the Farm: The Impact of Nano-scale Technologies on Food and Agriculture <br />
<br />
Report Prepared for the South Centre - The Potential Impacts of Nano-Scale Technologies on Commodity Markets: The Implications for Commodity Dependent Developing Countries<br />
<br />
<br />
<br />
'''Johns Hopkins (Berman Institute)''' <br />
<br />
http://www.lse.ac.uk/collections/humanRights/research/groups/Bioethics.htm<br />
<br />
Berman Institute scholar calls for a new legal, ethical framework for research with human tissue specimens<br />
What’s known on the subject: There is growing concern and confusion about the use of “banked” human tissue and cells for research. Several court cases involving the use of human tissue specimens, recent stories in the news, as well as the popularity of a book, The Immortal Life of Henrietta Lacks, all reflect a growing interest in the rights and expectations of the people who provide tissue samples and DNA for research.<br />
What this article adds: This review contends that the current legal and ethical framework for the use of human tissue specimens in research fails to consider the role or preferences of the tissue contributors, and argues that courts have failed to apply a consistent legal framework in addressing disputes between contributors and recipients of the biological samples used in research. <br />
This paper proposes a framework that acknowledges the separate contexts and relationships inherent in that distinction, and sets out the social, legal and ethical perils of ignoring the role that tissue sample providers play in the research enterprise.<br />
<br />
<br />
<br />
'''LSE BIOS''' <br />
<br />
http://www.lse.ac.uk/collections/humanRights/research/groups/Bioethics.htm<br />
<br />
The Bioethics, Rights and Human Rights group is led by Dr Alasdair Cochrane.<br />
<br />
Members:<br />
<br />
Btihaj Ajana (BIOS)<br />
<br />
Perveen Ali (Department of Law)<br />
<br />
Rachel Bell (BIOS)<br />
<br />
Meg Clinch (BIOS)<br />
<br />
Caitlin Connors (BIOS)<br />
<br />
Dr Carrie Friese (BIOS)<br />
<br />
Dr Roberto Fumagalli (Department of Philosophy, Logic and Scientific Method)<br />
<br />
Professor Conor Gearty (Department of Law)<br />
<br />
Amy Hinterberger (BIOS)<br />
<br />
Professor Emily Jackson (Department of Law) <br />
<br />
Kerstin Klein (BIOS)<br />
<br />
Dean Peters (Department of Philosophy, Logic and Scientific Method)<br />
<br />
Dr Joelle Abi Rached (BIOS)<br />
<br />
Dr David Reubi (Public & Environmental Health Research Unit, London School of Hygiene and Tropical Medicine)<br />
<br />
Professor Nikolas Rose (BIOS)<br />
<br />
Dr Igor Stramignoni (Department of Law)<br />
<br />
Dr Sivaramjani Thambisetty (Department of Law)<br />
<br />
Dr Scott Vrecko (BIOS)<br />
<br />
Dr Ayo Wahlberg (BIOS)<br />
<br />
Jeremy Williams (Department of Government)<br />
<br />
Alasdair Cochrane joined the Centre for the Study of Human Rights in 2007. He teaches on the core course for the MSc Human Rights ‘Approaches to Human Rights’, as well as on an undergraduate option in Sociology, ‘Environmentalism: Theory Politics and Practice’. Prior to joining the Centre, Alasdair taught in the Department of Government at the LSE, where he completed his PhD. He holds a 1st Class BA in Politics from the University of Sheffield, an MSc in Political Theory, and a PGCHE, both from the LSE.<br />
Alasdair Cochrane’s research interests include the philosophical justification of rights, contemporary political theory, environmentalism, animal ethics and bioethics. <br />
<br />
Selected publications include: <br />
<br />
-“Ownership and Justice for Animals”, Utilitas, Vol. 21, No. 4 (Dec, 2009). <br />
<br />
-“Do Animals Have an Interest in Liberty?”, Political Studies Vol. 57, No. 3 (Oct, 2009). <br />
<br />
-“Animal Rights and Animal Experiments: An Interest-Based Approach”, Res Publica, Vol. 3, No. 3 (Sep. <br />
2007). <br />
<br />
-“Environmental Ethics”, Internet Encyclopedia of Philosophy, (www.iep.utm.edu). <br />
<br />
-Selected research projects under review and in preparation include:<br />
<br />
-“Undignified Bioethics” (paper)<br />
<br />
-“Evaluating the Political Conception of Human Rights” (paper)<br />
<br />
-“Are Human Rights Speciesist and Does it Matter?” (paper)<br />
<br />
-Animal Rights without Liberation (book)<br />
<br />
-An Introduction to Animals and Political Theory (book)<br />
<br />
<br />
<br />
'''The Hastings Center''' <br />
<br />
http://www.thehastingscenter.org/Publications/BriefingBook/Default.aspx<br />
<br />
The Hastings Center, founded in 1969, is an independent, non-partisan, non-profit bioethics research institute based in the United States. It is dedicated to the examination of essential questions in health care, biotechnology, and the environment. The center has over 200 fellows, including many physicians, attorneys, PhDs and bioethicists.<br />
<br />
Bioethics Briefing Book<br />
<br />
From Birth to Death and Bench to Clinic: The Hastings Center Bioethics Briefing Book for Journalists, Policymakers, and Campaigns contains 36 overviews of issues in bioethics of high public interest, such as abortion, health care reform, human and sports enhancement, organ transplantation, personalized medicine, medical error, and stem cells. The chapters, written by leading ethicists, are nonpartisan, presenting reasonable considerations from various perspectives that are grounded in good scientific and ethical facts. They each include recent news stories, clickable experts to contact, linked resources, and (where available) recent legislation and campaign positions. Greater detail on how to use the book is in the introduction. The three framing essays offer valuable insights into the historical and increasing relevance of bioethics to public policy.<br />
<br />
<br />
<br />
'''Biotechnology Regulatory Bill of India – Five Fallacies'''<br />
<br />
Find out the loopholes in the bill which can have disastrous effect not to India alone bu to whole world at: <br />
<br />
http://scienceray.com/technology/biotechnology-regulatory-bill-of-india-five-fallacies/<br />
<br />
<br />
Mind map<br />
<br />
[[File:Bioethisists_mindmap.jpg]]</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=FArhad&diff=2811FArhad2010-10-27T04:28:18Z<p>Farhad: /* Bacteria based on indian myth:(The Holy Trinity- group ass) */</p>
<hr />
<div>== '''Journal''' ==<br />
<br />
<br />
<br />
<br />
'''Day 1'''<br />
<br />
After a very long time I had again opened my mind to biology. The last time I had studied biology was in the 10th grade and for the first half hour of the class everything pretty much went over my head. It had been a long time since I had heard these words and they actually sounded like Greek to me. But slowly everything I had learned in the past came back to me.<br />
<br />
In the first class we discussed about general information regarding the first theories of evolution and how they were replaced by others as we come to this day. WE also talked about DNA and its purpose.<br />
<br />
<br />
<br />
'''Day 2'''<br />
<br />
Today we talked about Mendel’s laws of segregation and independence. A very important point is that you don’t need to be a scientist or have a PhD. to discover things. We got to know how genes are passed down from one generation to another. Also alleles are outputs of genes (allele=pea being round or wrinkled.) The terminology used may take some time to get used to. It is amazing to actually see a cell splitting into 2. We then talked about chromosomes and how they decide the characteristics of a person.<br />
<br />
If Genome=book,<br />
<br />
Then DNA=volume,<br />
<br />
And Chromosome=library<br />
<br />
We also saw a video that talked about where gen. engineering would be about 30 yrs. from now. another important thing to consider is the ethics of the topic. Is creating new species good or bad for the world? Is it really progress or just an illusion of progress that we are blindly following that will lead us to our end???...<br />
<br />
<br />
<br />
'''Day 3'''<br />
<br />
Today we started off with seeing how gene mutation is not a good thing. For eg. Cigarette smoking causes the gene p53 to permanently mutate thus causing lung cancer.we then talked about the basic requirements for being genetic material, which are as follows<br />
<br />
1 information storage-Dna has 4 proteins that can be arranged in any way creating different codes<br />
<br />
2 accurate replication-there is a chance of 1 ni a million that the gene is defective, and if it’s so it gets disposed.<br />
<br />
3 it must be expressed as a phenotype- A phenotype is any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, or behavior<br />
<br />
4 it should be able to change –i.e. every individual has different characteristics therefore DNA is different<br />
<br />
DNA is like a symbol for bio like an atom for chem. DNA stands for dioxyribose nucleic acid. It consists of a sugar phosphate backbone and ATGC base pairs. The base pairs are what create code of the DNA for creating proteins.<br />
(Sugar=dioxy ribose, base pairs=nucleic acid) <br />
<br />
A=adenine<br />
<br />
T=thymine<br />
<br />
G=guanine<br />
<br />
C=cytosine<br />
<br />
The proportion of A & T is always equal. Similarly G=C. DNA replication is called semi conservative replication. In this process the DNA is split into its 2 separate helical structures (unzipped )and each of the single helix join to the respective base pair. Thus forming 2 similar DNA 2ble helixes. <br />
All somatic cells (non sex cells) have the same amount DNA specific organism. On the other hand sex cells (e.g. sperm) there is only half the total amount of DNA. The other half is in the sex cells of the mate. Thus the child gets 1 half each of the parents’ genes. Also genetic engineering is not creation of genes but just modifying the original genes to create a different protein.<br />
<br />
<br />
<br />
'''Day 4'''<br />
<br />
Today we talked about proteins. Proteins are polymers of amino acids. There are 20 types of amino acids, 8 of which cannot be produced by man. Thus they need to be consumed.the shape of he protein is very sensitive to the environment.(eg. An egg on heating becomes solid. <br />
<br />
There are 2 types of proteins based on their function:<br />
<br />
-Structural proteins ( hair, muscle collagen, etc.)<br />
<br />
-Enzymes <br />
<br />
enzymes are surfaces for reactions to occur. They act as catylists for reactions in the body. Enzyme names usually end with the letters “ase” eg .polymerase. proteins are also present in the nucleus.thus the DNA contains the gene and the proteins in the nucleus are the phenotype.<br />
<br />
<br />
<br />
'''Day 5'''<br />
<br />
As we talked yesterday gene= DNA and the protein= phenotype(expression). Today we talked about the process of protein creation using DNA. In the nucleus one of the helix of the DNA gets replicated to form RNA(RNA=1/2DNA).RNA is the set of instructions for producing protein. The RNA travels outside the nucleus and goes to the ribosome. The ribosome is like the factory for producing proteins. There are free proteins in the cell in pairs of 3 called codons that act as input for the ribosome. The protein pair is selected according to the code in the RNA(ATC produces a certain protein.) There are 20 types of proteins and only 4 codes in the RNA. Thus the RNA is in pairs of 3 to create enough no of codes for the 20 proteins.<br />
<br />
In DNA only 1 of the 2 helix is used for production, however it is a double helix for easy replication. When DNA is replicated, each of the daughter DNA has 1 of the helix of the parent DNA. Also the other helix decides where in the body the protein is used. <br />
<br />
<br />
<br />
'''Day 6'''<br />
<br />
Today we talked about the genome and genome sequencing. The first type of genome sequencing was hierarchal sequencing where there are certain landmarks in the genome which are used for genome sequencing. The other method is called shotgun sequencing. longer sequences get subdivided into smaller fragments, and subsequently reassembled to give the overall sequence.98% of the RNA produced does not even leave the nucleus. The walls of the nucleus act as as a purifier.they are like a simple on off switch. we also talked about bacteria that have a self defence against<br />
<br />
<br />
<br />
'''Day 7'''<br />
<br />
We talked about recombinant DNA. Recombinant DNA is DNA that is artificially created from two or more sources and is incorporated into a single recombinant molecule. Recombinant DNA (rDNA) is a form of DNA that does not exist naturally, but is created by combining DNA sequences that would not normally occur together. <br />
<br />
Most of the bacteria have a restriction enzyme which cuts up foreign DNA. Therefore it is sometimes difficult to splice DNA. This process of splicing can create new types of organisms. This is what synthetic biology is based on. Usually a bacteria called E.coli is used for this as it is not dangerous to experiment on. Synthetic bio. Has many applications. It is used to study particular sequences that are very tiny(the sequence is put in the bacteria and amplified), to express phenotypes, to increase the quantities of proteins , etc. <br />
<br />
<br />
<br />
'''Day 8'''<br />
<br />
Isolating genes was always done from the phenotype to theto the DNA, but that changed while trying to cure muscular dystrophy. The doctor tried to sequence the gene from the dNA to the phenotype. This is called reverse genetics. He found that a small gene on the x chromosome was missing. This gene was responsible for production of distrophin which connects the muscle fiber to the cells. Distrophin can be replaced by urotrophin , which can be produced by a drug. Thus the problem was cured. In the nucleus mRNA of about 14,600 base pairs is formed, most of which ars not required. the introns remove about 79 peaces from the mRNA by gene splicing in the nucleus itself.<br />
<br />
The DNA library is a volume of the genome. Hybrid DNA is a combination of 2 DNA from 2 different places. The geme and a vecter is combined and introduced into the bacteria. the bacteria takes the new gene and adds it to the original gene. The bacteria is allowed to grow and half the DNA of the new bactrria is introduced so that the full(double helix) DNA is fished out. Thus hybrid DNA is created.<br />
<br />
<br />
<br />
'''Day 9'''<br />
<br />
Today we talked about transgenetics which is DNA of more than 1 species. The the method used is called gene splicing which was first done by Boyle. While working with fruit flies he found that a certain gene called the homiobox genes were responsible for descision of what grows where. Thus by changing this gene he could change the position of different body parts. Thus started synthetic biology which was literally engeneering biology.<br />
<br />
<br />
<br />
'''Day 10'''<br />
<br />
Today we talked about creating a hypothetical bacteriaof our own. We also given a talk on hybrids and new creatures. The concept of hybrids has existed since many ages. The available technology and advancements in biology has made it possible to create such hybrids. Radical plastic surgens do exactly this. They add extra parts to the body through surgery.<br />
<br />
<br />
<br />
'''Day 11'''<br />
<br />
Today we saw a video of craig venter on ted talks. He was talking about his recent discoveries in biotechnology and how they went about doing it. We also talked about different bioartists and their approach to biology<br />
<br />
<br />
<br />
'''Day 12''' <br />
<br />
Today we went to NCBS for the first time.we had gone to meet the person who would help us create the new bacteria and understand how to go about doing it. <br />
<br />
<br />
<br />
'''Day 13'''<br />
<br />
Today we saw the different parts that make a functioning gene. it was shocking to see its resemblance to electronic parts and circuits. we also found out about the parts regestry and how to search it. The pats registry is a large collection of already existing dna. We also talked about bioremediation which is creation of an organism that solves environmental problems. Plants are better at bioremediation as they can be plantrd and removed easily thus not disturbing the ecology of an area . We also learnt about PCR (polymerase chain reaction) which was discovered by Kary Mullis. In DNA the base pairs are held together by an H bond. This bond is brokrn at 80 degrees celcious. The polymerase is used to duplicate the DNA and produce 2 strands of DNA. hut at 80 degrees celcious te polymerase coagulatees. thus we introduce an extremophile (organism that survives in extreme climates) that is genetically engeneered to produce polymerase. thus making it a chain reaction.<br />
<br />
<br />
<br />
'''Day 14'''<br />
<br />
Today we talked about gene scilencing. In this process some of the genes get turned off. This happens at the transcription level. Scilencing occurs when 2 strands of mRNA are created that are complementary to each other. Thus they recombine and are not allowed to leave the nucleus. Thus the protein is not created.<br />
<br />
We also researched on different bioartists that use biological phinominons as a form of art.today we looked at George gessart, Adam Zeretsky , Eduardo Katz, Petrissia Piccinini and so on. It is amazing to see how biologyitself was a form of art. And each bioart work had a deeper understanding to it.<br />
<br />
<br />
<br />
'''Day 15'''<br />
<br />
I had an appointment with an eye doctor so I couldn’t go for class. But today was the day we got our wiki pages created. In the evening I asked for my password and got it the same day so I didn’t lose out on a lot. They were also told about the 2 foreign faculty that was coming to aid us: Daisy and James.<br />
<br />
<br />
<br />
'''Day 16'''<br />
<br />
Today we didn’t d much. We saw a BBC docmentry : Secrets of Life,The race for the Double Helix. It talked aabout the three groups of scientists involved in finding the double helix structure of DNA and their contributions to the finding. Seeing this documentary made me realize that discovery is like a rat race of who finds what first and who should be credited for it. Also from the previous example of Kary Mullis and the 2 scientiststhst discovered the structure of the double helix, that one doesn’t need to be the smartest to discover something, he just needs to have some knowledge of the subject and a lot of luck.<br />
<br />
<br />
<br />
'''Day 17'''<br />
<br />
Today we saw the different parts that make a functioning gene and their uses. It was shocking to see its resemblance to electronic parts and circuits. we also found out about the parts regestry and how to search it. The pats registry is a large collection of already existing dna. We also researched about how to create yeast cultures. We found the following:<br />
<br />
<br />
'''Preparation or Agar:'''<br />
<br />
-Heat 7 gm of agar in 250 ml of water till it completely desolves.<br />
<br />
-Let it set.<br />
<br />
<br />
'''Preparing yeast culture:'''<br />
<br />
-Heat yeast in water to activate it.<br />
<br />
-sterilize loop.<br />
<br />
-dip in yeast and streak to the agar.<br />
<br />
-keep it aside to grow (24hrs).<br />
<br />
This process failed as we added very little agar (1 gm). Thus the yeast didn’t grow.<br />
<br />
<br />
<br />
'''Day 18'''<br />
<br />
Today we read our first scientific paper on repricilator gene. The gene works as a cycle. There are 3 main proteins that activate 3 different genes, which are produced by those 3 genes. 1 repressor affects the 2nd and the 2nd affects the 3rd. the 3rd in turn affects the first, Thus forming a feedback loop. The Bacteria works as an oscillator circuit using the time for triggering as the time between the action. The terms used in the paper were very confusing and did not make sense at first but slowly came to my understanding. My conclusion is that scientific papers are complicated ways of saying something simple. <br />
<br />
We also tried to grow yeast again his time we tried 3 different concentrations of agar:<br />
<br />
1.4gm/250ml<br />
<br />
4.3gm/250ml<br />
<br />
10gm/250ml<br />
<br />
thee middle concentration was best suited for yeast growth.<br />
<br />
<br />
<br />
'''Day 19'''<br />
<br />
Today we went for a discussion of: Evolution as opposed to design. The speaker talked about the design problem in evolution and whether the design was meant to be or just a coincidence. He gave the example of the eye and the telescope and said that if the telescope had a maker then so did the eye. The only difference is that we know who made the telescope. We also talked about natural and artificial. This raised a big question in my head that if man would interfere in anyway then it would become artificial. Then that would make everything artificial as man has interacted with and changed almost everything. Then that means nothing natural exists….<br />
<br />
<br />
<br />
'''Day 20-24'''<br />
<br />
We spent the next 4 days making our own lab equipment. We made 2 centrifuges, a microscope and an incubator using locally available materials. It took several trials and errors but we finally made all 3. I was working on the incubator and it was a little frustrating to get the perfect temperature.<br />
<br />
<br />
<br />
'''Day 25''' <br />
<br />
Today we worked on collecting all the info of the last 3 weeks. This is what we came up with:<br />
<br />
-We started off by creating bio-art sculptures that used, living organisms. We were told to create art without killing the organism, thus trying to integrate the two (art and biology) together and also having a kind of pet for the summer! <br />
<br />
-Coming from an art background, we tried to add meaning to why we did what we did.<br />
<br />
-After this we came up with ideas for bacteria and an explanation for how they functioned.<br />
<br />
-We created imaginary machines that CAN NOT exist. The idea was to open our minds to the extreme possibilities so as to get new ideas: for our final project.<br />
<br />
-As we went through all the previous works of Igem competitions we realised that almost all the projects fell under 3 major categories, which were: <br />
<br />
<br />
1. Purifiers <br />
<br />
2. Display/sensors/ indicators<br />
<br />
3. Production of energy<br />
<br />
We believed that it would be good to create an organism that would not fall in any of these categories.<br />
<br />
These are all the possibilities that we have come up with till now, hoping to have a excellent outcome. <br />
<br />
<br />
<br />
'''Day 26,27'''<br />
<br />
absent<br />
<br />
<br />
<br />
'''Day 28'''<br />
<br />
I was absent the last 2 days so I was a little lost. But with help I caught up quite fast. Today was also the day I met James and Daisy. Today’s assignment was to come up with an organism for iGEA(genetically engineered art) which was a new compition we started in srishti. We came up with E. cloudy. <br />
<br />
<br />
<br />
'''Day 29'''<br />
<br />
Today we presented our bacteria for iGEA. We were also given conics to read and pich out intresting myths which could be related to synth. biology. All the ones we selscted fell under tese catagories:<br />
Bio prospecting<br />
<br />
Karma<br />
<br />
Ecosystems<br />
<br />
Immunization against a disaster<br />
<br />
Soma<br />
<br />
Jugad (being very prominent)<br />
<br />
<br />
<br />
'''Day 30, 31'''<br />
Using the myths we read through we were told to a create a bacteria that retells the story. We depicted the story of Brahma, Vishnu and Shiva.(The holy trinity)<br />
<br />
<br />
<br />
'''Day 32''' <br />
<br />
Today we looked at the myths that had been created by synthetic biology for the past and the future.<br />
<br />
We were also told to make a scientific diagram for our mythical bacteria. that is to put it in complicated words. <br />
<br />
<br />
<br />
'''Day33'''<br />
<br />
Today we created a mindmap of the so called “actors” of bio technology and who was on which side. <br />
<br />
We also had 2 artists from Level10 comics to talk about the process of making a comic and the steps involved. They also showed us some of their works.<br />
<br />
<br />
<br />
'''Day 34'''<br />
<br />
Each of us was given a topic to do further research in. my topic was Bioethicists<br />
<br />
<br />
<br />
<br />
== '''Bio artists''' ==<br />
<br />
<br />
<br />
===Stellarc:===<br />
<br />
Stellar tries to integrate the biological and technological advances using the human body as the test subject. He tries to show the thin line that exists today between technology and the body which will be broken very soon.<br />
<br />
<br />
<br />
===Orlan:===<br />
<br />
Orlan again uses her own body as a canvas. But instead of technology she uses plastic surgery. If fine art is a visual medium, then Orlan herself is a walking exhibit. Orlan embraces the technology of the time by undergoing these procedures but rejects everything they stand for. Instead of making herself “pretty”, she makes herself grossly disfigured. Orlan is the only artist working so radically with her own body, asking questions about the status of the body in society.<br />
<br />
<br />
<br />
===Patricia Piccinini:===<br />
<br />
The work is quite interesting because of<br />
<br />
1. It’s life like feeling.<br />
<br />
2. Also at first one thinks it is completely impossible & imaginary but at closer inspection realise we are not far from achieving what she has made and that creating such animals are quite possible.<br />
<br />
3. Her art creates ethical debates about the advancements in technology & biology and its relation to nature. And how it is the responsibility of the creator for the new creatures uncertain ethical and physical results.<br />
<br />
<br />
<br />
<br />
== '''My assignments''' ==<br />
<br />
<br />
<br />
<br />
===Living sculpture:(living furniture)===<br />
<br />
<br />
Most of the furniture that we use in places like the lawn or at the beach are made of wood that has been cut from living trees. this living sculpture has both a use and aesthetics. Instead of cutting trees why not grow the according to the shape you need. <br />
<br />
The concept of tree shaping requires one to bend the tree in a desirable shape when it is a small plant. As the tree grows the shape is retained and the bark hardens to form the required shape. This can be called ecofriendly furniture. As the tree branches out, the leaves give shade. It is also cooler below the tree. Also since the tree produces oxygen, the air under the tree is fresh. My final project is to make a living chair. <br />
<br />
"[[File:Tree_shaping.jpg]]"<br />
<br />
I am starting by bending smaller plants and make in a simple loop(1st June). I used string to hold the shape and check after a month.<br />
<br />
[[File:Roll_2.JPG]] [[File:Roll_4.JPG]]<br />
<br />
After a moonth: The plant retains the shape but still needs some time to maintain that shape. <br />
<br />
<br />
===Hypothetical bacteria:(Pressure sensitive Thermo Bacteria)===<br />
<br />
<br />
The Srishti School of art design and tech. has created bacteria that emits heat when pressure is applied on it. It consists of tiny turbine like particles on it’s cell walls. When pressure is applied the cell produces an enzyme that causes the turbines to spin. These cells are tightly packed together in a tiny porous container. The activated turbines hit each other producing heat. The collected heat is magnified by the bacteria and is concentrated at the point of pressure. The temp ranges from 100 to 500 degrees.<br />
<br />
[[File:Bact_0.jpg]]<br />
[[File:Bact1.jpg]]<br />
<br />
The porous container itself is a living organism which concentrates all the heat on the point where the pressure is and spreads the heat across the area where pressure is. both the bacteria live along with each other as symbiotes. The heat producing bacteria feeds on the nutrients supplied by outer shell which is made of sugars and fatty acids. On the other hand the outer shell depends on the thermo bacteria for its shape and heat. Using some amount of the heat produced by the thermo bacteria, the porous outer structure converts cellulose into simple sugars which is food for both the organisms has pores that are about 0.01 nm in diameter all over it which are used to vent out all the extra heat in the form of steam (water is one of the byproducts of converting cellulose into sugar.)<br />
<br />
The organism reproduces by binary fission. When the shell is overloaded with the bacteria it expands until it breaks into 2 pieces. The 2 pieces join to themselves to form 2 separate structures. The outer structure does not break unless there is an internal pressure applied and it immediately joins when it breaks and grows to its normal size in 5 hours to incorporate more bacteria. The bacteria can be killed using an electric charge of 20 volts (D.C.), thus its growth can be controlled. <br />
<br />
This organism can be used for security purposes, as they are too small to be seen and produce enough heat to burn the body. If the amount of heat given out (number of collisions between spindles) can be controlled it can be used for various reasons e.g. Cooking, hot tubs, heated chairs, etc. And being organisms that can reproduce, they don’t need to be replaced.<br />
<br />
<br />
<br />
===Imagenary machine:(Projector bacteria)===<br />
<br />
<br />
The bacteria simply projects ones thoughts to a tangible 2D presentation. These bacteria live in the brain. It is a long egg like structure with 2 antennas. These bacteria are fixed on a circular moving belt. The bacteria pick up brain waves with the antenna and produce an image corresponding to the wave. <br />
<br />
[[File:Bact_3.jpg]]<br />
<br />
The optic nerve of the right eye touches one of the bacteria and picks up the image. As the rotating belt moves the optic nerve picks up other images and forms a stop motion of the thoughts in the mind on the retina. The image on the retina is inverted.<br />
<br />
The bacteria secrete an enzyme that runs along the optic nerve and makes the retina emit light. The image on the retina gets projected on to the lens of the right eye and is diverged by the lens thus magnifying the images it gets projected. The user of the bacteria can voluntarily secrete an enzyme that makes the optic nerve move away from the bacteria, thus stopping the projection and the eye starts to function normally. The bacteria reproduce by binary fission. One of the daughter bacteria replaces the parent and the second bacterium gets attatched to belt and acts as food for the bacteria.<br />
<br />
<br />
<br />
===DIY Equipnent===<br />
<br />
[[DIY Incubator]]<br />
[[DIY Sterlisation Hood]]<br />
[[DIY Water Bath]]<br />
[[ReacTable]]<br />
<br />
<br />
<br />
===iGEA:(E.Cloudy)===<br />
<br />
Bacteria which help coordinate your music with the weather [[File:Ec1.jpg|150px|left]]<br />
<br />
<br />
<br />
Escheriscia Cloudy or E. Cloudy is a Bacteria which is temperature sensitive and produces electricity. Its unique mix of qualities has been used to program a machine which plays music play lists of the user’s choice depending on the weather.<br />
<br />
The E.Cloudy bacterium have been created by combining two existing BioBrick parts – <br />
<br />
-BBa_K098995, responsible for the thermo sensitivity.(designed by the Harvard 2008 igem team)<br />
<br />
-BBa_K499271, responsible for the electricity.( designed by Boris Kirov igem 2010 )<br />
<br />
'''How the two BioBricks are connected'''<br />
<br />
•The thermo sensitive complex produces a certain protein on exposure to heat.<br />
This protein triggers off the second complex, making it generate a current<br />
<br />
'''How the machine works'''<br />
<br />
•The temperature sensitive bacteria creates current depending on the climate temp (more temp = more current). <br />
<br />
•The current passes through an amplifier to get a readable current. <br />
<br />
•As current passes through the voltmeter the needle moves increasingly. <br />
<br />
•Each temp range triggers the playing of a certain play list( ex a range of 0-10= soothing play list/ energetic play list depending on the user).<br />
<br />
•The machine has its own software which is loaded onto a computer or laptop. The machine is connected to the computer with a USB cable. <br />
<br />
[[File:Picture1.jpg|600px|]]<br />
<br />
'''Deeper into the Bacteria'''<br />
<br />
•The bacteria self reproduce.<br />
<br />
•They are in a way cannibalistic;<br />
Every time a bacteria reproduces, the mother bacteria is consumed by the child.<br />
[[File:Ec2.jpg|250px|right]]<br />
<br />
<br />
'''How it could Fail and Why this over a fully mechanical system?'''<br />
<br />
The system could malfunction if –<br />
<br />
•The bacterial container got contaminated by anything that could kill or reduce capacity of the bacteria.<br />
<br />
•We don’t know if the electricity would kill the bacteria. <br />
<br />
'''Why this?''' <br />
<br />
The same machine can be made using a thermometer, however, with a thermometer, there arises a chance of it getting ruined permanently. <br />
Also it can be looked upon as an alternative, a novelty, an exploration. <br />
How it ties into the criteria detailed by the contest <br />
<br />
•Social critique – creates moods, makes you question your own mood and keeps you conscious of the weather and its changes.<br />
<br />
•This ties into remix culture – apart from the obvious remixing of genes that the original escheriscia coli have undergone, looking it at it from an artistic angle, it’s sort of like replacing your weather man’s report with your own bacterial weather report! <br />
<br />
<br />
'''The effects of this bacterial product on the world.'''<br />
<br />
We have divided the consequence of introducing this product into the market into categories such as – <br />
<br />
'''Socio-Cultural'''<br />
<br />
We feel that this product has high potential to enter popular culture. It’s something which would help take individualism to a new level. It could be a new way to bring nature closer to us and observe it better. <br />
<br />
'''Economic - Financial'''<br />
<br />
The circuitry of this product wouldn’t be expensive, but producing the bacteria maybe the one to raise the price.<br />
•Who would be able to afford it? <br />
<br />
•What percentage of the population<br />
does this group make up?<br />
<br />
•Why would they want to buy it? (novelty and interest could lead to a social phenomenon!)<br />
<br />
•Does this say anything about us as consumers?<br />
<br />
•How much of an effect would it have on our economy? <br />
<br />
'''Technology'''<br />
<br />
We’ve seen bacteria producing fuel and the idea of the bacterial battery. Could energy producing bacteria be our future power houses? <br />
<br />
How would a product integrating living cells into a non-living machine be received by the tech industry? <br />
<br />
'''Science'''<br />
<br />
Could this product trigger off another set of ideas that could be beneficial to other sciences? We think it’s a possibility. <br />
<br />
'''Art'''<br />
<br />
Art is deceptive, it can pack a hard punch without seeming like it. <br />
<br />
Art has a lot to do with creating a sense of awareness, to make people question things around them. <br />
<br />
The concept behind this product (apart from being aware of the weather it creates awareness in how two very different genes, from possibly to very different organisms have been put together to create a machine) could lead us to questioning our rights to remix things (also, is it ok to mix the machine with living cells?) , our rights to play with natural selection, can we define this as a form of natural selection? <br />
<br />
<br />
<br />
===Bacteria based on indian myth:(The Holy Trinity)===<br />
<br />
<br />
When was the last time you ever read an Indian mythological story and asked your self – what if I can do that? Indian Mythology is known to be the most culturally rich, colourful, dramatic and at the same time metaphorically ambitious story, ever told. The numbers of different versions are more than the number of sarees that came off Draupadi! It’s like a roller coaster ride of emotions which at the end of every story brings in ‘balance’.<br />
<br />
As an Artist and Designer, whenever we read an Indian mythological story I have to say it’s quite amazing because these are some stories that have characters that can pretty much do whatever they want! Gods.... Isn’t that what we all want? To do whatever we like? And not have to worry about consequences? And just know that at the end of it all there will be balance? I think that’s some food for thought.<br />
<br />
As a team, we first read through the most famous stories in Indian mythology, and then had a fascinating discussion with a learned scholar in mythology and history. Arshia (the scholar) helped us put our facts together in the most fun filled way which after a few drinks turned out to be a very satisfying knowledge-full night.<br />
<br />
Our task now (which is the most interesting part) was to find links and parallels to any myth and use synthetic biology to fill the gap! I find that highly fascinating. SO we went through a few myths and as soon as we landed on Shiva’s third eye, there was a full stop. Shiva’s third eye is the destroyer, when he opens it; disaster is all over the place. So the last you want to do it tick him off. We took that in a metaphorical sense and thought about what if that third eye was a way for us to see when our real eyes are shut? So what if I had bacteria that could communicate with thoughts through neuron activity and when I’m wired up to a projector, it displays my thought in 3D space. Then communication would be in its most pure form since there is a lot of loss when converting thought to word or deed. Then what if I wired up to another person and started communicating with thought! Or if I left messages for someone on a platform and they could later wire up and receive it. But as usual there’s always a ‘BUT’, and the first one here is privacy. Privacy is by far the most delicate issue here. SO we kept this on hold for the time being and instead of looking at parts of a myth we moved away and looked at the Big Picture.<br />
<br />
[[File:Collages.jpg|400px|Left|]]<br />
[[File:Main 2.JPG|400px|right|]]<br />
<br />
The Holy Trinity – Brahma, the creator, Vishnu the Preserver and Shiva the destroyer. These are the first and foremost gods that rule the heavens, earth and hell. As you’re reading this don’t those three words –creator, preserver and destroyer burst out of your imagination and find its way to synthetic biology? Well, that’s exactly what happened to us. So here’s our idea.<br />
<br />
[[File:Collages2.jpg|400px|Left|]]<br />
<br />
In a over populated culture of bacteria. There is ‘imbalance’ since there more bacteria to eat than the nutrition available. So the ‘gods’ are summoned! The VISH-gene bacteria (the preserver) now gets into action by producing a chemical to which ONLY the SHIV-gene bacteria (the destroyer) can read. This then activates the SHIV-gene bacteria to in turn produce a chemical which start disrupting the bacterial cells in the colony. The ‘gods’ bacteria are of course resistant to this chemical. The SHIV-gene bacteria once activated has no control over killing the other cells. So once he has destroyed ample number of cells, he needs to be stopped, which ONLY the BRAHM-gene can do. So now the VISH-gene bacteria produces another chemical which ONLY the BRAHM-gene bacteria can read and this in turn activates the BRAHM-gene bacteria to produce a chemical to deactivate the SHIV-gene bacteria. Now there’s been too many bacteria killed so after a while of reproduction the optimum level is reached and ‘balance’ is restored. The subjects are happy and so are the gods. Soon after reproduction hastens up and there is over population again so the whole process is initiated making it a loop. <br />
<br />
[[File:Main 1.JPG|400px|Right|]]<br />
<br />
BRAHM-gene bacteria are identified with the presence of the BRAHM-gene. When the BBRAHM- gene replicates it does not transfer it’s genetic material completely, instead it retains one part of the gene, so the other bacteria now is the VISH-gene bacteria. When the BRAHM-gene bacteria replicates for the second time it does not transfer the BRAHM-gene at all making the new organism the SHIV-gene. <br />
<br />
We’d like to think that this mythological concept, besides being fascinating will definitely find its way to a good purpose in the world of Synthetic Biology. So wait up until then.<br />
<br />
<br />
'''Scientific reprisentation'''<br />
<br />
[[File:Bvs.jpg]] [[File:Bvs2.jpg]]<br />
<br />
'''07) The promise of Synthetic Biology:'''<br />
<br />
<br />
Such is the promise of synthetic biology, which, according to the people who have tried to explain it to me, is basically a marketing term for all kinds of research in which scientists tinker with biological bits to make useful things — sort of like living Lego blocks.<br />
<br />
The gift of man-made life — biofuels made of algae, tumor-seeking microbial missiles — comes wrapped in a risk: What if the oil-eating bug mutates, as the horror-movie version inevitably does, and starts eating other things — like us?<br />
<br />
It's perhaps not surprising that when bioethicists describe synthetic biology, they sound like the characters in Jurassic Park.<br />
"When dealing with biological entities," notes Thomas Murray, president of the Hastings Center, a bioethics organization, "life has a tendency to find a way."<br />
<br />
Accidents at power plants are bad enough. But a leak from a bioreactor could be worse, since bacteria can learn new tricks when you're not looking. Microbes excel at exchanging DNA, Murray notes — "like microbial French kissing." That bug we introduce into the ocean to sip the spill might end up swapping DNA with other living things. "We have a ways to go," he says, "before we can really know what risks we're running if we release these organisms into the environment."<br />
<br />
Without public oversight, we are certain to wake up one day to news of some private breakthrough that rattles our bones: a human-animal hybrid, a cloned child, a fetus grown solely to harvest its parts.<br />
<br />
As laboratories incubate new blends of man and machine — creatures whose creators used a keyboard — it seems mad to say that philosophy should not intervene.<br />
<br />
The path of progress cuts through the four-way intersection of the moral, medical, religious and political — and whichever way you turn, you are likely to run over someone's deeply held beliefs. Venter's bombshell revived the oldest of ethical debates, over whether scientists were playing God or proving he does not exist because someone re-enacted Genesis in suburban Maryland.<br />
Others dismiss the worry on the grounds that creating new forms of life is not the same as creating life. One doctor friend of mine suggested that "they haven't created life in any sense of the word, other than a person playing a cassette has invented the tape recorder."<br />
<br />
<br />
"It is vital that we as a society consider, in a thoughtful manner, the significance of this kind of scientific development," Obama writes.<br />
<br />
"Synthetic biology certainly raises deep philosophical and moral questions about the human relationship to nature," according to Gregory Kaebnick, a Hastings Center scholar who is managing the project. "It's not clear what the answers to those questions are. If by 'nature' we mean the world around us, more or less as we found it, we may well decide that synthetic biology does not really change the human relationship to nature—and may even help us preserve what is left of it."<br />
<br />
Myth: Cellulosic ethanol is a decade or more away.<br />
Fact: The world's first cellulosic ethanol production facility -- owned and operated by Iogen in Ottawa, Canada -- has been converting wheat straw into ethanol since 2004. Abengoa Bioenergy is completing construction of a commercial-scale cellulosic ethanol facility, located in Salamanca, Spain, that will by the end of 2007 begin producing 1.2 million gallons of cellulosic ethanol from wheat straw each year.<br />
<br />
<br />
Conclusion:<br />
People are bound to disagree about when scientists are crossing some moral Rubicon. That is all the more reason to debate, in public and in advance, where those boundaries lie — rather than doing so after the fact, when researchers are celebrating some technical triumph and the rest of us are wondering what price we will pay for it.<br />
<br />
'''Information from:'''<br />
<br />
'''http://www.time.com/time/magazine/article/0,9171,1997447,00.html'''<br />
<br />
'''http://machineslikeus.com/.../moral-issues-raised-synthetic-biology-subject-hastings -center-workshop - .html'''<br />
<br />
'''http://www.economist.com/node/16163154/comments?page=1.html'''<br />
<br />
===bioethicists:===<br />
<br />
<br />
<br />
'''Biodesign India'''<br />
<br />
Redesigning life for novel applications<br />
<br />
http://biodesignindia.org/index.htm<br />
<br />
<br />
The evolving synthetic biology community in our country needs to discuss unique ideas, interest groups, synergies, funding avenues and useful applications. The key goal will be to identify areas where India has potential to take global leadership.<br />
<br />
<br />
<br />
'''Etc group'''<br />
<br />
http://www.etcgroup.org/en/issues/biotechnology<br />
<br />
ETC Group is not fundamentally opposed to genetic engineering, but we have profound concerns about the way it is being foisted upon the world. In the current social, economic and political context, genetic engineering is not safe, and involves unacceptable levels of risk to people and the environment. For ETC Group, the fundamental issue is control.<br />
<br />
Reports:<br />
<br />
Patenting the "Climate Genes" ...and Capturing the Climate Agenda <br />
<br />
Direct-to-Consumer DNA Testing and the Myth of Personalized Medicine: Spit Kits, SNP Chips and Human Genomics<br />
<br />
Terminator: The Sequel<br />
<br />
ETC Group Report on Geoengineering Climate Change<br />
<br />
Extreme Genetic Engineering: An Introduction to Synthetic Biology<br />
<br />
Nanotech Rx-Medical applications of Nano-scale technologies: What Impact on Marginalized communities? <br />
<br />
A Tiny Primer on Nano-scale Technologies ...and The Little BANG Theory <br />
<br />
Down on the Farm: The Impact of Nano-scale Technologies on Food and Agriculture <br />
<br />
Report Prepared for the South Centre - The Potential Impacts of Nano-Scale Technologies on Commodity Markets: The Implications for Commodity Dependent Developing Countries<br />
<br />
<br />
<br />
'''Johns Hopkins (Berman Institute)''' <br />
<br />
http://www.lse.ac.uk/collections/humanRights/research/groups/Bioethics.htm<br />
<br />
Berman Institute scholar calls for a new legal, ethical framework for research with human tissue specimens<br />
What’s known on the subject: There is growing concern and confusion about the use of “banked” human tissue and cells for research. Several court cases involving the use of human tissue specimens, recent stories in the news, as well as the popularity of a book, The Immortal Life of Henrietta Lacks, all reflect a growing interest in the rights and expectations of the people who provide tissue samples and DNA for research.<br />
What this article adds: This review contends that the current legal and ethical framework for the use of human tissue specimens in research fails to consider the role or preferences of the tissue contributors, and argues that courts have failed to apply a consistent legal framework in addressing disputes between contributors and recipients of the biological samples used in research. <br />
This paper proposes a framework that acknowledges the separate contexts and relationships inherent in that distinction, and sets out the social, legal and ethical perils of ignoring the role that tissue sample providers play in the research enterprise.<br />
<br />
<br />
<br />
'''LSE BIOS''' <br />
<br />
http://www.lse.ac.uk/collections/humanRights/research/groups/Bioethics.htm<br />
<br />
The Bioethics, Rights and Human Rights group is led by Dr Alasdair Cochrane.<br />
<br />
Members:<br />
<br />
Btihaj Ajana (BIOS)<br />
<br />
Perveen Ali (Department of Law)<br />
<br />
Rachel Bell (BIOS)<br />
<br />
Meg Clinch (BIOS)<br />
<br />
Caitlin Connors (BIOS)<br />
<br />
Dr Carrie Friese (BIOS)<br />
<br />
Dr Roberto Fumagalli (Department of Philosophy, Logic and Scientific Method)<br />
<br />
Professor Conor Gearty (Department of Law)<br />
<br />
Amy Hinterberger (BIOS)<br />
<br />
Professor Emily Jackson (Department of Law) <br />
<br />
Kerstin Klein (BIOS)<br />
<br />
Dean Peters (Department of Philosophy, Logic and Scientific Method)<br />
<br />
Dr Joelle Abi Rached (BIOS)<br />
<br />
Dr David Reubi (Public & Environmental Health Research Unit, London School of Hygiene and Tropical Medicine)<br />
<br />
Professor Nikolas Rose (BIOS)<br />
<br />
Dr Igor Stramignoni (Department of Law)<br />
<br />
Dr Sivaramjani Thambisetty (Department of Law)<br />
<br />
Dr Scott Vrecko (BIOS)<br />
<br />
Dr Ayo Wahlberg (BIOS)<br />
<br />
Jeremy Williams (Department of Government)<br />
<br />
Alasdair Cochrane joined the Centre for the Study of Human Rights in 2007. He teaches on the core course for the MSc Human Rights ‘Approaches to Human Rights’, as well as on an undergraduate option in Sociology, ‘Environmentalism: Theory Politics and Practice’. Prior to joining the Centre, Alasdair taught in the Department of Government at the LSE, where he completed his PhD. He holds a 1st Class BA in Politics from the University of Sheffield, an MSc in Political Theory, and a PGCHE, both from the LSE.<br />
Alasdair Cochrane’s research interests include the philosophical justification of rights, contemporary political theory, environmentalism, animal ethics and bioethics. <br />
<br />
Selected publications include: <br />
<br />
-“Ownership and Justice for Animals”, Utilitas, Vol. 21, No. 4 (Dec, 2009). <br />
<br />
-“Do Animals Have an Interest in Liberty?”, Political Studies Vol. 57, No. 3 (Oct, 2009). <br />
<br />
-“Animal Rights and Animal Experiments: An Interest-Based Approach”, Res Publica, Vol. 3, No. 3 (Sep. <br />
2007). <br />
<br />
-“Environmental Ethics”, Internet Encyclopedia of Philosophy, (www.iep.utm.edu). <br />
<br />
-Selected research projects under review and in preparation include:<br />
<br />
-“Undignified Bioethics” (paper)<br />
<br />
-“Evaluating the Political Conception of Human Rights” (paper)<br />
<br />
-“Are Human Rights Speciesist and Does it Matter?” (paper)<br />
<br />
-Animal Rights without Liberation (book)<br />
<br />
-An Introduction to Animals and Political Theory (book)<br />
<br />
<br />
<br />
'''The Hastings Center''' <br />
<br />
http://www.thehastingscenter.org/Publications/BriefingBook/Default.aspx<br />
<br />
The Hastings Center, founded in 1969, is an independent, non-partisan, non-profit bioethics research institute based in the United States. It is dedicated to the examination of essential questions in health care, biotechnology, and the environment. The center has over 200 fellows, including many physicians, attorneys, PhDs and bioethicists.<br />
<br />
Bioethics Briefing Book<br />
<br />
From Birth to Death and Bench to Clinic: The Hastings Center Bioethics Briefing Book for Journalists, Policymakers, and Campaigns contains 36 overviews of issues in bioethics of high public interest, such as abortion, health care reform, human and sports enhancement, organ transplantation, personalized medicine, medical error, and stem cells. The chapters, written by leading ethicists, are nonpartisan, presenting reasonable considerations from various perspectives that are grounded in good scientific and ethical facts. They each include recent news stories, clickable experts to contact, linked resources, and (where available) recent legislation and campaign positions. Greater detail on how to use the book is in the introduction. The three framing essays offer valuable insights into the historical and increasing relevance of bioethics to public policy.<br />
<br />
<br />
<br />
'''Biotechnology Regulatory Bill of India – Five Fallacies'''<br />
<br />
Find out the loopholes in the bill which can have disastrous effect not to India alone bu to whole world at: <br />
<br />
http://scienceray.com/technology/biotechnology-regulatory-bill-of-india-five-fallacies/<br />
<br />
<br />
Mind map<br />
<br />
[[File:Bioethisists_mindmap.jpg]]</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=FArhad&diff=2810FArhad2010-10-27T04:24:19Z<p>Farhad: </p>
<hr />
<div>== '''Journal''' ==<br />
<br />
<br />
<br />
<br />
'''Day 1'''<br />
<br />
After a very long time I had again opened my mind to biology. The last time I had studied biology was in the 10th grade and for the first half hour of the class everything pretty much went over my head. It had been a long time since I had heard these words and they actually sounded like Greek to me. But slowly everything I had learned in the past came back to me.<br />
<br />
In the first class we discussed about general information regarding the first theories of evolution and how they were replaced by others as we come to this day. WE also talked about DNA and its purpose.<br />
<br />
<br />
<br />
'''Day 2'''<br />
<br />
Today we talked about Mendel’s laws of segregation and independence. A very important point is that you don’t need to be a scientist or have a PhD. to discover things. We got to know how genes are passed down from one generation to another. Also alleles are outputs of genes (allele=pea being round or wrinkled.) The terminology used may take some time to get used to. It is amazing to actually see a cell splitting into 2. We then talked about chromosomes and how they decide the characteristics of a person.<br />
<br />
If Genome=book,<br />
<br />
Then DNA=volume,<br />
<br />
And Chromosome=library<br />
<br />
We also saw a video that talked about where gen. engineering would be about 30 yrs. from now. another important thing to consider is the ethics of the topic. Is creating new species good or bad for the world? Is it really progress or just an illusion of progress that we are blindly following that will lead us to our end???...<br />
<br />
<br />
<br />
'''Day 3'''<br />
<br />
Today we started off with seeing how gene mutation is not a good thing. For eg. Cigarette smoking causes the gene p53 to permanently mutate thus causing lung cancer.we then talked about the basic requirements for being genetic material, which are as follows<br />
<br />
1 information storage-Dna has 4 proteins that can be arranged in any way creating different codes<br />
<br />
2 accurate replication-there is a chance of 1 ni a million that the gene is defective, and if it’s so it gets disposed.<br />
<br />
3 it must be expressed as a phenotype- A phenotype is any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, or behavior<br />
<br />
4 it should be able to change –i.e. every individual has different characteristics therefore DNA is different<br />
<br />
DNA is like a symbol for bio like an atom for chem. DNA stands for dioxyribose nucleic acid. It consists of a sugar phosphate backbone and ATGC base pairs. The base pairs are what create code of the DNA for creating proteins.<br />
(Sugar=dioxy ribose, base pairs=nucleic acid) <br />
<br />
A=adenine<br />
<br />
T=thymine<br />
<br />
G=guanine<br />
<br />
C=cytosine<br />
<br />
