Self Certified Genius of the World

      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...

      I was watching another alien invasion movie today. And I feel that this whole Martians/venusians or Alpha centaurians are vulnerable is a big problem with the whole genre. I believe that no civilization can really discover space travel without first discovering the secrets of health and disease. And if they have discovered that, then it is only a matter of time before they realize that they dont need huge machines and energy expensive robots and exoskeletons etc. All that they will do is send an earth-rover initially equipped with a small biological specimen collector/analyzer and find out the genetic makeup of earthlings. Once they do that, they will obviously realize that humans are susceptible to a lot of diseases. They dont need to understand english, they dont need to communicate with us (who the hell except us wants to anyway ?). It is our (rather Hollywood's) stupidity to think that Aliens would come to Earth and stand before us and in a comma...

Found this stupid letter to all atheists on the internet. Just had to send a reply. So here it is. My responses to the 'questions' preceded by "----". Dear Atheist, Do you think its a coincidence that... of billions of stars and planets in the many galaxies, only earth has life, and abundance of it? ---- what makes you think so ? the sun is 400 times the size of the earth's moon, 400 times further away from earth than the moon, yet they look both proportionally the same size in our sky? ---- Do you know how other moons look from their planets ? the sun lights the days nicely, while the moon glimmers in the night sweetly and the clouds bring forth rain to water our crops, which bring forth food in your stomach? ---- Mostly due to eart...

I have been doing some thinking recently on the corruption rampant in India. Why is nobody doing anything about it ? It is not that we lack the infrastructure to deal with it. Far from it. What we lack is in my opinion the will to police it. So, the real question is why are we not policing it ? After much thought on this matter, I have come to the conclusion that till now corruption was in the National security interest. Till now. Recent events tell us that it has lost that quality and hence, corruption will become punishable once again. Let me explain. Fig 1. Fictitious 'National average bribe taken' around the time of 1993 Bombay blasts. Imagine you are responsible for finding out terrorist or insurgency activities. How would you go about it ? You cannot have information about all the citizens of any country at your disposal. So, the easier way out is to have some kind of statistical test which will predict if terrorist activity is going to happen soon. How would you do that ...