Difference between revisions of "FArhad"

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People are bound to disagree about when scientists are crossing some moral Rubicon. That is all the more reason to debate, in public and in advance, where those boundaries lie — rather than doing so after the fact, when researchers are celebrating some technical triumph and the rest of us are wondering what price we will pay for it.
 
People are bound to disagree about when scientists are crossing some moral Rubicon. That is all the more reason to debate, in public and in advance, where those boundaries lie — rather than doing so after the fact, when researchers are celebrating some technical triumph and the rest of us are wondering what price we will pay for it.
  
Information from:
+
'''Information from:'''
 +
 
 
'''http://www.time.com/time/magazine/article/0,9171,1997447,00.html'''
 
'''http://www.time.com/time/magazine/article/0,9171,1997447,00.html'''
  

Revision as of 05:52, 24 June 2010

Journal

Day 1

After a very long time I had again opened my mind to biology. The last time I had studied biology was in the 10th grade and for the first half hour of the class everything pretty much went over my head. It had been a long time since I had heard these words and they actually sounded like Greek to me. But slowly everything I had learned in the past came back to me.

In the first class we discussed about general information regarding the first theories of evolution and how they were replaced by others as we come to this day. WE also talked about DNA and its purpose.


Day 2

Today we talked about Mendel’s laws of segregation and independence. A very important point is that you don’t need to be a scientist or have a PhD. to discover things. We got to know how genes are passed down from one generation to another. Also alleles are outputs of genes (allele=pea being round or wrinkled.) The terminology used may take some time to get used to. It is amazing to actually see a cell splitting into 2. We then talked about chromosomes and how they decide the characteristics of a person.

If Genome=book,

Then DNA=volume,

And Chromosome=library

We also saw a video that talked about where gen. engineering would be about 30 yrs. from now. another important thing to consider is the ethics of the topic. Is creating new species good or bad for the world? Is it really progress or just an illusion of progress that we are blindly following that will lead us to our end???...


Day 3

Today we started off with seeing how gene mutation is not a good thing. For eg. Cigarette smoking causes the gene p53 to permanently mutate thus causing lung cancer.we then talked about the basic requirements for being genetic material, which are as follows

1 information storage-Dna has 4 proteins that can be arranged in any way creating different codes

2 accurate replication-there is a chance of 1 ni a million that the gene is defective, and if it’s so it gets disposed.

3 it must be expressed as a phenotype- A phenotype is any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, or behavior

4 it should be able to change –i.e. every individual has different characteristics therefore DNA is different

DNA is like a symbol for bio like an atom for chem. DNA stands for dioxyribose nucleic acid. It consists of a sugar phosphate backbone and ATGC base pairs. The base pairs are what create code of the DNA for creating proteins. (Sugar=dioxy ribose, base pairs=nucleic acid)

A=adenine

T=thymine

G=guanine

C=cytosine

The proportion of A & T is always equal. Similarly G=C. DNA replication is called semi conservative replication. In this process the DNA is split into its 2 separate helical structures (unzipped )and each of the single helix join to the respective base pair. Thus forming 2 similar DNA 2ble helixes. All somatic cells (non sex cells) have the same amount DNA specific organism. On the other hand sex cells (e.g. sperm) there is only half the total amount of DNA. The other half is in the sex cells of the mate. Thus the child gets 1 half each of the parents’ genes. Also genetic engineering is not creation of genes but just modifying the original genes to create a different protein.


Day 4

Today we talked about proteins. Proteins are polymers of amino acids. There are 20 types of amino acids, 8 of which cannot be produced by man. Thus they need to be consumed.the shape of he protein is very sensitive to the environment.(eg. An egg on heating becomes solid.

There are 2 types of proteins based on their function:

-Structural proteins ( hair, muscle collagen, etc.)

-Enzymes

enzymes are surfaces for reactions to occur. They act as catylists for reactions in the body. Enzyme names usually end with the letters “ase” eg .polymerase. proteins are also present in the nucleus.thus the DNA contains the gene and the proteins in the nucleus are the phenotype.


Day 5

As we talked yesterday gene= DNA and the protein= phenotype(expression). Today we talked about the process of protein creation using DNA. In the nucleus one of the helix of the DNA gets replicated to form RNA(RNA=1/2DNA).RNA is the set of instructions for producing protein. The RNA travels outside the nucleus and goes to the ribosome. The ribosome is like the factory for producing proteins. There are free proteins in the cell in pairs of 3 called codons that act as input for the ribosome. The protein pair is selected according to the code in the RNA(ATC produces a certain protein.) There are 20 types of proteins and only 4 codes in the RNA. Thus the RNA is in pairs of 3 to create enough no of codes for the 20 proteins.