The proportion of A & T is always equal. Similarly G=C. DNA replication is called semi conservative replication. In this process the DNA is split into its 2 separate helical structures (unzipped )and each of the single helix join to the respective base pair. Thus forming 2 similar DNA 2ble helixes. <br />
All somatic cells (non sex cells) have the same amount DNA specific organism. On the other hand sex cells (e.g. sperm) there is only half the total amount of DNA. The other half is in the sex cells of the mate. Thus the child gets 1 half each of the parents’ genes. Also genetic engineering is not creation of genes but just modifying the original genes to create a different protein.<br />
<br />
<br />
<br />
'''Day 4'''<br />
<br />
Today we talked about proteins. Proteins are polymers of amino acids. There are 20 types of amino acids, 8 of which cannot be produced by man. Thus they need to be consumed.the shape of he protein is very sensitive to the environment.(eg. An egg on heating becomes solid. <br />
<br />
There are 2 types of proteins based on their function:<br />
<br />
-Structural proteins ( hair, muscle collagen, etc.)<br />
<br />
-Enzymes <br />
<br />
enzymes are surfaces for reactions to occur. They act as catylists for reactions in the body. Enzyme names usually end with the letters “ase” eg .polymerase. proteins are also present in the nucleus.thus the DNA contains the gene and the proteins in the nucleus are the phenotype.<br />
<br />
<br />
<br />
'''Day 5'''<br />
<br />
As we talked yesterday gene= DNA and the protein= phenotype(expression). Today we talked about the process of protein creation using DNA. In the nucleus one of the helix of the DNA gets replicated to form RNA(RNA=1/2DNA).RNA is the set of instructions for producing protein. The RNA travels outside the nucleus and goes to the ribosome. The ribosome is like the factory for producing proteins. There are free proteins in the cell in pairs of 3 called codons that act as input for the ribosome. The protein pair is selected according to the code in the RNA(ATC produces a certain protein.) There are 20 types of proteins and only 4 codes in the RNA. Thus the RNA is in pairs of 3 to create enough no of codes for the 20 proteins.<br />
<br />
In DNA only 1 of the 2 helix is used for production, however it is a double helix for easy replication. When DNA is replicated, each of the daughter DNA has 1 of the helix of the parent DNA. Also the other helix decides where in the body the protein is used. <br />
<br />
<br />
<br />
'''Day 6'''<br />
<br />
Today we talked about the genome and genome sequencing. The first type of genome sequencing was hierarchal sequencing where there are certain landmarks in the genome which are used for genome sequencing. The other method is called shotgun sequencing. longer sequences get subdivided into smaller fragments, and subsequently reassembled to give the overall sequence.98% of the RNA produced does not even leave the nucleus. The walls of the nucleus act as as a purifier.they are like a simple on off switch. we also talked about bacteria that have a self defence against<br />
<br />
<br />
<br />
'''Day 7'''<br />
<br />
We talked about recombinant DNA. Recombinant DNA is DNA that is artificially created from two or more sources and is incorporated into a single recombinant molecule. Recombinant DNA (rDNA) is a form of DNA that does not exist naturally, but is created by combining DNA sequences that would not normally occur together. <br />
<br />
Most of the bacteria have a restriction enzyme which cuts up foreign DNA. Therefore it is sometimes difficult to splice DNA. This process of splicing can create new types of organisms. This is what synthetic biology is based on. Usually a bacteria called E.coli is used for this as it is not dangerous to experiment on. Synthetic bio. Has many applications. It is used to study particular sequences that are very tiny(the sequence is put in the bacteria and amplified), to express phenotypes, to increase the quantities of proteins , etc. <br />
<br />
<br />
<br />
'''Day 8'''<br />
<br />
Isolating genes was always done from the phenotype to theto the DNA, but that changed while trying to cure muscular dystrophy. The doctor tried to sequence the gene from the dNA to the phenotype. This is called reverse genetics. He found that a small gene on the x chromosome was missing. This gene was responsible for production of distrophin which connects the muscle fiber to the cells. Distrophin can be replaced by urotrophin , which can be produced by a drug. Thus the problem was cured. In the nucleus mRNA of about 14,600 base pairs is formed, most of which ars not required. the introns remove about 79 peaces from the mRNA by gene splicing in the nucleus itself.<br />
<br />
The DNA library is a volume of the genome. Hybrid DNA is a combination of 2 DNA from 2 different places. The geme and a vecter is combined and introduced into the bacteria. the bacteria takes the new gene and adds it to the original gene. The bacteria is allowed to grow and half the DNA of the new bactrria is introduced so that the full(double helix) DNA is fished out. Thus hybrid DNA is created.<br />
<br />
<br />
<br />
'''Day 9'''<br />
<br />
Today we talked about transgenetics which is DNA of more than 1 species. The the method used is called gene splicing which was first done by Boyle. While working with fruit flies he found that a certain gene called the homiobox genes were responsible for descision of what grows where. Thus by changing this gene he could change the position of different body parts. Thus started synthetic biology which was literally engeneering biology.<br />
<br />
<br />
<br />
'''Day 10'''<br />
<br />
Today we talked about creating a hypothetical bacteriaof our own. We also given a talk on hybrids and new creatures. The concept of hybrids has existed since many ages. The available technology and advancements in biology has made it possible to create such hybrids. Radical plastic surgens do exactly this. They add extra parts to the body through surgery.<br />
<br />
<br />
<br />
'''Day 11'''<br />
<br />
Today we saw a video of craig venter on ted talks. He was talking about his recent discoveries in biotechnology and how they went about doing it. We also talked about different bioartists and their approach to biology<br />
<br />
<br />
<br />
'''Day 12''' <br />
<br />
Today we went to NCBS for the first time.we had gone to meet the person who would help us create the new bacteria and understand how to go about doing it. <br />
<br />
<br />
<br />
'''Day 13'''<br />
<br />
Today we saw the different parts that make a functioning gene. it was shocking to see its resemblance to electronic parts and circuits. we also found out about the parts regestry and how to search it. The pats registry is a large collection of already existing dna. We also talked about bioremediation which is creation of an organism that solves environmental problems. Plants are better at bioremediation as they can be plantrd and removed easily thus not disturbing the ecology of an area . We also learnt about PCR (polymerase chain reaction) which was discovered by Kary Mullis. In DNA the base pairs are held together by an H bond. This bond is brokrn at 80 degrees celcious. The polymerase is used to duplicate the DNA and produce 2 strands of DNA. hut at 80 degrees celcious te polymerase coagulatees. thus we introduce an extremophile (organism that survives in extreme climates) that is genetically engeneered to produce polymerase. thus making it a chain reaction.<br />
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<br />
<br />
'''Day 14'''<br />
<br />
Today we talked about gene scilencing. In this process some of the genes get turned off. This happens at the transcription level. Scilencing occurs when 2 strands of mRNA are created that are complementary to each other. Thus they recombine and are not allowed to leave the nucleus. Thus the protein is not created.<br />
<br />
We also researched on different bioartists that use biological phinominons as a form of art.today we looked at George gessart, Adam Zeretsky , Eduardo Katz, Petrissia Piccinini and so on. It is amazing to see how biologyitself was a form of art. And each bioart work had a deeper understanding to it.<br />
<br />
<br />
<br />
'''Day 15'''<br />
<br />
I had an appointment with an eye doctor so I couldn’t go for class. But today was the day we got our wiki pages created. In the evening I asked for my password and got it the same day so I didn’t lose out on a lot. They were also told about the 2 foreign faculty that was coming to aid us: Daisy and James.<br />
<br />
<br />
<br />
'''Day 16'''<br />
<br />
Today we didn’t d much. We saw a BBC docmentry : Secrets of Life,The race for the Double Helix. It talked aabout the three groups of scientists involved in finding the double helix structure of DNA and their contributions to the finding. Seeing this documentary made me realize that discovery is like a rat race of who finds what first and who should be credited for it. Also from the previous example of Kary Mullis and the 2 scientiststhst discovered the structure of the double helix, that one doesn’t need to be the smartest to discover something, he just needs to have some knowledge of the subject and a lot of luck.<br />
<br />
<br />
<br />
'''Day 17'''<br />
<br />
Today we saw the different parts that make a functioning gene and their uses. It was shocking to see its resemblance to electronic parts and circuits. we also found out about the parts regestry and how to search it. The pats registry is a large collection of already existing dna. We also researched about how to create yeast cultures. We found the following:<br />
<br />
<br />
'''Preparation or Agar:'''<br />
<br />
-Heat 7 gm of agar in 250 ml of water till it completely desolves.<br />
<br />
-Let it set.<br />
<br />
<br />
'''Preparing yeast culture:'''<br />
<br />
-Heat yeast in water to activate it.<br />
<br />
-sterilize loop.<br />
<br />
-dip in yeast and streak to the agar.<br />
<br />
-keep it aside to grow (24hrs).<br />
<br />
This process failed as we added very little agar (1 gm). Thus the yeast didn’t grow.<br />
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<br />
<br />
'''Day 18'''<br />
<br />
Today we read our first scientific paper on repricilator gene. The gene works as a cycle. There are 3 main proteins that activate 3 different genes, which are produced by those 3 genes. 1 repressor affects the 2nd and the 2nd affects the 3rd. the 3rd in turn affects the first, Thus forming a feedback loop. The Bacteria works as an oscillator circuit using the time for triggering as the time between the action. The terms used in the paper were very confusing and did not make sense at first but slowly came to my understanding. My conclusion is that scientific papers are complicated ways of saying something simple. <br />
<br />
We also tried to grow yeast again his time we tried 3 different concentrations of agar:<br />
<br />
1.4gm/250ml<br />
<br />
4.3gm/250ml<br />
<br />
10gm/250ml<br />
<br />
thee middle concentration was best suited for yeast growth.<br />
<br />
<br />
<br />
'''Day 19'''<br />
<br />
Today we went for a discussion of: Evolution as opposed to design. The speaker talked about the design problem in evolution and whether the design was meant to be or just a coincidence. He gave the example of the eye and the telescope and said that if the telescope had a maker then so did the eye. The only difference is that we know who made the telescope. We also talked about natural and artificial. This raised a big question in my head that if man would interfere in anyway then it would become artificial. Then that would make everything artificial as man has interacted with and changed almost everything. Then that means nothing natural exists….<br />
<br />
<br />
<br />
'''Day 20-24'''<br />
<br />
We spent the next 4 days making our own lab equipment. We made 2 centrifuges, a microscope and an incubator using locally available materials. It took several trials and errors but we finally made all 3. I was working on the incubator and it was a little frustrating to get the perfect temperature.<br />
<br />
<br />
<br />
'''Day 25''' <br />
<br />
Today we worked on collecting all the info of the last 3 weeks. This is what we came up with:<br />
<br />
-We started off by creating bio-art sculptures that used, living organisms. We were told to create art without killing the organism, thus trying to integrate the two (art and biology) together and also having a kind of pet for the summer! <br />
<br />
-Coming from an art background, we tried to add meaning to why we did what we did.<br />
<br />
-After this we came up with ideas for bacteria and an explanation for how they functioned.<br />
<br />
-We created imaginary machines that CAN NOT exist. The idea was to open our minds to the extreme possibilities so as to get new ideas: for our final project.<br />
<br />
-As we went through all the previous works of Igem competitions we realised that almost all the projects fell under 3 major categories, which were: <br />
<br />
<br />
1. Purifiers <br />
<br />
2. Display/sensors/ indicators<br />
<br />
3. Production of energy<br />
<br />
We believed that it would be good to create an organism that would not fall in any of these categories.<br />
<br />
These are all the possibilities that we have come up with till now, hoping to have a excellent outcome. <br />
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<br />
<br />
'''Day 26,27'''<br />
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absent<br />
<br />
<br />
<br />
'''Day 28'''<br />
<br />
I was absent the last 2 days so I was a little lost. But with help I caught up quite fast. Today was also the day I met James and Daisy. Today’s assignment was to come up with an organism for iGEA(genetically engineered art) which was a new compition we started in srishti. We came up with E. cloudy. <br />
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<br />
<br />
'''Day 29'''<br />
<br />
Today we presented our bacteria for iGEA. We were also given conics to read and pich out intresting myths which could be related to synth. biology. All the ones we selscted fell under tese catagories:<br />
Bio prospecting<br />
<br />
Karma<br />
<br />
Ecosystems<br />
<br />
Immunization against a disaster<br />
<br />
Soma<br />
<br />
Jugad (being very prominent)<br />
<br />
<br />
<br />
'''Day 30, 31'''<br />
Using the myths we read through we were told to a create a bacteria that retells the story. We depicted the story of Brahma, Vishnu and Shiva.(The holy trinity)<br />
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<br />
<br />
'''Day 32''' <br />
<br />
Today we looked at the myths that had been created by synthetic biology for the past and the future.<br />
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We were also told to make a scientific diagram for our mythical bacteria. that is to put it in complicated words. <br />
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<br />
<br />
'''Day33'''<br />
<br />
Today we created a mindmap of the so called “actors” of bio technology and who was on which side. <br />
<br />
We also had 2 artists from Level10 comics to talk about the process of making a comic and the steps involved. They also showed us some of their works.<br />
<br />
<br />
<br />
'''Day 34'''<br />
<br />
Each of us was given a topic to do further research in. my topic was Bioethicists<br />
<br />
<br />
<br />
<br />
== '''Bio artists''' ==<br />
<br />
<br />
<br />
===Stellarc:===<br />
<br />
Stellar tries to integrate the biological and technological advances using the human body as the test subject. He tries to show the thin line that exists today between technology and the body which will be broken very soon.<br />
<br />
<br />
<br />
===Orlan:===<br />
<br />
Orlan again uses her own body as a canvas. But instead of technology she uses plastic surgery. If fine art is a visual medium, then Orlan herself is a walking exhibit. Orlan embraces the technology of the time by undergoing these procedures but rejects everything they stand for. Instead of making herself “pretty”, she makes herself grossly disfigured. Orlan is the only artist working so radically with her own body, asking questions about the status of the body in society.<br />
<br />
<br />
<br />
===Patricia Piccinini:===<br />
<br />
The work is quite interesting because of<br />
<br />
1. It’s life like feeling.<br />
<br />
2. Also at first one thinks it is completely impossible & imaginary but at closer inspection realise we are not far from achieving what she has made and that creating such animals are quite possible.<br />
<br />
3. Her art creates ethical debates about the advancements in technology & biology and its relation to nature. And how it is the responsibility of the creator for the new creatures uncertain ethical and physical results.<br />
<br />
<br />
<br />
<br />
== '''My assignments''' ==<br />
<br />
<br />
<br />
<br />
===Living sculpture:(living furniture)===<br />
<br />
<br />
Most of the furniture that we use in places like the lawn or at the beach are made of wood that has been cut from living trees. this living sculpture has both a use and aesthetics. Instead of cutting trees why not grow the according to the shape you need. <br />
<br />
The concept of tree shaping requires one to bend the tree in a desirable shape when it is a small plant. As the tree grows the shape is retained and the bark hardens to form the required shape. This can be called ecofriendly furniture. As the tree branches out, the leaves give shade. It is also cooler below the tree. Also since the tree produces oxygen, the air under the tree is fresh. My final project is to make a living chair. <br />
<br />
"[[File:Tree_shaping.jpg]]"<br />
<br />
I am starting by bending smaller plants and make in a simple loop(1st June). I used string to hold the shape and check after a month.<br />
<br />
[[File:Roll_2.JPG]] [[File:Roll_4.JPG]]<br />
<br />
After a moonth: The plant retains the shape but still needs some time to maintain that shape. <br />
<br />
<br />
===Hypothetical bacteria:(Pressure sensitive Thermo Bacteria)===<br />
<br />
<br />
The Srishti School of art design and tech. has created bacteria that emits heat when pressure is applied on it. It consists of tiny turbine like particles on it’s cell walls. When pressure is applied the cell produces an enzyme that causes the turbines to spin. These cells are tightly packed together in a tiny porous container. The activated turbines hit each other producing heat. The collected heat is magnified by the bacteria and is concentrated at the point of pressure. The temp ranges from 100 to 500 degrees.<br />
<br />
[[File:Bact_0.jpg]]<br />
[[File:Bact1.jpg]]<br />
<br />
The porous container itself is a living organism which concentrates all the heat on the point where the pressure is and spreads the heat across the area where pressure is. both the bacteria live along with each other as symbiotes. The heat producing bacteria feeds on the nutrients supplied by outer shell which is made of sugars and fatty acids. On the other hand the outer shell depends on the thermo bacteria for its shape and heat. Using some amount of the heat produced by the thermo bacteria, the porous outer structure converts cellulose into simple sugars which is food for both the organisms has pores that are about 0.01 nm in diameter all over it which are used to vent out all the extra heat in the form of steam (water is one of the byproducts of converting cellulose into sugar.)<br />
<br />
The organism reproduces by binary fission. When the shell is overloaded with the bacteria it expands until it breaks into 2 pieces. The 2 pieces join to themselves to form 2 separate structures. The outer structure does not break unless there is an internal pressure applied and it immediately joins when it breaks and grows to its normal size in 5 hours to incorporate more bacteria. The bacteria can be killed using an electric charge of 20 volts (D.C.), thus its growth can be controlled. <br />
<br />
This organism can be used for security purposes, as they are too small to be seen and produce enough heat to burn the body. If the amount of heat given out (number of collisions between spindles) can be controlled it can be used for various reasons e.g. Cooking, hot tubs, heated chairs, etc. And being organisms that can reproduce, they don’t need to be replaced.<br />
<br />
<br />
<br />
===Imagenary machine:(Projector bacteria)===<br />
<br />
<br />
The bacteria simply projects ones thoughts to a tangible 2D presentation. These bacteria live in the brain. It is a long egg like structure with 2 antennas. These bacteria are fixed on a circular moving belt. The bacteria pick up brain waves with the antenna and produce an image corresponding to the wave. <br />
<br />
[[File:Bact_3.jpg]]<br />
<br />
The optic nerve of the right eye touches one of the bacteria and picks up the image. As the rotating belt moves the optic nerve picks up other images and forms a stop motion of the thoughts in the mind on the retina. The image on the retina is inverted.<br />
<br />
The bacteria secrete an enzyme that runs along the optic nerve and makes the retina emit light. The image on the retina gets projected on to the lens of the right eye and is diverged by the lens thus magnifying the images it gets projected. The user of the bacteria can voluntarily secrete an enzyme that makes the optic nerve move away from the bacteria, thus stopping the projection and the eye starts to function normally. The bacteria reproduce by binary fission. One of the daughter bacteria replaces the parent and the second bacterium gets attatched to belt and acts as food for the bacteria.<br />
<br />
<br />
<br />
===DIY Equipnent===<br />
<br />
[[DIY Incubator]]<br />
[[DIY Sterlisation Hood]]<br />
[[DIY Water Bath]]<br />
[[ReacTable]]<br />
<br />
<br />
<br />
===iGEA:(E.Cloudy)===<br />
<br />
Bacteria which help coordinate your music with the weather [[File:Ec1.jpg|150px|left]]<br />
<br />
<br />
<br />
Escheriscia Cloudy or E. Cloudy is a Bacteria which is temperature sensitive and produces electricity. Its unique mix of qualities has been used to program a machine which plays music play lists of the user’s choice depending on the weather.<br />
<br />
The E.Cloudy bacterium have been created by combining two existing BioBrick parts – <br />
<br />
-BBa_K098995, responsible for the thermo sensitivity.(designed by the Harvard 2008 igem team)<br />
<br />
-BBa_K499271, responsible for the electricity.( designed by Boris Kirov igem 2010 )<br />
<br />
'''How the two BioBricks are connected'''<br />
<br />
•The thermo sensitive complex produces a certain protein on exposure to heat.<br />
This protein triggers off the second complex, making it generate a current<br />
<br />
'''How the machine works'''<br />
<br />
•The temperature sensitive bacteria creates current depending on the climate temp (more temp = more current). <br />
<br />
•The current passes through an amplifier to get a readable current. <br />
<br />
•As current passes through the voltmeter the needle moves increasingly. <br />
<br />
•Each temp range triggers the playing of a certain play list( ex a range of 0-10= soothing play list/ energetic play list depending on the user).<br />
<br />
•The machine has its own software which is loaded onto a computer or laptop. The machine is connected to the computer with a USB cable. <br />
<br />
[[File:Picture1.jpg|600px|]]<br />
<br />
'''Deeper into the Bacteria'''<br />
<br />
•The bacteria self reproduce.<br />
<br />
•They are in a way cannibalistic;<br />
Every time a bacteria reproduces, the mother bacteria is consumed by the child.<br />
[[File:Ec2.jpg|250px|right]]<br />
<br />
<br />
'''How it could Fail and Why this over a fully mechanical system?'''<br />
<br />
The system could malfunction if –<br />
<br />
•The bacterial container got contaminated by anything that could kill or reduce capacity of the bacteria.<br />
<br />
•We don’t know if the electricity would kill the bacteria. <br />
<br />
'''Why this?''' <br />
<br />
The same machine can be made using a thermometer, however, with a thermometer, there arises a chance of it getting ruined permanently. <br />
Also it can be looked upon as an alternative, a novelty, an exploration. <br />
How it ties into the criteria detailed by the contest <br />
<br />
•Social critique – creates moods, makes you question your own mood and keeps you conscious of the weather and its changes.<br />
<br />
•This ties into remix culture – apart from the obvious remixing of genes that the original escheriscia coli have undergone, looking it at it from an artistic angle, it’s sort of like replacing your weather man’s report with your own bacterial weather report! <br />
<br />
<br />
'''The effects of this bacterial product on the world.'''<br />
<br />
We have divided the consequence of introducing this product into the market into categories such as – <br />
<br />
'''Socio-Cultural'''<br />
<br />
We feel that this product has high potential to enter popular culture. It’s something which would help take individualism to a new level. It could be a new way to bring nature closer to us and observe it better. <br />
<br />
'''Economic - Financial'''<br />
<br />
The circuitry of this product wouldn’t be expensive, but producing the bacteria maybe the one to raise the price.<br />
•Who would be able to afford it? <br />
<br />
•What percentage of the population<br />
does this group make up?<br />
<br />
•Why would they want to buy it? (novelty and interest could lead to a social phenomenon!)<br />
<br />
•Does this say anything about us as consumers?<br />
<br />
•How much of an effect would it have on our economy? <br />
<br />
'''Technology'''<br />
<br />
We’ve seen bacteria producing fuel and the idea of the bacterial battery. Could energy producing bacteria be our future power houses? <br />
<br />
How would a product integrating living cells into a non-living machine be received by the tech industry? <br />
<br />
'''Science'''<br />
<br />
Could this product trigger off another set of ideas that could be beneficial to other sciences? We think it’s a possibility. <br />
<br />
'''Art'''<br />
<br />
Art is deceptive, it can pack a hard punch without seeming like it. <br />
<br />
Art has a lot to do with creating a sense of awareness, to make people question things around them. <br />
<br />
The concept behind this product (apart from being aware of the weather it creates awareness in how two very different genes, from possibly to very different organisms have been put together to create a machine) could lead us to questioning our rights to remix things (also, is it ok to mix the machine with living cells?) , our rights to play with natural selection, can we define this as a form of natural selection? <br />
<br />
<br />
<br />
===Bacteria based on indian myth:(The Holy Trinity- group ass)===<br />
<br />
<br />
When was the last time you ever read an Indian mythological story and asked your self – what if I can do that? Indian Mythology is known to be the most culturally rich, colourful, dramatic and at the same time metaphorically ambitious story, ever told. The numbers of different versions are more than the number of sarees that came off Draupadi! It’s like a roller coaster ride of emotions which at the end of every story brings in ‘balance’.<br />
<br />
As an Artist and Designer, whenever we read an Indian mythological story I have to say it’s quite amazing because these are some stories that have characters that can pretty much do whatever they want! Gods.... Isn’t that what we all want? To do whatever we like? And not have to worry about consequences? And just know that at the end of it all there will be balance? I think that’s some food for thought.<br />
<br />
As a team, we first read through the most famous stories in Indian mythology, and then had a fascinating discussion with a learned scholar in mythology and history. Arshia (the scholar) helped us put our facts together in the most fun filled way which after a few drinks turned out to be a very satisfying knowledge-full night.<br />
<br />
Our task now (which is the most interesting part) was to find links and parallels to any myth and use synthetic biology to fill the gap! I find that highly fascinating. SO we went through a few myths and as soon as we landed on Shiva’s third eye, there was a full stop. Shiva’s third eye is the destroyer, when he opens it; disaster is all over the place. So the last you want to do it tick him off. We took that in a metaphorical sense and thought about what if that third eye was a way for us to see when our real eyes are shut? So what if I had bacteria that could communicate with thoughts through neuron activity and when I’m wired up to a projector, it displays my thought in 3D space. Then communication would be in its most pure form since there is a lot of loss when converting thought to word or deed. Then what if I wired up to another person and started communicating with thought! Or if I left messages for someone on a platform and they could later wire up and receive it. But as usual there’s always a ‘BUT’, and the first one here is privacy. Privacy is by far the most delicate issue here. SO we kept this on hold for the time being and instead of looking at parts of a myth we moved away and looked at the Big Picture.<br />
<br />
[[File:Collages.jpg|400px|Left|]]<br />
[[File:Main 2.JPG|400px|right|]]<br />
<br />
The Holy Trinity – Brahma, the creator, Vishnu the Preserver and Shiva the destroyer. These are the first and foremost gods that rule the heavens, earth and hell. As you’re reading this don’t those three words –creator, preserver and destroyer burst out of your imagination and find its way to synthetic biology? Well, that’s exactly what happened to us. So here’s our idea.<br />
<br />
[[File:Collages2.jpg|400px|Left|]]<br />
<br />
In a over populated culture of bacteria. There is ‘imbalance’ since there more bacteria to eat than the nutrition available. So the ‘gods’ are summoned! The VISH-gene bacteria (the preserver) now gets into action by producing a chemical to which ONLY the SHIV-gene bacteria (the destroyer) can read. This then activates the SHIV-gene bacteria to in turn produce a chemical which start disrupting the bacterial cells in the colony. The ‘gods’ bacteria are of course resistant to this chemical. The SHIV-gene bacteria once activated has no control over killing the other cells. So once he has destroyed ample number of cells, he needs to be stopped, which ONLY the BRAHM-gene can do. So now the VISH-gene bacteria produces another chemical which ONLY the BRAHM-gene bacteria can read and this in turn activates the BRAHM-gene bacteria to produce a chemical to deactivate the SHIV-gene bacteria. Now there’s been too many bacteria killed so after a while of reproduction the optimum level is reached and ‘balance’ is restored. The subjects are happy and so are the gods. Soon after reproduction hastens up and there is over population again so the whole process is initiated making it a loop. <br />
<br />
[[File:Main 1.JPG|400px|Right|]]<br />
<br />
BRAHM-gene bacteria are identified with the presence of the BRAHM-gene. When the BBRAHM- gene replicates it does not transfer it’s genetic material completely, instead it retains one part of the gene, so the other bacteria now is the VISH-gene bacteria. When the BRAHM-gene bacteria replicates for the second time it does not transfer the BRAHM-gene at all making the new organism the SHIV-gene. <br />
<br />
We’d like to think that this mythological concept, besides being fascinating will definitely find its way to a good purpose in the world of Synthetic Biology. So wait up until then.<br />
<br />
<br />
'''Scientific reprisentation'''<br />
<br />
[[File:Bvs.jpg]] [[File:Bvs2.jpg]]<br />
<br />
'''07) The promise of Synthetic Biology:'''<br />
<br />
<br />
Such is the promise of synthetic biology, which, according to the people who have tried to explain it to me, is basically a marketing term for all kinds of research in which scientists tinker with biological bits to make useful things — sort of like living Lego blocks.<br />
<br />
The gift of man-made life — biofuels made of algae, tumor-seeking microbial missiles — comes wrapped in a risk: What if the oil-eating bug mutates, as the horror-movie version inevitably does, and starts eating other things — like us?<br />
<br />
It's perhaps not surprising that when bioethicists describe synthetic biology, they sound like the characters in Jurassic Park.<br />
"When dealing with biological entities," notes Thomas Murray, president of the Hastings Center, a bioethics organization, "life has a tendency to find a way."<br />
<br />
Accidents at power plants are bad enough. But a leak from a bioreactor could be worse, since bacteria can learn new tricks when you're not looking. Microbes excel at exchanging DNA, Murray notes — "like microbial French kissing." That bug we introduce into the ocean to sip the spill might end up swapping DNA with other living things. "We have a ways to go," he says, "before we can really know what risks we're running if we release these organisms into the environment."<br />
<br />
Without public oversight, we are certain to wake up one day to news of some private breakthrough that rattles our bones: a human-animal hybrid, a cloned child, a fetus grown solely to harvest its parts.<br />
<br />
As laboratories incubate new blends of man and machine — creatures whose creators used a keyboard — it seems mad to say that philosophy should not intervene.<br />
<br />
The path of progress cuts through the four-way intersection of the moral, medical, religious and political — and whichever way you turn, you are likely to run over someone's deeply held beliefs. Venter's bombshell revived the oldest of ethical debates, over whether scientists were playing God or proving he does not exist because someone re-enacted Genesis in suburban Maryland.<br />
Others dismiss the worry on the grounds that creating new forms of life is not the same as creating life. One doctor friend of mine suggested that "they haven't created life in any sense of the word, other than a person playing a cassette has invented the tape recorder."<br />
<br />
<br />
"It is vital that we as a society consider, in a thoughtful manner, the significance of this kind of scientific development," Obama writes.<br />
<br />
"Synthetic biology certainly raises deep philosophical and moral questions about the human relationship to nature," according to Gregory Kaebnick, a Hastings Center scholar who is managing the project. "It's not clear what the answers to those questions are. If by 'nature' we mean the world around us, more or less as we found it, we may well decide that synthetic biology does not really change the human relationship to nature—and may even help us preserve what is left of it."<br />
<br />
Myth: Cellulosic ethanol is a decade or more away.<br />
Fact: The world's first cellulosic ethanol production facility -- owned and operated by Iogen in Ottawa, Canada -- has been converting wheat straw into ethanol since 2004. Abengoa Bioenergy is completing construction of a commercial-scale cellulosic ethanol facility, located in Salamanca, Spain, that will by the end of 2007 begin producing 1.2 million gallons of cellulosic ethanol from wheat straw each year.<br />
<br />
<br />
Conclusion:<br />
People are bound to disagree about when scientists are crossing some moral Rubicon. That is all the more reason to debate, in public and in advance, where those boundaries lie — rather than doing so after the fact, when researchers are celebrating some technical triumph and the rest of us are wondering what price we will pay for it.<br />
<br />
'''Information from:'''<br />
<br />
'''http://www.time.com/time/magazine/article/0,9171,1997447,00.html'''<br />
<br />
'''http://machineslikeus.com/.../moral-issues-raised-synthetic-biology-subject-hastings -center-workshop - .html'''<br />
<br />
'''http://www.economist.com/node/16163154/comments?page=1.html'''<br />
<br />
<br />
<br />
<br />
===bioethicists:===<br />
<br />
<br />
<br />
'''Biodesign India'''<br />
<br />
Redesigning life for novel applications<br />
<br />
http://biodesignindia.org/index.htm<br />
<br />
<br />
The evolving synthetic biology community in our country needs to discuss unique ideas, interest groups, synergies, funding avenues and useful applications. The key goal will be to identify areas where India has potential to take global leadership.<br />
<br />
<br />
<br />
'''Etc group'''<br />
<br />
http://www.etcgroup.org/en/issues/biotechnology<br />
<br />
ETC Group is not fundamentally opposed to genetic engineering, but we have profound concerns about the way it is being foisted upon the world. In the current social, economic and political context, genetic engineering is not safe, and involves unacceptable levels of risk to people and the environment. For ETC Group, the fundamental issue is control.<br />
<br />
Reports:<br />
<br />
Patenting the "Climate Genes" ...and Capturing the Climate Agenda <br />
<br />
Direct-to-Consumer DNA Testing and the Myth of Personalized Medicine: Spit Kits, SNP Chips and Human Genomics<br />
<br />
Terminator: The Sequel<br />
<br />
ETC Group Report on Geoengineering Climate Change<br />
<br />
Extreme Genetic Engineering: An Introduction to Synthetic Biology<br />
<br />
Nanotech Rx-Medical applications of Nano-scale technologies: What Impact on Marginalized communities? <br />
<br />
A Tiny Primer on Nano-scale Technologies ...and The Little BANG Theory <br />
<br />
Down on the Farm: The Impact of Nano-scale Technologies on Food and Agriculture <br />
<br />
Report Prepared for the South Centre - The Potential Impacts of Nano-Scale Technologies on Commodity Markets: The Implications for Commodity Dependent Developing Countries<br />
<br />
<br />
<br />
'''Johns Hopkins (Berman Institute)''' <br />
<br />
http://www.lse.ac.uk/collections/humanRights/research/groups/Bioethics.htm<br />
<br />
Berman Institute scholar calls for a new legal, ethical framework for research with human tissue specimens<br />
What’s known on the subject: There is growing concern and confusion about the use of “banked” human tissue and cells for research. Several court cases involving the use of human tissue specimens, recent stories in the news, as well as the popularity of a book, The Immortal Life of Henrietta Lacks, all reflect a growing interest in the rights and expectations of the people who provide tissue samples and DNA for research.<br />
What this article adds: This review contends that the current legal and ethical framework for the use of human tissue specimens in research fails to consider the role or preferences of the tissue contributors, and argues that courts have failed to apply a consistent legal framework in addressing disputes between contributors and recipients of the biological samples used in research. <br />
This paper proposes a framework that acknowledges the separate contexts and relationships inherent in that distinction, and sets out the social, legal and ethical perils of ignoring the role that tissue sample providers play in the research enterprise.<br />
<br />
<br />
<br />
'''LSE BIOS''' <br />
<br />
http://www.lse.ac.uk/collections/humanRights/research/groups/Bioethics.htm<br />
<br />
The Bioethics, Rights and Human Rights group is led by Dr Alasdair Cochrane.<br />
<br />
Members:<br />
<br />
Btihaj Ajana (BIOS)<br />
<br />
Perveen Ali (Department of Law)<br />
<br />
Rachel Bell (BIOS)<br />
<br />
Meg Clinch (BIOS)<br />
<br />
Caitlin Connors (BIOS)<br />
<br />
Dr Carrie Friese (BIOS)<br />
<br />
Dr Roberto Fumagalli (Department of Philosophy, Logic and Scientific Method)<br />
<br />
Professor Conor Gearty (Department of Law)<br />
<br />
Amy Hinterberger (BIOS)<br />
<br />
Professor Emily Jackson (Department of Law) <br />
<br />
Kerstin Klein (BIOS)<br />
<br />
Dean Peters (Department of Philosophy, Logic and Scientific Method)<br />
<br />
Dr Joelle Abi Rached (BIOS)<br />
<br />
Dr David Reubi (Public & Environmental Health Research Unit, London School of Hygiene and Tropical Medicine)<br />
<br />
Professor Nikolas Rose (BIOS)<br />
<br />
Dr Igor Stramignoni (Department of Law)<br />
<br />
Dr Sivaramjani Thambisetty (Department of Law)<br />
<br />
Dr Scott Vrecko (BIOS)<br />
<br />
Dr Ayo Wahlberg (BIOS)<br />
<br />
Jeremy Williams (Department of Government)<br />
<br />
Alasdair Cochrane joined the Centre for the Study of Human Rights in 2007. He teaches on the core course for the MSc Human Rights ‘Approaches to Human Rights’, as well as on an undergraduate option in Sociology, ‘Environmentalism: Theory Politics and Practice’. Prior to joining the Centre, Alasdair taught in the Department of Government at the LSE, where he completed his PhD. He holds a 1st Class BA in Politics from the University of Sheffield, an MSc in Political Theory, and a PGCHE, both from the LSE.<br />
Alasdair Cochrane’s research interests include the philosophical justification of rights, contemporary political theory, environmentalism, animal ethics and bioethics. <br />
<br />
Selected publications include: <br />
<br />
-“Ownership and Justice for Animals”, Utilitas, Vol. 21, No. 4 (Dec, 2009). <br />
<br />
-“Do Animals Have an Interest in Liberty?”, Political Studies Vol. 57, No. 3 (Oct, 2009). <br />
<br />
-“Animal Rights and Animal Experiments: An Interest-Based Approach”, Res Publica, Vol. 3, No. 3 (Sep. <br />
2007). <br />
<br />
-“Environmental Ethics”, Internet Encyclopedia of Philosophy, (www.iep.utm.edu). <br />
<br />
-Selected research projects under review and in preparation include:<br />
<br />
-“Undignified Bioethics” (paper)<br />
<br />
-“Evaluating the Political Conception of Human Rights” (paper)<br />
<br />
-“Are Human Rights Speciesist and Does it Matter?” (paper)<br />
<br />
-Animal Rights without Liberation (book)<br />
<br />
-An Introduction to Animals and Political Theory (book)<br />
<br />
<br />
<br />
'''The Hastings Center''' <br />
<br />
http://www.thehastingscenter.org/Publications/BriefingBook/Default.aspx<br />
<br />
The Hastings Center, founded in 1969, is an independent, non-partisan, non-profit bioethics research institute based in the United States. It is dedicated to the examination of essential questions in health care, biotechnology, and the environment. The center has over 200 fellows, including many physicians, attorneys, PhDs and bioethicists.<br />
<br />
Bioethics Briefing Book<br />
<br />
From Birth to Death and Bench to Clinic: The Hastings Center Bioethics Briefing Book for Journalists, Policymakers, and Campaigns contains 36 overviews of issues in bioethics of high public interest, such as abortion, health care reform, human and sports enhancement, organ transplantation, personalized medicine, medical error, and stem cells. The chapters, written by leading ethicists, are nonpartisan, presenting reasonable considerations from various perspectives that are grounded in good scientific and ethical facts. They each include recent news stories, clickable experts to contact, linked resources, and (where available) recent legislation and campaign positions. Greater detail on how to use the book is in the introduction. The three framing essays offer valuable insights into the historical and increasing relevance of bioethics to public policy.<br />
<br />
<br />
<br />
'''Biotechnology Regulatory Bill of India – Five Fallacies'''<br />
<br />
Find out the loopholes in the bill which can have disastrous effect not to India alone bu to whole world at: <br />
<br />
http://scienceray.com/technology/biotechnology-regulatory-bill-of-india-five-fallacies/<br />
<br />
<br />
Mind map<br />
<br />
[[File:Bioethisists_mindmap.jpg]]</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=FArhad&diff=2809FArhad2010-10-27T04:17:54Z<p>Farhad: </p>
<hr />
<div>== '''Journal''' ==<br />
<br />
<br />
<br />
<br />
'''Day 1'''<br />
<br />
After a very long time I had again opened my mind to biology. The last time I had studied biology was in the 10th grade and for the first half hour of the class everything pretty much went over my head. It had been a long time since I had heard these words and they actually sounded like Greek to me. But slowly everything I had learned in the past came back to me.<br />
<br />
In the first class we discussed about general information regarding the first theories of evolution and how they were replaced by others as we come to this day. WE also talked about DNA and its purpose.<br />
<br />
<br />
<br />
'''Day 2'''<br />
<br />
Today we talked about Mendel’s laws of segregation and independence. A very important point is that you don’t need to be a scientist or have a PhD. to discover things. We got to know how genes are passed down from one generation to another. Also alleles are outputs of genes (allele=pea being round or wrinkled.) The terminology used may take some time to get used to. It is amazing to actually see a cell splitting into 2. We then talked about chromosomes and how they decide the characteristics of a person.<br />
<br />
If Genome=book,<br />
<br />
Then DNA=volume,<br />
<br />
And Chromosome=library<br />
<br />
We also saw a video that talked about where gen. engineering would be about 30 yrs. from now. another important thing to consider is the ethics of the topic. Is creating new species good or bad for the world? Is it really progress or just an illusion of progress that we are blindly following that will lead us to our end???...<br />
<br />
<br />
<br />
'''Day 3'''<br />
<br />
Today we started off with seeing how gene mutation is not a good thing. For eg. Cigarette smoking causes the gene p53 to permanently mutate thus causing lung cancer.we then talked about the basic requirements for being genetic material, which are as follows<br />
<br />
1 information storage-Dna has 4 proteins that can be arranged in any way creating different codes<br />
<br />
2 accurate replication-there is a chance of 1 ni a million that the gene is defective, and if it’s so it gets disposed.<br />
<br />
3 it must be expressed as a phenotype- A phenotype is any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, or behavior<br />
<br />
4 it should be able to change –i.e. every individual has different characteristics therefore DNA is different<br />
<br />
DNA is like a symbol for bio like an atom for chem. DNA stands for dioxyribose nucleic acid. It consists of a sugar phosphate backbone and ATGC base pairs. The base pairs are what create code of the DNA for creating proteins.<br />
(Sugar=dioxy ribose, base pairs=nucleic acid) <br />
<br />
A=adenine<br />
<br />
T=thymine<br />
<br />
G=guanine<br />
<br />
C=cytosine<br />
<br />
The proportion of A & T is always equal. Similarly G=C. DNA replication is called semi conservative replication. In this process the DNA is split into its 2 separate helical structures (unzipped )and each of the single helix join to the respective base pair. Thus forming 2 similar DNA 2ble helixes. <br />
All somatic cells (non sex cells) have the same amount DNA specific organism. On the other hand sex cells (e.g. sperm) there is only half the total amount of DNA. The other half is in the sex cells of the mate. Thus the child gets 1 half each of the parents’ genes. Also genetic engineering is not creation of genes but just modifying the original genes to create a different protein.<br />
<br />
<br />
<br />
'''Day 4'''<br />
<br />
Today we talked about proteins. Proteins are polymers of amino acids. There are 20 types of amino acids, 8 of which cannot be produced by man. Thus they need to be consumed.the shape of he protein is very sensitive to the environment.(eg. An egg on heating becomes solid. <br />
<br />
There are 2 types of proteins based on their function:<br />
<br />
-Structural proteins ( hair, muscle collagen, etc.)<br />
<br />
-Enzymes <br />
<br />
enzymes are surfaces for reactions to occur. They act as catylists for reactions in the body. Enzyme names usually end with the letters “ase” eg .polymerase. proteins are also present in the nucleus.thus the DNA contains the gene and the proteins in the nucleus are the phenotype.<br />
<br />
<br />
<br />
'''Day 5'''<br />
<br />
As we talked yesterday gene= DNA and the protein= phenotype(expression). Today we talked about the process of protein creation using DNA. In the nucleus one of the helix of the DNA gets replicated to form RNA(RNA=1/2DNA).RNA is the set of instructions for producing protein. The RNA travels outside the nucleus and goes to the ribosome. The ribosome is like the factory for producing proteins. There are free proteins in the cell in pairs of 3 called codons that act as input for the ribosome. The protein pair is selected according to the code in the RNA(ATC produces a certain protein.) There are 20 types of proteins and only 4 codes in the RNA. Thus the RNA is in pairs of 3 to create enough no of codes for the 20 proteins.<br />
<br />
In DNA only 1 of the 2 helix is used for production, however it is a double helix for easy replication. When DNA is replicated, each of the daughter DNA has 1 of the helix of the parent DNA. Also the other helix decides where in the body the protein is used. <br />
<br />
<br />
<br />
'''Day 6'''<br />
<br />
Today we talked about the genome and genome sequencing. The first type of genome sequencing was hierarchal sequencing where there are certain landmarks in the genome which are used for genome sequencing. The other method is called shotgun sequencing. longer sequences get subdivided into smaller fragments, and subsequently reassembled to give the overall sequence.98% of the RNA produced does not even leave the nucleus. The walls of the nucleus act as as a purifier.they are like a simple on off switch. we also talked about bacteria that have a self defence against<br />
<br />
<br />
<br />
'''Day 7'''<br />
<br />
We talked about recombinant DNA. Recombinant DNA is DNA that is artificially created from two or more sources and is incorporated into a single recombinant molecule. Recombinant DNA (rDNA) is a form of DNA that does not exist naturally, but is created by combining DNA sequences that would not normally occur together. <br />
<br />
Most of the bacteria have a restriction enzyme which cuts up foreign DNA. Therefore it is sometimes difficult to splice DNA. This process of splicing can create new types of organisms. This is what synthetic biology is based on. Usually a bacteria called E.coli is used for this as it is not dangerous to experiment on. Synthetic bio. Has many applications. It is used to study particular sequences that are very tiny(the sequence is put in the bacteria and amplified), to express phenotypes, to increase the quantities of proteins , etc. <br />
<br />
<br />
<br />
'''Day 8'''<br />
<br />
Isolating genes was always done from the phenotype to theto the DNA, but that changed while trying to cure muscular dystrophy. The doctor tried to sequence the gene from the dNA to the phenotype. This is called reverse genetics. He found that a small gene on the x chromosome was missing. This gene was responsible for production of distrophin which connects the muscle fiber to the cells. Distrophin can be replaced by urotrophin , which can be produced by a drug. Thus the problem was cured. In the nucleus mRNA of about 14,600 base pairs is formed, most of which ars not required. the introns remove about 79 peaces from the mRNA by gene splicing in the nucleus itself.<br />
<br />
The DNA library is a volume of the genome. Hybrid DNA is a combination of 2 DNA from 2 different places. The geme and a vecter is combined and introduced into the bacteria. the bacteria takes the new gene and adds it to the original gene. The bacteria is allowed to grow and half the DNA of the new bactrria is introduced so that the full(double helix) DNA is fished out. Thus hybrid DNA is created.<br />
<br />
<br />
<br />
'''Day 9'''<br />
<br />
Today we talked about transgenetics which is DNA of more than 1 species. The the method used is called gene splicing which was first done by Boyle. While working with fruit flies he found that a certain gene called the homiobox genes were responsible for descision of what grows where. Thus by changing this gene he could change the position of different body parts. Thus started synthetic biology which was literally engeneering biology.<br />
<br />
<br />
<br />
'''Day 10'''<br />
<br />
Today we talked about creating a hypothetical bacteriaof our own. We also given a talk on hybrids and new creatures. The concept of hybrids has existed since many ages. The available technology and advancements in biology has made it possible to create such hybrids. Radical plastic surgens do exactly this. They add extra parts to the body through surgery.<br />
<br />
<br />
<br />
'''Day 11'''<br />
<br />
Today we saw a video of craig venter on ted talks. He was talking about his recent discoveries in biotechnology and how they went about doing it. We also talked about different bioartists and their approach to biology<br />
<br />
<br />
<br />
'''Day 12''' <br />
<br />
Today we went to NCBS for the first time.we had gone to meet the person who would help us create the new bacteria and understand how to go about doing it. <br />
<br />
<br />
<br />
'''Day 13'''<br />
<br />
Today we saw the different parts that make a functioning gene. it was shocking to see its resemblance to electronic parts and circuits. we also found out about the parts regestry and how to search it. The pats registry is a large collection of already existing dna. We also talked about bioremediation which is creation of an organism that solves environmental problems. Plants are better at bioremediation as they can be plantrd and removed easily thus not disturbing the ecology of an area . We also learnt about PCR (polymerase chain reaction) which was discovered by Kary Mullis. In DNA the base pairs are held together by an H bond. This bond is brokrn at 80 degrees celcious. The polymerase is used to duplicate the DNA and produce 2 strands of DNA. hut at 80 degrees celcious te polymerase coagulatees. thus we introduce an extremophile (organism that survives in extreme climates) that is genetically engeneered to produce polymerase. thus making it a chain reaction.<br />
<br />
<br />
<br />
'''Day 14'''<br />
<br />
Today we talked about gene scilencing. In this process some of the genes get turned off. This happens at the transcription level. Scilencing occurs when 2 strands of mRNA are created that are complementary to each other. Thus they recombine and are not allowed to leave the nucleus. Thus the protein is not created.<br />
<br />
We also researched on different bioartists that use biological phinominons as a form of art.today we looked at George gessart, Adam Zeretsky , Eduardo Katz, Petrissia Piccinini and so on. It is amazing to see how biologyitself was a form of art. And each bioart work had a deeper understanding to it.<br />
<br />
<br />
<br />
'''Day 15'''<br />
<br />
I had an appointment with an eye doctor so I couldn’t go for class. But today was the day we got our wiki pages created. In the evening I asked for my password and got it the same day so I didn’t lose out on a lot. They were also told about the 2 foreign faculty that was coming to aid us: Daisy and James.<br />
<br />
<br />
<br />
'''Day 16'''<br />
<br />
