http://www.hackteria.org/wiki/api.php?action=feedcontributions&user=Target022&feedformat=atomHackteria Wiki - User contributions [en]2024-03-28T16:53:54ZUser contributionsMediaWiki 1.28.0http://www.hackteria.org/wiki/index.php?title=Talk:Ethics&diff=3093Talk:Ethics2010-12-11T19:35:27Z<p>Target022: Replaced content with '>'</p>
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<div>></div>Target022http://www.hackteria.org/wiki/index.php?title=Talk:Design_%26_Technology&diff=3088Talk:Design & Technology2010-12-11T19:33:42Z<p>Target022: </p>
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<div>>16NIx1 &lt;a href=&quot;http://myqurbubblor.com/&quot;&gt;myqurbubblor&lt;/a&gt;, [url=http://ytrqhglyuenc.com/]ytrqhglyuenc[/url], [link=http://oizcdzrdgvoc.com/]oizcdzrdgvoc[/link], http://drwlhcbvesuy.com/</div>Target022http://www.hackteria.org/wiki/index.php?title=Talk:The_Specials&diff=3087Talk:The Specials2010-12-11T19:33:25Z<p>Target022: Replaced content with '>'</p>
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<div>></div>Target022http://www.hackteria.org/wiki/index.php?title=Week_Three&diff=3086Week Three2010-12-11T19:33:06Z<p>Target022: </p>
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<div>>=== May 30th ===<br />
<br />
'''We extracted DNA from human saliva and banana in our semi-functional, backyard science lab!<br />
<br />
It was sort of like a pre-introduction to science which we did ourselves!'''<br />
<br />
<br />
1) '''Extracting DNA from Banana:''' &lt;&lt;[[Read here]]<br />
<br />
2) '''Exracting DNA from Saliva:'''<br />
<br />
'''Images of our DNA we extracted from saliva:'''<br />
<br />
&lt;gallery&gt;<br />
File:NehasDNA.JPG|Neha's DNA<br />
File:KrupakarsDNA.JPG|Krupakar's DNA<br />
File:DhruvsDNA.JPG|Dhruv's DNA<br />
File:SandeepsDNA.JPG|Sandeep's DNA<br />
&lt;/gallery&gt;<br />
<br />
*All DNA pictures have been uploaded. Take your pick [[Special:ListFiles|here]]<br />
<br />
<br />
===May 31st===<br />
<br />
Some interesting articles:<br />
<br />
'''The Promise and Perils of Synthetic Biology:'''<br />
<br />
http://www.thenewatlantis.com/publications/the-promise-and-perils-of-synthetic-biology<br />
<br />
'''Molecular Synthetic Biology:'''<br />
<br />
http://www.nature.com/msb/journal/v2/n1/full/msb4100104.html <br />
<br />
'''The photosensitive stripes are made of bacteria:'''<br />
<br />
http://www.edgarlissel.de/data/mnemosyne_II_01e.html<br />
<br />
===June 3rd===<br />
<br />
'''The Registry of Parts Exercise'''<br />
<br />
To research a feasible idea among the various ideas that came up during the brainstorming session and present a dummy procedure on how to achieve the result on the basis of the scientific knowledge acquired in the two and a half weeks into iGEM.<br />
<br />
Sanya:<br />
Bacteria that indicates rise in and regulates body temperature.[[Media:Light.jpg]]<br />
<br />
[[Upasana]]: Temperature regulating bacteria<br />
<br />
All That Glitters: [[Neha's Bacterial Jewelery]]<br />
<br />
===June 5th===<br />
<br />
'''Beginning laboratory procedures:''' Introducing ourselves to understand working in a professional laboratory.<br />
<br />
1) [[Bacterial Transformation : The Process]] | [[The Bacterial Transformation Gallery]]<br />
<br />
2) Preparing the Plasmid (miniprep)<br />
<br />
3) Digesting the DNA<br />
<br />
4) Running the gel (Gel Electrophoresis)<br />
<br />
5) Elution</div>Target022http://www.hackteria.org/wiki/index.php?title=Talk:Coloreria&diff=3085Talk:Coloreria2010-12-11T19:32:47Z<p>Target022: Replaced content with '>'</p>
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<div>></div>Target022http://www.hackteria.org/wiki/index.php?title=The_promise_of_Synthetic_Biology&diff=3084The promise of Synthetic Biology2010-12-11T19:32:33Z<p>Target022: </p>
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<div>>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 />
&quot;When dealing with biological entities,&quot; notes Thomas Murray, president of the Hastings Center, a bioethics organization, &quot;life has a tendency to find a way.&quot;<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 — &quot;like microbial French kissing.&quot; That bug we introduce into the ocean to sip the spill might end up swapping DNA with other living things. &quot;We have a ways to go,&quot; he says, &quot;before we can really know what risks we're running if we release these organisms into the environment.&quot;<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 &quot;they haven't created life in any sense of the word, other than a person playing a cassette has invented the tape recorder.&quot;<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 />
'''http://www.time.com/time/magazine/article/0,9171,1997447,00.html'''<br />
<br />
<br />
&quot;It is vital that we as a society consider, in a thoughtful manner, the significance of this kind of scientific development,&quot; Obama writes.<br />
<br />
&quot;Synthetic biology certainly raises deep philosophical and moral questions about the human relationship to nature,&quot; according to Gregory Kaebnick, a Hastings Center scholar who is managing the project. &quot;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.&quot;<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.</div>Target022http://www.hackteria.org/wiki/index.php?title=Talk:A_synopsis&diff=3083Talk:A synopsis2010-12-11T19:32:13Z<p>Target022: Replaced content with '>'</p>
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<div><br />
=='''Journal'''==<br />
<br />
'''10 May 2010'''<br />
Got up this morning and while I completely woke up with my morning coffee I caught myself curious about what iGem had in store for me. I had done biology a long time ago in high school and the concept of genetic modification really interested me. Biology catching up with me in design school was just awesome. I liked the idea that I would be creating something at a different level. New mediums are always exciting. <br />
<br />
Walked into class and was confronted with a lot of information. Some of it was a recap from what I have done before and a lot of it was new. We raced through about few hundred years of micro biology and the important events that influenced thought and perception of cells and life and their creation. <br />
<br />
I was also given some insight into the possibility that genetic engineering and modification might not be a very positive thing. There are many risks and costs involved. Im sure that everyone else must have also had some thoughts on this matter. But do the people in power of using and spreading this technology and knowledge have the same? IF they do, what and how do they plan to use it? <br />
<br />
I left back to my apartment, craving for another cup of coffee but still excited about what the next few weeks were going to bring. <br />
<br />
'''11 May 2010'''<br />
<br />
Information, information, information!!! There was so much of it. Termanologies were flying out quite fast, I was a little overwhelmed with it all. I was trying to take it all in and make sense of it at the same time.<br />
It was reinforcing to learn that Mendel was a monk and that Leeuwenhoek was a cloth merchant!! <br />
<br />
I was a little startled to notice that the functioning (reading and manufacturing of information) of a Genome was similar to programing. A,C,T,G were like 1 and 0 Could we eventually be messing around with life like we do with computers? We were already kind of doing it now. <br />
Where is it going to go? I am a little skeptical about humans. <br />
<br />
<br />
'''12 May 2010'''<br />
We learnt about mutation today, how the change of even a single base pair in the DNA sequence can cause a very significant phenotypical change. I was a little startled to learn that smoking causes a change in a particular gene which can cause a permanent change, possibly causing cancer. Left class contemplating how chemicals, which are non living, combined in certain ways to create life. Where is the line where so called non-living things become living.<br />
<br />
<br />
'''13 May 2010'''<br />
Proteins was the topic of the day today. I do some of what I learned in school, especially about the two main types of structurally different proteins, enzymes and structural proteins. The importance of temperature and ph levels are important for proteins. If the two factors are either too high or too low there is a chance for the protein to denature permanently, like how once an egg is cooked it hardens permanently. The factors are important for the optimum functioning of enzymes also. which is why it is dangerous if the human core body temperature is too low or too high, most body functions begin to break down. <br />
<br />
<br />
'''14 May 2010'''<br />
Most of the processes in the body run on or are dependent on proteins. Each protein performs a particular task. All the information to produce a particular protein for a particular task is encoded into the genome of an individual. The store for all the information is in the genome of that individual. As discussed before small changes in the sequence can cause major in the individual. <br />
<br />
<br />
'''17 May 2010'''<br />
We went further into genome sequencing and an understanding of what a genome is; and how useful this understanding of various sections of the genome and what phenotypical change it corresponds to, could be in understanding our bodies. People suffering from genetically related disorders or diseases can be treated to some extent using gene therapy which was an outcome of learning about and isolating genes. Its something like fixing a bug or glitch in a software by comparing it with a correctly written one. The same principals of understanding what gene does what can be used to create genetically modified crops (BT brinjal) and even pets (like the glofish... google it) <br />
<br />
For our next assignment we had to 'create' a creature (any creature). This was just way cool. I knew it was just on paper, but the prospect of kind of playing god was exciting. <br />
<br />
Oh yeah I think we are gonna extract DNA tomorrow, quite excited. <br />
<br />
<br />
'''18 May 2010'''<br />
We started watching the BBC series of the cell; what a journey!!!. It left me a little dazed to think about millions of tiny little creatures evolving to such and extent that it makes me. &quot;I&quot; am a collection of millions, no billions of these cells working together. So who am &quot;I&quot;. <br />
<br />
Recombinant dna is the created from two or more sources of genetic information and 'glued' to form a single man made DNA polymer. What is man made?? if man is the product of the evolution of these cells, then maybe creating recombinant DNA is part of a higher process of evolution. <br />
<br />
<br />
'''20 May 2010'''<br />
Missed yesterday because I was sick and I'm still not feeling that great today either, but we were going to present our organisms today and I was quite excited to see what everyone had come up with also. I liked aarons organism, which would copy the genetic material of other organism to improve itself. I came up with a hypothetical 'booster cell' which attached itself to other cells of the body and provides them with more energy in the form of atp, so that the cell can function faster/more efficiently. <br />
<br />
'''21 May 2010'''<br />
Our initial assignment was to create an organism, and I thought most of the concepts that came out were quite cool. <br />
We had a discussion on the purpose. The purpose of organisms that exist today. We had all assigned a specific purpose in 'relation to humans' to the organisms that we created, so for the next assignment we had to create an organism which 'had no purpose'. No purpose? My mind went back to the the discussion of purpose and the meaning of purpose, both Aaron's as well as Yashas points of view, though contradictory, made sense to me, so I was left a little mind boggled.(I kind of agreed with yashas though) Decided ill ponder the idea for a while longer before I decide on anything, lets see what I come up with. <br />
<br />
'''22 May 2010'''<br />
Craig Venter announced the the creation of the first synthetic cell (synthetic cell? my mind went back to the whole, what is man made and what is not conundrum). Well now humans can create cells that they can 'program', how far will this technology go? If it develops as fast as todays technology, I may be able to experience some of its products. How will it be used, I wonder. <br />
<br />
<br />
'''28 May 2010'''<br />
Ha ha, its quite funny, no one seems to know much about what we are supposed to know by now, me not being the exception. It was quite embarrassing to be sitting there clueless. Im sure yashas is cursing everyone on the inside. Except for aaron, no one else seems to have really got anything done. In my defence I had no clue we had to write a journal like this, I was up till 4 am last night doing the log, remembering days of high school and law school where just was writing notes, and which is what I did. Its quite dry in contrast to Aarons work, and this happens to be my first log entry that is reflective rather than an account or notes of what happened in class.</div>Target022http://www.hackteria.org/wiki/index.php?title=Talk:DIY_Microfluidics&diff=3080Talk:DIY Microfluidics2010-12-11T19:30:45Z<p>Target022: Blanked the page</p>
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<div><br />
Extracting DNA from Banana<br />
<br />
'''What you need'''<br />
# 3 glass or clear plastic cups<br />
# A cup of water<br />
<br />
# A banana<br />
# A spoon<br />
# An eyedropper<br />
# A strainer<br />
# A funnel<br />
# A toothpick<br />
# A tablespoon of salt<br />
# 3 Tablespoons of liquid detergent containing Sodium Laurel Sulphate (look at back of the bottle)<br />
# A third of a cup of rubbing alcohol<br />
<br />
'''What you need to do'''<br />
# Put the rubbing alcohol in the freezer to chill it.<br />
# Mash the banana up with the spoon.<br />
# Strain the pulp through the funnel into one of the empty glasses (You might need some water to help it through.)<br />
# In another glass stir the detergent and salt together.<br />
# Mix the banana pulp and the salty detergent together for about a minute. Try to avoid bubbles.<br />
# When it settles, gently pour the alcohol down the side of the cup over the back end of the spoon. The alcohol should form a layer over the mixture.<br />
# Soon, you'll see tiny white strands of millions DNA gathering between the two layers.<br />
# Pick them out with the toothpick. They should be white, whiter than the rest of the banana pulp. Admire!</div>Target022http://www.hackteria.org/wiki/index.php?title=Talk:SynthBioWorkshop2010&diff=3077Talk:SynthBioWorkshop20102010-12-11T19:29:47Z<p>Target022: Blanked the page</p>
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<div><br />
&lt;strong&gt;Synthetic Biology for Artists and Designers 2&lt;/strong&gt;<br />
<br />
&lt;strong&gt;10th May 2010<br />
&lt;/strong&gt;<br />
• Biology - individual understanding and definition.<br />
• Brief History of Biology - Scientists/Microbiologists (Video)<br />
? Anton Von Leeuwenhoek<br />
? Gregor Mendel<br />
? Robert Hooke<br />
? Louis Pasteur<br />
? John Baptiste Van Helmont<br />
? Joseph Jackson Lister<br />
? Theodore Schwann<br />
? Rosalyn Franklin<br />
? Watson &amp; Crick<br />
• Evolution – Brief understanding and controversies<br />
• DNA, Protein – Introduction<br />
• Bacteria E.Coli<br />
• Readings – PDF<br />
? Scientific America – Engineering Life<br />
? Synthesizing DNA of microorganisms for various purposes<br />
? Sequencing of DNA<br />
? Cost factors involved<br />
? Comparison to Moore’s Law<br />
? Human Genome<br />
• Video – (BBC)-The Cell-The Hidden Kingdom<br />
Homework - Reading (PDF)<br />
1. Life: What a concept!<br />
<br />
&lt;strong&gt;11th May 2010&lt;/strong&gt;<br />
<br />
• Recap of yesterday’s learning<br />
• Video lecture by David Sadava<br />
? Expression of genes<br />
? Phenotypes and Alleles<br />
? The Nucleus<br />
? Totipotent Cells<br />
? Cloning<br />
? Genes, chromosomes<br />
? Human genetic information<br />
? Cell processing<br />
• Introduction to Synthetic Biology by Andrew Hessels<br />
• Video – Darwin’s theory on evolution<br />
Homework<br />
1.<br />
2.<br />
<br />
&lt;strong&gt;12th May 2010&lt;/strong&gt;<br />
<br />
• Video Lecture by David Sadava<br />
? Epidemiology<br />
? Lung Cancer gene<br />
? Mutations<br />
? Requirements of a DNA<br />
? Responsibilities of a Protein<br />
? Variety in DNA<br />
? Somatic and Sex Cells<br />
? Virus<br />
? DNA &amp; its properties<br />
? Structure of a DNA<br />
? Replication of DNA<br />
• Video of Watson and his story of the discovery of the DNA model at TED.com<br />
• Readings – Applying engineering to biology<br />
• Reading – Adventures in Synthetic Biology<br />
Homework<br />
1. Reading<br />
2. Online Research<br />
<br />
&lt;strong&gt;13th May 2010&lt;/strong&gt;<br />
<br />
1. Video Lecture by David Sadava<br />
? Spider web theory of protein<br />
? Protein production<br />
? Structure of protein<br />
? Synthesis of Protein<br />
? Human protein synthesis<br />
? Types of proteins<br />
? Expression of Proteins<br />
? Gene – Protein relationship<br />
? Metabolism<br />
? Thermodynamics<br />
? Mechanism, Cell Theory and Evolution<br />
? Ricin and its discovery<br />
? RNA and its role<br />
? Transcription and Translation<br />
? Nirenberg’s Experiment<br />
? Mutations and changes in base pairs<br />
• Video tutorial on DNA replication<br />
• Video tutorial on Protein synthesis<br />
Homework<br />
1. Exercise – Make a piece of art form using any LIVING form that should have the<br />
capability to grow over a period of two months.<br />
<br />
&lt;strong&gt;14th May 2010&lt;/strong&gt;<br />
<br />
1. Video Lecture by David Sadava<br />
Genomes – further details<br />
?<br />
Mutations &amp; Mutagens<br />
?<br />
Cancers caused by mutation of genes by radiation<br />
?<br />
Genetic Damage<br />
?<br />
Leukaemia<br />
?<br />
Scientist Renato del Bucco’s work<br />
?<br />
Hierarchical sequencing<br />
?<br />
Shotgun sequencing – Craig Ventor<br />
?<br />
Bioinformatics<br />
?<br />
Information from a genetic sequence<br />
?<br />
a. Coding sequence<br />
b. Protein amino acid sequence<br />
c. Gene control sequences<br />
Sequential Genomics<br />
?<br />
First genome to be sequenced<br />
?<br />
Hypothetical suggestion of 24000 genes in a human being<br />
?<br />
Synthetic Biology - making artificial genes to bring about a desired result<br />
?<br />
Scientist Werner Arber<br />
?<br />
Restriction Endonuclease<br />
?<br />
How a bacteria prevents Viral infections<br />
?<br />
DNA Mapping<br />
?<br />
Recombinant DNA<br />
?<br />
Stanley Cohen &amp; Herbert Boyer’s Experiment<br />
?<br />
Goals for making rDNA<br />
?<br />
Transgenic animals and plants<br />
?<br />
Naked and Vector DNA<br />
?<br />
<br />
&lt;strong&gt;17th May 2010-05-17&lt;/strong&gt;<br />
<br />
1. Video Lecture by David Sadava<br />
? Isolation of genes<br />
? PKU and dystrophy<br />
? Methods of analyzing DNA<br />
? Reverse Genetics<br />
? Dystrophine Gene and Utrophine<br />
? Gene Therapy<br />
? Nucleic Acid Hybridization<br />
? Genome Library<br />
? DNA Microarray<br />
? Metastasis<br />
2. Exercise - Think of your own creature. Design it. Explain detailed mechanisms using<br />
diagrams. This organism could be hypothetical. Name it.<br />
3. Make a scientific paper on your creature<br />
4. Demonstration of Gabriel’s current prototype of visually representing genetic sequenced<br />
data of a human mitochondria.<br />
Homework – develop and complete creature.<br />
<br />
&lt;strong&gt;18th May 2010&lt;/strong&gt;<br />
<br />
1. Video Documentary – BBC – The Cell – Chemistry of Life<br />
2. Video Documentary – BBC – The Cell – The Spark of Life<br />
3. Discussion of Creatures, peer feedback and progress<br />
<br />
&lt;strong&gt;19th May 2010&lt;/strong&gt;<br />
<br />
&lt;object width=&quot;400&quot; height=&quot;300&quot;&gt;&lt;param name=&quot;allowfullscreen&quot; value=&quot;true&quot; /&gt;&lt;param name=&quot;allowscriptaccess&quot; value=&quot;always&quot; /&gt;&lt;param name=&quot;movie&quot; value=&quot;http://vimeo.com/moogaloop.swf?clip_id=12045337&amp;server=vimeo.com&amp;show_title=1&amp;show_byline=1&amp;show_portrait=0&amp;color=&amp;fullscreen=1&quot; /&gt;&lt;embed src=&quot;http://vimeo.com/moogaloop.swf?clip_id=12045337&amp;server=vimeo.com&amp;show_title=1&amp;show_byline=1&amp;show_portrait=0&amp;color=&amp;fullscreen=1&quot; type=&quot;application/x-shockwave-flash&quot; allowfullscreen=&quot;true&quot; allowscriptaccess=&quot;always&quot; width=&quot;400&quot; height=&quot;300&quot;&gt;&lt;/embed&gt;&lt;/object&gt;&lt;a href=&quot;http://vimeo.com/12045337&quot;&gt;Center for Genomic Gastronomy @ Srishti, Bangalore, India&lt;/a&gt; from &lt;a href=&quot;http://vimeo.com/user3901760&quot;&gt;genomic gastronomy&lt;/a&gt; on &lt;a href=&quot;http://vimeo.com&quot;&gt;Vimeo&lt;/a&gt;.<br />
<br />
1. Presentation by Zac on The center for Genomic Gastronomy<br />
? What is Biotechnolgy<br />
? Perspective of food by all living things<br />
? Geohackers, Biohackers, Geoengineers, Planetcrafters<br />
? Agriculture Biodiversity<br />
? Agrinformatics<br />
? Metadata and food Genomes<br />
? Food System Adaptation<br />
? Agriculture Terrorism<br />
? First world eating issues<br />
? Cuisinformatics<br />
2. Extraction of DNA<br />
<br />
&lt;strong&gt;20th May 2010&lt;/strong&gt;<br />
<br />
1. Presentation of Abstracts of New Creatures<br />
? The Booster Cell<br />
? Supercule<br />
? Thermo Cell<br />
2. Exercise – Create another new creature which does not necessarily have to be a<br />
microorganism or even possible to exist. Completely hypothetical, imaginary of fantastical is<br />
great!<br />
<br />
&lt;strong&gt;21st May 2010&lt;/strong&gt;<br />
<br />
Minutes of the Class<br />
1. Discussion of ideation on creation of machines.<br />
<br />
&lt;strong&gt;22nd May 2010&lt;/strong&gt;<br />
<br />
Minutes of the Class<br />
1. Video Documentary by Craig Ventor<br />
? Scientific Breakthrough – First fully Synthetic Cell to be cultutred.<br />
? Genome copied from Mycoplasma Genatalium<br />
? Genome synthetically prepared in the lab<br />
? Introduced into yeast cells to complete transformation<br />
? Introduced into host bacterial cell which transforms to new organism<br />
? Watermarked with 46 authors, web address and mail ID<br />
? Significance – vaccine production and Oil Spill reduction<br />
2. Artist &amp; other Research<br />
? Stellarc<br />
? Symbiotica<br />
? Orlan<br />
<br />
&lt;strong&gt;25th May 2010&lt;/strong&gt;<br />
<br />
1. Visit to NCBS<br />
? Tour of the Campus<br />
? Meeting with PhD student Mehra and Navneet<br />
? Introduction to the lab space<br />
? Discussion over Science Institutes and their pros and cons<br />
? Tour of other labs with various workflow instruments<br />
<br />
&lt;strong&gt;26th May 2010&lt;/strong&gt;<br />
<br />
Minutes of the Class<br />
1. Video Tutorial by David Sadava<br />
? Bioremediation – using organism to improve the environment<br />
? Fluorescence in nature and different organisms<br />
? TNT used as example<br />
? Degraded by Psuedomonas Putida<br />
? Integrated Pest Management<br />
? Bacteria in decomposition<br />
? Bacteria in Waste Water Treatment<br />
? Extremophiles<br />
? PCR and its significance<br />
2. List of materials required to build the art form made from a living organism<br />
3. Artist &amp; other Research<br />
? Institution of Applied Autonomy<br />
? Center for Post Natural History<br />
? George Gessert<br />
<br />
&lt;strong&gt;27th May 2010&lt;/strong&gt;<br />
<br />
Minutes of the Class<br />
1. Video Documentary by Kary Mullis on the making of the PCR<br />
2. Artist &amp; other Research<br />
? Adam Zaretsky<br />
? Eduardo Kac<br />
? Patricia Piccinni<br />
3. Field work on material for art form construction.<br />
<br />
&lt;strong&gt; 1st June &lt;/strong&gt;<br />
<br />
Yeast Growing<br />
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<div><br />
I have been a student of art for as long as I remember- different mediums of self expression have engulfed me at different points in time, but largely I have been a performing artist presently studying the visual arts. The varying disciplines often create a conflict and often create solutions to the same self created conflicts as well. To inculcate science within the realms of ethics, aesthetics, philosophy and love, which are all integral to art seems like a direction towards a journey I want to explore. The symbiotic relationships as well as the independence of the elements in nature intrigue me. There is a need to be in sync with nature and using science as a tool to facilitate that process than curbing it's natural creativity is what I hope to achieve.<br />
<br />
Contact: avnisethi@gmail.com<br />
<br />
'''15th May 2009'''<br />
<br />
I was a little apprehensive of where this project and interaction would go, but I am only glad to encounter its strong philosophical backbone integrated with biology. There were some readings that have caught my attention and I have drawn the following understandings from them: -<br />
<br />
* The artist is like a conduit between specialized knowledge fields and other members of a public sphere meaning to say that one is not taking away or challenging the role of a specialist but as an artist one is only enhancing the specialized knowledge with considerations that specialties might not accommodate.<br />
<br />
* Artists agree to engage/associate/learn from and in society and public places. In such situations autonomy is always conditional, always negotiable.<br />
<br />
* Art more often than not occupies a place in metalanguage since it has a higher relationship with the symbolic therefore connecting us to realms such as ethics, aesthetics society, philosophy. This might be the purpose of even calling something art.<br />
<br />
<br />
'''16th May 2009'''<br />
<br />
These sketches are a completely fictional scientific logic of how I would want to create a bacterium called actinodopaine. This bacteria would detect the neuro-transmitter in humans called Dopamine that is secreted while feeling love. Once it detects this it would emit the odour of wet earth as a result of rain.<br />
<br />
[[File:Page 1.jpg]] [[File:Page 2.jpg]] [[File:Page 3.jpg]] <br />
<br />
This idea was inspired by a basic instinct of human beings to love and be loved, but very seldom in these fast paced times is there the time or motivation to demonstrate it.<br />
<br />
<br />
'''18th May 2009'''<br />
<br />
'''I wonder whether I am tampering with Nature through sheer neglect and ignorance?'''<br />
<br />
There is very little that I know about biology and whenever I come across the terms that ring a bell since high school I get extremely excited. Its a great way to learn and educate oneself, through curosity. But I wonder how far does 'curiosity to learn' justify the ethical reponsibilities that one must undertake while interacting with life.<br />
<br />
On the other hand its all beautiful and why not indulge, for doing is a way of thinking, a way of questioning!<br />
<br />
<br />
<br />
'''19th May 2009'''<br />
<br />
When one sees, one believes and that is the principle science works on, today I probably saw why that happens or where scientists come from. It for sure blows your mind away to see in real/experience science and its wonders. Today was the first day spent at National Centre for Biological Sciences (NCBS).<br />
<br />
There seem to be possibilities of translating the 'Actinodopaine' into a woking idea. Some notes to understand this better: -<br />
<br />
* Actinomyocetes is the bacteria that is responsible for the smell of rain.<br />
* It is found in soil, therefore growing a culture might not be difficult, except the emittion of the smell would happen under specific circumstances.<br />
* Unlike other bacteria, a particular gene is not responsible for the smell produced but the entire bacterium does the function.<br />
* Therefore, one cannot cut the specific sequnce to join it to another.<br />
* On the other hand, to detect neuro-transmitters such as dopamine, samples of sweat could be tested.<br />
<br />
- There was a mention of producing these results in E. Coli through an enzyme.<br />
<br />
<br />
'''20th May 2009'''<br />
<br />
Neuro science it was today! A look into various neuro mapping techniques, very cool rat reponding to smell videos and more interesting people.<br />
<br />
<br />
'''21st May 2009'''<br />
<br />
Here we are trying to 'design' the working of a bacteria on a white board. No matter how absurd it sounds i think it worked. We got some facts right and hopefully will get lots more!<br />
<br />
<br />
'''26th May 2009'''<br />
<br />
So we have things sorted, in terms of understanding how Geosmin works and the various conditions in which we can get farnysol diphosphate to react with the enzyme so as to create geosmin and the rest needs to be done by Mukund's lab to actually make the enzyme or order it which can take upto 1 months of work, which also means we need to start working on a parallel track that helps us understand some other basics.<br />
<br />
We also met Mr. Krishnan today, who seemed like an insightful man, one of those people who look at things from more than one framework. He spoke about a host of things including mutant fruitflies, biophysics,cell membranes,the scope of &quot;art&quot; in science and other intriguing things. but of course it had to trigger other very messy thoughts. Soon after this meeting I felt totally lost and obsolete. <br />
<br />
There was no room for dialogue with him, no articulation of what we are trying to do. So my task for the next few days is to articulate what is it that we're doing, we've had extensive discussions about this but yet it seems like I dont know.<br />
<br />
<br />
'''27th May 2009'''<br />
<br />
In one of my frantic emails to a friend who I know knows the science of words well and I have spoken about this project extensively, I said I needed help in understanding what I am doing. Below written is his reply which I think I should keep going back to:<br />
<br />
<br />
'''&quot;'''''You are not clearly not doing an art piece, for if you were you would be viewing the bacteria devoid of it's scientific attributes. You are however applying artistic methods(I think this is where it rests) to scientific matter. One can go on about this, and catch one self in semantic games. At bottom you are giving science-and it's methods a new orientation, a new approach. Perhaps the articulation would require an understanding od methodology. What is this artistic re-orientation of matters concerning science, and what is the difference between art and science. That is where your philosophy comes in. I think you should observe your self. You are your best experiment. See your methods, and compare it the method, you let's say approach a painting you creating or a dance you choreographed.'''''&quot;'''<br />
<br />
<br />
'''28th May 2009'''<br />
<br />
My bioart presentation- A chicken in a kaliedoscope.<br />
<br />
The project essentially raised ethical questions and possibly brought to the forefront the 'murky' grounds we could be entering with our attempt at synthetic biology.<br />
<br />
<br />
'''29th May 2009'''<br />
<br />
I went over a couple of comments on the CinK piece, (1). it is discussed and argued over, which is a good thing, if nothing else it could be a conversation starter for the much awaited conversation I wanted to be part of (2). It urges me to think and study another discipline totally in detail before i have any further conversations about it. -ETHICS- It seems like its the new big bad word.<br />
<br />
I certainly feel ethics are contextual and that certain values get converted into ethics in certain situation and dont in certain others. In a case like that i should be wary of making sweeping statements of what is ethical and what is not.<br />
<br />
But I certainly want to question the role of the artist and the role of the scientist. Is it utmostly important that he/'''she''' work with organisms and that they woulddn't do so if they could work with metal? Is it mandatory that human beings need to be saved using invasive techniques from carcinogenic waste created by human beings themselves? So then is it mandatory for artist to work with only metal since they'll hurt 'life' while working with chickens? Is expression using whatever it takes to do so unexceptable?<br />
<br />
I cant answer any of these questions using the framework of ethics, i dont claim to know them. But I certainly can answer each of these question from a personal insight which is hopefully integrated with sensitivity, honesty and a sense of responsibility.<br />
<br />
<br />
'''9th June 2009'''<br />
<br />
I seem lost and completely disconnected, I don't know what Bacteria Transformation or any of that is and why anybody should do it, although I am not uninterested, I just need a little bit of help from people around me. Its reaching a mystical stage where the cloak has begun to enter our process.</div>Target022http://www.hackteria.org/wiki/index.php?title=Talk:Gel_Electrophorosis&diff=3072Talk:Gel Electrophorosis2010-12-11T19:28:29Z<p>Target022: Blanked the page</p>
