Self Certified Genius of the World

   One of the earliest essays I wrote on the co-translational folding concept. This was for a course on protein folding that Prof Balaram takes at IISc. I am reproducing it in full, with missing punctuation marks added. At one point, I say that I have not been able to find out why it is assumed that refolding is a good substitute for in vivo protein folding. I did know even then, but I chose not to talk about it. I did so, since I cannot talk about the topic without calling everyone involved an idiot. Also, I have omitted the references as I cannot bring myself to format them properly. Rest assured that nothing I said in the essay is without literature support. Co-translational folding Introduction    Protein folding is one of the major unsolved problems of molecular biology. The problem is as follows : given that a gene encodes a unique structure (which performs a unique function), how does this information conversion take place ? it is assumed (barrin...

   Here I was, engrossed in my work (well mostly), and planning the months ahead with crystallization and other things related to a drug that I want to develop in the current lab. And suddenly, I hear that my father had a stroke. His earlier cardiac problems in some sense gave some reason to be afraid for his life. So, abandoning all plans, I came rushing back only to realize that almost all was well. As in any stroke, it is not the near future that is affected. It forces you to think about the far future, and what faculties of the brain have been lost and things like that. I guess everyone copes in their own way with what happens after a stroke. We had our fears and doubts about what may or may not have been lost. I dont have scans of the actual MRI, but it looks very much like this one taken from some sciguru web-site on singing after stroke ( http://www.sciguru.com/newsitem/10176/Singing-after-stroke-Why-rhythm-and-formulaic-phrases-may-be-more-important-melody ) . My fat...

 This is the true and untold story of how a planet very like ours became the world of the ultra-rationalist Vulcans. Perhaps there is something to be learnt in this story and maybe even implement it on our own planet. So, here it goes....   Once upon a long long time ago (clever amalgamation of two of the most common starting lines in fairy tales, dont you think ?), there was a planet called XM234. It was inhabited by intelligent beings very similar to us. They had two hands, two legs and pretty much everything we have, including round ears. There were a multitude of religions on XM234, and each held their own belief to be supreme. There were wars and famines and floods and corruption and all manner of evil that we see in our own world. In this world, was born a boy named Zara Vulcan. He was peculiar in having slightly pointed ears, not too noticeable though. Just a small tapering which you could discern if you looked closely at his photo for a long t...

    PZ Myers the Saint of Atheism has started a nice little regular column on his blog called "Why I am an Atheist" ( http://freethoughtblogs.com/pharyngula ). There have been so many people writing to him, and him posting them, that the original post is now lost in the sands of time. Anyways, I thought since I am an atheist too, why not chronicle my journey into atheism. After all, whats the point of calling myslef a self-certified genius and not acting narcissistic ? So, here we go :     I am Krishna Dev Oruganty, and I was born and brought up in India. My first experiments with the deity began around the age of 7 or 8. My grandmother had died around the time. I had not had much contact with my grandma, since we were in Delhi and she was in A.P, miles away. I remember that my mother and father were upset when they got the telegram (remember those?), and my father even booked an airplane ticket to go to A.P. I envied him for flying like that, an...

    When we were in school, we had to study both English prose and poetry. I found the poetry part quite boring, as I could not really understand any of it. Some people, I guess, get so engrossed in making things rhyme that they lose track of what the heck they were trying to say. That was my opinion of most poetry. The only guy I kind of liked at the time was Ogden Nash. But wait a minute, a quick search in google reveals that "am I a child or an adult" was actually written by Margaret Lawrence. OK, forget everything I said about Ogden Nash. BTW, Margaret Lawrence apparently wrote that poem when she started an illicit affair with her teacher at the age of 14. Some people have all the fun in the world. Forget about that too, because this post is all about science, thats right, fooled you didnt I ? Or maybe I harmed my own blog by twisting my own arguments, hmmm needs some thinking...    Anyways, the actual content of the post is not so much the poem, but t...