Today we didn’t d much. We saw a BBC docmentry : Secrets of Life,The race for the Double Helix. It talked aabout the three groups of scientists involved in finding the double helix structure of DNA and their contributions to the finding. Seeing this documentary made me realize that discovery is like a rat race of who finds what first and who should be credited for it. Also from the previous example of Kary Mullis and the 2 scientiststhst discovered the structure of the double helix, that one doesn’t need to be the smartest to discover something, he just needs to have some knowledge of the subject and a lot of luck.<br />
<br />
<br />
<br />
'''Day 17'''<br />
<br />
Today we saw the different parts that make a functioning gene and their uses. It was shocking to see its resemblance to electronic parts and circuits. we also found out about the parts regestry and how to search it. The pats registry is a large collection of already existing dna. We also researched about how to create yeast cultures. We found the following:<br />
<br />
<br />
'''Preparation or Agar:'''<br />
<br />
-Heat 7 gm of agar in 250 ml of water till it completely desolves.<br />
<br />
-Let it set.<br />
<br />
<br />
'''Preparing yeast culture:'''<br />
<br />
-Heat yeast in water to activate it.<br />
<br />
-sterilize loop.<br />
<br />
-dip in yeast and streak to the agar.<br />
<br />
-keep it aside to grow (24hrs).<br />
<br />
This process failed as we added very little agar (1 gm). Thus the yeast didn’t grow.<br />
<br />
<br />
<br />
'''Day 18'''<br />
<br />
Today we read our first scientific paper on repricilator gene. The gene works as a cycle. There are 3 main proteins that activate 3 different genes, which are produced by those 3 genes. 1 repressor affects the 2nd and the 2nd affects the 3rd. the 3rd in turn affects the first, Thus forming a feedback loop. The Bacteria works as an oscillator circuit using the time for triggering as the time between the action. The terms used in the paper were very confusing and did not make sense at first but slowly came to my understanding. My conclusion is that scientific papers are complicated ways of saying something simple. <br />
<br />
We also tried to grow yeast again his time we tried 3 different concentrations of agar:<br />
<br />
1.4gm/250ml<br />
<br />
4.3gm/250ml<br />
<br />
10gm/250ml<br />
<br />
thee middle concentration was best suited for yeast growth.<br />
<br />
<br />
<br />
'''Day 19'''<br />
<br />
Today we went for a discussion of: Evolution as opposed to design. The speaker talked about the design problem in evolution and whether the design was meant to be or just a coincidence. He gave the example of the eye and the telescope and said that if the telescope had a maker then so did the eye. The only difference is that we know who made the telescope. We also talked about natural and artificial. This raised a big question in my head that if man would interfere in anyway then it would become artificial. Then that would make everything artificial as man has interacted with and changed almost everything. Then that means nothing natural exists….<br />
<br />
<br />
<br />
'''Day 20-24'''<br />
<br />
We spent the next 4 days making our own lab equipment. We made 2 centrifuges, a microscope and an incubator using locally available materials. It took several trials and errors but we finally made all 3. I was working on the incubator and it was a little frustrating to get the perfect temperature.<br />
<br />
<br />
<br />
'''Day 25''' <br />
<br />
Today we worked on collecting all the info of the last 3 weeks. This is what we came up with:<br />
<br />
-We started off by creating bio-art sculptures that used, living organisms. We were told to create art without killing the organism, thus trying to integrate the two (art and biology) together and also having a kind of pet for the summer! <br />
<br />
-Coming from an art background, we tried to add meaning to why we did what we did.<br />
<br />
-After this we came up with ideas for bacteria and an explanation for how they functioned.<br />
<br />
-We created imaginary machines that CAN NOT exist. The idea was to open our minds to the extreme possibilities so as to get new ideas: for our final project.<br />
<br />
-As we went through all the previous works of Igem competitions we realised that almost all the projects fell under 3 major categories, which were: <br />
<br />
<br />
1. Purifiers <br />
<br />
2. Display/sensors/ indicators<br />
<br />
3. Production of energy<br />
<br />
We believed that it would be good to create an organism that would not fall in any of these categories.<br />
<br />
These are all the possibilities that we have come up with till now, hoping to have a excellent outcome. <br />
<br />
<br />
<br />
'''Day 26,27'''<br />
<br />
absent<br />
<br />
<br />
<br />
'''Day 28'''<br />
<br />
I was absent the last 2 days so I was a little lost. But with help I caught up quite fast. Today was also the day I met James and Daisy. Today’s assignment was to come up with an organism for iGEA(genetically engineered art) which was a new compition we started in srishti. We came up with E. cloudy. <br />
<br />
<br />
<br />
'''Day 29'''<br />
<br />
Today we presented our bacteria for iGEA. We were also given conics to read and pich out intresting myths which could be related to synth. biology. All the ones we selscted fell under tese catagories:<br />
Bio prospecting<br />
<br />
Karma<br />
<br />
Ecosystems<br />
<br />
Immunization against a disaster<br />
<br />
Soma<br />
<br />
Jugad (being very prominent)<br />
<br />
<br />
<br />
'''Day 30, 31'''<br />
Using the myths we read through we were told to a create a bacteria that retells the story. We depicted the story of Brahma, Vishnu and Shiva.(The holy trinity)<br />
<br />
<br />
<br />
'''Day 32''' <br />
<br />
Today we looked at the myths that had been created by synthetic biology for the past and the future.<br />
<br />
We were also told to make a scientific diagram for our mythical bacteria. that is to put it in complicated words. <br />
<br />
<br />
<br />
'''Day33'''<br />
<br />
Today we created a mindmap of the so called “actors” of bio technology and who was on which side. <br />
<br />
We also had 2 artists from Level10 comics to talk about the process of making a comic and the steps involved. They also showed us some of their works.<br />
<br />
<br />
<br />
'''Day 34'''<br />
<br />
Each of us was given a topic to do further research in. my topic was Bioethicists<br />
<br />
<br />
<br />
<br />
== '''Bio artists''' ==<br />
<br />
<br />
<br />
===Stellarc:===<br />
<br />
Stellar tries to integrate the biological and technological advances using the human body as the test subject. He tries to show the thin line that exists today between technology and the body which will be broken very soon.<br />
<br />
<br />
<br />
===Orlan:===<br />
<br />
Orlan again uses her own body as a canvas. But instead of technology she uses plastic surgery. If fine art is a visual medium, then Orlan herself is a walking exhibit. Orlan embraces the technology of the time by undergoing these procedures but rejects everything they stand for. Instead of making herself “pretty”, she makes herself grossly disfigured. Orlan is the only artist working so radically with her own body, asking questions about the status of the body in society.<br />
<br />
<br />
<br />
===Patricia Piccinini:===<br />
<br />
The work is quite interesting because of<br />
<br />
1. It’s life like feeling.<br />
<br />
2. Also at first one thinks it is completely impossible & imaginary but at closer inspection realise we are not far from achieving what she has made and that creating such animals are quite possible.<br />
<br />
3. Her art creates ethical debates about the advancements in technology & biology and its relation to nature. And how it is the responsibility of the creator for the new creatures uncertain ethical and physical results.<br />
<br />
<br />
<br />
<br />
== '''My assignments''' ==<br />
<br />
<br />
<br />
<br />
===Living sculpture:(living furniture)===<br />
<br />
<br />
Most of the furniture that we use in places like the lawn or at the beach are made of wood that has been cut from living trees. this living sculpture has both a use and aesthetics. Instead of cutting trees why not grow the according to the shape you need. <br />
<br />
The concept of tree shaping requires one to bend the tree in a desirable shape when it is a small plant. As the tree grows the shape is retained and the bark hardens to form the required shape. This can be called ecofriendly furniture. As the tree branches out, the leaves give shade. It is also cooler below the tree. Also since the tree produces oxygen, the air under the tree is fresh. My final project is to make a living chair. <br />
<br />
"[[File:Tree_shaping.jpg]]"<br />
<br />
I am starting by bending smaller plants and make in a simple loop(1st June). I used string to hold the shape and check after a month.<br />
<br />
[[File:Roll_2.JPG]] [[File:Roll_4.JPG]]<br />
<br />
After a moonth: The plant retains the shape but still needs some time to maintain that shape. <br />
<br />
<br />
===Hypothetical bacteria:(Pressure sensitive Thermo Bacteria)===<br />
<br />
<br />
The Srishti School of art design and tech. has created bacteria that emits heat when pressure is applied on it. It consists of tiny turbine like particles on it’s cell walls. When pressure is applied the cell produces an enzyme that causes the turbines to spin. These cells are tightly packed together in a tiny porous container. The activated turbines hit each other producing heat. The collected heat is magnified by the bacteria and is concentrated at the point of pressure. The temp ranges from 100 to 500 degrees.<br />
<br />
[[File:Bact_0.jpg]]<br />
[[File:Bact1.jpg]]<br />
<br />
The porous container itself is a living organism which concentrates all the heat on the point where the pressure is and spreads the heat across the area where pressure is. both the bacteria live along with each other as symbiotes. The heat producing bacteria feeds on the nutrients supplied by outer shell which is made of sugars and fatty acids. On the other hand the outer shell depends on the thermo bacteria for its shape and heat. Using some amount of the heat produced by the thermo bacteria, the porous outer structure converts cellulose into simple sugars which is food for both the organisms has pores that are about 0.01 nm in diameter all over it which are used to vent out all the extra heat in the form of steam (water is one of the byproducts of converting cellulose into sugar.)<br />
<br />
The organism reproduces by binary fission. When the shell is overloaded with the bacteria it expands until it breaks into 2 pieces. The 2 pieces join to themselves to form 2 separate structures. The outer structure does not break unless there is an internal pressure applied and it immediately joins when it breaks and grows to its normal size in 5 hours to incorporate more bacteria. The bacteria can be killed using an electric charge of 20 volts (D.C.), thus its growth can be controlled. <br />
<br />
This organism can be used for security purposes, as they are too small to be seen and produce enough heat to burn the body. If the amount of heat given out (number of collisions between spindles) can be controlled it can be used for various reasons e.g. Cooking, hot tubs, heated chairs, etc. And being organisms that can reproduce, they don’t need to be replaced.<br />
<br />
<br />
<br />
===Imagenary machine:(Projector bacteria)===<br />
<br />
<br />
The bacteria simply projects ones thoughts to a tangible 2D presentation. These bacteria live in the brain. It is a long egg like structure with 2 antennas. These bacteria are fixed on a circular moving belt. The bacteria pick up brain waves with the antenna and produce an image corresponding to the wave. <br />
<br />
[[File:Bact_3.jpg]]<br />
<br />
The optic nerve of the right eye touches one of the bacteria and picks up the image. As the rotating belt moves the optic nerve picks up other images and forms a stop motion of the thoughts in the mind on the retina. The image on the retina is inverted.<br />
<br />
The bacteria secrete an enzyme that runs along the optic nerve and makes the retina emit light. The image on the retina gets projected on to the lens of the right eye and is diverged by the lens thus magnifying the images it gets projected. The user of the bacteria can voluntarily secrete an enzyme that makes the optic nerve move away from the bacteria, thus stopping the projection and the eye starts to function normally. The bacteria reproduce by binary fission. One of the daughter bacteria replaces the parent and the second bacterium gets attatched to belt and acts as food for the bacteria.<br />
<br />
<br />
<br />
===DIY Equipnent===<br />
<br />
[[DIY Incubator]]<br />
[[DIY Sterlisation Hood]]<br />
[[DIY Water Bath]]<br />
[[ReacTable]]<br />
<br />
<br />
<br />
===iGEA:(E.Cloudy)===<br />
<br />
Bacteria which help coordinate your music with the weather <br />
<br />
[[File:Ec1.jpg]]<br />
<br />
Escheriscia Cloudy or E. Cloudy is a Bacteria which is temperature sensitive and produces electricity. Its unique mix of qualities has been used to program a machine which plays music play lists of the user’s choice depending on the weather.<br />
<br />
The E.Cloudy bacterium have been created by combining two existing BioBrick parts – <br />
<br />
-BBa_K098995, responsible for the thermo sensitivity.(designed by the Harvard 2008 igem team)<br />
<br />
-BBa_K499271, responsible for the electricity.( designed by Boris Kirov igem 2010 )<br />
<br />
'''How the two BioBricks are connected'''<br />
<br />
•The thermo sensitive complex produces a certain protein on exposure to heat.<br />
This protein triggers off the second complex, making it generate a current<br />
<br />
'''How the machine works'''<br />
<br />
•The temperature sensitive bacteria creates current depending on the climate temp (more temp = more current). <br />
<br />
•The current passes through an amplifier to get a readable current. <br />
<br />
•As current passes through the voltmeter the needle moves increasingly. <br />
<br />
•Each temp range triggers the playing of a certain play list( ex a range of 0-10= soothing play list/ energetic play list depending on the user).<br />
<br />
•The machine has its own software which is loaded onto a computer or laptop. The machine is connected to the computer with a USB cable. <br />
<br />
[[File:Picture1.jpg]]<br />
<br />
'''Deeper into the Bacteria'''<br />
<br />
•The bacteria self reproduce.<br />
<br />
•They are in a way cannibalistic;<br />
Every time a bacteria reproduces, the mother bacteria is consumed by the child.<br />
[[File:Ec2.jpg]]<br />
<br />
<br />
'''How it could Fail and Why this over a fully mechanical system?'''<br />
<br />
The system could malfunction if –<br />
<br />
•The bacterial container got contaminated by anything that could kill or reduce capacity of the bacteria.<br />
<br />
•We don’t know if the electricity would kill the bacteria. <br />
<br />
'''Why this?''' <br />
<br />
The same machine can be made using a thermometer, however, with a thermometer, there arises a chance of it getting ruined permanently. <br />
Also it can be looked upon as an alternative, a novelty, an exploration. <br />
How it ties into the criteria detailed by the contest <br />
<br />
•Social critique – creates moods, makes you question your own mood and keeps you conscious of the weather and its changes.<br />
<br />
•This ties into remix culture – apart from the obvious remixing of genes that the original escheriscia coli have undergone, looking it at it from an artistic angle, it’s sort of like replacing your weather man’s report with your own bacterial weather report! <br />
<br />
<br />
'''The effects of this bacterial product on the world.'''<br />
<br />
We have divided the consequence of introducing this product into the market into categories such as – <br />
<br />
'''Socio-Cultural'''<br />
<br />
We feel that this product has high potential to enter popular culture. It’s something which would help take individualism to a new level. It could be a new way to bring nature closer to us and observe it better. <br />
<br />
'''Economic - Financial'''<br />
<br />
The circuitry of this product wouldn’t be expensive, but producing the bacteria maybe the one to raise the price.<br />
•Who would be able to afford it? <br />
<br />
•What percentage of the population<br />
does this group make up?<br />
<br />
•Why would they want to buy it? (novelty and interest could lead to a social phenomenon!)<br />
<br />
•Does this say anything about us as consumers?<br />
<br />
•How much of an effect would it have on our economy? <br />
<br />
'''Technology'''<br />
<br />
We’ve seen bacteria producing fuel and the idea of the bacterial battery. Could energy producing bacteria be our future power houses? <br />
<br />
How would a product integrating living cells into a non-living machine be received by the tech industry? <br />
<br />
'''Science'''<br />
<br />
Could this product trigger off another set of ideas that could be beneficial to other sciences? We think it’s a possibility. <br />
<br />
'''Art'''<br />
<br />
Art is deceptive, it can pack a hard punch without seeming like it. <br />
<br />
Art has a lot to do with creating a sense of awareness, to make people question things around them. <br />
<br />
The concept behind this product (apart from being aware of the weather it creates awareness in how two very different genes, from possibly to very different organisms have been put together to create a machine) could lead us to questioning our rights to remix things (also, is it ok to mix the machine with living cells?) , our rights to play with natural selection, can we define this as a form of natural selection? <br />
<br />
<br />
<br />
===Bacteria based on indian myth:(The Holy Trinity- group ass)===<br />
<br />
<br />
When was the last time you ever read an Indian mythological story and asked your self – what if I can do that? Indian Mythology is known to be the most culturally rich, colourful, dramatic and at the same time metaphorically ambitious story, ever told. The numbers of different versions are more than the number of sarees that came off Draupadi! It’s like a roller coaster ride of emotions which at the end of every story brings in ‘balance’.<br />
<br />
As an Artist and Designer, whenever we read an Indian mythological story I have to say it’s quite amazing because these are some stories that have characters that can pretty much do whatever they want! Gods.... Isn’t that what we all want? To do whatever we like? And not have to worry about consequences? And just know that at the end of it all there will be balance? I think that’s some food for thought.<br />
<br />
As a team, we first read through the most famous stories in Indian mythology, and then had a fascinating discussion with a learned scholar in mythology and history. Arshia (the scholar) helped us put our facts together in the most fun filled way which after a few drinks turned out to be a very satisfying knowledge-full night.<br />
<br />
Our task now (which is the most interesting part) was to find links and parallels to any myth and use synthetic biology to fill the gap! I find that highly fascinating. SO we went through a few myths and as soon as we landed on Shiva’s third eye, there was a full stop. Shiva’s third eye is the destroyer, when he opens it; disaster is all over the place. So the last you want to do it tick him off. We took that in a metaphorical sense and thought about what if that third eye was a way for us to see when our real eyes are shut? So what if I had bacteria that could communicate with thoughts through neuron activity and when I’m wired up to a projector, it displays my thought in 3D space. Then communication would be in its most pure form since there is a lot of loss when converting thought to word or deed. Then what if I wired up to another person and started communicating with thought! Or if I left messages for someone on a platform and they could later wire up and receive it. But as usual there’s always a ‘BUT’, and the first one here is privacy. Privacy is by far the most delicate issue here. SO we kept this on hold for the time being and instead of looking at parts of a myth we moved away and looked at the Big Picture.<br />
<br />
[[File:Collages.jpg|400px|Left|]]<br />
[[File:Main 2.JPG|400px|right|]]<br />
<br />
The Holy Trinity – Brahma, the creator, Vishnu the Preserver and Shiva the destroyer. These are the first and foremost gods that rule the heavens, earth and hell. As you’re reading this don’t those three words –creator, preserver and destroyer burst out of your imagination and find its way to synthetic biology? Well, that’s exactly what happened to us. So here’s our idea.<br />
<br />
[[File:Collages2.jpg|400px|Left|]]<br />
<br />
In a over populated culture of bacteria. There is ‘imbalance’ since there more bacteria to eat than the nutrition available. So the ‘gods’ are summoned! The VISH-gene bacteria (the preserver) now gets into action by producing a chemical to which ONLY the SHIV-gene bacteria (the destroyer) can read. This then activates the SHIV-gene bacteria to in turn produce a chemical which start disrupting the bacterial cells in the colony. The ‘gods’ bacteria are of course resistant to this chemical. The SHIV-gene bacteria once activated has no control over killing the other cells. So once he has destroyed ample number of cells, he needs to be stopped, which ONLY the BRAHM-gene can do. So now the VISH-gene bacteria produces another chemical which ONLY the BRAHM-gene bacteria can read and this in turn activates the BRAHM-gene bacteria to produce a chemical to deactivate the SHIV-gene bacteria. Now there’s been too many bacteria killed so after a while of reproduction the optimum level is reached and ‘balance’ is restored. The subjects are happy and so are the gods. Soon after reproduction hastens up and there is over population again so the whole process is initiated making it a loop. <br />
<br />
[[File:Main 1.JPG|400px|Right|]]<br />
<br />
BRAHM-gene bacteria are identified with the presence of the BRAHM-gene. When the BBRAHM- gene replicates it does not transfer it’s genetic material completely, instead it retains one part of the gene, so the other bacteria now is the VISH-gene bacteria. When the BRAHM-gene bacteria replicates for the second time it does not transfer the BRAHM-gene at all making the new organism the SHIV-gene. <br />
<br />
We’d like to think that this mythological concept, besides being fascinating will definitely find its way to a good purpose in the world of Synthetic Biology. So wait up until then.<br />
<br />
<br />
'''Scientific reprisentation'''<br />
<br />
[[File:Bvs.jpg]] [[File:Bvs2.jpg]]<br />
<br />
'''07) The promise of Synthetic Biology:'''<br />
<br />
<br />
Such is the promise of synthetic biology, which, according to the people who have tried to explain it to me, is basically a marketing term for all kinds of research in which scientists tinker with biological bits to make useful things — sort of like living Lego blocks.<br />
<br />
The gift of man-made life — biofuels made of algae, tumor-seeking microbial missiles — comes wrapped in a risk: What if the oil-eating bug mutates, as the horror-movie version inevitably does, and starts eating other things — like us?<br />
<br />
It's perhaps not surprising that when bioethicists describe synthetic biology, they sound like the characters in Jurassic Park.<br />
"When dealing with biological entities," notes Thomas Murray, president of the Hastings Center, a bioethics organization, "life has a tendency to find a way."<br />
<br />
Accidents at power plants are bad enough. But a leak from a bioreactor could be worse, since bacteria can learn new tricks when you're not looking. Microbes excel at exchanging DNA, Murray notes — "like microbial French kissing." That bug we introduce into the ocean to sip the spill might end up swapping DNA with other living things. "We have a ways to go," he says, "before we can really know what risks we're running if we release these organisms into the environment."<br />
<br />
Without public oversight, we are certain to wake up one day to news of some private breakthrough that rattles our bones: a human-animal hybrid, a cloned child, a fetus grown solely to harvest its parts.<br />
<br />
As laboratories incubate new blends of man and machine — creatures whose creators used a keyboard — it seems mad to say that philosophy should not intervene.<br />
<br />
The path of progress cuts through the four-way intersection of the moral, medical, religious and political — and whichever way you turn, you are likely to run over someone's deeply held beliefs. Venter's bombshell revived the oldest of ethical debates, over whether scientists were playing God or proving he does not exist because someone re-enacted Genesis in suburban Maryland.<br />
Others dismiss the worry on the grounds that creating new forms of life is not the same as creating life. One doctor friend of mine suggested that "they haven't created life in any sense of the word, other than a person playing a cassette has invented the tape recorder."<br />
<br />
<br />
"It is vital that we as a society consider, in a thoughtful manner, the significance of this kind of scientific development," Obama writes.<br />
<br />
"Synthetic biology certainly raises deep philosophical and moral questions about the human relationship to nature," according to Gregory Kaebnick, a Hastings Center scholar who is managing the project. "It's not clear what the answers to those questions are. If by 'nature' we mean the world around us, more or less as we found it, we may well decide that synthetic biology does not really change the human relationship to nature—and may even help us preserve what is left of it."<br />
<br />
Myth: Cellulosic ethanol is a decade or more away.<br />
Fact: The world's first cellulosic ethanol production facility -- owned and operated by Iogen in Ottawa, Canada -- has been converting wheat straw into ethanol since 2004. Abengoa Bioenergy is completing construction of a commercial-scale cellulosic ethanol facility, located in Salamanca, Spain, that will by the end of 2007 begin producing 1.2 million gallons of cellulosic ethanol from wheat straw each year.<br />
<br />
<br />
Conclusion:<br />
People are bound to disagree about when scientists are crossing some moral Rubicon. That is all the more reason to debate, in public and in advance, where those boundaries lie — rather than doing so after the fact, when researchers are celebrating some technical triumph and the rest of us are wondering what price we will pay for it.<br />
<br />
'''Information from:'''<br />
<br />
'''http://www.time.com/time/magazine/article/0,9171,1997447,00.html'''<br />
<br />
'''http://machineslikeus.com/.../moral-issues-raised-synthetic-biology-subject-hastings -center-workshop - .html'''<br />
<br />
'''http://www.economist.com/node/16163154/comments?page=1.html'''<br />
<br />
<br />
<br />
<br />
===bioethicists:===<br />
<br />
<br />
<br />
'''Biodesign India'''<br />
<br />
Redesigning life for novel applications<br />
<br />
http://biodesignindia.org/index.htm<br />
<br />
<br />
The evolving synthetic biology community in our country needs to discuss unique ideas, interest groups, synergies, funding avenues and useful applications. The key goal will be to identify areas where India has potential to take global leadership.<br />
<br />
<br />
<br />
'''Etc group'''<br />
<br />
http://www.etcgroup.org/en/issues/biotechnology<br />
<br />
ETC Group is not fundamentally opposed to genetic engineering, but we have profound concerns about the way it is being foisted upon the world. In the current social, economic and political context, genetic engineering is not safe, and involves unacceptable levels of risk to people and the environment. For ETC Group, the fundamental issue is control.<br />
<br />
Reports:<br />
<br />
Patenting the "Climate Genes" ...and Capturing the Climate Agenda <br />
<br />
Direct-to-Consumer DNA Testing and the Myth of Personalized Medicine: Spit Kits, SNP Chips and Human Genomics<br />
<br />
Terminator: The Sequel<br />
<br />
ETC Group Report on Geoengineering Climate Change<br />
<br />
Extreme Genetic Engineering: An Introduction to Synthetic Biology<br />
<br />
Nanotech Rx-Medical applications of Nano-scale technologies: What Impact on Marginalized communities? <br />
<br />
A Tiny Primer on Nano-scale Technologies ...and The Little BANG Theory <br />
<br />
Down on the Farm: The Impact of Nano-scale Technologies on Food and Agriculture <br />
<br />
Report Prepared for the South Centre - The Potential Impacts of Nano-Scale Technologies on Commodity Markets: The Implications for Commodity Dependent Developing Countries<br />
<br />
<br />
<br />
'''Johns Hopkins (Berman Institute)''' <br />
<br />
http://www.lse.ac.uk/collections/humanRights/research/groups/Bioethics.htm<br />
<br />
Berman Institute scholar calls for a new legal, ethical framework for research with human tissue specimens<br />
What’s known on the subject: There is growing concern and confusion about the use of “banked” human tissue and cells for research. Several court cases involving the use of human tissue specimens, recent stories in the news, as well as the popularity of a book, The Immortal Life of Henrietta Lacks, all reflect a growing interest in the rights and expectations of the people who provide tissue samples and DNA for research.<br />
What this article adds: This review contends that the current legal and ethical framework for the use of human tissue specimens in research fails to consider the role or preferences of the tissue contributors, and argues that courts have failed to apply a consistent legal framework in addressing disputes between contributors and recipients of the biological samples used in research. <br />
This paper proposes a framework that acknowledges the separate contexts and relationships inherent in that distinction, and sets out the social, legal and ethical perils of ignoring the role that tissue sample providers play in the research enterprise.<br />
<br />
<br />
<br />
'''LSE BIOS''' <br />
<br />
http://www.lse.ac.uk/collections/humanRights/research/groups/Bioethics.htm<br />
<br />
The Bioethics, Rights and Human Rights group is led by Dr Alasdair Cochrane.<br />
<br />
Members:<br />
<br />
Btihaj Ajana (BIOS)<br />
<br />
Perveen Ali (Department of Law)<br />
<br />
Rachel Bell (BIOS)<br />
<br />
Meg Clinch (BIOS)<br />
<br />
Caitlin Connors (BIOS)<br />
<br />
Dr Carrie Friese (BIOS)<br />
<br />
Dr Roberto Fumagalli (Department of Philosophy, Logic and Scientific Method)<br />
<br />
Professor Conor Gearty (Department of Law)<br />
<br />
Amy Hinterberger (BIOS)<br />
<br />
Professor Emily Jackson (Department of Law) <br />
<br />
Kerstin Klein (BIOS)<br />
<br />
Dean Peters (Department of Philosophy, Logic and Scientific Method)<br />
<br />
Dr Joelle Abi Rached (BIOS)<br />
<br />
Dr David Reubi (Public & Environmental Health Research Unit, London School of Hygiene and Tropical Medicine)<br />
<br />
Professor Nikolas Rose (BIOS)<br />
<br />
Dr Igor Stramignoni (Department of Law)<br />
<br />
Dr Sivaramjani Thambisetty (Department of Law)<br />
<br />
Dr Scott Vrecko (BIOS)<br />
<br />
Dr Ayo Wahlberg (BIOS)<br />
<br />
Jeremy Williams (Department of Government)<br />
<br />
Alasdair Cochrane joined the Centre for the Study of Human Rights in 2007. He teaches on the core course for the MSc Human Rights ‘Approaches to Human Rights’, as well as on an undergraduate option in Sociology, ‘Environmentalism: Theory Politics and Practice’. Prior to joining the Centre, Alasdair taught in the Department of Government at the LSE, where he completed his PhD. He holds a 1st Class BA in Politics from the University of Sheffield, an MSc in Political Theory, and a PGCHE, both from the LSE.<br />
Alasdair Cochrane’s research interests include the philosophical justification of rights, contemporary political theory, environmentalism, animal ethics and bioethics. <br />
<br />
Selected publications include: <br />
<br />
-“Ownership and Justice for Animals”, Utilitas, Vol. 21, No. 4 (Dec, 2009). <br />
<br />
-“Do Animals Have an Interest in Liberty?”, Political Studies Vol. 57, No. 3 (Oct, 2009). <br />
<br />
-“Animal Rights and Animal Experiments: An Interest-Based Approach”, Res Publica, Vol. 3, No. 3 (Sep. <br />
2007). <br />
<br />
-“Environmental Ethics”, Internet Encyclopedia of Philosophy, (www.iep.utm.edu). <br />
<br />
-Selected research projects under review and in preparation include:<br />
<br />
-“Undignified Bioethics” (paper)<br />
<br />
-“Evaluating the Political Conception of Human Rights” (paper)<br />
<br />
-“Are Human Rights Speciesist and Does it Matter?” (paper)<br />
<br />
-Animal Rights without Liberation (book)<br />
<br />
-An Introduction to Animals and Political Theory (book)<br />
<br />
<br />
<br />
'''The Hastings Center''' <br />
<br />
http://www.thehastingscenter.org/Publications/BriefingBook/Default.aspx<br />
<br />
The Hastings Center, founded in 1969, is an independent, non-partisan, non-profit bioethics research institute based in the United States. It is dedicated to the examination of essential questions in health care, biotechnology, and the environment. The center has over 200 fellows, including many physicians, attorneys, PhDs and bioethicists.<br />
<br />
Bioethics Briefing Book<br />
<br />
From Birth to Death and Bench to Clinic: The Hastings Center Bioethics Briefing Book for Journalists, Policymakers, and Campaigns contains 36 overviews of issues in bioethics of high public interest, such as abortion, health care reform, human and sports enhancement, organ transplantation, personalized medicine, medical error, and stem cells. The chapters, written by leading ethicists, are nonpartisan, presenting reasonable considerations from various perspectives that are grounded in good scientific and ethical facts. They each include recent news stories, clickable experts to contact, linked resources, and (where available) recent legislation and campaign positions. Greater detail on how to use the book is in the introduction. The three framing essays offer valuable insights into the historical and increasing relevance of bioethics to public policy.<br />
<br />
<br />
<br />
'''Biotechnology Regulatory Bill of India – Five Fallacies'''<br />
<br />
Find out the loopholes in the bill which can have disastrous effect not to India alone bu to whole world at: <br />
<br />
http://scienceray.com/technology/biotechnology-regulatory-bill-of-india-five-fallacies/<br />
<br />
<br />
Mind map<br />
<br />
[[File:Bioethisists_mindmap.jpg]]</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=People&diff=2808People2010-10-27T04:04:58Z<p>Farhad: </p>
<hr />
<div>[[Avni]]<br />
<br />
[[Shreya Kumar]]<br />
<br />
[[Samrajni Patil]]<br />
<br />
[[Mohor Mukherjee]]<br />
<br />
[[Sankhalina Nath]]<br />
<br />
[[Sayed Nooshin]]<br />
<br />
[[Karthik Ilango]]<br />
<br />
[[Aaron Joseph]]<br />
<br />
[[fArhad]]<br />
<br />
[[Diya Sharma]]<br />
<br />
[[Akshitta kohli]]</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=Farhad_Mehta&diff=2807Farhad Mehta2010-10-27T03:53:27Z<p>Farhad: Created page with '== '''Journal''' == '''Day 1''' After a very long time I had again opened my mind to biology. The last time I had studied biology was in the 10th grade and for the first ha...'</p>
<hr />
<div>== '''Journal''' ==<br />
<br />
<br />
<br />
<br />
'''Day 1'''<br />
<br />
After a very long time I had again opened my mind to biology. The last time I had studied biology was in the 10th grade and for the first half hour of the class everything pretty much went over my head. It had been a long time since I had heard these words and they actually sounded like Greek to me. But slowly everything I had learned in the past came back to me.<br />
<br />
In the first class we discussed about general information regarding the first theories of evolution and how they were replaced by others as we come to this day. WE also talked about DNA and its purpose.<br />
<br />
<br />
<br />
'''Day 2'''<br />
<br />
Today we talked about Mendel’s laws of segregation and independence. A very important point is that you don’t need to be a scientist or have a PhD. to discover things. We got to know how genes are passed down from one generation to another. Also alleles are outputs of genes (allele=pea being round or wrinkled.) The terminology used may take some time to get used to. It is amazing to actually see a cell splitting into 2. We then talked about chromosomes and how they decide the characteristics of a person.<br />
<br />
If Genome=book,<br />
<br />
Then DNA=volume,<br />
<br />
And Chromosome=library<br />
<br />
We also saw a video that talked about where gen. engineering would be about 30 yrs. from now. another important thing to consider is the ethics of the topic. Is creating new species good or bad for the world? Is it really progress or just an illusion of progress that we are blindly following that will lead us to our end???...<br />
<br />
<br />
<br />
'''Day 3'''<br />
<br />
Today we started off with seeing how gene mutation is not a good thing. For eg. Cigarette smoking causes the gene p53 to permanently mutate thus causing lung cancer.we then talked about the basic requirements for being genetic material, which are as follows<br />
<br />
1 information storage-Dna has 4 proteins that can be arranged in any way creating different codes<br />
<br />
2 accurate replication-there is a chance of 1 ni a million that the gene is defective, and if it’s so it gets disposed.<br />
<br />
3 it must be expressed as a phenotype- A phenotype is any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, or behavior<br />
<br />
4 it should be able to change –i.e. every individual has different characteristics therefore DNA is different<br />
<br />
DNA is like a symbol for bio like an atom for chem. DNA stands for dioxyribose nucleic acid. It consists of a sugar phosphate backbone and ATGC base pairs. The base pairs are what create code of the DNA for creating proteins.<br />
(Sugar=dioxy ribose, base pairs=nucleic acid) <br />
<br />
A=adenine<br />
<br />
T=thymine<br />
<br />
G=guanine<br />
<br />
C=cytosine<br />
<br />
The proportion of A & T is always equal. Similarly G=C. DNA replication is called semi conservative replication. In this process the DNA is split into its 2 separate helical structures (unzipped )and each of the single helix join to the respective base pair. Thus forming 2 similar DNA 2ble helixes. <br />
All somatic cells (non sex cells) have the same amount DNA specific organism. On the other hand sex cells (e.g. sperm) there is only half the total amount of DNA. The other half is in the sex cells of the mate. Thus the child gets 1 half each of the parents’ genes. Also genetic engineering is not creation of genes but just modifying the original genes to create a different protein.<br />
<br />
<br />
<br />
'''Day 4'''<br />
<br />
Today we talked about proteins. Proteins are polymers of amino acids. There are 20 types of amino acids, 8 of which cannot be produced by man. Thus they need to be consumed.the shape of he protein is very sensitive to the environment.(eg. An egg on heating becomes solid. <br />
<br />
There are 2 types of proteins based on their function:<br />
<br />
-Structural proteins ( hair, muscle collagen, etc.)<br />
<br />
-Enzymes <br />
<br />
enzymes are surfaces for reactions to occur. They act as catylists for reactions in the body. Enzyme names usually end with the letters “ase” eg .polymerase. proteins are also present in the nucleus.thus the DNA contains the gene and the proteins in the nucleus are the phenotype.<br />
<br />
<br />
<br />
'''Day 5'''<br />
<br />
As we talked yesterday gene= DNA and the protein= phenotype(expression). Today we talked about the process of protein creation using DNA. In the nucleus one of the helix of the DNA gets replicated to form RNA(RNA=1/2DNA).RNA is the set of instructions for producing protein. The RNA travels outside the nucleus and goes to the ribosome. The ribosome is like the factory for producing proteins. There are free proteins in the cell in pairs of 3 called codons that act as input for the ribosome. The protein pair is selected according to the code in the RNA(ATC produces a certain protein.) There are 20 types of proteins and only 4 codes in the RNA. Thus the RNA is in pairs of 3 to create enough no of codes for the 20 proteins.<br />
<br />
In DNA only 1 of the 2 helix is used for production, however it is a double helix for easy replication. When DNA is replicated, each of the daughter DNA has 1 of the helix of the parent DNA. Also the other helix decides where in the body the protein is used. <br />
<br />
<br />
<br />
'''Day 6'''<br />
<br />
Today we talked about the genome and genome sequencing. The first type of genome sequencing was hierarchal sequencing where there are certain landmarks in the genome which are used for genome sequencing. The other method is called shotgun sequencing. longer sequences get subdivided into smaller fragments, and subsequently reassembled to give the overall sequence.98% of the RNA produced does not even leave the nucleus. The walls of the nucleus act as as a purifier.they are like a simple on off switch. we also talked about bacteria that have a self defence against<br />
<br />
<br />
<br />
'''Day 7'''<br />
<br />
We talked about recombinant DNA. Recombinant DNA is DNA that is artificially created from two or more sources and is incorporated into a single recombinant molecule. Recombinant DNA (rDNA) is a form of DNA that does not exist naturally, but is created by combining DNA sequences that would not normally occur together. <br />
<br />
Most of the bacteria have a restriction enzyme which cuts up foreign DNA. Therefore it is sometimes difficult to splice DNA. This process of splicing can create new types of organisms. This is what synthetic biology is based on. Usually a bacteria called E.coli is used for this as it is not dangerous to experiment on. Synthetic bio. Has many applications. It is used to study particular sequences that are very tiny(the sequence is put in the bacteria and amplified), to express phenotypes, to increase the quantities of proteins , etc. <br />
<br />
<br />
<br />
'''Day 8'''<br />
<br />
Isolating genes was always done from the phenotype to theto the DNA, but that changed while trying to cure muscular dystrophy. The doctor tried to sequence the gene from the dNA to the phenotype. This is called reverse genetics. He found that a small gene on the x chromosome was missing. This gene was responsible for production of distrophin which connects the muscle fiber to the cells. Distrophin can be replaced by urotrophin , which can be produced by a drug. Thus the problem was cured. In the nucleus mRNA of about 14,600 base pairs is formed, most of which ars not required. the introns remove about 79 peaces from the mRNA by gene splicing in the nucleus itself.<br />
<br />
The DNA library is a volume of the genome. Hybrid DNA is a combination of 2 DNA from 2 different places. The geme and a vecter is combined and introduced into the bacteria. the bacteria takes the new gene and adds it to the original gene. The bacteria is allowed to grow and half the DNA of the new bactrria is introduced so that the full(double helix) DNA is fished out. Thus hybrid DNA is created.<br />
<br />
<br />
<br />
'''Day 9'''<br />
<br />
Today we talked about transgenetics which is DNA of more than 1 species. The the method used is called gene splicing which was first done by Boyle. While working with fruit flies he found that a certain gene called the homiobox genes were responsible for descision of what grows where. Thus by changing this gene he could change the position of different body parts. Thus started synthetic biology which was literally engeneering biology.<br />
<br />
<br />
<br />
'''Day 10'''<br />
<br />
Today we talked about creating a hypothetical bacteriaof our own. We also given a talk on hybrids and new creatures. The concept of hybrids has existed since many ages. The available technology and advancements in biology has made it possible to create such hybrids. Radical plastic surgens do exactly this. They add extra parts to the body through surgery.<br />
<br />
<br />
<br />
'''Day 11'''<br />
<br />
Today we saw a video of craig venter on ted talks. He was talking about his recent discoveries in biotechnology and how they went about doing it. We also talked about different bioartists and their approach to biology<br />
<br />
<br />
<br />
'''Day 12''' <br />
<br />
Today we went to NCBS for the first time.we had gone to meet the person who would help us create the new bacteria and understand how to go about doing it. <br />
<br />
<br />
<br />
'''Day 13'''<br />
<br />
Today we saw the different parts that make a functioning gene. it was shocking to see its resemblance to electronic parts and circuits. we also found out about the parts regestry and how to search it. The pats registry is a large collection of already existing dna. We also talked about bioremediation which is creation of an organism that solves environmental problems. Plants are better at bioremediation as they can be plantrd and removed easily thus not disturbing the ecology of an area . We also learnt about PCR (polymerase chain reaction) which was discovered by Kary Mullis. In DNA the base pairs are held together by an H bond. This bond is brokrn at 80 degrees celcious. The polymerase is used to duplicate the DNA and produce 2 strands of DNA. hut at 80 degrees celcious te polymerase coagulatees. thus we introduce an extremophile (organism that survives in extreme climates) that is genetically engeneered to produce polymerase. thus making it a chain reaction.<br />
<br />
<br />
<br />
'''Day 14'''<br />
<br />
Today we talked about gene scilencing. In this process some of the genes get turned off. This happens at the transcription level. Scilencing occurs when 2 strands of mRNA are created that are complementary to each other. Thus they recombine and are not allowed to leave the nucleus. Thus the protein is not created.<br />
<br />
We also researched on different bioartists that use biological phinominons as a form of art.today we looked at George gessart, Adam Zeretsky , Eduardo Katz, Petrissia Piccinini and so on. It is amazing to see how biologyitself was a form of art. And each bioart work had a deeper understanding to it.<br />
<br />
<br />
<br />
'''Day 15'''<br />
<br />
I had an appointment with an eye doctor so I couldn’t go for class. But today was the day we got our wiki pages created. In the evening I asked for my password and got it the same day so I didn’t lose out on a lot. They were also told about the 2 foreign faculty that was coming to aid us: Daisy and James.<br />
<br />
<br />
<br />
'''Day 16'''<br />
<br />
Today we didn’t d much. We saw a BBC docmentry : Secrets of Life,The race for the Double Helix. It talked aabout the three groups of scientists involved in finding the double helix structure of DNA and their contributions to the finding. Seeing this documentary made me realize that discovery is like a rat race of who finds what first and who should be credited for it. Also from the previous example of Kary Mullis and the 2 scientiststhst discovered the structure of the double helix, that one doesn’t need to be the smartest to discover something, he just needs to have some knowledge of the subject and a lot of luck.<br />
<br />
<br />
<br />
'''Day 17'''<br />
<br />
Today we saw the different parts that make a functioning gene and their uses. It was shocking to see its resemblance to electronic parts and circuits. we also found out about the parts regestry and how to search it. The pats registry is a large collection of already existing dna. We also researched about how to create yeast cultures. We found the following:<br />
<br />
<br />
'''Preparation or Agar:'''<br />
<br />
-Heat 7 gm of agar in 250 ml of water till it completely desolves.<br />
<br />
-Let it set.<br />
<br />
<br />
'''Preparing yeast culture:'''<br />
<br />
-Heat yeast in water to activate it.<br />
<br />
-sterilize loop.<br />
<br />
-dip in yeast and streak to the agar.<br />
<br />
-keep it aside to grow (24hrs).<br />
<br />
This process failed as we added very little agar (1 gm). Thus the yeast didn’t grow.<br />
<br />
<br />
<br />
'''Day 18'''<br />
<br />
Today we read our first scientific paper on repricilator gene. The gene works as a cycle. There are 3 main proteins that activate 3 different genes, which are produced by those 3 genes. 1 repressor affects the 2nd and the 2nd affects the 3rd. the 3rd in turn affects the first, Thus forming a feedback loop. The Bacteria works as an oscillator circuit using the time for triggering as the time between the action. The terms used in the paper were very confusing and did not make sense at first but slowly came to my understanding. My conclusion is that scientific papers are complicated ways of saying something simple. <br />
<br />
We also tried to grow yeast again his time we tried 3 different concentrations of agar:<br />
<br />
1.4gm/250ml<br />
<br />
4.3gm/250ml<br />
<br />
10gm/250ml<br />
<br />
thee middle concentration was best suited for yeast growth.<br />
<br />
<br />
<br />
'''Day 19'''<br />
<br />
Today we went for a discussion of: Evolution as opposed to design. The speaker talked about the design problem in evolution and whether the design was meant to be or just a coincidence. He gave the example of the eye and the telescope and said that if the telescope had a maker then so did the eye. The only difference is that we know who made the telescope. We also talked about natural and artificial. This raised a big question in my head that if man would interfere in anyway then it would become artificial. Then that would make everything artificial as man has interacted with and changed almost everything. Then that means nothing natural exists….<br />
<br />
<br />
<br />
'''Day 20-24'''<br />
<br />
We spent the next 4 days making our own lab equipment. We made 2 centrifuges, a microscope and an incubator using locally available materials. It took several trials and errors but we finally made all 3. I was working on the incubator and it was a little frustrating to get the perfect temperature.<br />
<br />
<br />
<br />
'''Day 25''' <br />
<br />
Today we worked on collecting all the info of the last 3 weeks. This is what we came up with:<br />
<br />
-We started off by creating bio-art sculptures that used, living organisms. We were told to create art without killing the organism, thus trying to integrate the two (art and biology) together and also having a kind of pet for the summer! <br />
<br />
-Coming from an art background, we tried to add meaning to why we did what we did.<br />
<br />
-After this we came up with ideas for bacteria and an explanation for how they functioned.<br />
<br />
-We created imaginary machines that CAN NOT exist. The idea was to open our minds to the extreme possibilities so as to get new ideas: for our final project.<br />
<br />
-As we went through all the previous works of Igem competitions we realised that almost all the projects fell under 3 major categories, which were: <br />
<br />
<br />
1. Purifiers <br />
<br />
2. Display/sensors/ indicators<br />
<br />
3. Production of energy<br />
<br />
We believed that it would be good to create an organism that would not fall in any of these categories.<br />
<br />
These are all the possibilities that we have come up with till now, hoping to have a excellent outcome. <br />
<br />
<br />
<br />
'''Day 26,27'''<br />
<br />
absent<br />
<br />
<br />
<br />
'''Day 28'''<br />
<br />
I was absent the last 2 days so I was a little lost. But with help I caught up quite fast. Today was also the day I met James and Daisy. Today’s assignment was to come up with an organism for iGEA(genetically engineered art) which was a new compition we started in srishti. We came up with E. cloudy. <br />
<br />
<br />
<br />
'''Day 29'''<br />
<br />
Today we presented our bacteria for iGEA. We were also given conics to read and pich out intresting myths which could be related to synth. biology. All the ones we selscted fell under tese catagories:<br />
Bio prospecting<br />
<br />
Karma<br />
<br />
Ecosystems<br />
<br />
Immunization against a disaster<br />
<br />
Soma<br />
<br />
Jugad (being very prominent)<br />
<br />
<br />
<br />
'''Day 30, 31'''<br />
Using the myths we read through we were told to a create a bacteria that retells the story. We depicted the story of Brahma, Vishnu and Shiva.(The holy trinity)<br />
<br />
<br />
<br />
'''Day 32''' <br />
<br />
Today we looked at the myths that had been created by synthetic biology for the past and the future.<br />
<br />
We were also told to make a scientific diagram for our mythical bacteria. that is to put it in complicated words. <br />
<br />
<br />
<br />
'''Day33'''<br />
<br />
Today we created a mindmap of the so called “actors” of bio technology and who was on which side. <br />
<br />
We also had 2 artists from Level10 comics to talk about the process of making a comic and the steps involved. They also showed us some of their works.<br />
<br />
<br />
<br />
'''Day 34'''<br />
<br />
Each of us was given a topic to do further research in. my topic was Bioethicists<br />
<br />
<br />
<br />
<br />
== '''Bio artists''' ==<br />
<br />
<br />
<br />
'''Stellarc:'''<br />
<br />
Stellar tries to integrate the biological and technological advances using the human body as the test subject. He tries to show the thin line that exists today between technology and the body which will be broken very soon.<br />
<br />
<br />
<br />
'''Orlan:'''<br />
<br />
Orlan again uses her own body as a canvas. But instead of technology she uses plastic surgery. If fine art is a visual medium, then Orlan herself is a walking exhibit. Orlan embraces the technology of the time by undergoing these procedures but rejects everything they stand for. Instead of making herself “pretty”, she makes herself grossly disfigured. Orlan is the only artist working so radically with her own body, asking questions about the status of the body in society.<br />
<br />
<br />
<br />
'''Patricia Piccinini:'''<br />
<br />
The work is quite interesting because of<br />
<br />
1. It’s life like feeling.<br />
<br />
2. Also at first one thinks it is completely impossible & imaginary but at closer inspection realise we are not far from achieving what she has made and that creating such animals are quite possible.<br />
<br />
3. Her art creates ethical debates about the advancements in technology & biology and its relation to nature. And how it is the responsibility of the creator for the new creatures uncertain ethical and physical results.<br />
<br />
<br />
<br />
== '''My assignments''' ==<br />
<br />
<br />
<br />
<br />
'''01) Living sculpture:''' (living furniture)<br />
<br />
<br />
Most of the furniture that we use in places like the lawn or at the beach are made of wood that has been cut from living trees. this living sculpture has both a use and aesthetics. Instead of cutting trees why not grow the according to the shape you need. <br />
<br />
The concept of tree shaping requires one to bend the tree in a desirable shape when it is a small plant. As the tree grows the shape is retained and the bark hardens to form the required shape. This can be called ecofriendly furniture. As the tree branches out, the leaves give shade. It is also cooler below the tree. Also since the tree produces oxygen, the air under the tree is fresh. My final project is to make a living chair. <br />
