The article correctly describes the current flaws in biology research. Today, it is more of observation-based.. Like, you collect tons of data and then infer something (most of the times, unamusing). Rather, our approach should be hypothesis-based. The fields like physics, economics make use of mathematics to abstract the details.. Physics has laws, mathematics has laws.. But biology has only observations.. How can we expect to make huge intellectual leaps in biology without any laws or abstraction.. Why can’t we predict things in biology rather we just describe the observed phenomena..

Today, biologists need a heavy dose of courage and guts to leave the usual and make bold predictions about future. That’s how the field will progress. They are describing every phenomena in detail-and-detail-and-detail.. Can you ever use the knowledge from two distinct field of biology and then combine them to provide some meaningful sentences.. But, we can do that in physics… Combine any field with any other and then invent/predict/innovate…

We, biologists, need to build on existing knowledge and abstract information. And must not probe further and further because the detail will never end.. And further, by doing so, we can never expect to unify biology..

Click here to see the article.

Here is the preprint version of my review paper on the field of Synthetic Biology…

Abstract: Synthetic Biology will bring a new paradigm in science as it attempts to approach biology through standard engineering principles such as decoupling of problems, standardization of components and abstraction of information. It has enabled scientists to create life from the scratch, hence helping unlock the mysteries of biology. The viability of living organisms which use unnatural molecules is also being explored. Unconventional projects such as DNA playing tic-tac-toe, bacterial photographic film, etc. are taking biology to its extremes. On a serious note, the field holds a promise of mass production of cheap anti-malarial drug along with the possibility of programming E. coli to seek-and-destroy tumors in the body. However, the inherent property of self-replication and the complexity of biological systems make the field a challenging one. In addition to this, there are other major technical and ethical challenges which need to be addressed before the field realizes its true potential.

Click Here to download the full paper.

Drew Endy has suggested that problems such as our inability to avoid or manage biological complexity, the current tedious and unreliable construction of synthetic biological systems and the apparent spontaneous physical variation of biological system behavior can be solved using concepts such as standardization, decoupling and abstraction [1].

But, he suggested that evolution can be quite hard to tackle. This is because our synthetic genetic circuits become non-operational due to mutations. Sometimes, mutations can render an artificial biological system non-working in less than 5 hours. So, the problem of mutations (evolution) has been a quite difficult for synthetic biologists. It has also been suggested that we should learn from viruses, bacteria about how they manage to function normally in spite of the effect of evolution over the generations.

Here, I propose an entirely different approach to tackle evolution. According to me the concept of hierarchy and decentralization can solve the problem of abnormal behaviour of biological system due to mutations. I here talk of biological systems such as Standard Biological Parts(SBP).

I really think that SBP should create a hierarchy into the parts. Like, the parts should be defined on various levels with higher level parts employing low-level parts for its functioning. Then, we can create a redundancy of low-level parts into high-level parts so that even if a low-level part gets mutated and becomes non-functional, the high level part must keep on working normally.

A beautiful example of this approach can be TCP/IP protocol. Internet works on this protocol and thus is not dependent on any single node for its functioning. It is completey decentralised. So, even if one node (or even many nodes) come off the network, the network still functions in the normal way.

So, let us say we are making a biological equivalent of an AND gate which is composed of transistors. Then, if we design the AND gate in such a way that it is not dependent on any single transistor, we can expect the AND gate to work normally even if some of the transistors get mutated and become non-functional.

We can then scale this up. Like, we may then want to design some specific biological part e.g. an amplifier which consists of AND gates. Then, we design the amplifier in such a way that it becomes decentralized and is not dependent on any specific AND gate for its working. Now, even if a AND gate composed of many transistors gets completely un-operational due to mutations in all transistors, the amplifier will work normally.

Using this approach we can expect the increase the working life SBP quite dramatically. Also, this would enable the SBPs to work in diverse conditions.

What do you say about this approach?

REFERENCE
[1] Drew Endy, “Foundations of engineering Biology”, Nature 2005.

An article on Synthetic Biology which summarizes all the latest researches in the field. It could be a good article for the layman. Click here to access it.

Of late, I’ve been reading on the internet that Mathematics is going to become one of the major tool to help virtually any science field. It even is being applied to humanities. I wonder how it will help biology.

Basically, maths helps in modelling. Modelling in a sense that using maths we can construct models of the processes. After a model has been built, we may do many things with it. One example might be to use that model for predictions or use the model for optimise certain process.

Now, as we are progressing towards convergence of biology with other fields such as information science, nanotechnology, etc., the models of biological processes will become indispensable. In the future, more and more biology work such as genetic circuit design, population modelling, etc. will be done on the computer. And the software on the computer will be designed using maths. So, in near future, a biologist with mathematical skills will be in great demand and will be in much better position to do inter-disiplinary research than his counterparts.

I have decided to buy and read the book ‘Nonlinear dynamics & chaos by Steven H. Strogatz’. It is an excellent book and I expect to learn a lot from that book.

RESOURCES

1. Math will rock the World.
2. Why Math in Synthetic Bio?

Hey,

Just like we teach people how do things by demonstrations, in the same way ants teach them. I wonder if they have sufficient intelligence/complexity to understand and teach how to find food. But, indeed researchers have found that ants teach each other about how to find food. Ants collectively are quite intelligent. They can build colonies, collaborate, have definite hierarchy and now they can teach and learn too. I guess we have enough to learn from ants. The field of collective intelligence will just get hotter.

Check this article: http://www.livescience.com/animalworld/060111_ant_lessons.html

I always knew that.. The reseach just confirmed my belief that I may also be a genius
See: http://www.livescience.com/history/060111_genius_like_us.html

I unearthed this link from my website’s log in the section of refferers. It has all the stuff on Synthetic Biology nicely categorized into various categories. Basically, it is a site for students who are preparing for iGEM 2006. Don’t miss out to check this site.

Click here.

What is the future of human evolution? Where are humans headed towards?

According to this article, There are few likely scenarios:
1. Humans divide into two different species
2. Humans get replaced by Artificial Intelligence through natural selection
3. Humans merge with machines to give rise to cyborgs
4. Humans spread to different planets and stars
5. Humans modify themselves genetically and give rise to super-humans

What according to you is the most likely? IMO, humans will advance the biological engineering to such extent that they will soon be much more intelligent, powerful and skilled than normal humans. And then to prevent death, they will soon use the computer technology to encode themselves into bits-n-bytes. Thus, the property of life and death which arises due to physical existence of an organism will soon become an extinct property since organism can then exist as information only.

But, then, I guess natural selection will operate on parameters other than just survival. Or will evolution one day won’t matter at all because humans (or whatever name which they are called by in future) would have taken control of evolution? I guess if humans go on killing evolution, a day will come when this will affect themselves in unimaginable ways.

BTW, I am discussing the same topic here and here.

Ants were the first organisms to hack the biology. It has been discovered that Ants Use Antibiotics to Fight Pests. Great! And we thought humans are the only organisms to fool bacteria into producing antibiotics. Some Ants culture bacteria inside tiny glands between head and first pair of legs. Then these bacteria produce antibiotics to kill parasite which affect ants’ farms.

Check out the complete article here.