ArtScience IGEM team
-bacteria that prevents corrosion
-Time keeper or clock
-Related to weather - smell of rain
-Bacteria that is resistant to Scientific Probing/Instruments
-Mirror of bacteria
-Another creature made from bacteria
-Bacteria and sound
- Bacteria visualizations. (Both colour changes and 'choreographed' movement)
-Neuro transmitters- bacteria as sensors for emotions
-Bacteria that detects cravings
-Self mutating Bacteria
-Bacteria creates an identity
-Bacteria becoming material on death
-Constructing a 'Bacterial Ecology'
-Bacteria that acts like oil
- A lubricant - A liquid that can withstand high temperatures
- Facilitate a group of children to design their 'perfect creature' through visual/tactile media and then draw from these experiences and ideas to build another structure.
- Basic information on micro biology-synthetic biology becomes accessible in the forms of brochures/charts/posters in the team's work space.
-The gist of the Pentacost readings were that artists work with the symbolic and that the Artist's consent to work and learn in public is important. -We also discussed the political and cultural implications of Scientific Authority. -We also looked at Tuur Van Balen's Urban Geography project -Most of the Ideas[see above] today, dealt with the use of bacteria as -a) A sensor or Reactor - (to Inputs,emotions,light..etc) -b) A Producer (of energy, proteins..etc) -c) A Material
-Is there Any way in which we can look at Bacteria from a purely non-symbiotic / non-anthropomorphic viewpoint? -Can we use our technological "progress" to give a non-selfish gift back to our ecological siblings?
-Replace financial transactions with Bacteria
Here's some creatures we created using techno-scientific jargon and aesthetics:
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Today's reading was called Speculative Fabulations for Technoculture's Generation by Donna Haraway.
-The article is primarily a review of the Australian artist Patricia Piccinini's work and a recapitulation of Haraway's philosophies .
-One of the things enduring about the reading was her appeal to "love" our creations, not in a tech.no- phillic sense but in a more nurturing and caring way.
Hybrid creatures from mythology:
People at NCBS-study
-Molecules -MacroMolecules -Cells -Tissues -Organs(very few people in NCBS study organs) Organs on their own might themselves not be Intersting -Body -Populations(Families, Groups of Individuals- Populations in really large Scales) -Ancient DNA.(Samples from fossils)
Powders cutting DNA, Sequencing DNA Machines: Microscopes, Influencing movement of molecules Electrophysiology- Studying Neurons
All the process' are used to answer all the questions.
DNA sequencing is very slow, so nothing much seems to be happening. To truely understand this, you need to go through an entire excercise.
Microscope -4 people
DNA experiment -5 people
Everybody wants to do both and then we can switch
Tomorrow at about 10 in the morning we go through microscopy and half a round of DNA
and on wednesday we finish the DNA experiment
for the last 10 years the image is acquired on film or CCD chips once the image is done we look at the digital image and we can look at the file and then extract the images.
use MATLAB for image processing.
What are the big questions in Biology?
what were the big questions in biology
-Evolution -Cell structure? (became important after the microscope). -Before darwin it was about classifications and taxonomy. -traits of offspring-how this information was transmitted. -Homunculus-babies grow into bigger babies.
-Where are these instructions stored?
studying diseases-they saw aberrations in chromosomes studying chromosomes during meiosis
In the 40;s the big question was -how does DNA store and transmit information -DNA contains information ATCG: -Allows you to replicate the information.
Hargobind Khurana figured out - -How to read the information -the series of letters help you make a protien-insulin
Since the 40,50's the questions haven't changed that much:
-If you give me the full genome of the organism- I have no idea what that means-I can guess what protiens it produces... how does an animal form from the genome? No idea. How signals in cells work? No Idea. Can you make life from scratch? No idea.
Today in factories, we can synthesize every molecule in a cell but we cannot synthezice a cell
we can synthezise a virus(not a living thing)
we cannot make a cell?
cells do self organizations.
cells don't need to make themselves from scratch-It happened once in history
that is THE BIG questions of synthetic biology
how does the brain work is the other big questions
Mukund works with E-Coli . Ecoli has been studied for about 100 years, we know almost everything about E-coli( genes, proteins, shape and structure) E coli has 4000 genes, it can make 4000 different protiens the length of its genes is 4 million base pairs you need atleast 3 letters to make an amino acid
it however only makes a 1000 protiens
There's some stuff called Junk dna, which is primarily misunderstood
we take genes and the switches that regulate them and make these circuit
make a DNA(switch) Gene(switch) DNA(switch)
then inject this into a cell
the cell runs the program.
