ArtScience IGEM team

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Revision as of 11:41, 20 May 2009 by NehaBhat (talk | contribs) (Workshop)
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People

Akash Hirosh

Dhruv Nawani

Nikhil Patil

Upasana Simha

Sandeep Mathew

Sanya Rai Gupta

Avni Sethi

Neha Bhat

Gautam Vishwanath

Krupakar Dhinakaran

Ideas

-bacteria that prevents corrosion

-Time keeper or clock

-Combustible bacteria

-Related to weather - smell of rain

-Bacteria that is resistant to Scientific Probing/Instruments

-Mirror of bacteria

-Buoyant bacteria

-Interactive bacteria(painting)

-Another creature made from bacteria

-Bacteria and sound

 - Bacteria visualizations. (Both colour changes and 'choreographed' movement)

-Neuro transmitters- bacteria as sensors for emotions

-Glue

-Bacteria that detects cravings

-Magnetic bacteria

-Self mutating Bacteria

-Lie detector

-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.

Workshop

-May 15

-We discussed two Claire Pentacost Readings-Beyond Face and Critical Inventory of BioArt .

-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


-May 16

Here's some creatures we created using techno-scientific jargon and aesthetics:


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.

May 17th:

Hybrid creatures from mythology:


Mukund

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)


Process

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


--Switch--->Controller---->genes------>


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

oscillator

memory.

positive feedback.

Also understanding real cells:


Building instrumentation

Making cells from scratch.


-May 19

We spent the day in NCBS picking up some standard biological techniques-Gel electrophoresis And looking at some of the microscopy equipment at NCBS.

Mukund's Brief Overview on Synthetic Biology Basics

Gel electrophoresis:

  • 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.

Discussion over Lunch

The whole group including Mukund and Yashas sat together at lunch and we 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.





Readings

Art and Politics

Claire Pentecost::Beyond Face[1]

Claire Pentecost::Outfitting the Laboratory of the Symbolic: Towards a Critical Inventory of BioArt[2]

Donna Haraway::Speculative Fabulations for Technoculture's Generations[3]

Art

GeneAeshetics, The Art of Joe Davis[4]

Adam Zaretsky[5]

Patricia Piccinini[6]

Science

What are bacteria?[7]

Planet of the Bacteria[8]

Introductory Video Lectures in Biology[9]

Design & Technology

Urban BioGeography[10]

Designer Bacteria may have a future in Fashion[11]

Sunlight to Oil via Designer Bacteria[12]

Loop.ph-Design Research Studio[13]

Laughing in a sine curve- Abhishek Hazra[[14]

Some interesting bio-design stuff by Brandon Ballangee and the likes. [[15]]

Synthetic Biology:

Extracting DNA at home [16]

Harvard 2006: Explaining their process[[17]]

The Synthetic Biology Comic[[18]] The .pdf version is here:[19]

Introduction to Biological Engineering Design [20]

Introduction to Synthetic Biology[21]

Ibio Seminars [22]


General Design Links

http://psd.tutsplus.com/drawing/the-role-of-sketching-in-the-design-process/

http://www.wallwisher.com/wall/iGemSrishti