Project iGEM 2010

IGEM 2010


Day One 10th May 2010

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!

(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.)

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.

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.

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.

Day Two 11th May 2010

Recap of yesterday to keep us on track.

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.

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!

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!

Andrew Hessels - Introduction to Synthetic Biology. 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.

Day Three 12th May 2010

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.

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.

Day Four 13th May 2010

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!

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.

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.

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.

Day Five 14th May 2010

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.

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.

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.

Tomorrow we extract DNA.

Day Six 17th May 2010

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.

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!

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.

Extraction of DNA did not happen. Tomorrow we extract DNA!

Day Seven 18th May 2010

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.

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.

Day Eight 19th May 2010

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.

Why is Innovation disruptive – because it challenges assumptions and creates hybrids?

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.

Day Nine 20th May 2010

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!

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.

Day Ten 21st May 2010

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.

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.

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.

My conclusion: THERE IS NO DEFINITE EXPLANATION.

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.

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.

Day Eleven 24th May 2010

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.

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. 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.

25th May 2010

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.

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.

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.

26th May 2010

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.

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.

27th &amp; 28th May 2010

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.

This is going to take a while but I surely want to do it.

31st May 2010

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.

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.

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!

1st June 2010

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. 1. Build an incubator 2. Find some bacteria – E.Coli preferably 3. Grow the bacteria 4. Recombine its DNA with plastic binding proteins 5. Then check to see if it can break down or degrade protein.

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.

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.

2nd June 2010

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. 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.

7th, 8th, 9th &amp; 10th June 2010

THE CENTRIFUGE

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. 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. Next stop extract DNA again and run it in the centrifuge

11th June 2010

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. 12th June 2010 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! 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.

14th June 2010

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.

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.

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.

15th June 2010

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.

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.

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? 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!

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! 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.

So we started brainstorming like there is no tomorrow and a few lines to keep us on track were...
 * What is the iGEA competition - the International Genetically Engineered Art Competition?
 * What categories are there?
 * What prizes can be won? How do people communicate their work?
 * What might be disqualified from entering?

Karthik, Nooshin and I came up with this.

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.
 * Best Social Critique – there can be no art without critique from a third person
 * Best Visual Aesthetics – the world runs on this
 * Most Innovative Concept – Everyone looks for a new concept
 * Most Thought Provoking – Little difference from concept because this is a thought, it could or could not be a concept
 * Best Use of Colour – This spells out A-R-T
 * Best Abstract – Every single artist and designer will smile at this category
 * Most ECO – we need a better world and it starts from here
 * Best Pattern &amp; Texture – this award is for those who love to play the fool while experimenting
 * Gestalt Award – The mother of them all. Gestalt completes the whole competition.

16th June 2010 Today we finalized on what iGEA would be if it ran. The awards were boiled down to the following
 * Best Ecosystem
 * Best New Emotion
 * Best Social Critique
 * Best Pop-Culture
 * Shooting Star (short-lived, burning bright)
 * Remix Culture
 * Grand Prize: Gestalt Award
 * Honours: Critics Choice for Visual Aesthetics
 * Honours: Genetic Raspberry Award

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.

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.

23rd June

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’.

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.

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.

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.



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.

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.



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.

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.

28th June 2010

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.

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.

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.

I’m happy. We can call ourselves a team now.