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== About ==
 +
We consider ourselves amateurs/novices within the context of the IGEM competition. Our endeavor as “outsiders” is to bring our training in the arts and design to synthetic biology. Over this summer, we learnt the tools and techniques of synthetic biology and developed a piece of life which reflects our concerns, namely, the cultural, ethical and aesthetic implications of Synthetic Biology. Using a DIY approach and getting our hands “wet” was a critical element in the learning process. This approach allowed us to engage in constructive discussions with scientists working in the field. Our construct synthesizes Geosmin, an enzyme normally produced by cyanobacteria and actinobacteria. The biosynthesis of geosmin from farnesyl diphosphate is catalyzed by a single enzyme germacradienol/germacrene D synthase. E. coli, does not bear a gene that codes for germacradienol/germacrene D synthase. We have expressed this gene in different strains of  E. coli, under control of the pTrc  promoter present in the pTrc99a vector. Geosmin is responsible for producing the earthy smell that occurs in the air when rain falls after a dry spell of weather.
  
 
== People ==
 
== People ==
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==Ideas==
 
==Ideas==
  
-bacteria that prevents corrosion
+
[[File:Whiteboard.jpg|820px|none|Click for a closer look]]
 
 
-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'
+
Major Outcomes -
  
-Bacteria that acts like oil
+
* [[Ideas for Bacteria.]]
  - 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.
 
* 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.
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== Workshop ==
 
== Workshop ==
  
-'''May 15'''
 
 
-We discussed two Claire Pentacost Readings-[http://www.clairepentecost.org/beyond_face.htm Beyond Face ] and [http://www.clairepentecost.org/lab%20of%20symbolic_text.htm 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 [http://www.tuurvanbalen.com/projects/urbanbiogeography 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:
 
<gallery>
 
File:Non-standard_registry_of_names.jpg|IUpasana's Non Standard Regisitry of Names
 
File:Upasana.jpg|Upasana's Ideas
 
File:Bacteria_own.jpg|Neha's ''Materialistica Destructica''
 
File:DOC160509-16052009101732_Page_07.jpg|Neha's Graph
 
File:Page_1.jpg| Avni's ''actinodopaine''
 
File:Description_of_the_Amebitoni_Bacteria.png|Amebitoni_Bacteria
 
File:2.jpg|Immuno Bacteria
 
File:Sanya1.jpg|Plastico Collecticus
 
File:bactiprint.jpg|Id bacteria-Akash
 
File:bacteria.jpg|
 
</gallery>
 
 
 
Today's reading was called [http://www.patriciapiccinini.net/essay.php?id=30 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:
 
<gallery>
 
File:anubis - jackal god of mummification.jpg| Anubis- Egyptian Jackal God of Mummification
 
File:aker.jpg| Double headed Lion- Egyptian Earth god
 
File:Bastet-_goddess_of_fire.jpg‎| Bastet - Egyptian Goddess of Fire
 
File:Bes - dwarf god of music and dance.jpg| Bes - Egyptian dwarf god of music and dance
 
File:Khepera-_beetle_god_of_rising_sun.jpg‎| Khepera - Egyptian Beetle God of Rising Sun
 
File:Montu-_falcon_headed_god_of_war.jpg| Montu - Egyptian God of War
 
File:Nuva_&_Fuxi_-_half_snakehuman_-_repaired_the_sky.gif| Nuva and Fuxi- Japanese who repaired the sky
 
File:Rainbow_snake-a_kangaroo's_head,_a_crocodile's_tail_and_a_python's_body,_all_decorated_with_water_lilies_and_waving_tendrils..jpg| Australian Rainbow Snake - Kangaroo's head, Crocodile's tail, Python's body
 
File:baku.jpg|-Japanese mythology: Devours nighmares; Elephant head+ Lion's mane+ body and tail of horse
 
File:Futakuchi-onna.jpg|J.M.-Two mouthed woman
 
File:Sanzuniao-Three_legged_bird.jpg‎| Chinese three legged bird
 
File:Yukionna.jpg|J.M.-Snow Goddess; can transform into mist when threatened
 
File:993.jpg| Lord Ganesha has the head of an elephant and the body of a human.
 
File:be2.jpg| Nagas
 
File:Kalki75.jpg| Kalki is Lord Vishnu in his final avatar. He is half white horse and half human.
 
File:Brahma.jpg| Lord Brahma the creator.
 
File:Hanuman12.jpg| Hanuman has the face of a monkey and the body of a human.
 
File:kala_rahu_1.jpg| Rahu has a floating head and is believed to eat the sun and the moon and thereby cause eclipses.
 
File:kali.jpg| Kali
 
File:krishna1baby.jpg| Lord Krishna
 
File:lakshmi parvati and saraswati.jpg| The three goddesses lakshmi, parvati and saraswati.
 
