Tuesday, April 26, 2005

Publication or pain! (continued….)

They want 600 USD. Publication fee (page charges) for one of my papers. Hey! that’s equivalent to 3 month's salary of mine. Every one knows that we are always at fund crunch. But ...But. What else can we do except paying the money? If we don’t pay it, the whole process will get delayed. Publication of another paper depends upon it. So...I don’t know...I can’t help ....but keep my fingers crossed.

There is lot of discussions on new models of science publication. There is a fierce debate on public access to science. But where will the money come from? One can say that every article should free to access. Then the authors have to pay the publication fees. Are we in position to pay that? Definitely not. Not for all our articles. Our funding agencies do not provide us that much of money. BMC waive the publication fees fro authors from third world countries. However other journals don’t. We are always at disadvantage.

Any way, the good news, in all this mess, is that the computational paper have got a good review. Hope this one will get published soon.

Monday, April 18, 2005

Publications or disasters??

Last month I communicated two papers. Two more papers are ready. I am waiting for the permission from my boss to post them. It’s the worst time. A time of incubation; when all the hard work of last 5 years will be judged through these papers.

It reminds me some mails that I exchanged with one of my friend few months back.
One night he wrote me a mail. It was like this:

He was preparing for his professional exams while sitting on his bed. The table lamp was kept on the bed. All on a sudden he realized that the bed sheet had caught fire from the heat of the light of the table lamp. So he was amazed. He saw such an incident for the first time.

So I shot back a mail immediately to him. It was like this:

Ok, you do a few things. First, look into literature databases to know whether some one has already published such incident or not. Then you change the bed sheet of different colors but made up of same material. Then check, whether they are catching fire or not. Then use bed sheets of different materials. Try the same thing. Again do the experiments with various types of lamps and with varying exposure time. Repeat all those experiments at least thrice. Then jot down the data. Do factor analysis or cluster analysis which one you find suitable. Dig out the statistically significant observations. Then write down the whole story in a scientific paper format. Let your friends (?) read it and scratch your back. Then send it to a journal.

Now you wait. Wait another month. Mean while you can open your author account every day, just to make your day ugly. Then on an auspicious day, you get the reply from the editor with referee’s comments. And the fun begins now. One referee has raised really good questions. You get stimulated. You can even write down a new grant application based on this idea.

But hey! Wait. Read the comments of the second referee. He has asked, what happens if you spread cow dung over a bed sheet and then keep it bellow a lamp? Now you are in soup. Where does this cow dung come from? You scratch your head. Got agitated, then depressed. Any way, after two three days you start exploring the literature databases. This time your search command is: Cow dung AND bed sheet. Pfuuuuu….. After three four days of toil you write down all the answers to referees comment and re-write the whole paper a bit. And then re-submit it. Now pray again. Pray early in the morning and even before you go to sleep. If you are lucky you may get the article published just before your next promotion.

So it got published. And you are happy and excited. In the evening you ring up your girl friend and break the news: honey I have got a publication. Her reply: “so what?

You cannot help. When rape is inevitable enjoy it.

Hey I don’t say that; neither the story. HA HA HA!!!!
Abstraction, Theory and Biology:

Two three days back I posted a question in the Internet regarding use of ATP as energy currency in cell. It is quite amazing that only ATP is extensively used for energy storage, though all other nucleotides can be used energy storage molecules. This question must have an answer. Either I am ignorant or it has not been solved yet (most probably the first one). However I only got 4 replies and that too inconclusive. Even one person reminded that: "Always remember, biology, of all the sciences, has the fewest Laws."

This is a typical attitude I have always observed amongst many of the biologist. If any life form is dictated my physcio-chemical processes, then every thing can be explained by natural laws. We may be ignorant about many of them right now or may be we have not tried to explain them in the proper fashion. That’s the basic principle of Biochemistry. However I found that many of the biologists forget this and treat biology just as a compilation of observations. They always provide the lame logic that living system is too complex. (Remember here they usually use the word "complex" in layman’s term; not as complex system as defined in physics). In there believe system they are actually still in the age of "vitalism".

It is true that the history of development of Biology is quite different from other sciences like physics or chemistry. Historically Biology has developed as Natural History- compilation of information regarding living organisms. In the early days of biology there were very few options to setup any reductionist experiment with living systems. At the same time religion has a great shadow over people even who are working in the field of other pure sciences. Biologists were not exception. And as we are also part of this living world, it is always socially and psychologically problematic for us to consider that living systems are governed by natural laws.

