Samrajni Patil

2011 - Nanotechnology - BIOMOD

 To read special entries click here &gt; The Specials

Useful Links

Journal
'''10th May 2010 '''

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!

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.

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 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!

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. 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.

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.

We were also constantly trying to make sense of how we can contribute our skills as artists and designers to this world. 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.

11th May 2010

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.

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.

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.

17th May 2010

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!

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.

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.

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).

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...

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.

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.

24th May 2010

Our previous ideas for creatures while crazy weren't crazy enough, so we set out to intensify their crazy quotient.

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.



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.

A colony of these creatures can be used to harvest energy to power whole cities.

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!

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.

25th May 2010

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.

However what caught me was that he had to kill the mice before he worked on slices of their brain. 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.

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!

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.

30th May 2010

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.

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.



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! However, I didn't see reaction as pronounced as I was hoping!

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!

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

1st June 2010

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!

2nd June 2010

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).

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! :)

3rd June 2010

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!

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.

We also tried a new formula for the agar plates, we changed the agar:water proportions to see which one gave the best results. 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.

7th - 12th June 2010

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.

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.

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.

Can't wait for Monday!:)

14th, 15th and 16th June 2010

Alexandra and James are here! We presented a slideshow of our progress until now and they showed us their work.

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.

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.

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.

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.

Anyway, we finally ended up questioning where genetic engineering will take us in the future? an evolutionary glass ceiling?

Here's my interpretation of how our group poster could look -



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.

17th, 18th and 19th June 2010

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!

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.

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.

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. 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?

23rd June 2020

The soma bacteria

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“. 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.

Now we come to the working of the bacteria:

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. 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.

June 21st to 26th 2010

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 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.

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!

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)

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.

We made a poster for our bacteria.

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.

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.

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!!!!

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!

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!!!!!

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.

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.

28th June 2010

With all the information ready to be used, we spilt up into teams again to work on our mythical stories. We chose a few characters from the list of characters we'd researched on and began weaving stories around them. 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. 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 could be different. 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 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 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.

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 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.

Our story is based on Venter, the Transhumanists and the National Institutes of Health (USA).

30th June 2010

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? Which part of the demography would show real interest in our project? How could we start DOING things?

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 to find so many differing views and some with unique reasoning but with tangents coming into the common notions.

This day was also the day we finalised the idea of trying to develop an ecosystem as our final project idea for the competition.

1st July 2010

We went to the lab today. We prepared the e.coli cultures for performing the GFP gene transfer the next day.

2nd July 2010

This day we did the gene transfer. It was really cool since we got to do a lot of the procedures ourselves.

3rd July 2010

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!

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!

8th July 2010

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. Yashas suggested making a movie for the movie competition. We took pictures of potential locations to shoot in Bangalore.

All of us had something or the other to finish before next saturday.

14th July 2010

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 take pictures of good shooting spots for our movie if and when they go out.