File:narasimha2.jpg| Narasimha is believed to possess the head of a lion and the body of a human. He is one of the avatars that lord Vishnu takes.
 
File:Valkyrie.jpg|Valkyrie
 
File:medusa.png|Medusa
 
File:colossus.jpg|Colossus
 
File:Leviathan.jpg|Leviathan
 
File:mantacore.jpg|Mantacore
 
File:hydra.jpg|Hydra
 
File:lucifer.jpg|Lucifer
 
File:Freyja.jpg|Freyja
 
File:Heimdall.jpg|Heimdall
 
File:centaur.jpg|Centaur
 
 
 
</gallery>
 
 
 
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
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{| border=&quot;0&quot; cellspacing=&quot;0&quot; cellpadding=&quot;4&quot; align=&quot;center&quot;
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![[Week One]]
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![[Week Two]]
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![[Week Three]]
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![[Week Four]]
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|-
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![[Week Five]]
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![[Week Six]]
 +
![[Week Seven]]
 +
![[Week Eight]]
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|}
  
There's some stuff called Junk dna, which is primarily misunderstood
+
&lt;br/&gt;
  
 +
=== Other ===
  
--Switch--->Controller---->genes------>
+
http://www.historyforkids.org/scienceforkids/biology/cells/doing/dna.htm
  
 +
It is helpful to have an idea of how the other teams are progressing. So, if anyone comes across interesting iGEM team wikis/sites - please put up the links here.
  
we take genes and the switches that regulate them and make these circuit
+
http://igem.uwaterloo.ca/The_UW_iGEM_Team
  
make a DNA(switch) Gene(switch) DNA(switch)
+
The IBB Pune Team's wiki
 +
[http://2009.igem.org/Team:IBB_Pune#]
  
then inject this into a cell
+
[http://2008.igem.org/Team:NYMU-Taipei NYMU-Taipei's 2008 Wiki]
 
 
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 Electrophorosis]]
 
 
 
*([[Talk:ArtScience_IGEM_team|Click here to discuss]])
 
 
 
-[[Streaking and Spreading to obtain bacterial colonies]]
 
 
 
[[Imaging]]
 
 
 
*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]].
 
 
 
'''Flow Cytometry'''
 
 
 
* 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.
 
 
 
 
 
 
 
<gallery>
 
File:Brain.jpg|Brain cell of a fruitfly under a confocal microscope.
 
</gallery>
 
 
 
'''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??)
 
 
 
----
 
 
 
 
 
<gallery>
 
File:DSC01409.JPG
 
File:DSC01410.JPG
 
File:DSC01411.JPG
 
File:DSC01412.JPG
 
File:DSC01418.JPG
 
File:DSC01419.JPG
 
File:DSC01420.JPG
 
File:DSC01422.JPG
 
File:DSC01424.JPG
 
File:DSC01425.JPG
 
File:DSC01426.JPG
 
File:DSC01427.JPG
 
File:DSC01428.JPG
 
File:DSC01429.JPG
 
File:DSC01430.JPG
 
File:DSC01431.JPG
 
File:DSC01432.JPG
 
File:DSC01433.JPG
 
File:DSC01438.JPG
 
File:DSC01443.JPG
 
File:DSC01456.JPG
 
File:DSC01457.JPG
 
File:DSC01458.JPG
 
File:DSC01459.JPG
 
File:DSC01460.JPG
 
File:DSC01463.JPG
 
File:DSC01466.JPG
 
File:DSC01468.JPG
 
File:DSC01470.JPG
 
File:DSC01471.JPG
 
File:DSC01472.JPG
 
File:DSC_7960.jpg
 
File:DSC_7959.jpg
 
File:DSC_7955.jpg
 
File:DSC_7947.jpg
 
File:DSC_7936.jpg
 
File:DSC_7928.jpg
 
File:A.jpg
 
File:DSC_7963.jpg
 
File:DSC_7976.jpg
 
File:DSC_7977.jpg
 
File:DSC_7980.jpg
 
File:DSC_7985.jpg
 
</gallery>
 
  
 
== Readings ==
 
== Readings ==
  
 +
'''[[Art and Politics]]'''
  
'''Art and Politics'''
+
'''[[Art]]'''
 
 
Claire Pentecost::Beyond Face[http://www.clairepentecost.org/beyond_face.htm]
 
 
 
Claire Pentecost::Outfitting the Laboratory of the Symbolic: Towards a Critical Inventory of BioArt[http://www.clairepentecost.org/lab%20of%20symbolic_text.htm]
 
 
 
Donna Haraway::Speculative Fabulations for Technoculture's Generations[http://www.patriciapiccinini.net/essay.php?id=30]
 
 
 
'''Art'''
 
 
 
