'Virudh' : whom should we stand against?

He (and his wife and his daughter-in-law) fought silently: with their lips tight; with complete faith of Indian legal system; with complete trust on human values. However, at the end, he killed the killer of his innocent son. The story did not stop here. The court went through all the evidences and the judge declared, “on behalf of the whole judicial system, I apologize to you”. And he was declared innocent. Claps! Claps!

This is the new Mahesh Manjrekar creation: Amitabh Bachchan-Sharmila Tagore starrer - 'Virudh'. It’s a neat, well-crafted movie. Technically perfect. Every shots seem to be so natural. And you definitely get dragged into the life of Mr. Patabardhan. (Even though I watched it in a CD, copied from the movie hall).

As they fought for the justice for their murdered son, this world turned naked: friends, police, court, lawyers, and politicians. And at the end, he picked up the gun. But with a different mental status: Not to take the revenge; not to spread hatred. Rather just to establish that his dead son was innocent and was murdered for this bravery.


Mr. Manjerekar (and every one who has shed their tears while watching this movie)!!! I have just two questions:

• Is the GUN, the ultimate weapon to establish justice?

• The eternal question of “justice for an individual” and “justice for the society”. Is it wrong for a poor, jobless, hungry man, to loot a shop, just to feed his hungry children?

Ohhhh…..am writing after almost 2 months of gap. If you still want to read the story of the movie, here is the link.

MST


In continuation of the last blog, here is something from Brazil. They call it MST: a movement of landless workers in Brazil. Economic status of Brazil is well known to people who are informed about the IMF sponsored global reform in economy. I am not adding any extra lines on that. I am not much aware of the political lines of MST. I just stumbled upon a photo feature on MST at the BBC site. It is worth spending few minutes over it. Happy surfing.

Leyla Zana


Majority of my educated friends are disinterested in politics. For them politics is a dirty business of personal grit, power and money. This is the opinion that is aired even by our media and well percolated in our young minds. However, this attitude only shows our total ignorance about our societies, its history and present developments. It is nothing but just the reflection of a life with our eyes closed and head dipped in the mud of our day-to-day living. We, who are fortunate enough to enjoy the best things of life, just forget the pain and humiliation that majority of the human race on earth are facing every day.


While surfing through the Internet, I tumbled upon some web pages on Kurd people and Leyla Zana. Leyla Zana, who transformed herself from a simple village girl into the voice of Kurdish struggle for independent identity. I know there must be lots of propaganda going there on her name. But one thing is true: it is not her hunger for power or money, but her desire to fight against oppression and humiliation that she and her family faced, dragged her in politics. Hundreds of men and women are fighting every day against such personal odds. They are fighting for their own identities, their culture, their nationality, and language. It is not just power politics; rather it’s the politics for survival as an independent human being. Do we care about it?

3 cheers for Google:


Services provided by Google amaze me. They are really creative. I am using my Gmail account for almost 5 months now. Gmail is supposed to provide Contextual text advertisements. I have noticed such contextual advertisement in my mail pages. However, today I noticed something more interesting.


Usually, between our friends, we write mails in our vernacular, i.e Bengali. We use the English script to write Bengali terms in mails. In those mail pages, Gmail provide advertisements related to Bengali themes. It indicates that Google not only sniff our mail, but also can correlate words with dialects and languages. What an innovation!!! Keep it up Google.

Am drifting!!!

Do I suffer from OCD? That’s a funny question. Isn’t it? If I ask this question to Srini, he will definitely come up with few more questions to make a proper diagnosis. And them he will refer me to some one in the psychiatry department here in AIIMS. I don’t want to go through this entire ordeal.


For your kind information, the last time I visited a clinic, for my self, was 3 years back. That too for my sever tooth ache. I managed some SR here in dental, and thought that they are going to fix my problem. So on a painful morning I went to meet him. After juggling through the mass hysteria at the dental OPD, I managed to enter the clinic and say hello to my friend. He just referred me to a cute girl. Supposedly, a JR. She took a good look in side my mouth and said “too poor oral hygiene”. That’s all. Afterwards I never visited any clinic.


Let’s come back to OCD. When ever I lock a room, I definitely check it back at least twice. When ever am working late at night, I check the lab taps thrice or four times. Are they closed? Can you say these are symptoms of OCD? Now days, I check my mail box at least ten times a day. I open my publisher’s sites to check the status of my papers. At least thrice a day. I know my hairs are getting thinner and gray. But that does not mean that I have to check them out every time I stand in front of a mirror. Ha!!! Am doing all this. No; these are no way symptoms of OCD. Neither I find it glamorous to have some sort of psychological problem, nor do I want to label my self as insane to prove my intellectuality. I just have lots of time. It is the time to think incoherently; time to sleep endlessly; time to sip the rum. I want to drift this way unless I find a new nest. Then it will be hectic. I know.

To be pure!

Does science believe in Cult? Definitely NO. But scientists do. And therefore the scientific notions are many a time driven by such dogmatic believes. I first faced the problem while writing the recent article that has got accepted in Immunology.

