Team:ArtScienceBangalore/Notebook

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Latest revision as of 03:57, 6 October 2011

Notebook

Building our own BioLab

The thing that sets us apart from most IGEM teams is our ultra-tight budget and our desperate attempts at making our own lab equipment. In Hindi, this is called [http://en.wikipedia.org/wiki/Jugaad "Jugaad"]. Apart from the pleasure of having your own incubator which is pink in color, these exercises help us understand the science better. In these images, we have our microscopes, laminar air flow, a centrifuge and an incubator. We built our own lab by constructing a geodesic 10 feet dome which will house the entire lab and will function as the future ArtScienceBLR headquarters / community BIOlab.

Experiments at NCBS

We worked in the labs at NCBS, under the watchful eye of Navneet Rai.

The BioGeographer's toolkit

Every BioGeographer needs a toolkit to collect and store their samples.

The First Prototype:

Slab to store Epindorf tubes after soil sampling:

The Epindorf Bag

Soil Sampler ..for stylish soil extraction

The Post-Natural BioGeographer

Sidharta poses with his Soil Sampling toolkit

Outreach with (skeptical) Friends

Watching some David Cronenberg

[http://en.wikipedia.org/wiki/David_Cronenberg David Cronenberg's] strange explorations on technology and it's effects on humans are a good place to start for the budding synthetic biologist.

"Shivers (a movie directed by David Cronenberg) is about a doctor’s attempts to bring out the inner sexual animal in man, using a parasite. He fooled his co-workers, and sponsors, into thinking that he was working on creating an alternative to organ transplant, by using parasites. The doctor was unable to accurately predict what the modified parasite would do. This lead to the parasite spreading from his teenaged mistress to quite a few other residents of a “sterile” high-end apartment block, and spreading uncontrollable sexual desire. This movie, to me, highlighted the unpredictable nature of the effects, the consequences of any modifications that we make in any organisms. It also highlights the unpredictability of the behaviour of the organisms. The behaviour of the modified organism in the laboratory is not adequate enough to predict its behaviour in the outside (real) world. The parasites modified an entire society and, in a manner, the entire purpose of a community. How will this sudden change in the very purpose of their lives affect the community? Will it have adverse effects on their functioning? What about their environment? How will the delicate balance of nature be affected? Would it be affected? Who are we to change the very nature of the place we call home so drastically?"

-[http://hackteria.org/wiki/index.php/Prakrithy_Pradeep Prakrithy's diary]

"In the afternoon we watched a movie called Shivers. I cant say it is going to be one of my favorite movies. Though the movie had a pretty interesting story to it, the gory details put me off. One thing i liked a lot about the movie though was that even though it was a 1976 movie, The idea of developing science to such an extent was incredible. The movie shows how a scientist thought of replacing organs in the bodies with parasites. Parasites, which can take over the same function as that organ in the human body. But it didn't work out as he planned and hence the parasites took over the human body and lead it to nasty sexual desires. Aaron and his group apparently had worked on the same concept as the movie for one of their projects last year. They changed the mood patterns in ants and recorded how their entire life style. Same way The scientist in the movie had introduced the parasites into the humans lives. But Madhul raised a very interesting question today. She asked if changing these life style patterns in living things is a good thing or a bad thing. Because in the movie, it lead to mayhem but probably in the ant colony it lead to a good things cause there was no discrimination between the soldiers or the worker ants,or the worker ants and the queen. Which goes back to the question asked on day 4. Whether we have the right to modify lives of living things. This got me thinking a lot. And modifying life can have many different perceptions. I think there should be some laws on how we can modify life patterns in living organisms such that their lives aren't harmed or are caused discomfort"

-[http://hackteria.org/wiki/index.php/Achala_Basu Achala's diary]

We also watched The Fly...and here are some reactions!

Reading [http://www.stanford.edu/dept/HPS/Haraway/CyborgManifesto.html Donna Haraway's cyborg Manifesto](Yawn)

CENTER

Donna Haraway's Cyborg Manifesto coaxes the reader to reconsider stereotypes, assumptions and the true meaning of titular constructs like gender, divinity and organic.The writing style seemed poetic at first but I grew tiresome of her choice of words quickly. Although the manifesto made a few interesting points it was so overladen with unnecessarily esoteric terms that the read was more tedious than interesting. I spent far more time looking up Greek and Latin words than reading the actual article.