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<div><br />
[[File:DSC 8333.jpg|400px|thumb|center|Action is the best teacher]]<br />
<br />
'''Who am I?'''<br />
<br />
A bio-enthusiast with an inclination towards the world of art, I believe that there's an increasing need for artists who don't create '''art just for art's sake'''.<br />
After having majored in Biology in school, I opted for an education in art and design to discover the potential of a lesser acknowleged science (that being art) in mainstream science.<br />
<br />
'''What do I aim to do?'''<br />
<br />
With a penchant for writing and organising, from little safety pins to giant libraries, I hope to a part of the major revolution in education systems around the globe, which I hope to start!<br />
Ambitious? Whimsical? Maybe, but isn't it enthusiasm that makes the world go round?<br />
<br />
'''Reaching me:'''<br />
neha.n.bhat@gmail.com<br />
<br />
'''Idea-generation:<br />
'''<br />
Conveying ideas using non-textual tools: Creating a bacteria out of one's imagination<br />
<br />
[[File:DOC160509-16052009101732_Page_03.jpg|200px|thumb|left|Materialistica Destructilla and Reactant A-Pictorial Depiction]]<br />
<br />
[[File:DOC160509-16052009101732_Page_05.jpg|200px|thumb|left|Self-destruction on crossing the intolerance point ]]<br />
<br />
[[File:DOC160509-16052009101732 Page 07.jpg|200px|thumb|left|Graphical Representation]]<br />
<br />
A bacteria programmed to reproduce proportionately to the level of liquid silver/Reactant A characteristic only to the Indian currency. A intolerance point will be identified beyond which the bacteria cannot reproduce and starts a process of self-destruction. Its like paying for a life. How far can money take us? Won't it all end in self-destruction?<br />
The graph depicts the relation between the reactant and the mass of the bacteria.It also illustrates the 'intolerance point'.<br />
<br />
Thinking, seeking, doing:<br />
<br />
'''Reflections from two days at NCBS: '''<br />
<br />
I am learning. I am experimenting.<br />
More than that ‘upper’ stuff that I say I'm doing and all that I'm supposed to , I’m seeing things I’ve never seen before but always wanted to. From my school days, I’ve always been interested in biology and ‘doing things’ on my own. I absolutely detested the textbook method of learning and desired, passionately during those hours of rigorous memory-based learning, a space to understand science from through the ‘doing’ way. I longed for botany classes in the garden and learning through seeing .At the end of it all, I wanted to gain a mastery of over the lab. I wanted to overcome the morbidity of dissection and be the one who could do it the best. Like, complete control over something else’s life. Now, I don’t even understand why anything other than a member of the human species is referred to as ‘something’. You never call a dog ‘someone’.<br />
<br />
These two days of seeing so much long-desired passion, being manifested, although through someone else’s reality is giving me a path to tread. It is making me imagine myself in the shoes of the biologists.<br />
<br />
Somewhere, my understanding of the value of art seems to have diluted. Its not that I’m trivialising art in front of science, but I’m just a little lost as to where art ( actually, the commercial definition of it) seems to figure in science. Maybe it’s the constant interactions with fact-based people at NCBS, who seem to function on the power of proof. “Evidence that something works. Past-life theory isn’t a theory. Art is so subjective, its power-driven”. <br />
<br />
This is making me question what I’m doing as a student of art. Its making me realise that my understanding of art hasn’t really progressed much in the one year I have spent in the field ,beyond what it was before Srishti.I know what an artist’s output can be, career-wise. But I feel, I’m not dwelling on the right questions. I know the larger picture but not enough. Unlike some biologists I have met, who can argue their opinion, I feel I lack the understanding to argue my opinions out. Some of my counterparts in the same field as me seem to be doing this very thing pretty well, and I need to learn from that.<br />
<br />
'''A week into iGEM:'''<br />
<br />
My previous concerns seem to be slowly fading away. Oh no, they're not gone and I hope they don't to, since they're what keep me thinking. But there are new concerns. Like can artists's really get away with 'whatever they want to do'?<br />
Avni's Chicken Kailedoscope just made me think about the whole big hoo-haa about what we're doing. I mean, democratisation of knowledge, really? <br />
Again, I have many takes on this. Maybe its my lack of 'one stream of thought' (owing to dipping my hands and feet in art,bio,design all together), but I agree and don't agree with that statement all together.<br />
This might have been just a ramble, but I thought it was worth typing down.<br />
<br />
'''On Ethics and Art:'''<br />
<br />
My main issue with the chicken was not the project itself but what happens to it after the span of that hour of presentation. <br />
Most art projects end up framed in a gallery and viewed by a select few over wine and cheese. <br />
But is that really the point of what we're trying to do?<br />
<br />
'''As the synthetic biology industry hurtles into the future, civil society organizations are now asking if we shouldn't at least have widespread debate and legally-binding regulation before we rush into this great unknown?'''<br />
<br />
Now this statement (from a Genetic-Engineering article) creates this extreme commercial view of the field. Will what we do also end up like this? Will research heads choose specific projects to convert it into another money-making mania in the hands of moneymakers?<br />
And are implementing laws the solution?<br />
I think not.<br />
<br />
Getting our hands wet: <br />
<br />
Doing simple experiments like extracting our DNA from saliva and fruit helped in enforcing some momentum in 'doing' as opposed to the week of ideating that we went through. <br />
<br />
-Our Electrophoresis machine dosn't seem to work! (After 3 rounds of procedure-repeats, no satisfactory results!) <br />
This will be given to Navneet at NCBS tomorrow to see what an expert a do with it.<br />
<br />
-Study a bacterial idea thoroughly and come up with a dummy model.<br />
<br />
-Go to the registry and study the parts that need to make it.<br />
<br />
'''Food for thought:'''<br />
<br />
&quot;Scientists creating new life-forms cannot be allowed to act as judge and jury,&quot; explained Sue Mayer, director of GeneWatch. &quot;The implications are too serious to be left to well-meaning but self interested scientists. Public debate and policing is needed.&quot;<br />
<br />
&quot;Its like a book everyone is talking about but no one has read&quot;.<br />
<br />
'''Learning through doing:'''<br />
<br />
All that I have ever wanted to do in a biology I am learning to do. Those hundreds of pages of the biology textbook that I rote-learned in school without having even looked at a cell (other than probably, the ocassional onion peel) under the microscope are resufacing as I isolate,incubate,centrifuge and transform for hours together in a professional lab at a centre for breakthrough research!<br />
<br />
'''Experiments failed:'''<br />
<br />
'''Failure 1:'''<br />
<br />
The plasmids we prepared all by ourselves, following procedures from a book (Yes, it was like cooking) turned out too less in concentration. Was it an error in our understanding or our handling of lab equipment, we still don't know and probably we never will. I feel like repeating that 3 hour process as many times as possible to achieve that perfect concentration.<br />
<br />
However, I don't think that is such a negative thing after all. I can operate the centrifuge machine,the vortex mixer, micropipettes,the nanodrop all by myself.Unlike the initial absolute hesitation upon entering lab space, I am confident enough to handle professional procedures with the requisite guidance.<br />
<br />
'''Failure 2:'''<br />
<br />
So we continued the experiment with the plasmids prepared by Navneet and performed ligation all by ourselves. Since we thought dividing ourselves into groups of two or four won't lead to any greater results, we performed the whole procedure as one group. Probably the adage ' Too many cooks spoil the broth' proved true after all.<br />
However, it is also a fact that the chances of this experiment giving the required result is very low even in the case of practicing professionals!<br />
<br />
<br />
'''The Wait:'''<br />
<br />
Its been a slow week after the ending of our lysis experiment at NCBS. We're trying to work on things other than science parallely. However, as the beginning of our second year of college is approaching, I sense our group's energy dissipating.<br />
<br />
There is an increasing lack of motivation, since we still dont' know where we are going and I don't think everyone understands that this is what the trial-and-error system of learning is all about.<br />
How we plan to coordinate cirriculum work and this project, is also proving to be a major challenge.<br />
<br />
[[File:Bacteria own.jpg|200px|thumb|left|Materialistic Destructilla-Biological Information-Page1]]<br />
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[[File:Bacteria own2jpg.jpg|200px|thumb|left|Biological Information-Page 2]]<br />
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[[File:TheArtScientistA.jpg|200px|thumb|left|'TheArtScientist'-Page 1<br />
<br />
A satirical view on today's ArtScientist]]<br />
<br />
<br />
[[File:The Art ScientistB.jpg|200px|thumb|left|TheArtScientist-Page 2]]<br />
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[[File:NehasDNA.JPG|200px|thumb|left|DNA extracted from my saliva]]</div>Target022http://www.hackteria.org/wiki/index.php?title=Sayed_Nooshin&diff=3064Sayed Nooshin2010-12-11T19:25:32Z<p>Target022: </p>
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<div><br />
'''Log book'''<br />
<br />
May 10<br />
<br />
First day of class we were introduced to the basics of the cell and its different organelles. Learned about the history of biology and about eminent people like Antony Van Leeuwenhoek, Robert Hooke , Louis Pasteur, Theodore Shwann, Gregor Mendel, Watson &amp; Crick, George Church and Craig Venter. Introduction to the theories of evolution as well as DNA and its function. Did some research on E-coli . We were given readings to go through to better our understanding of DNA, Human genome and such. Watched a BBC documentary based on the cell. Typical day but not a bad start to who knows whats in store for us later.<br />
<br />
May 11<br />
<br />
Today we watched a video lecture by David Sadava. Talked about the nucleus, genes, chromosomes genetic information phenotypes and genotypes. We were first introduced to synthetic biology today. A reading called Introduction to Synthetic Biology. Watched a video on the Darwinian theory of evolution. Lots of info pouring in and lots more to come. Learned something important today though :- Always be sceptical of what you read.<br />
<br />
May 12<br />
<br />
Video lecture by David Sadava on the capacity of the DNA to mutate, experiments giving insight on it, How lung cancer was caused by damage to the DNA due to smoking. Function and structure of DNA in different types of cells including viruses. DNA double helix structure. Cell theory proposed by 2 german scientists – Jakob Matthias Schleiden and Theodore Schwann. Viruses are composed of dna and protein. Discussed theories of evolution. Watched a video on tedtalks on Watson where he describes how they happened to come up with the DNA model. Two readings for the day – applying engineering to biology and adventures in Synthetic biology, the latter being a comic strip on the know hows of synthetic biology.<br />
<br />
May 13<br />
<br />
Todays lecture video was about proteins. How it is produced, the role of dna in producing it, the process and its properties.Watched a video showing the process in real time. Lecture touched Ricin, a poisonous substance and its discovery its chemical structure and experients done with ricin. This substance kills by inhibiting gene and is found in castor oil. We were getting somewhere with all the research that we’d been doing on our subject matter. Gained a slight picture of what we are dealing with and also a little know how on how to do it as well.<br />
<br />
May 14<br />
<br />
Video lecture talked about DNA sequencing and the different methods of doing it. Craig Venter explained his method but could not comprehend it completely but I have a general picture of how the sequences for different functions and organs are on specific sequences of the DNA. Learned the humans cannot produce 8 of the 20 amino acids required because of some defect in the DNA. Other bacteria produce it for us. Naked and Vector DNA. Cohen and Boyers experiment with bacteria and viruses. DNA recombinant technology where a required gene can be isolated and introduced into the dna of bacteria , for instance to induce resistance to antibiotics.PKU presence of a certain enzyme causes mental retardation . <br />
<br />
May 17<br />
<br />
Lecture on isolating the gene . Muscular dystrophy is a progressive reduction of the muscles and its function. It is caused by a missing sequence of DNA in chromosomes. Reverse genetics is when the gene is figured out before the protein is. This is contrary to the traditional method where the protein is analysed to produce what gene made it. He talks about Nucleic Acid Hybridization wherein the the complementary pairs to the target base is filtered and isolated. This in turn binds with another pair (a complement) that is the same as the target pair. If nothing binds then the outside dna does not have the dna with the same sequence.<br />
<br />
May 18<br />
<br />
Watched two more parts of the BBC The cell documentary .It goes on to describe the application of synthetic biology and showed graphic visuals of how the mRNA transfers genetic info to the ribosomes so as they can produce the required protein. Saw some interesting prospects of synthetic biology. Bio diesel.<br />
<br />
May 19<br />
<br />
We had a presentation by Zackery Denfeld about genetically modified organisms like Glofish, that are now commercially available for purchase.These are not for consumption though. We extracted our first DNA, with the help of pril and rubbing alcohol. <br />
<br />
May 20<br />
<br />
Our ideas on the new creature were discussed. The ideating was done in groups of two. Lots of crazy ideas, bacterial holograms, bacterial sonic sheets (idea was they are to be used instead of conventional speakers. Just a strip of paper containing bacteria that can produce sounds. Can be connected to playback devices). This involved a lot of playing with the mind. Since we were asked to come up with anything, our options were huge and since we had to come up with abstract or almost impossible it was a lot of conceptual exploration. I enjoyed this quite a bit.</div>Target022http://www.hackteria.org/wiki/index.php?title=Talk:Read_here&diff=3063Talk:Read here2010-12-11T19:25:05Z<p>Target022: Blanked the page</p>
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'''Aim''' <br />
<br />
To be able to view the DNA bands under ultra violet light.<br />
<br />
<br />
'''Apparatus'''<br />
<br />
*beaker<br />
*pippette<br />
*casting plate<br />
*electricity generator<br />
*comb and comb stand<br />
*nitrile gloves<br />
*UV light box<br />
<br />
<br />
'''Material'''<br />
<br />
*Agarose<br />
*Buffer solution- TAE(Tris-Cl, Acetic Acid, Ethylene diamene tetra acetic acid)1.0x pH 8<br />
*Ethidium Bromide (5.25 mg/ml in H2O)<br />
*A low molecular weight dye, bromophenol blue<br />
*Antibiotic resitant gene(from ampicilin)<br />
<br />
<br />
'''Preperation'''<br />
<br />
* Make a 1% agarose solution in 100ml TAE, for typical DNA fragments. For 3-4 kb solution of DNA a solution as low as 0.7% is used. <br />
* Heat this mixtue to 37 degree C and let it cool.<br />
* Now on wear gloves and add EtBr of 0.5 ug/ml concentration.<br />
* Stir the solution and pour it into the the casting plate.<br />
* Now insert the comb at one side of the gel about 10mm away from the side.<br />
* Once the gel has cooled down and become solid, pull the comb out.<br />
* The holes that remain are the wells. The DNA samples travel ahead through these wells.<br />
* Put the gel along with the casting plate in a tank with TAE, EtBr at the same concentration can be added.<br />
* The gel must be completely covered by TAE and placed such that the wells are at the end electrode passing negative charge.<br />
<br />
<br />
'''Images'''<br />
<br />
&lt;gallery&gt;<br />
File:DSC01420.JPG<br />
File:DSC01425.JPG<br />
File:DSC01456.JPG<br />
&lt;/gallery&gt;<br />
<br />
'''Procedure'''<br />
<br />
* Using a micropippette inject 2.5µl solution with the DNA ladder into the first well (DNA ladder-DNA of previously known lengths) along with the low molecular weight blue dye.<br />
* In the same way now inject the DNA samples mixed with the blue dye into the other wells.<br />
* Now a current is applied, about 100V for 30 minutes.<br />
* Lastly place the slab of gel on a UV light box and observe.<br />
* One can also capture a digital image of the same.<br />
<br />
<br />
'''Safety measures'''<br />
<br />
* The chemicals used are highly toxic therefore the use of gloves inevitable.<br />
* The disposal of tplatic waste used during the process or even chemical should be done in a seperate bin and ultimately to its correct destination (incineration).<br />
* Washing hands with soap must not be forgotten.<br />
<br />
<br />
'''Observations'''<br />
<br />
(1). A ladder is observed as the first column and bands of DNA in the others.<br />
(2).DNA markings are observed to have moved from the negative electrode to the positive electrode.<br />
(3). The bands are various shades of orange when seen under the UV light since EtBr gets collected between two strands of a DNA. <br />
(3). The smaller DNA is seen to move faster towards the positive electrode where as the bigger DNA are slower.<br />
<br />
<br />
'''Conclusion'''<br />
<br />
Through the process of Gel Electrophorosis one can observe the DNA bands under UV light and also say that DNA carries negative charge.</div>Target022http://www.hackteria.org/wiki/index.php?title=The_Specials&diff=3061The Specials2010-12-10T17:25:47Z<p>Target022: </p>
<hr />
<div><br />
Coming soon, my thoughts on the talk about Darwin's theory of evolution.</div>Target022http://www.hackteria.org/wiki/index.php?title=Samrajni_Patil&diff=3060Samrajni Patil2010-12-10T17:25:01Z<p>Target022: </p>
<hr />
<div><br />
''' To read special entries click here &gt;''' [[The Specials]]<br />
<br />
<br />
[[ Useful Links ]]<br />
<br />
== '''Journal''' ==<br />
<br />
<br />
'''10th May 2010<br />
'''<br />
<br />
Honestly all I knew about this competition was that it had something to do with biology and it was the memory of how much I used to love biology back in the tenth grade that motivated me to take it up. Also, there's a bit of a science fiction fan inside me!<br />
<br />
We started work today. The majority of us being purely Art students came with the little knowledge that high school biology provides. We learned that we have missed out on a lot of details and that there is a sea of information out there that we need to know in order to fully and effectively exercise our creative skills.<br />
<br />
Although I love biology I realised that I remember very little of what I had been taught, so I asked myself, how much do I remember? Though it seemed like a lot, the group discussion made me realise that it was hardly anything; most of what I remembered was either jumbled <br />
up with something else or was too vague and flimsy, and there was also quiet a lot of stuff that came out of no where...spontaneous generation? ha!...figments of my imagination!<br />
<br />
We spoke about each of our perceptions on biology, a system, cells, DNA, genes and proteins, genetic splicing and what genetic engineering is all about.<br />
The theories on the origin of life and from where or how living cells came into existence, especially with so much diversity was another thing we discussed. Every theory makes sense in its own way, even with Pasteur's simple experiment to disprove the theory of spontaneous generation, no one can explain how the first cells, if there is a first that is, came into existence. As Karthik pointed out our brains are practically hardwired with the theory of cause and reaction, it is only natural that we assume that everything has an origin, things can't just pop out of nowhere. I personally believe that we don't know enough to disregard or discard seemingly irrational theories. Anything is possible.<br />
<br />
The bbc documentary on cells gave us substantial insight into the history of the discovery of the cell and about the invention of the microscope; about Antonie van Leeuwenhoek and the other pioneers who planted major landmarks in the world of science.<br />
<br />
We were also constantly trying to make sense of how we can contribute our skills as artists and designers to this world. <br />
When we started to learn about what genetic engineers did and about gene splicing and gene sequencing, it made sense, it's all an art; a gene sequence is like a colour, mixing different sequences would produce different results, i.e. different colours, the way you compose them on a canvas is the art. Once you get a hang of how to make the different colours, you can compose it anyway you like.<br />
<br />
----<br />
<br />
<br />
'''11th May 2010'''<br />
<br />
I got my kiddie microscope to class today, it isn't too bad, magnifies up to 600x. We placed a droplet of muddy water on the slide and we were able to see what looked like little translucent worms, but we weren't sure if it was just the dust and scratches on the lens or if it was in the water. Then we tried placing a thin piece of sliced leaf and saw the pores on its surface. We tried making a microscope using an old Logitech webcam, it was interesting to know that all we had to do after dismantling the webcam was invert the lens! This made me realise that there's a lot of old stuff in all our homes which we could play around with and create new things; recycle and rebuild for some other purposes. <br />
<br />
Then we watched videos on the Mendelian theory, how he observed and theorised the process of genetic inheritance using the pea plants, we were given examples of how this works in human beings. We learned about genomes, chromosomes and genes, a chromosome is sort of like a complex pack of genes. A gene in itself contains strands of DNA, which in turn contain pairs of bases-ATs and CGs. <br />
<br />
For me, the coolest part was that Mendel was a monk and Antonie van Leeuwenhoek was an apprentice to a cloth merchant; and both of them are now seen as the forefathers of today’s ''Science''. Growing up in a time when the Arts and the Sciences were perceived as immiscible (for the most part), it was empowering and reassuring to learn that just about anyone could be the next person to go down in history for discovering or coming up with an idea that could prove to be invaluable to the world.<br />
<br />
----<br />
<br />
<br />
'''17th May 2010'''<br />
<br />
Apart from watching more videos about genetics, our task today was to create an imaginary creature. It could be absolutely useless and whimsical. These kinds of assignments are my personal favourite! <br />
<br />
I've thought about this many times (although not in this context).Ever since I was little I remember imagining creatures; watching cartoons and TV shows with things that you wouldn't really see living on your planet makes you wonder and makes you dream about your own little (or really huge) creatures. Recently while watching Avatar I was constantly imagining things and I was really excited to do this exercise.<br />
<br />
So my creature would be something that floats or flies. I wanted it to be translucent with a slight portion of its insides visible to us on the outside, I wanted it to be roughly the size of a medium sized bubble or a tennis ball. I wanted it to be a wobbly sphere.<br />
<br />
Now, I didn't want my creature to be completely useless, since we are in great need of air purifiers, especially in big cities like Bangalore, why not create something that fed on the pollutants. Every time the pollution increased in the atmosphere these little creatures start sprouting out. It's their source of nutrition. I decided to name it Purgcaelum. It's latin for purify air (purg and caelum respectively).<br />
<br />
[[File:Purgcaelum.jpg]]<br />
<br />
I found that Nitrogen oxides are major pollutants, so I wanted Purgcaelum to be able to turn the nitrogen oxides into ammonia that could be helpful to plants. I wanted it to perform the role of nitrogen fixing bacteria! I'm not sure about how scientifically possible this task is though...<br />
<br />
''We're also doing a living art piece.'' Using any medium of portrayal, we're going to take a living thing and study it's pattern of growth or behaviour. As against cruelty towards living things as I am, I decided to study fireflies to see how I could control their behaviour (I will let them free ofcourse). Finding them around where I live however, is very difficult. I'm not even sure if it's their habitat. <br />
<br />
After a lot of research, I found that sadly '''fireflies all around the world are endangered'''. Well, seeing a firefly in itself was a huge deal for me as a kid, forget catching one. I haven't seen one in years. It's extrememly sad. We should save them.<br />
<br />
----<br />
<br />
<br />
'''24th May 2010'''<br />
<br />
Our previous ideas for creatures while crazy weren't crazy enough, so we set out to intensify their crazy quotient. <br />
<br />
I thought up a whole new idea. And this is most definitely not possible, atleast won't be (I think) for many many years. And it is that, my creature is able to carry out the process of nuclear fission with in its body. It has a lining of concrete to protect its out membranes from exposure to the radiation and for it to coexist peacefully with the other organisms. Now why it needs this process is to create enough energy to produce enough pressure to survive both in shallow waters and in the deepest parts of the ocean. It has a highly developed pressure sensor. <br />
<br />
<br />
[[File:PhotoFish11.jpg]] [[File:PhotoFish22.jpg]]<br />
<br />
<br />
Very little of the earth's seabed/ oceanbed has been explored by mankind due to the high amounts of pressure and this creature would be just the thing we need to look into the unexplored. It also has photogrpahic memory which we can easily access since its brain can be hacked into by humans. Again it is sphereical in shape with many pressure nodules on it's surface, it has eyes, a mouth and breathes as well. The nodules also act as the pressure sensors. <br />
<br />
A colony of these creatures can be used to harvest energy to power whole cities. <br />
<br />
Just got back to college today after four days of being ill, I missed out on the DNA extraction, but was explained the process of how it happens and how it looks. I never imagined it to be so simple, the very term 'DNA extraction' sounds like one needs an entire lab (like dexter's lab) to facilitate it! <br />
<br />
This made me think on a more philosophical note; all the things that we think are really difficult, that are complicated and almost impossible to do are sometimes and most of the times the simplest and easiest to do, while the ones which we wrongly assume to be easy end up being really tough while doing them.<br />
<br />
----<br />
<br />
<br />
'''25th May 2010'''<br />
<br />
We FINALLY went to the National Centre for Biological Sciences (NCBS) today! This place is bea-uti-full!!!!! It's so fancy, shiny labs, awesome rooftop cafes, and a dinning hall with inexpensive yummy food (or so I heard). We were supposed to meet up with Mukund, but couldn't since he was busy but we did get to meet another scientist, Shorab(I not sure about the spelling...) who spoke to us about the experiment he was working at that moment(literally, he'd even timed himself and the alarm went off for him to go back while he was in the middle of our discussion). It was to do with mice brains and their brain activity, he said a lot of things about the synapse, which I cannot recall since a very little of it made sense...but it did sound very interesting. <br />
<br />
However what caught me was that he had to kill the mice before he worked on slices of their brain. <br />
He said that they're anesthetised before they're killed so I don't think they feel pain; they are not employing cruel methods, so that's good. <br />
<br />
We met another scientist, who showed us around the labs and told us what the different machines do. It was amusing to find out that half the machines in the lab were only used to mix ingredients! <br />
<br />
Also, we had a very interesting conversation in the morning at NCBS, it was about how a scientific institue could afford to be so luxurious while a majority of our country was starving and shelterless. How does our government prioritize? Does it even prioritize? We came up with many explainations to this, but I wonder, are we in a position, as a 3rd party, as outsiders to both the groups in question, to make assumptions about the situations. I think we need to listen to both stories and the government's story, and only then can we make a fair judgement. <br />
<br />
<br />
----<br />
<br />
<br />
'''30th May 2010'''<br />
<br />
Finding fireflies is super hard! So while I'm still on the look out for them, I decided to try my music test on ants. I took two different kinds of ants. I'm not sure I can identify them because there are 632 different species of ants in India! All I can say is that on was a big black ant, with a longer body, while the other was smaller with a boxier body. <br />
<br />
I put them in the glass bottle I'd saved for the fireflies with a two long leaves for company. The bigger one was more active on the whole, while the smaller one was mellow. I strated off playing really loud hip hop! It didn't seem to faze them much, the big one became more limited in it's exploration of the bottle while the smaller one hid under one of the leaves. It was very still through out. Next I gave them same quiet time. The big one resumed running around, the small one was still under the leaf. I started playing 3oh!3, then tweaked it by increasing the pitch (which was very very disturbing) and this time I played it on ear phones and I hung one ear phone into the bottle midway. Again they did the same thing, the little one was still under the leaf and the big one froze up on one of the leaves. I took the ear phone out and played it out loud, same reaction. <br />
<br />
[[File:AntonLeaf.jpg]]<br />
<br />
Now here's the interesting part, I played Explosions in the sky, who are a lot more soothing to human ears than 3oh!3 and the little guy actually came out from under the leaf, I don't know if it was just him getting used to the music but at one point it was as though he was coordinating his leg and antennae movement to the music. It probably was just coincidence or my imagination going wild but just to double check I'm going to repeat this experiment with different ants. Let's see what happens! <br />
However, I didn't see reaction as pronounced as I was hoping! <br />
<br />
Moving on, hre's another idea. Instead of plastic, we could use bacteria. Bacteria which we could use in all the ways we use plastic, for bags, containers, clothes etc etc. The best part is that it's biodegradble! When the bacteria start dying we just put the product in a compost bin and use it as manure! <br />
<br />
I had an inkling that there is already something like this out there, and yes there is, so take a look at this, it may not be exactly what I'm talking about but it's close enough to what I'm saying! http://www.scientificamerican.com/article.cfm?id=turning-bacteria-into-plastic-factories-replacing-fossil-fuels<br />
<br />
<br />
----<br />
<br />
<br />
'''1st June 2010'''<br />
<br />
We tried to grow yeast today! We went up to the Aditi Lab and made some agar. We then tried colonising three different forms of yeast on the agar plates. One plate was smeared with dry yeast mixed with room temperature water, one with yeast in warm water and another with just dry yeast. We will leave it undisturbed for two days and see what happens! <br />
<br />
<br />
----<br />
<br />
<br />
<br />
'''2nd June 2010'''<br />
<br />
<br />
Today, we went for a talk and presentation on Darwin's theory of evolution by Dr. Narsimhan at the National Institute of Advanced Studies. It was mainly a discussion about how much chance and how much design is involved in the making of the world. The presentation definitely brought on some questions and confusion, which I will write about in detail soon (which I will post in my Special entries section). <br />
<br />