<br />
"[[File:Tree_shaping.jpg]]"<br />
<br />
I am starting by bending smaller plants and make in a simple loop(1st June). I used string to hold the shape and check after a month.<br />
<br />
[[File:Roll_2.JPG]] [[File:Roll_4.JPG]]<br />
<br />
After a moonth: The plant retains the shape but still needs some time to maintain that shape. <br />
<br />
<br />
'''02) Hypothetical bacteria:''' (Pressure sensitive Thermo Bacteria)<br />
<br />
<br />
The Srishti School of art design and tech. has created bacteria that emits heat when pressure is applied on it. It consists of tiny turbine like particles on it’s cell walls. When pressure is applied the cell produces an enzyme that causes the turbines to spin. These cells are tightly packed together in a tiny porous container. The activated turbines hit each other producing heat. The collected heat is magnified by the bacteria and is concentrated at the point of pressure. The temp ranges from 100 to 500 degrees.<br />
<br />
[[File:Bact_0.jpg]]<br />
[[File:Bact1.jpg]]<br />
<br />
The porous container itself is a living organism which concentrates all the heat on the point where the pressure is and spreads the heat across the area where pressure is. both the bacteria live along with each other as symbiotes. The heat producing bacteria feeds on the nutrients supplied by outer shell which is made of sugars and fatty acids. On the other hand the outer shell depends on the thermo bacteria for its shape and heat. Using some amount of the heat produced by the thermo bacteria, the porous outer structure converts cellulose into simple sugars which is food for both the organisms has pores that are about 0.01 nm in diameter all over it which are used to vent out all the extra heat in the form of steam (water is one of the byproducts of converting cellulose into sugar.)<br />
<br />
The organism reproduces by binary fission. When the shell is overloaded with the bacteria it expands until it breaks into 2 pieces. The 2 pieces join to themselves to form 2 separate structures. The outer structure does not break unless there is an internal pressure applied and it immediately joins when it breaks and grows to its normal size in 5 hours to incorporate more bacteria. The bacteria can be killed using an electric charge of 20 volts (D.C.), thus its growth can be controlled. <br />
<br />
This organism can be used for security purposes, as they are too small to be seen and produce enough heat to burn the body. If the amount of heat given out (number of collisions between spindles) can be controlled it can be used for various reasons e.g. Cooking, hot tubs, heated chairs, etc. And being organisms that can reproduce, they don’t need to be replaced.<br />
<br />
<br />
<br />
'''03) Imagenary machine:'''(Projector bacteria)<br />
<br />
<br />
The bacteria simply projects ones thoughts to a tangible 2D presentation. These bacteria live in the brain. It is a long egg like structure with 2 antennas. These bacteria are fixed on a circular moving belt. The bacteria pick up brain waves with the antenna and produce an image corresponding to the wave. <br />
<br />
[[File:Bact_3.jpg]]<br />
<br />
The optic nerve of the right eye touches one of the bacteria and picks up the image. As the rotating belt moves the optic nerve picks up other images and forms a stop motion of the thoughts in the mind on the retina. The image on the retina is inverted.<br />
<br />
The bacteria secrete an enzyme that runs along the optic nerve and makes the retina emit light. The image on the retina gets projected on to the lens of the right eye and is diverged by the lens thus magnifying the images it gets projected. The user of the bacteria can voluntarily secrete an enzyme that makes the optic nerve move away from the bacteria, thus stopping the projection and the eye starts to function normally. The bacteria reproduce by binary fission. One of the daughter bacteria replaces the parent and the second bacterium gets attatched to belt and acts as food for the bacteria.<br />
<br />
<br />
<br />
'''04) Incubator:'''<br />
<br />
click:[[DIY Incubator]]<br />
<br />
<br />
<br />
'''05) iGEA:''' (E.Cloudy)<br />
<br />
Bacteria which help coordinate your music with the weather <br />
<br />
[[File:Ec1.jpg]]<br />
<br />
Escheriscia Cloudy or E. Cloudy is a Bacteria which is temperature sensitive and produces electricity. Its unique mix of qualities has been used to program a machine which plays music play lists of the user’s choice depending on the weather.<br />
<br />
The E.Cloudy bacterium have been created by combining two existing BioBrick parts – <br />
<br />
-BBa_K098995, responsible for the thermo sensitivity.(designed by the Harvard 2008 igem team)<br />
<br />
-BBa_K499271, responsible for the electricity.( designed by Boris Kirov igem 2010 )<br />
<br />
'''How the two BioBricks are connected'''<br />
<br />
•The thermo sensitive complex produces a certain protein on exposure to heat.<br />
This protein triggers off the second complex, making it generate a current<br />
<br />
'''How the machine works'''<br />
<br />
•The temperature sensitive bacteria creates current depending on the climate temp (more temp = more current). <br />
<br />
•The current passes through an amplifier to get a readable current. <br />
<br />
•As current passes through the voltmeter the needle moves increasingly. <br />
<br />
•Each temp range triggers the playing of a certain play list( ex a range of 0-10= soothing play list/ energetic play list depending on the user).<br />
<br />
•The machine has its own software which is loaded onto a computer or laptop. The machine is connected to the computer with a USB cable. <br />
<br />
[[File:Picture1.jpg]]<br />
<br />
'''Deeper into the Bacteria'''<br />
<br />
•The bacteria self reproduce.<br />
<br />
•They are in a way cannibalistic;<br />
Every time a bacteria reproduces, the mother bacteria is consumed by the child.<br />
[[File:Ec2.jpg]]<br />
<br />
<br />
'''How it could Fail and Why this over a fully mechanical system?'''<br />
<br />
The system could malfunction if –<br />
<br />
•The bacterial container got contaminated by anything that could kill or reduce capacity of the bacteria.<br />
<br />
•We don’t know if the electricity would kill the bacteria. <br />
<br />
'''Why this?''' <br />
<br />
The same machine can be made using a thermometer, however, with a thermometer, there arises a chance of it getting ruined permanently. <br />
Also it can be looked upon as an alternative, a novelty, an exploration. <br />
How it ties into the criteria detailed by the contest <br />
<br />
•Social critique – creates moods, makes you question your own mood and keeps you conscious of the weather and its changes.<br />
<br />
•This ties into remix culture – apart from the obvious remixing of genes that the original escheriscia coli have undergone, looking it at it from an artistic angle, it’s sort of like replacing your weather man’s report with your own bacterial weather report! <br />
<br />
<br />
'''The effects of this bacterial product on the world.'''<br />
<br />
We have divided the consequence of introducing this product into the market into categories such as – <br />
<br />
'''Socio-Cultural'''<br />
<br />
We feel that this product has high potential to enter popular culture. It’s something which would help take individualism to a new level. It could be a new way to bring nature closer to us and observe it better. <br />
<br />
'''Economic - Financial'''<br />
<br />
The circuitry of this product wouldn’t be expensive, but producing the bacteria maybe the one to raise the price.<br />
•Who would be able to afford it? <br />
<br />
•What percentage of the population<br />
does this group make up?<br />
<br />
•Why would they want to buy it? (novelty and interest could lead to a social phenomenon!)<br />
<br />
•Does this say anything about us as consumers?<br />
<br />
•How much of an effect would it have on our economy? <br />
<br />
'''Technology'''<br />
<br />
We’ve seen bacteria producing fuel and the idea of the bacterial battery. Could energy producing bacteria be our future power houses? <br />
<br />
How would a product integrating living cells into a non-living machine be received by the tech industry? <br />
<br />
'''Science'''<br />
<br />
Could this product trigger off another set of ideas that could be beneficial to other sciences? We think it’s a possibility. <br />
<br />
'''Art'''<br />
<br />
Art is deceptive, it can pack a hard punch without seeming like it. <br />
<br />
Art has a lot to do with creating a sense of awareness, to make people question things around them. <br />
<br />
The concept behind this product (apart from being aware of the weather it creates awareness in how two very different genes, from possibly to very different organisms have been put together to create a machine) could lead us to questioning our rights to remix things (also, is it ok to mix the machine with living cells?) , our rights to play with natural selection, can we define this as a form of natural selection? <br />
<br />
<br />
<br />
'''06) Bacteria based on indian myth:''' (The Holy Trinity- group ass)<br />
<br />
<br />
When was the last time you ever read an Indian mythological story and asked your self – what if I can do that? Indian Mythology is known to be the most culturally rich, colourful, dramatic and at the same time metaphorically ambitious story, ever told. The numbers of different versions are more than the number of sarees that came off Draupadi! It’s like a roller coaster ride of emotions which at the end of every story brings in ‘balance’.<br />
<br />
As an Artist and Designer, whenever we read an Indian mythological story I have to say it’s quite amazing because these are some stories that have characters that can pretty much do whatever they want! Gods.... Isn’t that what we all want? To do whatever we like? And not have to worry about consequences? And just know that at the end of it all there will be balance? I think that’s some food for thought.<br />
<br />
As a team, we first read through the most famous stories in Indian mythology, and then had a fascinating discussion with a learned scholar in mythology and history. Arshia (the scholar) helped us put our facts together in the most fun filled way which after a few drinks turned out to be a very satisfying knowledge-full night.<br />
<br />
Our task now (which is the most interesting part) was to find links and parallels to any myth and use synthetic biology to fill the gap! I find that highly fascinating. SO we went through a few myths and as soon as we landed on Shiva’s third eye, there was a full stop. Shiva’s third eye is the destroyer, when he opens it; disaster is all over the place. So the last you want to do it tick him off. We took that in a metaphorical sense and thought about what if that third eye was a way for us to see when our real eyes are shut? So what if I had bacteria that could communicate with thoughts through neuron activity and when I’m wired up to a projector, it displays my thought in 3D space. Then communication would be in its most pure form since there is a lot of loss when converting thought to word or deed. Then what if I wired up to another person and started communicating with thought! Or if I left messages for someone on a platform and they could later wire up and receive it. But as usual there’s always a ‘BUT’, and the first one here is privacy. Privacy is by far the most delicate issue here. SO we kept this on hold for the time being and instead of looking at parts of a myth we moved away and looked at the Big Picture.<br />
<br />
[[File:Collages.jpg|400px|Left|]]<br />
[[File:Main 2.JPG|400px|right|]]<br />
<br />
The Holy Trinity – Brahma, the creator, Vishnu the Preserver and Shiva the destroyer. These are the first and foremost gods that rule the heavens, earth and hell. As you’re reading this don’t those three words –creator, preserver and destroyer burst out of your imagination and find its way to synthetic biology? Well, that’s exactly what happened to us. So here’s our idea.<br />
<br />
[[File:Collages2.jpg|400px|Left|]]<br />
<br />
In a over populated culture of bacteria. There is ‘imbalance’ since there more bacteria to eat than the nutrition available. So the ‘gods’ are summoned! The VISH-gene bacteria (the preserver) now gets into action by producing a chemical to which ONLY the SHIV-gene bacteria (the destroyer) can read. This then activates the SHIV-gene bacteria to in turn produce a chemical which start disrupting the bacterial cells in the colony. The ‘gods’ bacteria are of course resistant to this chemical. The SHIV-gene bacteria once activated has no control over killing the other cells. So once he has destroyed ample number of cells, he needs to be stopped, which ONLY the BRAHM-gene can do. So now the VISH-gene bacteria produces another chemical which ONLY the BRAHM-gene bacteria can read and this in turn activates the BRAHM-gene bacteria to produce a chemical to deactivate the SHIV-gene bacteria. Now there’s been too many bacteria killed so after a while of reproduction the optimum level is reached and ‘balance’ is restored. The subjects are happy and so are the gods. Soon after reproduction hastens up and there is over population again so the whole process is initiated making it a loop. <br />
<br />
[[File:Main 1.JPG|400px|Right|]]<br />
<br />
BRAHM-gene bacteria are identified with the presence of the BRAHM-gene. When the BBRAHM- gene replicates it does not transfer it’s genetic material completely, instead it retains one part of the gene, so the other bacteria now is the VISH-gene bacteria. When the BRAHM-gene bacteria replicates for the second time it does not transfer the BRAHM-gene at all making the new organism the SHIV-gene. <br />
<br />
We’d like to think that this mythological concept, besides being fascinating will definitely find its way to a good purpose in the world of Synthetic Biology. So wait up until then.<br />
<br />
<br />
'''Scientific reprisentation'''<br />
<br />
[[File:Bvs.jpg]] [[File:Bvs2.jpg]]<br />
<br />
'''07) The promise of Synthetic Biology:'''<br />
<br />
<br />
Such is the promise of synthetic biology, which, according to the people who have tried to explain it to me, is basically a marketing term for all kinds of research in which scientists tinker with biological bits to make useful things — sort of like living Lego blocks.<br />
<br />
The gift of man-made life — biofuels made of algae, tumor-seeking microbial missiles — comes wrapped in a risk: What if the oil-eating bug mutates, as the horror-movie version inevitably does, and starts eating other things — like us?<br />
<br />
It's perhaps not surprising that when bioethicists describe synthetic biology, they sound like the characters in Jurassic Park.<br />
"When dealing with biological entities," notes Thomas Murray, president of the Hastings Center, a bioethics organization, "life has a tendency to find a way."<br />
<br />
Accidents at power plants are bad enough. But a leak from a bioreactor could be worse, since bacteria can learn new tricks when you're not looking. Microbes excel at exchanging DNA, Murray notes — "like microbial French kissing." That bug we introduce into the ocean to sip the spill might end up swapping DNA with other living things. "We have a ways to go," he says, "before we can really know what risks we're running if we release these organisms into the environment."<br />
<br />
Without public oversight, we are certain to wake up one day to news of some private breakthrough that rattles our bones: a human-animal hybrid, a cloned child, a fetus grown solely to harvest its parts.<br />
<br />
As laboratories incubate new blends of man and machine — creatures whose creators used a keyboard — it seems mad to say that philosophy should not intervene.<br />
<br />
The path of progress cuts through the four-way intersection of the moral, medical, religious and political — and whichever way you turn, you are likely to run over someone's deeply held beliefs. Venter's bombshell revived the oldest of ethical debates, over whether scientists were playing God or proving he does not exist because someone re-enacted Genesis in suburban Maryland.<br />
Others dismiss the worry on the grounds that creating new forms of life is not the same as creating life. One doctor friend of mine suggested that "they haven't created life in any sense of the word, other than a person playing a cassette has invented the tape recorder."<br />
<br />
<br />
"It is vital that we as a society consider, in a thoughtful manner, the significance of this kind of scientific development," Obama writes.<br />
<br />
"Synthetic biology certainly raises deep philosophical and moral questions about the human relationship to nature," according to Gregory Kaebnick, a Hastings Center scholar who is managing the project. "It's not clear what the answers to those questions are. If by 'nature' we mean the world around us, more or less as we found it, we may well decide that synthetic biology does not really change the human relationship to nature—and may even help us preserve what is left of it."<br />
<br />
Myth: Cellulosic ethanol is a decade or more away.<br />
Fact: The world's first cellulosic ethanol production facility -- owned and operated by Iogen in Ottawa, Canada -- has been converting wheat straw into ethanol since 2004. Abengoa Bioenergy is completing construction of a commercial-scale cellulosic ethanol facility, located in Salamanca, Spain, that will by the end of 2007 begin producing 1.2 million gallons of cellulosic ethanol from wheat straw each year.<br />
<br />
<br />
Conclusion:<br />
People are bound to disagree about when scientists are crossing some moral Rubicon. That is all the more reason to debate, in public and in advance, where those boundaries lie — rather than doing so after the fact, when researchers are celebrating some technical triumph and the rest of us are wondering what price we will pay for it.<br />
<br />
'''Information from:'''<br />
<br />
'''http://www.time.com/time/magazine/article/0,9171,1997447,00.html'''<br />
<br />
'''http://machineslikeus.com/.../moral-issues-raised-synthetic-biology-subject-hastings -center-workshop - .html'''<br />
<br />
'''http://www.economist.com/node/16163154/comments?page=1.html'''<br />
<br />
<br />
<br />
<br />
'''08) bioethicists:'''<br />
<br />
<br />
<br />
'''Biodesign India'''<br />
<br />
Redesigning life for novel applications<br />
<br />
http://biodesignindia.org/index.htm<br />
<br />
<br />
The evolving synthetic biology community in our country needs to discuss unique ideas, interest groups, synergies, funding avenues and useful applications. The key goal will be to identify areas where India has potential to take global leadership.<br />
<br />
<br />
<br />
'''Etc group'''<br />
<br />
http://www.etcgroup.org/en/issues/biotechnology<br />
<br />
ETC Group is not fundamentally opposed to genetic engineering, but we have profound concerns about the way it is being foisted upon the world. In the current social, economic and political context, genetic engineering is not safe, and involves unacceptable levels of risk to people and the environment. For ETC Group, the fundamental issue is control.<br />
<br />
Reports:<br />
<br />
Patenting the "Climate Genes" ...and Capturing the Climate Agenda <br />
<br />
Direct-to-Consumer DNA Testing and the Myth of Personalized Medicine: Spit Kits, SNP Chips and Human Genomics<br />
<br />
Terminator: The Sequel<br />
<br />
ETC Group Report on Geoengineering Climate Change<br />
<br />
Extreme Genetic Engineering: An Introduction to Synthetic Biology<br />
<br />
Nanotech Rx-Medical applications of Nano-scale technologies: What Impact on Marginalized communities? <br />
<br />
A Tiny Primer on Nano-scale Technologies ...and The Little BANG Theory <br />
<br />
Down on the Farm: The Impact of Nano-scale Technologies on Food and Agriculture <br />
<br />
Report Prepared for the South Centre - The Potential Impacts of Nano-Scale Technologies on Commodity Markets: The Implications for Commodity Dependent Developing Countries<br />
<br />
<br />
<br />
'''Johns Hopkins (Berman Institute)''' <br />
<br />
http://www.lse.ac.uk/collections/humanRights/research/groups/Bioethics.htm<br />
<br />
Berman Institute scholar calls for a new legal, ethical framework for research with human tissue specimens<br />
What’s known on the subject: There is growing concern and confusion about the use of “banked” human tissue and cells for research. Several court cases involving the use of human tissue specimens, recent stories in the news, as well as the popularity of a book, The Immortal Life of Henrietta Lacks, all reflect a growing interest in the rights and expectations of the people who provide tissue samples and DNA for research.<br />
What this article adds: This review contends that the current legal and ethical framework for the use of human tissue specimens in research fails to consider the role or preferences of the tissue contributors, and argues that courts have failed to apply a consistent legal framework in addressing disputes between contributors and recipients of the biological samples used in research. <br />
This paper proposes a framework that acknowledges the separate contexts and relationships inherent in that distinction, and sets out the social, legal and ethical perils of ignoring the role that tissue sample providers play in the research enterprise.<br />
<br />
<br />
<br />
'''LSE BIOS''' <br />
<br />
http://www.lse.ac.uk/collections/humanRights/research/groups/Bioethics.htm<br />
<br />
The Bioethics, Rights and Human Rights group is led by Dr Alasdair Cochrane.<br />
<br />
Members:<br />
<br />
Btihaj Ajana (BIOS)<br />
<br />
Perveen Ali (Department of Law)<br />
<br />
Rachel Bell (BIOS)<br />
<br />
Meg Clinch (BIOS)<br />
<br />
Caitlin Connors (BIOS)<br />
<br />
Dr Carrie Friese (BIOS)<br />
<br />
Dr Roberto Fumagalli (Department of Philosophy, Logic and Scientific Method)<br />
<br />
Professor Conor Gearty (Department of Law)<br />
<br />
Amy Hinterberger (BIOS)<br />
<br />
Professor Emily Jackson (Department of Law) <br />
<br />
Kerstin Klein (BIOS)<br />
<br />
Dean Peters (Department of Philosophy, Logic and Scientific Method)<br />
<br />
Dr Joelle Abi Rached (BIOS)<br />
<br />
Dr David Reubi (Public & Environmental Health Research Unit, London School of Hygiene and Tropical Medicine)<br />
<br />
Professor Nikolas Rose (BIOS)<br />
<br />
Dr Igor Stramignoni (Department of Law)<br />
<br />
Dr Sivaramjani Thambisetty (Department of Law)<br />
<br />
Dr Scott Vrecko (BIOS)<br />
<br />
Dr Ayo Wahlberg (BIOS)<br />
<br />
Jeremy Williams (Department of Government)<br />
<br />
Alasdair Cochrane joined the Centre for the Study of Human Rights in 2007. He teaches on the core course for the MSc Human Rights ‘Approaches to Human Rights’, as well as on an undergraduate option in Sociology, ‘Environmentalism: Theory Politics and Practice’. Prior to joining the Centre, Alasdair taught in the Department of Government at the LSE, where he completed his PhD. He holds a 1st Class BA in Politics from the University of Sheffield, an MSc in Political Theory, and a PGCHE, both from the LSE.<br />
Alasdair Cochrane’s research interests include the philosophical justification of rights, contemporary political theory, environmentalism, animal ethics and bioethics. <br />
<br />
Selected publications include: <br />
<br />
-“Ownership and Justice for Animals”, Utilitas, Vol. 21, No. 4 (Dec, 2009). <br />
<br />
-“Do Animals Have an Interest in Liberty?”, Political Studies Vol. 57, No. 3 (Oct, 2009). <br />
<br />
-“Animal Rights and Animal Experiments: An Interest-Based Approach”, Res Publica, Vol. 3, No. 3 (Sep. <br />
2007). <br />
<br />
-“Environmental Ethics”, Internet Encyclopedia of Philosophy, (www.iep.utm.edu). <br />
<br />
-Selected research projects under review and in preparation include:<br />
<br />
-“Undignified Bioethics” (paper)<br />
<br />
-“Evaluating the Political Conception of Human Rights” (paper)<br />
<br />
-“Are Human Rights Speciesist and Does it Matter?” (paper)<br />
<br />
-Animal Rights without Liberation (book)<br />
<br />
-An Introduction to Animals and Political Theory (book)<br />
<br />
<br />
<br />
'''The Hastings Center''' <br />
<br />
http://www.thehastingscenter.org/Publications/BriefingBook/Default.aspx<br />
<br />
The Hastings Center, founded in 1969, is an independent, non-partisan, non-profit bioethics research institute based in the United States. It is dedicated to the examination of essential questions in health care, biotechnology, and the environment. The center has over 200 fellows, including many physicians, attorneys, PhDs and bioethicists.<br />
<br />
Bioethics Briefing Book<br />
<br />
From Birth to Death and Bench to Clinic: The Hastings Center Bioethics Briefing Book for Journalists, Policymakers, and Campaigns contains 36 overviews of issues in bioethics of high public interest, such as abortion, health care reform, human and sports enhancement, organ transplantation, personalized medicine, medical error, and stem cells. The chapters, written by leading ethicists, are nonpartisan, presenting reasonable considerations from various perspectives that are grounded in good scientific and ethical facts. They each include recent news stories, clickable experts to contact, linked resources, and (where available) recent legislation and campaign positions. Greater detail on how to use the book is in the introduction. The three framing essays offer valuable insights into the historical and increasing relevance of bioethics to public policy.<br />
<br />
<br />
<br />
'''Biotechnology Regulatory Bill of India – Five Fallacies'''<br />
<br />
Find out the loopholes in the bill which can have disastrous effect not to India alone bu to whole world at: <br />
<br />
http://scienceray.com/technology/biotechnology-regulatory-bill-of-india-five-fallacies/<br />
<br />
<br />
Mind map<br />
<br />
[[File:Bioethisists_mindmap.jpg]]</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=People&diff=2806People2010-10-27T03:52:15Z<p>Farhad: </p>
<hr />
<div>[[Avni]]<br />
<br />
[[Shreya Kumar]]<br />
<br />
[[Samrajni Patil]]<br />
<br />
[[Mohor Mukherjee]]<br />
<br />
[[Sankhalina Nath]]<br />
<br />
[[Sayed Nooshin]]<br />
<br />
[[Karthik Ilango]]<br />
<br />
[[Aaron Joseph]]<br />
<br />
[[fArhad]]<br />
<br />
[[Farhad Mehta]]<br />
<br />
[[Diya Sharma]]<br />
<br />
[[Akshitta kohli]]</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=Old_Main_Page&diff=2804Old Main Page2010-10-22T10:02:53Z<p>Farhad: </p>
<hr />
<div><!-- Labs--><br />
<div class="alertBox"><br />
{| class="alert"<br />
! Labs<br />
|-<br />
|'''Hackteria Lab - Dock18 - April 2010''' <br />
[[Hackteria Lab - Dock18 - 6-9 April 2010]]<br />
<br />
[[File:forum_hackteria.jpg|300px]]<br />
<br />
|}<br />
</div><br />
<!-- Labs end --><br />
<br />
<!-- Workshops--><br />
<div class="alertBox"><br />
{| class="alert"<br />
! Workshops<br />
|-<br />
|'''Workshop:''' <br />
[[hackteria & lab_hacking @ NK, Berlin]]<br />
30. May - 3. June 2009<br />
[[File:Flyer_nk_web.jpg|300px]]<br />
<br />
<br />
[http://www.myspace.com/enka52 NK, Berlin]<br />
|-<br />
| '''Workshop: '''<br />
[[File:Igemworkshoppngwiki.png|http://hackteria.org/index.php/ArtScience_IGEM_team]]<br />
<br />
[http://hackteria.org/index.php/ArtScience_IGEM_team Synthetic Biology for Artists and Designers@CEMA,NCBS]<br />
<br />
15. May-01. July<br />
|<br />
|-<br />
|'''Workshop:''' <br />
[[Bioelectronics for artists @ CEMA]]<br />
20. July - 28. July 2009<br />
[[File:amobae_workshop.jpg|300px]]<br />
|<br />
|-<br />
|'''Workshop:''' <br />
[[bioelectronix for artists @ videotage, Hong Kong]]<br />
<br />
14. Nov - 15. Nov 2009<br />
[[File:bioelectronix_videotage.jpg|300px]]<br />
|<br />
|-<br />
|'''Workshop:''' <br />
[[bioelectronix for artists @ piksel09]]<br />
<br />
19. Nov - 21. Nov 2009<br />
[[File:bioelectronix_piksel.jpg|300px]]<br />
|<br />
|-<br />
|'''Workshop:''' <br />
[[bioelectronix for artists @ playaround09, Taipei]]<br />
<br />
7. Nov - 11. Dez 2009<br />
[[File:bioelectronix_playaround.jpg|300px]]<br />
|}<br />
</div><br />
<!-- Workshops end --><br />
<br />
<!-- People --><br />
<div class="alertBox"><br />
{| class="alert"<br />
! '''People: Artists and Designers working with Biology, Bio-technology and Bio-Ethics'''<br />
|-<br />
| Symbiotica<br />
|-<br />
| [http://www.critical-art.net/ Critical Arts Ensemble]<br />
|-<br />
| Dunne and Raby<br />
|-<br />
| Joe Davis<br />
|-<br />
|Eduardo Kac<br />
|-<br />
|[http://www.philross.org/ Phil Ross]<br />
|-<br />
|Stelarc<br />
|-<br />
|Beatriz D' Costa<br />
|-<br />
|[http://www.art.cfa.cmu.edu/people/2787-RichardPell Rich Pell]<br />
|-<br />
|[http://www.postnatural.org/http://www.postnatural.org/ Center for Post Natural History]<br />
|-<br />
|Natalie Jermejenko<br />
|-<br />
|[http://www.hostprods.net Andy Gracie]<br />
|-<br />
|[http://www.dusseiller.ch/labs Marc Dusseiller aka dusjagr]<br />
|-<br />
|[http://biomusic.labbs.net Jay Barros //BioMusic - Sounds of Science //]<br />
|-<br />
|Guy Ben-Aury<br />
|-<br />
|Gabriel Harp<br />
|-<br />
|Anab Jain<br />
|-<br />
|[http://www.heavythinking.org Verena Friedrich]<br />
|-<br />
|Anthony Hall<br />
|-<br />
|[http://www.emutagen.com Adam Zaretsky]<br />
|-<br />
|Brandon Ballangee<br />
|-<br />
|C-Labs<br />
|-<br />
|[http://residualsoup.org/boo-chapple.html Boo Chapple]<br />
|-<br />
|Marta de Menezes<br />
|-<br />
|Victoria Vesna<br />
|-<br />
|[http://www.o-o-e.org/ The Office of Experiments]<br />
|-<br />
|[http://thedepartment.in The Department of Fun and Games]<br />
|-<br />
|[http://www.allisonx.com Allison Kudla]<br />
|-<br />
|}<br />
</div><br />
<!-- People ends --><br />
<br />
<!-- Links --><br />
<div class="alertBox"><br />
{| class="alert"<br />
! Tools<br />
|-<br />
|BioBricks [http://www.biobricks.org]<br />
|-<br />
|GeneSynthetic[http://www.genesynthetic.com/page_main.shtml]<br />
|-<br />
|<br />
DIY Bio Blog[http://diybio4beginners.blogspot.com/]<br />
|}<br />
</div><br />
<!-- Links ends --><br />
<br />
<!-- Papers--><br />
<div class="alertBox"><br />
{| class="alert"<br />
! Papers,Conferences and Journals<br />
|-<br />
|Leonardo<br />
|-<br />
|Synthetic Biology 3 Zurich[http://www.syntheticbiology3.ethz.ch/extra/SBProceedings.pdf]<br />
|-<br />
|Biointer''phases''[http://biointerphases.org/]<br />
|-<br />
|Lab on a Chip[http://www.rsc.org/publishing/journals/LC/]<br />
|}<br />
</div><br />
<!-- Papers ends --><br />
<br />
<br />
<br />
== Welcome to Hackteria.org ==<br />
<br />
<br />
Hackteria is a collection of DIY Biology, Open Source Art Projects that use Biology, LifeSciences, Biotechnology.<br />
<br />
[[File:hackteria_banner.jpg]]<br />
<br />
[[editing the hackteria wiki]]<br />
<br />
<!-- Projects --><br />
<div class="alertBox1"><br />
{| class="alert"<br />
!Projects<br />
<br />
|-<br />
|'''Project 1: [[The Bacterial Net- Microbial Telecommunications.]]'''<br />
[[Image:2.jpg|120px|left]]<br />
Quorum sensing is a type of decision-making process used by decentralized groups to coordinate behavior. Many species of bacteria use quorum sensing to coordinate their gene expression according to the local density of their population.The Bacterial Net attempts to transfer this decision making process over the Internet. Using Microcontollers and sensors to detect bacterial population and a public web service http://www.pachube.com that helps transfer sensor information. The Bacterial Net is an exploration in bringing the Internet into the Natural Ecosystem. <br />
<br />
|-<br />
|'''Project 2: [[Bioelectronix]]'''<br />
<br />
[[Image:bioelectronics_after_casting.jpg|120px|left]]<br />
<br />
Integrating electronics into biological culture devices needs different approaches. the use of silicone-rubbers for sealing off the wet/humid bio-part from the silicon circuits and sensors allows the making of hybrid bioelectronic devices. <br />
|-<br />
| '''Project 3: [[Synthetic Biology for Artists and Designers: A primer]]'''<br />
[[File:synbio_cover.jpg|120px|left]]<br />
An Illustrated [http://hackteria.org/wiki/images/a/a1/Handbook.pdf <strong>handbook</strong>] that shows you how to work with MIT's parts registry<br />
|-<br />
| '''Project 4: [[ArtScience IGEM team]]'''<br />
[[File:Whiteboard.jpg|120px|left]]<br />
<br />
<br />
|-<br />
|'''Project 5: [[DIY microscopy]]'''<br />
[[File:cam_ani_sm.gif|left]]<br />
<br />
a small hack to the optics of a standard webcam with an adjustable focus-lens, allows to create video data, with a magnification of around 100 to 400x (depending on the model) at a working distance of a few mm. The highest magnifications can be achieved by inverting (putting upside down) the lens. Addition of good lighting by the use of leds allows to create images using a bright-field method (shine through the stuff) or dark field method (look at the reflections and scattering). <br />
<br />
|-<br />
|'''Project 6:[[DIY $25 Gel Box]]'''<br />
[[File:DSC 8050.jpg|120px|left]]<br />
Building your own Electrophoresis Gel Box is easy. Here's how you do it!<br />
<br />
|-<br />
| '''Project 7: [[bio habitats]]'''<br />
[[File:biohabitat.jpg|120px|left]]<br />
instead of using standard lab culture tools, such as flasks or petri-dishes, artists might want to design their own devices to culture and inhabitate living organisms and keep them alive. simple devices can be cast in silicone to incorporate all the necessary environemtal conditions for long time survival of microorganisms.<br />
<br />
|-<br />
| '''Project 8: [[DIY Microfluidics]]'''<br />
[[File:Microfluidicwikiimage.png|120px|left]]<br />
<br />
|-<br />
| '''Project 9: [[DIY Plant Tissue culture and Engineering]]'''<br />
[[File:plant_culture.jpg|120px|left]]<br />
<br />
|-<br />
| '''Project 10: [[Pd_microscope]]'''<br />
[[File:pd_microscope.png|120px|left]]<br />
Pd_microscope is the software package that you can use to control your DIY microscope. It's a work in progress<br />
<br />
|-<br />
| '''Project 11: [[DIY spectroscopy]]'''<br />
[[File:spektral_tag1.jpg|120px|left]]<br />
Spectroscopy means the analysis of natural phenomena according to its energy distribution. In case of the electromagnetic spectra, ranging from x-ray, visible light, infrated to radio frequencies, this can be used to analyse chemical compounds, follow biochemical reactions or get information of the composition of stars. This project tries utilize webcams, CD/DVD and some construction material, to get a spectral analysis of ultra-violett and visible light sources, which might be used to follow enzymatic and metabolic reactions in cultured microorganisms and bacteria.<br />
<br />
|-<br />
| '''Project 12: [[ArtScienceBangalore 2010-Synthetic Biology for Artists and Designers]]'''<br />
[[File:Asb_2010_group.jpg|150px|left]]<br />
A bunch of regular people with very little idea of Synthetic Biology but ready to pick up eveything about it.<br />
<br />
|-<br />
| '''Project 13: [[DIY handheld centrifuge]]'''<br />
[[File:HandHeldCent.jpg |120px|left]]<br />
<br />
|-<br />
| '''Project 14: [[DIY table top centrifuge]]'''<br />
[[File:Table_top.JPG|120px|left]]<br />
<br />
|-<br />
| '''Project 15: [[DIY Incubator]]'''<br />
[[File:DSC03096.JPG|120px|left]]<br />
<br />
<br />
|-<br />
| '''Project 16: [[DIY Fermentation or the Art of making Wine]]'''<br />
[[File:diy_fermentation.jpg|120px|left]]<br />
<br />
|-<br />
| '''Project 17: [[Hacked Optical Mouse]]'''<br />
[[File:optical_mouse_hack.jpg|120px|left]]<br />
<br />
|-<br />
| '''Project 18: [[DIY Sterlisation Hood]]'''<br />
[[File:DSC03946.JPG |120px|left]]<br />
<br />
|-<br />
| '''Project 19: [[DIY Water Bath]]'''<br />
[[File:DSC04040.JPG|120px|left]]<br />
<br />
|-<br />
| '''Project 20: [[GFP Protocol Jugaad]]'''<br />
[[File:MG_7283.JPG|120px|left]]<br />
Home made GFP bacteria<br />
<br />
|-<br />
| '''Project 21: [[ReacTable]]'''<br />
[[File:DSC04180.JPG|120px|left]]<br />
Gives information and protocals of equipment and bacteria put on it<br />
<br />
</div><br />
<!-- Projects end --></div>Farhadhttp://www.hackteria.org/wiki/index.php?title=File:DSC04180.JPG&diff=2803File:DSC04180.JPG2010-10-22T10:02:15Z<p>Farhad: </p>
<hr />
<div></div>Farhadhttp://www.hackteria.org/wiki/index.php?title=ReacTable&diff=2802ReacTable2010-10-22T10:01:25Z<p>Farhad: </p>
<hr />
<div>== Introbuction ==<br />
<br />
<br />
This is a multi touch table that reads markers placed on the screen and does a corresponding action. Thus reading the object on the screen and functioning accordingly. The table uses reactivision software. This application was designed to track specially designed fiducial markers. By downloading the TUIO library you can cerate a program that operates on these markers. the table uses infra red light for finger tracking.<br />
a webcam takes in the feed and runs it through reactivision. It is then processed in processing and displayed again on the screen.<br />
<br />
'''We used this to give information and protocals when a certian object was put on it.'''<br />
<br />
<br />
<br />
===How reacTIVision works===<br />
<br />
In a nutshell the system works like this: reacTIVision tracks specially designed fiducial markers in a real time video stream. The source image frame is first converted to a black&white image with an adaptive thresholding algorithm. Then this image is segmented into a tree of alternating black and white regions (region adjacency graph). This graph is then searched for unique left heavy depth sequences, which have been encoded into the fiducial symbol. Finally the found tree sequences are matched to a dictionary to retrieve an unique ID number. The fiducial design allows the efficient calculation of the marker's center point as well as its orientation. OSC messages implementing the TUIO protocol encode the fiducials' presence, location, orientation and identity and transmit this data to the client applications. <br />
Additionally reacTIVision uses the result of the image segmentation in order to retrieve and identify small round white blobs as finger tips on the surface. A quick and dirty shape matching algorithm selects the actual finger blobs from the possible region candidates. A complementary blob tracking algorithm is also taking advantage of the same data in order to track eventually not recognized fiducials, for example where fast movements destroy the actual fiducial structure in the image.<br />
<br />
<br />
<br />
<br />
== Building the table ==<br />
<br />
<br />
===table & surface===<br />
<br />
A camera and a projector with wide-angle lenses need to be placed underneath the table, so they can both cover the entire surface. [[File:Reactivision03.png|400px|right|]]Alternatively a mirror can be used in order to achieve a larger projection distance. For the interactive surface itself a normal perspex board can be used in conjunction with some ordinary tracing paper on the top side for the projection. This material is completely transparent for objects and finger tips in direct contact with the surface. In order to avoid direct reflections of the light source and projector lamp, the lower side of the surface should have a matte finish, while maintaing the overall transparency. <br />
<br />
<br />
===illumination===<br />
<br />
For the tracking, the objects need to be properly illuminated, so the camera and thus the computer vision application can see them correctly. For the projection onto a table, the surface needs to be dark though, so the user can see the projected image well enough. Since these two necessary steps logically exclude each other, the solution is to operate in two different spectra: <br />
The projection has to be visible to the user, so the computer vision component needs to operate in a different, invisible spectrum such as near infrared in the range of 850nm. Most CCD cameras are perfectly sensitive within the near IR spectrum, therefore infrared LED lamps can be used to illuminate the table. All light from the visible spectrum needs to be filtered in the camera, so the computer vision algorithm is not disturbed by the projection. Eventually an existing infrared blocker needs to be removed from the camera sensor. <br />
<br />
<br />
===camera===<br />
<br />
You should make sure that the camera has an acceptable lens and sensor size. For lowest latency and best performance we recommend firewire cameras from the top range, such as industrial cameras with a high framerate, resolution and sensor size. These cameras usually also come with high quality C-mount lenses. Cheaper firewire cameras, such as the unibrain fire-i also allow optional wide-angle lenses. From the large range of available USB cameras we recommend to use high end models with a native resolution of at least 640x480 at a frame rate of 30Hz. A very affordable and relatively good camera for this purpose is the Sony PS3eye, which is also working well under Windows, Linux and Mac OSX. DV cameras supporting full-frame mode are suitable, while those with interlaced mode only, will not work at all. an IR bypass filter needs to be placed on the lens instead of the ordinary camera filter if you are using 2 different spectra<br />
[[File:DSC04178.JPG|200 px|right|frame|IR LEDs along side of perspex board]]<br />
<br />
<br />
=== How Our box functions ===<br />
<br />
[[File:DSC04188.JPG|200 px|left]]<br />
1. We used a simple wood box(3 x 1.5 x 2.5 ft) painted black on the inside so there is less reflection of light. We used a projector to project onto a mirror which reflects the projection onto the screen.The keystone setting on the projector is set at -120 so that the projection on the screen is a rectangular shape.<br />
<br />
2. We couldn't find an IR bulb so we placed IR LEDs on 2 opposite sides of the perspex board so that the IR light refracts in the perspex board. When a finger is placed on the screen, it forms a blob of IR light on the inside of the box and is read by the webcam. <br />
<br />
3. We made a stand for the laptop on top of the projector and used the laptop webcam itself as the image was pretty clear. We used a processed photography negative as the IR bypass filter on the webcam.<br />
<br />
<br />
<br />
== Using reacTIVision ==<br />
<br />
[http://www.reactivision.sourceforge.netlink download reacTIVisiom here]<br />
<br />
===Fiducial Symbols===<br />
<br />
[[File:Reactivision02.png|300px|right|]]<br />
This application was designed to track specially designed fiducial markers. You will find the default "amoeba" fiducial set within the document "default.pdf" within the symbols folder of the reactivision download. Print this document and attach the labels to any object you want to track. The default fiducial tracking engine is using Ross Bencina's fidtrack library which is basically a newer high-performance implementation of Enrico Costanza's d-touch concept. Alternatively you can use the "classic" or the "dtouch" sets. See below how to configure the application using these older symbol sets. <br />
<br />
<br />
===Finger Tracking===<br />
<br />
Since reacTIVision was initially designed for fiducial tracking, its thresholder and segmentation modules are optimized for this task. Finger tracking was added at a later stage, and is taking advantage of the existing image processing infrastructure with almost no additional performance overhead. On the other hand it might seem difficult to set up reacTIVision in order to achieve good tracking performance for both the fiducial symbols and the finger tips. When used with diffused illumination, the setup needs strong and even illumination in order to achieve the necessary contrast for finger tracking, also the overall image control such as brightness, gain and shutter speed will improve the tracking quality (O key). Another important control parameter is the threshold "gradient gate" which should be set as low as possible, just before too much image noise becomes visible (G key). Finally the finger tracking can be configured by adjusting the average finger size and tracking sensitivity (F key). <br />
<br />
<br />
===Application Handling===<br />
<br />
[[File:Cam_settings.JPG|300px|right|frame|webcam streaming on laptop]]<br />
Common settings can be edited within the file "reacTIVision.xml" where all changes are stored automatically when closing the application. Under Mac OS X the XML configuration file can be found within the application bundle's Resources folder. Select "Show Package Contents" from the application's context menu in order to access and edit the file. <br />
<br />
The reacTIVision application usually sends the TUIO messages to port 3333 on locahost (127.0.0.1) You can change this setting by adding or editing the XML tag <tuio host="127.0.0.1" port="3333"> to the configuration. <br />
<br />
The <fiducial engine="amoeba" tree="default"/> XML tag lets you select the fiducial engine or an alternative amoeba tree order. The default engine is using the fastest and effective 'amoeba' fiducial set. Add the 'classic' option in order to use Ross' initial d-touch reimplementation. You can select Enrico's original d-touch engine by providing the 'dtouch' option. <br />
<br />
The display attribute defines the default screen upon startup. The <image display="dest" equalize="false" gradient="32" /> lets you adjust the default gradient gate value. reacTIVision comes with a background subtraction module, which in some cases can simplify the recognition performance of both the finger and fiducial tracking. Within the running application you can toggle this with the 'E' key or recalculate the background subtraction by hitting the SPACE bar. <br />
<br />
The camera options can be adjusted by pressing the 'O' key. On Windows and Mac OS this will show a system dialog that allows the adjustment of the available camera parameters. On Linux (Mac OS X when using IEEE1394 cameras), the available camera settings can be adjusted with a simple on screen display.<br />
The overall camera settings can be configured within the camera.xml configuration file. Please note that for Windows and the Quicktime mode on Mac OS X this only allows the configuration of the image size. For IEEE1394 cameras on Mac OS X as well as all camera types on Linux all image parameters can be fully configured using this configuration file.<br />
<br />
<br />
===Calibration and Distortion===<br />
<br />
Some tables, such as the reacTable are using wide-angle or fish-eye lens in order to increase the area visible to the camera at a minimal distance. These lenses unfortunately distort the image and reacTIVision can correct that distortion and the overall alignment of the image. For the calibration print and place one of these rectangular or square calibration sheets on the table and adjust the grid points to the grid printed on the sheet. <br />
<br />
To calibrate reacTIVision switch to calibration mode hitting 'C'. Use the keys A,D,W,X to move within grid, moving with the cursor keys will adjust the grid point. <br />
'J' resets the whole calibration grid, 'U' resets the selected point and 'K' reverts to the saved grid. <br />
To check if the distortion is working properly press 'R'. This will show the fully distorted live video image in the target window. Of course the distortion algorithm only corrects the found positions instead of the full image.<br />
<br />
<br />
<br />
== TUIO in Processing ==<br />
<br />
<br />
=== Installation ===<br />
<br />
Copy the complete contents of this distribution to a folder named TUIO to the libraries folder of your Processing sketchbook. In order to use this library, you will need to provide the according import statement within the header of your Processing sketch: <br />
import TUIO.*; <br />
<br />
<br />
=== Application Programming Interface ===<br />
<br />
First you need to create an instance of the TuioProcessing client, providing the instance of your sketch to the constructor using the this argument. The TuioProcessing client immediately starts listening to incoming TUIO messages and generates higher level events based on the object and cursor movements. <br />
TuioProcessing tuioClient = new TuioProcessing(this);<br />
<br />
Therefore your sketch needs to implement the following methods in order to be able to receive these TUIO events properly: <br />
<br />
-addTuioObject(TuioObject tobj) this is called when an object becomes visible <br />
<br />
-removeTuioObject(TuioObject tobj) an object was removed from the table <br />
<br />
-updateTuioObject(TuioObject tobj) an object was moved on the table surface <br />
<br />
-addTuioCursor(TuioCursor tcur) this is called when a new cursor is detected <br />
<br />
-removeTuioCursor(TuioCursor tcur) a cursor was removed from the table <br />
<br />
-updateTuioCursor(TuioCursor tcur) a cursor was moving on the table surface <br />
<br />
-refresh(TuioTime bundleTime) this method is called after each bundle,<br />
<br />
<br />
use it to repaint your screen for example: <br />
<br />
Each TuioObject or TuioCursor is identified with a unique SessionID, which it maintains over its lifetime. Additionally each TuioObject carries a SymbolID that corresponds to its attached fiducial marker number. The CursorID of the TuioCursor is always a number in the range of all currently detected cursors. You can retrieve these ID numbers with the according getSessionID(), getSymbolID() or getCursorID() methods. <br />
<br />
The TuioObject and TuioCursor references are updated automatically by the TuioProcessing client and are always referencing the same instance over the object's or cursor's lifetime. All the TuioObject and TuioCursor attributes are encapsulated, and can be accessed with methods such as getX(), getY() and getAngle(). There exist further methods for the retrieval of speed and acceleration values, please see the provided example sketches for a complete list. TuioObject and TuioCursor also have some additional convenience methods for the calculation of distances and angles between objects. The getPath() method returns a Vector of TuioPoint representing the movement path of the object. Please refer to the documentation of the TUIO Java reference implementations for further details on all the available methods. <br />
<br />
Alternatively, the TuioProcessing class contains some methods for the polling of the current object and cursor states. There are methods which return either a list or individual TuioObject and TuioCursor objects. <br />
<br />
-getTuioObjects() returns a Vector of all currently present TuioObjects <br />
<br />
-getTuioCursors() returns a Vector of all currently present TuioCursors <br />
<br />
-getTuioObject(long s_id) returns a TuioObject or NULL depending on its presence <br />
<br />
-getTuioCursor(long s_id) returns a TuioCursor or NULL depending on its presence<br />
<br />
<br />
=== Our Program ===<br />
<br />
<br />
[[File:React_table_flow_chart.JPG|400px|]]<br />
<br />
In our program each marker is attached to an image that discribes a cretian equipment and how it is used. the fudicial is stuck onto the equipment.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=File:DSC04188.JPG&diff=2801File:DSC04188.JPG2010-10-22T09:57:42Z<p>Farhad: </p>
<hr />
<div></div>Farhadhttp://www.hackteria.org/wiki/index.php?title=File:DSC04178.JPG&diff=2800File:DSC04178.JPG2010-10-22T09:55:24Z<p>Farhad: uploaded a new version of "File:DSC04178.JPG"</p>
<hr />
<div></div>Farhadhttp://www.hackteria.org/wiki/index.php?title=File:DSC04178.JPG&diff=2799File:DSC04178.JPG2010-10-22T09:40:04Z<p>Farhad: </p>
<hr />
<div></div>Farhadhttp://www.hackteria.org/wiki/index.php?title=ReacTable&diff=2798ReacTable2010-10-20T09:37:40Z<p>Farhad: </p>
<hr />
<div>== Introbuction ==<br />
<br />
<br />
This is a multi touch table that reads markers placed on the screen and does a corresponding action. Thus reading the object on the screen and functioning accordingly. The table uses reactivision software. This application was designed to track specially designed fiducial markers. By downloading the TUIO library you can cerate a program that operates on these markers. the table uses infra red light for finger tracking.<br />
a webcam takes in the feed and runs it through reactivision. It is then processed in processing and displayed again on the screen.<br />
<br />
'''We used this to give information and protocals when a certian object was put on it.'''<br />
<br />
<br />
<br />
===How reacTIVision works===<br />
<br />
In a nutshell the system works like this: reacTIVision tracks specially designed fiducial markers in a real time video stream. The source image frame is first converted to a black&white image with an adaptive thresholding algorithm. Then this image is segmented into a tree of alternating black and white regions (region adjacency graph). This graph is then searched for unique left heavy depth sequences, which have been encoded into the fiducial symbol. Finally the found tree sequences are matched to a dictionary to retrieve an unique ID number. The fiducial design allows the efficient calculation of the marker's center point as well as its orientation. OSC messages implementing the TUIO protocol encode the fiducials' presence, location, orientation and identity and transmit this data to the client applications. <br />
Additionally reacTIVision uses the result of the image segmentation in order to retrieve and identify small round white blobs as finger tips on the surface. A quick and dirty shape matching algorithm selects the actual finger blobs from the possible region candidates. A complementary blob tracking algorithm is also taking advantage of the same data in order to track eventually not recognized fiducials, for example where fast movements destroy the actual fiducial structure in the image.<br />
<br />
<br />
<br />
<br />
== Building the table ==<br />
<br />
<br />
===table & surface===<br />
<br />
A camera and a projector with wide-angle lenses need to be placed underneath the table, so they can both cover the entire surface. [[File:Reactivision03.png|400px|right|]]Alternatively a mirror can be used in order to achieve a larger projection distance. For the interactive surface itself a normal perspex board can be used in conjunction with some ordinary tracing paper on the top side for the projection. This material is completely transparent for objects and finger tips in direct contact with the surface. In order to avoid direct reflections of the light source and projector lamp, the lower side of the surface should have a matte finish, while maintaing the overall transparency. <br />
<br />
<br />
===illumination===<br />
<br />
For the tracking, the objects need to be properly illuminated, so the camera and thus the computer vision application can see them correctly. For the projection onto a table, the surface needs to be dark though, so the user can see the projected image well enough. Since these two necessary steps logically exclude each other, the solution is to operate in two different spectra: <br />
The projection has to be visible to the user, so the computer vision component needs to operate in a different, invisible spectrum such as near infrared in the range of 850nm. Most CCD cameras are perfectly sensitive within the near IR spectrum, therefore infrared LED lamps can be used to illuminate the table. All light from the visible spectrum needs to be filtered in the camera, so the computer vision algorithm is not disturbed by the projection. Eventually an existing infrared blocker needs to be removed from the camera sensor. <br />
<br />
<br />
===camera===<br />
<br />