GeneAeshetics, The Art of Joe Davis[http://www.clondiag.com/frame.php?page=/art/joe.davis/index.php?docid=0]
 
 
 
Adam Zaretsky[http://www.emutagen.com/]
 
 
 
Patricia Piccinini[http://www.patriciapiccinini.net/]
 
 
 
'''Science'''
 
 
 
What are bacteria?[http://www.disknet.com/indiana_biolab/b004.htm]
 
 
 
Planet of the Bacteria[http://www.stephenjaygould.org/library/gould_bacteria.html]
 
 
 
Introductory Video Lectures in Biology[http://videolectures.net/mit7012f04_introduction_biology/]
 
 
 
'''Design & Technology'''
 
 
 
Urban BioGeography[http://www.tuurvanbalen.com/projects/urbanbiogeography]
 
 
 
Designer Bacteria may have a future in Fashion[http://www.nytimes.com/2001/08/19/style/designer-bacteria-may-have-a-future-in-fashion.html]
 
 
 
Sunlight to Oil via Designer Bacteria[http://www.thinkgene.com/light-oil-with-bacteria/]
 
 
 
Loop.ph-Design Research Studio[http://loop.ph/bin/view/Loop/WebHome]
 
 
 
Laughing in a sine curve- Abhishek Hazra[[http://abhishekhazra.blogspot.com/2009/04/laughing-in-sine-curve.html]
 
 
 
Some interesting bio-design stuff by Brandon Ballangee and the likes. [[http://io9.com/photogallery/biotechnique/1000502846]]
 
 
 
'''Synthetic Biology:
 
'''
 
 
 
Gel Electrophoresis [http://en.wikipedia.org/wiki/Gel_electrophoresis]
 
 
 
Extracting DNA at home [http://nature.ca/genome/05/051/pdfs/DNAextract_e.pdf]
 
 
 
Harvard 2006: Explaining their process[[http://parts2.mit.edu/wiki/index.php/Harvard_2006]]
 
 
 
The Synthetic Biology Comic[[http://www.nature.com/nature/comics/syntheticbiologycomic/]] The .pdf version is here:[http://mit.edu/endy/www/scraps/comic/AiSB.vol1.pdf]
 
 
 
Introduction to Biological Engineering Design [http://openwetware.org/wiki/20.20]
 
 
 
Introduction to Synthetic Biology[http://openwetware.org/wiki/Intertech:iSB2008:Materials]
 
  
Ibio Seminars [http://www.ibioseminars.org/]
+
'''[[Science]]'''
  
 +
'''[[Ethics]]'''
  
'''General Design Links'''
+
'''[[Design &amp; Technology]]'''
  
http://psd.tutsplus.com/drawing/the-role-of-sketching-in-the-design-process/
+
'''[[Synthetic Biology]]'''
  
http://www.wallwisher.com/wall/iGemSrishti
+
'''[[General Design Links]]'''

Latest revision as of 18:01, 10 December 2010

Hackteria banner1.png

About

We consider ourselves amateurs/novices within the context of the IGEM competition. Our endeavor as “outsiders” is to bring our training in the arts and design to synthetic biology. Over this summer, we learnt the tools and techniques of synthetic biology and developed a piece of life which reflects our concerns, namely, the cultural, ethical and aesthetic implications of Synthetic Biology. Using a DIY approach and getting our hands “wet” was a critical element in the learning process. This approach allowed us to engage in constructive discussions with scientists working in the field. Our construct synthesizes Geosmin, an enzyme normally produced by cyanobacteria and actinobacteria. The biosynthesis of geosmin from farnesyl diphosphate is catalyzed by a single enzyme germacradienol/germacrene D synthase. E. coli, does not bear a gene that codes for germacradienol/germacrene D synthase. We have expressed this gene in different strains of E. coli, under control of the pTrc promoter present in the pTrc99a vector. Geosmin is responsible for producing the earthy smell that occurs in the air when rain falls after a dry spell of weather.

People

Akash Hirosh

Dhruv Nawani

Nikhil Patil

Upasana Simha

Sandeep Mathew

Sanya Rai Gupta

Avni Sethi

Neha Bhat

Gautam Vishwanath

Krupakar Dhinakaran

Ideas

Click for a closer look

Major Outcomes -

  • 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

Week One Week Two Week Three Week Four
Week Five Week Six Week Seven Week Eight

<br/>

Other

http://www.historyforkids.org/scienceforkids/biology/cells/doing/dna.htm

It is helpful to have an idea of how the other teams are progressing. So, if anyone comes across interesting iGEM team wikis/sites - please put up the links here.

http://igem.uwaterloo.ca/The_UW_iGEM_Team

The IBB Pune Team's wiki [1]

NYMU-Taipei's 2008 Wiki

Readings

Art and Politics

Art

Science

Ethics

Design & Technology

Synthetic Biology

General Design Links