If you are wondering why am I posting after so long then the short answer is “I was (or rather am) busy”. I am here at National Center for Biological Studies, Bangalore for one month winter internship under Dr Mukund Thattai. My work is very interesting and am learning new things daily. The place is really energetic and exciting. I will post more frequently once I complete the research internship. Till then, keep waiting…

This post will be under construction until I enter a grad school…

General Resources:

* http://career.berkeley.edu/default.stm
* http://www.petersons.com/graduate
* http://college.wsj.com/

Graduate Programs:

* http://csbi.mit.edu/
* http://bioegrad.berkeley.edu/
* http://www.sanger.ac.uk/careers/phd/fouryearphd.shtml

Hi All,

I am happy to inform you that my research paper titled “Evolved cellular automata for protein secondary structure prediction imitate the determinants for folding observed in nature” has been published in the journal In Silico Biology.

The details of the publication are as following:

Paras Chopra and Andreas Bender. Evolved cellular automata for protein secondary structure prediction imitate the determinants for folding observed in nature. In Silico Biol. 7, 0007 (2006).

Abstract: We demonstrate the first application of cellular automata to the secondary structure predictions of proteins. Cellular automata use localized interactions to simulate global phenomena, which resembles the protein folding problem where individual residues interact locally to define the global protein conformation. The protein’s amino acid sequence was input into the cellular automaton and rules for updating states were evolved using a genetic algorithm. An optimized accuracy (Q3) for the RS126 and CB513 dataset of 58.21% and 56.51%, respectively, could be obtained. Thus, the current work demonstrates the applicability of a rather simple algorithm on a problem as complex as protein secondary structure prediction.

Full text link: http://www.bioinfo.de/isb/2006/07/0007/

Your feedback/comments are welcome and appreciated.

Regards,
Paras Chopra

Here is a news story covering the article on tumor growth titled: “Tumor Morphology and Phenotypic Evolution Driven by Selective Pressure from the Microenvironment”

A site (just like this one) dedicated to Biohacking. Check it out at: http://biohackery.com

This can be a source of inspiration for biohackers. The website has a collection of classical papers in genetics (Mendel, Morgan – the site has it all). Check out: http://www.esp.org/foundations/genetics/classical/

Read this interesting news. It may be relevant to AI theorists and experimenters.

A man with one watch knows the time.
A man with two watches is never sure.

- A version of Murphy’s Law

But this law is much truer in reality. Today my long held conviction was shattered when I realized that the Big Bang theory is not the reality of world. It is merely a hypothesis and other theories do exist.

It is not that I have started rejecting Big Bang as a viable model of our universe. It is the most popular model which has made several predictions which match with the observations. But the key point here is the word popular. Any belief held by 99% of the population does not convert it into a fact.

The other theories, clubbed as Alternative Cosmology Theories, also make predictions which match with observations and are equally interesting. So when I came to know about these theories I really realized that theories are theories after all.

So, when I knew only about the Big Bang model I was happy and satisfied to know about the universe as the theory told me but now, since I know that alternative explanations for the same set of observations do exist, I am unsure of what my universe really is. Please note that I am in now way promoting alternative cosmology theories. It is just the fact that I, now, have realized that no theory should be taken as a fact, no matter what.

By the way, check out the basics of these Alternative Theories at:
http://en.wikipedia.org/wiki/Plasma_cosmology
http://en.wikipedia.org/wiki/Steady_state_theory
http://en.wikipedia.org/wiki/Quasi-steady_state_cosmology

From Moshe Pritsker:

Journal of Visualized Experiments (JoVE), www.myjove.com, FREE journal publishing video-protocols

JoVE is a newly founded online research journal that publishes video-articles on biological experiments (video-protocols). Video-articles include step-by-step instructions on experiments, and short discussions by experts describing possible technical problems and modifications.

JoVE invites article submissions in all areas of biology. Its editorial board includes a number of distinguished scientists, leading experts in their fields. JoVE employs the OPEN-SOURCE model: submission is free, and all video-articles published are freely available online.