You should make sure that the camera has an acceptable lens and sensor size. For lowest latency and best performance we recommend firewire cameras from the top range, such as industrial cameras with a high framerate, resolution and sensor size. These cameras usually also come with high quality C-mount lenses. Cheaper firewire cameras, such as the unibrain fire-i also allow optional wide-angle lenses. From the large range of available USB cameras we recommend to use high end models with a native resolution of at least 640x480 at a frame rate of 30Hz. A very affordable and relatively good camera for this purpose is the Sony PS3eye, which is also working well under Windows, Linux and Mac OSX. DV cameras supporting full-frame mode are suitable, while those with interlaced mode only, will not work at all. an IR bypass filter needs to be placed on the lens instead of the ordinary camera filter if you are using 2 different spectra<br />
<br />
<br />
=== How Our box functions ===<br />
<br />
1. We used a simple wood box(3 x 1.5 x 2.5 ft) painted black on the inside so there is less reflection of light. We used a projector to project onto a mirror which reflects the projection onto the screen.The keystone setting on the projector is set at -120 so that the projection on the screen is a rectangular shape.<br />
<br />
2. We couldn't find an IR bulb so we placed IR LEDs on 2 opposite sides of the perspex board so that the IR light refracts in the perspex board. When a finger is placed on the screen, it forms a blob of IR light on the inside of the box and is read by the webcam. <br />
<br />
3. We made a stand for the laptop on top of the projector and used the laptop webcam itself as the image was pretty clear. We used a processed photography negative as the IR bypass filter on the webcam.<br />
<br />
<br />
<br />
== Using reacTIVision ==<br />
<br />
[http://www.reactivision.sourceforge.netlink download reacTIVisiom here]<br />
<br />
===Fiducial Symbols===<br />
<br />
[[File:Reactivision02.png|300px|right|]]<br />
This application was designed to track specially designed fiducial markers. You will find the default "amoeba" fiducial set within the document "default.pdf" within the symbols folder of the reactivision download. Print this document and attach the labels to any object you want to track. The default fiducial tracking engine is using Ross Bencina's fidtrack library which is basically a newer high-performance implementation of Enrico Costanza's d-touch concept. Alternatively you can use the "classic" or the "dtouch" sets. See below how to configure the application using these older symbol sets. <br />
<br />
<br />
===Finger Tracking===<br />
<br />
Since reacTIVision was initially designed for fiducial tracking, its thresholder and segmentation modules are optimized for this task. Finger tracking was added at a later stage, and is taking advantage of the existing image processing infrastructure with almost no additional performance overhead. On the other hand it might seem difficult to set up reacTIVision in order to achieve good tracking performance for both the fiducial symbols and the finger tips. When used with diffused illumination, the setup needs strong and even illumination in order to achieve the necessary contrast for finger tracking, also the overall image control such as brightness, gain and shutter speed will improve the tracking quality (O key). Another important control parameter is the threshold "gradient gate" which should be set as low as possible, just before too much image noise becomes visible (G key). Finally the finger tracking can be configured by adjusting the average finger size and tracking sensitivity (F key). <br />
<br />
<br />
===Application Handling===<br />
<br />
[[File:Cam_settings.JPG|300px|right|frame|webcam streaming on laptop]]<br />
Common settings can be edited within the file "reacTIVision.xml" where all changes are stored automatically when closing the application. Under Mac OS X the XML configuration file can be found within the application bundle's Resources folder. Select "Show Package Contents" from the application's context menu in order to access and edit the file. <br />
<br />
The reacTIVision application usually sends the TUIO messages to port 3333 on locahost (127.0.0.1) You can change this setting by adding or editing the XML tag <tuio host="127.0.0.1" port="3333"> to the configuration. <br />
<br />
The <fiducial engine="amoeba" tree="default"/> XML tag lets you select the fiducial engine or an alternative amoeba tree order. The default engine is using the fastest and effective 'amoeba' fiducial set. Add the 'classic' option in order to use Ross' initial d-touch reimplementation. You can select Enrico's original d-touch engine by providing the 'dtouch' option. <br />
<br />
The display attribute defines the default screen upon startup. The <image display="dest" equalize="false" gradient="32" /> lets you adjust the default gradient gate value. reacTIVision comes with a background subtraction module, which in some cases can simplify the recognition performance of both the finger and fiducial tracking. Within the running application you can toggle this with the 'E' key or recalculate the background subtraction by hitting the SPACE bar. <br />
<br />
The camera options can be adjusted by pressing the 'O' key. On Windows and Mac OS this will show a system dialog that allows the adjustment of the available camera parameters. On Linux (Mac OS X when using IEEE1394 cameras), the available camera settings can be adjusted with a simple on screen display.<br />
The overall camera settings can be configured within the camera.xml configuration file. Please note that for Windows and the Quicktime mode on Mac OS X this only allows the configuration of the image size. For IEEE1394 cameras on Mac OS X as well as all camera types on Linux all image parameters can be fully configured using this configuration file.<br />
<br />
<br />
===Calibration and Distortion===<br />
<br />
Some tables, such as the reacTable are using wide-angle or fish-eye lens in order to increase the area visible to the camera at a minimal distance. These lenses unfortunately distort the image and reacTIVision can correct that distortion and the overall alignment of the image. For the calibration print and place one of these rectangular or square calibration sheets on the table and adjust the grid points to the grid printed on the sheet. <br />
<br />
To calibrate reacTIVision switch to calibration mode hitting 'C'. Use the keys A,D,W,X to move within grid, moving with the cursor keys will adjust the grid point. <br />
'J' resets the whole calibration grid, 'U' resets the selected point and 'K' reverts to the saved grid. <br />
To check if the distortion is working properly press 'R'. This will show the fully distorted live video image in the target window. Of course the distortion algorithm only corrects the found positions instead of the full image.<br />
<br />
<br />
<br />
== TUIO in Processing ==<br />
<br />
<br />
=== Installation ===<br />
<br />
Copy the complete contents of this distribution to a folder named TUIO to the libraries folder of your Processing sketchbook. In order to use this library, you will need to provide the according import statement within the header of your Processing sketch: <br />
import TUIO.*; <br />
<br />
<br />
=== Application Programming Interface ===<br />
<br />
First you need to create an instance of the TuioProcessing client, providing the instance of your sketch to the constructor using the this argument. The TuioProcessing client immediately starts listening to incoming TUIO messages and generates higher level events based on the object and cursor movements. <br />
TuioProcessing tuioClient = new TuioProcessing(this);<br />
<br />
Therefore your sketch needs to implement the following methods in order to be able to receive these TUIO events properly: <br />
<br />
-addTuioObject(TuioObject tobj) this is called when an object becomes visible <br />
<br />
-removeTuioObject(TuioObject tobj) an object was removed from the table <br />
<br />
-updateTuioObject(TuioObject tobj) an object was moved on the table surface <br />
<br />
-addTuioCursor(TuioCursor tcur) this is called when a new cursor is detected <br />
<br />
-removeTuioCursor(TuioCursor tcur) a cursor was removed from the table <br />
<br />
-updateTuioCursor(TuioCursor tcur) a cursor was moving on the table surface <br />
<br />
-refresh(TuioTime bundleTime) this method is called after each bundle,<br />
<br />
<br />
use it to repaint your screen for example: <br />
<br />
Each TuioObject or TuioCursor is identified with a unique SessionID, which it maintains over its lifetime. Additionally each TuioObject carries a SymbolID that corresponds to its attached fiducial marker number. The CursorID of the TuioCursor is always a number in the range of all currently detected cursors. You can retrieve these ID numbers with the according getSessionID(), getSymbolID() or getCursorID() methods. <br />
<br />
The TuioObject and TuioCursor references are updated automatically by the TuioProcessing client and are always referencing the same instance over the object's or cursor's lifetime. All the TuioObject and TuioCursor attributes are encapsulated, and can be accessed with methods such as getX(), getY() and getAngle(). There exist further methods for the retrieval of speed and acceleration values, please see the provided example sketches for a complete list. TuioObject and TuioCursor also have some additional convenience methods for the calculation of distances and angles between objects. The getPath() method returns a Vector of TuioPoint representing the movement path of the object. Please refer to the documentation of the TUIO Java reference implementations for further details on all the available methods. <br />
<br />
Alternatively, the TuioProcessing class contains some methods for the polling of the current object and cursor states. There are methods which return either a list or individual TuioObject and TuioCursor objects. <br />
<br />
-getTuioObjects() returns a Vector of all currently present TuioObjects <br />
<br />
-getTuioCursors() returns a Vector of all currently present TuioCursors <br />
<br />
-getTuioObject(long s_id) returns a TuioObject or NULL depending on its presence <br />
<br />
-getTuioCursor(long s_id) returns a TuioCursor or NULL depending on its presence<br />
<br />
<br />
=== Our Program ===<br />
<br />
<br />
[[File:React_table_flow_chart.JPG|400px|]]<br />
<br />
In our program each marker is attached to an image that discribes a cretian equipment and how it is used. the fudicial is stuck onto the equipment.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=Old_Main_Page&diff=2797Old Main Page2010-10-20T09:31:11Z<p>Farhad: </p>
<hr />
<div><!-- Labs--><br />
<div class="alertBox"><br />
{| class="alert"<br />
! Labs<br />
|-<br />
|'''Hackteria Lab - Dock18 - April 2010''' <br />
[[Hackteria Lab - Dock18 - 6-9 April 2010]]<br />
<br />
[[File:forum_hackteria.jpg|300px]]<br />
<br />
|}<br />
</div><br />
<!-- Labs end --><br />
<br />
<!-- Workshops--><br />
<div class="alertBox"><br />
{| class="alert"<br />
! Workshops<br />
|-<br />
|'''Workshop:''' <br />
[[hackteria & lab_hacking @ NK, Berlin]]<br />
30. May - 3. June 2009<br />
[[File:Flyer_nk_web.jpg|300px]]<br />
<br />
<br />
[http://www.myspace.com/enka52 NK, Berlin]<br />
|-<br />
| '''Workshop: '''<br />
[[File:Igemworkshoppngwiki.png|http://hackteria.org/index.php/ArtScience_IGEM_team]]<br />
<br />
[http://hackteria.org/index.php/ArtScience_IGEM_team Synthetic Biology for Artists and Designers@CEMA,NCBS]<br />
<br />
15. May-01. July<br />
|<br />
|-<br />
|'''Workshop:''' <br />
[[Bioelectronics for artists @ CEMA]]<br />
20. July - 28. July 2009<br />
[[File:amobae_workshop.jpg|300px]]<br />
|<br />
|-<br />
|'''Workshop:''' <br />
[[bioelectronix for artists @ videotage, Hong Kong]]<br />
<br />
14. Nov - 15. Nov 2009<br />
[[File:bioelectronix_videotage.jpg|300px]]<br />
|<br />
|-<br />
|'''Workshop:''' <br />
[[bioelectronix for artists @ piksel09]]<br />
<br />
19. Nov - 21. Nov 2009<br />
[[File:bioelectronix_piksel.jpg|300px]]<br />
|<br />
|-<br />
|'''Workshop:''' <br />
[[bioelectronix for artists @ playaround09, Taipei]]<br />
<br />
7. Nov - 11. Dez 2009<br />
[[File:bioelectronix_playaround.jpg|300px]]<br />
|}<br />
</div><br />
<!-- Workshops end --><br />
<br />
<!-- People --><br />
<div class="alertBox"><br />
{| class="alert"<br />
! '''People: Artists and Designers working with Biology, Bio-technology and Bio-Ethics'''<br />
|-<br />
| Symbiotica<br />
|-<br />
| [http://www.critical-art.net/ Critical Arts Ensemble]<br />
|-<br />
| Dunne and Raby<br />
|-<br />
| Joe Davis<br />
|-<br />
|Eduardo Kac<br />
|-<br />
|[http://www.philross.org/ Phil Ross]<br />
|-<br />
|Stelarc<br />
|-<br />
|Beatriz D' Costa<br />
|-<br />
|[http://www.art.cfa.cmu.edu/people/2787-RichardPell Rich Pell]<br />
|-<br />
|[http://www.postnatural.org/http://www.postnatural.org/ Center for Post Natural History]<br />
|-<br />
|Natalie Jermejenko<br />
|-<br />
|[http://www.hostprods.net Andy Gracie]<br />
|-<br />
|[http://www.dusseiller.ch/labs Marc Dusseiller aka dusjagr]<br />
|-<br />
|[http://biomusic.labbs.net Jay Barros //BioMusic - Sounds of Science //]<br />
|-<br />
|Guy Ben-Aury<br />
|-<br />
|Gabriel Harp<br />
|-<br />
|Anab Jain<br />
|-<br />
|[http://www.heavythinking.org Verena Friedrich]<br />
|-<br />
|Anthony Hall<br />
|-<br />
|[http://www.emutagen.com Adam Zaretsky]<br />
|-<br />
|Brandon Ballangee<br />
|-<br />
|C-Labs<br />
|-<br />
|[http://residualsoup.org/boo-chapple.html Boo Chapple]<br />
|-<br />
|Marta de Menezes<br />
|-<br />
|Victoria Vesna<br />
|-<br />
|[http://www.o-o-e.org/ The Office of Experiments]<br />
|-<br />
|[http://thedepartment.in The Department of Fun and Games]<br />
|-<br />
|[http://www.allisonx.com Allison Kudla]<br />
|-<br />
|}<br />
</div><br />
<!-- People ends --><br />
<br />
<!-- Links --><br />
<div class="alertBox"><br />
{| class="alert"<br />
! Tools<br />
|-<br />
|BioBricks [http://www.biobricks.org]<br />
|-<br />
|GeneSynthetic[http://www.genesynthetic.com/page_main.shtml]<br />
|-<br />
|<br />
DIY Bio Blog[http://diybio4beginners.blogspot.com/]<br />
|}<br />
</div><br />
<!-- Links ends --><br />
<br />
<!-- Papers--><br />
<div class="alertBox"><br />
{| class="alert"<br />
! Papers,Conferences and Journals<br />
|-<br />
|Leonardo<br />
|-<br />
|Synthetic Biology 3 Zurich[http://www.syntheticbiology3.ethz.ch/extra/SBProceedings.pdf]<br />
|-<br />
|Biointer''phases''[http://biointerphases.org/]<br />
|-<br />
|Lab on a Chip[http://www.rsc.org/publishing/journals/LC/]<br />
|}<br />
</div><br />
<!-- Papers ends --><br />
<br />
<br />
<br />
== Welcome to Hackteria.org ==<br />
<br />
<br />
Hackteria is a collection of DIY Biology, Open Source Art Projects that use Biology, LifeSciences, Biotechnology.<br />
<br />
[[File:hackteria_banner.jpg]]<br />
<br />
[[editing the hackteria wiki]]<br />
<br />
<!-- Projects --><br />
<div class="alertBox1"><br />
{| class="alert"<br />
!Projects<br />
<br />
|-<br />
|'''Project 1: [[The Bacterial Net- Microbial Telecommunications.]]'''<br />
[[Image:2.jpg|120px|left]]<br />
Quorum sensing is a type of decision-making process used by decentralized groups to coordinate behavior. Many species of bacteria use quorum sensing to coordinate their gene expression according to the local density of their population.The Bacterial Net attempts to transfer this decision making process over the Internet. Using Microcontollers and sensors to detect bacterial population and a public web service http://www.pachube.com that helps transfer sensor information. The Bacterial Net is an exploration in bringing the Internet into the Natural Ecosystem. <br />
<br />
|-<br />
|'''Project 2: [[Bioelectronix]]'''<br />
<br />
[[Image:bioelectronics_after_casting.jpg|120px|left]]<br />
<br />
Integrating electronics into biological culture devices needs different approaches. the use of silicone-rubbers for sealing off the wet/humid bio-part from the silicon circuits and sensors allows the making of hybrid bioelectronic devices. <br />
|-<br />
| '''Project 3: [[Synthetic Biology for Artists and Designers: A primer]]'''<br />
[[File:synbio_cover.jpg|120px|left]]<br />
An Illustrated [http://hackteria.org/wiki/images/a/a1/Handbook.pdf <strong>handbook</strong>] that shows you how to work with MIT's parts registry<br />
|-<br />
| '''Project 4: [[ArtScience IGEM team]]'''<br />
[[File:Whiteboard.jpg|120px|left]]<br />
<br />
<br />
|-<br />
|'''Project 5: [[DIY microscopy]]'''<br />
[[File:cam_ani_sm.gif|left]]<br />
<br />
a small hack to the optics of a standard webcam with an adjustable focus-lens, allows to create video data, with a magnification of around 100 to 400x (depending on the model) at a working distance of a few mm. The highest magnifications can be achieved by inverting (putting upside down) the lens. Addition of good lighting by the use of leds allows to create images using a bright-field method (shine through the stuff) or dark field method (look at the reflections and scattering). <br />
<br />
|-<br />
|'''Project 6:[[DIY $25 Gel Box]]'''<br />
[[File:DSC 8050.jpg|120px|left]]<br />
Building your own Electrophoresis Gel Box is easy. Here's how you do it!<br />
<br />
|-<br />
| '''Project 7: [[bio habitats]]'''<br />
[[File:biohabitat.jpg|120px|left]]<br />
instead of using standard lab culture tools, such as flasks or petri-dishes, artists might want to design their own devices to culture and inhabitate living organisms and keep them alive. simple devices can be cast in silicone to incorporate all the necessary environemtal conditions for long time survival of microorganisms.<br />
<br />
|-<br />
| '''Project 8: [[DIY Microfluidics]]'''<br />
[[File:Microfluidicwikiimage.png|120px|left]]<br />
<br />
|-<br />
| '''Project 9: [[DIY Plant Tissue culture and Engineering]]'''<br />
[[File:plant_culture.jpg|120px|left]]<br />
<br />
|-<br />
| '''Project 10: [[Pd_microscope]]'''<br />
[[File:pd_microscope.png|120px|left]]<br />
Pd_microscope is the software package that you can use to control your DIY microscope. It's a work in progress<br />
<br />
|-<br />
| '''Project 11: [[DIY spectroscopy]]'''<br />
[[File:spektral_tag1.jpg|120px|left]]<br />
Spectroscopy means the analysis of natural phenomena according to its energy distribution. In case of the electromagnetic spectra, ranging from x-ray, visible light, infrated to radio frequencies, this can be used to analyse chemical compounds, follow biochemical reactions or get information of the composition of stars. This project tries utilize webcams, CD/DVD and some construction material, to get a spectral analysis of ultra-violett and visible light sources, which might be used to follow enzymatic and metabolic reactions in cultured microorganisms and bacteria.<br />
<br />
|-<br />
| '''Project 12: [[ArtScienceBangalore 2010-Synthetic Biology for Artists and Designers]]'''<br />
[[File:Asb_2010_group.jpg|150px|left]]<br />
A bunch of regular people with very little idea of Synthetic Biology but ready to pick up eveything about it.<br />
<br />
|-<br />
| '''Project 13: [[DIY handheld centrifuge]]'''<br />
[[File:HandHeldCent.jpg |120px|left]]<br />
<br />
|-<br />
| '''Project 14: [[DIY table top centrifuge]]'''<br />
[[File:Table_top.JPG|120px|left]]<br />
<br />
|-<br />
| '''Project 15: [[DIY Incubator]]'''<br />
[[File:DSC03096.JPG|120px|left]]<br />
<br />
<br />
|-<br />
| '''Project 16: [[DIY Fermentation or the Art of making Wine]]'''<br />
[[File:diy_fermentation.jpg|120px|left]]<br />
<br />
|-<br />
| '''Project 17: [[Hacked Optical Mouse]]'''<br />
[[File:optical_mouse_hack.jpg|120px|left]]<br />
<br />
|-<br />
| '''Project 18: [[DIY Sterlisation Hood]]'''<br />
[[File:DSC03946.JPG |120px|left]]<br />
<br />
|-<br />
| '''Project 19: [[DIY Water Bath]]'''<br />
[[File:DSC04040.JPG|120px|left]]<br />
<br />
|-<br />
| '''Project 20: [[GFP Protocol Jugaad]]'''<br />
[[File:MG_7283.JPG|120px|left]]<br />
Home made GFP bacteria<br />
<br />
|-<br />
| '''Project 21: [[ReacTable]]'''<br />
[[File:Reactivision02.png|120px|left]]<br />
Gives information and protocals of equipment and bacteria put on it<br />
<br />
</div><br />
<!-- Projects end --></div>Farhadhttp://www.hackteria.org/wiki/index.php?title=ReacTable&diff=2796ReacTable2010-10-20T09:13:33Z<p>Farhad: </p>
<hr />
<div>== Introbuction ==<br />
<br />
<br />
This is a multi touch table that reads markers placed on the screen and does a corresponding action. Thus reading the object on the screen and functioning accordingly. The table uses reactivision software. This application was designed to track specially designed fiducial markers. By downloading the TUIO library you can cerate a program that operates on these markers. the table uses infra red light for finger tracking.<br />
a webcam takes in the feed and runs it through reactivision. It is then processed in processing and displayed again on the screen.<br />
<br />
'''We used this to give information and protocals when a certian object was put on it.'''<br />
<br />
<br />
<br />
===How reacTIVision works===<br />
<br />
In a nutshell the system works like this: reacTIVision tracks specially designed fiducial markers in a real time video stream. The source image frame is first converted to a black&white image with an adaptive thresholding algorithm. Then this image is segmented into a tree of alternating black and white regions (region adjacency graph). This graph is then searched for unique left heavy depth sequences, which have been encoded into the fiducial symbol. Finally the found tree sequences are matched to a dictionary to retrieve an unique ID number. The fiducial design allows the efficient calculation of the marker's center point as well as its orientation. OSC messages implementing the TUIO protocol encode the fiducials' presence, location, orientation and identity and transmit this data to the client applications. <br />
Additionally reacTIVision uses the result of the image segmentation in order to retrieve and identify small round white blobs as finger tips on the surface. A quick and dirty shape matching algorithm selects the actual finger blobs from the possible region candidates. A complementary blob tracking algorithm is also taking advantage of the same data in order to track eventually not recognized fiducials, for example where fast movements destroy the actual fiducial structure in the image.<br />
<br />
<br />
<br />
<br />
== Building the table ==<br />
<br />
<br />
===table & surface===<br />
<br />
A camera and a projector with wide-angle lenses need to be placed underneath the table, so they can both cover the entire surface. [[File:Reactivision03.png|400px|right|]]Alternatively a mirror can be used in order to achieve a larger projection distance. For the interactive surface itself a normal perspex board can be used in conjunction with some ordinary tracing paper on the top side for the projection. This material is completely transparent for objects and finger tips in direct contact with the surface. In order to avoid direct reflections of the light source and projector lamp, the lower side of the surface should have a matte finish, while maintaing the overall transparency. <br />
<br />
<br />
===illumination===<br />
<br />
For the tracking, the objects need to be properly illuminated, so the camera and thus the computer vision application can see them correctly. For the projection onto a table, the surface needs to be dark though, so the user can see the projected image well enough. Since these two necessary steps logically exclude each other, the solution is to operate in two different spectra: <br />
The projection has to be visible to the user, so the computer vision component needs to operate in a different, invisible spectrum such as near infrared in the range of 850nm. Most CCD cameras are perfectly sensitive within the near IR spectrum, therefore infrared LED lamps can be used to illuminate the table. All light from the visible spectrum needs to be filtered in the camera, so the computer vision algorithm is not disturbed by the projection. Eventually an existing infrared blocker needs to be removed from the camera sensor. <br />
<br />
<br />
===camera===<br />
<br />
You should make sure that the camera has an acceptable lens and sensor size. For lowest latency and best performance we recommend firewire cameras from the top range, such as industrial cameras with a high framerate, resolution and sensor size. These cameras usually also come with high quality C-mount lenses. Cheaper firewire cameras, such as the unibrain fire-i also allow optional wide-angle lenses. From the large range of available USB cameras we recommend to use high end models with a native resolution of at least 640x480 at a frame rate of 30Hz. A very affordable and relatively good camera for this purpose is the Sony PS3eye, which is also working well under Windows, Linux and Mac OSX. DV cameras supporting full-frame mode are suitable, while those with interlaced mode only, will not work at all. an IR bypass filter needs to be placed on the lens instead of the ordinary camera filter if you are using 2 different spectra<br />
<br />
<br />
=== How Our box functions ===<br />
<br />
1. We used a simple wood box(3 x 1.5 x 2.5 ft) painted black on the inside so there is less reflection of light. We used a projector to project onto a mirror which reflects the projection onto the screen.The keystone setting on the projector is set at -120 so that the projection on the screen is a rectangular shape.<br />
<br />
2. We couldn't find an IR bulb so we placed IR LEDs on 2 opposite sides of the perspex board so that the IR light refracts in the perspex board. When a finger is placed on the screen, it forms a blob of IR light on the inside of the box and is read by the webcam. <br />
<br />
3. We made a stand for the laptop on top of the projector and used the laptop webcam itself as the image was pretty clear. We used a processed photography negative as the IR bypass filter on the webcam.<br />
<br />
<br />
<br />
== Using reacTIVision ==<br />
<br />
<br />
===Fiducial Symbols===<br />
<br />
[[File:Reactivision02.png|300px|right|]]<br />
This application was designed to track specially designed fiducial markers. You will find the default "amoeba" fiducial set within the document "default.pdf" within the symbols folder of the reactivision download. Print this document and attach the labels to any object you want to track. The default fiducial tracking engine is using Ross Bencina's fidtrack library which is basically a newer high-performance implementation of Enrico Costanza's d-touch concept. Alternatively you can use the "classic" or the "dtouch" sets. See below how to configure the application using these older symbol sets. <br />
<br />
<br />
===Finger Tracking===<br />
<br />
Since reacTIVision was initially designed for fiducial tracking, its thresholder and segmentation modules are optimized for this task. Finger tracking was added at a later stage, and is taking advantage of the existing image processing infrastructure with almost no additional performance overhead. On the other hand it might seem difficult to set up reacTIVision in order to achieve good tracking performance for both the fiducial symbols and the finger tips. When used with diffused illumination, the setup needs strong and even illumination in order to achieve the necessary contrast for finger tracking, also the overall image control such as brightness, gain and shutter speed will improve the tracking quality (O key). Another important control parameter is the threshold "gradient gate" which should be set as low as possible, just before too much image noise becomes visible (G key). Finally the finger tracking can be configured by adjusting the average finger size and tracking sensitivity (F key). <br />
<br />
<br />
===Application Handling===<br />
<br />
[[File:Cam_settings.JPG|300px|right|frame|webcam streaming on laptop]]<br />
Common settings can be edited within the file "reacTIVision.xml" where all changes are stored automatically when closing the application. Under Mac OS X the XML configuration file can be found within the application bundle's Resources folder. Select "Show Package Contents" from the application's context menu in order to access and edit the file. <br />
<br />
The reacTIVision application usually sends the TUIO messages to port 3333 on locahost (127.0.0.1) You can change this setting by adding or editing the XML tag <tuio host="127.0.0.1" port="3333"> to the configuration. <br />
<br />
The <fiducial engine="amoeba" tree="default"/> XML tag lets you select the fiducial engine or an alternative amoeba tree order. The default engine is using the fastest and effective 'amoeba' fiducial set. Add the 'classic' option in order to use Ross' initial d-touch reimplementation. You can select Enrico's original d-touch engine by providing the 'dtouch' option. <br />
<br />
The display attribute defines the default screen upon startup. The <image display="dest" equalize="false" gradient="32" /> lets you adjust the default gradient gate value. reacTIVision comes with a background subtraction module, which in some cases can simplify the recognition performance of both the finger and fiducial tracking. Within the running application you can toggle this with the 'E' key or recalculate the background subtraction by hitting the SPACE bar. <br />
<br />
The camera options can be adjusted by pressing the 'O' key. On Windows and Mac OS this will show a system dialog that allows the adjustment of the available camera parameters. On Linux (Mac OS X when using IEEE1394 cameras), the available camera settings can be adjusted with a simple on screen display.<br />
The overall camera settings can be configured within the camera.xml configuration file. Please note that for Windows and the Quicktime mode on Mac OS X this only allows the configuration of the image size. For IEEE1394 cameras on Mac OS X as well as all camera types on Linux all image parameters can be fully configured using this configuration file.<br />
<br />
<br />
===Calibration and Distortion===<br />
<br />
Some tables, such as the reacTable are using wide-angle or fish-eye lens in order to increase the area visible to the camera at a minimal distance. These lenses unfortunately distort the image and reacTIVision can correct that distortion and the overall alignment of the image. For the calibration print and place one of these rectangular or square calibration sheets on the table and adjust the grid points to the grid printed on the sheet. <br />
<br />
To calibrate reacTIVision switch to calibration mode hitting 'C'. Use the keys A,D,W,X to move within grid, moving with the cursor keys will adjust the grid point. <br />
'J' resets the whole calibration grid, 'U' resets the selected point and 'K' reverts to the saved grid. <br />
To check if the distortion is working properly press 'R'. This will show the fully distorted live video image in the target window. Of course the distortion algorithm only corrects the found positions instead of the full image.<br />
<br />
<br />
<br />
== TUIO in Processing ==<br />
<br />
<br />
=== Installation ===<br />
<br />
Copy the complete contents of this distribution to a folder named TUIO to the libraries folder of your Processing sketchbook. In order to use this library, you will need to provide the according import statement within the header of your Processing sketch: <br />
import TUIO.*; <br />
<br />
<br />
=== Application Programming Interface ===<br />
<br />
First you need to create an instance of the TuioProcessing client, providing the instance of your sketch to the constructor using the this argument. The TuioProcessing client immediately starts listening to incoming TUIO messages and generates higher level events based on the object and cursor movements. <br />
TuioProcessing tuioClient = new TuioProcessing(this);<br />
<br />
Therefore your sketch needs to implement the following methods in order to be able to receive these TUIO events properly: <br />
<br />
-addTuioObject(TuioObject tobj) this is called when an object becomes visible <br />
<br />
-removeTuioObject(TuioObject tobj) an object was removed from the table <br />
<br />
-updateTuioObject(TuioObject tobj) an object was moved on the table surface <br />
<br />
-addTuioCursor(TuioCursor tcur) this is called when a new cursor is detected <br />
<br />
-removeTuioCursor(TuioCursor tcur) a cursor was removed from the table <br />
<br />
-updateTuioCursor(TuioCursor tcur) a cursor was moving on the table surface <br />
<br />
-refresh(TuioTime bundleTime) this method is called after each bundle,<br />
<br />
<br />
use it to repaint your screen for example: <br />
<br />
Each TuioObject or TuioCursor is identified with a unique SessionID, which it maintains over its lifetime. Additionally each TuioObject carries a SymbolID that corresponds to its attached fiducial marker number. The CursorID of the TuioCursor is always a number in the range of all currently detected cursors. You can retrieve these ID numbers with the according getSessionID(), getSymbolID() or getCursorID() methods. <br />
<br />
The TuioObject and TuioCursor references are updated automatically by the TuioProcessing client and are always referencing the same instance over the object's or cursor's lifetime. All the TuioObject and TuioCursor attributes are encapsulated, and can be accessed with methods such as getX(), getY() and getAngle(). There exist further methods for the retrieval of speed and acceleration values, please see the provided example sketches for a complete list. TuioObject and TuioCursor also have some additional convenience methods for the calculation of distances and angles between objects. The getPath() method returns a Vector of TuioPoint representing the movement path of the object. Please refer to the documentation of the TUIO Java reference implementations for further details on all the available methods. <br />
<br />
Alternatively, the TuioProcessing class contains some methods for the polling of the current object and cursor states. There are methods which return either a list or individual TuioObject and TuioCursor objects. <br />
<br />
-getTuioObjects() returns a Vector of all currently present TuioObjects <br />
<br />
-getTuioCursors() returns a Vector of all currently present TuioCursors <br />
<br />
-getTuioObject(long s_id) returns a TuioObject or NULL depending on its presence <br />
<br />
-getTuioCursor(long s_id) returns a TuioCursor or NULL depending on its presence<br />
<br />
<br />
=== Our Program ===<br />
<br />
<br />
[[File:React_table_flow_chart.JPG|400px|]]<br />
<br />
In our program each marker is attached to an image that discribes a cretian equipment and how it is used. the fudicial is stuck onto the equipment.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=File:Reactivision02.png&diff=2795File:Reactivision02.png2010-10-20T09:00:25Z<p>Farhad: </p>
<hr />
<div></div>Farhadhttp://www.hackteria.org/wiki/index.php?title=ReacTable&diff=2794ReacTable2010-10-20T08:58:49Z<p>Farhad: </p>
<hr />
<div>== Introbuction ==<br />
<br />
<br />
This is a multi touch table that reads markers placed on the screen and does a corresponding action. Thus reading the object on the screen and functioning accordingly. The table uses reactivision software. This application was designed to track specially designed fiducial markers. By downloading the TUIO library you can cerate a program that operates on these markers. the table uses infra red light for finger tracking.<br />
a webcam takes in the feed and runs it through reactivision. It is then processed in processing and displayed again on the screen.<br />
<br />
'''We used this to give information and protocals when a certian object was put on it.'''<br />
<br />
<br />
<br />
===How reacTIVision works===<br />
<br />
In a nutshell the system works like this: reacTIVision tracks specially designed fiducial markers in a real time video stream. The source image frame is first converted to a black&white image with an adaptive thresholding algorithm. Then this image is segmented into a tree of alternating black and white regions (region adjacency graph). This graph is then searched for unique left heavy depth sequences, which have been encoded into the fiducial symbol. Finally the found tree sequences are matched to a dictionary to retrieve an unique ID number. The fiducial design allows the efficient calculation of the marker's center point as well as its orientation. OSC messages implementing the TUIO protocol encode the fiducials' presence, location, orientation and identity and transmit this data to the client applications. <br />
Additionally reacTIVision uses the result of the image segmentation in order to retrieve and identify small round white blobs as finger tips on the surface. A quick and dirty shape matching algorithm selects the actual finger blobs from the possible region candidates. A complementary blob tracking algorithm is also taking advantage of the same data in order to track eventually not recognized fiducials, for example where fast movements destroy the actual fiducial structure in the image.<br />
<br />
<br />
<br />
<br />
== Building the table ==<br />
<br />
<br />
===table & surface===<br />
<br />
A camera and a projector with wide-angle lenses need to be placed underneath the table, so they can both cover the entire surface. [[File:Reactivision03.png|400px|right|]]Alternatively a mirror can be used in order to achieve a larger projection distance. For the interactive surface itself a normal perspex board can be used in conjunction with some ordinary tracing paper on the top side for the projection. This material is completely transparent for objects and finger tips in direct contact with the surface. In order to avoid direct reflections of the light source and projector lamp, the lower side of the surface should have a matte finish, while maintaing the overall transparency. <br />
<br />
<br />
===illumination===<br />
<br />
For the tracking, the objects need to be properly illuminated, so the camera and thus the computer vision application can see them correctly. For the projection onto a table, the surface needs to be dark though, so the user can see the projected image well enough. Since these two necessary steps logically exclude each other, the solution is to operate in two different spectra: <br />
The projection has to be visible to the user, so the computer vision component needs to operate in a different, invisible spectrum such as near infrared in the range of 850nm. Most CCD cameras are perfectly sensitive within the near IR spectrum, therefore infrared LED lamps can be used to illuminate the table. All light from the visible spectrum needs to be filtered in the camera, so the computer vision algorithm is not disturbed by the projection. Eventually an existing infrared blocker needs to be removed from the camera sensor. <br />
<br />
<br />
===camera===<br />
<br />
You should make sure that the camera has an acceptable lens and sensor size. For lowest latency and best performance we recommend firewire cameras from the top range, such as industrial cameras with a high framerate, resolution and sensor size. These cameras usually also come with high quality C-mount lenses. Cheaper firewire cameras, such as the unibrain fire-i also allow optional wide-angle lenses. From the large range of available USB cameras we recommend to use high end models with a native resolution of at least 640x480 at a frame rate of 30Hz. A very affordable and relatively good camera for this purpose is the Sony PS3eye, which is also working well under Windows, Linux and Mac OSX. DV cameras supporting full-frame mode are suitable, while those with interlaced mode only, will not work at all. an IR bypass filter needs to be placed on the lens instead of the ordinary camera filter if you are using 2 different spectra<br />
<br />
<br />
=== How Our box functions ===<br />
<br />
1. We used a simple wood box(3 x 1.5 x 2.5 ft) painted black on the inside so there is less reflection of light. We used a projector to project onto a mirror which reflects the projection onto the screen.The keystone setting on the projector is set at -120 so that the projection on the screen is a rectangular shape.<br />
<br />
2. We couldn't find an IR bulb so we placed IR LEDs on 2 opposite sides of the perspex board so that the IR light refracts in the perspex board. When a finger is placed on the screen, it forms a blob of IR light on the inside of the box and is read by the webcam. <br />
<br />
3. We made a stand for the laptop on top of the projector and used the laptop webcam itself as the image was pretty clear. We used a processed photography negative as the IR bypass filter on the webcam.<br />
<br />
<br />
<br />
== Using reacTIVision ==<br />
<br />
<br />
===Fiducial Symbols===<br />
<br />
This application was designed to track specially designed fiducial markers. You will find the default "amoeba" fiducial set within the document "default.pdf" within the symbols folder of the reactivision download. Print this document and attach the labels to any object you want to track. The default fiducial tracking engine is using Ross Bencina's fidtrack library which is basically a newer high-performance implementation of Enrico Costanza's d-touch concept. Alternatively you can use the "classic" or the "dtouch" sets. See below how to configure the application using these older symbol sets. <br />
<br />
<br />
===Finger Tracking===<br />
<br />
Since reacTIVision was initially designed for fiducial tracking, its thresholder and segmentation modules are optimized for this task. Finger tracking was added at a later stage, and is taking advantage of the existing image processing infrastructure with almost no additional performance overhead. On the other hand it might seem difficult to set up reacTIVision in order to achieve good tracking performance for both the fiducial symbols and the finger tips. When used with diffused illumination, the setup needs strong and even illumination in order to achieve the necessary contrast for finger tracking, also the overall image control such as brightness, gain and shutter speed will improve the tracking quality (O key). Another important control parameter is the threshold "gradient gate" which should be set as low as possible, just before too much image noise becomes visible (G key). Finally the finger tracking can be configured by adjusting the average finger size and tracking sensitivity (F key). <br />
<br />
<br />
===Application Handling===<br />
<br />
[[File:Cam_settings.JPG|300px|right|frame|webcam streaming on laptop]]<br />
Common settings can be edited within the file "reacTIVision.xml" where all changes are stored automatically when closing the application. Under Mac OS X the XML configuration file can be found within the application bundle's Resources folder. Select "Show Package Contents" from the application's context menu in order to access and edit the file. <br />
<br />
The reacTIVision application usually sends the TUIO messages to port 3333 on locahost (127.0.0.1) You can change this setting by adding or editing the XML tag <tuio host="127.0.0.1" port="3333"> to the configuration. <br />
<br />
The <fiducial engine="amoeba" tree="default"/> XML tag lets you select the fiducial engine or an alternative amoeba tree order. The default engine is using the fastest and effective 'amoeba' fiducial set. Add the 'classic' option in order to use Ross' initial d-touch reimplementation. You can select Enrico's original d-touch engine by providing the 'dtouch' option. <br />
<br />
The display attribute defines the default screen upon startup. The <image display="dest" equalize="false" gradient="32" /> lets you adjust the default gradient gate value. reacTIVision comes with a background subtraction module, which in some cases can simplify the recognition performance of both the finger and fiducial tracking. Within the running application you can toggle this with the 'E' key or recalculate the background subtraction by hitting the SPACE bar. <br />
<br />
The camera options can be adjusted by pressing the 'O' key. On Windows and Mac OS this will show a system dialog that allows the adjustment of the available camera parameters. On Linux (Mac OS X when using IEEE1394 cameras), the available camera settings can be adjusted with a simple on screen display.<br />
The overall camera settings can be configured within the camera.xml configuration file. Please note that for Windows and the Quicktime mode on Mac OS X this only allows the configuration of the image size. For IEEE1394 cameras on Mac OS X as well as all camera types on Linux all image parameters can be fully configured using this configuration file.<br />
<br />
<br />
===Calibration and Distortion===<br />
<br />
Some tables, such as the reacTable are using wide-angle or fish-eye lens in order to increase the area visible to the camera at a minimal distance. These lenses unfortunately distort the image and reacTIVision can correct that distortion and the overall alignment of the image. For the calibration print and place one of these rectangular or square calibration sheets on the table and adjust the grid points to the grid printed on the sheet. <br />
<br />
To calibrate reacTIVision switch to calibration mode hitting 'C'. Use the keys A,D,W,X to move within grid, moving with the cursor keys will adjust the grid point. <br />
'J' resets the whole calibration grid, 'U' resets the selected point and 'K' reverts to the saved grid. <br />
To check if the distortion is working properly press 'R'. This will show the fully distorted live video image in the target window. Of course the distortion algorithm only corrects the found positions instead of the full image.<br />
<br />
<br />
<br />
== TUIO in Processing ==<br />
<br />
<br />
=== Installation ===<br />
<br />
Copy the complete contents of this distribution to a folder named TUIO to the libraries folder of your Processing sketchbook. In order to use this library, you will need to provide the according import statement within the header of your Processing sketch: <br />
import TUIO.*; <br />
<br />
<br />
=== Application Programming Interface ===<br />
<br />
First you need to create an instance of the TuioProcessing client, providing the instance of your sketch to the constructor using the this argument. The TuioProcessing client immediately starts listening to incoming TUIO messages and generates higher level events based on the object and cursor movements. <br />
TuioProcessing tuioClient = new TuioProcessing(this);<br />
<br />
Therefore your sketch needs to implement the following methods in order to be able to receive these TUIO events properly: <br />
<br />
addTuioObject(TuioObject tobj) this is called when an object becomes visible <br />
<br />
removeTuioObject(TuioObject tobj) an object was removed from the table <br />
<br />
updateTuioObject(TuioObject tobj) an object was moved on the table surface <br />
<br />
addTuioCursor(TuioCursor tcur) this is called when a new cursor is detected <br />
<br />
removeTuioCursor(TuioCursor tcur) a cursor was removed from the table <br />
<br />
updateTuioCursor(TuioCursor tcur) a cursor was moving on the table surface <br />
<br />
refresh(TuioTime bundleTime) this method is called after each bundle,<br />
<br />
<br />
use it to repaint your screen for example: <br />
<br />
Each TuioObject or TuioCursor is identified with a unique SessionID, which it maintains over its lifetime. Additionally each TuioObject carries a SymbolID that corresponds to its attached fiducial marker number. The CursorID of the TuioCursor is always a number in the range of all currently detected cursors. You can retrieve these ID numbers with the according getSessionID(), getSymbolID() or getCursorID() methods. <br />
<br />
The TuioObject and TuioCursor references are updated automatically by the TuioProcessing client and are always referencing the same instance over the object's or cursor's lifetime. All the TuioObject and TuioCursor attributes are encapsulated, and can be accessed with methods such as getX(), getY() and getAngle(). There exist further methods for the retrieval of speed and acceleration values, please see the provided example sketches for a complete list. TuioObject and TuioCursor also have some additional convenience methods for the calculation of distances and angles between objects. The getPath() method returns a Vector of TuioPoint representing the movement path of the object. Please refer to the documentation of the TUIO Java reference implementations for further details on all the available methods. <br />
<br />
Alternatively, the TuioProcessing class contains some methods for the polling of the current object and cursor states. There are methods which return either a list or individual TuioObject and TuioCursor objects. <br />
<br />
getTuioObjects() returns a Vector of all currently present TuioObjects <br />
<br />
getTuioCursors() returns a Vector of all currently present TuioCursors <br />
<br />
getTuioObject(long s_id) returns a TuioObject or NULL depending on its presence <br />
<br />
getTuioCursor(long s_id) returns a TuioCursor or NULL depending on its presence</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=File:Cam_settings.JPG&diff=2793File:Cam settings.JPG2010-10-20T08:14:30Z<p>Farhad: uploaded a new version of "File:Cam settings.JPG"</p>
<hr />
<div></div>Farhadhttp://www.hackteria.org/wiki/index.php?title=File:Cam_settings.JPG&diff=2792File:Cam settings.JPG2010-10-20T08:09:41Z<p>Farhad: uploaded a new version of "File:Cam settings.JPG"</p>
<hr />
<div></div>Farhadhttp://www.hackteria.org/wiki/index.php?title=ReacTable&diff=2791ReacTable2010-10-20T08:04:01Z<p>Farhad: </p>
<hr />
<div>== Introbuction ==<br />
<br />
<br />
This is a multi touch table that reads markers placed on the screen and does a corresponding action. Thus reading the object on the screen and functioning accordingly. The table uses reactivision software. This application was designed to track specially designed fiducial markers. By downloading the TUIO library you can cerate a program that operates on these markers. the table uses infra red light for finger tracking.<br />
a webcam takes in the feed and runs it through reactivision. It is then processed in processing and displayed again on the screen.<br />
<br />
'''We used this to give information and protocals when a certian object was put on it.'''<br />
<br />
<br />
<br />
===How reacTIVision works===<br />
<br />
In a nutshell the system works like this: reacTIVision tracks specially designed fiducial markers in a real time video stream. The source image frame is first converted to a black&white image with an adaptive thresholding algorithm. Then this image is segmented into a tree of alternating black and white regions (region adjacency graph). This graph is then searched for unique left heavy depth sequences, which have been encoded into the fiducial symbol. Finally the found tree sequences are matched to a dictionary to retrieve an unique ID number. The fiducial design allows the efficient calculation of the marker's center point as well as its orientation. OSC messages implementing the TUIO protocol encode the fiducials' presence, location, orientation and identity and transmit this data to the client applications. <br />
Additionally reacTIVision uses the result of the image segmentation in order to retrieve and identify small round white blobs as finger tips on the surface. A quick and dirty shape matching algorithm selects the actual finger blobs from the possible region candidates. A complementary blob tracking algorithm is also taking advantage of the same data in order to track eventually not recognized fiducials, for example where fast movements destroy the actual fiducial structure in the image.<br />
<br />
<br />
<br />
<br />
== Building the table ==<br />
<br />
<br />
===table & surface===<br />
<br />
A camera and a projector with wide-angle lenses need to be placed underneath the table, so they can both cover the entire surface. [[File:Reactivision03.png|400px|right|]]Alternatively a mirror can be used in order to achieve a larger projection distance. For the interactive surface itself a normal perspex board can be used in conjunction with some ordinary tracing paper on the top side for the projection. This material is completely transparent for objects and finger tips in direct contact with the surface. In order to avoid direct reflections of the light source and projector lamp, the lower side of the surface should have a matte finish, while maintaing the overall transparency. <br />
<br />
<br />
===illumination===<br />
<br />
For the tracking, the objects need to be properly illuminated, so the camera and thus the computer vision application can see them correctly. For the projection onto a table, the surface needs to be dark though, so the user can see the projected image well enough. Since these two necessary steps logically exclude each other, the solution is to operate in two different spectra: <br />
The projection has to be visible to the user, so the computer vision component needs to operate in a different, invisible spectrum such as near infrared in the range of 850nm. Most CCD cameras are perfectly sensitive within the near IR spectrum, therefore infrared LED lamps can be used to illuminate the table. All light from the visible spectrum needs to be filtered in the camera, so the computer vision algorithm is not disturbed by the projection. Eventually an existing infrared blocker needs to be removed from the camera sensor. <br />
<br />
<br />
===camera===<br />
<br />
You should make sure that the camera has an acceptable lens and sensor size. For lowest latency and best performance we recommend firewire cameras from the top range, such as industrial cameras with a high framerate, resolution and sensor size. These cameras usually also come with high quality C-mount lenses. Cheaper firewire cameras, such as the unibrain fire-i also allow optional wide-angle lenses. From the large range of available USB cameras we recommend to use high end models with a native resolution of at least 640x480 at a frame rate of 30Hz. A very affordable and relatively good camera for this purpose is the Sony PS3eye, which is also working well under Windows, Linux and Mac OSX. DV cameras supporting full-frame mode are suitable, while those with interlaced mode only, will not work at all.<br />
<br />
== Using reacTIVision ==<br />
<br />
<br />
===Fiducial Symbols===<br />
<br />
This application was designed to track specially designed fiducial markers. You will find the default "amoeba" fiducial set within the document "default.pdf" within the symbols folder. Print this document and attach the labels to any object you want to track. The default fiducial tracking engine is using Ross Bencina's fidtrack library which is basically a newer high-performance implementation of Enrico Costanza's d-touch concept. Alternatively you can use the "classic" or the "dtouch" sets. See below how to configure the application using these older symbol sets. <br />
<br />
<br />
===Finger Tracking===<br />
<br />