As I had wrote in the last blog, the first question that I asked was why every body missing the real point. The mistake that I was questioning, in the article, is quite obvious. Every body knows selection can be both positive and negative. So just looking for positive selection of mutations can not give a picture on antigenic selection of an antibody clone. But every one was just following the trend and churning out papers. Even Dr. Rath frankly told us that he had also thought that the method used by people is wrong. But no one was questioning it.

Let me give another example of this trend. It is really amazing to note the symmetry and organization of a living system. But how does such an organized structures emerge out of basic molecules? The questions regarding emergence of living from non-living has always intrigued scientists. Similarly, if such organized structure emerges spontaneously, then why does it break into pieces? And why does it replicate? (Remember, replication has a huge cost in terms of energy and material). These questions are still unanswered.

But I want to draw attentions to some related thing. Many a time biology teachers ask students to explain whether biological systems are in contradiction with second law of thermodynamics. They argue that life is an organized form of bio-molecules. So with organized structure there is loss of entropy. But the process is spontaneous. Does the whole thing fits in the second law of thermodynamics? Their expected answer is that the organism is loosing entropy but the environment is gaining it due to the metabolic process. Even one can find many long articles on this line. Now, for me, asking such a question is stupid. In our thermodynamics classes, we first learn about different types of systems and their definitions: open system, closed system and isolated system. And in simplest terms second law of thermodynamics states that when an internal constrain of an isolated system is removed the entropy of the system increases. And every one knows that all concepts of thermodynamics are actually based on isolated systems. Life is no way an isolated system. So kindly dont ask such a question.

But there is a long history behind such seemingly stupid question. Most probably it all started with Shrödinger. In his book, "what is life?", he wrote -"living systems seems to feed on negative entropy " (I don’t remember the exact line, rather just the gross meaning). But what is negative entropy? No one had heard about it before. No one had deduced it. Is it possible? It’s the beginning of a new era dealing with "negative entropy". So we developed the term negantropy. However such concepts have not been able to solve the problems related to living systems. Rather we realized strongly that classical thermodynamics is not going to help us much to deduce ‘life’. I think all these debates actually trickled down in diluted form to Biologists. And may be that’s the origin of such a question that a biology student still faces in there college viva.

I am writing all this words just for me. Just to remind me not to get trapped in the club of cults. Being a member of this society one is always at risk of loosing ones own thought process and just ending up as a follower of a leader. We really need some psychological aerobics every day to get out of it and to keep ones thoughts pure.

Yahoo!!!


Ultimately THE PAPER has got accepted in Immunology. I worked on it for last 2 years. It was rigorous experience. Doing calculations, reading a lot of diverse papers, writing codes, writing the article and repeated polishing of the draft. Then getting painful rejections. Opps!!


It all started in a very funny way. I applied for a poster presentation in a conference on mathematical biology in IIT Kanpur. They changed my category into an oral presentation. I was just dumb. What Am I going to talk? That was my first question. And then I started this work.
Then I hit another roadblock. After giving a preliminary shape to the work, I was wondering. I am challenging a silly mistake that has been repeated by scientists for almost in 200 papers. How could they do that? I must be missing something very important!!!


After checking and rechecking, we are at the simplest conclusion: scientists, just like any other human being, love to follow cults. Chang and Casali formulated the statistical method. It is easy to use. Every one started to use it without even bothering to check its correctness. Although Dunwalter challenged it, every one kept using it. It seems no body go through literatures thoroughly.


Working on this paper was a nice experience for other reasons too. I posted questions all over the Internet. Even I posted a SOS in our JU alumni yahoo groups. And the response was enormous. Even one Pittsburgh statistician advised me to have a teacher in statistics, as my basics are so poor. Yes, I know am badly in need of a teacher. Rather a mentor. Thanks to Tapan, he helped me a lot to understand the basics of the likelihood estimation. Dr. Rath from NII gave us the most important review of the article. And thanks to the referee who went thoroughly and made some beautiful corrections.


Phuuuu…we should celebrate now. Definitely with Bacardy.

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.

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.

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.

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.

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!!!!!

My home page

Biomed central and Public library of science are trying to build a style of scientific publishing which can make us free of large publication houses and provide free immidiate access to research results. Lots of information is avialable in these two sites about public access to scientific information. Very recently a interview is publeshed, which gives some detail accounts of the personal history of biomed central: Interview with Vitek Tracz: Essential for Science
Srini sent me this link. Thank you srini. Its worth reading.

They say its the easiest way to publish on net. They say viewers of blogs is increasing . But till today I am not feeling comfortable with blogging. I still find maintaining my web site much easier. Write a few lines of HTML and publish it. This blog is just like a web site. But its hard for me to remember it web address. Its not geting listed any where. Even google search can not find it out. Then what are the advantages of a blog. I really dont understand. May be some day i will understand the real utility of blogs.
Forget about blogs. Lets discuss about experiments. I am trying to digest my recombinant antibody by pepsin. Its a mouse human chimeric antibody and binds to Hepatitis B surface antigen. I want to digest it with both papain and pepsin to confirm that, its structure is similar to a normal antibody. Apart from this molecule I have generated a scFv-Fc fusion molecule too. I will digest with pepsin to confirm that the disulphide bond is actually at the hinge region. Wish me good luck.
Biplab
Please visit my HOME PAGE
http://www.biplabbose.wb.st