A video-based approach is employed to allow for explicit demonstration on “how experiments are really done”, which remains unclear or misinterpreted from traditional publications in print. This is to increase reproducibility and decrease the traditionally high failure rate of biological studies. This approach can be especially important for scientific fields where experimental procedures are highly sensitive and difficult for standardization, e.g. neuroscience or stem cell biology. The JoVE’s approach is also expected to facilitate adoption of new technologies, e.g. genomics and proteomics, and thus lead to significant savings in time in resources in the academic and industrial research.

Sample article on a behavior assay in mouse model: http://www.myjove.com/index.stt?comp=c18jdh42&ID=104&VID=53

Philosophy and motivation:

Mastery of scientific techniques has undeniably become a craft in itself. Looking at a particular drawing, a portrait, most people can easily identify gender, age, facial features of a person described. They know the concept and might even know that one needs specific tools, brush and paints, to draw a picture. However, only very few people will be capable of drawing the same picture since it requires years of training and such qualities as talent, which are difficult to predict or measure. A similar situation exists in biological research where the mastery in experimental techniques is not sufficient but necessary for advancement.

Generally speaking, each field has its concept and methods. Concepts are generally accepted ideas that direct field’s practices. DNA replication, gene code, transcription, cell cycle, cell differentiation are examples of biological concepts. Methods comprise tools and procedures. Examples of methods in biology include DNA purification, polymerase chain reaction, isolation and propagation of cell cultures and cell transplantation. Current biological concepts are simple to explain and understand. On the other hand, learning methods is very time-consuming, and performance levels achieved are often difficult to predict. Learning and applying new techniques at the expert’s level is often a hard and tedious journey.

Interestingly, the described situation persists despite the fact that descriptions of techniques and procedures ( “protocols” ) are available in the scientific literature, which is mostly accessed through PubMed. Theoretically, these protocols should be written in a clear instructive manner and, therefore, understood by every researcher. However, in biological experiments, there are multiple unforeseen variables in details such as specific reagents, equipment, specimens, previous scientist’s experience, reader’s interpretation and others, which cannot be foreseen by writers of protocols. Thus, in reality, reading and even understanding protocols does not convert one into an expert. Similarly, reading a manual on drawing techniques does not make one a painter. However, biology is not an art. It is a science, and its experimental procedures, although complex, consist of rationally determined sets of basic operations that are known to every practitioner.

Solution to the problem

Video-based visualization of biological techniques and procedures can provide a solution to the problem described. For example, the nature of equipment and biological samples employed becomes more obvious in visualized demonstrations. Visual instructions are less prone to misinterpretations on “how to do the experiment”, as compared to written protocols. In addition, visualization significantly reduce the language barrier, which is especially important for non-native English speakers, abroad and in US where they comprise more than 50% of staff in many academic and industry laboratories.

Open-source model

The JoVE database should be built with the contribution of the entire scientific community using a “open source” model, which is prevalent in the sharing of information such as in Linux, Wikipedia, etc. Due to the large number and tremendous diversity of biological research techniques, the production of these video-based instructions for all these techniques will require the effort and contribution of the entire scientific community.

Similarly, every scientist planning on a biological experiment will be able to access the database, find videos relevant to their work and use them as protocols. High effectiveness of visualized instructions will decrease failure rates for biological experiments, and, thus, facilitate significant savings in time and reagents’ cost. Thus, we can expect that JoVE will become an essential tool for every biological researcher, as Google became an integral part of every Internet user’s life.

Suppose we discover or invent or whatever the final Ultimate theory. But even then could it offer us an answer to the most basic question: Why there is something rather than nothing?

I believe that no theory can offer such an explanation. This is because a theory (Y) is based on a set of observations or axioms (X).

So, if X => Y, we would still need to explain X. Then we can say W => X. See, it is an infinite regress.

The only superfluous solution which the Ultimate theory can hope to provide is something like Y => W. So it makes a circular theory which does no better explaining the universe.