Later that day we went to NCBS again, we met Mukund (finally!) and he showed us around the area where we will be working. He also suggested that we make our own lab equipment! So this should be really cool! :)<br />
<br />
<br />
----<br />
<br />
<br />
'''3rd June 2010'''<br />
<br />
<br />
We started work on building our lab equipment. We did some research on how to build incubators and centrifuges. I always felt that we needed something super fancy to make things happen but this course has kept surprising me with how much we can do with stuff we have lying around at home!<br />
<br />
We had a look at what had happened to the yeast on the agar plates (to see if there were any colonies) and only one had some kind of growth, the one sprinkled with dry yeast was the only one that showed some kind of development while the rest were not so successful. <br />
<br />
We also tried a new formula for the agar plates, we changed the agar:water proportions to see which one gave the best results.<br />
I think the one with 5g of agar to 250ml of water worked the best, it wasn't too dry and hard nor was it too gooey. <br />
<br />
----<br />
<br />
<br />
'''7th - 12th June 2010'''<br />
<br />
<br />
This week was mostly about constructing our lab equipment, with the centrifuge not cooperating with our attempts at trying to make it work, it was a little crazy and at times frustrating. We got a table top mixer, we tried connecting a pipe to it's blade which we were hoping would spin, but the pipe was almost impossible to keep stable on the blade without making it permanent, and since we weren't sure about whether the rest of the idea would work or not, we needed something temporary, so after a lot of trial and error, we figured that all we need was the axis on which the blade rotated, if we could fix a round disc or metal trips on the part where the blade goes it would prove to be a lot easier, and as it happens it was a lot easier. We also had to deal with strong vibration and we were able to do away with them as well. Once the sealant used for covering the bottoms of the test tube holders has dried completely we will try this out, it should work. <br />
<br />
Simultaneously, we made a hand held centrifuge using a hand blender. This was relatively easier to make since we had learned how to dodge certain problems from the table top version. It's quiet effective on chalk powder and poster paint but we still haven't tried it on actual DNA. I hope it works, this one's sort of like my baby :D. <br />
<br />
The incubator was stubborn too, we only got it to maintain a near steady 37 degrees C on saturday. We realised that the thermocole ice box didn't really need aluminium foil lining and a light bulb beacuse these made the temperature rise over 100 C, with the clinical thermometer bursting! We also figured that it needed an industrial thermometer and four fans instead of the initially estimated, one. With four fans and a mosquito repellor providing heat our team mates were able to notice an almost steady temp. of 37 degrees C which was exactly around what we were hoping to achieve. Now all we need to do is see if the mosquito repellor affects the specimens in the petri dishes, if it does, then we will have to find an alternate source of low heat. I was thinking maybe a few Christmas lights or the little blubs used in torches, I think they would provide enough heat and we we could just use batteries to power it; making it more portable. <br />
<br />
Can't wait for Monday!:)<br />
<br />
----<br />
<br />
<br />
'''14th, 15th and 16th June 2010'''<br />
<br />
<br />
Alexandra and James are here! We presented a slideshow of our progress until now and they showed us their work.<br />
<br />
On the first day, we spoke about our ideas and categorised them under the categories made by the Design for the First World competition. From what I gathered from the discussions that we had, trying to &quot;solve&quot; a problem is such a western thought and while critiquing western design it wouldn't really help us to think in exactly the same way that has been there. And this does make sense. <br />
<br />
On the second day, we were asked to look up a previous Igem teams' project and imagine that this idea was actually being put into effect sometime in the future. We chose Team ULB-Brussels' project Glucoli, a bacteria which secretes a biodegradable and natural adhesive. My initial idea behind proposing to use this team's project in context was that, this product could be used as an innovative way to kill people. Since our exercise was to report the repercussions of the product as a news report, I felt that this idea would make a good story to report. Later my team mates and I changed it up a little to make a new story. However, I think a little more organisation from our side would have been more justifiable to our portrayal of the situation.<br />
<br />
On the third day, we were split into groups again, this time it was to actually take part in the competition we had designed the day before which is for bio-artists and designers. It's called IGEA, the International Genetically Engineered Art Competition.<br />
<br />
Our team was supposed to make a piece of art that fit into the categories - a Social Critique and an example of the Remix culture. We came up with many ideas, one of mine was to question our idea of personal space and hygiene. We're always so fussy about personal space and hygiene, especially me, and I wondered what would happen if we knew just how many people had touched every single object around us before we touched it. Would we be disgusted? would we feel like perpetually living under a wash basin? Or would it make us feel more at home? Less lonely, more connected? While this idea was a social critique, we couldn't see how it could connect to Remix culture. <br />
<br />
Anyway, we finally ended up questioning where genetic engineering will take us in the future? an evolutionary glass ceiling? <br />
<br />
Here's my interpretation of how our group poster could look -<br />
<br />
<br />
<br />
[[File:EvoMan_small.jpg]]<br />
<br />
''I don't know whom to credit the original(unmodified) picture to, I hope whoever it is doesn't mind and isn't offended that I modified it.''<br />
<br />
----<br />
<br />
<br />
'''17th, 18th and 19th June 2010'''<br />
<br />
<br />
On Thursday, we had a presentation on telling stories. We watched clips of the movies The Man in the White Suit and Spirited Away (A Japanese anime....which was very interesting). We also looked at Polish film posters. Generally film posters aim at easy readability, and a sort of in your face message, but these posters were abstract, unless you knew what the movie was about you wouldn't know what the poster was trying to convey. So in a way I think this a clever strategy; you go watch the movie just to decipher the poster! Makes you wonder about how Polish people think....they must have a really interesting thought process! <br />
<br />
We were also supposed to re-work on our presentations and present them on Friday. Our group decided to take up a new idea since all of us felt that the previous idea was too generic. Our final idea was to make bacteria which tell you what the weather is like by playing a certain music playlist. We called it E.Cloudy. <br />
<br />
We went critical on this project. We looked at almost every aspect of what could go wrong with it and what could become popular. We listed it out and I think this really helped us sort out the project. In the end it worked out well, but we hoped to make a 3D model which we couldn't, but we will some time soon. <br />
<br />
On Saturday, we read some stories from the Amar Chitrakata books about Shiva and the other Gods. I'm not an extreme feminist but some parts of the story set something off in my head and I just couldn't get around the fact that women were treated and perceived in the way that I perceived them in the stories. Maybe it's just me, but yeah this was sort of annoying. However I didn't know a lot of these stories so it definitely was good to read them. <br />
Anyway our idea behind reading these was to see what hybrids and genetic engineering we could find in our Hindu mythologies. One of the groups that presented had worked on how sages in history would go into a state of trance due to the internally produced DMT (which I think is really awesome! :D) and there were also talks about Shiva's third eye, and this led me to think about all the other Gods, like Hanuman, Brahma and Garuda, all of whom are very modern images of science fiction. It brings you to question how our ancestors imagined these things, what made them believe that these things were in existence and were possible, was there a time when such people (or Gods?) did exist? <br />
<br />
----<br />
<br />
'''23rd June 2020''' <br />
<br />
The soma bacteria <br />
<br />
This idea of the soma bacteria is primarily inspired by the popular Hindu myth of the samudra manthan , commonly known as “the churning of the ocean“.<br />
The phrase “soma bacteria” comes from the drink of “soma”, which is a drink primarily behaving as an anesthetic in the famous mythical incident of Samudra manthan. <br />
<br />
'''Now we come to the working of the bacteria:'''<br />
<br />
The soma bacteria are not just one bacterium but a pair of bacteria, which are co- dependent, and they are unstable in the absence of each other. One bacterium is harmful in relation to the human body, whereas the other one is harmless, but it is to be noted that it is not of a curative nature. The habitat of these bacteria is common rust. While they live in their rusty habitat, they live in colonies but there is no activity of exchange taking place. <br />
The minute it comes in contact with the human body, the bacteria get activated at once. It commutes throughout the human body, causing harm. The minute it comes in contact with a WBC, the two bacteria start exchanging their genetic material rapidly. While the WBC recognizes that one bacterium is harmless, it also realizes that the other one is harmful. But due to the rapid state of exchange of genetic material, the WBC is unable to recognize the harmful one and try and kill it. While the harmless bacterium contains a protein, which the WBC cannot counter, it cannot kill either of the bacteria. Thus, the WBC can never destroy the soma bacteria at any given time.<br />
<br />
----<br />
<br />
'''June 21st to 26th 2010'''<br />
<br />
<br />
'''Monday''' - Daisy's Birthday!!!!! Happy Birthday! :D This day, we looked at how we could organise potential synth bio material we had collected from the myths we'd read. We looked at<br />
categorises such as Soma ( a durg like substance believed by some to be a drink of immortality and and by some as an anesthetic, a drink that keeps you happy), jugaad ( I finally know what this word means!!!), Karma and Immunisation against a Disaster, etc. <br />
<br />
Later in the day, we tried to take the way the myths were told and use them in context of a synth bio scenario. Anusha, Diya and I teamed up to come up with something. Our initial idea sprang out of us questioning the role of Priests. We wanted to create a bacteria that specifically killed priests. We thought we could make bacteria which lived in Camphor, which in Inida we use to burn and use as little lamps in temples!<br />
<br />
We also went over to Yashas' place to hear Arshia Satta talk about Shiva and clarify our doubts on the mythologies we'd been reading. Further thoughts on this will come up in my specials page! (Look at the begining of my page)<br />
<br />
'''Tuesday''' - We started making our stories more scientific. We decided on bacteria which rapidly switched genetic material and dodged WBCs in the human body. They need to do this since one of the bacterium in the pair of the co-dependant bacteria is seen as harmful by the WBCs while the other one which produces histamine isn't seen as a foreign body. This bacteria lives on iron and feeds off the haemoglobin in the RBCs. <br />
<br />
We made a poster for our bacteria. <br />
<br />
'''Wednesday''' - we re-iterated our poster for our bacteria since it wasn't very vocal. This time I think it made more sense. This day we also made an enormous mind map which included everyone related to synthetic biology. <br />
<br />
'''Thursday''' - We finished making our power point presentation on the Biobricks that would come into play to make the Samudra Manthan bacteria possible. We were supposed to present it to Mukund and seek scientific opinion but he had to cancel for some reason. We will hopefully present to him next week. <br />
<br />
We also met the Level 10 Comics guys today and what was really nice about their work was that it was based in familiar spaces. Their stories about Bangalore (and an illustration which showed Mallya Hospital in ruins after a zombie attack) were brilliant, it was a different expirience than compared to stories about Cities in countries we've never been to, localising these stories we've been hearing and watching in cartoons and movies is another thing! It was fun! Next time I'm somewhere close to the Vidhan Sauda I can't help but start imagining half dead people and blood all over the place!!! And I think this is the only time when I'll be soo excited to see such mayhem in our city!!!!<br />
<br />
We were also invited to a play by Aditi at Alliance Francaise that evening. It was called The Clearing. It was awesome! I loved it! It was a story weaved around a plant called lantana! <br />
<br />
'''Friday''' - We spoke about designing entire ecosystems, if it's possible and has anyone done it before successfully? we thought about designing ecosystems that include our mythological bacteria. In our case for our Samdura Manthan Bacteria I felt that it would work well as a weapon. So if we used in in darts and bullets they could be really lethal!!!!!<br />
<br />
We found out that due to a political situation in the City we would have to leave early, so we split research work on the various actors we'd included in our giant mind map with which we will design a comic story on Monday! My task was to investigate America, Obama, the CIA etc and all their connections with Synthetic Biology. <br />
<br />
'''Saturday''' - Farhad, Aaron and I extracted my DNA. We were supposed to use the Hand Held Centrifuge, but the Centrifuge's Twist and Lock contraption seems to have melted beacuse of the heat created by the extra friction caused by the weight that it wasn't meant to take. We will send the blender back to the company to have the Locking system fixed. Only then can we see if our centrifuge works on actual DNA.<br />
<br />
----<br />
<br />
<br />
'''28th June 2010'''<br />
<br />
With all the information ready to be used, we spilt up into teams again to work on our mythical stories.<br />
We chose a few characters from the list of characters we'd researched on and began weaving stories around them.<br />
One of the scenarios that my team ( Akshitta, Anusha and Karthik along with me) thought up was about an utpoian world. Utopia; an ideal place or state.<br />
The dream world; everything you want happpens and you're always happy, but who's dream world or ideal space are we talking about? Everyone's ideal space <br />
could be different. <br />
Another thing was that Akshitta and Anusha felt that such a world wouldn't last long, they felt that not everyone would want and be satisfied by <br />
the materialistic convinience that our imagined world was going to provide for mankind. We spoke to Avy about our idea and he too felt that the utopia that<br />
this place offered would hold no interest to him since the material things that this world offers make little or no difference to his well being. <br />
<br />
We did understand this concept, we spoke A LOT. There were conflicts and there were points where everyone was in agreement with each other but we didn't really <br />
realise in the heat of the moment. In the end we decided to use this story in some way or the other since it was capable of creating so much conflict. <br />
<br />
Our story is based on Venter, the Transhumanists and the National Institutes of Health (USA).<br />
<br />
<br />
'''30th June 2010'''<br />
<br />
This day we looked at 'Human Practices'. How would people react to the things we were doing? How could we communicate what we're doing to the common public, hold their interest?<br />
Which part of the demography would show real interest in our project? How could we start DOING things?<br />
<br />
We decided to start off by interviewing the people we found around Srishti and a small bit of Aditi. We interviewed teachers, lecturers and some students. It was interesting<br />
to find so many differing views and some with unique reasoning but with tangents coming into the common notions. <br />
<br />
This day was also the day we finalised the idea of trying to develop an ecosystem as our final project idea for the competition. <br />
<br />
<br />
'''1st July 2010'''<br />
<br />
We went to the lab today. We prepared the e.coli cultures for performing the GFP gene transfer the next day. <br />
<br />
<br />
'''2nd July 2010'''<br />
<br />
This day we did the gene transfer. It was really cool since we got to do a lot of the procedures ourselves. <br />
<br />
<br />
'''3rd July 2010'''<br />
<br />
We went to check up on our cultures. We looked at the modified cultures under UV light and they were glowing!!!!!! This was our first proper success as a team!<br />
<br />
Now we break for holidays and it's also the last day that James was with us. We hope that Daisy and him can come back again in September!<br />
<br />
<br />
'''8th July 2010'''<br />
<br />
A few of us who were still in the city met up to discuss what was left to be done, things we could finish off before we met the next saturday. <br />
Yashas suggested making a movie for the movie competition. We took pictures of potential locations to shoot in Bangalore.<br />
<br />
All of us had something or the other to finish before next saturday. <br />
<br />
<br />
'''14th July 2010'''<br />
<br />
We all met up to see where we were at. The Stories needed to be finished and emailed to James. The Jugaad lab was supposed to be set up and tried. We also told everyone to <br />
take pictures of good shooting spots for our movie if and when they go out.</div>Target022http://www.hackteria.org/wiki/index.php?title=Mohor_Mukherjee&diff=3059Mohor Mukherjee2010-12-10T17:23:36Z<p>Target022: </p>
<hr />
<div><br />
'''iGEM 2010'''<br />
<br />
<br />
'''An overview''':<br />
<br />
'''Designers and biology'''. Confusion in minds. Well stepping out of the visual world depicting our minds and stepping into synthetic biology was not exactly a big leap but it was a sure headed decision. Not like I was an avid biology lover but I never really had an issue as long as I could make sense of it. I consider it to be just another part how our system works besides the political, the geographical, the economical etc. And to bind all this together is design. Which to be or to not be considered is related to everything. Hence here we as a part of a design school taking part in a synthetic biology project.<br />
<br />
<br />
'''JOURNAL'''<br />
<br />
<br />
'''10th May'''<br />
<br />
Landing into '''Bioland''', Basement Computer Room, Srishti School of Art, Design &amp; Technology. Our very enthusiastic facilitator Yashas and most of the participants as residents , not to forget Avy walking in and out with “you have intruded my land look”. So we start our iGEM project. Discussions, questions, vague ideas were predominant topics of the day. Soon we moved on to our much awaited introduction with Dr.David Sadava’s lecture videos. Interesting...mind-boggling and a heavy start to the project. Basics of biology-'''cell theory''' are what we learnt about today. Memories were brought back of sitting in school and attending biology classes and scribbling here and there. By lunch break I was sick. <br />
<br />
'''11th May'''<br />
<br />
Down with fever. :(<br />
But I was doing research on '''e.coli, evolution, Darwin and articles about Genetics.'''<br />
<br />
'''12th May'''<br />
<br />
Back to catching up with yesterday’s work. Saw the '''webcam''' that has been used as a '''microscope'''. Quite interesting. Learning more about chromosomes, their functions, '''allele''', genes, mutations, how duplications in biology are termed as replications and in depth about genetic material. So by the end of the day I was already humming some random tune saying '''ATGC..ATGC..ATGC'''.......!<br />
<br />
'''13th May'''<br />
<br />
Writing the chemical form of a '''protein molecule''' showing the bonds brought back memories and built up some kind of enthusiasm contrarily. '''Biochemical pathway''', '''thermodynamics''' led the way of learning today to '''gene transcription''', '''gene translation, genetic coding and descent with modification.''' Atleast it got me to wonder if each of us are results of some genetic mutation while having a discussion with Anusha. Learnt about ricin and how Sadava describes it with his expressions as “scary”...”poisonous”! <br />
In the process as a start to our experiments &quot;we need to extract DNA asap!&quot; –Yashas.<br />
<br />
'''14th May'''<br />
<br />
An extensive discussion on '''genetic damage and cancer''' was intriguing. Further it led to '''bio-informatics, hierarchical sequencing, shot-gun sequencing and of-course re-combinant DNA.''' It’s been four days and we are quite loaded with biological terms. Hoping to have them on our finger tips soon.<br />
<br />
'''17th May'''<br />
<br />
Didn’t know that biology could be so experimental..to the extent of '''reverse genetics'''! An intensive study of how synthetic DNA can be used to make new genes! Besides, today we had to design our own organism and it could be even fantastical! Yay! So I am thinking....<br />
<br />
'''19th May'''<br />
<br />
“Innovation is disruptive because it challenges assumptions and creates hybrids” – learning of the day from Zack besides having extracted Aaron’s DNA from his cheek cells.<br />
Zack gave us a talk about food production and eating disorders and led us to knowing terms like '''biohackers''', geohackers etc. He gave us an insight into cross species cookbooks, transgenic food etc. It feels quite good to be exposed to so much of knowledge. Hopefully I can make use of it someday.<br />
<br />
'''20th May'''<br />
<br />
I think I know what my organism does by now. I haven’t named it as yet but I am quite kicked about its functionalities. '''It gets produced in our saliva after a particular number of chewings. It’s an organism that cleans our environment with the help of its 99% water content.''' So basically those ugly gutkha and pan stains dissolve and clears up. Yay! <br />
<br />
'''21st May''' <br />
<br />
We are working on our next assignment of '''designing a machine that may or may not have any functions.''' Realised how difficult it is to think about something of the kind without a purpose. Finally came up with this machine that '''reads the stress or lack of concentration in your head and takes you for a puzzle walk'''. It was more like transferring into a different world to get rid of the mental block. This puzzle walk sounds a little crazy since it takes one for a physical walk...so one might be in mid air but does not interrupt the surroundings. The walk is entirely in a different world once the machine starts functioning! I really wish I could make something of the kind in reality.<br />
<br />
'''24th May'''<br />
<br />
I finally have a drawing of my organism. And I have named it also. It’s called '''CLEAGUEW''' (one which cleans gutkha and chewing gum). This is what it looks like :<br />
<br />
[[File:CLEAGUEW1.jpg]]<br />
<br />
'''25th May'''<br />
<br />
We visited NCBS today. The place is so welcoming to work at. It was really nice to just hang around. Over hanging around we found ourselves a place under the trees to have a discussion. The topic started with our take on the campus and its environment. The discussion eventually turned towards whether its a '''worthy investment''' considering the existence of a large amount of poverty stricken population in the country. I don’t think it was a worthy discussion to have being a third party. Whichever sides we take is going to have its pros and cons..so I didn’t even consider commenting. Mainly because each statement we say is going to be contradictory because we don’t have any kind of first hand proof with us.<br />
Eventually over lunch we started varied discussions with people there. We got into a hard core discussion with education reformation in the country and the regular issues etc. It was quite nice to have these '''discussions''' and look at '''varied view points''',and most importantly from different age-groups.<br />
<br />
'''26th May'''<br />
<br />
We are back to seeing David Sadava after a long break! The video got me adding to my research book again. I like it! We learnt about '''bio-remediation''' and how pseudomonas putida helps to break down trinitrotoluene present in landmines. Further it was about '''extremophiles''', radiation repair system, bacteria used for mining etc. <br />
We learnt extensively about Polymerase Chain Reaction or '''PCR''' and Kary Mullis’s fantastic work on it.<br />
Learning really fantastic things here over summer but homesickness calls quite often. Nevertheless, got to hang in there. <br />
<br />
'''27th May'''<br />
<br />
We have started working on another assignment which wants us to create an art piece using a live organism. As for my first attempt I shall be trying to grow yeast on a plant and watch the consequences. I really don’t know whether it’s going to work out but I want to try it out. The nearby bakeries or groceries do not have yeast for the next couple of days! Wow! <br />
<br />
'''28th May'''<br />
<br />
Attending class was more for working on the living organism project and further researches.<br />
<br />
'''31st May'''<br />
<br />
My plant is here. I found very little yeast from somewhere the other day. Hence it’s not working. Tomorrow Samrajni is getting me yeast! So yay! I hope things work my way!<br />
<br />
'''1st June'''<br />
<br />
Sam gifts me a box of dried yeast! yay! not so yay actually cause I think my mind has changed and it doesn't really make sense of <br />
growing yeast on plants. So I am looking around,staring,wondering about this again. :( <br />
Though today we have made an attempt to grow yeast on agar and left it for good in the aditi lab for the next 2 days.<br />
<br />
'''2nd June'''<br />
<br />
It was an added exposure to go to NIAS and hear the talk on the analysis of the design of Darwin's theory.My mind was quite set that<br />
it is going to be all greek to me. But in the course of the lecture I proved myself partially incorrect. I enjoyed the knowledge that<br />
I gained about so many people and the instances that were provided (for e.g about the stone and the watch etc). Further the questions thrown at the lecturer clarified certain things that I did not understand clearly too.<br />
We learnt that the eye must have had a designer just like that of a telescope.In contrary it was also told that in the context of developments it has been demonstrated that the eye is a result of gradual evolution.The lecture also had this question whether god Vishwakarma is a creator or designer. This has actually given me food for thought.<br />
<br />
'''3rd June'''<br />
<br />
We need to build our lab in the space given to us at NCBS. So we got down to making mind-maps on how to go about it. The first thing we have decided is to make an incubator day after! :)<br />
<br />
'''5th June'''<br />
<br />
Responsibility needs to be given from what it seems! Because initially we didn't even have the ice-box to work with and that's the main structure to make an incubator. In the process we destroyed two thermometers,one burst in the microwave and the other cracked and burst in the to-be incubator ice-box. Yashas says the beginning of our success is showing because of such failures(destruction he means!).<br />
<br />
'''7th June'''<br />
<br />
There’s a new ice-box to make a new incubator. So the earlier one is our guinea pig incubator!hence no assault to be made on this one till we are sure of our ways and means. A mixer-grinder has been bought to make the centrifuge. Being unsure of certain things...we are going quite slow in terms of constructiveness. :(<br />
<br />
'''8th June'''<br />
<br />
Experimenting and observing continues. Shreya has been making a stand for our webcam microscope and Aaron has finally been successful in making a soft-box! so that's pretty much our progress for the day.<br />
<br />
'''9th June'''<br />
<br />
I am supposed to be helping Shreya make the microscope holder.Today's aim was to make the movement of the holder flexible and mechanically sensible. I gave Shreya few ideas ,though she didn't want any and kept shoo-ing me away from helping her! Work on the incubator and centrifuge continues on the other side. I didn't help at all on that side considering the fact that people were already working at it and it made no sense standing and staring or poking my nose in.<br />
<br />
'''10th June'''<br />
<br />
One month of working for iGEM! congratulations to us! The centrifuge has been made with a hand-blender and it works amazingly! Besides, four fans are being used to keep the temperature in control inside the incubator. Tomorrow the incubator must be working in full swing provided the temperature remains around 37 degrees.<br />
Shreya's microscope holder's motion has some technical difficulties.She has used large nuts and bolts from the top which has brought in imbalance in motion. We need exact focus otherwise the video is going to create problems. I had suggested to her initially to use a pulley system so that there is one point of control thereby reducing any kind of imbalance.So more or less we are done with building our equipments.<br />
<br />
'''11th June'''<br />
<br />
The usual running around to check if everything works fine continues. Yashas has asked me to build a new microscope after me and Aaron were done struggling to make Mr. Ravindra's surveillance camera work as one. Had this surveillance camera worked,it would have served the purpose amazingly! but I guess the wires were all funky and the capacitor was apparently burned. So all the effort to match the colour codes of the usb to the camera wire went fruitless more because two wires of the camera had the same colour,although I enjoyed the permutation combination process.<br />
<br />
'''12th June'''<br />
<br />
James and Daisy are coming on Monday to facilitate us, hence as an introduction to our work we have to brief them about our progress till now. I was a part of the group which had to put together the brain-stormings that we had done so far. I had a good time going over everyone's work once again and making mind-maps for them.<br />
<br />
'''14th June'''<br />
<br />
They are here..yay! We went over our work then we went over their's. It was really awesome. Further we had to brainstorm on four sub-headings under the topic '''The rest saving the west.'''Mostly we came up with problem solving ideas and in the process forgot to keep in mind about the rest saving the west. Tomorrow we push this further as an abstraction. <br />
<br />
'''15th June'''<br />
<br />
A very intense day in terms of thinking. We learnt about '''Dr.Jay Keasling''' and his saying '''save the world,one molecule at a time.'''We got an indepth understanding of an individual's intent like a bio-researcher,a garage bio-hacker,a disgruntled researcher to Bin Laden genetics inc. i.e from honourable to dishonourable intents. Further we brainstormed about the '''impacts of synthetic biology''' and moved on the notes of increasing imbalance,bio-errorism,bio-terrorism,unexpected trouble of war,an artist's responsibility etc and concluded it by including the fact that '''just because we can make it,should we?'''. <br />
Besides, we also did a reverse engineering workshop and worked on the second exercise of '''IGEA'''-international genetically engineered art!In groups of three we came up with ideas for igea. My group's idea of igea was called '''ZOOBOTART'''! We had thorn art,flower art and pigment art under the Plant category and collage art,light art,dye art and movement art under Microbes. We categorised the awards under various sub-headings such as '''static &amp; dynamic''',concept,aesthetics etc and also an '''ecosystem''' in which atleast three genetically modified organisms have to be used and they survive interdependently. We also came up with certain criteria's of disqualifications such as death of the organism under any extreme condition or intention of any harmful feature etc.<br />
<br />
'''16th June'''<br />
<br />
