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.