Self Certified Genius of the World

   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...

      I was reading "Essentials of Statistical Thermodynamics" by Nash today. Several things that he said made me realize a lot of truths about Stat ThermoDyn. He starts by saying that thermodynamics teaches us what happens and how much of it happens, but it does not tell us why it happens. Most such textbooks would probably say the same thing, and then proceed to drown us in jargon and all manner of equations. My favorite part is when these oh-so-smart guys shove my ignorance in my face by sating things like "It is trivial to extrapolate from this 3 term equation to a 30 term equation". And I am left wondering what the hell happened. Needless to say, from that point onwards I am too annoyed to make sense of anything. So Nash takes us through the subject with minimal assumptions and the Boltzmann distribution almost seems like a natural extension of basic probability which actually it is. So, reading his book got me thinking about a lot of other things and I ende...