In DNA only 1 of the 2 helix is used for production, however it is a double helix for easy replication. When DNA is replicated, each of the daughter DNA has 1 of the helix of the parent DNA. Also the other helix decides where in the body the protein is used.


Day 6

Today we talked about the genome and genome sequencing. The first type of genome sequencing was hierarchal sequencing where there are certain landmarks in the genome which are used for genome sequencing. The other method is called shotgun sequencing. longer sequences get subdivided into smaller fragments, and subsequently reassembled to give the overall sequence.98% of the RNA produced does not even leave the nucleus. The walls of the nucleus act as as a purifier.they are like a simple on off switch. we also talked about bacteria that have a self defence against


Day 7

We talked about recombinant DNA. Recombinant DNA is DNA that is artificially created from two or more sources and is incorporated into a single recombinant molecule. Recombinant DNA (rDNA) is a form of DNA that does not exist naturally, but is created by combining DNA sequences that would not normally occur together.

Most of the bacteria have a restriction enzyme which cuts up foreign DNA. Therefore it is sometimes difficult to splice DNA. This process of splicing can create new types of organisms. This is what synthetic biology is based on. Usually a bacteria called E.coli is used for this as it is not dangerous to experiment on. Synthetic bio. Has many applications. It is used to study particular sequences that are very tiny(the sequence is put in the bacteria and amplified), to express phenotypes, to increase the quantities of proteins , etc.


Day 8

Isolating genes was always done from the phenotype to theto the DNA, but that changed while trying to cure muscular dystrophy. The doctor tried to sequence the gene from the dNA to the phenotype. This is called reverse genetics. He found that a small gene on the x chromosome was missing. This gene was responsible for production of distrophin which connects the muscle fiber to the cells. Distrophin can be replaced by urotrophin , which can be produced by a drug. Thus the problem was cured. In the nucleus mRNA of about 14,600 base pairs is formed, most of which ars not required. the introns remove about 79 peaces from the mRNA by gene splicing in the nucleus itself.

The DNA library is a volume of the genome. Hybrid DNA is a combination of 2 DNA from 2 different places. The geme and a vecter is combined and introduced into the bacteria. the bacteria takes the new gene and adds it to the original gene. The bacteria is allowed to grow and half the DNA of the new bactrria is introduced so that the full(double helix) DNA is fished out. Thus hybrid DNA is created.


Day 9

Today we talked about transgenetics which is DNA of more than 1 species. The the method used is called gene splicing which was first done by Boyle. While working with fruit flies he found that a certain gene called the homiobox genes were responsible for descision of what grows where. Thus by changing this gene he could change the position of different body parts. Thus started synthetic biology which was literally engeneering biology.


Day 10

Today we talked about creating a hypothetical bacteriaof our own. We also given a talk on hybrids and new creatures. The concept of hybrids has existed since many ages. The available technology and advancements in biology has made it possible to create such hybrids. Radical plastic surgens do exactly this. They add extra parts to the body through surgery.


Day 11

Today we saw a video of craig venter on ted talks. He was talking about his recent discoveries in biotechnology and how they went about doing it. We also talked about different bioartists and their approach to biology


Day 12

Today we went to NCBS for the first time.we had gone to meet the person who would help us create the new bacteria and understand how to go about doing it.


Day 13

My assignments

01) Living sculpture: (living furniture)


Most of the furniture that we use in places like the lawn or at the beach are made of wood that has been cut from living trees. this living sculpture has both a use and aesthetics. Instead of cutting trees why not grow the according to the shape you need.

The concept of tree shaping requires one to bend the tree in a desirable shape when it is a small plant. As the tree grows the shape is retained and the bark hardens to form the required shape. This can be called ecofriendly furniture. As the tree branches out, the leaves give shade. It is also cooler below the tree. Also since the tree produces oxygen, the air under the tree is fresh. My final project is to make a living chair.

"Tree shaping.jpg"

I am starting by bending smaller plants and make in a simple loop(1st June). I used string to hold the shape and check after a month.

Roll 2.JPG Roll 4.JPG

After a moonth: The plant retains the shape but still needs some time to maintain that shape.


02) Hypothetical bacteria: (Pressure sensitive Thermo Bacteria)


The Srishti School of art design and tech. has created bacteria that emits heat when pressure is applied on it. It consists of tiny turbine like particles on it’s cell walls. When pressure is applied the cell produces an enzyme that causes the turbines to spin. These cells are tightly packed together in a tiny porous container. The activated turbines hit each other producing heat. The collected heat is magnified by the bacteria and is concentrated at the point of pressure. The temp ranges from 100 to 500 degrees.