-Bisu's Diary

Some Early Speculative ideas:

Spicy Bacteria-by Prakrithy

Biswajit's Insulin Bacteria

A collection of ideas after a "Soil Mapping Brainstorming session"

Urban Bacterial Theater

Desire Line Drawing Capture the paths of people on a park using Stop Motion Sample along those paths

Hospital Waste Samples Human Parts thrown out back? Nurse Costume

Family History

Super Hero Saving the Day Radiation / Mutation i.e. Spiderman, Incredible Hulk

Disaster Mapping Fukishima, Chernobyl, Bhopal etc... E-Waste Sites

Retracing a walk Recursion / Remembering Gandhi Sea March Silk Road Ghengis Kahn

Topography / BioTrekking

Farmer / Drought / IR Mapping

Costume = Bullet Belt

Blood Soil Conflict Areas / Borders Israel / Palestine Kashmir Tropic of Cancer - Bhuj

Tea Plantation Basket Costume for Collecting samples Terroir

Ant Hills / Termite Mounds Costume = A Bacteria Zoologist / Arcehologist

Paranormal Activity Soil Ghost Hunters

Soul in the Soil Graveyard / Tower of Silence

Sending Soil on a Journey Put a potted plant on a train and take samples at each end

Soil Sadu Ask for soil samples instead of alms Wiseman / karma

Culture Soil Compare different cultures / paint clothes

National PCR Compare national data (GDP, GINI) with PCR data

Sunrise Sampling Grab samples as the sun comes up across the world

Airplane dust Collect samples on the plane

Sea beds Since it is no ones land. International waters

Oil Refinery / Shipping Ports Look for oil contamination / Map the flow of energy

Shadows & Soils Micro-climates on ONE site based on where sun hits or doesn't

Zoology of the Future

Old vs New Old vs. New Airport in BLR Oldest Building in BLR and site that is being built on now Schools vs. Old Age Homes

Royal Soil Difference between "holy" soil & normal soil

Neighborhood Soil

Cultural Soils

Walking / Imagery of Feet

Lake / Garbage Disposal

Evolution Mapping the evolution of borders/city limits Soil samples along different border

Trace a day Follow a cow/street dog/goat across the city, and take soil samples along the path say, every 30 mins. Follow people from "contrasting" walks of life