Since reacTIVision was initially designed for fiducial tracking, its thresholder and segmentation modules are optimized for this task. Finger tracking was added at a later stage, and is taking advantage of the existing image processing infrastructure with almost no additional performance overhead. On the other hand it might seem difficult to set up reacTIVision in order to achieve good tracking performance for both the fiducial symbols and the finger tips. When used with diffused illumination, the setup needs strong and even illumination in order to achieve the necessary contrast for finger tracking, also the overall image control such as brightness, gain and shutter speed will improve the tracking quality (O key). Another important control parameter is the threshold "gradient gate" which should be set as low as possible, just before too much image noise becomes visible (G key). Finally the finger tracking can be configured by adjusting the average finger size and tracking sensitivity (F key). <br />
<br />
<br />
===Application Handling===<br />
<br />
[[File:Cam_settings.JPG|400px|right]]<br />
Common settings can be edited within the file "reacTIVision.xml" where all changes are stored automatically when closing the application. Under Mac OS X the XML configuration file can be found within the application bundle's Resources folder. Select "Show Package Contents" from the application's context menu in order to access and edit the file. <br />
<br />
The reacTIVision application usually sends the TUIO messages to port 3333 on locahost (127.0.0.1) You can change this setting by adding or editing the XML tag <tuio host="127.0.0.1" port="3333"> to the configuration. <br />
<br />
The <fiducial engine="amoeba" tree="default"/> XML tag lets you select the fiducial engine or an alternative amoeba tree order. The default engine is using the fastest and effective 'amoeba' fiducial set. Add the 'classic' option in order to use Ross' initial d-touch reimplementation. You can select Enrico's original d-touch engine by providing the 'dtouch' option. <br />
<br />
The display attribute defines the default screen upon startup. The <image display="dest" equalize="false" gradient="32" /> lets you adjust the default gradient gate value. reacTIVision comes with a background subtraction module, which in some cases can simplify the recognition performance of both the finger and fiducial tracking. Within the running application you can toggle this with the 'E' key or recalculate the background subtraction by hitting the SPACE bar. <br />
<br />
The camera options can be adjusted by pressing the 'O' key. On Windows and Mac OS this will show a system dialog that allows the adjustment of the available camera parameters. On Linux (Mac OS X when using IEEE1394 cameras), the available camera settings can be adjusted with a simple on screen display.<br />
The overall camera settings can be configured within the camera.xml configuration file. Please note that for Windows and the Quicktime mode on Mac OS X this only allows the configuration of the image size. For IEEE1394 cameras on Mac OS X as well as all camera types on Linux all image parameters can be fully configured using this configuration file. <br />
<br />
<br />
===TUIO vs. MIDI===<br />
<br />
The application can alternatively send MIDI messages, which allows to map any object dimension (xpos, ypos, angle) to a MIDI control via an XML configuration file. Adding and removing objects can be mapped to simple note ON/OFF events. Keep in mind though that MIDI has less bandwidth and data resolution compared to Open Sound Contol, so the MIDI feature is meant as an convenient alternative in some cases, but TUIO still will be the primary messaging layer. <br />
<br />
Adding <midi config="midi/demo.xml"/> to reacTIVision.xml switches to MIDI mode and specifies the MIDI configuration file that contains the mappings and MIDI device selection. An example configuration file "demo.xml" along with an example PD patch "demo.pd" can be found in the "midi" folder. You can list all available MIDI devices with the "-l midi" option.<br />
<br />
<br />
===Calibration and Distortion===<br />
<br />
Some tables, such as the reacTable are using wide-angle or fish-eye lens in order to increase the area visible to the camera at a minimal distance. These lenses unfortunately distort the image and reacTIVision can correct that distortion and the overall alignment of the image. For the calibration print and place one of these rectangular or square calibration sheets on the table and adjust the grid points to the grid printed on the sheet. <br />
<br />
To calibrate reacTIVision switch to calibration mode hitting 'C'. Use the keys A,D,W,X to move within grid, moving with the cursor keys will adjust the grid point. <br />
'J' resets the whole calibration grid, 'U' resets the selected point and 'K' reverts to the saved grid. <br />
To check if the distortion is working properly press 'R'. This will show the fully distorted live video image in the target window. Of course the distortion algorithm only corrects the found positions instead of the full image.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=File:Cam_settings.JPG&diff=2790File:Cam settings.JPG2010-10-20T08:00:00Z<p>Farhad: </p>
<hr />
<div></div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_handheld_centrifuge&diff=2789DIY handheld centrifuge2010-10-20T07:38:46Z<p>Farhad: </p>
<hr />
<div>== INTRODUCTIONS ==<br />
<br />
A centrifuge is a rotating body with very high RPM. The vial holders at the edge of the body spinning at high rpm are used to separate substances of different densities.<br />
<br />
<br />
<br />
== You will need, ==<br />
<br />
1. A hand-blender <br />
<br />
2. A circular disc/ a fan/ wheel or anything which is fit enough to spin on the blender's blade. It needs to be a little bigger than a tea-cup's saucer. <br />
<br />
3. PVC pipe; long enough to cut out six pieces which would fit test-tubes inside, the width will need to be a little larger than that of the test-tube. <br />
<br />
4. Pipe caps to seal off the bottom of each pipe-piece.<br />
<br />
5. Synthetic wire, about 2mm thick.<br />
<br />
6. A drill, with a 1 or 2mm drill bit. <br />
<br />
7. A cutter and a mini hack saw.<br />
<br />
<br />
<br />
<br />
== PROCEDURE ==<br />
<br />
<br />
<br />
=== How our centrifuge functions ===<br />
<br />
we have used a hand blender with rpm and attatched a disk onto it to make our frtating body. to this disk we have connected holders for the vials, thus making a centrifuge.<br />
<br />
<br />
<br />
=== Making a Hand-held Centrifuge ===<br />
<br />
<br />
<br />
'''To make the rotating body,'''<br />
<br />
1. If the blender's blade is surrounded by a border, saw it off, it'll be easier to fix the disc/wheel/fan this way.<br />
<br />
2. Take the disc/ wheel/fan place it over the blades of the blender, make sure it's centered. Mark the points of the blades on the disc/wheel/fan.<br />
<br />
3. Drill holes in the disc/wheel/fan where the points were marked, use a cutter and make the holes wide enough to fix the blades into them.<br />
<br />
4. If there is no provision on the disc/wheel/fan to tie the test-tube holders, make six holes on the edge of the disc/wheel/fan to do so.<br />
<br />
5. Now, fix the disc/wheel/fan onto the blender's blades. To secure use Emseal around, over and under the area where the blades protrude out of the disc/wheel/fan.<br />
<br />
6. Let it dry completely.(Making sure it's dry is very important.)<br />
<br />
<br />
'''To make Test-tube holders,'''<br />
<br />
7. Cut up the PVC pipes into six pieces.<br />
<br />
8. Drill two holes at the edge of the pipe, one at each end of the Diameter of the pipe. <br />
<br />
9. Fix the Pipe caps at the bottom of each pipe, if they are loose, seal them off with the sealant.<br />
<br />
10.Pass one wire through each hole, knot it so it doesn't slip through the hole.<br />
<br />
'''Finally,'''<br />
<br />
11. Once the sealant on the blender's blade has dried up completely, tie up the ends of each wire in the pipes onto the holes on the edge of the disc/wheel/fan. Make sure the knots are all very strong.<br />
<br />
<br />
<br />
=== Picture Reference : ===<br />
<br />
[[File:BlenderBlade.jpg|frame|none|saw off border of the blade]] <br />
[[File:FixingBlade.jpg|frame|none|mark the points of the blade]] <br />
[[File:DiscOnBlade.jpg|frame|none|fix disk on blade]] <br />
[[File:HandHeldCent.jpg|frame|none|final product]]<br />
<br />
<br />
<br />
== PRECAUTIONS ==<br />
<br />
<br />
1. Handle blade and other sharp objects with care.<br />
<br />
2. While operating final product hold away from body and face, if possible use a protective shield, ex: a riding helmet. <br />
<br />
3. Be careful while testing the product for the first time, use plastic test tubes or similar objects rather than a glass test tube; there is a chance of the caps on the holders giving way and the test tube shooting out; this could be extremely dangerous to any one standing around the area(trust us). <br />
<br />
4. Make sure the blender's motor doesn't get too hot, when hot allow it too cool down before using again.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_table_top_centrifuge&diff=2788DIY table top centrifuge2010-10-20T07:27:37Z<p>Farhad: </p>
<hr />
<div>== INTRODUCTION ==<br />
<br />
A centrifuge is a rotating body with very high RPM. The vial holders at the edge of the body spinning at high rpm are used to separate substances of different densities.<br />
<br />
<br />
<br />
== You will need, ==<br />
<br />
1. '''Blender''' – One which has variable speeds would be better<br />
<br />
2. '''Jar''' – a small one, since we’ll need only the bottom part that attaches to the blender<br />
<br />
3. '''Strips of metal''' – make sure the edges are completely filed off to be safer<br />
<br />
4. '''Test tube holders''' – I used PVC pipes here with caps that fit very snugly <br />
<br />
5. '''Latches''' – Small in size to fasten the tubes to the metal strips<br />
<br />
<br />
<br />
<br />
== PROCEDURE ==<br />
<br />
<br />
===How our centrifuge works===<br />
<br />
The first thing I would like to say about this project is PLEASE DO NOT TRY THIS AT HOME! <br />
<br />
Well now, if you had to take that seriously then this would barely be a do-it-yourself workshop! I’ve had good fun making this centrifuge and one thing I’ve learned for sure is anything that spins very fast can cause serious damage! So for what it matters, please DO take extra precaution while trying to make this.<br />
<br />
I went about this using the basic principal of the centrifuge which is that anything that spins has a force that pushes away from it called the ‘centrifugal force’ so if I have a motor than spins then anything attached to it will be thrown away. <br />
<br />
<br />
<br />
=== To make a centrifuge ===<br />
<br />
As simple as it sounds but that’s all you need. Follow these few steps and you’ll have your centrifuge up and running in no time!<br />
<br />
<br />
'''1. '''<br />
Dismantle the upper portion of the jar so that we remain with only the unit that attaches to the blender<br />
<br />
'''2. '''<br />
Make a hole in the center of the two metal strips. This hole has to be exactly in the center so measuring it will be a good option. If it’s not in the center then it could cause imbalance during rotation. The size of the hole has to have the same diameter as the center spinning portion in the jar.<br />
<br />
'''3. '''<br />
Make holes on either side of the metal strips using the latches as a mark since they will be screwed into the metal strip.<br />
<br />
'''4. '''<br />
Make a hole in the test tube holder using the latch again since it will be screwed into it.<br />
<br />
'''Assembly-'''<br />
Fit the jar on to the blender and lock it. Screw one end of the latch to the test tube holder and the other onto the metal strip on all four sides. Place both the metal strips onto the blender and screw them in. Make sure to tighten all the screws as much as possible. To be on the safer side use the adhesive to fix the screws of the latch on the metal strip and the test tube holders. At high speeds, wear and tear is maximum, due to friction. So double check to ensure everything is completely secure.<br />
<br />
<br />
== PRECAUTIONS ==<br />
<br />
<br />
1. ALWAYS wear safety glasses. Seriously you never know what could go flying and get into your eyes. <br />
<br />
2. It would be good to keep a large board in front of you when testing the centrifuge for the first time or until you get comfortable.<br />
<br />
3. Test the centrifuge with a dummy test tube which is NOT glass to make sure all goes well.<br />
<br />
4. ALWAYS run the centrifuge slowly and at short intervals, and then later pick up speed.<br />
<br />
5. ALWAYS run your centrifuge BALANCED, i.e tubes on either sides at all times.<br />
<br />
6. Finally remember to have fun!</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_Incubator&diff=2787DIY Incubator2010-10-20T06:58:04Z<p>Farhad: </p>
<hr />
<div>== INTRODUCTION ==<br />
<br />
<br />
An incubator is an isolated storage place that is used for cultivating bacteria. The incubator maintains optimal temperature of the atmosphere inside it. Incubators are essential for a lot of experimental work in cell biology, microbiology and molecular biology and are used to culture both bacterial as well as eukaryotic cells. The simplest incubators are insulated boxes with an adjustable heater, typically going up to 60 to 65 °C (140 to 150 °F), though some can go slightly higher (generally to no more than 100 °C). The most commonly used temperature both for bacteria such as the frequently used E. Coli cells is approximately 37 °C, as these organisms grow well under such conditions. They also need a circulation system for equal distribution of heat in the box.<br />
<br />
We made a simple incubator that maintains a temperature of 37 °C using materials that are easily available. This incubator will be used cultivate E.Coli.<br />
<br />
<br />
<br />
<br />
== You will need, ==<br />
<br />
<br />
1. Styrofoam box.(doesn't conduct heat)....................[[File:Box.JPG]]<br />
<br />
2. heating element.(bulb,heating pad,etc.).................[[File:Bulbs.JPG]]<br />
<br />
3. cabinet fans.(depending on size of box).................[[File:Fan.JPG]]<br />
<br />
4. thermometer.(between 20 °C to 100 °C).................[[File:Thermometer.JPG]]<br />
<br />
5. 12V adaptor.(for powering fans)............................[[File:Adapter.JPG]]<br />
<br />
6. conducting wire.(adapter to fans)..........................[[File:Wire.JPG]]<br />
<br />
7. insulation tape.<br />
<br />
<br />
<br />
== PROCEDURE ==<br />
<br />
<br />
===How our box functions===<br />
<br />
The styrofoam box is an insulated box that keeps the heat locked inside. The heating element is introduced into the box to produce heat. The cabinet fans are used to circulate the heat inside and keep the temperature same everywhere in the box. A thermometer is introduced into the box through a perfect fitting hole in the box to measure the temperature inside. the hole is then well sealed and insulated. Neither the heating element nor the fan must be too close to the thermometer. '''The fans and heating element must be placed in such a way that the required temperature is achieved'''(Not as easy as it seems). once the placement is finalized, stick the fans and the heat source in place using arelldite. The lis of the box must be sealed properly so as to not let any exchange take place(duct tape). The incubator is ready to use.<br />
<br />
<br />
<br />
<br />
===Our Process===<br />
<br />
<br />
'''Day 1'''<br />
<br />
We first experimented with a dummy styrofoam box that we got at a juice centre. we first started with a 75 watt bulb and 1 fan. the fan was placed exactly opposite to the bulb. We also used a layer of al foil to increase heat.The temp reading showed 108°C. and the thermometer bursted. WE then scraped the Al foil idea.<br />
<br />
<br />
'''Day 2'''<br />
<br />
[[File:DSC02976.JPG|right|]]<br />
We then tried using a 40 watt bulb in the dommy with 3 fans.We placed the fans in such a way that the air circulated evenly through the box. The trmperature shot up to 40°C in the first 20 minutes and then remained constant at 60°C. We thought of having an outlet for the heat to escape and use the fan as an exhaust. This was not safe as there might be a possibality that some microbes may enter the incubator. so we used a bulb of lower wattage.<br />
<br />
<br />
<br />
'''Day 3'''<br />
<br />
We used a 0 watt bulb in the dummy box along with 3 fans. the new box had also arrived so we tried the same combination in the new box since it was bigger. The readings were as follows:<br />
<br />
[[File:DSC03091.jpg]]<br />
<br />
'''Dummy Box''' <br />
<br />
Time(min).............Temp(°C)<br />
<br />
0..............................33<br />
<br />
1..............................34<br />
<br />
3..............................35<br />
<br />
5..............................36<br />
<br />
6..............................37<br />
<br />
8..............................38<br />
<br />
10.............................39<br />
<br />
13.............................40<br />
<br />
17.............................41<br />
<br />
20.............................42<br />
<br />
29.............................43<br />
<br />
43.............................44<br />
<br />
65.............................45(const)<br />
<br />
<br />
<br />
'''Final box'''<br />
<br />
Time(min).............Temp(°C)<br />
<br />
0..............................31<br />
<br />
2..............................32<br />
<br />
3..............................33<br />
<br />
4..............................34<br />
<br />
5..............................35<br />
<br />
7..............................36<br />
<br />
9..............................37<br />
<br />
11.............................38<br />
<br />
15.............................39<br />
<br />
21.............................40<br />
<br />
33.............................41<br />
<br />
53.............................42(const)<br />
<br />
<br />
<br />
'''Day 4'''<br />
<br />
today we used 4 fans to reduce temp. The final temp came to 40°C. We also jumped to the conclusion that each fan reduces the temp of about 20°C, which was wrong.<br />
<br />
<br />
<br />
'''Day 5'''<br />
<br />
[[File:DSC03125.JPG|right|]]<br />
Today we tried to redoce the wattage further by using a mosquito repelent heater. we also used 4 fans in such a way that the air circulates in 2 circles. the temperatures recorded were as follows:<br />
<br />
<br />
<br />
<br />
Time(min).............Temp(°C) <br />
<br />
0..............................29<br />
<br />
1..............................30<br />
<br />
2..............................31<br />
<br />
4..............................32<br />
<br />
5..............................33<br />
<br />
6..............................34<br />
<br />
8..............................35<br />
<br />
11.............................36<br />
<br />
20.............................37<br />
<br />
60.............................37(const)<br />
<br />
Thus we got a constant temperature of 37°C which es the apt temp for E.coli.<br />
<br />
<br />
<br />
===Ref photos===<br />
<br />
[[File:DSC02904.JPG|250px|]]<br />
[[File:DSC02908.JPG|250px|]]<br />
[[File:DSC02914.JPG|250px|]]<br />
[[File:DSC02921.JPG|250px|]]<br />
[[File:DSC02934.JPG|250px|]]<br />
[[File:DSC02984.JPG|250px|]]<br />
[[File:DSC02986.JPG|250px|]]<br />
[[File:DSC02988.JPG|250px|]]<br />
[[File:DSC02995.JPG|250px|]]<br />
[[File:DSC03079.JPG|250px|]]<br />
[[File:DSC03096.JPG|250px|]]<br />
[[File:DSC03100.JPG|250px|]]<br />
[[File:DSC03129.JPG|250px|]]<br />
<br />
<br />
<br />
== PRECAUTIONS ==<br />
<br />
1. Do not put fans rihgt in front of heater as its constant temperature will drop over time.<br />
<br />
2. Do not use a normal thermometre, it cannot take temperature more than 108°F and might burst.<br />
<br />
3. If by any chance the thermometer breakes and the mercury spills, dispose it safely without touching it directly.<br />
<br />
4. Switch off main power before doing connections.<br />
<br />
5. Run the incubator for about half an hour before use</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_Sterlisation_Hood&diff=2786DIY Sterlisation Hood2010-10-20T04:57:08Z<p>Farhad: </p>
<hr />
<div>== INTRODUCTION ==<br />
<br />
<br />
A sterilisation hood is a transparent box that maintains a sterile environment within it. Sterile hoods aim to keep the microbes out of the air, or in other words, to make a Sterile space. This enables specimens to be worked with/prepared in controlled conditions. It uses a heppa filter and a laminar air flow system to achieve this. There is also a UV light that is run for about half an hour before the experiment starts to kill any living bacteria in the hood. there is a small opeaning for the hands to go in and work. equipment in the hood is not taken out to avoid contamination. Trust me this sounds easy but you need alot of patience and material to do this.<br />
<br />
<br />
<br />
== You will need, ==<br />
<br />
<br />
1) Acrylic sheets-4mm (6 pcs)....2 of dimension 57X61 (cms)-Sides <br />
<br />
................................................2 of dimension 57X80 (cms)-Top & Bottom<br />
<br />
................................................1 of dimension 62X80 (cms)-Back<br />
<br />
................................................1 of dimension 65X80 (cms)-Front<br />
<br />
<br />
<br />
<br />
2) Uv light(15 watts)......................[[File:IMG_7998.JPG]]<br />
<br />
<br />
3) Car heppa filter.........................[[File:IMG_7989.JPG]] <br />
<br />
<br />
<br />
4) Exhaust fan..............................[[File:Ex_fan.JPG]]<br />
<br />
<br />
5) Connector pipes(7cm diam)........[[File:DSC03925.JPG]]<br />
<br />
<br />
6) Wooden blocks.........................[[File:DSC03928.JPG]]<br />
<br />
<br />
<br />
7) L angles..................................[[File:DSC03929.JPG]]<br />
<br />
<br />
<br />
8) Nuts and bolts.........................[[File:DSC03923.JPG]]<br />
<br />
<br />
<br />
9) Uv filter (Car cooling film)...........[[File:Filter.JPG]]<br />
<br />
<br />
<br />
10) M-seal and silica gel(for acrylic sheets)<br />
<br />
<br />
<br />
<br />
== PROCEDURE ==<br />
<br />
<br />
===How our hood works===<br />
<br />
The hood is made of acrylic sheets. The back of the box has 2 holes at the top right and bottom left corners for the air flow. There is a UV light attached on the top face of the box. It is difficult to find a UV light, so you can use a black light bulb but it is not nearly as effective as the real thing. our air filter uses a simple car heppa filter and an industrial exhaust fan. the fan pulls the air through the heppa filter and blows it back into the box through PVC pipes. We put the fan close to the heppa filter and connected the fan horizontally so the pull is more powerful and effective. the front of the hood was held to the box with L angles so that it can slide up & down. The front is stopped at a height of 16cm. with wooden blocks for the hands to go in. you can also make 2 holes and connect them to gloves to reduce contamination. we also tried to make a robot arm that is put in the hood and does the work in the hood.<br />
<br />
<br />
<br />
===To make a sterile hood,===<br />
<br />
<br />
'''Makig the laminar air flow''' [[File:DSC03712.JPG|150px|right|]]<br />
<br />
<br />
1. First make the box around the exhaust fan. (We used sun board but you can use something else).the fan needs about 4-5cm distance from the faces of the box. <br />
<br />
2. For the fan box take 4 pieces of sun board(fan width+8cm x fan length) and stick them to the sides of the fan in such a way that the fan is in the centre of the pieces. Pull out the wires from or of the pieces.<br />
<br />
3. Take 2 square pieces(fan length) and cut a hole(pipe diameter) in them. stick them on both open sides of the fan.Seal all sides with M-seal. [[File:DSC03721.JPG|170px|right|]] <br />
<br />
4. Take the acrylic sheet with dimension 62x80 cm which is the back side of the box and drill three holes in it. One for the air filter [[File:DSC03708.JPG|170px||]](top right), the second one for the pvc pipe(bottom left) and the third one(bottom right) for the wire of the Uv light to pass.<br />
While doing this '''make sure that the filter, the pipe and the wire exactly fit into the holes and there is no extra space.''' <br />
<br />
5. Stick the heppa filter into the top right hole, on the inside with araldite.<br />
<br />
6. Connect the heppa filter to the fan box and then to the inlet at the right bottom corner using the pipes and L shape connectors. Keep the fan close to the filter to increase power.keep the setup as close as possable to the acrylic sheet.<br />
<br />
7. Thus the air filter at the top right hole is connected to the inlet via the fan.<br />
<br />
8. Seal all the connections and joints with M-seal.<br />
<br />
<br />
'''Making the box''' [[File:DSC03715.JPG|170px|right|]]<br />
<br />
9. The two acrylic sheets of dimension 57X61 cm forms the sides of the box. Two sheets of dimensions 57X80 cm form the top and bottom of the box. One of dimension 61x80 cm is used for the back of the box and the one of dimension 65x80 cm for the front of the box.<br />
<br />
10. Stick the 2 sides of the hood to the base using super glue in such a way that the 2 sides are on the base and wait for it to dry. You need to use support for it to dry in a right angle.<br />
<br />
11. Once it is dry put a layer of silica gel on both sides without moving the support to set it firmly in place. <br />
<br />
12. The sides and the air flow system will take about 5 to 7 hours to set.<br />
<br />
13. Once everything is set and dry attach the back sheet with the air flow system to the sides and the base with super glue and then silica gel. Try to keep the back against a wall for support.<br />
<br />
14. Stick the top in the same way and wait for the gel to completely solidify.<br />
<br />
15. After ensuring that all the sides are stuck to the base properly , connect the L angles on the sides of the box and two on the base using nuts and bolts for good support for the front cover. [[File:DSC03787.JPG|170px|right|]]<br />
<br />
16. Drill holes on the top sheet and connect the UV tube to the box with nuts and bolts.<br />
<br />
17. Drill holes and make stoppers with the wooden blocks using nuts and bolts at about 16cms from the base.<br />
<br />
18. Finally put the front sheet by making it slide through the L angles.<br />
<br />
19. Cover the box with UV filter once it is built. Do not cover the front screen.<br />
<br />
20. Your hood is ready.<br />
<br />
<br />
===Process Pictures===<br />
<br />
[[File:DSC03699.JPG|180px|]]<br />
[[File:DSC03707.JPG]]<br />
[[File:DSC03708.JPG]]<br />
[[File:DSC03719.JPG|180px|]]<br />
[[File:DSC03717.JPG]]<br />
[[File:DSC03727.JPG]]<br />
[[File:DSC03728.JPG]]<br />
[[File:DSC03729.JPG]]<br />
[[File:DSC03731.JPG]]<br />
[[File:DSC03734.JPG]]<br />
[[File:DSC03736.JPG]]<br />
[[File:DSC03738.JPG]]<br />
[[File:DSC03739.JPG]]<br />
[[File:P1090748.JPG]]<br />
[[File:DSC03750.JPG]]<br />
[[File:DSC03787.JPG]]<br />
[[File:DSC03791.JPG]]<br />
[[File:DSC03796.JPG]]<br />
[[File:DSC03944.JPG]]<br />
[[File:DSC03945.JPG]]<br />
<br />
<br />
<br />
<br />
== PRECAUTIONS: ==<br />
<br />
<br />
1. Make sure that the holes drilled on the back side of the box are of perfect size so that there are less chances of contamination.<br />
<br />
2. Seal all the gaps in the box with m-seal.<br />
<br />
3. While drilling holes in the acrylic sheet make sure that there is proper support so that the sheet doesn’t bend or break.<br />
<br />
4. While sealing the pipes connected to the fan, first seal the pipes together with m-seal and then connect the whole thing.<br />
<br />
5. The Uv light is switched off while it is being connected.<br />
<br />
6. Do not run Uv light for a long time. Stay away when Uv light is running.<br />
<br />
7. Make sure the front shutter is held up securely with the stoppers before conducting the experiment.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_Sterlisation_Hood&diff=2785DIY Sterlisation Hood2010-10-20T04:56:01Z<p>Farhad: </p>
<hr />
<div><br />
== INTRODUCTION ==<br />
<br />
<br />
A sterilisation hood is a transparent box that maintains a sterile environment within it. Sterile hoods aim to keep the microbes out of the air, or in other words, to make a Sterile space. This enables specimens to be worked with/prepared in controlled conditions. It uses a heppa filter and a laminar air flow system to achieve this. There is also a UV light that is run for about half an hour before the experiment starts to kill any living bacteria in the hood. there is a small opeaning for the hands to go in and work. equipment in the hood is not taken out to avoid contamination. Trust me this sounds easy but you need alot of patience and material to do this.<br />
<br />
<br />
<br />
== '''You will need, ''' ==<br />
<br />
<br />
1) Acrylic sheets-4mm (6 pcs)....2 of dimension 57X61 (cms)-Sides <br />
<br />
................................................2 of dimension 57X80 (cms)-Top & Bottom<br />
<br />
................................................1 of dimension 62X80 (cms)-Back<br />
<br />
................................................1 of dimension 65X80 (cms)-Front<br />
<br />
<br />
<br />
<br />
2) Uv light(15 watts)......................[[File:IMG_7998.JPG]]<br />
<br />
<br />
3) Car heppa filter.........................[[File:IMG_7989.JPG]] <br />
<br />
<br />
<br />
4) Exhaust fan..............................[[File:Ex_fan.JPG]]<br />
<br />
<br />
5) Connector pipes(7cm diam)........[[File:DSC03925.JPG]]<br />
<br />
<br />
6) Wooden blocks.........................[[File:DSC03928.JPG]]<br />
<br />
<br />
<br />
7) L angles..................................[[File:DSC03929.JPG]]<br />
<br />
<br />
<br />
8) Nuts and bolts.........................[[File:DSC03923.JPG]]<br />
<br />
<br />
<br />
9) Uv filter (Car cooling film)...........[[File:Filter.JPG]]<br />
<br />
<br />
<br />
10) M-seal and silica gel(for acrylic sheets)<br />
<br />
<br />
<br />
<br />
== PROCEDURE ==<br />
<br />
<br />
===How our hood works===<br />
<br />
The hood is made of acrylic sheets. The back of the box has 2 holes at the top right and bottom left corners for the air flow. There is a UV light attached on the top face of the box. It is difficult to find a UV light, so you can use a black light bulb but it is not nearly as effective as the real thing. our air filter uses a simple car heppa filter and an industrial exhaust fan. the fan pulls the air through the heppa filter and blows it back into the box through PVC pipes. We put the fan close to the heppa filter and connected the fan horizontally so the pull is more powerful and effective. the front of the hood was held to the box with L angles so that it can slide up & down. The front is stopped at a height of 16cm. with wooden blocks for the hands to go in. you can also make 2 holes and connect them to gloves to reduce contamination. we also tried to make a robot arm that is put in the hood and does the work in the hood.<br />
<br />
<br />
<br />
===To make a sterile hood,===<br />
<br />
<br />
'''Makig the laminar air flow''' [[File:DSC03712.JPG|150px|right|]]<br />
<br />
<br />
1. First make the box around the exhaust fan. (We used sun board but you can use something else).the fan needs about 4-5cm distance from the faces of the box. <br />
<br />
2. For the fan box take 4 pieces of sun board(fan width+8cm x fan length) and stick them to the sides of the fan in such a way that the fan is in the centre of the pieces. Pull out the wires from or of the pieces.<br />
<br />
3. Take 2 square pieces(fan length) and cut a hole(pipe diameter) in them. stick them on both open sides of the fan.Seal all sides with M-seal. [[File:DSC03721.JPG|170px|right|]] <br />
<br />
4. Take the acrylic sheet with dimension 62x80 cm which is the back side of the box and drill three holes in it. One for the air filter [[File:DSC03708.JPG|170px||]](top right), the second one for the pvc pipe(bottom left) and the third one(bottom right) for the wire of the Uv light to pass.<br />
While doing this '''make sure that the filter, the pipe and the wire exactly fit into the holes and there is no extra space.''' <br />
<br />
5. Stick the heppa filter into the top right hole, on the inside with araldite.<br />
<br />
6. Connect the heppa filter to the fan box and then to the inlet at the right bottom corner using the pipes and L shape connectors. Keep the fan close to the filter to increase power.keep the setup as close as possable to the acrylic sheet.<br />
<br />
7. Thus the air filter at the top right hole is connected to the inlet via the fan.<br />
<br />
8. Seal all the connections and joints with M-seal.<br />
<br />
<br />
'''Making the box''' [[File:DSC03715.JPG|170px|right|]]<br />
<br />
9. The two acrylic sheets of dimension 57X61 cm forms the sides of the box. Two sheets of dimensions 57X80 cm form the top and bottom of the box. One of dimension 61x80 cm is used for the back of the box and the one of dimension 65x80 cm for the front of the box.<br />
<br />
10. Stick the 2 sides of the hood to the base using super glue in such a way that the 2 sides are on the base and wait for it to dry. You need to use support for it to dry in a right angle.<br />
<br />
11. Once it is dry put a layer of silica gel on both sides without moving the support to set it firmly in place. <br />
<br />
12. The sides and the air flow system will take about 5 to 7 hours to set.<br />
<br />
13. Once everything is set and dry attach the back sheet with the air flow system to the sides and the base with super glue and then silica gel. Try to keep the back against a wall for support.<br />
<br />
14. Stick the top in the same way and wait for the gel to completely solidify.<br />
<br />
15. After ensuring that all the sides are stuck to the base properly , connect the L angles on the sides of the box and two on the base using nuts and bolts for good support for the front cover. [[File:DSC03787.JPG|170px|right|]]<br />
<br />
16. Drill holes on the top sheet and connect the UV tube to the box with nuts and bolts.<br />
<br />
17. Drill holes and make stoppers with the wooden blocks using nuts and bolts at about 16cms from the base.<br />
<br />
18. Finally put the front sheet by making it slide through the L angles.<br />
<br />
19. Cover the box with UV filter once it is built. Do not cover the front screen.<br />
<br />
20. Your hood is ready.<br />
<br />
<br />
===PROCESS PICTURES:===<br />
<br />
[[File:DSC03699.JPG|180px|]]<br />
[[File:DSC03707.JPG]]<br />
[[File:DSC03708.JPG]]<br />
[[File:DSC03719.JPG|180px|]]<br />
[[File:DSC03717.JPG]]<br />
[[File:DSC03727.JPG]]<br />
[[File:DSC03728.JPG]]<br />
[[File:DSC03729.JPG]]<br />
[[File:DSC03731.JPG]]<br />
[[File:DSC03734.JPG]]<br />
[[File:DSC03736.JPG]]<br />
[[File:DSC03738.JPG]]<br />
[[File:DSC03739.JPG]]<br />
[[File:P1090748.JPG]]<br />
[[File:DSC03750.JPG]]<br />
[[File:DSC03787.JPG]]<br />
[[File:DSC03791.JPG]]<br />
[[File:DSC03796.JPG]]<br />
[[File:DSC03944.JPG]]<br />
[[File:DSC03945.JPG]]<br />
<br />
<br />
<br />
<br />
== PRECAUTIONS: ==<br />
<br />
<br />
1. Make sure that the holes drilled on the back side of the box are of perfect size so that there are less chances of contamination.<br />
<br />
2. Seal all the gaps in the box with m-seal.<br />
<br />
3. While drilling holes in the acrylic sheet make sure that there is proper support so that the sheet doesn’t bend or break.<br />
<br />
4. While sealing the pipes connected to the fan, first seal the pipes together with m-seal and then connect the whole thing.<br />
<br />
5. The Uv light is switched off while it is being connected.<br />
<br />
6. Do not run Uv light for a long time. Stay away when Uv light is running.<br />
<br />
7. Make sure the front shutter is held up securely with the stoppers before conducting the experiment.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_Water_Bath&diff=2784DIY Water Bath2010-10-20T04:52:44Z<p>Farhad: </p>
<hr />
<div>== Introduction==<br />
<br />
<br />
A laboratory water bath is a tool used to maintain a very stable temperature much like an incubator. It is used to give indirect heat to the chemicals or bacteria and maintains that temperature. Water baths can hold often temperatures within a tenth of a degree Celsius; the water is often circulated. Sometimes beads are used as a waterless option. We use it to give bacteria heat shock thus loosening its cell wall. Our experiment needs a waterbath constant at 42°C so the maximum temperature of the waterbath.<br />
<br />
<br />
<br />
== '''You will need,''' ==<br />
<br />
<br />
<br />
1. Bucket.........................[[File:DSC03955.JPG]]<br />
<br />
<br />
<br />
2. Aquarium heater............[[File:DSC03953.JPG]]<br />
<br />
<br />
<br />
3. Tape...........................[[File:DSC03956.JPG]]<br />
<br />
<br />
<br />
4. Thermocole sheet...........[[File:DSC03960.JPG]]<br />
<br />
<br />
<br />
5. Thermometer.................[[File:Thermometer.JPG]]<br />
<br />
<br />
<br />
6. Boiled Water<br />
<br />
<br />
<br />
==Procedure==<br />
<br />
<br />
==='''How our water bath works'''===<br />
<br />
Our water bath uses a simple aquarium heater who's thermostat is hacked to cutoff at 42°C. A simple bucket is used as the container for the water bath as it does not allow the heat to escape.<br />
<br />
<br />
==='''To make a water bath,'''===<br />
<br />
1. Remove the glass casing of the aquarium heater without breaking it.<br />
<br />
2. Unscrew the connecter screw and use it to pull out the thermostat adjustment. Be careful not to break it, just bend it slightly.<br />
<br />
3. With sand paper file the tip of the thermostat adjustment. Be careful as every mm that you file off increases the temperature greatly.<br />
<br />
4. Keep filing and checking till the right temperature is achieved. (In our case it was 42 C. and was achieved after about 5 tries.)<br />
<br />
5. Once the temperature is achieved seal off the heater the same way you opened it and place it into the glass casing and properly seal the edge so that there is no chance of water seeping in.<br />
<br />
6. Next clean the bucket with detol and half fill with boiled water.<br />
<br />
7. Attach a lid to the bucket to reduce heat loss.<br />
<br />
8. Make a small hole on the lid for the thermometer. It is important that the thermometer is dipped in the water.<br />
<br />
9. Stick the aquarium heater in the bucket and make shure that the heating element is completely submerged. For safety do not put the opened side underwater.<br />
<br />
10. You can make the float using thermocol with holes bog enough for the vials to fit into.<br />
Your water bath is ready.<br />
<br />
<br />
==='''PROCESS PICTURES:'''===<br />
<br />
[[File:DSC03963.JPG|frame|none|Remove the glass casing of the aquarium heater]]<br />
[[File:DSC03967.JPG|frame|none|Unscrew the connecter screw]]<br />
[[File:DSC03974.JPG|frame|none|use it to pull out the thermostat adjustment]]<br />
[[File:DSC03980.JPG|frame|none|With sand paper file the tip of the thermostat adjustment. Be careful as every mm that you file off increases the temperature greatly]]<br />
[[File:DSC03988.JPG|frame|none|Once the temperature is achieved scew it the same way it was opened]]<br />
[[File:DSC03990.JPG|frame|none|place it into the glass casing and properly seal the edge]]<br />
[[File:DSC03993.JPG|frame|none|]]<br />
[[File:DSC03997.JPG|frame|none|clean the bucket with detol]]<br />
[[File:DSC03998.JPG|frame|none|]]<br />
[[File:DSC04003.JPG|frame|none|half fill with boiled water.]]<br />
[[File:DSC04006.JPG|frame|none|]]<br />
[[File:DSC04013.JPG|frame|none|Attach a lid to the bucket]]<br />
[[File:DSC04015.JPG|frame|none|]]<br />
[[File:DSC04023.JPG|frame|none|]]<br />
[[File:DSC04028.JPG|frame|none|Make a small hole on the lid for the thermometer]]<br />
[[File:DSC04031.JPG|frame|none|Stick the aquarium heater in the bucket and make shure that the heating element is completely submerged]]<br />
[[File:DSC04032.JPG|frame|none|]]<br />
[[File:DSC04035.JPG|frame|none|]]<br />
[[File:DSC04040.JPG|frame|none|And it's ready]]<br />
<br />
<br />
<br />
=='''PRECAUTIONS:'''==<br />
<br />
1. Try not to crack the outer casing while opening it for the first time. I know it is difficult but try.<br />
<br />
2. Never let the water touch the circuit or the heating element<br />
<br />
3. Do not dip hot glass in water it will crack and the circuit will burst.<br />
<br />
4. Do not touch heating coil after use.<br />
<br />
5. Be careful to not file the thermostat adjustment too much or you will have to shut it down manually every time it goes above the required temperature.<br />
<br />
6. Only half fill the bucket so that water doesn’t touch the open side of the circuit.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_Water_Bath&diff=2783DIY Water Bath2010-10-20T04:50:15Z<p>Farhad: </p>
<hr />
<div><br />
== Introduction==<br />
<br />
<br />
A laboratory water bath is a tool used to maintain a very stable temperature much like an incubator. It is used to give indirect heat to the chemicals or bacteria and maintains that temperature. Water baths can hold often temperatures within a tenth of a degree Celsius; the water is often circulated. Sometimes beads are used as a waterless option. We use it to give bacteria heat shock thus loosening its cell wall. Our experiment needs a waterbath constant at 42°C so the maximum temperature of the waterbath.<br />
<br />
<br />
<br />
=='''You will need,'''==<br />
<br />
<br />
1. Bucket.........................[[File:DSC03955.JPG]]<br />
<br />
<br />
<br />
2. Aquarium heater............[[File:DSC03953.JPG]]<br />
<br />
<br />
<br />
3. Tape...........................[[File:DSC03956.JPG]]<br />
<br />
<br />
<br />
4. Thermocole sheet...........[[File:DSC03960.JPG]]<br />
<br />
<br />
<br />
5. Thermometer.................[[File:Thermometer.JPG]]<br />
<br />
<br />
<br />
6. Boiled Water<br />
<br />
<br />
<br />
==Procedure==<br />
<br />
<br />
==='''How our water bath works'''===<br />
<br />
Our water bath uses a simple aquarium heater who's thermostat is hacked to cutoff at 42°C. A simple bucket is used as the container for the water bath as it does not allow the heat to escape.<br />
<br />
<br />
==='''To make a water bath,'''===<br />
<br />
1. Remove the glass casing of the aquarium heater without breaking it.<br />
<br />
2. Unscrew the connecter screw and use it to pull out the thermostat adjustment. Be careful not to break it, just bend it slightly.<br />
<br />
3. With sand paper file the tip of the thermostat adjustment. Be careful as every mm that you file off increases the temperature greatly.<br />
<br />
4. Keep filing and checking till the right temperature is achieved. (In our case it was 42 C. and was achieved after about 5 tries.)<br />
<br />
5. Once the temperature is achieved seal off the heater the same way you opened it and place it into the glass casing and properly seal the edge so that there is no chance of water seeping in.<br />
<br />
6. Next clean the bucket with detol and half fill with boiled water.<br />
<br />
7. Attach a lid to the bucket to reduce heat loss.<br />
<br />
8. Make a small hole on the lid for the thermometer. It is important that the thermometer is dipped in the water.<br />
<br />
9. Stick the aquarium heater in the bucket and make shure that the heating element is completely submerged. For safety do not put the opened side underwater.<br />
<br />
10. You can make the float using thermocol with holes bog enough for the vials to fit into.<br />
Your water bath is ready.<br />
<br />
<br />
==='''PROCESS PICTURES:'''===<br />
<br />
[[File:DSC03963.JPG|frame|none|Remove the glass casing of the aquarium heater]]<br />
[[File:DSC03967.JPG|frame|none|Unscrew the connecter screw]]<br />
[[File:DSC03974.JPG|frame|none|use it to pull out the thermostat adjustment]]<br />
[[File:DSC03980.JPG|frame|none|With sand paper file the tip of the thermostat adjustment. Be careful as every mm that you file off increases the temperature greatly]]<br />
[[File:DSC03988.JPG|frame|none|Once the temperature is achieved scew it the same way it was opened]]<br />
[[File:DSC03990.JPG|frame|none|place it into the glass casing and properly seal the edge]]<br />
[[File:DSC03993.JPG|frame|none|]]<br />
[[File:DSC03997.JPG|frame|none|clean the bucket with detol]]<br />
[[File:DSC03998.JPG|frame|none|]]<br />
[[File:DSC04003.JPG|frame|none|half fill with boiled water.]]<br />
[[File:DSC04006.JPG|frame|none|]]<br />
[[File:DSC04013.JPG|frame|none|Attach a lid to the bucket]]<br />
[[File:DSC04015.JPG|frame|none|]]<br />
[[File:DSC04023.JPG|frame|none|]]<br />
[[File:DSC04028.JPG|frame|none|Make a small hole on the lid for the thermometer]]<br />
[[File:DSC04031.JPG|frame|none|Stick the aquarium heater in the bucket and make shure that the heating element is completely submerged]]<br />
[[File:DSC04032.JPG|frame|none|]]<br />
[[File:DSC04035.JPG|frame|none|]]<br />
[[File:DSC04040.JPG|frame|none|And it's ready]]<br />
<br />
<br />
<br />
=='''PRECAUTIONS:'''==<br />
<br />
1. Try not to crack the outer casing while opening it for the first time. I know it is difficult but try.<br />
<br />
2. Never let the water touch the circuit or the heating element<br />
<br />
3. Do not dip hot glass in water it will crack and the circuit will burst.<br />
<br />
4. Do not touch heating coil after use.<br />
<br />
5. Be careful to not file the thermostat adjustment too much or you will have to shut it down manually every time it goes above the required temperature.<br />
<br />
6. Only half fill the bucket so that water doesn’t touch the open side of the circuit.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=ReacTable&diff=2782ReacTable2010-10-20T04:10:17Z<p>Farhad: /* Building the table */</p>
<hr />
<div>== Introbuction ==<br />
<br />
<br />
This is a multi touch table that reads markers placed on the screen and does a corresponding action. Thus reading the object on the screen and functioning accordingly. The table uses reactivision software. This application was designed to track specially designed fiducial markers. By downloading the TUIO library you can cerate a program that operates on these markers. the table uses infra red light for finger tracking.<br />
a webcam takes in the feed and runs it through reactivision. It is then processed in processing and displayed again on the screen.<br />
<br />
'''We used this to give information and protocals when a certian object was put on it.'''<br />
<br />
<br />
<br />
===How reacTIVision works===<br />
<br />
In a nutshell the system works like this: reacTIVision tracks specially designed fiducial markers in a real time video stream. The source image frame is first converted to a black&white image with an adaptive thresholding algorithm. Then this image is segmented into a tree of alternating black and white regions (region adjacency graph). This graph is then searched for unique left heavy depth sequences, which have been encoded into the fiducial symbol. Finally the found tree sequences are matched to a dictionary to retrieve an unique ID number. The fiducial design allows the efficient calculation of the marker's center point as well as its orientation. OSC messages implementing the TUIO protocol encode the fiducials' presence, location, orientation and identity and transmit this data to the client applications. <br />
Additionally reacTIVision uses the result of the image segmentation in order to retrieve and identify small round white blobs as finger tips on the surface. A quick and dirty shape matching algorithm selects the actual finger blobs from the possible region candidates. A complementary blob tracking algorithm is also taking advantage of the same data in order to track eventually not recognized fiducials, for example where fast movements destroy the actual fiducial structure in the image.<br />
<br />
<br />
<br />
<br />
== Building the table ==<br />
<br />
<br />
===table & surface===<br />
<br />
A camera and a projector with wide-angle lenses need to be placed underneath the table, so they can both cover the entire surface. [[File:Reactivision03.png|400px|right|]]Alternatively a mirror can be used in order to achieve a larger projection distance. For the interactive surface itself a normal perspex board can be used in conjunction with some ordinary tracing paper on the top side for the projection. This material is completely transparent for objects and finger tips in direct contact with the surface. In order to avoid direct reflections of the light source and projector lamp, the lower side of the surface should have a matte finish, while maintaing the overall transparency. <br />
<br />
<br />
===illumination===<br />
<br />
For the tracking, the objects need to be properly illuminated, so the camera and thus the computer vision application can see them correctly. For the projection onto a table, the surface needs to be dark though, so the user can see the projected image well enough. Since these two necessary steps logically exclude each other, the solution is to operate in two different spectra: <br />
The projection has to be visible to the user, so the computer vision component needs to operate in a different, invisible spectrum such as near infrared in the range of 850nm. Most CCD cameras are perfectly sensitive within the near IR spectrum, therefore infrared LED lamps can be used to illuminate the table. All light from the visible spectrum needs to be filtered in the camera, so the computer vision algorithm is not disturbed by the projection. Eventually an existing infrared blocker needs to be removed from the camera sensor. <br />
<br />
<br />
===camera===<br />
<br />
You should make sure that the camera has an acceptable lens and sensor size. For lowest latency and best performance we recommend firewire cameras from the top range, such as industrial cameras with a high framerate, resolution and sensor size. These cameras usually also come with high quality C-mount lenses. Cheaper firewire cameras, such as the unibrain fire-i also allow optional wide-angle lenses. From the large range of available USB cameras we recommend to use high end models with a native resolution of at least 640x480 at a frame rate of 30Hz. A very affordable and relatively good camera for this purpose is the Sony PS3eye, which is also working well under Windows, Linux and Mac OSX. DV cameras supporting full-frame mode are suitable, while those with interlaced mode only, will not work at all.<br />
<br />
== Using reacTIVision ==<br />
<br />
<br />
===Fiducial Symbols===<br />
<br />
This application was designed to track specially designed fiducial markers. You will find the default "amoeba" fiducial set within the document "default.pdf" within the symbols folder. Print this document and attach the labels to any object you want to track. The default fiducial tracking engine is using Ross Bencina's fidtrack library which is basically a newer high-performance implementation of Enrico Costanza's d-touch concept. Alternatively you can use the "classic" or the "dtouch" sets. See below how to configure the application using these older symbol sets. <br />
<br />
<br />
===Finger Tracking===<br />
<br />
Since reacTIVision was initially designed for fiducial tracking, its thresholder and segmentation modules are optimized for this task. Finger tracking was added at a later stage, and is taking advantage of the existing image processing infrastructure with almost no additional performance overhead. On the other hand it might seem difficult to set up reacTIVision in order to achieve good tracking performance for both the fiducial symbols and the finger tips. When used with diffused illumination, the setup needs strong and even illumination in order to achieve the necessary contrast for finger tracking, also the overall image control such as brightness, gain and shutter speed will improve the tracking quality (O key). Another important control parameter is the threshold "gradient gate" which should be set as low as possible, just before too much image noise becomes visible (G key). Finally the finger tracking can be configured by adjusting the average finger size and tracking sensitivity (F key). <br />
<br />
<br />
===Application Handling===<br />
<br />
Common settings can be edited within the file "reacTIVision.xml" where all changes are stored automatically when closing the application. Under Mac OS X the XML configuration file can be found within the application bundle's Resources folder. Select "Show Package Contents" from the application's context menu in order to access and edit the file. <br />
<br />
The reacTIVision application usually sends the TUIO messages to port 3333 on locahost (127.0.0.1) You can change this setting by adding or editing the XML tag <tuio host="127.0.0.1" port="3333"> to the configuration. <br />
<br />
The <fiducial engine="amoeba" tree="default"/> XML tag lets you select the fiducial engine or an alternative amoeba tree order. The default engine is using the fastest and effective 'amoeba' fiducial set. Add the 'classic' option in order to use Ross' initial d-touch reimplementation. You can select Enrico's original d-touch engine by providing the 'dtouch' option. <br />
<br />
The display attribute defines the default screen upon startup. The <image display="dest" equalize="false" gradient="32" /> lets you adjust the default gradient gate value. reacTIVision comes with a background subtraction module, which in some cases can simplify the recognition performance of both the finger and fiducial tracking. Within the running application you can toggle this with the 'E' key or recalculate the background subtraction by hitting the SPACE bar. <br />
<br />
The camera options can be adjusted by pressing the 'O' key. On Windows and Mac OS this will show a system dialog that allows the adjustment of the available camera parameters. On Linux (Mac OS X when using IEEE1394 cameras), the available camera settings can be adjusted with a simple on screen display.<br />
The overall camera settings can be configured within the camera.xml configuration file. Please note that for Windows and the Quicktime mode on Mac OS X this only allows the configuration of the image size. For IEEE1394 cameras on Mac OS X as well as all camera types on Linux all image parameters can be fully configured using this configuration file. <br />
<br />
<br />
===TUIO vs. MIDI===<br />
<br />
The application can alternatively send MIDI messages, which allows to map any object dimension (xpos, ypos, angle) to a MIDI control via an XML configuration file. Adding and removing objects can be mapped to simple note ON/OFF events. Keep in mind though that MIDI has less bandwidth and data resolution compared to Open Sound Contol, so the MIDI feature is meant as an convenient alternative in some cases, but TUIO still will be the primary messaging layer. <br />
<br />
Adding <midi config="midi/demo.xml"/> to reacTIVision.xml switches to MIDI mode and specifies the MIDI configuration file that contains the mappings and MIDI device selection. An example configuration file "demo.xml" along with an example PD patch "demo.pd" can be found in the "midi" folder. You can list all available MIDI devices with the "-l midi" option.<br />
<br />
<br />
===Calibration and Distortion===<br />
<br />
Some tables, such as the reacTable are using wide-angle or fish-eye lens in order to increase the area visible to the camera at a minimal distance. These lenses unfortunately distort the image and reacTIVision can correct that distortion and the overall alignment of the image. For the calibration print and place one of these rectangular or square calibration sheets on the table and adjust the grid points to the grid printed on the sheet. <br />
<br />
