Diwali 2009

Diwali 2009, 6.30 PM: I am sitting in my room in New York City and sipping tea. You can’t burst crackers here. No houses around me are decorated with lights. No candles or diyas. To any observer it will be just another day. But, there is traffic in a different domain. Lot of texts are being exchanged, lot of phone calls to old, forgotten friends are being made. Lot of Diwali dinner invitations being sent. Ya, we are celebrating Diwali. Not out loud with crackers, but at our homes or at friends' homes – by gathering together, eating food and lighting some diyas. If it was not for my friends, I would not have cared to do anything this Diwali. But, I am getting a feel of it now. I am getting emotional about it.

Happy

To come early to the lab, go back late.. work hard the whole day, exercise for an hour and read something before sleeping is what gives me ultimate peace and happiness. Nothing matches it.

P.S. - What would give me most pain is to see that somebody else has published what I was about to. So, I should stop blogging and get back to work.

How close to science we actually are?

How will a charged ion move in a uniform magnetic field (assuming only classical physics)? An easy question for most engineering graduates. What keeps the Sun burning? Nuclear fusion of course. But, how about this - why does coke lose dissolved CO2 when salt is added to it? Why do clothes become darker in color when wet? For the past three months, I have been wondering what reaction coordinate best represents protein unfolding. But have I (we) ever wondered what is the best reaction coordinate for our age? A reaction coordinate describing protein unfolding basically is an index to determine the age of the protein - how close it is to unfolding. We take the number of living years as the reaction coordinate for our age. We just assume it is by law, we don't question it, and it is universally used. But, you can die anytime - from 40s to 90s. There is a large standard deviation in this reaction coordinate. But we don't stop to ponder about another one. We would accept it without much thought, just like we accept our surroundings without much thought as to why things happen the way they do. Rather, while pursuing something in the scientific field we focus on more abstract things like, motion of a charged ion (which none of us can see but only know exists because of what we have read), or nuclear fusion, or protein folding. We are very far away from Science, which, losely defined, is understanding the physical nature of the environment around us. I recently heard that JEE is not what it used to be. Now its all multiple choice questions. The idea is to negate the coaching classes' influence. But I dont think they have managed to eliminate these institutes' influence. What if JEE is made into a test of knowledge of how well we understand things around us. Simple questions from what we see daily. Coaching classes will fail because there is no set course to attack this. And interesting would be - who emerge as toppers. Maybe rustic kids who have much more time to ponder about things, have to work with their hands to milk cows and do not sit in isolated air-conditioned environments.

Take a roller and level down the rugged free energy landscape. it has to be flat.. ergodicity is required.. 

Rickshaw walas of IIT

Only two rickshaws were permitted to operate in the IIT Delhi campus. I never rode on them because paying as much as Rs 3-5 for going from one place in the campus to another seemed a lot to me. But I did ride them once. That one day in my fourth year, I took a rickshaw to go from the insti to the kailash gate (kailash gate was the exit from the campus to the Aurobindo marg). I took the rickshaw because my sister was getting married and our entire family from different parts of India had come. Because of the proximity of my campus from my sister's house, I many a times used to sneek out of some ceremonies and marriage preparations to attend classes (although I did skip many). Well, all that is quite extraneous. I have a habit of writing a lot of extraneous stuff. Ok, so when the rickshaw wala dropped me at the gate, I asked him 'bhaiya, kitna kama lete ho' (how much you end up earning?). He stated somewhere between 80-120 rupees. I replied 'par bhahar to aur zyada kama sakte ho' (you can earn much more if you operate outside the campus). To which he replied, 'haan, par yahan log tameez se baat karte hain, bhahar koi dhang se baat nahi karta'. For a rikshaw wala a rupee is much more valuable for us engineers. So, he is paying a big price for the dignity he gets in the campus.

The brain (2)

I stayed back in the lab till 11 PM yesterday to start some simulations. I was hungry, tired but I wanted to start the runs so that I get the night time for my runs. But, today morning I noticed that 8 of my codes have stopped running in the middle of the run because the hard drives had got completely full. It took me a few hours in the morning to clean up the space. I had to call Orbitz to smoothen an issue with an airline ticket and they kept me on hold for 45 mins. When I was finally ready to start my sims, I noticed that some other person had started his sims on the computers I was using. I searched for other nodes where I can restart the sims. While I was trying to run sims, old, unpleasant incidents started coming to my mind and I wanted to shout at somebody. Reminded me of theme of the book 'The Sphere' by Michael Crichton. How delicate is our brain's composure. And how we choose to exhume old incidents as excuses to be angry when the reason is the present.

RNA as logic gates

We have our departmental seminars every Tuesday. Yesterday's talk was one of the most impressive I have ever seen. The professor was making logic gates in cells using RNA molecules. Unlike in proteins, if sequence of an RNA molecule is known, you can predict its structure using available algorithms. From the structure, you can determine how the molecule will respond to a ligand. So, the Professor's lab was attaching RNA molecules of known response to different ligands to genes. In one conformation, the RNA molecule suppressed the gene and in another it did not. And so by introducing some concentration of a ligand, you can in principle have an on-off mechanism. This idea can be used to make different logic gates. The interesting part was that it was not a chimerical hypothesis, but a real experimental work. We were shown experimental evidence that the logic gates can be made and do work as desired! Quite amazing. Another interesting thing was that the speaker was not an old, senile-looking professor but a young, pretty girl who anyone would mistake as a graduate student.