Bact 0.jpg Bact1.jpg

The porous container itself is a living organism which concentrates all the heat on the point where the pressure is and spreads the heat across the area where pressure is. both the bacteria live along with each other as symbiotes. The heat producing bacteria feeds on the nutrients supplied by outer shell which is made of sugars and fatty acids. On the other hand the outer shell depends on the thermo bacteria for its shape and heat. Using some amount of the heat produced by the thermo bacteria, the porous outer structure converts cellulose into simple sugars which is food for both the organisms has pores that are about 0.01 nm in diameter all over it which are used to vent out all the extra heat in the form of steam (water is one of the byproducts of converting cellulose into sugar.)

The organism reproduces by binary fission. When the shell is overloaded with the bacteria it expands until it breaks into 2 pieces. The 2 pieces join to themselves to form 2 separate structures. The outer structure does not break unless there is an internal pressure applied and it immediately joins when it breaks and grows to its normal size in 5 hours to incorporate more bacteria. The bacteria can be killed using an electric charge of 20 volts (D.C.), thus its growth can be controlled.

This organism can be used for security purposes, as they are too small to be seen and produce enough heat to burn the body. If the amount of heat given out (number of collisions between spindles) can be controlled it can be used for various reasons e.g. Cooking, hot tubs, heated chairs, etc. And being organisms that can reproduce, they don’t need to be replaced.


03) Imagenary machine:(Projector bacteria)


The bacteria simply projects ones thoughts to a tangible 2D presentation. These bacteria live in the brain. It is a long egg like structure with 2 antennas. These bacteria are fixed on a circular moving belt. The bacteria pick up brain waves with the antenna and produce an image corresponding to the wave.

Bact 3.jpg

The optic nerve of the right eye touches one of the bacteria and picks up the image. As the rotating belt moves the optic nerve picks up other images and forms a stop motion of the thoughts in the mind on the retina. The image on the retina is inverted.

The bacteria secrete an enzyme that runs along the optic nerve and makes the retina emit light. The image on the retina gets projected on to the lens of the right eye and is diverged by the lens thus magnifying the images it gets projected. The user of the bacteria can voluntarily secrete an enzyme that makes the optic nerve move away from the bacteria, thus stopping the projection and the eye starts to function normally. The bacteria reproduce by binary fission. One of the daughter bacteria replaces the parent and the second bacterium gets attatched to belt and acts as food for the bacteria.


04) Bacteria based on indian myth: (The Holy Trinity- group ass)


When was the last time you ever read an Indian mythological story and asked your self – what if I can do that? Indian Mythology is known to be the most culturally rich, colourful, dramatic and at the same time metaphorically ambitious story, ever told. The numbers of different versions are more than the number of sarees that came off Draupadi! It’s like a roller coaster ride of emotions which at the end of every story brings in ‘balance’.

As an Artist and Designer, whenever we read an Indian mythological story I have to say it’s quite amazing because these are some stories that have characters that can pretty much do whatever they want! Gods.... Isn’t that what we all want? To do whatever we like? And not have to worry about consequences? And just know that at the end of it all there will be balance? I think that’s some food for thought.

As a team, we first read through the most famous stories in Indian mythology, and then had a fascinating discussion with a learned scholar in mythology and history. Arshia (the scholar) helped us put our facts together in the most fun filled way which after a few drinks turned out to be a very satisfying knowledge-full night.

Our task now (which is the most interesting part) was to find links and parallels to any myth and use synthetic biology to fill the gap! I find that highly fascinating. SO we went through a few myths and as soon as we landed on Shiva’s third eye, there was a full stop. Shiva’s third eye is the destroyer, when he opens it; disaster is all over the place. So the last you want to do it tick him off. We took that in a metaphorical sense and thought about what if that third eye was a way for us to see when our real eyes are shut? So what if I had bacteria that could communicate with thoughts through neuron activity and when I’m wired up to a projector, it displays my thought in 3D space. Then communication would be in its most pure form since there is a lot of loss when converting thought to word or deed. Then what if I wired up to another person and started communicating with thought! Or if I left messages for someone on a platform and they could later wire up and receive it. But as usual there’s always a ‘BUT’, and the first one here is privacy. Privacy is by far the most delicate issue here. SO we kept this on hold for the time being and instead of looking at parts of a myth we moved away and looked at the Big Picture.

Collages.jpg

Main 2.JPG

The Holy Trinity – Brahma, the creator, Vishnu the Preserver and Shiva the destroyer. These are the first and foremost gods that rule the heavens, earth and hell. As you’re reading this don’t those three words –creator, preserver and destroyer burst out of your imagination and find its way to synthetic biology? Well, that’s exactly what happened to us. So here’s our idea.