The '''iGEA''' competition was scheduled for today. We got about six hours to present our pieces in groups of three. Further each group had to work under certain constraints of sub-categories of awards. For example my group had to work keeping in mind '''social critique''' and remix('''genetic jockeying'''). Samrajni,Kartik and I brainstormed for the initial hour and discussed intensely about ideas,concepts,contradictions,societal issues etc. We discussed various ideas,such as that of - a calf starts producing milk just ten days after its birth, a spray that can show one how much bacteria surrounds us even when we sit at a table and put our hands on it, a plant that produces leather and fur,a tree that can make noise when it is being cut to reduce deforestation and finally a hybrid human that can fly and have a shell to protect itself. We moved ahead with our last idea keeping in mind our category for the award also. The idea of a hybrid human already exists,but we took it forward thinking of social critique as to where this process ends,even though at this moment it is hypothetical to an extent! Sam made an awesome hybrid figure using m-seal! The hybrid had bat wings to fly and a snail shell to protect itself. The wings to fly were incorporated keeping in mind that the world is running out of it's natural resources and soon self sustaining methods are required and this could be one of them.<br />
<br />
Further in the process of the presentation Yashas pointed out the practicality of the idea as an issue. He brought up the fact that how many people will be able to afford such a change considering the fact that it is going to be an expensive investment. And this topic is to be dealt with further, tomorrow. <br />
<br />
I liked the presentation that Aaron and Nooshin put up. The concept of taking out formaldehyde from ants was quite interesting. <br />
Quite a tiring day but I enjoyed the kind of thinking we were doing! :)<br />
<br />
'''17th June'''<br />
<br />
We heard Zack's revised lecture on Genomic Gastronomy at NCBS. This lecture gave us a deeper understanding of his project from the previous one. Agro-informatics,agro-terrorism,cuisinformatics were some of the sub topics that he covered. Further Daisy and James presented their work. The lectures left us with immense food for thought. Hearing the lectures twice over actually helped us to think beyond the superficial level. <br />
In the latter half of the day we were to re-think our ideas on iGEA and present it tomorrow according to the guidelines. <br />
We were thinking about how can RBC's be produced artificially to help save the ones suffering from '''thalassaemia'''.Instead of undergoing blood transfusion every other day,how about a permanent remedy! <br />
Soon we also came up with the idea of a weather sensitive music playing bacteria! The idea sounded comparitively more artistic. We went ahead to create a presentation,a stop motion to put up our work for iGEA.<br />
<br />
'''18th June'''<br />
<br />
'''E.cloudy''' is what we called our bacteria. It produces electricity on sensing the weather temperature.The temperature sensitive bacteria creates current depending on the weather temperature hence the intensity of the current is directly proportional to the weather temperature.<br />
The current passes through an amplifier and then through a voltmeter to read the current and detect the playlist.Each temperature range triggers the playing of a certain play list.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. Hence this brings into consideration the question of whether the person owns a laptop or a computer or not. Also the circuit set-up of the system wouldn't be very expensive but producing the bacteria is might be an expensive affair. Besides,this machine brings together man and nature by making him conscious of the weather and the temperature around him inspite of keeping him related with what he depends on the most,technology.<br />
<br />
'''19th June'''<br />
<br />
It feels so weirdly awesome to read about the epics and the mythologies. Surprisingly Daisy has bought them and we have been going over them. Atleast I have been reading them with immense enthusiasm inspite of it being told as a weird looking comic strip. I finished reading the five stories about Shiva and tomorrow I am going to read ''the Devotees of Vishnu''. I have read them when I was young or the stories were told to me by my Mother, but going over them now once again brought some kind of an ecstatic feeling! <br />
We are going over these to bring in a sense of hybrids and get some ideas from our so creative and fantastical ancestors! I wonder what has happened to us though!<br />
<br />
'''21st June'''<br />
<br />
Having read the books on mythology I somehow did not feel any kind of satisfaction in reading them. I continuously felt that I was being given an overview of the part of the epics. It has aroused this feeling of going back to them and reading the epics over again! and guess what aroused this feeling...Synthetic Biology! We had to retell one of the myths by using a bacteria that we can engineer..or atleast attempt to. <br />
We also met Arshia(she is a scholar who deals with religion and myths) who further stressed on one point that if one is not sure about the myths the shouldn't tell the stories on assumptions because from what it seemed more than half of us were gaining our knowledge out of the comic books. She also brought up the topic of 'anti's', anti's in the sense of opposites... '''GOD - anti. GOD''', GIRL- anti.GIRL(boy) etc.<br />
<br />
'''22nd June'''<br />
<br />
We had a reflection on yesterday’s discussion with Arshia and came up with thought’s that there are so many ways of being right! And also quoting Samrajni, “ Is Genetic Engineering like science’s imagination?” . <br />
Further we came up with the idea to build on the existence of Shiva’s third eye as our mythological story for synthetic biology. Eventually the idea was modified to a story revolving around Brahma,Vishnu and Shiva as bacterias. In the process of brainstorming we learnt about the '''e.coli synthetic PREDATOR-PREY ecosystem''', which communicate bi-directionally through '''quorum sensing''' and regulate each other’s gene expression and survival via '''engineered gene circuits'''.<br />
We made a poster as an attempt to depict our story. We called our story the HOLY TRINITY. <br />
''To read more about the holy trinity please click here.'' &gt; [[THE HOLY TRINITY]]<br />
<br />
By end of the day we had to re-do our poster for tomorrow in a much more dramatic way like our b-grade bollywood movie posters!<br />
<br />
<br />
'''23rd June'''<br />
<br />
We re-worked on our poster summarising the entire working of our Brahma-Vishnu and Shiva bacteria into a dramatic bollywood look-alike poster. Through the day we all researched on '''synthetic biology NOW''' and came up with people who are involved,people who are working,organisations who have invested etc in the field of synthetic biology. In the process we came across this article: &gt; [[The promise of Synthetic Biology]].<br />
<br />
'''24th June'''<br />
<br />
We had to work on the bio-bricks of what our bacteria does. There were bio-bricks that we found between Vishnu and Brahma &amp; Vishnu and Shiva. There are others that we need. Here is the slide that gives the details.<br />
<br />
[[File:Tht.jpg|400px|]]<br />
<br />
In the evening we met again at Alliance Française to watch a play on ecology called ‘The Clearing’. It potrayed the ethics that bind society and nature in a very day to day basis. <br />
<br />
'''25th June'''<br />
<br />
We further worked on the people involved in synth-bio NOW and divided ourselves for the headings to research on. I looked into &gt; [[Synthetic Biology in India.]]<br />
<br />
'''28th June'''<br />
<br />
Story-building around Daisy Ginsberg,Drew Endy and the Indian Government! We(Aaron,Diya &amp; me) have come up with a story..stay tuned to read the final version of it.. <br />
<br />
'''29th June'''<br />
<br />
Floosy,Dendy,Himmesh and Dhanmohan are coming along quite well with the story...we are working on it..so hang in there having read the teaser:<br />
<br />
'''The Genetic Laboratory at Stanford University. Dr Brew Dendy standing at the corner of the room, one hand in his lab coat and the other on his forehead.‘I think I should face it the way it comes’, he says to himself to calm himself down...'''<br />
'''Dendy had a slight hint of this change in his behaviour but not to a level where someone like Floosy who he has been meeting for work would notice.He needs to do something about it...something else comes to his mind...'''<br />
<br />
'''30th June'''<br />
<br />
I have been reading this huge article on '''Synthesizing Law for Synthetic Biology''' since last evening and there is a lot that I learnt. I have never read an almost forty page article with the same enthusiasm all through. I have taken out some of the stuff which I felt was worth noting out of it. Please click on this &gt; [[A synopsis]] to have an overview of how laws and rules have been discussed in synthetic biology.<br />
<br />
Further as a group Akshitta,Aaron and me built a '''Winogradsky Column''' for observation over the next few months. It was really interesting to use the common things that we found around us (eg.,eggs,newspaper,pond water) to create a column of microorganisms and wait to see it evolve over time. <br />
<br />
From a group brainstorm we came up with the following:<br />
• Presentation<br />
• Seeing is believing<br />
• ECOSYSTEM<br />
• Reactions- if they are feasible<br />
• The HEAT sensitive ecosystem<br />
• Carbon foot-prints<br />
• Telling stories<br />
• WHERE IS OUR WORLD GOING?<br />
• An overview- standing and looking at the earth- TERRARIUM<br />
• Statement as artists and designers<br />
• Balance- humans are a part of it.<br />
• Even though we genetically engineer (modify) the bacteria,they still survive.<br />
• Sphere exists inspite of the chaos<br />
• Complementary-balance<br />
• Transfer of energy from the human makes the ecosystem run.<br />
• Loop-&gt; balance<br />
• How else can the ecosystem INTERACT? <br />
<br />
'''1st july'''<br />
<br />
We start our experimentation hands on today at NCBS. We divided ourselves into 2 groups and being a part of the group which wasn’t doing the experiment in the first half we went to hear a talk on the STRING THEORY AND THE QUEST FOR QUANTUM SPACETIME by Rajesh Gopakumar. Not having come from a science background was making things a little difficult for me to understand but his approach was really well grounded. In the sense ,he started by going over the very basics,like the laws of physics;gravity;Newton’s Law;Einstenian gravity;gravity and geometry;gravity in a quantum world etc.He spoke about the Einstenian and the Newtonian laws’ limitations and explanations for them. <br />
<br />
[[PEOPLE IN THE PROCESS]]</div>Target022http://www.hackteria.org/wiki/index.php?title=Ethics&diff=3058Ethics2010-12-10T17:23:02Z<p>Target022: </p>
<hr />
<div>>Playing God for Fun and Profit[http://radar.oreilly.com/2008/02/play-god-for-fun-and-profit-mo.html]<br />
<br />
The Ethics of DNA databasing[http://www.economist.com/debate/days/view/284#pro_statement_anchor]</div>Target022http://www.hackteria.org/wiki/index.php?title=Sankhalina_Nath&diff=3057Sankhalina Nath2010-12-10T17:22:33Z<p>Target022: </p>
<hr />
<div><br />
== The iGem Journal. ==<br />
<br />
<br />
'''10th may 2010'''<br />
<br />
It all started with weird notions like spontaneous generation where people believed that living beings came into being spontaneously out of thin air. Better an idiotic start then no start at all! I once read in this book called “Between Eternities” that saying that life as it is now on earth happened just by chance without a designer/creator is like saying that ink was spilled on paper and beautiful poetry came out of nowhere when there was no ink and paper to begin with.<br />
<br />
And to look at the present scenario it is like “Whoa!!” Carrying out experiment after experiment to prove guesswork seems like one tedious and draining task. If one is not passionate enough it is better not to set sail in this ocean.At least I wouldn’t dare to.<br />
<br />
'''11th may 2010'''<br />
<br />
We now know that the basic building blocks of living matter are proteins which are organic compounds made of amino acids arranged in a liner chain and folded into a globular form. <br />
<br />
The studies started with the discovery of microorganisms when Robert Hooke invented the first microscope which detected these tiny organisms. Based on these studies Hooke published Micrographia which had amazing illustrations of these tiny creatures. Brilliant artwork.<br />
Then there was Antonie Van Leeuwenhoek who was the first person to observe and study single celled organisms. He studied sperm cells and according to him there were tiny human beings inside sperms which grow up to be a full sized human being. Quite a male chauvinistic pig, I must say.<br />
<br />
'''13th may 2010'''<br />
<br />
Charles Darwin held deep interest in living beings and went on to study them in their natural habitats to find out where all of us have come from. This led to the theory of evolution”. But he never found out whether the chicken came first or the egg.<br />
<br />
Meanwhile Gregor Mendel started his experiments with pea plants to see how characteristics are transferred from one generation to the next. He found out that there were some dominant characteristics and some recessive. And these were carried by genes from generation to generation transferring characteristics while in the process never changing their form. It must be strange for people in those times to even think about comparing themselves with peas, let alone accepting the fact that certain processes in the human body are similar to pea plants like gene transfer.<br />
<br />
'''14th may 2010'''<br />
<br />
Genes may be of two different types known as alleles; a dominant allele and a recessive allele. Organisms are distinguished by its phenotype which is what it looks like and genotype which is what allele it has. An organism is called homozygous if it contains the same allele in both the homologous chromosomes and heterozygous if it contains one dominant allele and one recessive allele… blah, blah, blah. Too much of gene talk is happening, and it tends to go over my head when it gets this monotonous. I won’t be surprised if this “guy with the tie” is accused of putting someone into a coma just by lecturing them.<br />
<br />
'''18th may 2010'''<br />
<br />
After the invention of better and more powerful microscopes biologists started revealing that all complex living beings are made up of cells and all cells exist because of division of pre existing cells and before division everything in the cell is doubled.<br />
Inside the cell there is a nucleus. All the genetic material of a living being is present inside the nucleus of a cell in the form of chromosomes which is made up of DNA molecules with are double stranded helical structures. The strands are made up of a sugar and a phosphate. Joining the two strands is the four different types of proteins called bases. They are adenine, thymine, guanine and cytosine. A always pairs up with T and C always pair up with G and vice versa.<br />
Human beings have 26 different pairs of chromosomes. The gonads are the only cells which have half the number of chromosomes as compared to all other cells in the body.<br />
<br />
Facts, facts and some more facts, is getting thrown left, right and centre and honestly now my mind involuntarily shuts down to anything remotely related to even a single cell of this “guy with the tie”. I digested whatever I could from his lectures, but now I can’t help it anymore.<br />
<br />
'''19th may 2010'''<br />
<br />
By the process of transcription an equivalent RNA copy of a DNA sequence is made. This RNA goes out of the nucleus and by the process of translation ribosome synthesizes protein by consuming ATP. This is how proteins are made inside the cell according to the information present in the DNA.<br />
<br />
I found it quite a cool assembly line kind of arrangement. And I read somewhere that the human DNA, if straightened, would be between three and nine feet long. We are beautiful and awesome machines.<br />
<br />
'''20th may 2010'''<br />
<br />
It is possible for a gene to cross over from one chromosome to another. So this makes the joining of pieces of different genetic material possible. This way if a gene for a particular characteristic in an organism is joined with the DNA of another organism, it is possible to make the organism imbibe that characteristic from the host organism in most of the cases. This fact enabled man hack into natural systems and tweak them. I am still in the process of thinking how right or wrong that is. For right now, no comments.<br />
<br />
'''21st may 2010'''<br />
<br />
Today I am summarizing the crazy ideas that I have until now which look insanely impossible. But then again quoting one of my most favorite quotes by Sir Arthur Conan Doyle I have to say “How often have I said to you that when you have eliminated the impossible, whatever remains, however improbable, must be the truth”.<br />
<br />
So here it goes…<br />
<br />
1. Primitive man frozen in permafrost brought back to life by cloning.<br />
<br />
2. A 3D organic printer which can print out anything organic with just few cartridges of the basic organic elements i.e. carbon, hydrogen, oxygen, nitrogen, calcium, sulphur and phosphorus.<br />
<br />
3. An organism with a million protective outer shells and a super fast capability to regenerate.<br />
<br />
That’s all the craziness I can enlist for right now.<br />
<br />
'''24th may 2010'''<br />
<br />
Today it was craziness part two. We had to design a wacky organism and write an abstract for it. Mine goes as follows:<br />
<br />
Dopaminium Duali<br />
<br />
I am publishing through this paper the results of my genetically engineered machine experiments on microorganisms which resulted in the genetically modified organism called Dopaminium Duali.<br />
<br />
It is a single celled bacteria generally found in our atmosphere. This bacterium is found to be the only bacterium where there are different male and female forms found. The females are responsible for food consumption and digestion where as the males are responsible for reproduction. The male bacterium doesn’t have a digestive system of its own and so it mates with the female just for the sake of nutrition.<br />
This organism doesn’t mate for reproduction. The males reproduce in a unique fashion of quaternary fission where the parent cell after the fission divides into for daughter cells where three are males and one is always a female. Because of this imbalance in the number of males and females there is a big amount of competition for the females.<br />
<br />
In order to attract the females the males need to release strong pheromones; the stronger the better. This organism is capable of latching onto the human body harmlessly and makes it increase its production of dopamine and endorphins which in turn it consumes and turns into its pheromones. It does so by releasing capsaicin into the human body which is a chemical known to increase the endorphin levels. This chemical is also found in chilies. D. Duali females have been found in large numbers on chilly plants which consumes capsaicin from the plants.<br />
<br />
Because of this property if this bacterium can be cultured and sprayed in gloomy places like mental hospitals and offices in a small way it can actually lift people’s spirits up and make the world a happier, less stressful place to live in.<br />
<br />
'''26th may 2010'''<br />
<br />
It was kind of like a research day. We looked up a few bio-artists like Stelarc who has an ear implanted in his arm (one needs to be a little extra eccentric to do that!!) and Orlan who has altered her own body several times by the means of plastic surgery. These two artists have taken extreme measures to alter their bodies and although it might look downright crazy to someone who just sees them, to look at it from their point of view those modifications are just means of exploration of their own bodies and taking them to another level. <br />
<br />
I have one metal plate, five screws and one nail in my ankle which facilitated the healing of my bi-malleolar fracture in my right ankle. Now it is my choice whether I want to keep them or take them out for which I have to go through another surgery. Which means; another session of spinal anesthesia, excruciating pain, pain killers, IV drips, cast, not being able to walk for a month, again trying to walk limping and all that jazz. But I want to do it, even though the metal doesn’t affect me or my daily life in any way at all, because I somehow don’t want a foreign material inside my body. <br />
<br />
When I see my situation in contrast to what these artists are doing I can see it is the desire that drives them and me. The only difference is I am ready to go through pain to take out something foreign out of my body, while they are going through similar kind of pain to implant some into theirs.<br />
<br />
'''28th may 2010'''<br />
<br />
I had kept a packet of bread and an omelet to go bad 10 days ago. The omelet is showing no signs of getting mould, while inside the packet of bread I can not only see moldy bread but the mould is perspiring. The entire surface is covered dark greenish mould. The mould is taking all the nutrition it can from the bread slices and at the same time destroying the surface. The omelet is in a glass and all the fat has accumulated at the bottom while the omelet is kind of floating.<br />
<br />
[[File:DSC09045.JPG]]<br />
<br />
<br />
I hate animals or rotting food. I wish it was a cooking project.<br />
<br />
'''31st may 2010'''<br />
<br />
Today we looked up some unique artists like Tuur Van Balen, Alexandra Daisy Ginsberg and James King. I really like James King’s work specially his projects called “Potential Pharmacy” and “Dressing the Meat of Tomorrow”. I like the fun but no nonsense way in which King presents his projects. They have a sense of humor attached to them but at the same time we can easily see through the serious message behind them. On the other hand most of Daisy’s work looked like they meant to raise questions about where we as human beings stand with respect to biotechnology.<br />
<br />
It is amazing how art can describe certain simple facts of science which science itself fails to illustrate with all its accurate facts and calculations and diagrams.</div>Target022http://www.hackteria.org/wiki/index.php?title=Diya_Sharma&diff=3056Diya Sharma2010-12-10T17:21:47Z<p>Target022: </p>
<hr />
<div><br />
''10th May 2010'''<br />
Our first official day of class, I was absolutely clueless, unanswered questions were still dancing at the back of my mind, there was no formal announcement as to what we will be doing for the next few months. The only thing I understood in the first class was ‘’E-COLI’, probably the only thing I was clear about.<br />
Once the class got over, I was preoccupied with thoughts as to how things will fall in place.<br />
<br />
'''11th May 2010'''<br />
Today was a little clearer, after watching bbc-‘the cell’ video, we brushed up our basic terminologies, and we started following a sequence of watching video lectures by David Sadava. Readings kept coming our way; the one, which interests me most, was life ‘what a concept’.<br />
<br />
'''12th May 2010'''<br />
As days past by, I kept catching up on details about the cell, nucleus DNA, functioning of organisms and microorganisms (essential biological terms) etc. Something which had a defined working we could relate better, like Mendel’s pea experiment, Moore’s law etc, I saw people in these classes sitting with their eyes wide open, and not falling asleep. Thus it was concluded sitting in a practical class people paid unasked attention.<br />
<br />
'''17th May 2010'''<br />
We started brainstorming on our abstract bacteria/organism/product .it took us hardly few minutes to come up with an initial idea. Each day we kept modifying it, and thought of other possibilities, what we discovered by the end was all of our ideas were practically possible to an extent; we could carry it forward to the next level.<br />
<br />
<br />
'''Become a lie detector:''' Introducing the all-new lirteutheria!<br />
<br />
'''Warning:''' sometimes ignorance is bliss, after using lietrutheria; you may be hurt when its obvious that someone is lying to you.<br />
<br />
'''Body:''' lie detector lietrutheria consists of a round plastic transparent lid, 4 cockroaches, 2 facing each other, other 2 in opposite directions. These four-legged organisms are attached to the lid.<br />
<br />
'''Working:''' Lietrutheria, as a whole, moves in a particular direction, if a person says the truth i.e. cockroaches will coordinate and move, if one organism moves frontward the other will move backward, and the ones at the bottom will move sideward, to make the round lid move <br />
If a person is lying, each organism will move in the direction to which they are facing, i.e. each of them move in different directions, which results in no movement, the lid starts wobbling. <br />
<br />
'''Durability:''' This product will remain with you throughout your life, the cockroaches keep reproducing.<br />
When a couple of cockroaches mate (front two pair), they begin to battle with each other using their antennae. The male will then bring up his wings and ruffle them. The female feeds on secretions in the male’s dorsal glands, located on his abdomen. The male will follow by going behind the female and will touch her reproductive organs. Once that is done, they will both face each other; their back ends will come in contact and the reproduction begins. This process will take about one hour. The male will send his sperm directly into the female. <br />
Female cockroaches will either store these cases away in a safe corner of confined areas or they will carry them inside or outside their bodies until the eggs are born. Initial 2 months the babies don’t work, once they are on their feet they help the parent cockroach.<br />
<br />
'''Storage:''' The cockroach is among the most cosmopolitan of all pests and insects. They are often seen and inhabit human home, therefore the product can be stored anywhere in the house. Preferable if kept in small, dark places. They prefer coming out only at night, therefore avoid using it in daytime. Keep them in the kitchen so that they can clear of the junk as their daily food.<br />
<br />
'''Safety:''' They do not sting or bite, Roaches have a unique figure that allows them to run away quickly and to successfully hide themselves by contracting their bodies to fit in tight spots. The cockroach will not use its wings to escape but will instead dart into holes and cracks. Therefore lietrutheria is human friendly!<br />
<br />
'''Usage:''' Often used by police and security experts. This product is also useful for managers, employers, and for anyone to use in everyday situations where telling the truth from a lie can help -prevent you from being a victim of fraud/scams and other deceptions. Therapists, to test their patients, also use it.<br />
[[File:diyads2.jpg]]<br />
<br />
'''18th May 2010'''<br />
The bbc-‘the cell’ documentary was informative yet not boring, therefore we decided to download the 2nd and 3rd part to it. <br />
<br />
<br />
<br />
'''19th May 2010'''<br />
The grand day, where we practically did something with our hands, we extracted our DNA, with the help of pril (washing liquid), alcohol, and human spit. It was exciting to perform your first practical experiment even though it was at a small scale. It took me back to the school days where we used to fight for the seat next to the lab assistant just to see how the experiment is being performed.<br />
<br />
'''22nd May 2010'''<br />
The day when I thought I would take an off as the weather was not in my favor of attending today’s class, I received a call demanding everyone in class, we had zack’s talk on genetically modified organisms, which later lead to gender bias discussion, that’s when all the girls of the class raised their voice. I was glad I didn’t miss that day in particular. <br />
<br />
'''25th May 2010'''<br />
Finally our picnic trip to ncbs (national centre for biological sciences), a place where someone would dream to work, explored the place for while, and then got involved in a discussion with an educator, the debate was wether the present education system does any good or not. Another topic of his concern was we being designers took up synthetic biology for this term. <br />
It was shocking to see, how people without demanding money are making efforts on their own just bring the best output possible from the present generation.<br />
<br />
'''27th may 2010''' <br />
Time to create another hypothetical machine, mind boggling took place along with clash of ideas. While I as thinking, I clipped my hair and handful broke, and that minute I wondered what if there exists a machine, which could fix the hair that fall, and continue to grow them in the same manner.<br />
<br />
[[File:diy2.jpg]]<br />
<br />
'''28th May 2010'''<br />
When scientists were out of the game, artists came in for a while, we read about Stelarc, Orlan, Adam zerestky, Petricia Piccinini and Eduardo Kac. I personally liked petricia’s work she uses hyper realistic sculpture of customized life form. Patricia piccinini examines the relationship between science, nature, science and technology. She challenges our classification of life by displaying the relationship and differences between the organic, natural and our constructed material world. Gives an idea that stuff is actually happening and is therefore representative of the world today.<br />
<br />
'''31st June 2010''' <br />
Practical working begins, everyone is off on an all new journey with their yet to be built sculptures. I am working with extracted tooth, which disgust me to the extent that I can vomit. Teeth, which have accumulated germs and dirt. The bacteria that cause tooth decay utilize sugars (glucose, sucrose, fructose, lactose, or cooked starches) as their food source; therefore if we apply the above in liquid form it will help the bacteria survive longer. The waste products created during the digestion of these sugars are the acids (especially lactic acid) that cause the demineralization of tooth enamel and dentin.<br />
Dr kashinatha shetty, cosmetic dentist near our locality, helped me gain the above knowledge.<br />
<br />
'''1st June 2010'''<br />
Entry to the lab. Hurray! We started growing yeast in three different ways. Our group followed the technique of dry yeast pallets in agar water, and then the yeast was left to grow in the lab for a day. Though this is not required on an immediate note, but the names of the chemical compounds marked on the test tubes made me go back to my 10th class chemistry classes, few of us started asking each other the full forms, it lead to a quiz and also brushed up our organic chemistry. It was fun.<br />
<br />
'''2nd June 2010'''<br />
Thanks to Avni, for exposing us to a very interesting talk at NIAS (national institute of advanced studies) on theory of evolution by Charles Darwin. The presenter was bombarded with questions, asking whether there exists a creator or not. Some strongly believed there was no requirement of a creator. An example of an eye was given, stating even an organ like an eye, progressed with the help of evolution.<br />
<br />
'''3rd June 2010'''<br />
Brain storming along with research was our first step to build our very own lab. We listed down the materials required to build an incubator and a centrifuge, it was difficult to gulp the fact that one could build such stuff with absolute junk. Documentation also tagged along all this while.<br />
<br />
'''23rd June 2020'''<br />
<br />
The soma bacteria <br />
<br />
This idea of the soma bacteria is primarily inspired by the popular Hindu myth of the samudra manthan , commonly known as “the churning of the ocean“.<br />
The phrase “soma bacteria” comes from the drink of “soma”, which is a drink primarily behaving as an anesthetic in the famous mythical incident of Samudra manthan. <br />
<br />
'''Now we come to the working of the bacteria:'''<br />
The soma bacteria are not just one bacterium but a pair of bacteria, which are co- dependent, and they are unstable in the absence of each other. One bacterium is harmful in relation to the human body, whereas the other one is harmless, but it is to be noted that it is not of a curative nature. The habitat of these bacteria is common rust. While they live in their rusty habitat, they live in colonies but there is no activity of exchange taking place. <br />
The minute it comes in contact with the human body, the bacteria get activated at once. It commutes throughout the human body, causing harm. The minute it comes in contact with a WBC, the two bacteria start exchanging their genetic material rapidly. While the WBC recognizes that one bacterium is harmless, it also realizes that the other one is harmful. But due to the rapid state of exchange of genetic material, the WBC is unable to recognize the harmful one and try and kill it. While the harmless bacterium contains a protein, which the WBC cannot counter, it cannot kill either of the bacteria. Thus, the WBC can never destroy the soma bacteria at any given time.</div>Target022http://www.hackteria.org/wiki/index.php?title=GFP_Protocol_Jugaad&diff=3055GFP Protocol Jugaad2010-12-10T17:21:02Z<p>Target022: </p>
<hr />
<div><br />