Earlier during the day, I had the opportunity to have lunch with her. It is a new thing in our department that the invited speaker is taken to lunch by some grad students. I was not interested initially, but there was one open slot and the dept secy asked me to take it (somehow I am a default inclusion if there is a need of a grad student for any such extraneous thing in our Dept). Well, I enjoyed the lunch though. During the lunch, our discussion mainly revolved around how to prepare applications for faculty positions, as she had done it only some 5 odd years back. And, she mentioned more than once that the kind of applications they get at their university for faculty positions are of very high quality and sometimes makes her wonder how her application got through. And, more than once the thought crossed my mind that there could be some favorable bias towards a pretty, young girl. And when it did, I smiled and nodded. But, later during the day, she completed bowled  us over with her presentation. I was guilty of my prejudice but she had seeded it with her humbleness...

What is life

I think we give too much importance to ourselves when we ask if we are the only planet with life or what makes us living or what gives us a conciousness or when we wonder that there must be a soul or a spirit that makes us different from all the other innate objects around us. I have started beliving that seemingly complex problems have simple solutions. What makes them complex is our inability to identify that solution. What makes them complex is the problem's ability to overwhelm us so that we don't think of simple answers but keep digging deeper and deeper. I think the answer to 'what life is' is pretty simple. We are simply designs of a feed-forward control. It is a nature's experiment. 

First, Universe is evolving - into what - I don't know - but different entities in it are playing a role in its evolution by the interactions they impose on each other. All non-living things follow a simple cause-effect relationship, and that's how the universe has been evolving (as far as I understand). It is a linear mechanism. But, to change the way it evolves, if nature decided to introduce a feed-forward device then it would be us, the living beings. If we try to list the most basics of what is required to have a feed-forward control, we find that those characterstics very well overlap with and are unique to living beings. Before I explain further, let me briefly write about what I mean by a feed forward device or mechanism. In control systems, a feed forward mechanism is basically identifying a signal upstream and using it to change the process downstream. It is what Macbeth did. Extrapolating the present signals to improve his future way of living. A device that pre-empts a happening is a feed-forward device. It's like you look at the inputs and pre-empt the effect and work accordingly. 

Every action of living beings is a pre-emptive action. For example, we eat food before our body is totally starved. We sleep before we lose all our ability to function. Complex devices like humans, even pre-empt the need to learn by sending their kids to schools (which in other species happens only by experience). The kids who go to school at the age of 3 do not understand why they are being sent away from home and so cry and resent. But, the society understands that learning by only experience later on in life would be wasteful (at least in some part) and even dangerous. We reproduce before we are dead. We dress up even before we can feel the cold outside and so on and so forth. The above is broadly applicable to all life-forms. Now if I try to list the basics of what a feed forward mechanism would require - it is an amazing match. First, you need to understand what effects an input will cause to have a feed forward mechanism. For that you need to store the input - brain. Analyze it - brain. Have to analyze many many different kinds of inputs - a learning mind, memory. Need to execute what our analysis of inputs predicts - for that we need mobility, energy, modes of communication. What else is life? All the basic requirements for a feed-forward device exactly match the basic characterstics of all living beings. Over it, nature was clever enough that it should not be needed to keep re-inventing the wheel, so is introduced reproduction. 

Lets go back to how we design a chemical plant in a process control class. There is a reaction in a reactor with some input streams and some output streams. To get a desired output, we need to constantly tune the input. So, we attach a feed back loop to the reactor. This is simple cause-effect relationship. Then, to reduce the lag time associated with it - we start noticing the quality of the input feeds and use them to tune the reaction conditions. That's feeding forward. This feed-forward control requires modeling of the reaction - so a model predictive control is required. That's how a chemical plant improves performance. Quite parallel to what nature did. But, I don't know what is the Universe evolving into and what for. 

PhD comics guy coming to Columbia.. yeah!

1000 days in the ice

This is clearly the most inspiring story I have ever read. An amazing account of scientific acuteness coupled with courage, determination, patience and perseverance of one person. http://ngm.nationalgeographic.com/2009/01/nansen/sides-text/1

The jump

I sped down the white slope, climbed a mound, slowed down a little, and reached its top - a little jump, something funny in my stomach, skis back on the ground, and balance regained. The next mound, brimming with confidence, I sped up its slope, but dint slow down. A terrific jump, but lost my balance, hit the ground - and boom, blast, dhchaak - my skis detached, face in the snow, nose and lips bleeding, different parts of the body hurting, but nevertheless,  a charmed escape with no broken bones - something to gild a tall story.. the scars remain though - medals of bravery or reminders of bravado

Talks

Giving talks to our research group always looked a piece of cake to me. Now it is getting tougher. The manner in which I present has changed significantly, and consequently the manner in which my professor responds has changed a lot too. Earlier my presentations used to be bare results on the current work, hinting to something, pointing to a possible new direction. Now in my slides I try to explain a physical phenomenon or some previous experimental work, using my simulation results. And when I do it, I get a taste of acuteness my professor. The entire discussion becomes challenging, and sometimes I get to know that some of the work I have done has no physical significance at all. That still hurts, even though I have seen this now many times in the past 2 years.