To calibrate reacTIVision switch to calibration mode hitting 'C'. Use the keys A,D,W,X to move within grid, moving with the cursor keys will adjust the grid point. <br />
'J' resets the whole calibration grid, 'U' resets the selected point and 'K' reverts to the saved grid. <br />
To check if the distortion is working properly press 'R'. This will show the fully distorted live video image in the target window. Of course the distortion algorithm only corrects the found positions instead of the full image.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=ReacTable&diff=2781ReacTable2010-10-20T04:09:18Z<p>Farhad: </p>
<hr />
<div>== Introbuction ==<br />
<br />
<br />
This is a multi touch table that reads markers placed on the screen and does a corresponding action. Thus reading the object on the screen and functioning accordingly. The table uses reactivision software. This application was designed to track specially designed fiducial markers. By downloading the TUIO library you can cerate a program that operates on these markers. the table uses infra red light for finger tracking.<br />
a webcam takes in the feed and runs it through reactivision. It is then processed in processing and displayed again on the screen.<br />
<br />
'''We used this to give information and protocals when a certian object was put on it.'''<br />
<br />
<br />
<br />
===How reacTIVision works===<br />
<br />
In a nutshell the system works like this: reacTIVision tracks specially designed fiducial markers in a real time video stream. The source image frame is first converted to a black&white image with an adaptive thresholding algorithm. Then this image is segmented into a tree of alternating black and white regions (region adjacency graph). This graph is then searched for unique left heavy depth sequences, which have been encoded into the fiducial symbol. Finally the found tree sequences are matched to a dictionary to retrieve an unique ID number. The fiducial design allows the efficient calculation of the marker's center point as well as its orientation. OSC messages implementing the TUIO protocol encode the fiducials' presence, location, orientation and identity and transmit this data to the client applications. <br />
Additionally reacTIVision uses the result of the image segmentation in order to retrieve and identify small round white blobs as finger tips on the surface. A quick and dirty shape matching algorithm selects the actual finger blobs from the possible region candidates. A complementary blob tracking algorithm is also taking advantage of the same data in order to track eventually not recognized fiducials, for example where fast movements destroy the actual fiducial structure in the image.<br />
<br />
<br />
<br />
<br />
== Building the table ==<br />
<br />
<br />
===table & surface===<br />
<br />
A camera and a projector with wide-angle lenses need to be placed underneath the table, so they can both cover the entire surface. [[File:Reactivision03.png|200px|right|]]Alternatively a mirror can be used in order to achieve a larger projection distance. For the interactive surface itself a normal perspex board can be used in conjunction with some ordinary tracing paper on the top side for the projection. This material is completely transparent for objects and finger tips in direct contact with the surface. In order to avoid direct reflections of the light source and projector lamp, the lower side of the surface should have a matte finish, while maintaing the overall transparency. <br />
<br />
<br />
===illumination===<br />
<br />
For the tracking, the objects need to be properly illuminated, so the camera and thus the computer vision application can see them correctly. For the projection onto a table, the surface needs to be dark though, so the user can see the projected image well enough. Since these two necessary steps logically exclude each other, the solution is to operate in two different spectra: <br />
The projection has to be visible to the user, so the computer vision component needs to operate in a different, invisible spectrum such as near infrared in the range of 850nm. Most CCD cameras are perfectly sensitive within the near IR spectrum, therefore infrared LED lamps can be used to illuminate the table. All light from the visible spectrum needs to be filtered in the camera, so the computer vision algorithm is not disturbed by the projection. Eventually an existing infrared blocker needs to be removed from the camera sensor. <br />
<br />
<br />
===camera===<br />
<br />
You should make sure that the camera has an acceptable lens and sensor size. For lowest latency and best performance we recommend firewire cameras from the top range, such as industrial cameras with a high framerate, resolution and sensor size. These cameras usually also come with high quality C-mount lenses. Cheaper firewire cameras, such as the unibrain fire-i also allow optional wide-angle lenses. From the large range of available USB cameras we recommend to use high end models with a native resolution of at least 640x480 at a frame rate of 30Hz. A very affordable and relatively good camera for this purpose is the Sony PS3eye, which is also working well under Windows, Linux and Mac OSX. DV cameras supporting full-frame mode are suitable, while those with interlaced mode only, will not work at all.<br />
<br />
<br />
<br />
<br />
== Using reacTIVision ==<br />
<br />
<br />
===Fiducial Symbols===<br />
<br />
This application was designed to track specially designed fiducial markers. You will find the default "amoeba" fiducial set within the document "default.pdf" within the symbols folder. Print this document and attach the labels to any object you want to track. The default fiducial tracking engine is using Ross Bencina's fidtrack library which is basically a newer high-performance implementation of Enrico Costanza's d-touch concept. Alternatively you can use the "classic" or the "dtouch" sets. See below how to configure the application using these older symbol sets. <br />
<br />
<br />
===Finger Tracking===<br />
<br />
Since reacTIVision was initially designed for fiducial tracking, its thresholder and segmentation modules are optimized for this task. Finger tracking was added at a later stage, and is taking advantage of the existing image processing infrastructure with almost no additional performance overhead. On the other hand it might seem difficult to set up reacTIVision in order to achieve good tracking performance for both the fiducial symbols and the finger tips. When used with diffused illumination, the setup needs strong and even illumination in order to achieve the necessary contrast for finger tracking, also the overall image control such as brightness, gain and shutter speed will improve the tracking quality (O key). Another important control parameter is the threshold "gradient gate" which should be set as low as possible, just before too much image noise becomes visible (G key). Finally the finger tracking can be configured by adjusting the average finger size and tracking sensitivity (F key). <br />
<br />
<br />
===Application Handling===<br />
<br />
Common settings can be edited within the file "reacTIVision.xml" where all changes are stored automatically when closing the application. Under Mac OS X the XML configuration file can be found within the application bundle's Resources folder. Select "Show Package Contents" from the application's context menu in order to access and edit the file. <br />
<br />
The reacTIVision application usually sends the TUIO messages to port 3333 on locahost (127.0.0.1) You can change this setting by adding or editing the XML tag <tuio host="127.0.0.1" port="3333"> to the configuration. <br />
<br />
The <fiducial engine="amoeba" tree="default"/> XML tag lets you select the fiducial engine or an alternative amoeba tree order. The default engine is using the fastest and effective 'amoeba' fiducial set. Add the 'classic' option in order to use Ross' initial d-touch reimplementation. You can select Enrico's original d-touch engine by providing the 'dtouch' option. <br />
<br />
The display attribute defines the default screen upon startup. The <image display="dest" equalize="false" gradient="32" /> lets you adjust the default gradient gate value. reacTIVision comes with a background subtraction module, which in some cases can simplify the recognition performance of both the finger and fiducial tracking. Within the running application you can toggle this with the 'E' key or recalculate the background subtraction by hitting the SPACE bar. <br />
<br />
The camera options can be adjusted by pressing the 'O' key. On Windows and Mac OS this will show a system dialog that allows the adjustment of the available camera parameters. On Linux (Mac OS X when using IEEE1394 cameras), the available camera settings can be adjusted with a simple on screen display.<br />
The overall camera settings can be configured within the camera.xml configuration file. Please note that for Windows and the Quicktime mode on Mac OS X this only allows the configuration of the image size. For IEEE1394 cameras on Mac OS X as well as all camera types on Linux all image parameters can be fully configured using this configuration file. <br />
<br />
<br />
===TUIO vs. MIDI===<br />
<br />
The application can alternatively send MIDI messages, which allows to map any object dimension (xpos, ypos, angle) to a MIDI control via an XML configuration file. Adding and removing objects can be mapped to simple note ON/OFF events. Keep in mind though that MIDI has less bandwidth and data resolution compared to Open Sound Contol, so the MIDI feature is meant as an convenient alternative in some cases, but TUIO still will be the primary messaging layer. <br />
<br />
Adding <midi config="midi/demo.xml"/> to reacTIVision.xml switches to MIDI mode and specifies the MIDI configuration file that contains the mappings and MIDI device selection. An example configuration file "demo.xml" along with an example PD patch "demo.pd" can be found in the "midi" folder. You can list all available MIDI devices with the "-l midi" option.<br />
<br />
<br />
===Calibration and Distortion===<br />
<br />
Some tables, such as the reacTable are using wide-angle or fish-eye lens in order to increase the area visible to the camera at a minimal distance. These lenses unfortunately distort the image and reacTIVision can correct that distortion and the overall alignment of the image. For the calibration print and place one of these rectangular or square calibration sheets on the table and adjust the grid points to the grid printed on the sheet. <br />
<br />
To calibrate reacTIVision switch to calibration mode hitting 'C'. Use the keys A,D,W,X to move within grid, moving with the cursor keys will adjust the grid point. <br />
'J' resets the whole calibration grid, 'U' resets the selected point and 'K' reverts to the saved grid. <br />
To check if the distortion is working properly press 'R'. This will show the fully distorted live video image in the target window. Of course the distortion algorithm only corrects the found positions instead of the full image.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=ReacTable&diff=2780ReacTable2010-10-20T04:07:02Z<p>Farhad: </p>
<hr />
<div>== Introbuction ==<br />
<br />
<br />
This is a multi touch table that reads markers placed on the screen and does a corresponding action. Thus reading the object on the screen and functioning accordingly. The table uses reactivision software. This application was designed to track specially designed fiducial markers. By downloading the TUIO library you can cerate a program that operates on these markers. the table uses infra red light for finger tracking.<br />
a webcam takes in the feed and runs it through reactivision. It is then processed in processing and displayed again on the screen.<br />
<br />
'''We used this to give information and protocals when a certian object was put on it.'''<br />
<br />
<br />
<br />
===How reacTIVision works===<br />
<br />
In a nutshell the system works like this: reacTIVision tracks specially designed fiducial markers in a real time video stream. The source image frame is first converted to a black&white image with an adaptive thresholding algorithm. Then this image is segmented into a tree of alternating black and white regions (region adjacency graph). This graph is then searched for unique left heavy depth sequences, which have been encoded into the fiducial symbol. Finally the found tree sequences are matched to a dictionary to retrieve an unique ID number. The fiducial design allows the efficient calculation of the marker's center point as well as its orientation. OSC messages implementing the TUIO protocol encode the fiducials' presence, location, orientation and identity and transmit this data to the client applications. <br />
Additionally reacTIVision uses the result of the image segmentation in order to retrieve and identify small round white blobs as finger tips on the surface. A quick and dirty shape matching algorithm selects the actual finger blobs from the possible region candidates. A complementary blob tracking algorithm is also taking advantage of the same data in order to track eventually not recognized fiducials, for example where fast movements destroy the actual fiducial structure in the image.<br />
<br />
<br />
<br />
<br />
== Building the table ==<br />
<br />
<br />
===table & surface===<br />
<br />
A camera and a projector with wide-angle lenses need to be placed underneath the table, so they can both cover the entire surface. Alternatively a mirror can be used in order to achieve a larger projection distance. For the interactive surface itself a normal perspex board can be used in conjunction with some ordinary tracing paper on the top side for the projection. This material is completely transparent for objects and finger tips in direct contact with the surface. In order to avoid direct reflections of the light source and projector lamp, the lower side of the surface should have a matte finish, while maintaing the overall transparency. <br />
<br />
<br />
===illumination===<br />
<br />
For the tracking, the objects need to be properly illuminated, so the camera and thus the computer vision application can see them correctly. For the projection onto a table, the surface needs to be dark though, so the user can see the projected image well enough. Since these two necessary steps logically exclude each other, the solution is to operate in two different spectra: <br />
The projection has to be visible to the user, so the computer vision component needs to operate in a different, invisible spectrum such as near infrared in the range of 850nm. Most CCD cameras are perfectly sensitive within the near IR spectrum, therefore infrared LED lamps can be used to illuminate the table. All light from the visible spectrum needs to be filtered in the camera, so the computer vision algorithm is not disturbed by the projection. Eventually an existing infrared blocker needs to be removed from the camera sensor. <br />
<br />
<br />
===camera===<br />
<br />
You should make sure that the camera has an acceptable lens and sensor size. For lowest latency and best performance we recommend firewire cameras from the top range, such as industrial cameras with a high framerate, resolution and sensor size. These cameras usually also come with high quality C-mount lenses. Cheaper firewire cameras, such as the unibrain fire-i also allow optional wide-angle lenses. From the large range of available USB cameras we recommend to use high end models with a native resolution of at least 640x480 at a frame rate of 30Hz. A very affordable and relatively good camera for this purpose is the Sony PS3eye, which is also working well under Windows, Linux and Mac OSX. DV cameras supporting full-frame mode are suitable, while those with interlaced mode only, will not work at all.<br />
<br />
<br />
<br />
<br />
== Using reacTIVision ==<br />
<br />
<br />
===Fiducial Symbols===<br />
<br />
This application was designed to track specially designed fiducial markers. You will find the default "amoeba" fiducial set within the document "default.pdf" within the symbols folder. Print this document and attach the labels to any object you want to track. The default fiducial tracking engine is using Ross Bencina's fidtrack library which is basically a newer high-performance implementation of Enrico Costanza's d-touch concept. Alternatively you can use the "classic" or the "dtouch" sets. See below how to configure the application using these older symbol sets. <br />
<br />
<br />
===Finger Tracking===<br />
<br />
Since reacTIVision was initially designed for fiducial tracking, its thresholder and segmentation modules are optimized for this task. Finger tracking was added at a later stage, and is taking advantage of the existing image processing infrastructure with almost no additional performance overhead. On the other hand it might seem difficult to set up reacTIVision in order to achieve good tracking performance for both the fiducial symbols and the finger tips. When used with diffused illumination, the setup needs strong and even illumination in order to achieve the necessary contrast for finger tracking, also the overall image control such as brightness, gain and shutter speed will improve the tracking quality (O key). Another important control parameter is the threshold "gradient gate" which should be set as low as possible, just before too much image noise becomes visible (G key). Finally the finger tracking can be configured by adjusting the average finger size and tracking sensitivity (F key). <br />
<br />
<br />
===Application Handling===<br />
<br />
Common settings can be edited within the file "reacTIVision.xml" where all changes are stored automatically when closing the application. Under Mac OS X the XML configuration file can be found within the application bundle's Resources folder. Select "Show Package Contents" from the application's context menu in order to access and edit the file. <br />
<br />
The reacTIVision application usually sends the TUIO messages to port 3333 on locahost (127.0.0.1) You can change this setting by adding or editing the XML tag <tuio host="127.0.0.1" port="3333"> to the configuration. <br />
<br />
The <fiducial engine="amoeba" tree="default"/> XML tag lets you select the fiducial engine or an alternative amoeba tree order. The default engine is using the fastest and effective 'amoeba' fiducial set. Add the 'classic' option in order to use Ross' initial d-touch reimplementation. You can select Enrico's original d-touch engine by providing the 'dtouch' option. <br />
<br />
The display attribute defines the default screen upon startup. The <image display="dest" equalize="false" gradient="32" /> lets you adjust the default gradient gate value. reacTIVision comes with a background subtraction module, which in some cases can simplify the recognition performance of both the finger and fiducial tracking. Within the running application you can toggle this with the 'E' key or recalculate the background subtraction by hitting the SPACE bar. <br />
<br />
The camera options can be adjusted by pressing the 'O' key. On Windows and Mac OS this will show a system dialog that allows the adjustment of the available camera parameters. On Linux (Mac OS X when using IEEE1394 cameras), the available camera settings can be adjusted with a simple on screen display.<br />
The overall camera settings can be configured within the camera.xml configuration file. Please note that for Windows and the Quicktime mode on Mac OS X this only allows the configuration of the image size. For IEEE1394 cameras on Mac OS X as well as all camera types on Linux all image parameters can be fully configured using this configuration file. <br />
<br />
<br />
===TUIO vs. MIDI===<br />
<br />
The application can alternatively send MIDI messages, which allows to map any object dimension (xpos, ypos, angle) to a MIDI control via an XML configuration file. Adding and removing objects can be mapped to simple note ON/OFF events. Keep in mind though that MIDI has less bandwidth and data resolution compared to Open Sound Contol, so the MIDI feature is meant as an convenient alternative in some cases, but TUIO still will be the primary messaging layer. <br />
<br />
Adding <midi config="midi/demo.xml"/> to reacTIVision.xml switches to MIDI mode and specifies the MIDI configuration file that contains the mappings and MIDI device selection. An example configuration file "demo.xml" along with an example PD patch "demo.pd" can be found in the "midi" folder. You can list all available MIDI devices with the "-l midi" option.<br />
<br />
<br />
===Calibration and Distortion===<br />
<br />
Some tables, such as the reacTable are using wide-angle or fish-eye lens in order to increase the area visible to the camera at a minimal distance. These lenses unfortunately distort the image and reacTIVision can correct that distortion and the overall alignment of the image. For the calibration print and place one of these rectangular or square calibration sheets on the table and adjust the grid points to the grid printed on the sheet. <br />
<br />
To calibrate reacTIVision switch to calibration mode hitting 'C'. Use the keys A,D,W,X to move within grid, moving with the cursor keys will adjust the grid point. <br />
'J' resets the whole calibration grid, 'U' resets the selected point and 'K' reverts to the saved grid. <br />
To check if the distortion is working properly press 'R'. This will show the fully distorted live video image in the target window. Of course the distortion algorithm only corrects the found positions instead of the full image.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=File:Reactivision03.png&diff=2779File:Reactivision03.png2010-10-20T03:57:54Z<p>Farhad: </p>
<hr />
<div></div>Farhadhttp://www.hackteria.org/wiki/index.php?title=ReacTable&diff=2778ReacTable2010-10-19T03:07:15Z<p>Farhad: </p>
<hr />
<div><br />
== Introbuction ==<br />
<br />
<br />
This is a multi touch table that reads markers placed on the screen and does a corresponding action. Thus reading the object on the screen and functioning accordingly. The table uses reactivision software. This application was designed to track specially designed fiducial markers. By downloading the TUIO library you can cerate a program that operates on these markers. the table uses infra red light for finger tracking.<br />
a webcam takes in the feed and runs it through reactivision. It is then processed in processing and displayed again on the screen.<br />
<br />
'''We used this to give information and protocals when a certian object was put on it.'''<br />
<br />
<br />
<br />
===How reacTIVision works===<br />
<br />
In a nutshell the system works like this: reacTIVision tracks specially designed fiducial markers in a real time video stream. The source image frame is first converted to a black&white image with an adaptive thresholding algorithm. Then this image is segmented into a tree of alternating black and white regions (region adjacency graph). This graph is then searched for unique left heavy depth sequences, which have been encoded into the fiducial symbol. Finally the found tree sequences are matched to a dictionary to retrieve an unique ID number. The fiducial design allows the efficient calculation of the marker's center point as well as its orientation. OSC messages implementing the TUIO protocol encode the fiducials' presence, location, orientation and identity and transmit this data to the client applications. <br />
Additionally reacTIVision uses the result of the image segmentation in order to retrieve and identify small round white blobs as finger tips on the surface. A quick and dirty shape matching algorithm selects the actual finger blobs from the possible region candidates. A complementary blob tracking algorithm is also taking advantage of the same data in order to track eventually not recognized fiducials, for example where fast movements destroy the actual fiducial structure in the image.<br />
<br />
<br />
<br />
<br />
== Building the table ==<br />
<br />
<br />
===table & surface===<br />
<br />
A camera and a projector with wide-angle lenses need to be placed underneath the table, so they can both cover the entire surface. Alternatively a mirror can be used in order to achieve a larger projection distance. For the interactive surface itself a normal perspex board can be used in conjunction with some ordinary tracing paper on the top side for the projection. This material is completely transparent for objects and finger tips in direct contact with the surface. In order to avoid direct reflections of the light source and projector lamp, the lower side of the surface should have a matte finish, while maintaing the overall transparency. <br />
<br />
<br />
===illumination===<br />
<br />
For the tracking, the objects need to be properly illuminated, so the camera and thus the computer vision application can see them correctly. For the projection onto a table, the surface needs to be dark though, so the user can see the projected image well enough. Since these two necessary steps logically exclude each other, the solution is to operate in two different spectra: <br />
The projection has to be visible to the user, so the computer vision component needs to operate in a different, invisible spectrum such as near infrared in the range of 850nm. Most CCD cameras are perfectly sensitive within the near IR spectrum, therefore infrared LED lamps can be used to illuminate the table. All light from the visible spectrum needs to be filtered in the camera, so the computer vision algorithm is not disturbed by the projection. Eventually an existing infrared blocker needs to be removed from the camera sensor. <br />
<br />
<br />
===camera===<br />
<br />
You should make sure that the camera has an acceptable lens and sensor size. For lowest latency and best performance we recommend firewire cameras from the top range, such as industrial cameras with a high framerate, resolution and sensor size. These cameras usually also come with high quality C-mount lenses. Cheaper firewire cameras, such as the unibrain fire-i also allow optional wide-angle lenses. From the large range of available USB cameras we recommend to use high end models with a native resolution of at least 640x480 at a frame rate of 30Hz. A very affordable and relatively good camera for this purpose is the Sony PS3eye, which is also working well under Windows, Linux and Mac OSX. DV cameras supporting full-frame mode are suitable, while those with interlaced mode only, will not work at all.<br />
<br />
<br />
<br />
<br />
== Using reacTIVision ==<br />
<br />
<br />
===Fiducial Symbols===<br />
<br />
This application was designed to track specially designed fiducial markers. You will find the default "amoeba" fiducial set within the document "default.pdf" within the symbols folder. Print this document and attach the labels to any object you want to track. The default fiducial tracking engine is using Ross Bencina's fidtrack library which is basically a newer high-performance implementation of Enrico Costanza's d-touch concept. Alternatively you can use the "classic" or the "dtouch" sets. See below how to configure the application using these older symbol sets. <br />
<br />
<br />
===Finger Tracking===<br />
<br />
Since reacTIVision was initially designed for fiducial tracking, its thresholder and segmentation modules are optimized for this task. Finger tracking was added at a later stage, and is taking advantage of the existing image processing infrastructure with almost no additional performance overhead. On the other hand it might seem difficult to set up reacTIVision in order to achieve good tracking performance for both the fiducial symbols and the finger tips. When used with diffused illumination, the setup needs strong and even illumination in order to achieve the necessary contrast for finger tracking, also the overall image control such as brightness, gain and shutter speed will improve the tracking quality (O key). Another important control parameter is the threshold "gradient gate" which should be set as low as possible, just before too much image noise becomes visible (G key). Finally the finger tracking can be configured by adjusting the average finger size and tracking sensitivity (F key). <br />
<br />
<br />
===Application Handling===<br />
<br />
Common settings can be edited within the file "reacTIVision.xml" where all changes are stored automatically when closing the application. Under Mac OS X the XML configuration file can be found within the application bundle's Resources folder. Select "Show Package Contents" from the application's context menu in order to access and edit the file. <br />
<br />
The reacTIVision application usually sends the TUIO messages to port 3333 on locahost (127.0.0.1) You can change this setting by adding or editing the XML tag <tuio host="127.0.0.1" port="3333"> to the configuration. <br />
<br />
The <fiducial engine="amoeba" tree="default"/> XML tag lets you select the fiducial engine or an alternative amoeba tree order. The default engine is using the fastest and effective 'amoeba' fiducial set. Add the 'classic' option in order to use Ross' initial d-touch reimplementation. You can select Enrico's original d-touch engine by providing the 'dtouch' option. <br />
<br />
The display attribute defines the default screen upon startup. The <image display="dest" equalize="false" gradient="32" /> lets you adjust the default gradient gate value. reacTIVision comes with a background subtraction module, which in some cases can simplify the recognition performance of both the finger and fiducial tracking. Within the running application you can toggle this with the 'E' key or recalculate the background subtraction by hitting the SPACE bar. <br />
<br />
The camera options can be adjusted by pressing the 'O' key. On Windows and Mac OS this will show a system dialog that allows the adjustment of the available camera parameters. On Linux (Mac OS X when using IEEE1394 cameras), the available camera settings can be adjusted with a simple on screen display.<br />
The overall camera settings can be configured within the camera.xml configuration file. Please note that for Windows and the Quicktime mode on Mac OS X this only allows the configuration of the image size. For IEEE1394 cameras on Mac OS X as well as all camera types on Linux all image parameters can be fully configured using this configuration file. <br />
<br />
<br />
===TUIO vs. MIDI===<br />
<br />
The application can alternatively send MIDI messages, which allows to map any object dimension (xpos, ypos, angle) to a MIDI control via an XML configuration file. Adding and removing objects can be mapped to simple note ON/OFF events. Keep in mind though that MIDI has less bandwidth and data resolution compared to Open Sound Contol, so the MIDI feature is meant as an convenient alternative in some cases, but TUIO still will be the primary messaging layer. <br />
<br />
Adding <midi config="midi/demo.xml"/> to reacTIVision.xml switches to MIDI mode and specifies the MIDI configuration file that contains the mappings and MIDI device selection. An example configuration file "demo.xml" along with an example PD patch "demo.pd" can be found in the "midi" folder. You can list all available MIDI devices with the "-l midi" option.<br />
<br />
<br />
===Calibration and Distortion===<br />
<br />
Some tables, such as the reacTable are using wide-angle or fish-eye lens in order to increase the area visible to the camera at a minimal distance. These lenses unfortunately distort the image and reacTIVision can correct that distortion and the overall alignment of the image. For the calibration print and place one of these rectangular or square calibration sheets on the table and adjust the grid points to the grid printed on the sheet. <br />
<br />
To calibrate reacTIVision switch to calibration mode hitting 'C'. Use the keys A,D,W,X to move within grid, moving with the cursor keys will adjust the grid point. <br />
'J' resets the whole calibration grid, 'U' resets the selected point and 'K' reverts to the saved grid. <br />
To check if the distortion is working properly press 'R'. This will show the fully distorted live video image in the target window. Of course the distortion algorithm only corrects the found positions instead of the full image.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=ReacTable&diff=2777ReacTable2010-10-19T03:01:17Z<p>Farhad: </p>
<hr />
<div>This is a multi touch table that reads markers placed on the screen and does a corresponding action. Thus reading the object on the screen and functioning accordingly. The table uses reactivision software. This application was designed to track specially designed fiducial markers. By downloading the TUIO library you can cerate a program that operates on these markers. the table uses infra red light for finger tracking.<br />
a webcam takes in the feed and runs it through reactivision. It is then processed in processing and displayed again on the screen.<br />
<br />
'''We used this to give information and protocals when a certian object was put on it.'''<br />
<br />
<br />
<br />
'''How reactivision works'''<br />
<br />
In a nutshell the system works like this: reacTIVision tracks specially designed fiducial markers in a real time video stream. The source image frame is first converted to a black&white image with an adaptive thresholding algorithm. Then this image is segmented into a tree of alternating black and white regions (region adjacency graph). This graph is then searched for unique left heavy depth sequences, which have been encoded into the fiducial symbol. Finally the found tree sequences are matched to a dictionary to retrieve an unique ID number. The fiducial design allows the efficient calculation of the marker's center point as well as its orientation. OSC messages implementing the TUIO protocol encode the fiducials' presence, location, orientation and identity and transmit this data to the client applications. <br />
Additionally reacTIVision uses the result of the image segmentation in order to retrieve and identify small round white blobs as finger tips on the surface. A quick and dirty shape matching algorithm selects the actual finger blobs from the possible region candidates. A complementary blob tracking algorithm is also taking advantage of the same data in order to track eventually not recognized fiducials, for example where fast movements destroy the actual fiducial structure in the image.<br />
<br />
<br />
<br />
<br />
== Building the table ==<br />
<br />
<br />
'''table & surface'''<br />
<br />
A camera and a projector with wide-angle lenses need to be placed underneath the table, so they can both cover the entire surface. Alternatively a mirror can be used in order to achieve a larger projection distance. For the interactive surface itself a normal perspex board can be used in conjunction with some ordinary tracing paper on the top side for the projection. This material is completely transparent for objects and finger tips in direct contact with the surface. In order to avoid direct reflections of the light source and projector lamp, the lower side of the surface should have a matte finish, while maintaing the overall transparency. <br />
<br />
<br />
'''illumination'''<br />
<br />
For the tracking, the objects need to be properly illuminated, so the camera and thus the computer vision application can see them correctly. For the projection onto a table, the surface needs to be dark though, so the user can see the projected image well enough. Since these two necessary steps logically exclude each other, the solution is to operate in two different spectra: <br />
The projection has to be visible to the user, so the computer vision component needs to operate in a different, invisible spectrum such as near infrared in the range of 850nm. Most CCD cameras are perfectly sensitive within the near IR spectrum, therefore infrared LED lamps can be used to illuminate the table. All light from the visible spectrum needs to be filtered in the camera, so the computer vision algorithm is not disturbed by the projection. Eventually an existing infrared blocker needs to be removed from the camera sensor. <br />
<br />
<br />
'''camera'''<br />
<br />
You should make sure that the camera has an acceptable lens and sensor size. For lowest latency and best performance we recommend firewire cameras from the top range, such as industrial cameras with a high framerate, resolution and sensor size. These cameras usually also come with high quality C-mount lenses. Cheaper firewire cameras, such as the unibrain fire-i also allow optional wide-angle lenses. From the large range of available USB cameras we recommend to use high end models with a native resolution of at least 640x480 at a frame rate of 30Hz. A very affordable and relatively good camera for this purpose is the Sony PS3eye, which is also working well under Windows, Linux and Mac OSX. DV cameras supporting full-frame mode are suitable, while those with interlaced mode only, will not work at all.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=ReacTable&diff=2776ReacTable2010-10-19T03:00:12Z<p>Farhad: </p>
<hr />
<div>This is a multi touch table that reads markers placed on the screen and does a corresponding action. Thus reading the object on the screen and functioning accordingly. The table uses reactivision software. This application was designed to track specially designed fiducial markers. By downloading the TUIO library you can cerate a program that operates on these markers. the table uses infra red light for finger tracking.<br />
a webcam takes in the feed and runs it through reactivision. It is then processed in processing and displayed again on the screen.<br />
<br />
'''We used this to give information and protocals when a certian object was put on it.'''<br />
<br />
<br />
<br />
'''How reactivision works'''<br />
<br />
In a nutshell the system works like this: reacTIVision tracks specially designed fiducial markers in a real time video stream. The source image frame is first converted to a black&white image with an adaptive thresholding algorithm. Then this image is segmented into a tree of alternating black and white regions (region adjacency graph). This graph is then searched for unique left heavy depth sequences, which have been encoded into the fiducial symbol. Finally the found tree sequences are matched to a dictionary to retrieve an unique ID number. The fiducial design allows the efficient calculation of the marker's center point as well as its orientation. OSC messages implementing the TUIO protocol encode the fiducials' presence, location, orientation and identity and transmit this data to the client applications. <br />
Additionally reacTIVision uses the result of the image segmentation in order to retrieve and identify small round white blobs as finger tips on the surface. A quick and dirty shape matching algorithm selects the actual finger blobs from the possible region candidates. A complementary blob tracking algorithm is also taking advantage of the same data in order to track eventually not recognized fiducials, for example where fast movements destroy the actual fiducial structure in the image.<br />
<br />
<br />
<br />
<br />
== building the table ==<br />
<br />
<br />
'''table & surface'''<br />
<br />
A camera and a projector with wide-angle lenses need to be placed underneath the table, so they can both cover the entire surface. Alternatively a mirror can be used in order to achieve a larger projection distance. For the interactive surface itself a normal perspex board can be used in conjunction with some ordinary tracing paper on the top side for the projection. This material is completely transparent for objects and finger tips in direct contact with the surface. In order to avoid direct reflections of the light source and projector lamp, the lower side of the surface should have a matte finish, while maintaing the overall transparency. <br />
<br />
<br />
'''illumination'''<br />
<br />
For the tracking, the objects need to be properly illuminated, so the camera and thus the computer vision application can see them correctly. For the projection onto a table, the surface needs to be dark though, so the user can see the projected image well enough. Since these two necessary steps logically exclude each other, the solution is to operate in two different spectra: <br />
The projection has to be visible to the user, so the computer vision component needs to operate in a different, invisible spectrum such as near infrared in the range of 850nm. Most CCD cameras are perfectly sensitive within the near IR spectrum, therefore infrared LED lamps can be used to illuminate the table. All light from the visible spectrum needs to be filtered in the camera, so the computer vision algorithm is not disturbed by the projection. Eventually an existing infrared blocker needs to be removed from the camera sensor. <br />
<br />
<br />
'''camera'''<br />
<br />
You should make sure that the camera has an acceptable lens and sensor size. For lowest latency and best performance we recommend firewire cameras from the top range, such as industrial cameras with a high framerate, resolution and sensor size. These cameras usually also come with high quality C-mount lenses. Cheaper firewire cameras, such as the unibrain fire-i also allow optional wide-angle lenses. From the large range of available USB cameras we recommend to use high end models with a native resolution of at least 640x480 at a frame rate of 30Hz. A very affordable and relatively good camera for this purpose is the Sony PS3eye, which is also working well under Windows, Linux and Mac OSX. DV cameras supporting full-frame mode are suitable, while those with interlaced mode only, will not work at all.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=ReacTable&diff=2773ReacTable2010-10-18T11:04:20Z<p>Farhad: </p>
<hr />
<div>This is a multi touch table that reads markers placed on the screen and does a corresponding action. Thus reading the object on the screen and functioning accordingly. The table uses reactivision software. This application was designed to track specially designed fiducial markers. By downloading the TUIO library you can cerate a program that operates on these markers. the table uses infra red light for finger tracking.<br />
a webcam takes in the feed and runs it through reactivision. It is then processed in processing and displayed again on the screen.<br />
<br />
'''We used this to give information and protocals when a certian object was put on it.'''<br />
<br />
<br />
<br />
'''How reactivision works'''<br />
<br />
In a nutshell the system works like this: reacTIVision tracks specially designed fiducial markers in a real time video stream. The source image frame is first converted to a black&white image with an adaptive thresholding algorithm. Then this image is segmented into a tree of alternating black and white regions (region adjacency graph). This graph is then searched for unique left heavy depth sequences, which have been encoded into the fiducial symbol. Finally the found tree sequences are matched to a dictionary to retrieve an unique ID number. The fiducial design allows the efficient calculation of the marker's center point as well as its orientation. OSC messages implementing the TUIO protocol encode the fiducials' presence, location, orientation and identity and transmit this data to the client applications. <br />
Additionally reacTIVision uses the result of the image segmentation in order to retrieve and identify small round white blobs as finger tips on the surface. A quick and dirty shape matching algorithm selects the actual finger blobs from the possible region candidates. A complementary blob tracking algorithm is also taking advantage of the same data in order to track eventually not recognized fiducials, for example where fast movements destroy the actual fiducial structure in the image.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=ReacTable&diff=2772ReacTable2010-10-18T10:58:16Z<p>Farhad: </p>
<hr />
<div>This is a multi touch table that reads markers placed on the screen and does a corresponding action. Thus reading the object on the screen and functioning accordingly. The table uses reactivision software. This application was designed to track specially designed fiducial markers. By downloading the TUIO library you can cerate a program that operates on these markers. the table uses infra red light for finger tracking.<br />
a webcam takes in the feed and runs it through reactivision. It is then processed in processing and displayed again on the screen.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_table_top_centrifuge&diff=2771DIY table top centrifuge2010-10-18T10:09:15Z<p>Farhad: </p>
<hr />
<div>A centrifuge is a rotating body with very high RPM. The vial holders at the edge of the body spinning at high rpm are used to separate substances of different densities.<br />
<br />
<br />
<br />
'''You will need,'''<br />
<br />
1. '''Blender''' – One which has variable speeds would be better<br />
<br />
2. '''Jar''' – a small one, since we’ll need only the bottom part that attaches to the blender<br />
<br />
3. '''Strips of metal''' – make sure the edges are completely filed off to be safer<br />
<br />
4. '''Test tube holders''' – I used PVC pipes here with caps that fit very snugly <br />
<br />
5. '''Latches''' – Small in size to fasten the tubes to the metal strips<br />
<br />
<br />
<br />
'''How our centrifuge works'''<br />
<br />
The first thing I would like to say about this project is PLEASE DO NOT TRY THIS AT HOME! <br />
<br />
Well now, if you had to take that seriously then this would barely be a do-it-yourself workshop! I’ve had good fun making this centrifuge and one thing I’ve learned for sure is anything that spins very fast can cause serious damage! So for what it matters, please DO take extra precaution while trying to make this.<br />
<br />
I went about this using the basic principal of the centrifuge which is that anything that spins has a force that pushes away from it called the ‘centrifugal force’ so if I have a motor than spins then anything attached to it will be thrown away. <br />
<br />
<br />
<br />
'''Procedure'''<br />
<br />
As simple as it sounds but that’s all you need. Follow these few steps and you’ll have your centrifuge up and running in no time!<br />
<br />
<br />
'''1. '''<br />
Dismantle the upper portion of the jar so that we remain with only the unit that attaches to the blender<br />
<br />
'''2. '''<br />
Make a hole in the center of the two metal strips. This hole has to be exactly in the center so measuring it will be a good option. If it’s not in the center then it could cause imbalance during rotation. The size of the hole has to have the same diameter as the center spinning portion in the jar.<br />
<br />
'''3. '''<br />
Make holes on either side of the metal strips using the latches as a mark since they will be screwed into the metal strip.<br />
<br />
'''4. '''<br />
Make a hole in the test tube holder using the latch again since it will be screwed into it.<br />
<br />
'''Assembly-'''<br />
Fit the jar on to the blender and lock it. Screw one end of the latch to the test tube holder and the other onto the metal strip on all four sides. Place both the metal strips onto the blender and screw them in. Make sure to tighten all the screws as much as possible. To be on the safer side use the adhesive to fix the screws of the latch on the metal strip and the test tube holders. At high speeds, wear and tear is maximum, due to friction. So double check to ensure everything is completely secure.<br />
<br />
'''5. '''<br />
DONE! Now you’re ready to spin. <br />
<br />
<br />
<br />
'''Precaution and Safety Measures'''<br />
<br />
1. ALWAYS wear safety glasses. Seriously you never know what could go flying and get into your eyes. <br />
<br />
2. It would be good to keep a large board in front of you when testing the centrifuge for the first time or until you get comfortable.<br />
<br />
3. Test the centrifuge with a dummy test tube which is NOT glass to make sure all goes well.<br />
<br />
4. ALWAYS run the centrifuge slowly and at short intervals, and then later pick up speed.<br />
<br />
5. ALWAYS run your centrifuge BALANCED, i.e tubes on either sides at all times.<br />
<br />
6. Finally remember to have fun!</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_table_top_centrifuge&diff=2770DIY table top centrifuge2010-10-18T10:08:44Z<p>Farhad: </p>
<hr />
<div>A centrifuge is a rotating body with very high RPM. The vial holders at the edge of the body spinning at high rpm are used to separate substances of different densities.<br />
<br />
<br />
<br />
'''You will need,'''<br />
<br />
1. '''Blender''' – One which has variable speeds would be better<br />
<br />
2. '''Jar''' – a small one, since we’ll need only the bottom part that attaches to the blender<br />
<br />
3. '''Strips of metal''' – make sure the edges are completely filed off to be safer<br />
<br />
4. '''Test tube holders''' – I used PVC pipes here with caps that fit very snugly <br />
<br />
5. '''Latches''' – Small in size to fasten the tubes to the metal strips<br />
<br />
<br />
<br />
'''How our centrifuge works'''<br />
<br />
The first thing I would like to say about this project is PLEASE DO NOT TRY THIS AT HOME! <br />
<br />
Well now, if you had to take that seriously then this would barely be a do-it-yourself workshop! I’ve had good fun making this centrifuge and one thing I’ve learned for sure is anything that spins very fast can cause serious damage! So for what it matters, please DO take extra precaution while trying to make this.<br />
<br />
I went about this using the basic principal of the centrifuge which is that anything that spins has a force that pushes away from it called the ‘centrifugal force’ so if I have a motor than spins then anything attached to it will be thrown away. <br />
<br />
<br />
<br />
'''Procedure'''<br />
As simple as it sounds but that’s all you need. Follow these few steps and you’ll have your centrifuge up and running in no time!<br />
<br />
'''1. '''<br />
Dismantle the upper portion of the jar so that we remain with only the unit that attaches to the blender<br />
<br />
'''2. '''<br />
Make a hole in the center of the two metal strips. This hole has to be exactly in the center so measuring it will be a good option. If it’s not in the center then it could cause imbalance during rotation. The size of the hole has to have the same diameter as the center spinning portion in the jar.<br />
<br />
'''3. '''<br />
Make holes on either side of the metal strips using the latches as a mark since they will be screwed into the metal strip.<br />
<br />
'''4. '''<br />
Make a hole in the test tube holder using the latch again since it will be screwed into it.<br />
<br />
'''Assembly-'''<br />
Fit the jar on to the blender and lock it. Screw one end of the latch to the test tube holder and the other onto the metal strip on all four sides. Place both the metal strips onto the blender and screw them in. Make sure to tighten all the screws as much as possible. To be on the safer side use the adhesive to fix the screws of the latch on the metal strip and the test tube holders. At high speeds, wear and tear is maximum, due to friction. So double check to ensure everything is completely secure.<br />
<br />
'''5. '''<br />
DONE! Now you’re ready to spin. <br />
<br />
<br />
<br />
'''Precaution and Safety Measures'''<br />
<br />
1. ALWAYS wear safety glasses. Seriously you never know what could go flying and get into your eyes. <br />
<br />
2. It would be good to keep a large board in front of you when testing the centrifuge for the first time or until you get comfortable.<br />
<br />
3. Test the centrifuge with a dummy test tube which is NOT glass to make sure all goes well.<br />
<br />
4. ALWAYS run the centrifuge slowly and at short intervals, and then later pick up speed.<br />
<br />
5. ALWAYS run your centrifuge BALANCED, i.e tubes on either sides at all times.<br />
<br />
6. Finally remember to have fun!</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_table_top_centrifuge&diff=2769DIY table top centrifuge2010-10-18T10:05:01Z<p>Farhad: </p>
<hr />
<div>The first thing I would like to say about this project is PLEASE DO NOT TRY THIS AT HOME! <br />
<br />
Well now, if you had to take that seriously then this would barely be a do-it-yourself workshop! I’ve had good fun making this centrifuge and one thing I’ve learned for sure is anything that spins very fast can cause serious damage! So for what it matters, please DO take extra precaution while trying to make this.<br />
<br />
I went about this using the basic principal of the centrifuge which is that anything that spins has a force that pushes away from it called the ‘centrifugal force’ so if I have a motor than spins then anything attached to it will be thrown away. <br />
<br />
<br />
<br />
'''You will need,'''<br />
<br />
1. '''Blender''' – One which has variable speeds would be better<br />
<br />
2. '''Jar''' – a small one, since we’ll need only the bottom part that attaches to the blender<br />
<br />
3. '''Strips of metal''' – make sure the edges are completely filed off to be safer<br />
<br />
4. '''Test tube holders''' – I used PVC pipes here with caps that fit very snugly <br />
<br />
5. '''Latches''' – Small in size to fasten the tubes to the metal strips<br />
<br />
<br />
'''Procedure'''<br />
As simple as it sounds but that’s all you need. Follow these few steps and you’ll have your centrifuge up and running in no time!<br />
<br />
'''1. '''<br />
Dismantle the upper portion of the jar so that we remain with only the unit that attaches to the blender<br />
<br />
'''2. '''<br />
Make a hole in the center of the two metal strips. This hole has to be exactly in the center so measuring it will be a good option. If it’s not in the center then it could cause imbalance during rotation. The size of the hole has to have the same diameter as the center spinning portion in the jar.<br />
<br />
'''3. '''<br />
Make holes on either side of the metal strips using the latches as a mark since they will be screwed into the metal strip.<br />
<br />
'''4. '''<br />
Make a hole in the test tube holder using the latch again since it will be screwed into it.<br />
<br />
'''Assembly-'''<br />
Fit the jar on to the blender and lock it. Screw one end of the latch to the test tube holder and the other onto the metal strip on all four sides. Place both the metal strips onto the blender and screw them in. Make sure to tighten all the screws as much as possible. To be on the safer side use the adhesive to fix the screws of the latch on the metal strip and the test tube holders. At high speeds, wear and tear is maximum, due to friction. So double check to ensure everything is completely secure.<br />
<br />
'''5. '''<br />
DONE! Now you’re ready to spin. <br />
<br />
<br />
<br />
'''Precaution and Safety Measures'''<br />
<br />
1. ALWAYS wear safety glasses. Seriously you never know what could go flying and get into your eyes. <br />
<br />
2. It would be good to keep a large board in front of you when testing the centrifuge for the first time or until you get comfortable.<br />
<br />
3. Test the centrifuge with a dummy test tube which is NOT glass to make sure all goes well.<br />
<br />
4. ALWAYS run the centrifuge slowly and at short intervals, and then later pick up speed.<br />
<br />
5. ALWAYS run your centrifuge BALANCED, i.e tubes on either sides at all times.<br />
<br />