@@ Line 24: / Line 24: @@
 '''Building our own BioLab'''
-One of our main aspects of doing igem everyear is making our own biolab from scrap, i.e jugaad.
+The thing that sets us apart from most IGEM teams is our ultra-tight budget and our desperate attempts at making our own lab equipment.
-Using alternatives and different methods to carry out a completely different purpose.
+In Hindi, this is called [http://en.wikipedia.org/wiki/Jugaad "Jugaad"]. Apart from the pleasure of having your own incubator which is pink in color, these exercises help us understand the science better. In these images, we have our microscopes, laminar air flow, a centrifuge  and an incubator. We built our own lab by constructing a geodesic
-We started off with building a microscope from a webcam, and soon we were making a centrifuge out of a hand blender.  We also made a laminar air flow, a desicator  and an incubator from different materials.
+feet dome which will house the entire lab and will function as the future ArtScienceBLR headquarters / community BIOlab.
-We built our own lab by constructing a geodesic 10 feet metal dome which we covered with tarp.
-Featured in this image is our own DIY microscope, sterile hood, incubator and a geodesic Biodome which houses our entire lab.
+[[File:microscope 1.0.jpg|800x533px]]
-[[File:microscope 1.0.jpg|350px]]
+[[File:centrifuge.jpg|800x533px]]
-[[File:centrifuge.jpg|350px]]
+[[File:laminar.jpg|800x533px]]
-[[File:laminar.jpg|350px]]
+[[File:incubator.jpg|800x533px]]
-[[File:incubator.jpg|350px]]
+[[File:dome.jpg|800x533px]]
-[[File:dome.jpg|350px]]
@@ Line 50: / Line 47: @@
 [[File:Lab_NCBS.jpg]]
-We worked in the labs at NCBS, under the guidance of Navneet Rai.
+We worked in the labs at NCBS, under the watchful eye of Navneet Rai.
 '''The BioGeographer's toolkit'''
-Before our expeditions to collect soil samples, we came up with a tool kit that holds all the essentials required to be carried on the field while working:
+Every BioGeographer needs a toolkit to collect and store their samples.
@@ Line 61: / Line 60: @@
 [[File:prototype.jpg|350px]]
-'''Fold-able cloth toolkit'''
- [[File:cloth toolkit.jpg|350px]]
@@ Line 77: / Line 69: @@
-'''Epindorf Bag'''
+'''The Epindorf Bag'''
 [[File:epindorf bag.jpg|350px]]
@@ Line 87: / Line 79: @@
 [[File:Soil_Sampler00.jpg]] [[File:Soil_Sampler01.jpg]]
@@ Line 100: / Line 93: @@
-'''Outreach with Friends'''
+'''Outreach with (skeptical) Friends'''
-[[File:Balloonmaps01.jpg| 900x500px]]
+[[File:Balloonmaps01c.png | 750x500px]]
 [[File:Balloonmaps02.jpg | 900x500px]]
 [[File:SoilSampling01.jpg | 900x500px]]
@@ Line 109: / Line 102: @@
-As we all know aerial photography is quite expensive; owing to our tight budget, we had to come up with a simple and cheaper way of the same- balloon mapping.
-We invited students from our campus to show them our cost effective way of aerial photography. They were quite impressed of how a easy it was to make a useful gadget out of simple day to day objects- helium filled balloons, a strong thread and a digital camera.
+'''Watching some David Cronenberg'''
+[http://en.wikipedia.org/wiki/David_Cronenberg David Cronenberg's] strange explorations on technology and it's effects on humans are a good place to start for the budding synthetic biologist.
-'''Watching some David Cronenberg'''
+[[File:Shivers_2.jpg]]
+'' "Shivers (a movie directed by David Cronenberg) is about a doctor’s attempts to bring out the inner sexual animal in man, using a parasite. He fooled his co-workers, and sponsors, into thinking that he was working on creating an alternative to organ transplant, by using parasites. The doctor was unable to accurately predict what the modified parasite would do. This lead to the parasite spreading from his teenaged mistress to quite a few other residents of a “sterile” high-end apartment block, and spreading uncontrollable sexual desire.
+This movie, to me, highlighted the unpredictable nature of the effects, the consequences of any modifications that we make in any organisms. It also highlights the unpredictability of the behaviour of the organisms. The behaviour of the modified organism in the laboratory is not adequate enough to predict its behaviour in the outside (real) world. The parasites modified an entire society and, in a manner, the entire purpose of a community.
+How will this sudden change in the very purpose of their lives affect the community? Will it have adverse effects on their functioning? What about their environment? How will the delicate balance of nature be affected? Would it be affected? Who are we to change the very nature of the place we call home so drastically?" ''
+-[http://hackteria.org/wiki/index.php/Prakrithy_Pradeep '''Prakrithy's diary''']