== '''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 &amp; 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>Target022http://www.hackteria.org/wiki/index.php?title=Ideas_for_Bacteria.&diff=3054Ideas for Bacteria.2010-12-10T17:20:30Z<p>Target022: </p>
<hr />
<div><br />
-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>Target022http://www.hackteria.org/wiki/index.php?title=A_synopsis&diff=3053A synopsis2010-12-10T17:20:03Z<p>Target022: </p>
<hr />
<div><br />
• By reimagining biology from the perspective of engineers, computer programmers, and hackers, synthetic biologists hope to move beyond the strictures imposed on genes,cells, and organisms by eons of evolution by natural selection.<br />
<br />
• Within five years of the first deliberate recombination of DNA, ambition for the field had vaulted towards '''the new era of ‘synthetic biology’ where not only existing genes are described and analyzed but also new gene arrangements can be constructed and evaluated.''' Synthetic biology has since moved well beyond this early conception of the field as one of rearranging genes. Now the field envisions not just the redesign of existing organisms, but even the de novo design and “programming” of genes and organisms.<br />
<br />
• The metaphor most congruent to the goals of synthetic biology is the gene as algorithm. In this conception of the gene, DNA encodes a set of instructions for carrying out functions via biochemistry just as a computer program encodes a set of instructions for carrying out functions via electricity.<br />
<br />
• French geneticists François Jacob and Jacques Monod established that some genes encode biochemical products that,in turn, regulate the expression of other genes. They proposed that '''“the genome contains not only a series of blue-prints, but a co-ordinated program of protein synthesis and the means of controlling its execution.”'''<br />
<br />
• One approach synthetic biology takes to ensure programmability is the deliberate reengineering of biological parts and systems to make them structurally simplified and functionally predictable. <br />
<br />
• Nevertheless, as important as this engineering science approach may be, the ethos of open science, and a concomitant distaste for intellectual property, represents what may be an even more significant influence in the development of synthetic biology.<br />
<br />
• '''PROPRIETARY SYNTHETIC BIOLOGY''':<br />
<br />
Synthetic biology promises to challenge fields beyond science and technology. '''It is sure to unsettle notions of how the intellectual property laws should apply to biotechnological inventions.''' Three ways in which synthetic biology may force change to legal doctrine are discussed below. '''First''', human designed DNA sequences, systems, cells, and organisms may avoid criticisms about patents claiming “products of nature.” '''Second''', synthetic DNA sequences may qualify for copyright protection as “original works of authorship fixed in a tangible medium of expression.” '''Third''', synthetic biology may create new routes to trademark protection of its resulting products and services by enabling the routine inclusion in DNA sequences (or other engineered biological structures) of distinctive motifs capable of serving as legally effective indications of source. <br />
<br />
• After the Diamond v. Chakrabarty decision in 1980,patent applications and issued patents claiming DNA sequences increased rapidly.Today, patenting DNA sequences is routine. The USPTO Utility Examination Guidelines state that “ a patent on a gene covers the isolated and purified gene but does not cover the gene as it occurs in nature.” The phrase “[‘isolated DNA’] or a similar term (e.g., ‘modified DNA’ or ‘purified DNA’) is widely used to distinguish the claimed DNA from its naturally occurring counterpart, i.e., genomic DNA encoding [the same polypeptide].”Such claims are “unquestionably patentable over the corresponding products of nature,” although they must also satisfy criteria of patentability other than being statutory patentable subject matter. Despite the longstanding Parke-Davis ruling, some have argued that DNA sequences should not constitute patentable subject matter because they are derived from natural (“genomic”) DNA sequences.Synthetic biology allows these concerns to be avoided entirely. Genes constructed using synthetic biological techniques will have their origins in human imagination and will, thus, not be products of nature. Even if the courts were to accede to the wishes of those opposing the patent eligibility of genes isolated from natural genomic sources, synthetic genes would remain patentable subject due to their non-natural origins. In fact, opposition to gene patents as products of nature would incentivize preferential investment in research, development, and patenting of synthetic genes. <br />
<br />
• Recent tumult regarding the patentability of isolated human genes is likely to raise the prospective value of synthetic genes. On May 12, 2009, the American Civil Liberties Union (ACLU) filed a lawsuit to challenge the eligibility of human genes for patent protection.As the complaint stated, <br />
'''Every person’s body contains human genes, passed down to each individual from his or her parents. These genes determine, in part, the structure and function of every human body. This case challenges the legality and constitutionality of granting patents over this most basic element of every person’s individuality.'''<br />
<br />
• However, synthetic biology can involve the design and construction of new, human designed DNA sequences. Here the synthetic biologist designs the particular DNA sequence, and “writes” it when she synthesizes the sequence.Since there is an author in this case, such DNA sequences should qualify as “original works of authorship.” Furthermore, although DNA sequences lack the explicit statutory recognition as copyrightable subject matter that computer software possesses, synthetic DNA sequences may be eligible for copyright protection under the expansive interpretation of “works of authorship” manifested by Congress in the legislative history of the 1976 amendments to the Copyright Act.<br />
<br />
• In a measured version of this conception, Endy has suggested that “synthetic biology provides an opportunity to test the hypothesis that the genomes encoding natural biological systems can be ‘rewritten,’ producing engineered surrogates that might usefully supplant some natural biological systems.” <br />
<br />
• Given that one of the primary goals of synthetic biology is to engineer cells and genes to become ever more like computers and computer software, as synthetic biology succeeds in making DNA appear more similar to computer software, DNA sequences will likely move towards copyrightability by analogy to computer software. Alternatively, '''if cells and organisms are already computers and genes are already software, then DNA sequences are already eligible for copyright protection.'''<br />
<br />
• A specific pattern or motif spliced into a synthetic DNA sequence could serve a trademark function if it identified the source of that DNA. To avoid the restrictions of the functionality doctrine, such a DNA trademark would best be placed outside of the coding (or functional) portion of the DNA sequence. '''As the field of synthetic biology becomes more commercially important, DNA trademarks are likely to play increasingly important roles as indicators of source.<br />
'''<br />
• Von Hippel has warned that, “with a few exceptions, innovators do not think that patents are very useful either for excluding imitators or for capturing royalties in most industries,”and that “the characteristics of present-day intellectual property regimes as actually experienced by innovators are far from the beneficial expectations of theorists and policy makers.” He notes a growing realization “that intellectual property rights are bad for innovation too in many cases.”<br />
<br />
• An increasing body of '''empirical research supports the hypothesis that intellectual property protection may harm, rather than spur, technological innovation. More than two decades ago, von Hippel reported that “empirical data seem to suggest that the patent grant has little value to innovators in most fields.”''' <br />
<br />
• Open biology and open synthetic biology represent non-proprietary modes of biotechnological innovation.<br />
<br />
• Moser has presented historical evidence showing that, at least during the nineteenth century, countries with patent systems did not experience significantly greater rates of technological innovation than countries without patent systems. <br />
<br />
• Yochai and Benkler have instead proposed that “commons-based strategies” may spur rates of innovation in fields such as software, agriculture, and drug development more than proprietary systems.145 Open biology and open synthetic biology represent non-proprietary modes of biotechnological innovation.<br />
<br />
• '''The International HapMap Project (IMHP)''' is a “partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United Kingdom, and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals.”The HapMap (or map of haplotypes) “is a catalog of common genetic variants that occur in human beings.”The IHMP is attempting to create a public domain database of haplotypes by encouraging researchers not to patent their research, but, instead, to contribute their haplotype data freely to the IHMP genetic database. ''By “making this information freely available, the [IHMP] will help biomedical researchers find genes involved in disease and responses to therapeutic drugs.”'' Researchers do not require licenses to gain access to the IHMP database, where data “can be downloaded with minimal constraints.”Although one of the goals of the IHMP is to minimize hindrances on genetic research caused by patents, it does not oppose patents claiming haplotypes “as long as this action does not prevent others from obtaining access to data from the [IHMP].<br />
<br />
• The first sentence in the Preface of both the Contributor and User Agreements begins with a broad statement of BBF’s mission and values: <br />
[The BBF] was established to foster and advance innovation,research, standardization, and education in synthetic biology through the open design, construction, distribution, understanding, and use of BioBrick™ compatible parts, namely standardized genetic materials and associated functional information,in ways that benefit the world.<br />
<br />
• Nightmare scenarios include '''“the malicious use of DNA sequences posted on the Internet to engineer a new virus or more devastating biological weapons.”<br />
'''<br />
• '''The preface signals that only beneficial uses should be made of synthetic biology, though the very need to state this positive value indicates an awareness of its opposite.'''<br />
<br />
• Section Two of the Contributor Agreement requires contributors to agree to let the BBF insert a “BioBrick™ Identification Tag” into the DNA sequence of any contributed BioBrick. Users must make related promises in Section Three of the User Agreement, agreeing not to remove any “BioBrick™ Identification Tag” from a BioBrick and to ensure that the BioBrick Agreement logo is displayed prominently whenever a BioBrick, or modification thereof, is made available, commercialized, or distributed; Section Five of the Contributor Agreement informs contributors of this user obligation. This trademark policing is intended to ensure that BioBricks remain both standardized, compatible, and accessible. Finally, the BioBrick Agreement provides for attribution. Section Five of the Contributor Agreement allows contributors to request that users attribute BioBricks to their contributors when those users describe those BioBricks. Section Three of the User Agreement requires that users promise to make such attributions to contributors.</div>Target022http://www.hackteria.org/wiki/index.php?title=Egyptian_Mythology&diff=3052Egyptian Mythology2010-12-10T17:19:38Z<p>Target022: </p>
<hr />
<div>>= RA =<br />
<br />
<br />
[[File:Ra.gif|160px|thumb|left|The Sun God]]<br />
<br />
<br />
The King of Gods and Sun God<br />
<br />
Hybrid of a man and a falcon's head<br />
<br />
Ra was the greatest of the gods and he kept his power in his secret name, which only he knew. He had started to grow old, and sometimes he dribbled. Isis collected some of his saliva and made it into a snake. She hid the snake where Ra would walk. When Ra trod on it, it bit him, and Ra screamed in pain. All the gods gathered round, but none could heal him. Isis said &quot;If you tell me your secret name, this will give me enough magic power to heal you.&quot; Ra didn't want to do this, but eventually the pain was so bad that he had to. Isis healed him, and ever since then she has the magic powers that Ra had.<br />
<br />
<br />
= HATHOR =<br />
<br />
<br />
[[File:Hathor2.gif|160px|thumb|left|Goddess of love]]<br />
<br />
<br />
Goddess of love, music and dance<br />
<br />
Contained cow horns and sundisk on her head<br />
<br />
Hathor was the goddess of joy, motherhood, and love. <br />
<br />
She looked after all women. <br />
<br />
She was the goddess of music and dancing<br />
<br />
<br />
<br />
<br />
<br />
= SEKHMET =<br />
<br />
<br />
[[File:Sekhmet.gif|80px|thumb|left|Goddess of Sun]]<br />
<br />
<br />
Goddess of the Sun<br />
<br />
Woman with a lion's head<br />
<br />
Sekhmet was the destructive Sun Goddess<br />
<br />
Egyptians knew that the Sun brought light but were also aware of the desert Sun which could kill people<br />
<br />
Ra, the Sun God, was angry with mankind, because they laughed at him. He said that he'd send down his anger as Sekhmet, the Eye of Ra. She went down to Earth, killing men, and drinking their blood. She started to frighten Ra, who only wanted to punish Mankind, not destroy them all. So he dyed some beer red, to look like blood. When Sekhmet saw the beer, she was thristy for blood, so she drank it all, got drunk and went to sleep. When she woke up, Ra persuaded her to stop killing Mankind.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
= NUT AND GEB =<br />
<br />
<br />
[[File:Nutgeb.gif|160px|thumb|left|Sky Goddess and Earth God]]<br />
<br />
<br />
Nut was the Goddess of the skies and Geb being the God of Earth<br />
<br />
Nut is shown in blue with the Golden Stars<br />
<br />
Geb contains the colour of plants and the fertile Nile mud<br />
<br />
Nut and Geb are separated, but each evening Nut comes down to meet Geb and this causes darkness. <br />
<br />
If storms came during the day, it was believed that Nut had come closer to the earth.<br />
<br />
<br />
<br />
= HORUS =<br />
<br />
<br />
[[File:Horus2.gif|160px|thumb|left|Horus, the son of Osiris]]<br />
<br />
<br />
Son of Osiris<br />
<br />
A hawk or Man with hawk's head with the crown of Egypt<br />
<br />
The Eye of Horus, healed by Thoth, was an amulet, or magic charm.</div>Target022http://www.hackteria.org/wiki/index.php?title=Bioelectronics_for_artists_@_CEMA&diff=3051Bioelectronics for artists @ CEMA2010-12-10T17:18:48Z<p>Target022: </p>
<hr />
<div><br />
== Abstract ==<br />
<br />
[[File:sample_hackteria_workshop.jpg|200px|left|]]<br />
<br />
<br />
The workshop is an experimental make-workshop with multilayered outcome for people interested in sound, DIY-biology, microscopy and simple technological interaction with living microorganisms. Participants will become involved in hacking webcams to be used for live-video microscopy, finding microorganisms from the urban environment, and then develop open hardware and software tools with which these organisms can be both viewed and become the subjects for simple interactions.<br />
<br />
more info a about [[DIY_microscopy]]<br />
<br />
== Call for participation ==<br />
<br />
The workshop &quot;Bioelectronics for Artists @ CEMA, Bangalore&quot; is open to the public to join. Feel free to contact us at yashas(AT)cema(DOT)in for more information. Artists are welcome to join in only partially if their schedules doesnt allow the whole 5 days.<br />
<br />
== Workshop mentors ==<br />
<br />
'''Yashas Shetty''' | [http://cema.srishti.ac.in/ CEMA], [http://thedepartment.in /DFG] India<br />
<br />
Yashas Shetty is an artist and composer based in Bangalore, India. He is currently an artist in residence at the National Center for Biological Sciences in Bangalore and faculty at the Srishti School of Art, Design and Technology. He helped found the Center for Experimental Media Arts at Srishti and has previously taught at design schools across India, His works look at the relationship between language,ecology and technology.<br />
<br />
'''Marc Dusseiller''' | [http://www.dusseiller.ch/labs/ dusjagr labs], [http://www.mechatronicart.ch/ SGMK], Switzerland<br />
<br />
Dr. Marc R. Dusseiller is a transdisciplinary scholar, lecturer for Micro- and Nanotechnology and artist. He works in an integral way to combine science, art and education. He performs DIY-workshops in lo-fi electronics, music and robotics, has made various short movies and is currently developing means to perform biological science (mammalian cell culture, microfluidics, live-microscopy) in a DIY fashion in your kitchen or your atelier. He is also co-organizing dock18, Room for Mediacultures, and various other engagments like the diy* festival as the president of the Swiss Mechatronic Art Society, SGMK.<br />
<br />
== Participants ==<br />
<br />
Joanne Hoffmann<br />
<br />
Kannan Mehta<br />
<br />
Avinash<br />
<br />
Navin<br />
<br />
Victor Vina<br />
<br />
kinshuk surjan<br />
<br />
Shikhar Srivastava<br />
<br />
Nitya Kumar<br />
<br />
[[User: Sem2490| Sandeep Mathew]]<br />
<br />
<br />
<br />
...<br />
<br />
== Presentations ==<br />
<br />
[[File:hackteria_CEMA_introduction.pdf]]<br />
<br />
[[File:hackteria_CEMA_bioelectronix_intro.pdf]]<br />
<br />
[[File:hackteria_CEMA_size_of_things.pdf]]<br />
<br />
[[File:hackteria_CEMA_microscopy.pdf]]<br />
<br />
<br />
== Schedule ==<br />
<br />
'''Friday, 24th July till Wednesday 29th July, 2009'''<br />
<br />
Day 1 | Friday<br />
• welcome/introduction and overview<br />
• inputs from participants<br />
• how big are the things we want to work with? first views of the microcosmos <br />
• microscopy overview<br />
• webcam hacking<br />
<br />
[[File:diy_microscope_steps.jpg|180px|building an inverted microscope setup for access and easy handling of biological species]]<br />
<br />
Day 2 | Saturday<br />
• intro to bioelectronix<br />
• webcam hacking, cont.<br />
• build a microscope<br />
• puredata for microscopy <br />
<br />
[[File:rotifer_in_space.jpg|180px|dirt sample with a rotifer in the left side of the image]]<br />
<br />
Day 3 | Monday<br />
• improve the microscope / leds, motors and sensors<br />
• design and build the bioelectronix device<br />
• BioArduino / control your bioelectronix device<br />
• observation and biohacking <br />
<br />
[[File:bioelectronix.jpg|180px|the combination of living organisms and electronix. tardigrade on a CMOS chip of a webcam]]<br />
<br />
Day 4 | Tuesday<br />
• intro to biosensors<br />
• bio2sound interfaces<br />
• sound2bio communication<br />
• brainstorm about concepts for installations/performances<br />
• urban walk and field research<br />
<br />
[[File:nematode_digicam.jpg|180px|building an inverted microscope setup for access and easy handling of biological species]]<br />
<br />
Day 5 | Wednesday<br />
• finish microscopes<br />
• investigate urban samples<br />
• open discussions<br />
• prepare installations/performances<br />
<br />
== Hardware ==<br />
<br />
== Software ==<br />
<br />
[[File:pd_microscope_close.png|300px]]<br />
<br />
pd patch for linux inculding arduino controls (v4l, v4l2, pdp, simple message system)<br />
<br />
[[File:pd_arduino_microscope_screenshot.png|300px]]<br />
<br />
[[File:hackteria_microscope.zip]]<br />
<br />
== Discussions ==<br />
<br />
So we get these nice videos and images... and now what?<br />
<br />
''Discussion on Day 4:''<br />
<br />
''Super Bio Mario Land''<br />
<br />
creating a computer game with a bio-generated landscape and moving organisms. a digital character will have to dodge and jump around the stuff<br />
<br />
''micro jam session''<br />
<br />
musical jamming with microorganisms. use the lifeforms to generate musical patterns and the human musican jams to it using normal instruments<br />
<br />
''bio-music videos / wormdancing''<br />
<br />
add music to various videos to tell stories... <br />
<br />
''microtorture chambers''<br />
<br />
no comment<br />
<br />
''universe to microverse''<br />
<br />
alien landscapes and local microenvironments<br />
<br />
<br />
<br />
== hackteria walk through Yelahanka neighbourhood ==<br />
<br />
[[File:hackteria_exploration_crew.jpg|300px]]<br />
<br />
[[File:sample 1.jpg|300px]] &lt;i&gt;water used to wash utensils at chai kadai <br />
<br />
[[File:sample 2.jpg|300px]]<br />
<br />
[[File:sample 3.jpg|300px]]<br />
<br />
[[File:sample 4.jpg|300px]]<br />
<br />
[[File:sample 5.jpg|300px]]<br />
<br />
[[File:sample 6.jpg|300px]]<br />
<br />
[[File:sample 7.jpg|300px]]<br />
<br />
[[File:sample 8.jpg|300px]]<br />
<br />
[[File:sample 9.jpg|300px]]<br />
<br />
[[File:sample 10.jpg|300px]]<br />
<br />
[[File:sample 11.jpg|300px]]<br />
<br />
[[File:sample 12.jpg|300px]]<br />
<br />
[[File:sample 13.jpg|300px]]<br />
<br />
[[File:sample 14.jpg|300px]]</div>Target022http://www.hackteria.org/wiki/index.php?title=Chloroform&diff=3050Chloroform2010-12-10T17:18:03Z<p>Target022: </p>
<hr />
<div><br />
Chloroform binds to any proteins present in the sample and thus carries out protein decontamination.</div>Target022http://www.hackteria.org/wiki/index.php?title=Aaron_Joseph&diff=3049Aaron Joseph2010-12-10T17:17:39Z<p>Target022: </p>
<hr />
<div><br />
[[File:MG_51381.jpg|frameless|border|center|1000px|]]<br />
<br />
<br />
<br />
'''Day One 10th May 2010'''<br />
<br />
It starts now! I’ve been waiting to work on this competition for a few months now. Somehow while writing this; I feel the excitement has just increased two folds after today’s session. Today we got introduced to the term ‘Biology’ by defining it in our own ways and not the way a science text book would. That’s quite interesting to me since I’ve known only one definition which I was expected to learn word to word. The first half of the day took us through a quick milestone check in the history of Biology. So we skimmed from the greatest discoverers of this subject, including Antoine von Leeuwenhoek, Charles Darwin, Robert Hooke, Louis Pasteur, Gregor Mendel, Hans Loncke, John Baptiste Van Helmont, Joseph Jackson Lister, Theodore Schwann, Rosalyn Franklin, James Watson and Francis Crick. All this that took place over a few hundred years we got done with it in a few hours!<br />
<br />
(EDIT: Hans Loncke really doesn't belong in this list. For the last 15 years or so, he has researched the work of Antonie van Leeuwenhoek, and has been rebuilding the microscopes van Leeuwenhoek used in the 17th and 18th century. He is considered one of the most knowledgeable persons on the subject of Antonie van Leeuwenhoek, and starred in the BBC's program 'The Cell'. Unlike the others in this list, he has not made any great breakthroughs in the field of biology. And unlike the others, he's still very much alive.)<br />
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Moving on to the more important parts, I read through a few documents on how synthetic biology is shaping the world now. How some of the most breakthrough discoveries are based on synthetic biology. From resurrecting a mammoth to engineering a man V2.0!. It gave me a good insight on the positive and scary sides of this kind of biology.<br />
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We also watched videos of today’s pioneers in this field of study and how they look at this subject, keeping in mind all the possible factors that come into play when synthetic biology needs to show progress. Estimations and foresights of cost and availability were part of the whole presentation. <br />
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I went back home with a smile on my face, because personally, 5 years ago I would never have imagined that we could reach this kind of progress in such little time, right after I got done with a fully fledged course in microbiology. I’m as fascinated as I was back then with this subject and now it’s gotten even better.<br />
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'''Day Two 11th May 2010'''<br />
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Recap of yesterday to keep us on track. <br />
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Today required me to be more sharp at remembering technical terms so I could familiarize myself with the different names involved in Genetic study. Since we will be working very closely with DNA and Genes, we sat tight and watched a few lectures on Genetics which took us through all the necessary jargons that we need to get accustomed with. Individual parts of a cell and how they contribute to the mechanism of keeping the cell to survive; these parts included the DNA, Genes, expression of genes, phenotypes, alleles, cloning and a few more. Mendel, the monk who put together the first jigsaw pieces had quite an impact on us, since we were browsing through all his work online as well as through available media. One of most important part was how we eventually came to learn about the Human Genome and the number of chromosomes in a human being. Also how a distinguishing chromosome makes a male or a female.<br />
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I learnt an interesting way of understanding how to look at a Nucleus. If we were to think a Genome as a Library, then the chromosome would act as the volumes in that library and the Gene would be the Chapters in each volume. I find that very simple to understand and really wish my faculty could put it across that way!<br />
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Moving on to synthetic biology I did a few readings on ‘How to kill synthetic biology’. This reading was a practical approach on how in many ways, many people think that this kind of a science could only end up spurring the ultimate fear which is WAR. So obviously enough people are trying to cut out supply or even make it highly cost inefficient. Another huge risk is the fact that companies are patenting any and every gene they isolate. Makes me come to think of a time when if I own a gene to rice then we’ll have to go back to the Barter system - I’ll give you rice, you give me corn! <br />
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Andrew Hessels - Introduction to Synthetic Biology.<br />
This video has surely shown me a hundred new doors for my mind to walk through. The ultimate fusion of computing technology, with a living organism by using programmable language, to control a living system. Come to look at it, there’s almost no difference between the functionality of a computer program and the commands in an organism. When I contemplate on the endless possibilities of this kind of progress, I usually end up logging back into facebook, just to distract myself. The result is always the same; we will inevitably end up in chaos, at least as far as I can think. Anyway keeping this topic at bay for the moment I enjoyed being exposed to the latest in synthetic biology. <br />
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'''Day Three 12th May 2010'''<br />
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Today’s class seemed a little boring to start with but it got interesting eventually as soon as David Sadava mentioned MUTATION and its permanent damages to a cell. Requirements of a DNA made things easy to understand when I asked myself why the big fuss about DNA? Once you get into the roller coaster of a DNA then you simply can’t leave out RNA and Proteins. Further on in the lecture I liked the way a Virus found its way into our learning. We’re always in awe of bacteria but when a virus makes an entry there’s simply no competition. <br />
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A statement that really got me thinking is when Watson said ‘The essence to life is Information’. I think that’s so simply put. Most of the time I keep asking myself - What is life? And that’s followed by a series of never ending answers which are mostly different perspectives. But nonetheless I found a new perspective to that question today and I think it’s going to stay for a while.<br />
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'''Day Four 13th May 2010''' <br />
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Spider web is stronger than steel! Now that’s something interesting. Look at the number of ways we can use that strength if only we can convert it something more malleable. It’s fascinating to know such small wonders in nature can be much mightier than what we are keep boasting about. I had a nice recap of many facts about human genetic information like we can only synthesize 12 out of the 20 amino acids that our bodies need. Something tells me that nature is not only smart but also plays a few games! <br />
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DNA replication – one of the most important processes that man has ever deciphered. The replication of the fundamental unit of LIFE. And all glory goes to the protein first at the job – POLYMERASE. I’m sure he’s sucking up some glory right now because there are more than a million cells dividing right now as I write this! Metabolism and thermodynamics were also important parts of today’s class and considering they are quite important topics I’m going to have to do more research on it. I also learnt the deadly effects of RICIN today and did have a few evil thoughts but otherwise there’s always so much to learn about our environment. <br />
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Today had a whole lot of jargons that I could easily recognize but the look on my friend’s faces was priceless. Promoter, Codons, Hormones and Transcription were some of them. Although after a quick animated video everything was back to sanity. We went over Nirenberg’s Experiment and other mutational effects in a cell which was quite exciting because as soon as I hear mutation I think of X-Men and the endless possibilities that we can explore.<br />
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Tomorrow we extract DNA! A simple Do-it-yourself technique that can be done anywhere, even at home. All we need is some dish washing liquid, salt and laboratory alcohol. So tomorrow’s going to be a thriller because someone’s DNA is going to be floating everywhere.<br />
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'''Day Five 14th May 2010''' <br />
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DNA extraction did not happen today. No alcohol, no salt. One we couldn’t find the other no one remembered to bring! Moving along, Genomes was an extended discussion today. Apart from that we went over mutations in further detail by using mutagens to understand it. Cancer quickly found its way into the discussion. Talking about genetic damage was inevitable. All this had to lead to sequencing of the Human Genome. I now know how to sequence my entire genome and look at all the commands that make me who I am. Sequential Genomics is something new I learned. Laying out an entire genome out there makes no sense until you know how to sequence it. I was really amazed that out of the 3.2 million base pairs that we own, only 2% of it codes for the most important element in our bodies – Protein. <br />
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Why do humans have only 24,000 genes? I think it’s a good question because it brought up some highly weird explanations in our class. I looked at Synthetic Biology very differently today. I always thought it was always about synthesizing a living organism. Now although this new definition may not b very different I still think it defines it much better. Synthetic Biology is making artificial genes to bring about a desired change in a living system. <br />
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We learnt about the process that’s making all the news ever since Stanley Cohen &amp; Herbert Boyer decided to put their inquisitiveness to an experiment – Recombinant DNA (rDNA). Cutting one DNA an infusing it into another that DOES NOT happen in nature can only be thought of by MAN! Well as strongly negative as it may sound, it’s been doing a whole of good to humanity. <br />
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Tomorrow we extract DNA.<br />
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'''Day Six 17th May 2010''' <br />
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Science has always fascinated me. In fact I personally feel that there’s no need to categorize the anything into science. Simply because everything that exists or doesn’t around you is part of science. Every single person has always wanted to know and explore his environment in some way or another. Maybe eventually he chooses to do what interests him more but science is always a part of everyone.<br />