6. Finally remember to have fun!</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_table_top_centrifuge&diff=2768DIY table top centrifuge2010-10-18T10:03:36Z<p>Farhad: </p>
<hr />
<div>The first thing I would like to say about this project is PLEASE DO NOT TRY THIS AT HOME! <br />
<br />
Well now, if you had to take that seriously then this would barely be a do-it-yourself workshop! I’ve had good fun making this centrifuge and one thing I’ve learned for sure is anything that spins very fast can cause serious damage! So for what it matters, please DO take extra precaution while trying to make this.<br />
<br />
I went about this using the basic principal of the centrifuge which is that anything that spins has a force that pushes away from it called the ‘centrifugal force’ so if I have a motor than spins then anything attached to it will be thrown away. <br />
<br />
<br />
<br />
'''You will need,'''<br />
<br />
<br />
1. '''Blender''' – One which has variable speeds would be better<br />
<br />
2. '''Jar''' – a small one, since we’ll need only the bottom part that attaches to the blender<br />
<br />
3. '''Strips of metal''' – make sure the edges are completely filed off to be safer<br />
<br />
4. '''Test tube holders''' – I used PVC pipes here with caps that fit very snugly <br />
<br />
5. '''Latches''' – Small in size to fasten the tubes to the metal strips<br />
<br />
<br />
<br />
As simple as it sounds but that’s all you need. Follow these few steps and you’ll have your centrifuge up and running in no time!<br />
<br />
<br />
'''1. '''<br />
Dismantle the upper portion of the jar so that we remain with only the unit that attaches to the blender<br />
<br />
'''2. '''<br />
Make a hole in the center of the two metal strips. This hole has to be exactly in the center so measuring it will be a good option. If it’s not in the center then it could cause imbalance during rotation. The size of the hole has to have the same diameter as the center spinning portion in the jar.<br />
<br />
'''3. '''<br />
Make holes on either side of the metal strips using the latches as a mark since they will be screwed into the metal strip.<br />
<br />
'''4. '''<br />
Make a hole in the test tube holder using the latch again since it will be screwed into it.<br />
<br />
'''Assembly-'''<br />
Fit the jar on to the blender and lock it. Screw one end of the latch to the test tube holder and the other onto the metal strip on all four sides. Place both the metal strips onto the blender and screw them in. Make sure to tighten all the screws as much as possible. To be on the safer side use the adhesive to fix the screws of the latch on the metal strip and the test tube holders. At high speeds, wear and tear is maximum, due to friction. So double check to ensure everything is completely secure.<br />
<br />
'''5. '''<br />
DONE! Now you’re ready to spin. <br />
<br />
<br />
<br />
'''Precaution and Safety Measures'''<br />
<br />
1. ALWAYS wear safety glasses. Seriously you never know what could go flying and get into your eyes. <br />
<br />
2. It would be good to keep a large board in front of you when testing the centrifuge for the first time or until you get comfortable.<br />
<br />
3. Test the centrifuge with a dummy test tube which is NOT glass to make sure all goes well.<br />
<br />
4. ALWAYS run the centrifuge slowly and at short intervals, and then later pick up speed.<br />
<br />
5. ALWAYS run your centrifuge BALANCED, i.e tubes on either sides at all times.<br />
<br />
6. Finally remember to have fun!</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_Sterlisation_Hood&diff=2767DIY Sterlisation Hood2010-10-18T09:58:35Z<p>Farhad: </p>
<hr />
<div>A sterilisation hood is a transparent box that maintains a sterile environment within it. Sterile hoods aim to keep the microbes out of the air, or in other words, to make a Sterile space. This enables specimens to be worked with/prepared in controlled conditions. It uses a heppa filter and a laminar air flow system to achieve this. There is also a UV light that is run for about half an hour before the experiment starts to kill any living bacteria in the hood. there is a small opeaning for the hands to go in and work. equipment in the hood is not taken out to avoid contamination. Trust me this sounds easy but you need alot of patience and material to do this.<br />
<br />
<br />
'''You will need, '''<br />
<br />
1) Acrylic sheets-4mm (6 pcs)....2 of dimension 57X61 (cms)-Sides <br />
<br />
................................................2 of dimension 57X80 (cms)-Top & Bottom<br />
<br />
................................................1 of dimension 62X80 (cms)-Back<br />
<br />
................................................1 of dimension 65X80 (cms)-Front<br />
<br />
<br />
<br />
<br />
2) Uv light(15 watts)......................[[File:IMG_7998.JPG]]<br />
<br />
<br />
3) Car heppa filter.........................[[File:IMG_7989.JPG]] <br />
<br />
<br />
<br />
4) Exhaust fan..............................[[File:Ex_fan.JPG]]<br />
<br />
<br />
5) Connector pipes(7cm diam)........[[File:DSC03925.JPG]]<br />
<br />
<br />
6) Wooden blocks.........................[[File:DSC03928.JPG]]<br />
<br />
<br />
<br />
7) L angles..................................[[File:DSC03929.JPG]]<br />
<br />
<br />
<br />
8) Nuts and bolts.........................[[File:DSC03923.JPG]]<br />
<br />
<br />
<br />
9) Uv filter (Car cooling film)...........[[File:Filter.JPG]]<br />
<br />
<br />
<br />
10) M-seal and silica gel(for acrylic sheets)<br />
<br />
<br />
<br />
<br />
'''How our hood works'''<br />
<br />
The hood is made of acrylic sheets. The back of the box has 2 holes at the top right and bottom left corners for the air flow. There is a UV light attached on the top face of the box. It is difficult to find a UV light, so you can use a black light bulb but it is not nearly as effective as the real thing. our air filter uses a simple car heppa filter and an industrial exhaust fan. the fan pulls the air through the heppa filter and blows it back into the box through PVC pipes. We put the fan close to the heppa filter and connected the fan horizontally so the pull is more powerful and effective. the front of the hood was held to the box with L angles so that it can slide up & down. The front is stopped at a height of 16cm. with wooden blocks for the hands to go in. you can also make 2 holes and connect them to gloves to reduce contamination. we also tried to make a robot arm that is put in the hood and does the work in the hood.<br />
<br />
<br />
<br />
'''PROCEDURE:'''<br />
<br />
<br />
'''Makig the laminar air flow''' [[File:DSC03712.JPG|150px|right|]]<br />
<br />
<br />
1. First make the box around the exhaust fan. (We used sun board but you can use something else).the fan needs about 4-5cm distance from the faces of the box. <br />
<br />
2. For the fan box take 4 pieces of sun board(fan width+8cm x fan length) and stick them to the sides of the fan in such a way that the fan is in the centre of the pieces. Pull out the wires from or of the pieces.<br />
<br />
3. Take 2 square pieces(fan length) and cut a hole(pipe diameter) in them. stick them on both open sides of the fan.Seal all sides with M-seal. [[File:DSC03721.JPG|170px|right|]] <br />
<br />
4. Take the acrylic sheet with dimension 62x80 cm which is the back side of the box and drill three holes in it. One for the air filter [[File:DSC03708.JPG|170px||]](top right), the second one for the pvc pipe(bottom left) and the third one(bottom right) for the wire of the Uv light to pass.<br />
While doing this '''make sure that the filter, the pipe and the wire exactly fit into the holes and there is no extra space.''' <br />
<br />
5. Stick the heppa filter into the top right hole, on the inside with araldite.<br />
<br />
6. Connect the heppa filter to the fan box and then to the inlet at the right bottom corner using the pipes and L shape connectors. Keep the fan close to the filter to increase power.keep the setup as close as possable to the acrylic sheet.<br />
<br />
7. Thus the air filter at the top right hole is connected to the inlet via the fan.<br />
<br />
8. Seal all the connections and joints with M-seal.<br />
<br />
<br />
'''Making the box''' [[File:DSC03715.JPG|170px|right|]]<br />
<br />
9. The two acrylic sheets of dimension 57X61 cm forms the sides of the box. Two sheets of dimensions 57X80 cm form the top and bottom of the box. One of dimension 61x80 cm is used for the back of the box and the one of dimension 65x80 cm for the front of the box.<br />
<br />
10. Stick the 2 sides of the hood to the base using super glue in such a way that the 2 sides are on the base and wait for it to dry. You need to use support for it to dry in a right angle.<br />
<br />
11. Once it is dry put a layer of silica gel on both sides without moving the support to set it firmly in place. <br />
<br />
12. The sides and the air flow system will take about 5 to 7 hours to set.<br />
<br />
13. Once everything is set and dry attach the back sheet with the air flow system to the sides and the base with super glue and then silica gel. Try to keep the back against a wall for support.<br />
<br />
14. Stick the top in the same way and wait for the gel to completely solidify.<br />
<br />
15. After ensuring that all the sides are stuck to the base properly , connect the L angles on the sides of the box and two on the base using nuts and bolts for good support for the front cover. [[File:DSC03787.JPG|170px|right|]]<br />
<br />
16. Drill holes on the top sheet and connect the UV tube to the box with nuts and bolts.<br />
<br />
17. Drill holes and make stoppers with the wooden blocks using nuts and bolts at about 16cms from the base.<br />
<br />
18. Finally put the front sheet by making it slide through the L angles.<br />
<br />
19. Cover the box with UV filter once it is built. Do not cover the front screen.<br />
<br />
20. Your hood is ready.<br />
<br />
<br />
<br />
'''PRECAUTIONS:'''<br />
<br />
1. Make sure that the holes drilled on the back side of the box are of perfect size so that there are less chances of contamination.<br />
<br />
2. Seal all the gaps in the box with m-seal.<br />
<br />
3. While drilling holes in the acrylic sheet make sure that there is proper support so that the sheet doesn’t bend or break.<br />
<br />
4. While sealing the pipes connected to the fan, first seal the pipes together with m-seal and then connect the whole thing.<br />
<br />
5. The Uv light is switched off while it is being connected.<br />
<br />
6. Do not run Uv light for a long time. Stay away when Uv light is running.<br />
<br />
7. Make sure the front shutter is held up securely with the stoppers before conducting the experiment.<br />
<br />
<br />
<br />
'''PROCESS PICTURES:'''<br />
<br />
[[File:DSC03699.JPG|180px|]]<br />
[[File:DSC03707.JPG]]<br />
[[File:DSC03708.JPG]]<br />
[[File:DSC03719.JPG|180px|]]<br />
[[File:DSC03717.JPG]]<br />
[[File:DSC03727.JPG]]<br />
[[File:DSC03728.JPG]]<br />
[[File:DSC03729.JPG]]<br />
[[File:DSC03731.JPG]]<br />
[[File:DSC03734.JPG]]<br />
[[File:DSC03736.JPG]]<br />
[[File:DSC03738.JPG]]<br />
[[File:DSC03739.JPG]]<br />
[[File:P1090748.JPG]]<br />
[[File:DSC03750.JPG]]<br />
[[File:DSC03787.JPG]]<br />
[[File:DSC03791.JPG]]<br />
[[File:DSC03796.JPG]]<br />
[[File:DSC03944.JPG]]<br />
[[File:DSC03945.JPG]]</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=GFP_Protocol_Jugaad&diff=2766GFP Protocol Jugaad2010-10-18T09:36:26Z<p>Farhad: /* Day 2: */</p>
<hr />
<div>== '''Materials''' ==<br />
<br />
<br />
'''The list below provides information about the materials supplied in the kit.'''<br />
<br />
The products should be stored as suggested. Use the kit within 6 months of arrival.<br />
<br />
<br />
'''Materials'''……………………... '''Quantity'''………….'''store at'''<br />
<br />
Ampicillin………………………..100 mg………….…..4°C<br />
<br />
Host ………………………………1 vial……..………...4°C<br />
<br />
Solution A………………………. 40 ml…………….….4°C<br />
<br />
Control DNA……………………...10 μl….…………..-20°C<br />
<br />
T4 DNA Ligase………………….…5 μl………………-20°C<br />
<br />
10X Ligase Assay Buffer ….……10 μl……….……..-20°C<br />
<br />
Insert………………………………20 μl………..…....-20°C<br />
<br />
Vector DNA………………………10 μl ………….….-20°C<br />
<br />
LB Broth……………………….....15 g ……………..…RT<br />
<br />
Agar………………………………...5 g……..………... RT<br />
<br />
1.5 ml vials……………………….25 Nos……….….... RT<br />
<br />
<br />
'''Equipment :'''<br />
<br />
-Centrifuge (preferably refrigerated)( [[DIY handheld centrifuge]] ).<br />
<br />
-UV transilluminator (312 nm).<br />
<br />
-Spectrophotometer.<br />
<br />
<br />
'''Glassware :'''<br />
<br />
-Capped centrifuge tubes.<br />
<br />
-Conical flask.<br />
<br />
-Petri plates.<br />
<br />
-Test tubes.<br />
<br />
<br />
'''Reagent :'''<br />
<br />
-Distilled water.<br />
<br />
<br />
'''Other Requirements:''' <br />
<br />
-Crushed ice.<br />
<br />
-Cuvette (of 1 cm pathlength).<br />
<br />
-Micropipette, Tips.<br />
<br />
-Thermometer.<br />
<br />
-Water bath. ( [[DIY Water Bath]] )<br />
<br />
-Incubator.([[DIY Incubator]] )<br />
<br />
-Sterilization Hood. ( [[DIY Sterlisation Hood]] )<br />
<br />
<br />
<br />
<br />
<br />
== '''Procedure:''' ==<br />
<br />
<br />
<br />
=== Day 1: ===<br />
<br />
'''Revival of Host'''<br />
<br />
'''1.''' Break open the lyophilized vial, add 0.1 ml of LB<br />
broth.<br />
<br />
[[File:MG_6822.JPG]] [[File:MG_6833.JPG]]<br />
<br />
'''2.''' Streak a loopful of the suspension onto LB plate & LB culture tubes.<br />
(in duplicates).<br />
<br />
[[File:MG_6792.JPG]] [[File:MG_6799.JPG]] <br />
<br />
[[File:MG_6808.JPG]] [[File:MG_6837.JPG]]<br />
<br />
[[File:MG_6841.JPG]] [[File:MG_6842.JPG]] <br />
<br />
[[File:MG_6859.JPG]][[File:MG_6843.JPG]] <br />
<br />
[[File:MG_6881.JPG]]<br />
<br />
<br />
<br />
'''3.''' Incubate the plates at 37°C, overnight.<br />
<br />
[[File:MG_6887.JPG]] [[File:MG_6898.JPG]] <br />
<br />
[[File:MG_6899.JPG]] [[File:MG_6901.JPG]]<br />
<br />
<br />
<br />
<br />
<br />
'''Ligation of Vector to Insert'''<br />
<br />
'''4.''' Thaw the ligase assay buffer, vector and insert DNA.<br />
<br />
'''Note:''' Thaw the ligase assay buffer vial on ice,<br />
store at -20°C immediately after use.<br />
<br />
'''5.''' Set up ligation reaction as follows:<br />
<br />
-Water : 11 μl<br />
<br />
-Vector DNA : 2 μl<br />
<br />
-Insert DNA : 4 μl<br />
<br />
-Ligase assay buffer : 2 μl<br />
<br />
-T4 DNA ligase : 1 μl<br />
<br />
Mix the contents by tapping gently and incubate at<br />
16°C waterbath, overnight.<br />
<br />
'''Note:''' Set up five ligation reactions simultaneously.<br />
<br />
[[File:MG_6927.JPG]] [[File:MG_6937.JPG]]<br />
<br />
[[File:MG_6955.JPG]]<br />
<br />
<br />
<br />
<br />
<br />
=== Day 2: ===<br />
<br />
<br />
'''Preparation of Competent Cells'''<br />
<br />
'''6.''' Incubate the culture tubes at 37°C. Grow until OD A600<br />
reaches 0.3, this takes about 2-3 hours.<br />
<br />
'''7.''' Chill the culture tubes on ice for 10-20 minutes.<br />
<br />
'''8.''' Transfer the culture aseptically into sterile vials. (5 vials with 0.5ml each)<br />
<br />
'''9.''' Spin down at 6000 rpm for 8 minutes,<br />
preferably in a refrigerated centrifuge at 4°C or spin at<br />
Room temperature (RT).<br />
<br />
'''10.''' Discard the supernatant.<br />
<br />
'''11.''' Resuspend the cell pellet very gently in small volume<br />
of ice-cold solution A (approximately 2 ml), using a<br />
pre-chilled pipette. Care must be taken not to remove<br />
the tubes from ice during resuspension. Add remaining<br />
33 ml of solution A, resuspend gently.<br />
<br />
'''12.''' Keep the vials on ice for 5 minutes.<br />
Centrifuge at 8000 rpm for 5 minutes at 4°C or spin at<br />
RT.<br />
<br />
'''13.''' Discard the supernatant and chill the tube on ice.<br />
Resuspend the pellet in 3 ml of ice-cold solution A.<br />
<br />
'''Note:''' Resuspension is to be done gently as cells<br />
are very fragile at this stage.<br />
<br />
[[File:MG_7020.JPG]] [[File:MG_7028.JPG]]<br />
<br />
[[File:DSC02293.JPG]] [[File:MG_7052.JPG]]<br />
<br />
[[File:MG_7075.JPG]] [[File:MG_7083.JPG]]<br />
<br />
[[File:DSC02295.JPG]] [[File:MG_7052.JPG]]<br />
<br />
[[File:MG_7174.JPG]]<br />
<br />
<br />
<br />
'''14.''' Heat inactivate the ligated samples at 65°C for<br />
10 minutes. Spin at 5000 rpm for 2 minutes and keep<br />
the vials on ice.<br />
<br />
'''15.''' Aliquot 2 μl (10 ng) of control DNA each into 5 ligation vials<br />
<br />
[[File:MG_7176.JPG]] [[File:MG_7177.JPG]]<br />
<br />
[[File:DSC02296.JPG]] [[File:MG_7174.JPG]]<br />
<br />
[[File:MG_7163.JPG]] [[File:MG_7028.JPG]]<br />
<br />
<br />
<br />
<br />
<br />
'''Transformation:'''<br />
<br />
<br />
'''16.''' Take a 2 vials of ligated sample and control DNA and 1 vial of only control DNA( positive control).<br />
To this add 200 μl each of competent cells. Tap the<br />
vials gently and incubate on ice for 20 minutes.<br />
<br />
<br />
'''17.''' Label the remaining 200 μl of competent cells as non transformed (negative control)<br />
cells, place on ice till the plating step (step<br />
23).<br />
<br />
'''18.''' Tap all the vials gently and incubate on ice for<br />
20 minutes.<br />
<br />
'''19.''' Heat shock the cells by placing the vial(s) in 42°C water<br />
bath for 2 minutes, then return the vials to ice and chill<br />
for 5 minutes.<br />
<br />
'''20.''' Add 0.5 ml of LB broth aseptically to the vial(s) and<br />
incubate at 37°C (shaker) for an hour. This is to allow<br />
bacteria to recover and express the protein.<br />
<br />
'''Note:''' While the heat shock treatment is going on, prepare the LB-Amp agar(200 μl in 200 ml of LB agar.)<br />
<br />
[[File:MG_7064.JPG]] [[File:MG_7133.JPG]]<br />
<br />
[[File:MG_7142.JPG]] [[File:MG_7143.JPG]]<br />
<br />
[[File:MG_7174.JPG]] [[File:MG_7175.JPG]]<br />
<br />
[[File:MG_7177.JPG]] [[File:MG_7174.JPG]]<br />
<br />
[[File:MG_7185.JPG]] [[File:MG_7191.JPG]]<br />
<br />
[[File:MG_7190.JPG]] [[File:MG_7186.JPG]]<br />
<br />
[[File:DSC02301.JPG]]<br />
<br />
<br />
<br />
'''21.''' liquify the already made LB-amp agar and pour about 20 to 25 ml of i in each plate.<br />
<br />
'''Note:''' Wait for agar to solidify again.<br />
<br />
'''22.''' Pipette 200 μl each from the vials transformed with the<br />
ligated mix onto LB-Amp plates and spread thoroughly<br />
using spreader/pipette.<br />
<br />
'''23.''' Pipette 200 μl of LB onto a LB -Amp plate and spread<br />
20 ìl of the cells transformed with control DNA. Label<br />
this as positive control plate.<br />
<br />
'''24.''' Plate 200 μl of non-transformed cells onto another<br />
LB-Amp plate to check for contamination. Label this<br />
as non-transformed (negative control) plate.<br />
<br />
'''25.''' Keep one plate with only LB-Amp Agar and nothing else. Name this as double negative control.<br />
<br />
'''26.''' Incubate the plates at 37°C, overnight.<br />
<br />
<br />
[[File:MG_7204.JPG]] [[File:MG_7206.JPG]]<br />
<br />
[[File:MG_7213.JPG]] [[File:MG_7221.JPG]]<br />
<br />
[[File:MG_7225.JPG]] [[File:3.JPG]]<br />
<br />
[[File:4.JPG]] [[File:5.JPG]]<br />
<br />
[[File:6.JPG]] [[File:7.JPG]]<br />
<br />
=== Day 3: ===<br />
<br />
<br />
'''Moment of Truth'''<br />
<br />
'''27.''' Observe the plates under UV-light (312 nm).<br />
<br />
'''Note:''' If observed add 254 nm of less intensity of glow<br />
could vary.<br />
<br />
'''Note:''' The 3 controls:<br />
<br />
'''Positive control:''' (Competent cells + Control DNA.)<br />
<br />
-If there are no colonies it means there is something wrong with the cells.<br />
<br />
'''Negative control:''' (only Competent cells.)<br />
<br />
-If there are no colonies it means the cells are contaminated.<br />
<br />
'''Double Negative control:''' (Empty LB-Amp plate.)<br />
<br />
-If there is growth then there is external contamination. <br />
<br />
<br />
[[File:MG_7281.JPG]] [[File:MG_7269.JPG]]<br />
<br />
[[File:MG_7282.JPG]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== '''Precautions:''' ==<br />
<br />
1. Work in a closed room with all the equipment in it. Don't run around for things.<br />
<br />
2. Keep the room clean. No eatables, foot wear allowed.<br />
<br />
3. Run UV light for about half an hour before starting experiment.<br />
<br />
'''Note:''' do not stand close to the UV when it is on. use a uv filter to cover all sides of the box and if posible cover the incubator and walls also.<br />
<br />
4. Clean hands with alcohol before starting anything. <br />
<br />
5. Before using glassware autoclave them (wrap in paper and boil in cooker for 3 wistles.)<br />
<br />
6. All work is done in the hood to avoid external contamination.<br />
<br />
7. Sterilize everything in alcahol and flame before use<br />
<br />
8. Keep someone beside you to give and take things from you while working in the hood. Don't keep moving your hands in and out of the hood.<br />
<br />
9. Keep hood closed when not in use<br />
<br />
10. When using the water bath run it till it reaches the required temp. and then use it.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=GFP_Protocol_Jugaad&diff=2765GFP Protocol Jugaad2010-10-18T09:33:16Z<p>Farhad: /* Day 2: */</p>
<hr />
<div>== '''Materials''' ==<br />
<br />
<br />
'''The list below provides information about the materials supplied in the kit.'''<br />
<br />
The products should be stored as suggested. Use the kit within 6 months of arrival.<br />
<br />
<br />
'''Materials'''……………………... '''Quantity'''………….'''store at'''<br />
<br />
Ampicillin………………………..100 mg………….…..4°C<br />
<br />
Host ………………………………1 vial……..………...4°C<br />
<br />
Solution A………………………. 40 ml…………….….4°C<br />
<br />
Control DNA……………………...10 μl….…………..-20°C<br />
<br />
T4 DNA Ligase………………….…5 μl………………-20°C<br />
<br />
10X Ligase Assay Buffer ….……10 μl……….……..-20°C<br />
<br />
Insert………………………………20 μl………..…....-20°C<br />
<br />
Vector DNA………………………10 μl ………….….-20°C<br />
<br />
LB Broth……………………….....15 g ……………..…RT<br />
<br />
Agar………………………………...5 g……..………... RT<br />
<br />
1.5 ml vials……………………….25 Nos……….….... RT<br />
<br />
<br />
'''Equipment :'''<br />
<br />
-Centrifuge (preferably refrigerated)( [[DIY handheld centrifuge]] ).<br />
<br />
-UV transilluminator (312 nm).<br />
<br />
-Spectrophotometer.<br />
<br />
<br />
'''Glassware :'''<br />
<br />
-Capped centrifuge tubes.<br />
<br />
-Conical flask.<br />
<br />
-Petri plates.<br />
<br />
-Test tubes.<br />
<br />
<br />
'''Reagent :'''<br />
<br />
-Distilled water.<br />
<br />
<br />
'''Other Requirements:''' <br />
<br />
-Crushed ice.<br />
<br />
-Cuvette (of 1 cm pathlength).<br />
<br />
-Micropipette, Tips.<br />
<br />
-Thermometer.<br />
<br />
-Water bath. ( [[DIY Water Bath]] )<br />
<br />
-Incubator.([[DIY Incubator]] )<br />
<br />
-Sterilization Hood. ( [[DIY Sterlisation Hood]] )<br />
<br />
<br />
<br />
<br />
<br />
== '''Procedure:''' ==<br />
<br />
<br />
<br />
=== Day 1: ===<br />
<br />
'''Revival of Host'''<br />
<br />
'''1.''' Break open the lyophilized vial, add 0.1 ml of LB<br />
broth.<br />
<br />
[[File:MG_6822.JPG]] [[File:MG_6833.JPG]]<br />
<br />
'''2.''' Streak a loopful of the suspension onto LB plate & LB culture tubes.<br />
(in duplicates).<br />
<br />
[[File:MG_6792.JPG]] [[File:MG_6799.JPG]] <br />
<br />
[[File:MG_6808.JPG]] [[File:MG_6837.JPG]]<br />
<br />
[[File:MG_6841.JPG]] [[File:MG_6842.JPG]] <br />
<br />
[[File:MG_6859.JPG]][[File:MG_6843.JPG]] <br />
<br />
[[File:MG_6881.JPG]]<br />
<br />
<br />
<br />
'''3.''' Incubate the plates at 37°C, overnight.<br />
<br />
[[File:MG_6887.JPG]] [[File:MG_6898.JPG]] <br />
<br />
[[File:MG_6899.JPG]] [[File:MG_6901.JPG]]<br />
<br />
<br />
<br />
<br />
<br />
'''Ligation of Vector to Insert'''<br />
<br />
'''4.''' Thaw the ligase assay buffer, vector and insert DNA.<br />
<br />
'''Note:''' Thaw the ligase assay buffer vial on ice,<br />
store at -20°C immediately after use.<br />
<br />
'''5.''' Set up ligation reaction as follows:<br />
<br />
-Water : 11 μl<br />
<br />
-Vector DNA : 2 μl<br />
<br />
-Insert DNA : 4 μl<br />
<br />
-Ligase assay buffer : 2 μl<br />
<br />
-T4 DNA ligase : 1 μl<br />
<br />
Mix the contents by tapping gently and incubate at<br />
16°C waterbath, overnight.<br />
<br />
'''Note:''' Set up five ligation reactions simultaneously.<br />
<br />
[[File:MG_6927.JPG]] [[File:MG_6937.JPG]]<br />
<br />
[[File:MG_6955.JPG]]<br />
<br />
<br />
<br />
<br />
<br />
=== Day 2: ===<br />
<br />
<br />
'''Preparation of Competent Cells'''<br />
<br />
'''6.''' Incubate the culture tubes at 37°C. Grow until OD A600<br />
reaches 0.3, this takes about 2-3 hours.<br />
<br />
'''7.''' Chill the culture tubes on ice for 10-20 minutes.<br />
<br />
'''8.''' Transfer the culture aseptically into sterile vials. (5 vials with 0.5ml each)<br />
<br />
'''9.''' Spin down at 6000 rpm for 8 minutes,<br />
preferably in a refrigerated centrifuge at 4°C or spin at<br />
Room temperature (RT).<br />
<br />
'''10.''' Discard the supernatant.<br />
<br />
'''11.''' Resuspend the cell pellet very gently in small volume<br />
of ice-cold solution A (approximately 2 ml), using a<br />
pre-chilled pipette. Care must be taken not to remove<br />
the tubes from ice during resuspension. Add remaining<br />
33 ml of solution A, resuspend gently.<br />
<br />
'''12.''' Keep the vials on ice for 5 minutes.<br />
Centrifuge at 8000 rpm for 5 minutes at 4°C or spin at<br />
RT.<br />
<br />
'''13.''' Discard the supernatant and chill the tube on ice.<br />
Resuspend the pellet in 3 ml of ice-cold solution A.<br />
<br />
'''Note:''' Resuspension is to be done gently as cells<br />
are very fragile at this stage.<br />
<br />
[[File:MG_7020.JPG]] [[File:MG_7028.JPG]]<br />
<br />
[[File:DSC02293.JPG]] [[File:MG_7052.JPG]]<br />
<br />
[[File:MG_7075.JPG]] [[File:MG_7083.JPG]]<br />
<br />
[[File:DSC02295.JPG]] [[File:MG_7052.JPG]]<br />
<br />
[[File:MG_7174.JPG]]<br />
<br />
<br />
<br />
'''14.''' Heat inactivate the ligated samples at 65°C for<br />
10 minutes. Spin at 5000 rpm for 2 minutes and keep<br />
the vials on ice.<br />
<br />
'''15.''' Aliquot 2 μl (10 ng) of control DNA each into 5 ligation vials<br />
<br />
[[File:MG_7176.JPG]] [[File:MG_7177.JPG]]<br />
<br />
[[File:DSC02296.JPG]] [[File:MG_7174.JPG]]<br />
<br />
[[File:MG_7163.JPG]] [[File:MG_7028.JPG]]<br />
<br />
<br />
<br />
<br />
<br />
'''Transformation:'''<br />
<br />
<br />
'''16.''' Take a 2 vials of ligated sample and control DNA and 1 vial of only control DNA( positive control).<br />
To this add 200 μl each of competent cells. Tap the<br />
vials gently and incubate on ice for 20 minutes.<br />
<br />
<br />
'''17.''' Label the remaining 200 μl of competent cells as non transformed (negative control)<br />
cells, place on ice till the plating step (step<br />
23).<br />
<br />
'''18.''' Tap all the vials gently and incubate on ice for<br />
20 minutes.<br />
<br />
'''19.''' Heat shock the cells by placing the vial(s) in 42°C water<br />
bath for 2 minutes, then return the vials to ice and chill<br />
for 5 minutes.<br />
<br />
'''20.''' Add 0.5 ml of LB broth aseptically to the vial(s) and<br />
incubate at 37°C (shaker) for an hour. This is to allow<br />
bacteria to recover and express the protein.<br />
<br />
'''Note:''' While the heat shock treatment is going on, prepare the LB-Amp agar(200 μl in 200 ml of LB agar.)<br />
<br />
[[File:MG_7064.JPG]] [[File:MG_7133.JPG]]<br />
<br />
[[File:MG_7142.JPG]] [[File:MG_7143.JPG]]<br />
<br />
[[File:MG_7174.JPG]] [[File:MG_7175.JPG]]<br />
<br />
[[File:MG_7177.JPG]] [[File:MG_7174.JPG]]<br />
<br />
[[File:MG_7185.JPG]] [[File:MG_7191.JPG]]<br />
<br />
[[File:MG_7190.JPG]] [[File:MG_7186.JPG]]<br />
<br />
[[File:DSC02301.JPG]]<br />
<br />
<br />
<br />
'''21.''' liquify the already made LB-amp agar and pour about 20 to 25 ml of i in each plate.<br />
<br />
'''Note:''' Wait for agar to solidify again.<br />
<br />
'''22.''' Pipette 200 μl each from the vials transformed with the<br />
ligated mix onto LB-Amp plates and spread thoroughly<br />
using spreader/pipette.<br />
<br />
'''23.''' Pipette 200 μl of LB onto a LB -Amp plate and spread<br />
20 ìl of the cells transformed with control DNA. Label<br />
this as positive control plate.<br />
<br />
'''24.''' Plate 200 μl of non-transformed cells onto another<br />
LB-Amp plate to check for contamination. Label this<br />
as non-transformed (negative control) plate.<br />
<br />
'''25.''' Keep one plate with only LB-Amp Agar and nothing else. Name this as double negative control.<br />
<br />
'''26.''' Incubate the plates at 37°C, overnight.<br />
<br />
<br />
[[File:MG_7204.JPG]] [[File:MG_7206.JPG]]<br />
<br />
[[File:MG_7213.JPG]] [[File:MG_7221.JPG]]<br />
<br />
[[File:MG_7225.JPG]] [[File:3.JPG]]<br />
<br />
[[File:4.JPG]] [[File:5.JPG]]<br />
<br />
[[File:6.JPG]] [[File:7.JPG]]<br />
<br />
=== Day 3: ===<br />
<br />
<br />
'''Moment of Truth'''<br />
<br />
'''27.''' Observe the plates under UV-light (312 nm).<br />
<br />
'''Note:''' If observed add 254 nm of less intensity of glow<br />
could vary.<br />
<br />
'''Note:''' The 3 controls:<br />
<br />
'''Positive control:''' (Competent cells + Control DNA.)<br />
<br />
-If there are no colonies it means there is something wrong with the cells.<br />
<br />
'''Negative control:''' (only Competent cells.)<br />
<br />
-If there are no colonies it means the cells are contaminated.<br />
<br />
'''Double Negative control:''' (Empty LB-Amp plate.)<br />
<br />
-If there is growth then there is external contamination. <br />
<br />
<br />
[[File:MG_7281.JPG]] [[File:MG_7269.JPG]]<br />
<br />
[[File:MG_7282.JPG]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== '''Precautions:''' ==<br />
<br />
1. Work in a closed room with all the equipment in it. Don't run around for things.<br />
<br />
2. Keep the room clean. No eatables, foot wear allowed.<br />
<br />
3. Run UV light for about half an hour before starting experiment.<br />
<br />
'''Note:''' do not stand close to the UV when it is on. use a uv filter to cover all sides of the box and if posible cover the incubator and walls also.<br />
<br />
4. Clean hands with alcohol before starting anything. <br />
<br />
5. Before using glassware autoclave them (wrap in paper and boil in cooker for 3 wistles.)<br />
<br />
6. All work is done in the hood to avoid external contamination.<br />
<br />
7. Sterilize everything in alcahol and flame before use<br />
<br />
8. Keep someone beside you to give and take things from you while working in the hood. Don't keep moving your hands in and out of the hood.<br />
<br />
9. Keep hood closed when not in use<br />
<br />
10. When using the water bath run it till it reaches the required temp. and then use it.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=GFP_Protocol_Jugaad&diff=2764GFP Protocol Jugaad2010-10-18T09:19:15Z<p>Farhad: /* Day 2: */</p>
<hr />
<div>== '''Materials''' ==<br />
<br />
<br />
'''The list below provides information about the materials supplied in the kit.'''<br />
<br />
The products should be stored as suggested. Use the kit within 6 months of arrival.<br />
<br />
<br />
'''Materials'''……………………... '''Quantity'''………….'''store at'''<br />
<br />
Ampicillin………………………..100 mg………….…..4°C<br />
<br />
Host ………………………………1 vial……..………...4°C<br />
<br />
Solution A………………………. 40 ml…………….….4°C<br />
<br />
Control DNA……………………...10 μl….…………..-20°C<br />
<br />
T4 DNA Ligase………………….…5 μl………………-20°C<br />
<br />
10X Ligase Assay Buffer ….……10 μl……….……..-20°C<br />
<br />
Insert………………………………20 μl………..…....-20°C<br />
<br />
Vector DNA………………………10 μl ………….….-20°C<br />
<br />
LB Broth……………………….....15 g ……………..…RT<br />
<br />
Agar………………………………...5 g……..………... RT<br />
<br />
1.5 ml vials……………………….25 Nos……….….... RT<br />
<br />
<br />
'''Equipment :'''<br />
<br />
-Centrifuge (preferably refrigerated)( [[DIY handheld centrifuge]] ).<br />
<br />
-UV transilluminator (312 nm).<br />
<br />
-Spectrophotometer.<br />
<br />
<br />
'''Glassware :'''<br />
<br />
-Capped centrifuge tubes.<br />
<br />
-Conical flask.<br />
<br />
-Petri plates.<br />
<br />
-Test tubes.<br />
<br />
<br />
'''Reagent :'''<br />
<br />
-Distilled water.<br />
<br />
<br />
'''Other Requirements:''' <br />
<br />
-Crushed ice.<br />
<br />
-Cuvette (of 1 cm pathlength).<br />
<br />
-Micropipette, Tips.<br />
<br />
-Thermometer.<br />
<br />
-Water bath. ( [[DIY Water Bath]] )<br />
<br />
-Incubator.([[DIY Incubator]] )<br />
<br />
-Sterilization Hood. ( [[DIY Sterlisation Hood]] )<br />
<br />
<br />
<br />
<br />
<br />
== '''Procedure:''' ==<br />
<br />
<br />
<br />
=== Day 1: ===<br />
<br />
'''Revival of Host'''<br />
<br />
'''1.''' Break open the lyophilized vial, add 0.1 ml of LB<br />
broth.<br />
<br />
[[File:MG_6822.JPG]] [[File:MG_6833.JPG]]<br />
<br />
'''2.''' Streak a loopful of the suspension onto LB plate & LB culture tubes.<br />
(in duplicates).<br />
<br />
[[File:MG_6792.JPG]] [[File:MG_6799.JPG]] <br />
<br />
[[File:MG_6808.JPG]] [[File:MG_6837.JPG]]<br />
<br />
[[File:MG_6841.JPG]] [[File:MG_6842.JPG]] <br />
<br />
[[File:MG_6859.JPG]][[File:MG_6843.JPG]] <br />
<br />
[[File:MG_6881.JPG]]<br />
<br />
<br />
<br />
'''3.''' Incubate the plates at 37°C, overnight.<br />
<br />
[[File:MG_6887.JPG]] [[File:MG_6898.JPG]] <br />
<br />
[[File:MG_6899.JPG]] [[File:MG_6901.JPG]]<br />
<br />
<br />
<br />
<br />
<br />
'''Ligation of Vector to Insert'''<br />
<br />
'''4.''' Thaw the ligase assay buffer, vector and insert DNA.<br />
<br />
'''Note:''' Thaw the ligase assay buffer vial on ice,<br />
store at -20°C immediately after use.<br />
<br />
'''5.''' Set up ligation reaction as follows:<br />
<br />
-Water : 11 μl<br />
<br />
-Vector DNA : 2 μl<br />
<br />
-Insert DNA : 4 μl<br />
<br />
-Ligase assay buffer : 2 μl<br />
<br />
-T4 DNA ligase : 1 μl<br />
<br />
Mix the contents by tapping gently and incubate at<br />
16°C waterbath, overnight.<br />
<br />
'''Note:''' Set up five ligation reactions simultaneously.<br />
<br />
[[File:MG_6927.JPG]] [[File:MG_6937.JPG]]<br />
<br />
[[File:MG_6955.JPG]]<br />
<br />
<br />
<br />
<br />
<br />
=== Day 2: ===<br />
<br />
<br />
'''Preparation of Competent Cells'''<br />
<br />
'''6.''' Incubate the culture tubes at 37°C. Grow until OD A600<br />
reaches 0.3, this takes about 2-3 hours.<br />
<br />
'''7.''' Chill the culture tubes on ice for 10-20 minutes.<br />
<br />
'''8.''' Transfer the culture aseptically into sterile vials. (5 vials with 0.5ml each)<br />
<br />
'''9.''' Spin down at 6000 rpm for 8 minutes,<br />
preferably in a refrigerated centrifuge at 4°C or spin at<br />
Room temperature (RT).<br />
<br />
'''10.''' Discard the supernatant.<br />
<br />
'''11.''' Resuspend the cell pellet very gently in small volume<br />
of ice-cold solution A (approximately 2 ml), using a<br />
pre-chilled pipette. Care must be taken not to remove<br />
the tubes from ice during resuspension. Add remaining<br />
33 ml of solution A, resuspend gently.<br />
<br />
'''12.''' Keep the vials on ice for 5 minutes.<br />
Centrifuge at 8000 rpm for 5 minutes at 4°C or spin at<br />
RT.<br />
<br />
'''13.''' Discard the supernatant and chill the tube on ice.<br />
Resuspend the pellet in 3 ml of ice-cold solution A.<br />
<br />
'''Note:''' Resuspension is to be done gently as cells<br />
are very fragile at this stage.<br />
<br />
[[File:MG_7020.JPG]] [[File:MG_7028.JPG]]<br />
<br />
[[File:DSC02293.JPG]] [[File:MG_7052.JPG]]<br />
<br />
[[File:MG_7075.JPG]] [[File:MG_7083.JPG]]<br />
<br />
[[File:DSC02295.JPG]] [[File:MG_7052.JPG]]<br />
<br />
[[File:MG_7174.JPG]]<br />
<br />
<br />
<br />
'''14.''' Heat inactivate the ligated samples at 65°C for<br />
10 minutes. Spin at 5000 rpm for 2 minutes and keep<br />
the vials on ice.<br />
<br />
'''15.''' Aliquot 2 μl (10 ng) of control DNA each into 5 ligation vials<br />
<br />
[[File:MG_7176.JPG]] [[File:MG_7177.JPG]]<br />
<br />
[[File:DSC02296.JPG]] [[File:MG_7174.JPG|300px]]<br />
<br />
[[File:MG_7163.JPG]] [[File:MG_7028.JPG]]<br />
<br />
<br />
<br />
<br />
<br />
'''Transformation:'''<br />
<br />
<br />
'''16.''' Take a 2 vials of ligated sample and control DNA and 1 vial of only control DNA( positive control).<br />
To this add 200 μl each of competent cells. Tap the<br />
vials gently and incubate on ice for 20 minutes.<br />
<br />
<br />
'''17.''' Label the remaining 200 μl of competent cells as non transformed (negative control)<br />
cells, place on ice till the plating step (step<br />
23).<br />
<br />
'''18.''' Tap all the vials gently and incubate on ice for<br />
20 minutes.<br />
<br />
'''19.''' Heat shock the cells by placing the vial(s) in 42°C water<br />
bath for 2 minutes, then return the vials to ice and chill<br />
for 5 minutes.<br />
<br />
'''20.''' Add 0.5 ml of LB broth aseptically to the vial(s) and<br />
incubate at 37°C (shaker) for an hour. This is to allow<br />
bacteria to recover and express the protein.<br />
<br />
'''Note:''' While the heat shock treatment is going on, prepare the LB-Amp agar(200 μl in 200 ml of LB agar.)<br />
<br />
[[File:MG_7064.JPG]] [[File:MG_7133.JPG]]<br />
<br />
[[File:MG_7142.JPG]] [[File:MG_7143.JPG]]<br />
<br />
[[File:MG_7174.JPG]] [[File:MG_7175.JPG]]<br />
<br />
[[File:MG_7177.JPG]] [[File:MG_7174.JPG]]<br />
<br />
[[File:MG_7185.JPG]] [[File:MG_7191.JPG]]<br />
<br />
[[File:MG_7190.JPG]] [[File:MG_7186.JPG]]<br />
<br />
[[File:DSC02301.JPG]]<br />
<br />
<br />
<br />
'''21.''' liquify the already made LB-amp agar and pour about 20 to 25 ml of i in each plate.<br />
<br />
'''Note:''' Wait for agar to solidify again.<br />
<br />
'''22.''' Pipette 200 μl each from the vials transformed with the<br />
ligated mix onto LB-Amp plates and spread thoroughly<br />
using spreader/pipette.<br />
<br />
'''23.''' Pipette 200 μl of LB onto a LB -Amp plate and spread<br />
20 ìl of the cells transformed with control DNA. Label<br />
this as positive control plate.<br />
<br />
'''24.''' Plate 200 μl of non-transformed cells onto another<br />
LB-Amp plate to check for contamination. Label this<br />
as non-transformed (negative control) plate.<br />
<br />
'''25.''' Keep one plate with only LB-Amp Agar and nothing else. Name this as double negative control.<br />
<br />
'''26.''' Incubate the plates at 37°C, overnight.<br />
<br />
<br />
[[File:MG_7204.JPG]] [[File:MG_7206.JPG]]<br />
<br />
[[File:MG_7213.JPG]] [[File:MG_7221.JPG]]<br />
<br />
[[File:MG_7225.JPG]] [[File:3.JPG]]<br />
<br />
[[File:4.JPG]] [[File:5.JPG]]<br />
<br />
[[File:6.JPG]] [[File:7.JPG]]<br />
<br />
=== Day 3: ===<br />
<br />
<br />
'''Moment of Truth'''<br />
<br />
'''27.''' Observe the plates under UV-light (312 nm).<br />
<br />
'''Note:''' If observed add 254 nm of less intensity of glow<br />
could vary.<br />
<br />
'''Note:''' The 3 controls:<br />
<br />
'''Positive control:''' (Competent cells + Control DNA.)<br />
<br />
-If there are no colonies it means there is something wrong with the cells.<br />
<br />
'''Negative control:''' (only Competent cells.)<br />
<br />
-If there are no colonies it means the cells are contaminated.<br />
<br />
'''Double Negative control:''' (Empty LB-Amp plate.)<br />
<br />
-If there is growth then there is external contamination. <br />
<br />
<br />
[[File:MG_7281.JPG]] [[File:MG_7269.JPG]]<br />
<br />
[[File:MG_7282.JPG]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
== '''Precautions:''' ==<br />
<br />
1. Work in a closed room with all the equipment in it. Don't run around for things.<br />
<br />
2. Keep the room clean. No eatables, foot wear allowed.<br />
<br />
3. Run UV light for about half an hour before starting experiment.<br />
<br />
'''Note:''' do not stand close to the UV when it is on. use a uv filter to cover all sides of the box and if posible cover the incubator and walls also.<br />
<br />
4. Clean hands with alcohol before starting anything. <br />
<br />
5. Before using glassware autoclave them (wrap in paper and boil in cooker for 3 wistles.)<br />
<br />
6. All work is done in the hood to avoid external contamination.<br />
<br />
7. Sterilize everything in alcahol and flame before use<br />
<br />
8. Keep someone beside you to give and take things from you while working in the hood. Don't keep moving your hands in and out of the hood.<br />
<br />
9. Keep hood closed when not in use<br />
<br />
10. When using the water bath run it till it reaches the required temp. and then use it.</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_Incubator&diff=2763DIY Incubator2010-10-18T09:09:06Z<p>Farhad: </p>
<hr />
<div>An incubator is an isolated storage place that is used for cultivating bacteria. The incubator maintains optimal temperature of the atmosphere inside it. Incubators are essential for a lot of experimental work in cell biology, microbiology and molecular biology and are used to culture both bacterial as well as eukaryotic cells. The simplest incubators are insulated boxes with an adjustable heater, typically going up to 60 to 65 °C (140 to 150 °F), though some can go slightly higher (generally to no more than 100 °C). The most commonly used temperature both for bacteria such as the frequently used E. Coli cells is approximately 37 °C, as these organisms grow well under such conditions. They also need a circulation system for equal distribution of heat in the box.<br />
<br />
We made a simple incubator that maintains a temperature of 37 °C using materials that are easily available. This incubator will be used cultivate E.Coli.<br />
<br />
<br />
<br />
<br />
'''You will need,'''<br />
<br />
<br />
1. Styrofoam box.(doesn't conduct heat)....................[[File:Box.JPG]]<br />
<br />
2. heating element.(bulb,heating pad,etc.).................[[File:Bulbs.JPG]]<br />
<br />
3. cabinet fans.(depending on size of box).................[[File:Fan.JPG]]<br />
<br />
4. thermometer.(between 20 °C to 100 °C).................[[File:Thermometer.JPG]]<br />
<br />
5. 12V adaptor.(for powering fans)............................[[File:Adapter.JPG]]<br />
<br />
6. conducting wire.(adapter to fans)..........................[[File:Wire.JPG]]<br />
<br />
7. insulation tape.<br />
<br />
<br />
<br />
<br />
'''How our box functions'''<br />
<br />
The styrofoam box is an insulated box that keeps the heat locked inside. The heating element is introduced into the box to produce heat. The cabinet fans are used to circulate the heat inside and keep the temperature same everywhere in the box. A thermometer is introduced into the box through a perfect fitting hole in the box to measure the temperature inside. the hole is then well sealed and insulated. Neither the heating element nor the fan must be too close to the thermometer. '''The fans and heating element must be placed in such a way that the required temperature is achieved'''(Not as easy as it seems). once the placement is finalized, stick the fans and the heat source in place using arelldite. The lis of the box must be sealed properly so as to not let any exchange take place(duct tape). The incubator is ready to use.<br />
<br />
<br />
<br />
<br />
'''Our Process'''<br />
<br />
<br />
'''Day 1'''<br />
<br />
We first experimented with a dummy styrofoam box that we got at a juice centre. we first started with a 75 watt bulb and 1 fan. the fan was placed exactly opposite to the bulb. We also used a layer of al foil to increase heat.The temp reading showed 108°C. and the thermometer bursted. WE then scraped the Al foil idea.<br />
<br />
<br />
'''Day 2'''<br />
<br />
We then tried using a 40 watt bulb in the dommy with 3 fans.We placed the fans in such a way that the air circulated evenly through the box. The trmperature shot up to 40°C in the first 20 minutes and then remained constant at 60°C. We thought of having an outlet for the heat to escape and use the fan as an exhaust. This was not safe as there might be a possibality that some microbes may enter the incubator. so we used a bulb of lower wattage.<br />
<br />
[[File:DSC02976.JPG]]<br />
<br />
<br />
'''Day 3'''<br />
<br />
We used a 0 watt bulb in the dummy box along with 3 fans. the new box had also arrived so we tried the same combination in the new box since it was bigger. The readings were as follows:<br />
<br />
[[File:DSC03091.jpg]]<br />
<br />
'''Dummy Box''' <br />
<br />
Time(min).............Temp(°C)<br />
<br />
0..............................33<br />
<br />
1..............................34<br />
<br />
3..............................35<br />
<br />
5..............................36<br />
<br />
6..............................37<br />
<br />
8..............................38<br />
<br />
10.............................39<br />
<br />
13.............................40<br />
<br />
17.............................41<br />
<br />
20.............................42<br />
<br />
29.............................43<br />
<br />
43.............................44<br />
<br />
65.............................45(const)<br />
<br />
<br />
<br />
'''Final box'''<br />
<br />
Time(min).............Temp(°C)<br />
<br />
0..............................31<br />
<br />
2..............................32<br />
<br />
3..............................33<br />
<br />
4..............................34<br />
<br />
5..............................35<br />
<br />
7..............................36<br />
<br />
9..............................37<br />
<br />
11.............................38<br />
<br />
15.............................39<br />
<br />
21.............................40<br />
<br />
33.............................41<br />
<br />
53.............................42(const)<br />
<br />
<br />
<br />
'''Day 4'''<br />
<br />
today we used 4 fans to reduce temp. The final temp came to 40°C. We also jumped to the conclusion that each fan reduces the temp of about 20°C, which was wrong.<br />
<br />
<br />
<br />
'''Day 5'''<br />
<br />
Today we tried to redoce the wattage further by using a mosquito repelent heater. we also used 4 fans in such a way that the air circulates in 2 circles. the temperatures recorded were as follows:<br />
<br />
[[File:DSC03125.JPG]]<br />
<br />
Time(min).............Temp(°C) <br />
<br />
0..............................29<br />
<br />
1..............................30<br />
<br />
2..............................31<br />
<br />
4..............................32<br />
<br />
5..............................33<br />
<br />
6..............................34<br />
<br />
8..............................35<br />
<br />
11.............................36<br />
<br />
20.............................37<br />
<br />
60.............................37(const)<br />
<br />
Thus we got a constant temperature of 37°C which es the apt temp for E.coli.<br />
<br />
<br />
<br />
'''Precautions'''<br />
<br />
1. Do not put fans rihgt in front of heater as its constant temperature will drop over time.<br />
<br />
2. Do not use a normal thermometre, it cannot take temperature more than 108°F and might burst.<br />
<br />
3. If by any chance the thermometer breakes and the mercury spills, dispose it safely without touching it directly.<br />
<br />
4. Switch off main power before doing connections.<br />
<br />
5. Run the incubator for about half an hour before use<br />
<br />
<br />
<br />
'''Ref photos'''<br />
<br />
[[File:DSC02904.JPG|250px|]]<br />
[[File:DSC02908.JPG|250px|]]<br />
[[File:DSC02914.JPG|250px|]]<br />
[[File:DSC02921.JPG|250px|]]<br />
[[File:DSC02934.JPG|250px|]]<br />
[[File:DSC02984.JPG|250px|]]<br />
[[File:DSC02986.JPG|250px|]]<br />
[[File:DSC02988.JPG|250px|]]<br />
[[File:DSC02995.JPG|250px|]]<br />
[[File:DSC03079.JPG|250px|]]<br />
[[File:DSC03096.JPG|250px|]]<br />
[[File:DSC03100.JPG|250px|]]<br />
[[File:DSC03129.JPG|250px|]]</div>Farhadhttp://www.hackteria.org/wiki/index.php?title=DIY_Sterlisation_Hood&diff=2762DIY Sterlisation Hood2010-10-18T09:05:25Z<p>Farhad: </p>
<hr />
<div>A sterilisation hood is a transparent box that maintains a sterile environment within it. Sterile hoods aim to keep the microbes out of the air, or in other words, to make a Sterile space. This enables specimens to be worked with/prepared in controlled conditions. It uses a heppa filter and a laminar air flow system to achieve this. There is also a UV light that is run for about half an hour before the experiment starts to kill any living bacteria in the hood. there is a small opeaning for the hands to go in and work. equipment in the hood is not taken out to avoid contamination. Trust me this sounds easy but you need alot of patience and material to do this.<br />
<br />
<br />
'''You will need, '''<br />
<br />
1) Acrylic sheets-4mm (6 pcs)....2 of dimension 57X61 (cms)-Sides <br />
<br />
................................................2 of dimension 57X80 (cms)-Top & Bottom<br />
<br />
................................................1 of dimension 62X80 (cms)-Back<br />
<br />
................................................1 of dimension 65X80 (cms)-Front<br />
<br />
<br />
<br />
<br />
2) Uv light(15 watts)......................[[File:IMG_7998.JPG]]<br />
<br />
<br />
3) Car heppa filter.........................[[File:IMG_7989.JPG]] <br />
<br />
<br />
<br />
4) Exhaust fan..............................[[File:Ex_fan.JPG]]<br />
<br />
<br />
5) Connector pipes(7cm diam)........[[File:DSC03925.JPG]]<br />
<br />
<br />
6) Wooden blocks.........................[[File:DSC03928.JPG]]<br />
<br />
<br />
<br />
7) L angles..................................[[File:DSC03929.JPG]]<br />
<br />
<br />
<br />
8) Nuts and bolts.........................[[File:DSC03923.JPG]]<br />
<br />
<br />
<br />
9) Uv filter (Car cooling film)...........[[File:Filter.JPG]]<br />
<br />
<br />
<br />
10) M-seal and silica gel(for acrylic sheets)<br />
<br />
<br />
<br />
<br />
'''How our hood works'''<br />
<br />
The hood is made of acrylic sheets. The back of the box has 2 holes at the top right and bottom left corners for the air flow. There is a UV light attached on the top face of the box. It is difficult to find a UV light, so you can use a black light bulb but it is not nearly as effective as the real thing. our air filter uses a simple car heppa filter and an industrial exhaust fan. the fan pulls the air through the heppa filter and blows it back into the box through PVC pipes. We put the fan close to the heppa filter and connected the fan horizontally so the pull is more powerful and effective. the front of the hood was held to the box with L angles so that it can slide up & down. The front is stopped at a height of 16cm. with wooden blocks for the hands to go in. you can also make 2 holes and connect them to gloves to reduce contamination. we also tried to make a robot arm that is put in the hood and does the work in the hood.<br />
<br />
<br />
<br />
'''PROCEDURE:'''<br />
<br />
<br />
'''Makig the laminar air flow''' [[File:DSC03712.JPG|150px|right|]]<br />
<br />
<br />
1. First make the box around the exhaust fan. (We used sun board but you can use something else).the fan needs about 4-5cm distance from the faces of the box. <br />
<br />
2. For the fan box take 4 pieces of sun board(fan width+8cm x fan length) and stick them to the sides of the fan in such a way that the fan is in the centre of the pieces. Pull out the wires from or of the pieces.<br />
<br />
3. Take 2 square pieces(fan length) and cut a hole(pipe diameter) in them. stick them on both open sides of the fan.Seal all sides with M-seal. [[File:DSC03721.JPG|170px|right|]] <br />
<br />
4. Take the acrylic sheet with dimension 62x80 cm which is the back side of the box and drill three holes in it. One for the air filter [[File:DSC03708.JPG|170px||]](top right), the second one for the pvc pipe(bottom left) and the third one(bottom right) for the wire of the Uv light to pass.<br />
While doing this '''make sure that the filter, the pipe and the wire exactly fit into the holes and there is no extra space.''' <br />
<br />
5. Stick the heppa filter into the top right hole, on the inside with araldite.<br />
<br />
6. Connect the heppa filter to the fan box and then to the inlet at the right bottom corner using the pipes and L shape connectors. Keep the fan close to the filter to increase power.keep the setup as close as possable to the acrylic sheet.<br />
<br />
7. Thus the air filter at the top right hole is connected to the inlet via the fan.<br />
<br />
8. Seal all the connections and joints with M-seal.<br />
<br />
<br />
'''Making the box''' [[File:DSC03715.JPG|170px|right|]]<br />
<br />
9. The two acrylic sheets of dimension 57X61 cm forms the sides of the box. Two sheets of dimensions 57X80 cm form the top and bottom of the box. One of dimension 61x80 cm is used for the back of the box and the one of dimension 65x80 cm for the front of the box.<br />
<br />
10. Stick the 2 sides of the hood to the base using super glue in such a way that the 2 sides are on the base and wait for it to dry. You need to use support for it to dry in a right angle.<br />
<br />
11. Once it is dry put a layer of silica gel on both sides without moving the support to set it firmly in place. <br />
<br />
12. The sides and the air flow system will take about 5 to 7 hours to set.<br />
<br />
13. Once everything is set and dry attach the back sheet with the air flow system to the sides and the base with super glue and then silica gel. Try to keep the back against a wall for support.<br />
<br />
14. Stick the top in the same way and wait for the gel to completely solidify.<br />
<br />
15. After ensuring that all the sides are stuck to the base properly , connect the L angles on the sides of the box and two on the base using nuts and bolts for good support for the front cover. [[File:DSC03787.JPG|170px|right|]]<br />
<br />
16. Drill holes on the top sheet and connect the UV tube to the box with nuts and bolts.<br />
<br />
17. Drill holes and make stoppers with the wooden blocks using nuts and bolts at about 16cms from the base.<br />
<br />
18. Finally put the front sheet by making it slide through the L angles.<br />
<br />
19. Cover the box with UV filter once it is built. Do not cover the front screen.<br />
<br />
20. Your hood is ready.<br />
<br />
<br />
<br />
'''PRECAUTIONS:'''<br />
<br />
1. Make sure that the holes drilled on the back side of the box are of perfect size so that there are less chances of contamination.<br />
<br />
2. Seal all the gaps in the box with m-seal.<br />
<br />
3. While drilling holes in the acrylic sheet make sure that there is proper support so that the sheet doesn’t bend or break.<br />
<br />
4. While sealing the pipes connected to the fan, first seal the pipes together with m-seal and then connect the whole thing.<br />
<br />
5. The Uv light is switched off while it is being connected.<br />
<br />
6. Do not run Uv light for a long time. Stay away when Uv light is running.<br />
<br />
7. Make sure the front shutter is held up securely with the stoppers before conducting the experiment.<br />
<br />
<br />
<br />
'''PROCESS PICTURES:'''<br />
<br />
[[File:DSC03699.JPG]]<br />
[[File:DSC03712.JPG]]<br />
[[File:DSC03707.JPG]]<br />
[[File:DSC03708.JPG]]<br />
[[File:DSC03713.JPG]]<br />
[[File:DSC03717.JPG]]<br />
[[File:DSC03715.JPG]]<br />
[[File:DSC03719.JPG]]<br />
[[File:DSC03721.JPG]]<br />
[[File:DSC03727.JPG]]<br />
[[File:DSC03728.JPG]]<br />
[[File:DSC03729.JPG]]<br />
[[File:DSC03731.JPG]]<br />
[[File:DSC03734.JPG]]<br />
[[File:DSC03736.JPG]]<br />
[[File:DSC03738.JPG]]<br />
[[File:DSC03739.JPG]]<br />
[[File:P1090748.JPG]]<br />
[[File:DSC03750.JPG]]<br />
[[File:DSC03787.JPG]]<br />
[[File:DSC03790.JPG]]<br />
[[File:DSC03791.JPG]]<br />
[[File:DSC03796.JPG]]<br />
[[File:DSC03944.JPG]]<br />
[[File:DSC03945.JPG]]</div>Farhad