+''"In the afternoon we watched a movie called Shivers. I cant say it is going to be one of my favorite movies. Though the movie had a pretty interesting story to it, the gory details put me off. One thing i liked a lot about the movie though was that even though it was a 1976 movie, The idea of developing science to such an extent was incredible. The movie shows how a scientist thought of replacing organs in the bodies with parasites. Parasites, which can take over the same function as that organ in the human body. But it didn't work out as he planned and hence the parasites took over the human body and lead it to nasty sexual desires. Aaron and his group apparently had worked on the same concept as the movie for one of their projects last year. They changed the mood patterns in ants and recorded how their entire life style. Same way The scientist in the movie had introduced the parasites into the humans lives. But Madhul raised a very interesting question today. She asked if changing these life style patterns in living things is a good thing or a bad thing. Because in the movie, it lead to mayhem but probably in the ant colony it lead to a good things cause there was no discrimination between the soldiers or the worker ants,or the worker ants and the queen. Which goes back to the question asked on day 4. Whether we have the right to modify lives of living things. This got me thinking a lot. And modifying life can have many different perceptions. I think there should be some laws on how we can modify life patterns in living organisms such that their lives aren't harmed or are caused discomfort"''
-Shivers (a movie directed by David Cronenberg) is about a doctor’s attempts to bring out the inner sexual animal in man, using a parasite. He fooled his co-workers, and sponsors, into thinking that he was working on creating an alternative to organ transplant, by using parasites. The doctor was unable to accurately predict what the modified parasite would do. This lead to the parasite spreading from his teenaged mistress to quite a few other residents of a “sterile” high-end apartment block, and spreading uncontrollable sexual desire.
+-[http://hackteria.org/wiki/index.php/Achala_Basu '''Achala's diary''']
-This movie highlighted the unpredictable nature of the effects, the consequences of any modifications that we make in any organisms. It also highlights the unpredictability of the behaviour of the organisms. The behaviour of the modified organism in the laboratory is not adequate enough to predict its behaviour in the outside (real) world. The parasites modified an entire society and, in a manner, the entire purpose of a community.
-We also watched The Fly...and here are a few of the reactions!
+We also watched The Fly...and here are some reactions!
@@ Line 126: / Line 127: @@
-'''Some Early Speculative ideas'''
+'''Reading [http://www.stanford.edu/dept/HPS/Haraway/CyborgManifesto.html Donna Haraway's cyborg Manifesto](Yawn)'''
+[[File:LisaFoo.gif | CENTER]]
+''Donna Haraway's Cyborg Manifesto coaxes the reader to reconsider stereotypes, assumptions and the true meaning of titular constructs like gender, divinity and organic.The writing style seemed poetic at first but I grew tiresome of her choice of words quickly. Although the manifesto made a few interesting points it was so overladen with unnecessarily esoteric terms that the read was more tedious than interesting. I spent far more time looking up Greek and Latin words than reading the actual article.''
+-'''Bisu's Diary'''
+'''Some Early Speculative ideas:'''
+<CENTER>[[File:speculating.jpg|350px]]</CENTER>
+'''Spicy Bacteria-by Prakrithy'''
 [[File:Spicy_Bacteria.jpg]]
-Spices like chillies & pepper feel "hot" beacuse they contain certain chemicals like capsaicin and piperine. Our body (mainly our mouth) feels a sensation of burning pain, as a result of these chemicals. Our sensory neurons contain a functional cDNA encoding for a capsaicin receptor. The receptor is a non-selective cation channel that is also activated by increases in temperature. Similarly, other spices will all have acting chemicals, mostly organic. Each spice will also have corresponding receptors, or mechanisms, to induce responses. Most of the spices and condiments used are plant parts. This implies that they do contain cells (living or dead. Cells contain DNA, which would be responsible for the production of the chemicals responsible for the flavours of the spices. We would be able to identify the exact DNA sequences that code for the necessary chemicals by DNA sequencing. Once the sequences are identified, they can be introduced into the DNA of a suitable, safe bacteria. This bacteria would produce the different chemicals (for the spices) in certain fixed quantities when introduced into the food. This would reduce the chances of dishes getting "spoilt" due to the usage of incorrect mixtures and quantities of spices.
+'''Biswajit's Insulin Bacteria'''
+[[File:Needle-Shy%3F.jpg]]
-''Brainstorm of Soil Mapping''
+''A collection of ideas after a "Soil Mapping Brainstorming session"''
 Urban Bacterial Theater
@@ Line 156: / Line 181: @@
 E-Waste Sites
-"Space Dusters" / Space Crashers = Mediorite Landing
 Retracing a walk
@@ Line 217: / Line 242: @@
 Micro-climates on ONE site based on where sun hits or doesn't
-Tracing the path of Ganga
 Zoology of the Future
-Junkyard is separated out by object - sample each site
 Old vs New
@@ Line 235: / Line 259: @@
 Walking / Imagery of Feet
-Defense Areas / BSF DRDO Air Force
 Lake / Garbage Disposal
@@ Line 247: / Line 271: @@
 Follow people from "contrasting" walks of life
-Deadly Differences
-Samples from different types'/societies'/religions' burial grounds/crematoriums
-Soil "Classes"
-Soils from different classes of places
-"Holy", Royal, "Dirty", Common, etc
-Life Soil
-Trace all locations in a persons life
-Birth, Education, Settlement, Entertainment, Employment, Retirement, Health, Death, Graveyard, Paranormal activity