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I learnt of isolation of genes. I don’t think it gets any better than this. Extracting the most highly simple pairs of compounds that are yet the source of all complexity on this planet. A good thing about this extraction is that it’s used for ‘gene therapy’. That means now we can help people live a normal life that they probably couldn’t, having a genetic disorder. Here’s where I also saw the high relativity of how a living system functions just like a programmed execution of a machine. The resemblance is striking. And needless to say now we can put the two together and create magic!<br />
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Our new exercise today was something I have been looking forward to for a while now. It’s the cool part of this whole competition. I have to create my own organism and design it fully! Now that’s talking like a designer. Here’s where all my technical and abstract thoughts are going to find one place to play. I can give this organism any feature or function I want to. It belongs to my jurisdiction. Sadism apart, I’m going to make some thoughts work in a positive way and let’s see what happens.<br />
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Extraction of DNA did not happen. Tomorrow we extract DNA!<br />
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'''Day Seven 18th May 2010''' <br />
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Today I’ve not been so happy watching two movies back to back. We finished the BBC series on The Cell. It was amazing. The whole journey of how man has reached this point in science makes come to think of how far we are going to get and will we ever stop. Everything said and done about man being the dominant species at this time and eventually he will succumb to the next step in evolution, well the difference here is that he is completely aware of this step and to a very far extent is in control of it. <br />
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We have come a very long way and the numbers of combinations that have been tried to get better are only half way done! I’m not a Human being biased person but I think man is by far the most highly evolved living organism and all credits to nature but on the other hand I sometimes feel nature maybe regretting this. <br />
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'''Day Eight 19th May 2010''' <br />
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Zac is a funny man. I’ve never come across or even thought of combining words such as Geohackers, Biohackers, Geoenginees and Planetcrafters. I learnt that food is inevitable a necessary evil, that we simply can’t do without. SO interestingly Zac’s presentation took me through a quick brief of how we handle this crisis of shortage of food on one side of the earth while there are famines on the other. I think eating habits are related to too many factors to isolate. Most importantly, they are cultural which already tells me that it’s going to be ages before any change can happen.<br />
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Why is Innovation disruptive – because it challenges assumptions and creates hybrids?<br />
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I see this smile on my face and wonder what it’s about. I remember, we extracted DNA today! Apparently I was the chosen guinea pig. No complaints at all, it was simply fascinating to look at those clumps of strands move up into the alcohol. Just couldn’t stop myself from a mental movie that flashed most of my life in front of me. This one was a good kind of flash because it highlighted only what makes me ME. <br />
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'''Day Nine 20th May 2010'''<br />
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Everybody was sick today! The famous Bangalore weather is back again. Suddenly changed from harsh hot to romantic cool and put everyone into a drowsy influenza dominant mood. The day still goes on. I presented my abstract on the new organism I cooked up, along with everyone else and I must say when you put a bunch of people together and get them to ideate, something really good always comes out, even if it was thought of individually. Everyone had this more or less cool creature that was loaded with some wicked features. Like for example thermo sensitive bacteria that can generate heat to ward off anything you want or a booster organism that gives you all the energy you need whenever you need it and of course my organism that’s a super organism which is smart enough to copy other organism DNAs, take the best out of it and put it in its own! <br />
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I’m beaming with ideas, need to pen them down and do some permutations with the features I can give a living thing. This is more fun than I thought. I’m positively sure there’ll come a day when these creatures will be merrily living around us.<br />
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'''Day Ten 21st May 2010''' <br />
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The sickness continues. I’m not sure if this is coincidence of just plain irony. We’re all putting our heads together and working on microorganisms at the delicate cellular level and there’s this humorous virus that infects most of us, thinking it will pass off as a practical joke! Most of down with the flu but still made it.<br />
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Today’s class got me thinking in a direction I’ve mostly ignored in a while now. Yesterday’s exercise was to brainstorm on a machine that could or could not have a form or function or even purpose for that matter. Now here’s where I’d like to think that verbal communication is the least effective. How does one think of creating anything without having thought of something relative to previous understanding? No matter what you think of, however random or bizarre it will always have its roots somewhere in relation with what you have already heard, seen or experienced of. What is imagination? It’s an extension of some point of relevance, so no matter how far fledged you think, the idea or thought is going to have some kind of inspiration from something or the other. So how do we think of creating a machine that has a mechanism without purpose? Isn’t purpose relative, which means if a mechanism exists, then a purpose will follow... Now the argument is that a purpose is assigned to a mechanism and hence the purpose does not exist by itself. I partially agree with this since it does make complete sense but on the other hand that’s like a hen vs. egg statement. Yes I know that a purpose is assigned to a mechanism and so therefore if the mechanism does not exist then so doesn’t the purpose. But then again the mechanism DOES exist, so we can talk about hypothetical situations but at the end of the day this is what reality is, or at least is perceived by us. So the fact that there are chlorophyll cells converting sunlight energy into food as a mechanism, their purpose is to provide nutrition to the plant. Now this can be said to the general understanding of the purpose of the chlorophyll cell that is assigned by us but at the same time if you don’t consider that opinion, the purpose STILL REMAINS THE SAME.<br />
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Another statement that came up was the fact that if according to relativity anything has infinite purpose then it also has NO purpose. This will definitely suffice mathematically. I completely agree with how this is deduced and how it makes full sense. So here again there are different aspects to looking at it, which simply makes it perceptual understanding. If I stand at the north side of this discussion I see that purpose is nothing but a fragmental extension of an existent mechanism and from the south end its nothing but a perception of what is assigned to a function. <br />
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My conclusion: THERE IS NO DEFINITE EXPLANATION.<br />
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This brings me back to designing a machine that has function without purpose. The only one thing that I can think of which fits the bill without any biases, is DARK MATTER. We don’t really have too much understanding to this subject; some claim it’s still a hypothesis, therefore i think it’s a good ‘feature’ to base my machine on.<br />
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So for now, I’m going to retire with the thought of creating a machine that has no connection with what I already know. I seriously hope something pops up in my dreams because I don’t think I’m going to able to manage this otherwise.<br />
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'''Day Eleven 24th May 2010''' <br />
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Somehow coincidences seem to be name of the game. I’ve been following a few recent developments in the field of Synthetic Biology and quite a few have been very significant, surprisingly coming together just when we are doing iGEM! Take for instance there was a recent article in the newspaper on how the DNA replaces the ‘chip’ followed by a nanorobotic Virus and to top it all off, Craig Ventor announces the first fully synthetic cell to be cultured! Now this is what I’ve been talking about for a while, very soon we’re going to have all our systems being run by living functions that can evolve. The thought really scares me but alongside that fear there is this futuristic view of how good things can be if only we can use this power constructively in a positive manner. Alas, that thought ends with a snigger, knowing there is no hope for something like that. <br />
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This completely synthetic cell is a baby of a computer! I’d like to relate this to Patricia Piccinni’s work of the hybrids she makes of future organisms. I’d really like to see what she could put together with a computer and a synthetic cell! In fact I’m going to try and do that myself. This cell also has a password that when cracked will reveal web addresses and email addresses and also names of the authors who put this organism together. This cell has great significance, like it can really help produce vaccines very quickly and so that in turn will help save many lives at the nick of time. It can also be used to clear up the massive oil spills that wipe out marine life. But here’s the catch, the kind of advanced technology can be misused by many to wipe out us humans all over again. I’ve always had this thought at the back of my head – we are always complaining about how we as humans are messing with nature and tearing it apart. How we are responsible for causing an imbalance by modifying and creating what would otherwise not happen ‘naturally’. Well here’s my thought, what if this was nature’s way of working? What if this is how nature planned to move evolution to the next step? What if nature knew that it could not bend its own rules so it evolved into the most sophisticated organism (Human Beings) that can eventually get the job done for it? What if nature could do only a certain amount of permutations with evolution and so we are its way out. Apparently, at this level of intelligence we are still using only 10% of the capacity of our brain, so what if nature has all this well planned out. It knows what’s headed its way and is very well prepared for it. And here we, the emotional beings that we are attach so much to this process and start categorizing it into ethics and morals and values and what not! A very long chain of thought follows these questions that contradict it in many ways because there are quite a number of different ways you can look at this. But all said and done I think I’m going to pursue these questions and start applying them wherever I possibly can just to see what answers I can get.<br />
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Stellarc, I’d like to say is one of those people who simply cannot see themselves living a mediocre life with materialistic possessions, so they get up, get out, and start mixing. I like some of his work and after a few of his reading s I can say he does think out of the box and experiments with almost anything which is good because variety does make things better. Orlan on the other hand is an artist I can probably never connect with. I think people like her are more or less society rejects. Allow me to explain. I think she has had some disturbing experience in her childhood or while growing up she simply did not fit in her environment repeatedly. At the same time she is not a kind of person who would express herself in a harsh manner since she is completely aware of the line that separates her from a lunatic and so this kind of art becomes her medium of expression. The pain she goes through helps subside her aggression, which of course she experiences in a very subtle and satisfying manner. I know these are purely judgemental but I’ve made these statements after trying to fit in her shoes as much as possible.<br />
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'''25th May 2010''' <br />
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We finally made it to NCBS today! I was nostalgic for almost the whole time. I remember coming here to submit my Entomology Thesis when I was college. And also remember trotting around the whole GKVK campus with my friends and collecting as many different varieties of insects as we could. The campus has grown I can see how trees add to the aesthetics of any place. The canteen had a lot of fresh air to get my gears running but I chose to be the listener when Avni and Karthik had a very interesting discussion that I felt started with a bang, then got lost somewhere, then came back to a point and finished off by just hanging in there. I remember being this enthusiastic about ‘how science institutions get funded’, (I had a snicker on my face when I wrote that). At the back of my head I can hear a voice tell me that there’s been an addition to the army of people that sit and discuss this when really nothing good comes out of it. I know I sound based but honestly these are more or less topics that you get passionate and aggressive about for a period of time in your life. Once you start to realize that the system is not going to change by sitting and talking about it then you start to leave the topic alone.<br />
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The rest of the day was quite spaced out. We went around looking at different labs and their equipments. I was very impressed with the fluorescent microscope but not with the fact that work on the Drosophila Melanogaster still reigns.<br />
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I think what I’ve taken back with me today is that everything we aspire to learn of master in life has a process which very simply put you does NOT have a shortcut. You can find alternative routes that will make it seem more convenient but I think that’s just an illusion.<br />
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'''26th May 2010'''<br />
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Welcome back David Sadava. Went back to his tutorials today. Almost forgot his brilliant humour! Today was very informative. The thought of disarming a landmine using a microorganism would sure never come to my head. And i remember once reading in a NAT GEO magazine, they did this article on this guy who had a record collection of landmines that he dug up. That was his job to go into the field and dig up live landmines! I'm sure this news will bring him some joy. <br />
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We did a good amount of study on the PCR today. Starting from Kary Mullis to how the PCR became a rage and is used massively world wide even till today. In a video where Kary Mullis spoke on TED talks I found it very interesting that he gave his invention very little importance but instead chose to spoke of how data gets manipulated in our world. That really got me thinking on exactly how am I supposed to believe ANY data that I recieve. How do I know that it wasnt tampered. He used the example of a weather reporting station that manipulated data on the weather and put us into this fear mode that we are depleting the ozone layer! Disturbuing, it's going to make me think a few times before i agree to any data information.<br />
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'''27th &amp; 28th May 2010'''<br />
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We started a new assignment today. To experiment and grow a living form over a long time and watch how it interacts and changes form or location. Complicated? Not really, its just about growing a living form and seeing how it finds it way to survive. I have a few ideas like if i had to grow a GFP bacteria in a tank large enough to hold a colony of bees then, after both the bacteria and the bees have grwon, the bacteria would probably attach to the bees legs and so if I had to keep this in a room lit by UV light then I would see glowing bees flying everywhere! I know it sounds far fledged but I think its doable if I can manage to keep the place out of human reach. My other idea was to grow a colony of ants in a closed environment and keep changing the a few factors in it, like remove or add things everyday and see how they grow with that. My thought behind this was to see how they will respond to constant changes in their comfort level.<br />
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This is going to take a while but I surely want to do it. <br />
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'''31st May 2010''' <br />
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NCBS here we come! Wait, Yashas just said ‘tomorrow’. I was really hoping we could go set up our OWN lab at NCBS today, but looks like Yashas wins again. One day I’m going to take a picture of him and make something really funny out of it. Actually I think I’m going to get everyone to make some funny stuff about him. <br />
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After three weeks of this competition, I finally like the work of an artist. Alexandra Daisy Ginserg. It’s very obvious, she’s more or less of this age, and has done tons of work in a very short time. I was going through her bio-data and she has achieved a list of valuable titles that I’m pretty impressed with. What is very promising is that she’s going to be joining us for this competition and facilitating this course! I’m definitely waiting for that to happen. I like the way she uses modern techniques to express her thoughts. It’s what I’d like to do myself, so I’m surely going to inspire from her. <br />
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I can’t stop thinking about what this very infamous scientist said, I quote, ‘I only wish I knew it was so important at that time’ – Raymond Gosling. He was the scientist that worked under Rosalyn Franklin of the structure of DNA and just like her got no recognition for it. But back then it was just working to get the structure of any other molecule as simple as sodium chloride. What really caught my attention was his simplicity to the fact that he realized how important it is to treat every moment of your effort with the high importance. We seldom do that. At least I definitely don’t. I have a brilliant program in my head that almost instantaneously categorizes everything bit of work I do and as soon as a piece of work does not meet the minimum ‘importance’ criteria, it’s conveniently forgotten. And of course the minimum criteria here are whether I would get immediate reward or recognition failing which, everything else can wait!<br />
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'''1st June 2010''' <br />
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I started today with a definite goal of figuring how I’m going to build on the art form exercise from scratch. So I’ve done my research which and here are a list of things I need to do.<br />
1. Build an incubator<br />
2. Find some bacteria – E.Coli preferably<br />
3. Grow the bacteria<br />
4. Recombine its DNA with plastic binding proteins<br />
5. Then check to see if it can break down or degrade protein.<br />
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Growing yeast on agar today was a nostalgic feeling. The best part is that I even forgot all the specifications of growing it. Thanks to the internet, it’s all available at a click. So we boiled, sterilized, transferred, inoculated and labelled all our stuff. <br />
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I enjoyed reading through bacterial transformation. I’m simply fascinated by the whole process, sometimes I think these organisms are far too intelligent than we think. Another treasure added to the collection of information on synthetic biology - A synthetic oscillatory network, the first synthetic biology paper submitted. This paper got me up on my toes. It had every single thing in the highest detail. I had to read four lines at a stretch and give it time to digest. The concept of a negative feedback was what got kept me thinking all night. It’s actually the most ideal mechanism of an input output system. A few things that I’m going to be researching on are a Promoter, Repressor, Negative Feedback and a Plasmid.<br />
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'''2nd June 2010''' <br />
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Having a campus spread out for more than 300acres can be deceiving sometimes. It took me half an hour just to figure out the entrance of the NIAS at IISC today. There was a debate on “Between Scylla and Charybdis : An analytical overview of the debate on the Design problem in the Theory of Evolution” by M.G. Narasimhan. I entered late but managed to catch the interesting parts of the debate. My understanding of the whole debate revolved the speculation of how much importance we give to the designer of life. The eye was taken as an example and just like the eye has a designer so does the designer have its own designer, hence it goes on and reaches infinity. So in a way in does makes sense that there is no point in discussing WHO made it but the fact that it IS made and the complexity that goes in its making. I think I’m going to spend my time unravelling and understanding the complexities involved in the making of life rather than who made it. I think what is far more interesting and important is that we as beings with the capacity to evolve should keep our eyes on that ball.<br />
The rest of the day was pretty quick at NCBS. We finally got to meet the big guy Mr. Mukund who will be facilitating us through iGEM and he took us around our space that we will be working at.<br />
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'''7th, 8th, 9th &amp; 10th June 2010''' <br />
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'''THE CENTRIFUGE'''<br />
<br />
In theory EVERYTHING is possible! I’ve used a centrifuge hundreds of times before. And like a device of royalty I’ve put it on and put it off whenever I’ve felt like. Now that I had to make it, showed how being on the other side is no joke at all. We started with brainstorming what to use. So the simplest mechanism would be anything that rotates, like a blender, table fan, exhaust fan, cycle wheel. We picked the blender since it already has a jar attached to it. So that makes it quite convenient. All we had to do now was to attach a few tubes around its rim and voila! We have a centrifuge. Like I said in theory everything is possible. It’s been a tough job. When we got into making each part with the available material around us, it got tougher than we thought. Our first obstacle – the blender was spinning way too fast, the motor was very powerful. This was a good and a bad thing. The good being that we would finish with a high speed centrifuge and the bad being that high speed meant high vibration, high friction, and high wear and tear and so we would need tremendously high attachment techniques. This however would eventually stay the same problem but we will figure a way to keep the tubes in place. So we took two metal strips bolted them together in the center and at the sides then used GI wire to fasten through the tubes and through the metal strip. I know a metal strip could be dangerous but filing the edges and keeping the bolts tight should help. Now GI wire is good for experimenting but eventually we had to shift to a safer method. We used hinges that come in a metal box to keep it closed and locked. This worked excellent since we just had to screw them on to the tubes and the metal strip. Now to test our patience the rotor gives up. So back to square one now we need a new rotor. We somehow managed to get an old rotor that worked fine fixed into the blender and this time it worked perfect! The tubes spun so fast i was sure to get some great results. Now the final part was to use a stopper on the outer end of the tubes to seal it closed. First thing that came out of Sam’s mouth – MSEAL. She just loves doing that. Want to stick anything? – MSEAL. I think someday when he boyfriend talks too much she’ll MSEAL his mouth!! Anyway so we used MSEAL to seal the bottom part of the tubes and after half hour of drying, we did our first test run. We used two glass test tubes without anything in them and after a few minutes of anticipation we ran it. The result? MSEAL breaks, test tube goes flying across the room and smashes into smithereens on the wall, almost exactly where David our workshop facilitator sits. Luckily enough, he wasn’t sitting there at that time! It took me a good half hour to get over that. I had cold feet until then. <br />
So later on we put everything aside and came back the next day with a fresh start. We secured all the bolts with adhesive and the bottom of the tubes with MSEAL again only this time it was rock solid before we started anything. We ran the blender and needless to say it worked like magic. It spun so fast, felt like a fan right at my face. This time we were sure as hell. The Jugaad centrifuge was alive.<br />
Next stop extract DNA again and run it in the centrifuge<br />
<br />
<br />
<br />
'''11th June 2010''' <br />
<br />
A brand new day after a little success. Today Mohor and me decided we’re going to make a Jugaad microscope. Shreya has already been working on one and has been sweating it out to finish it, which is more or less a great piece to use. But this time we’re going to learn from all the mistakes made to get this one right. So we started with a surveillance cam which was a super flop, then moved onto a buying an inexpensive webcam. Converting a webcam to a microscope is pretty easy. All you have to do is pull out the lens invert it and stick it right back on. The tough part is how to build a structure to keep the cam in place so you can use it to see objects without the slightest shake. I know this is going to take a while but we get at it immediately hoping to finish quick.<br />
12th June 2010 <br />
Designers James King and Daisy Ginsberg will be coming over to facilitate our team! I think that is really cool. I went through Daisy’s work and man has she accomplished a lot in very little time. James himself has done a lot too and I really like the way he represents his work visually. It’s time to make a good impression. We start collating our work to present to them when they come on Monday so all of know this has got be good. We quickly divide into groups and take up responsibilities. One group picture collation, the other content, the other brainstorming and another power point! <br />
It was fun today. I realized we go through everyday working on something or the other but what really pays off is when you sit down to put all that work together and it looks good! That’s a nice feeling. I like it.<br />
<br />
<br />
'''14th June 2010''' <br />
<br />
James and Daisy came over. I felt this good exchange of energy when they smiled at all of us. We started off by introducing ourselves and the work we’ve been doing so far. And they in turn showed us what they have been doing for many years now. I find their work quite fascinating because they really think far ahead in the future and if I have to match that with something else it would be similar thought of all the most famous people in the world, they thought for the future. <br />
<br />
Something interesting I learnt today was a phrase – The Rest saving the West. I find that very strange to believe and all credit goes to the west for that. The West has such a huge influence on our lifestyle that we barely even realize it anymore and to top that up we have numbers of designers coming from the west saying that they want to save the rest when actually it needs to be the other way around. Simply because if they think they need to save us, they have to realize that we adopt their cultures to become what they think needs help. So really they first need to help themselves.<br />
<br />
We brainstormed as a team on this and came up with a few good ideas. I’m not sure how far we can take this although.<br />
<br />
<br />
'''15th June 2010''' <br />
<br />
I don’t think Jugaad and me have started off on the right foot. I get the point of Jugaad but maybe there’s a reason why things should be less accessible. What happens when things are made easily by the wrong hands? What if the things made from Jugaad have high potential for disaster? I have a list of questions but I think the point is put across. For now I’m going to stick with it. <br />
<br />
We saw a video today called Kempinski. This really changed my perspective on Jugaad. The movie had this eerie feeling to it that almost made it seem real. I can’t stop myself form thinking of a future like that.<br />
<br />
Today’s new learnt topic – What happens when Synthetic Biology is hacked in a way we are not familiar with, so let’s call it ‘unethical hacking’. I have no idea what would come under ethical hacking but nonetheless for arguments sake, what if a backyard scientist hacked a cell and made it produce a protein which his son needs desperately. And on dosage his son dies. Now no one knows why the kid died and he’s been playing around with all the colony kids for a few weeks now and all those kids have gone back home and to their own schools. So roughly, how many people do you think have that bacterium in them? And how soon do you think until the worst happens?<br />
We did a fun exercise today in which we split up into teams and had to come up with unexpected errors or use of the previous iGEM team’s creations. So Karthik, Nooshin and I quickly ran through a few teams and closed in on the bacteria that can oxidize metal and then we cunningly found the best way to apply this – The BP Oil Spill! I know this may sound ridiculous but we presented this as the headlines from a local news channel. So the BP oil spill apparently was because a group of Anarchists decided to have an inside man at the BP stations and he cleverly used this bacterium to cause the spill! <br />
<br />
iGEM started in a classroom with a bunch of students and a faculty. There’s something very similar in this class we sit in. We are a bunch of students and we have three faculty! So off we go to invent and start the FIRST ever of its kind – iGEA which stand for International Genetically Engineered ART!<br />
The sound of it makes my head rush through a few years and look at five thousand participants being part of this globally recognized event. <br />
<br />
So we started brainstorming like there is no tomorrow and a few lines to keep us on track were...<br />
* What is the iGEA competition - the International Genetically Engineered Art Competition? <br />
* What categories are there? <br />
* What prizes can be won? How do people communicate their work? <br />
* What might be disqualified from entering? <br />
<br />
Karthik, Nooshin and I came up with this.<br />
<br />
* Best Social Critique – there can be no art without critique from a third person<br />
* Best Visual Aesthetics – the world runs on this<br />
* Most Innovative Concept – Everyone looks for a new concept<br />
* Most Thought Provoking – Little difference from concept because this is a thought, it could or could not be a concept<br />
* Best Use of Colour – This spells out A-R-T<br />
* Best Abstract – Every single artist and designer will smile at this category<br />
* Most ECO – we need a better world and it starts from here<br />
* Best Pattern &amp; Texture – this award is for those who love to play the fool while experimenting<br />
* Gestalt Award – The mother of them all. Gestalt completes the whole competition.<br />
The latter half of today went into this huge discussion of how to tell between an artist and scientist and after listening to everyone’s version of it. I’ve come to this strong conclusion. There is really NO difference between an artist and a designer. I think the ONLY valid point that can be considered is ‘how they present their work’ so to put it in simple words If you present your work in a scientific manner then you’re thinking like a scientist otherwise you’re thinking like an artist/designer. This is only because in every other way both an artist and a scientist have exactly the same thought pattern and process.<br />
<br />
<br />
'''16th June 2010'''<br />
<br />
