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.