Mohor Mukherjee

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iGEM 2010


An overview:

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.


JOURNAL


10th May

Landing into Bioland, Basement Computer Room, Srishti School of Art, Design & 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.

11th May

Down with fever. :( But I was doing research on e.coli, evolution, Darwin and articles about Genetics.

12th May

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.......!

13th May

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”! In the process as a start to our experiments "we need to extract DNA asap!" –Yashas.

14th May

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.

17th May

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....

19th May

“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. 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.

20th May

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!

21st May

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.

24th May

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 :

CLEAGUEW1.jpg

25th May

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. 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.

26th May

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. We learnt extensively about Polymerase Chain Reaction or PCR and Kary Mullis’s fantastic work on it. Learning really fantastic things here over summer but homesickness calls quite often. Nevertheless, got to hang in there.

27th May

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!

28th May

Attending class was more for working on the living organism project and further researches.

31st May

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!

1st June

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 growing yeast on plants. So I am looking around,staring,wondering about this again. :( 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.

2nd June

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 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 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. 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.

3rd June

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! :)

5th June

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!).

7th June

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. :(

8th June

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.

9th June

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.

10th June

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. 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.

11th June

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.

12th June

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.

14th June

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.

15th June

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?. 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 & 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.

16th June

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.

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.

I liked the presentation that Aaron and Nooshin put up. The concept of taking out formaldehyde from ants was quite interesting. Quite a tiring day but I enjoyed the kind of thinking we were doing! :)

17th June

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. In the latter half of the day we were to re-think our ideas on iGEA and present it tomorrow according to the guidelines. 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! 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.

18th June

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. 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.

19th June

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! 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!

21st June

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. 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.

22nd June

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?” . 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. We made a poster as an attempt to depict our story. We called our story the HOLY TRINITY. To read more about the holy trinity please click here. > THE HOLY TRINITY

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!


23rd June

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: > The promise of Synthetic Biology.

24th June

We had to work on the bio-bricks of what our bacteria does. There were bio-bricks that we found between Vishnu and Brahma & Vishnu and Shiva. There are others that we need. Here is the slide that gives the details.

Tht.jpg

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.

25th June

We further worked on the people involved in synth-bio NOW and divided ourselves for the headings to research on. I looked into > Synthetic Biology in India.

28th June

Story-building around Daisy Ginsberg,Drew Endy and the Indian Government! We(Aaron,Diya & me) have come up with a story..stay tuned to read the final version of it..

29th June

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:

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... 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...

30th June

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 > A synopsis to have an overview of how laws and rules have been discussed in synthetic biology.

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.

From a group brainstorm we came up with the following: • Presentation • Seeing is believing • ECOSYSTEM • Reactions- if they are feasible • The HEAT sensitive ecosystem • Carbon foot-prints • Telling stories • WHERE IS OUR WORLD GOING? • An overview- standing and looking at the earth- TERRARIUM • Statement as artists and designers • Balance- humans are a part of it. • Even though we genetically engineer (modify) the bacteria,they still survive. • Sphere exists inspite of the chaos • Complementary-balance • Transfer of energy from the human makes the ecosystem run. • Loop-> balance • How else can the ecosystem INTERACT?

1st july

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.

PEOPLE IN THE PROCESS