Today we finalized on what iGEA would be if it ran. The awards were boiled down to the following<br />
* Best Ecosystem <br />
* Best New Emotion <br />
* Best Social Critique <br />
* Best Pop-Culture <br />
* Shooting Star (short-lived, burning bright) <br />
* Remix Culture <br />
* Grand Prize: Gestalt Award<br />
* Honours: Critics Choice for Visual Aesthetics<br />
* Honours: Genetic Raspberry Award<br />
<br />
We had to chose the categories we were competing for and we got Best New Emotion and Best Pop Culture This time it was only Nooshin ad I since Karthik was off home for a family emergency. So Nooshin and I brainstormed by starting with a mind map on Pop Culture. Then we moved onto Emotions and a few interesting things came up like Crime as an emotion – What if crime was committed as an oblivious response to an emotion. SO just like you would approach that cute girl and ask her out because you have butterflies in your stomach for her, likewise there’s this guy who wants to kill another person because he experiences an emotion that drives him to it. The other thought was jailed in Pop Culture – if you look at this in a certain perspective then aren’t all of us prisoners of pop culture. We simply cannot do without it can we? So we imagined a penitentiary where all the in-mates are served the latest iPOD. They bathe in alcohol, feed on news of the latest hip item released and party all day long. Our third idea which happened to be the one we took forward was what would happen if we deprived something of a very important element in their lives? How would they cope with that? What changes would come along? What would they do about this change? Nooshin suggested ANTS since they already have a certain culture in their behaviours and their lives revolve around the production of Formaldehyde. So we took it as a good idea and moved forward. <br />
<br />
Ants communicate using a trail of formaldehyde everywhere they go and they have complex levels of communication otherwise. So we thought of engineering a bacterium to inhibit the production of formaldehyde and then see what happens. How the pop culture fit in here, we already knew that was going to have to be imaginary. This was’nt enough so our next level was to engineer the bacteria to not only inhibit the production of formaldehyde but also produce a coloured protein in response to the emotion of the ant.<br />
<br />
<br />
<br />
'''23rd June'''<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 I read an Indian mythological story I have to say it’s so cool because these are some stories that have characters that can pretty much do whatever they want! 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 />
<br />
[[File:Holy_Trinity_11.JPG|center|800px|]]<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 />
<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:Holy_Trinity_21.JPG|center|800px|]]<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 />
<br />
'''28th June 2010''' <br />
<br />
Today I’m happy. We started out the day like any other. Clueless. But at the end of this class there’s a beginning. Picking up from the assignment over the weekend, we put up all our research over the most important people and organizations on the board and then started arranging them in hierarchy. After all of it was up, we split into teams and picked three characters off the board. It was story building time! Mohor, Diya and I picked The Indian government, Drew Endy and Daisy Ginsberg. I find that to be a killer combination. Just putting these three characters together in the mind itself creates pages of stories. So we gathered around and put on our thinking caps. I think the excitement came from reading those Level 10 comics. I’m fascinatedly excited. The Story is going to come up in a day or two so until then... stay curious.<br />
<br />
Post Lunch I came and sat at my desk and looked at James across me. Without a second thought I asked to talk to him aside. After a brief chat I figured my instincts were right! He had no clue why there was such a huge communication gap between us and him. All this while we were under the impression that he and Daisy were leading us somewhere and they on the other hand were wondering why we as a team we were not coming up with any ideas for the main event! The Power of Expression! We quickly called a meeting in the cafeteria and in 15mins our team was a rolling stone. We all came to the common understanding that were going to put our heads together on this and use Yashas and James to tap us back on track in case we deter.<br />
<br />
MIND MAP out on the ground. We put all the most important learning’s on the floor for now and tomorrow we start connecting the dots. <br />
<br />
I’m happy. We can call ourselves a team now.<br />
<br />
[[is this a link]]<br />
[[Media:microscope.ogg]]</div>Target022http://www.hackteria.org/wiki/index.php?title=Hackteria_Lab_Commons&diff=3048Hackteria Lab Commons2010-12-10T17:16:33Z<p>Target022: </p>
<hr />
<div><br />
== First Ideas ==<br />
<br />
=== DIY Micromanipulator ===<br />
<br />
After observing the micro world I would like to interact. To do so we could build a mircomanipulator using intelligent materials:<br />
&lt;gallery&gt;<br />
File:Manip.jpg<br />
File:manip2.jpg<br />
File:rigidgrab.jpg|http://www.me.unm.edu/~lumia/Microgripperwebsite/main.htm<br />
File:stacked-parts.jpg|http://robotics.eecs.berkeley.edu/~ronf/milli-robot.html<br />
&lt;/gallery&gt;<br />
<br />
Check out the movies:<br />
<br />
[http://www.me.unm.edu/~lumia/Microgripperwebsite/Good%20gripping_solder%20ball.MOV UNM Gripper]<br />
<br />
[http://robotics.eecs.berkeley.edu/~ronf/MICROBOT/assemble_small.mpg Berkeley Gripper]<br />
<br />
Update, Thursday April 8th, 0:46, Urs&lt;br&gt;<br />
Some first results with most simple micromanipulator done. Building it was a matter of some 30 minutes (felt time). Hot glue, acrylic and coil wire. The results are ok. Difficult to adjust on the microscope lucifer due to the big magnification. Had some first interaction with a tardigrada. Not sure weather she/he/it liked it. At one point the tardigrada rose on the manipulator. From an engineering perspective the Micrometer scale is already quite challenging. The human hand is (when helped by a good visual feedback through the microscop) capable of executing quite sensitive movement. The manipulator (as for now) helps a litte. Think the lever construction is a good starting point for automated / remote interaction.<br />
&lt;br&gt;<br />
[[File:Manip1.jpg]]<br />
[[File:Manip3.jpg]]<br />
<br />
===Phototransitor Array===<br />
<br />
Instead of using a webcam I would like to experiment with an array of phototransitors. In combination with the laser projection microscope (by Marc) this could give a low res picture of the microcosmos. &lt;br&gt;<br />
<br />
Could look something like this:&lt;br&gt;<br />
[[File:IR sensor array small .jpg|240px]]<br />
<br />
I will bring some of these and some analog multiplexers... &lt;br&gt;<br />
[[File:AmbientLightSensor.png|240px]]<br />
<br />
Update, Thursday April 8th, 0:46, Urs&lt;br&gt;<br />
The phototransistor array is soldered together. While commercial digital cameras are in the mega (1'000'000) pixel range I thought that 20 pixels soldered and hard-wired by hand is already a lot. The ambient light photo transistor sensors work like a charm. Interfacing using 4 multiplexers (4061) was busy work. There is still a little glitch some where in the wiring. Still I am happy with the result and Marc is having fun while poking around with the laser on the DIY camera (which is always a good sign for me). The software was a little bit a pain (needs some (abstract) concentration which is some how difficult in creative sessions). Concatenating the pixel camera with the (identicaly looking) LED Display was no big deal. &lt;br&gt;<br />
&lt;br&gt;<br />
<br />
[[File:PhotoArray.jpg]]<br />
<br />
<br />
== '''mouse and blocks''' == <br />
<br />
I am interested in possible approaches for the visualization of nano effects in micro-scale.&lt;br&gt;<br />
first basic idea:<br />
&lt;br&gt;<br />
mouse and blocks - tardigrades which will be led by controlled obstacle patterns, made of magnetic nanoparticles. &lt;br&gt;<br />
first approach would be, trying to realize a controlled &quot;moses effekt&quot;(Dusseiller 2010), dividing water with the &lt;br&gt;<br />
help of magnetic nanoparticles.&lt;br&gt;<br />
&lt;br&gt;<br />
<br />
Stefan &lt;br&gt;<br />
<br />
== Spectroscopy ==<br />
<br />
I've got 4 of the photometer boards made up from this tutorial here -&gt; http://www.rsc.org/Education/EiC/issues/2007Sept/BuildYourOwnSpectrophotometer.asp and i have some extra 3140 opamps for making some more. I'd like to develop a couple of these into 'proper' spectrometers, develop a suitable (maybe PDMS based) organism container and see if there is a way to get spectroscopic data out of organic change.<br />
<br />
andy g<br />
<br />
== Tardigrade Farm ==<br />
<br />
I've been culturing tardigrades for a while now with moderate success, but I'd like to develop a proper 'tardigrade farm' for future hackteria use. These entails the making up of proper media such as Chalkey's and Soil extract, and it would be good if we can do this without needing a proper lab. It might also be necessary to develop a bespoke container and parallel chlorococcum (tardi food algae) culture. If the whole thing could be partially or completely automated it would be fun.<br />
<br />
andy g<br />
<br />
== Some general electronics ==<br />
<br />
I'm also hoping that someone can give me a hand for a couple of hours to get over my brain block in controlling some 12v solenoid valves from arduino. I'll bring the solenoid valves and the arduino if someone else brings the brain...<br />
<br />
andy g<br />
<br />
<br />
== Colonized Colonizer == <br />
<br />
<br />
Traffick or un/aware handling of organisms has been an underlaying reason for that what social sciences call as -colonialism- (we live in the realm of fungi!). I will like propose shared observations to compare _realtime_ (via video streaming) with some of our collegues in Colombia different micro-organisms, minerals, strains.. that could lead us to share thoughts on the many bio tactics introduced by colonialist strategies. There are many conceptual layers to it, from how much observation affects the experiments to micro biological &quot;peace&amp;love war&quot; on drugs. The fact that we open a parallel view across continents will lead our experimental approach. (still to much to elaborate on this.. but at least it express one possible vector i will like to put effort to implement for the sake of the continuity of our networked collaborative practices). --[[User:Alejo|Alejo]] 10:45, 3 April 2010 (UTC)<br />
<br />
<br />
== ++ Linux Drivers for webcams ==<br />
<br />
In case one has the need to reinstall gspca video based drivers, there is this guide that helped me out reconfigure a meesed up system:<br />
<br />
Karmic: get the latest drivers for gspca, uvc, usbvideo and other<br />
[http://stemp.wordpress.com/2009/11/03/karmic-get-the-latest-drivers-for-gspca-uvc-usbvideo-and-other/]<br />
<br />
For a list of supported webcams under linux see here -&gt; [http://linuxtv.org/wiki/index.php/Webcams]<br />
<br />
<br />
== Microscope-incubator-device == <br />
<br />
I would be interested in starting to work on a DIY-microscope-incubator-glovebox-device to be able to work with mammalian cells and to find out if it´s possible to do some basic live cell imaging. So generally, I would like to learn more about the culturing and incubation of cells over a longer period of time and to find out how if it´s possible in a DIY way at home/in the atelier.<br />
<br />
I´m very interested in visiting the light microscopy center of ETH Zurich. <br />
<br />
verena f<br />
<br />
Update, Thursday April 8th, 0:46, Urs&lt;br&gt;<br />
Felt some consensus seems to be there on the incubator. I am really happy about our progress on the rough concept of the incubator. Pieces are coming together and some really interesting synergies (like growing chamber = droplet = lens = biosphere) are there. Interconnections between functional units can be established. While technical aspects are ostensible thinking about the incubator concept as a representation of the ongoings in the HackteriaLab might be interesting (Ma be this is particularly true for verena looking into the Lab from outside).<br />
<br />
[[File:Incubator_1.jpg]]<br />
<br />
== Ideas about Hackteria Workshops ==<br />
<br />
One of the central idea of the hackteria project is the development and conduction of introductory workshops into the world of biological arts. while some artist have developed a strong relation to the biological science, introducing living media into their work and processes, the field is not very easy to enter for emerging artists. By the breaking down of biological techniques, simple instruction to set up a functional lab in an artists atelier and critical and theoretical reflection about these processes a hackteria workshop should help artists to start working independantly with biological media.<br />
<br />
here are some ideas and topics that might be interesting to condense into a introductory workshop format.<br />
<br />
*On the origin of species<br />
Evolution, variability, species, chimera, what is out there<br />
<br />
*bioelectronix<br />
Hybrid system, cybernetics, measurement and control, symbiosis<br />
<br />
*BioLab<br />
How to start a lab, tools, diy,<br />
<br />
*diy microscopy<br />
History of scientific instrumentation, microcosmos, visual experience<br />
<br />
*on instrumentation<br />
Spectroscopes, microscopes, absorbtion/emission, pumps, incubators<br />
<br />
*Genetic media<br />
Genetic code vs digital code, extraction, synthesis, sequencing, visualization of genetic information, privacy<br />
<br />
*Flesh! Animal tissue<br />
Life outside of the organism, cell culture, artificial organs, xenografting<br />
<br />
*on plants<br />
Growing<br />
<br />
*Synthetic biology<br />
Genetic manipulation, bacteria, viral transfection, biobricks, artificial life<br />
<br />
*Nanobiotechnology<br />
Analysis, interaction and manipulation of biological phenomena on the nanoscale, motorproteins, nanoparticles, lipids, new instruments<br />
<br />
*living colors<br />
Life as paint, patternig, growth patterns, time based, fluorescence<br />
<br />
== Questions ==<br />
<br />
I have some questions. I will ask questions.<br />
(I'll collect some of these &lt;s&gt;here&lt;/s&gt; over the next days and hope others will join as well. &lt;s&gt;We might also open up a separate Q&amp;A page ...?&lt;/s&gt;)<br />
<br />
The Topics &amp; Questions Section can be found on the [[BookOfHackteria]] subpage!<br />
<br />
[VK]<br />
<br />
== Experimental Cuisine ==<br />
<br />
A hackteria tardigrade recipe book...<br />
<br />
the following from - http://heywoodgould.com/pages/?p=180<br />
<br />
<br />
“Tardigrades produce a sugar called trehalose just before they go into a state of suspended animation,” Durg says. “Trehalose protects them against conditions of heat and dehydration, plus invasion by foreign bacteria and viruses. They also generate a large protein which rebuilds their cell structures.” He stops with an astonished look. “On the molecular level they are invulnerable!”<br />
<br />
What if the tardigrade’s protective powers could be transferred to human beings? Durg thought.<br />
<br />
“What if tardiigrades were the greatest health food ever invented?”<br />
<br />
He began experimenting. “I got a few wet branches in Prospect Park and made my first harvest,” he says. “Imagine my delight when, the tardigrades turned out to be pleasantly chewy like calamari.”<br />
<br />
Moistened with egg yolk and sprinkled with panko the tardigrades made a light, pleasant cutlet. Durg adapted other recipes, producing Tardigrada Parmigiana, Spicy Tarigrada Roll, Spaghetii and Tarigrada Balls…<br />
<br />
He reopened with a hard sell slogan: “Eat at Durg’s, Live Forever…”<br />
<br />
Response was immediate. Diners came away reporting new vigor.<br />
<br />
“I feel so good I might start bothering Barb again,” George H.W. Bush said.<br />
<br />
With a six month waiting list, Durg has to be brutal. The other night John McCain exploded when told he couldn’t have a table.<br />
<br />
“It’s your duty as an American to seat me,” he screamed at Durg. “Do you want Sarah Palin to be president?”<br />
<br />
At that, the entire restaurant arose in unison.<br />
<br />
William Shatner, 78, was the first to the door. “Come back, Senator,” he pleaded. “You can have my table.”<br />
<br />
== Magnetotactic bacteria ==<br />
<br />
Fascinating critters. The first idea for now is to try and see whether we can find any in Lake Zurich.<br />
Here's a short and simple set of instructions on where to go looking for such bacteria, how to catch them and how to look for them in samples under a microscope:<br />
<br />
[http://www.biophysics.uwa.edu.au/STAWA/ Magnetotactic Bacteria]<br />
<br />
These instructions say to look for magnetotactic bacteria in salt water, but we know that they can be found in freshwater, too, such as Magnetobacterium bavaricum (Chiemsee).<br />
<br />
[[File:mtnb-gg.gif]]<br />
<br />
Magnetotaxis, [http://www.homemade-labor.ch/weblog/archives/2010/04/hackteria_dock1.html as imagined by miss.gunst]<br />
<br />
== Some Links ==<br />
<br />
DIY Cleanroom http://www.iheartrobotics.com/2010/02/this-new-lab-diy-cleanroom.html<br />
<br />
== For Reference: The Biopunk Manifesto ==<br />
<br />
by Meredith Patterson, copied from [http://maradydd.livejournal.com/496085.html Meredith Patterson's LiveJournal]<br />
<br />
Scientific literacy is necessary for a functioning society in the modern age. Scientific literacy is not science education. A person educated in science can understand science; a scientifically literate person can *do* science. Scientific literacy empowers everyone who possesses it to be active contributors to their own health care, the quality of their food, water, and air, their very interactions with their own bodies and the complex world around them.<br />
<br />
Society has made dramatic progress in the last hundred years toward the promotion of education, but at the same time, the prevalence of citizen science has fallen. Who are the twentieth-century equivalents of Benjamin Franklin, Edward Jenner, Marie Curie or Thomas Edison? Perhaps Steve Wozniak, Bill Hewlett, Dave Packard or Linus Torvalds -- but the scope of their work is far narrower than that of the natural philosophers who preceded them. Citizen science has suffered from a troubling decline in diversity, and it is this diversity that biohackers seek to reclaim. We reject the popular perception that science is only done in million-dollar university, government, or corporate labs; we assert that the right of freedom of inquiry, to do research and pursue understanding under one's own direction, is as fundamental a right as that of free speech or freedom of religion. We have no quarrel with Big Science; we merely recall that Small Science has always been just as critical to the development of the body of human knowledge, and we refuse to see it extinguished.<br />
<br />
Research requires tools, and free inquiry requires that access to tools be unfettered. As engineers, we are developing low-cost laboratory equipment and off-the-shelf protocols that are accessible to the average citizen. As political actors, we support open journals, open collaboration, and free access to publicly-funded research, and we oppose laws that would criminalize the possession of research equipment or the private pursuit of inquiry.<br />
<br />
Perhaps it seems strange that scientists and engineers would seek to involve themselves in the political world -- but biohackers have, by necessity, committed themselves to doing so. The lawmakers who wish to curtail individual freedom of inquiry do so out of ignorance and its evil twin, fear -- the natural prey and the natural predator of scientific investigation, respectively. If we can prevail against the former, we will dispel the latter. As biohackers it is our responsibility to act as emissaries of science, creating new scientists out of everyone we meet. We must communicate not only the value of our research, but the value of our methodology and motivation, if we are to drive ignorance and fear back into the darkness once and for all.<br />
<br />
We the biopunks are dedicated to putting the tools of scientific investigation into the hands of anyone who wants them. We are building an infrastructure of methodology, of communication, of automation, and of publicly available knowledge.<br />
<br />
Biopunks experiment. We have questions, and we don't see the point in waiting around for someone else to answer them. Armed with curiosity and the scientific method, we formulate and test hypotheses in order to find answers to the questions that keep us awake at night. We publish our protocols and equipment designs, and share our bench experience, so that our fellow biopunks may learn from and expand on our methods, as well as reproducing one another's experiments to confirm validity. To paraphrase Eric Hughes, &quot;Our work is free for all to use, worldwide. We don't much care if you don't approve of our research topics.&quot; We are building on the work of the Cypherpunks who came before us to ensure that a widely dispersed research community cannot be shut down.<br />
<br />
Biopunks deplore restrictions on independent research, for the right to arrive independently at an understanding of the world around oneself is a fundamental human right. Curiosity knows no ethnic, gender, age, or socioeconomic boundaries, but the opportunity to satisfy that curiosity all too often turns on economic opportunity, and we aim to break down that barrier. A thirteen-year-old kid in South Central Los Angeles has just as much of a right to investigate the world as does a university professor. If thermocyclers are too expensive to give one to every interested person, then we'll design cheaper ones and teach people how to build them.<br />
<br />
Biopunks take responsibility for their research. We keep in mind that our subjects of interest are living organisms worthy of respect and good treatment, and we are acutely aware that our research has the potential to affect those around us. But we reject outright the admonishments of the precautionary principle, which is nothing more than a paternalistic attempt to silence researchers by inspiring fear of the unknown. When we work, it is with the betterment of the community in mind -- and that includes our community, your community, and the communities of people that we may never meet. We welcome your questions, and we desire nothing more than to empower you to discover the answers to them yourselves.<br />
<br />
The biopunks are actively engaged in making the world a place that everyone can understand. Come, let us research together.<br />
<br />
== Backalley DNA Sequencer ==<br />
<br />
I've been thinking about how to build a primitive but usable DNA sequencer for a while now. During the Hackteria Lab Days, I settled for an approach of how to do this and compiled a short text to introduce the project and outline the steps necessary to develop it. If anyone decides to try and build one too, I'd be thrilled to hear from them and exchange experience on the progress. Shoot me an email: thalheim at informatik dot hu dash berlin dot de<br />
<br />
'''Project goal<br />
<br />
The goal is to build a lowcost semi-automated DNA sequencer. We don't expect to get anywhere near the performance of a bleeding-edge device, but we do hope that the sequencer will permit to undertake small sequencing endeavours, such as sequencing of single human genes or exploratory metagenome sequencing.<br />
<br />
'''Motivation<br />
<br />
The motivation behind this project is to help enable enthuasiastic amateurs and citizen scientists. It's about the equivalent of going down to your local lake, taking a water sample and looking at the sample under the microscope. Just that now, you read the DNA sequences contained in the sample. This genomic information can then be analyzed further, for example by cross-checking against the wealth of publicly available sequence databases.<br />
<br />
'''Background<br />
<br />
The idea is to build the system around the method of Sanger sequencing. Sanger sequencing has gone out of fashion; the newer sequencers use a different approach that is better suited to parallelization and automation. However, Sanger sequencing is a relatively simple, low-tech method. The fabrication and chemicals involved are still very much accessible to a DIY approach today. Hence, this first attempt at building a low-cost DIY sequencer focuses on the Sanger method.<br />
<br />
The Sanger method works by selectively synthesizing DNA fragments that terminate on a given nucleotide. The result is a pool of DNA molecules of different lengths. The molecules of different lengths are then separated using gel electrophoresis. Knowing the lengths of the DNA molecules and the nucleotides they terminate on then permits a reconstruction of the original sequence.<br />
<br />
'''Technical overview<br />
<br />
The system can be built incrementally, adding a little automation at each step. Here's a short description of the final system, its components and what they do:<br />
<br />
* Gel slides - Instead of using the slab gel usually employed, the gels will be embedded in a custom-made plastic carrier. One option here is to laser-cut carriers that feature channels and wells into which the gel is poured. The alternative is to just cast a gel on a flat plastic carrier. The advantage of a channeled carrier is that it would require less gel, possibly decreasing the cost of a gel run.<br />
* Gel cast - Mold to cast the gels including a comb to create wells in the gel<br />
* Gel electrophoresis (GE) chamber<br />
* Power supply for gel electrophoresis<br />
* Transilluminator<br />
* Camera - monitors the gel in realtime to permit a shutdown the power supply before the samples run beyond the gel boundaries; takes images of a gel once it's done<br />
* Sensors for buffer fill levels and temperature<br />
* Buffer pump - can release fresh buffering solution into the GE chamber if the fill level drops below a certain threshold<br />
* Processing unit (desktop computer and/or arduino/similar) - receives input from the sensors and the camera, controls the power supply, buffer pump and transilluminator. When the buffering solution or gel overheat, it can regulate or shut down the power supply. The finished gel images are analysed to automatically reconstruct the sequence. This processing should also involve some kind of measurement for the quality of a run.<br />
* Contraption for automatically changing gel slides (probably involving some kind of stack for new gel slides and one for finished gel slides, and a mechanism to transfer a gel slide from the &quot;new&quot; stack into the GE chamber and then to the &quot;finished&quot; stack)<br />
<br />
The idea is for the user to pre-load a range of samples into the system (either directly onto the slides or via some kind of intermediate storage), turn on the system and then come back the next morning to find a file with the sequence information.<br />
<br />
The main improvement over manual Sanger sequencing is a) that gels can run on their own, without constant attention from the user and b) that the time-consuming and error-prone task of reconstructing the sequence from a gel is automated.<br />
<br />
'''Incremental project stages<br />
<br />
1. Gel slides, gel mold, agarose - evaluate whether it's possible to pour agarose gel into a channeled design with good results<br />
2. GE chamber, gel slides, gel mold, power supply, transilluminator - pretty much everything is done manually at this stage. Evaluate possible designs for the gel slides, GE chamber, and whether gels can be dry-loaded.<br />
3. Add camera and processing unit that can determine when a gel is finished and automatically shut down the power supply.<br />
4. Add software that can evaluate the quality of a gel and assemble the sequence from the gel image.<br />
5. Add temperature and fill-level sensors that are monitored by the processing unit, and software to regulate the power supply based on the temperature readings.<br />
6. Add buffer pump and software, such that the fill level of the GE chamber will be regulated automatically.<br />
7. Add contraption that can load and unload gels into and out of the GE chamber, plus software that controls the loading and unloading.<br />
<br />
All evaluation should initially be done with a DNA ladder and then with custom samples.<br />
<br />
'''Stage 1<br />
<br />
Materials needed<br />
<br />
* Suitable material (thinking polycarbonate at the moment)<br />
* Access to laser cutter<br />
* Agarose<br />
<br />
'''Stage 2<br />
<br />
Materials needed:<br />
<br />
* GE chamber<br />
* Gel slides<br />
* Power supply<br />
* Transilluminator<br />
* Gel mold<br />
* Agarose<br />
* DNA ladder<br />
* Buffer<br />
<br />
The objectives of this stage are:<br />
<br />
* Get a basic setup running<br />
* Determine designs and dimensions for the GE chamber, transilluminator, gel mold and gel slides<br />
<br />
'''Stages 3-7<br />
<br />
to do...<br />
<br />
'''Open Questions<br />
<br />
* Can a gel be &quot;dry-loaded&quot;?<br />
* Does the buffer solution have to be changed after every run because of contaminations? Or can it be reused for several runs?<br />
* What are suitable dimensions for the GE chamber and the gel slides?<br />
* What is a good and cost-effective design for the gel slides?</div>Target022http://www.hackteria.org/wiki/index.php?title=Hackteria_Lab_Participants&diff=3047Hackteria Lab Participants2010-12-10T17:16:07Z<p>Target022: </p>
<hr />
<div><br />
=== Participants ===<br />
<br />
<br />
==== ''Marc Dusseiller, Dr. aka dusjagr (CH)'' (organizer) ====<br />
<br />
Marc R. Dusseiller is a transdisciplinary scholar, lecturer for micro- and nanotechnology, cultural facilitator and artist. He works in an integral way to combine science, art and education. He performs DIY-workshops in lo-fi electronics, music and robotics, has made various short movies and is currently developing means to perform biological science (hackteria | open source biological art) in a DIY fashion in your kitchen or your atelier. He is also co-organizing [http://www.tock18.ch Dock18], Room for Mediacultures, and various other engagments like the diy* festival, national and international workshops for both artists and schools and children as the president of the [http://www.mechatronicart.ch Swiss Mechatronic Art Society, SGMK].<br />
<br />
[http://www.dusseiller.ch/labs/ dusjagr labs]<br />
<br />
[http://hackteria.org hackteria | Open Source Biological Art]<br />
<br />
==== ''Andy Gracie (Spain/UK)'' (co-organizer) ====<br />
<br />
Andy Gracie is an artist working between various disciplines including installation, sound, video and biological practice. His work is situated between the arts and the sciences, creating situations of exchange between organic and artificial systems. He has shown work across the UK and also in France, Spain, USA, Japan, Mexico and Australia, presented at numerous conferences and seminars and published a number of articles and papers.<br />
<br />
[http://www.hostprods.net/ Andy Gracie:hostprods]<br />
<br />
[http://hackteria.org hackteria | Open Source Biological Art]<br />
<br />
==== ''Mario Purkathofer aka wildprovider (CH/AU)'' (curator) ====<br />
Mit dem Hackteria Forum bietet das Dock18 unter der Leitung von Marc Dusseiller eine Plattform für die führenden Köpfe des Biohackings. Biohacking ist eine Disziplin die vor allem durch die Vernetzung verschiedener Wissenschaften und Praktiken mit Elektronik und digitalen Medien entsteht. Dieser interdisziplinäre Zugang verspricht eine Praxis jenseits von Kunst und Wissenschaft. Die Zugänge sind offen. <br />
<br />
Wesentlich ist die Auseinandersetzung mit lebendem Zeug.<br />
<br />
==== ''Antony Hall (UK)'' (confirmed) ====<br />
<br />
As an artist he works primarily with science and technology. Projects exist both as research and art. He has worked extensively within science education providing workshops and CPD sessions. Rather than creating individual 'art works' his work exists in the performance and re-creation of experiments. Specifically he investigates biological and physical phenomena; the behavior of liquids or animals for example. This takes the form of long-term research projects, residencies, performance, electro-acoustic sound art. Often working within contexts such as universities and museums, in collaboration with scientists.<br />
<br />
[http://www.variableg.org.uk/ Antony Hall:variableg]<br />
<br />
==== ''Alejo Duque (Colombia/CH)'' (confirmed) ====<br />
<br />
Passion drives me towards the attempt to interface &quot;place&quot; across all types of vectors and network protocols. While becoming the test ground. &lt;br /&gt; (colombian artist based in Switzerland - Ph.D candidate at EGS (www.egs.edu))<br />
<br />
http://co.lab.cohete.net/ &lt;br /&gt;<br />
http://bios.unloquer.org/ &lt;br /&gt;<br />