Physics developed with a well titrated methodology: Observation ----> Abstraction -----> Theorization ----> validation . Many a time such abstractions crossed the barrier of general understanding and proposed some audacious thesises. Many of them got proved experimentally long after it was theorized. And now they are the most essential tools in physics. Chemistry also followed a similar path, holding the hand of physics. And in both of the cases, Mathematics helped as a natural language for abstraction. And that’s why in physics and chemistry we strongly believe in abstraction and theorization. Definitely experimental observations are important but those are not independent of theory.

As I have noted earlier, biologist usually put more importance to information gathering. And usually leave the job of theorization to mathematicians/physicists/Chemists. It is true we really know very little about living system even in terms of just information and it takes a lot of energy and time to gather that information. But that does not mean that we should not use our valuable energy for abstraction. In fact, history has shown that, such abstractions actually help us to discover many principles, which are otherwise neglected. Our strong believe in thermodynamic theories are the best example. Our strong believe in the conservation of mass and energy led us to the discovery of many sub-atomic particles.

There are similar examples in Biology too.

Friday, April 08, 2005

In one of my last posts I wrote about the inter-relation between our biological existence and our culture. Recently there is a beautiful article on Pain in The Scientist. It deals with the inter-relation of biological and cultural aspects of Pain. Worth reading.

Sunday, April 03, 2005

One needs lots of patience and time to watch a full cricket match. Even an one-day mach. However when you have finished your Ph.D and have ample time to sit and pray for few “miracles” to happen, you can afford to watch a cricket match. That’s what I did today. The Kochi match between India and Pakisthan. The most interesting of this match is a placard displayed by a spectator. It says: “Dravid: The Great Wall of India”. I think, every one who is in the field of research should watch his maches and learn the attitude.

Friday, April 01, 2005

I could not stop the temptation to blog this one.
Long back I posted this one in my India Times Blog:
“The eternal questions!!!
The eternal questions that humanity still faces are: Who we are? where we from? and what we are supposed to do?
My journey in the field of science is nothing but a reflection of my personal life. For long time am trying to jot it down in a single home page. Its almost ready. Please visit My Home Page”

And some one responded to it in this way: “what do you think what really we are? an unique combination of some 30000 genes?are our intentions and willpower all encoded by our genes? i am interested to know how your journey in the field of science is a reflection of your personal life?”

So here is my answer to this query:

This is what my answer is. Not in details as I have to finish some of other works before my boss reaches here.

We all know that any living system is a open system with continuous flux of matter, energy and information from the surroundings. It will be foolish to think that all functions of a cell are just fixed by genetic encryption. Its not and its yes too. Any phenotype is the resultant of genotype and effect of environment. There is no confusion about it. So a single cell is the out come of inherited genetic (and epigenetic information) and environmental interactions. And an organism is combination of the outcomes of those individual cells. And be sure that combination is just not linear summation. It is not. It cannot be. Lets move one step ahead. The society is the end product of interaction between individuals. (Those individuals do follow the rule just stated above). So what do we get? Our society is the end product of interaction genotypes and environment. These things can be explained with lots of common example. Better I stop it here today.

There is another way of looking to the question raised. The way one think is definitely reflected in his/her actions. Again our thinking process, our believe systems are dependent on our interaction with society. Your actions thoughts cannot be separated from your social learning process. That’s why science is not above a scientist. There is a common saying that when you start reading a history book, first read the biography of the writer. That’s why it is always better to read science book from the very beginning, starting with acknowledgements and introductions. I hope I can convey my opinion. Take an example. How many Ph.D students in Biological sciences in India, pursuing research just to enjoy the challenge of learning? Or its just a way out for a greener future (in US / or just a mirage). If you don’t know the answer, ask some one from this field. I don’t have the statistics, but would love to do an survey.

haaaahhhh!!!!!! I should take a break now. I think I have lots to write on it. Bye

My home page

Phhuuu..!!! slowly and steadily am learning to post blogs and manage them. It does require time. Then you can always say, I waste lots of time in doing nothing. Just a glass of hot coffee and Wills. The NesCafe stall here in AIIMS is really cool. By the way, have you really wondered about the history of NesCafe. If you want to know a little bit more just look here. I love to read this histories. There are many such interesting corporate stories: Bata, Dabur......happy surfing!!!!!

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