   Was reading a Scientific American article on 15  answers to creationist nonsense ( http://www.scientificamerican.com/article.cfm?id=15-answers-to-creationist ). Nice article, but since it was published by reputable publishing house, they could not use words like Bullshit, which are slightly more appropriate for the subject. But, the article got me thinking about creationists and other things. The article goes on to say why doubts raised by creationists are not valid science. For example, macro evolutionary processes are not  understood, but the fact of macro evolution or speciation having occurred is beyond doubt. The article goes into greater details about these things. The final answer is on the "Paley principle". Simply stated it goes as follows : "a watch is a complex thing and tells time by a specific arrangement of a lot of smaller parts. Somebody must have put them into place otherwise it would not work. We work (or...

   Being a scientist, I am always in two-minds about my work. On one hand, given the current knowledge, I feel what I am doing is right. I take good care to have proper controls and etc etc when I do my work. So, it is most probably correct, as far as I know. But, since nobody knows everything, how sure can we really be about what we do ? And more importantly, how do we teach people to be incorrect in the 'correct' measure ?    And this is where the concept of collective accuracy and Individual accuracy comes into the picture. What it means is, Science as a whole is correct, but each fact taken or each scientist's contribution taken individually is almost always slightly incorrect. I dont think I need to give examples, all the revisions that the theory of atomic structure has undergone over the decades is quite well known. I dont remember now if I ever said this in the blog, but "Science is an asymptote to Truth". There you go. Remember that and be ha...

    Well, have been doing a lot of a MD simulations lately. My current favourite is implicit solvent simulations. The entire explicit solvent thing always seemed too brute force to me. Its not elegant, and nor is it computationally feasible for larger systems. Implicit solvent simulations suffer from their own problems, but I would consider their future much brighter. This is simply sue to the larger time scales that you can access using these simulations even on a normal desktop system. Larger time scales means better averages and thermodynamic properties are always averages, so better match with experiment.    Speaking of Implicit solvent simulations, Gromacs does a good job, as well as any other currently. I especially like the OBC model for calculating Born radii which I am glad to say, I copied to MUST_READ folder when it first came out. It might still be lying there, that is another thing, but at least I can appreciate when a good...

      This post has also been a long time in coming. I firmly reject the stupid notion that our emotions are anything other than chemical reactions occurring in the brain. So having all the hocus pocus of 'souls' and spirits etc out of the way, we can concentrate on the chemistry of neural activity. And when speaking of emotions, what better emotion than the most exalted and mysterious of these, 'love'. What the hell is it, by the way ? Hmm, its like being punched by the invisible man, you can feel it, but you cannot explain or predict it.      The 'punch in the face by invisible man' hypothesis of love is very apt for a discussion of the neurochemistry of love. Because every emotion has to have a sensory input, and no emotion can exist in vacuum. So, the real question we must ask ourselves is this : "What is the mechanism of formation of 'love'-like emotions in the brain ?". Is it different for 'love' of a laddoo for e...

   Well, enough of talk about non-scientific thinking. There is something about which I have wondered many times. The steps in doing any MD is as follows : Assign charges, atom type (sp3, sp2 etc with variations) and Van der Waals radii to each atom. Based on this, the parameters will be decided. As of now, most force fields use fixed charges which means their value does not change based on the environment. So, protonation states of His and others have to be determined empirically at this step. Following the parameter assignment to each atom, bond and torsion (together they constitute a force field), all short contacts etc need to be removed. Now, at this point, you place waters randomly around your protein and then 'energy minimize' your structure which relieves short contacts between waters and the protein. You can keep all atoms of the protein fixed, or allow some relaxation to take place at this step. Now, once the protein is ready (BTW, this is what is c...

Been a long time. Actually my original thought was to write my autobiographical sketch in parts and end it with the results of this year's CASP (and in my fantasies, I solve the protein folding problem by then). But reality struck me down and I started thinking, what if my programs suck big time in CASP ? So, abandoned the idea of my autobiographical sketch. Unfortunately, after college was where most of the fun began, as far as protein folding is concerned, so you people missed the fun part, but never mind, it will come at a later date. I do have a lot of small things to share, and I have been sending myself mails to remember them, so here they come: Saw this on Scientific american today : Take a cylinder with radius 'z' and height 'a'. What is the volume ? PiZZA... HEE HEE HEE... I like it... I've heard of the one billion euro project for future science or something like that. And most projects are interesting, but I had one of my own. I t...