Why not just have a bunch of Genes? Why have a network
cells need to be clever cell needs to process information/when it is hot AND wet do something
can we make a switch from scratch that responds only when the sugar is high AND temperature is high
What else can switches do that genes cannot do: There are something called emergent properties, the collection of
Also understanding real cells:
Making cells from scratch.
We spent the day in NCBS picking up some standard biological techniques-Gel electrophoresis And looking at some of the microscopy equipment at NCBS.
- One way to 'see' DNA is gel electrophoresis. DNA is negatively charged. When you put DNA into small holes called wells on one end of some Agarose gel(agarose comes from agar extracted from seaweed), and pass a current through the gel (with the positive end opposite to the wells) the DNA bands will squeeze themselves through the pores of the gel, try to reach the other end. The smallest bands of DNA will move the furthest, and the longest the least- creating a graduated set of rectangular marks that follow the width of the well.
- The marks are rectangular because they are a number DNA strands of the same length packed together, (like a stack of pancakes seen from the side)
- (Click here to discuss)
- Streaking and Spreading to obtain bacterial colonies
- There are many microscopes available to scientists. There are so many varieties, primarily because scientist require different resolutions for different cells or (whatever else they might want to look at really close up)
- There are point/line/disc scanning microscopes
- Generally,the software to operate microscopes are sold with the microscope. Some of them are 'CellQuest Pro' etc.
-Without optics, there is no biology
250nm- Wide field microscope 100nm-TIRF 50nm- 20nm-STED 1nm-AFM <1nm-Electron microscope -This is the only electron-based microscope; rest are photon-based: Costs Rs 3 crore,is manufactured in hundreds per year only in select countries like Japan and Germany.
Some basics of microscopy:
1.Pixel size in case of magnification should not exceed Theoritical resolution/2.3 2.Dwell time of laser= Time spent on one pixel to read it 3.Voxel- A 3-D pixel in microscopy 4.Resolution is the smallest distance possible between two objects before they look like one.
- One of the microscopes that we saw closely was a Confocal microscope. The specimen we viewed was a fixed cell of a fruit fly's brain.
- We viewed it under red and green laser as well as with its own florescence.
- We also saw a Transmission Electron Microscope and an Atomic Force microscope.
- Its a method that helps scientists count, sort and analyse particles that are too small and in very large quantities.
- The particles are usually in the order of 10 µm.
- The machine works by forcing the cells under very high presure along a narrow stream of liquid called the sheath flow.
- The Sheath flow has lasers that pass it perpendicularly.
- The machine counts the particles at very high speeds by counting the disturbances in the laser beam.
- By analyzing the way the lasers excite fluorescent cells, and create pulses of released photons it can sort the different particles.
- The released photons will have spectral qualities that are unique to its fluorochrome.
- It is necessary to know the properties of the dyes used on the particles in order to identify them.
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Brain cell of a fruitfly under a confocal microscope.
Discussion over Lunch
The whole group including Mukund and Yashas sat together at lunch and did a quick recap of the day's activities till then and what we learnt from engaging in each of them. We then discussed our ideas for the iGEM project. While doing this, we also discussed the feasibilty and success rate of each of them. The few major workable ideas that were arrived at were -
- Enabling E.coli to give out the smell of rain when it secretes dopomine (the enzyme reponsible for the emotion love) - Experimenting with sound and the bacteria's reactions to it in different forms.
The whole idea of using olfactory glands as a sensor for experiments rather than the usual visual or aural glands seems exciting.(during coffee??)
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Art and Politics
Claire Pentecost::Beyond Face
Claire Pentecost::Outfitting the Laboratory of the Symbolic: Towards a Critical Inventory of BioArt
Donna Haraway::Speculative Fabulations for Technoculture's Generations
GeneAeshetics, The Art of Joe Davis
What are bacteria?
Planet of the Bacteria
Introductory Video Lectures in Biology
Design & Technology
Designer Bacteria may have a future in Fashion
Sunlight to Oil via Designer Bacteria
Loop.ph-Design Research Studio
Laughing in a sine curve- Abhishek Hazra[
Some interesting bio-design stuff by Brandon Ballangee and the likes. []
Gel Electrophoresis 
Extracting DNA at home 
Harvard 2006: Explaining their process[]
Introduction to Biological Engineering Design 
Introduction to Synthetic Biology
Ibio Seminars 
General Design Links