http://soup.znerol.ch/ &lt;br /&gt;<br />
[[notes_ad|workshop notes]]<br />
<br />
==== ''Victor Mazon aka Animazon (DE/?)'' (confirmed) ====<br />
<br />
http://www.vimeo.com/animazon<br />
<br />
http://www.myspace.com/animazon<br />
<br />
<br />
==== ''Stefan Doepner (DE/SLO)'' (confirmed) ====<br />
<br />
[http://www.f18institut.org/ f18 Institute]<br />
<br />
==== ''Verena Friedrich (DE)'' (confirmed) ====<br />
<br />
...is an artist working in the field of installation, sculpture, electronics and robotics.<br />
Her work has been shown internationally at various media art festivals and exhibitions in Germany, Switzerland, Austria, Italy, Turkey, Japan and the USA. <br />
In 2009, she has been teaching (Visual Communication / Media) at the Academy of Art and Design Offenbach, Germany. <br />
Verena is based in Frankfurt/Main and Cologne, where she is currently taking part in the postgraduate study program of the Academy of Media Arts. <br />
For some time now she is interested in combining human material and technology.<br />
<br />
[http://www.heavythinking.org/ heavythinking.org]<br />
<br />
info@heavythinking.org<br />
<br />
tel +49 172 6656603<br />
<br />
==== ''Urs Gaudenz (CH)'' (confirmed) ====<br />
Urs Gaudenz is microengineer and worked for Swiss high tech companies in the field of micro sensor technology (sensirion.com) and brushless motor control. With his solid background in electronics, mechanics and software he is working in an interdisciplinary style between the disciplines. After several years of experience as a consultant in innovation management he is now engaged as lecturer for product innovation at the Lucerne University of Applied Science and Arts. He built his first diy microscopes based on a webcam and a cheap digital camera during a workshop with Marc in Berlin. He loves improvisation and he is always good for a surprise. <br />
<br />
[http://www.gaudi.ch/ Gaudi]<br />
<br />
<br />
==== ''Nick Fankhauser, Dr. aka nyk (CH)'' (confirmed) ====<br />
<br />
Scientist, bioinformatics, programmer and videoartist<br />
<br />
[http://www.nyk.ch/ The Empire of Nick]<br />
<br />
==== ''Effi Tanner (CH)'' (confirmed) ====<br />
<br />
Robotic artist, tatooist and ...<br />
<br />
[http://effi.me/ effi.me]<br />
<br />
<br />
<br />
==== ''Lisa Thalheim (AT/DE)'' (confirmed) ====<br />
<br />
Studied computer science at the Humboldt University in Berlin, worked and played for the last 12 years in the field of computer hacking &amp; reverse engineering, and since the first contact with a back-alley biolab project during a stay in Seattle, slowly meandered towards biotech and biohacking as another fascinating variety of society-transforming technology.<br />
<br />
==== ''Olivier (CH)'' (confirmed) ====<br />
<br />
Documentation and publication of the first issue of the Dock18'zine<br />
<br />
<br />
=== Guests ===<br />
<br />
<br />
==== ''Erik Reimhult, Dr. (CH/SE)'' (to be confirmed) ====<br />
<br />
Scientist working on Nanobiotechnologies, Biointerfaces, Colloids<br />
<br />
<br />
==== ''Gabor Csucs, Dr. (CH/HU)'' (to be confirmed) ====<br />
<br />
Scientist working on biointerfaces, cell biology and microscopy. Head of the light microscopy center, ETH Zürich<br />
<br />
[http://www.lmc.ethz.ch/ Light microscopy Center, ETH Zürich]<br />
<br />
<br />
<br />
==== ''Tobias Hoffmann aka kiilo (DE/CH)'' (confirmed) ====<br />
<br />
Tobias Hoffmann about himself: ''&quot;I have studied physics, special education, fine art and New Media, making music as well. I am working in the field of audiovisual processing with an emphasis on collaborating with other artists by using interaktive programs which allow „real-time jamming“'' <br />
<br />
http://kiilo.org<br />
http://playaround.cc/index.php<br />
<br />
==== ''Pei Wen Liu (TW/CH)'' (confirmed) ====<br />
<br />
Pei has dabbled in a variety of digital domains, but has concentrated on sound art, electronic music programming, and streaming video art since 1999. Her work has been influenced by neo-dada, freeform jazz as well as avant-garde electronic musicians and minimalist painters/composers. She has composed pieces for radio, animation, dance, theatre projects and installations.<br />
<br />
http://little-object.com<br />
http://playaround.cc<br />
<br />
==== ''Kirsty Boyle (AUS/CH)'' (confirmed) ====<br />
<br />
http://onnai.com<br />
<br />
http://openmaterials.org<br />
<br />
==== ''Rene Bauer (CH)'' (to be confirmed) ====<br />
<br />
Lecturer for Gamedesign, Gameart<br />
<br />
==== ''Verena Kuni, Dr. (DE)'' (confirmed - local and/or remote) ====<br />
<br />
Verena Kuni, scholar in art &amp; media theory, professor for visual culture at Goethe University, Frankfurt/Main (DE) with strong preferences for inter-, trans- and patadisciplinary approaches. Current projects are dedicated a.o. to transfers between media and material cultures; recycling invention; alternate uses of everyday technologies; toys and/as tools, philosophical toys; urban biotopes; cyborg entomologies and time bending. As miss.gunst she is running a.o. a web based oracle, a weekly art radio show on radio x/ffm and the HOME MADE LAB weblog.<br />
<br />
[http://www.kuni.org/v/index.html kuniverse] - <br />
[http://www.under-construction.cc www.under-construction.cc] - [http://www.visuelle-kultur.info www.visuelle-kultur.info] - [http://www.gunst.info GUNST] - <br />
[http://www.homemade-labor.ch/weblog HOME MADE LAB WEBLOG]<br />
<br />
=== Remote Collaborators ===<br />
<br />
==== Anyma, Fribourg (CH) ====<br />
<br />
Anyma organized a Research Week on digital and electronic art, DIY and lots of other fun projects at the same time in Fribourg. <br />
<br />
all info can be found on the [http://www.anyma.ch/2010/info/homemade-makers-forschungswoche-2010 Makers@Anyma website]<br />
<br />
<br />
==== UGM and HONF, Yogyakarta (Indonesia) ====<br />
<br />
[http://www.natural-fiber.com/ The House of Natural Fiber] will remotely calloborate on issues of microscopy, bacterial culture and<br />
<br />
==== more to be anounced ====</div>Target022http://www.hackteria.org/wiki/index.php?title=Design_%26_Technology&diff=3046Design & Technology2010-12-10T17:15:45Z<p>Target022: </p>
<hr />
<div><br />
Urban BioGeography[http://www.tuurvanbalen.com/projects/urbanbiogeography]<br />
<br />
Designer Bacteria may have a future in Fashion[http://www.nytimes.com/2001/08/19/style/designer-bacteria-may-have-a-future-in-fashion.html]<br />
<br />
Sunlight to Oil via Designer Bacteria[http://www.thinkgene.com/light-oil-with-bacteria/]<br />
<br />
Loop.ph-Design Research Studio[http://loop.ph/bin/view/Loop/WebHome]<br />
<br />
Laughing in a sine curve- Abhishek Hazra[[http://abhishekhazra.blogspot.com/2009/04/laughing-in-sine-curve.html]<br />
<br />
Some interesting bio-design stuff by Brandon Ballangee and the likes. [[http://io9.com/photogallery/biotechnique/1000502846]]</div>Target022http://www.hackteria.org/wiki/index.php?title=Is_this_a_link&diff=3045Is this a link2010-12-10T17:15:31Z<p>Target022: Blanked the page</p>
<hr />
<div></div>Target022http://www.hackteria.org/wiki/index.php?title=Akshitta_kohli&diff=3044Akshitta kohli2010-12-10T17:15:16Z<p>Target022: </p>
<hr />
<div><br />
== '''Daily log''' ==<br />
<br />
<br />
The first few days there was a lot of confusion about what exactly had to be done. The only knowledge I had was that it was something to do with synthetic biology. Now what exactly synthetic biology was...I had no idea. I was just familiar with the term biology. We started by seeing videos on cells and talked about various scientists, some of which I already knew about from my past knowledge about biology. In a week things had become clearer and now we were familiar with almost all the terms and terminologies related to biology.<br />
<br />
<br />
'''17th may'''<br />
<br />
Does lying about things do us any good? What if there was something which could immediately detect our lie?? What if our body could change colour depending on our moods?? These were the questions that came to me while I was thinking about my bacteria.<br />
So I came up with these bacteria which could detect a person’s lie and his state of nervousness by changing the person’s skin colour. I named it coloreria. While doing this I learnt a lot about the functioning of bacteria. Other things that interested me were the various mechanisms involved in the melanin formation and I was also fascinated by the fact that these bacteria can make people dark and light skinned based on their moods.To know more about the functioning of coloreria visit the link:<br />
[[coloreria]]<br />
<br />
<br />
'''18th may'''<br />
<br />
The day was spent in modifying our ideas on our hypothetical bacteria. The most interesting part of creating the bacteria was thinking about a mechanism for it to work. It was more like making it work on my own terms. It was interesting to add more features to the bacteria and decide their usability! While thinking about this there were other things that conquered my mind as well. It was the way society accepts colour. Every society has tended to assign some valuation to skin colour differences, especially when these have corresponded with existing economic and political differentiations.<br />
<br />
<br />
'''19th may'''<br />
<br />
Thinking of a machine....that could perform any abstract function was one of the tasks of the day. What will the machine do? How will it function? Why not make a machine that keeps eve teasers away? So we thought of a machine which could push back the eve teasers. We thought of a machine which can be attached to the intestine. So it absorbs a part of the waste while it passes through the intestine. Whenever any human with the machine in its intestine feels insecure the machine starts decaying the waste and it comes out of the body in the form of bad stink which pushes the eve teasers away. <br />
<br />
<br />
<br />
'''21st may'''<br />
<br />
Things are still not clear and we are thinking on making another hypothetical machine. Thought process was still going on...we were brainstorming on creating another machine and modifying our previous ideas. So why not make something that can act as a life saver. So I got stuck with the idea of an oxygen recycler. This is basically a machine which will extract oxygen from the plants during the day and store it so that it can be used later for a lot of other life saving purposes.<br />
<br />
<br />
'''24th may'''<br />
<br />
I started thinking about my sculpture in which we are asked to grow something that lives for a period of 2-3 months.So i thought of growing fungi. Now the next step was to think about how to grow it.I thought of growing them on fruits.Now the ideation is done...only implementation is left!<br />
<br />
<br />
'''25th may'''<br />
<br />
Today we went to the national centre for biological sciences. I had always dreamt of working in a place like ncbs. The place fascinated me a lot. It is quite a fancy place. We then had a huge discussion on whether government should spend that much of money on places like these or not. During lunch we met a very interesting person who is an educator and discussed with him the positives and negatives of the present system of education. He was quite curious to know that why we all being design students are taking part in a competition like igem. So there was one discussion after the other and it went on for quite a long time. So the day was given to discussions. Then we were introduced to the labs and the different microscopes in ncbs. We met a few people who quite willingly talked about their research work in ncbs.We saw a fly brain under a specialized microscope and saw the way all this information is read digitally. <br />
<br />
<br />
'''26th may'''<br />
<br />
Now that we had our basic knowledge about biology, it was time to know about some artists. We read about Stelarc and Orlan. I quite liked Orlan’s work. Her idea of Carnal Art is quite fascinating. It is a very unique way to put things across as it uses her body as a language. I think that she tried to change ideas of feminism by doing such experiments on herself. Her digital hybrids try to break the barriers of gender, caste, colour and creed.She treated her skin as the most treasured organ and experimented with it.By experimenting with her skin she tried to change the concept of beauty.<br />
<br />
<br />
'''27th may'''<br />
<br />
I started working on my sculpture today.I got fruits like papaya and sapota and left them to decay.I have cut papaya into pieces and then left it for decaying whereas sapota has been kept as it is.<br />
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'''28th may'''<br />
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Today we read about Adam Zeretsky , Petricia Piccinni and Eduardo Kac. Out of these artists Petricia Piccinni’s work fascinated me the most. I think she has tried to challenge the stereotypical mindsets with her work like by using an ugly looking old mermaid, rat like creatures coming out of the bum, breasts at the back and a lot more things like these. I really like the way she has created a beautiful relation between the ugly and the beautiful. Like in one of her works she displays a very beautiful relation between a small boy and an old ugly fish like creature.<br />
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'''31st may'''<br />
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It has been four days since i have started working on my sculpture. The papaya that i had kept has ripened fully and now it has started decaying. I can see some black fungi growing on the outer body of the papaya. The sapota has decayed and has become black and loose to touch. The fruits have started stinking. In a few days the fruits will start stinking even more and even the sight of it will disgust me. I hope it turns out the way I want it to.<br />
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'''1st June'''<br />
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Today we started with our first experiment. We tried to grow yeast in the lab. We used different techniques to grow yeast. In one of them we used dry yeast pallets in agar water and left the yeast to grow in the lab for 2 days. The process of growing yeast was quite interesting. Since I have worked in a lab earlier, I was familiar with all the lab equipments and the precautions that had to be taken care of while working. It was fun to work in the lab after a long time.<br />
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'''2nd June'''<br />
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We started our day by attending a talk in the National Institute of Advanced Studies (NIAS) on the theory of evolution given by Charles Darwin. It was quite an interesting talk. It basically presented the views of different theologians and scientists on the theory of evolution. A lot of people questioned the theory and believed that there exists a creator (God) who creates the living species. They tried to explain their point with interesting examples like that of an eye. According to some of them, the eye being a very complicated sense organ can only be the role of a creator. While there were others who did not believe in the concept of a creator at all. According to them even a complicated organ like the eye has been evolved through the process of evolution. They believed that eye initially had a very simple structure but due to the requirement of the successive generations , different features have been added to the eye by the process of evolution which has made it a complex organ. It was quite interesting to see how different people approach the idea of the creator(designer). Even after the talk ended there were a lot of questions in my mind that were unexplained. Though Darwin’s theory was a great success but the questions that it created about the role of a designer are still unexplained. Later in the day we went to ncbs and saw the place where we were supposed to work. Our most important task was to build our own lab.<br />
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'''3rd june'''<br />
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We started our day by thinking on the materials that we will require to build our own lab. So after listing everything down , we thought of making an incubator and wrote down all the stuff we would require to make one. I searched for different methods of making an incubator and found out quite interesting ways. Then we went to the lab to see the growth of our yeast. We saw all the three petridishes in which we had grown yeast but only one of them showed yeast growth...the other two were unaffected. So were happy that one third of our experiment was successful, which was a good start. We decided to work on the proportions and then tried to grow the yeast by the other two methods which were initially not successful. This time we first waited for the agar mixture to settle. We left it for an hour. After an hour the agar had completely settled and had formed a thick jelly. We put yeast in it and left it to grow for another two days.<br />
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'''7th June'''<br />
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The first thing was to see how our second attempt of growing yeast had turned out. It was interesting to see that apart from the yeast colonies there were colonies of some other fungi growing as well. So now we get back to making our incubator and centrifuge. We started with the incubator first. The most difficult part was to keep the temperature inside the incubator constant, so for that we thought of using a 75 watt bulb with an exhaust fan. Then we thought of different ways of fixing the fan inside the ice box. Then we left the incubator for a little while and started thinking about the centrifuge. We used a mixer for it. We started by using plastic tubes and made slits in the tube so as to fix it in the mixer blades. We tried and tried but didn’t work. Every time put the mixer on the tube used to fly off. So the thought process was still going on....<br />
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'''8th June'''<br />
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Still thinking .....how will the centrifuge work? Finally karthik managed to extract the base out of the jar of the mixer. So now we thought of putting a plate on top of the base which rotates with the base. Then attach the plastic tubes to which will act as test tube holders. So this is what we have planned. Now the incubator. Finally it was made..yay! but again the temperature inside the incubator was not constant and was high. So we thought of putting two more fans inside the incubator.Lets see how it works.<br />
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'''9th June'''<br />
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Making the incubator is fun!! Now we used a 40 watt bulb with 2 fans. The temperature reached to about 45 degrees. Then we thought of using another fan to reduce the temperature. We used a bigger box to put the fourth fan. It took us a lot of time to fix the fans. The whole day went in fixing the fans. We tried to connect the fans to a 9 volt adaptor but the speed of the fans got reduced. So we needed another adaptor and a bulb of zero wattage in case the 40watt doesn’t work. We were extremely tired and left all this for the next day.<br />
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'''10th June'''<br />
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Fixing the fans was one problem. There were four of them and every time we tried connecting it one or the other would stop. Then we got another 9 volt adaptor and connected two fans each to both the adaptors. Even after that one of the fans wasn’t working , so we checked all the wiring again. We did this more than thrice after which finally all of them were working properly. Once the fans started working , the wiring of one of the adaptors went loose. Now it was just getting to me. The whole day went fixing the fans in place. Then we used the 40 watt bulb first to see if it works. But the temperature again went to about 44 degrees. Then we used the zero watt bulb. There was not much change in the temperature. it went to about 42 degrees. <br />
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'''11th June'''<br />
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The next day we quickly started working on the incubator and some started working on the centrifuge. We thought of using the zero watt bulb as we could not think of anything else which would produce less heat than this. We tried different positions of the fans but none of them helped in reducing the temperature. The temperature was still stuck to 42 degrees. We were thinking on different ways to achieve perfect 37 degrees. Then Sudipto gave us an idea of using mosquito repellent instead of the bulb as it would produce less heat. So we left the rest of it for the next day.<br />
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'''12th June''' <br />
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We then used the mosquito repellent in the incubator instead of the bulb and recorded the temperature values. The temperature this time went to perfect 37 degrees this time. yay! Finally we built the incubator. The whole process of making the incubator was quite fun and we experimented with a lot of things in the process. <br />
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'''14th June'''<br />
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Daisy and James were finally here. We started off by showing them our work which was followed by a presentation of their work. After that we brainstormed under four sub headings under REST SAVING THE WEST. We started off by putting our hypothetical bacteria under one of the categories. Then we thought of other bacteria which could come under any of these categories. There were some which could not be put under any of the given categories , so we put them in a separate category.<br />
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'''15th June'''<br />
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Today we saw a really cool science fiction. We also talked about the impacts of synthetic biology which included bio-terrorism, bio-errorism etc. Then we looked at some of the projects in the old igem competitions. We really liked the project of the team EPF-laussane who had worked on light sensitive proteins and created something which worked as an on and off switch. We tried to look at it from a different perspective and came up with some of its uncommon uses. Then we transformed IGEM to IGEA- international genetically engineered art. We changed places of art and science. We were supposed to come up with ideas for IGEA. In groups of three we thought of the various categories that can come under IGEA. So we thought of categories like aesthetics, installation, static and dynamic art, modification etc. Then there was this category of ecosystem which required minimum of three microbes or plants to create an ecosystem.This would show their dependency on the environment and also how they would form a part of the ecological cycle.<br />
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'''16th June'''<br />
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Now that IGEA was designed. We were supposed to take part in it. We were divided into three groups and each group had to come up with a piece of art and was provided with certain constraints. Our group was given the topics ecosystem and shooting star. As soon as we got our topics we started brainstorming. All of us had a different understanding of an ecosystem. According to me an ecosystem runs on dependency . It is like a give and take relationship that the organisms in an ecosystem share. We were supposed to present it in 6 hours. We thought of presenting our idea in the form of a model which would represent four different ecosystems with proper functioning. But we could not take this idea further as we realised that our bacteria was not fitting in the categories given to us. Then we thought of another idea. But again faced the same problem...it was difficult for us to connect ecosystem and shooting star together. We thought and thought and then came up with this idea of a hookah as an ecosystem. We liked the idea and started thinking on the same lines. Then again we had to relate it to a shooting star and synthetic biology. No matter how much we tried coming up with ideas that day...but it wasn’t happening. So finally we got stuck with the idea of the hookah and thought of an organism that mixes in the hookah and whenever you take a drag, it just takes you through a journey of the past, present and future. We did not have any presentation or model to present our idea as it we could not come up with anything substantial till the end. We were extremely disappointed with ourselves and thought of working on our idea.<br />
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'''17th June'''<br />
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Finally we went to NCBS...but only to attend a talk by Zack on genomic gastronomy which was followed by a presentation by Daisy and James. We had seen both the presentations before but going through them for the second time induced a deeper understanding of it. After lunch we had a discussion about the way we felt about technology and the fact that are we scared of technology and its failures? There were some interesting answers to this. Some felt that technological disasters even if its a small disaster prepares us for a bigger disaster. I quite agree to this. Even if its a small disaster , it can teach us to handle a bigger disaster or even prevent it. Then we went back to college and were asked to rework on our previous ideas and present the final presentation the next morning. We had a lot to do. We thought of starting from the scratch. We again started brainstorming. We came up with an idea till the evening and thought of making a working model to show its working. Since our previous presentation was a failure, we gave our best and worked all night to come up with a good one.<br />
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'''18th June'''<br />
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We came up with a bacteria that is basically present in the air but gets activated when it enters the human body. It needs a minimum temperature of 37 degrees to survive. This bacteria induces different hormones each time it enters the human body and produces a different effect. It releases DMT (dimethyltriptamine) which helps the gland to produce its respective hormone and it mixes with the hormone to produce the effect. So it basically acts as a drug which gives you a different high every time it enters your body. We made a working model to show the working of the bacteria and also made a stop motion on psychedelic trans state. As they say hard work always pays...our work was appreciated by everyone and we were satisfied we what we did .Our failure pushed us to work hard!<br />
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'''19th June'''<br />
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Daisy had bought us books which had tales of Shiva. I have always been fascinated by mythological tales. I used to listen to them from my grandmother when I was a kid. These stories brought back all those memories. I read them with great interest and had faint memories of almost all of them. I remember listening to almost all of them from my grandmother.<br />
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'''21st June'''<br />
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Today we started our day by discussing about the mythological stories that we had read and tried to relate it metaphorically with synthetic biology. Then we came up with different themes based on our ideas. The themes were bio-prospecting, Ecosystems, Immunisation against a disaster, Karma, Epigenetics, Soma and Jugaad. Then we tried putting down the myths that we could think of which could come under these themes. I really liked the idea of Jugaad and it was fun to think of myths which could come under Jugaad. While coming up with the myths under Jugaad, I could approach the mythological stories that I had read in a different way. Half of the things that I could think of were based on Jugaad. Even today a major part of our life is based on Jugaad. In the evening , we attended a talk by Arshia who is a Sanskrit scholar. She told us a lot about mythology. She read us an extract from a play by Girish Kamad which was basically a conversation between Sita and her shadow/ image. It was quite an interesting play. I had a lot of doubts about the episode of the Samundra Manthan which slowly got cleared as the talk proceeded. I loved the way she defined a myth. She said that “'''a myth is a lie that tells the truth'''” which perfectly made sense to me. In the end, I had a talk with her about the Bhagvad Gita and she told me about the importance of Gita in one’s life. She said that it’s our choice to absorb what we want to from the Gita. She also told me about her learning’s from the Gita which gave me a different way to look at the Gita. I have tried reading the Gita, but have never read it beyond a particular chapter because every time I read it, I develop a new understanding for the same extract. After this talk my questions about the learning’s from the Gita were answered to a great extent.<br />
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'''22nd June'''<br />
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Today we had to work on myths. We chose one of the myths and tried to build a story around it. So we started thinking. I was really fascinated by the story of Sita in Ramayan where she leaves herself in the fire before she goes to live in exile. So it’s just her image that goes through the whole period of suffering. We started thinking of a bacteria that could produce an image or which could replicate in a certain manner. We framed a story in which a scientist succeeds in producing an image of a girl and the girl uses her image for managing half of her work. Then later in the story there was a conflict between the girl and her shadow where the shadow feels that she was the one who had gone through all the suffering while her real self was just at peace. We were not happy with our story but since we had to work in time limits, we made a poster depicting this story. Then each of the groups discussed their stories with Yashas, Daisy and James. They really liked the myth we had chosen but asked us to improve on the story and go into the details of it. Then we had to modify our stories and represent them using bacteria. When we went into the details of our story , we could not relate it to something that was practically possible. We thought and thought and while thinking about this we came up with the idea of the karmic cycle. We really liked it and changed our concept to that of the karmic cycle. We thought of a bacteria which would just be a representation of the karmic cycle. The karmic cycle is based on our karma(actions). It gets altered according to one’s karma and it ends only when our positive deeds balance out our negative deeds. We named our movie poster ”Tamso ma jyotirgamaya” which is taken from a Sanskrit phrase and it means “Lead Me From Darkness To Light”. The bacteria was named E-li. The bacteria travels towards the light and it replicates whenever the intensity of light changes. This replication is followed by the change in its size and its shadow. We introduced the concept of shadow as a metaphor. It being the bacteria’s indicator depicting its path to the light source. We could also relate it to a general human behaviour.It is our natural tendency to follow the light and leave the darkness behind. We tend to run away from the darkness but it does follow it. But the more we go toward enlightment , the intensity of darkness reduces.<br />
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'''23rd June'''<br />
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We started mind mapping. We made a mind map of the people who are in the field of synthetic biology, their current research and the organisations that are involved in this field etc. We also searched for biobricks for our respective bacteria.<br />
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'''24th June'''<br />
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Today all the three groups had a presentation on the biobricks which they had found. We also included some of the graphs that we had come up with while ideating for our bacteria. We could easily put our concept forward using those graphs. After this we again made a mind map and classified all our information in groups. Later in the day Suhas and Deepak from the level 10 comics came to visit us. We saw their work and it really inspired us. <br />
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'''25th June'''<br />
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We came back to our mind maps. We looked at the different headings and divided them amongst ourselves to work further on them. I researched on George church. Here is what I found out about him:[[George Church]]</div>Target022