Collages2.jpg

In a over populated culture of bacteria. There is ‘imbalance’ since there more bacteria to eat than the nutrition available. So the ‘gods’ are summoned! The VISH-gene bacteria (the preserver) now gets into action by producing a chemical to which ONLY the SHIV-gene bacteria (the destroyer) can read. This then activates the SHIV-gene bacteria to in turn produce a chemical which start disrupting the bacterial cells in the colony. The ‘gods’ bacteria are of course resistant to this chemical. The SHIV-gene bacteria once activated has no control over killing the other cells. So once he has destroyed ample number of cells, he needs to be stopped, which ONLY the BRAHM-gene can do. So now the VISH-gene bacteria produces another chemical which ONLY the BRAHM-gene bacteria can read and this in turn activates the BRAHM-gene bacteria to produce a chemical to deactivate the SHIV-gene bacteria. Now there’s been too many bacteria killed so after a while of reproduction the optimum level is reached and ‘balance’ is restored. The subjects are happy and so are the gods. Soon after reproduction hastens up and there is over population again so the whole process is initiated making it a loop.

Main 1.JPG

BRAHM-gene bacteria are identified with the presence of the BRAHM-gene. When the BBRAHM- gene replicates it does not transfer it’s genetic material completely, instead it retains one part of the gene, so the other bacteria now is the VISH-gene bacteria. When the BRAHM-gene bacteria replicates for the second time it does not transfer the BRAHM-gene at all making the new organism the SHIV-gene.

We’d like to think that this mythological concept, besides being fascinating will definitely find its way to a good purpose in the world of Synthetic Biology. So wait up until then.


05) The promise of Synthetic Biology:


Such is the promise of synthetic biology, which, according to the people who have tried to explain it to me, is basically a marketing term for all kinds of research in which scientists tinker with biological bits to make useful things — sort of like living Lego blocks.

The gift of man-made life — biofuels made of algae, tumor-seeking microbial missiles — comes wrapped in a risk: What if the oil-eating bug mutates, as the horror-movie version inevitably does, and starts eating other things — like us?

It's perhaps not surprising that when bioethicists describe synthetic biology, they sound like the characters in Jurassic Park. "When dealing with biological entities," notes Thomas Murray, president of the Hastings Center, a bioethics organization, "life has a tendency to find a way."

Accidents at power plants are bad enough. But a leak from a bioreactor could be worse, since bacteria can learn new tricks when you're not looking. Microbes excel at exchanging DNA, Murray notes — "like microbial French kissing." That bug we introduce into the ocean to sip the spill might end up swapping DNA with other living things. "We have a ways to go," he says, "before we can really know what risks we're running if we release these organisms into the environment."

Without public oversight, we are certain to wake up one day to news of some private breakthrough that rattles our bones: a human-animal hybrid, a cloned child, a fetus grown solely to harvest its parts.

As laboratories incubate new blends of man and machine — creatures whose creators used a keyboard — it seems mad to say that philosophy should not intervene.

The path of progress cuts through the four-way intersection of the moral, medical, religious and political — and whichever way you turn, you are likely to run over someone's deeply held beliefs. Venter's bombshell revived the oldest of ethical debates, over whether scientists were playing God or proving he does not exist because someone re-enacted Genesis in suburban Maryland. Others dismiss the worry on the grounds that creating new forms of life is not the same as creating life. One doctor friend of mine suggested that "they haven't created life in any sense of the word, other than a person playing a cassette has invented the tape recorder."


"It is vital that we as a society consider, in a thoughtful manner, the significance of this kind of scientific development," Obama writes.

"Synthetic biology certainly raises deep philosophical and moral questions about the human relationship to nature," according to Gregory Kaebnick, a Hastings Center scholar who is managing the project. "It's not clear what the answers to those questions are. If by 'nature' we mean the world around us, more or less as we found it, we may well decide that synthetic biology does not really change the human relationship to nature—and may even help us preserve what is left of it."

Myth: Cellulosic ethanol is a decade or more away. Fact: The world's first cellulosic ethanol production facility -- owned and operated by Iogen in Ottawa, Canada -- has been converting wheat straw into ethanol since 2004. Abengoa Bioenergy is completing construction of a commercial-scale cellulosic ethanol facility, located in Salamanca, Spain, that will by the end of 2007 begin producing 1.2 million gallons of cellulosic ethanol from wheat straw each year.


Conclusion: People are bound to disagree about when scientists are crossing some moral Rubicon. That is all the more reason to debate, in public and in advance, where those boundaries lie — rather than doing so after the fact, when researchers are celebrating some technical triumph and the rest of us are wondering what price we will pay for it.

Information from:

http://www.time.com/time/magazine/article/0,9171,1997447,00.html

http://machineslikeus.com/.../moral-issues-raised-synthetic-biology-subject-hastings -center-workshop - .html

http://www.economist.com/node/16163154/comments?page=1.html