Friday, February 29, 2008

Random thoughts on leap day

I just had to have a post dated February 29th, for who knows what would happen four years from now right? So, here are a few random thoughts in my head at this time.

1. I recently yielded to temptation and bought my first camera. Nothing fancy, just a point and shoot Nikon coolpix. The other day I took the following picture.



What a geek I have become! Multicolored pens arranged in a row at the edge of my desk. Not only that, I have become an organization freak, obsessively cross-referencing and filing my notes away for I am tired of reinventing the wheel every few days, just because I am not able to find notes or references.

2. I went to look at the site stats for this blog yesterday and found this.

An anomalous peak that screws the scale so much that it renders the rest of the landscape totally flat. The reason is that DP linked to my “Experimenting with Box.net” post. I write all these beautiful (even if I do say so myself) science posts that almost nobody reads and they link to the “freak of nature” ARR post :)). [*]

3. Speaking of science posts, a blogger that DP likes a lot has this cool post on caricatures of seminar speakers, do read if you have not already.

4. Also, blogging break coming up. I start traveling next week. Seminar in Boston, then onto New Orleans. None of the talks are written so I guess I will be married to win edt and powerpoint for the next few days.

[*] Aside for A, all other readers ignore: I know you did this. But why is there no hat tip acknowledgement? Feeling cowardly are we?:)

Sunday, February 24, 2008

From birds and fish to cells

A physicist’s view of collective transport in biological systems

Let me motivate what I want to say today with a couple of videos. First up, an amateur video of a flock of starlings in Scotland.

Or see this one, where the flock cohesively responds to a predator. A Starling is a small bird, shown in the picture alongside, about the size and shape of a “myna” if you are familiar with it. They fly in flocks that do amazing things as a collective entity as you just saw in the above example. Understanding how they do this is field of active research as indicated by this cover of the October issue of Physics Today. I will tell you a little bit about how they do that subsequently. But you might say to me, “They are birds, and they have brains, albeit “bird brains”, so they see, process that information somehow and do stuff. Why would a physicist concern herself with that?” So, to make my point even more clear, let me show you one more video.

video

This one is a microscopic movie of a bacterial swarm (obtained from here). Do you see the complex flow patterns they exhibit? These guys clearly do not have brains. It might be that this rich collective behavior originates in more chemistry than physics, but clearly not biology. And to make my point that it is indeed just physics, I ask you to look at this other video (obtained from here)

videoDo you see the similarity in the flow pattern to that seen in the bacteria? Can you guess what you are looking at? It is just a vibrated monolayer of some centimeter long metal rods! Whatever is going on here is clearly just physics. Moreover, one can mathematically represent the motion of the bacteria/birds and those of the rods by the same set of equations! What I want to do in the rest of this post is to give you a flavor of some of the physics behind these and other collective phenomena in biological systems.

When looking at fish schools or bird flocks, the first postulate that comes to mind is that the phenomenon is “follow the leader”, with one bird/fish doing its own thing, and the others following. But as stated above, the things that birds/fish do is “mathematically similar” to what the bacteria do. So “follow the leader” seems an unlikely scenario. The logical next question to ask would be, “What are the minimal rules that can give rise to this kind of behavior?” We have known the answer to this question for a while now [1]. The rules are the following – Each member of the flock does each of three things a) Alignment : Adjust my direction of motion so that I am going in the same direction as my neighbors, b) Velocity matching : I adjust my speed so that I am going with the same speed as my neighbors c) Cohesion : I try to keep the distance from my neighbors the same at all times. With these basic rules and simple boundary conditions for entities at the edge of the flock, like “If there is food, turn towards it” and “If there is danger, turn away from it”, most of the complex patterns exhibited by these groups of organisms can be reproduced!

But these are just rules. So, the next question to ask would be, “Can these rules come about from just physical interactions?” Let us ignore the boundary conditions associated with food/predator for the moment, they clearly are chemistry and other higher processes and focus on the bulk flocking rules. What is a unifying thing between the birds, the fish the bacteria and so on? What they are, are objects that have a non-spherical shape that actively move through a medium (air/water etc.). Now what does that mean? They exert a force on the medium [2]. The medium responds, i.e., the fact that my bird/fish/bacterium is pushing on the fluid induces a flow in the fluid itself. This response now propagates through the fluid. So, a bird/fish/bacterium that is elsewhere will feel this change in the fluid, in terms of the local flow field and pressure gradients. And it will adjust its own force on the fluid accordingly, and this whole things feeds back to the other entities in the flock. This phenomenon is called hydrodynamic interaction. And this is the dominant interaction that produces the three aspects of flocks that is listed in the previous paragraph!

Further, I want to make the case that this quest for minimal mechanisms for collective behavior is not just restricted to animal group behavior on the different scales encompassed from birds to bacteria. For this, see the famous video below.

This is a video of a neutrophil chasing a bacterium and then gobbling it, the immune system of your body at work. I know what you are thinking, “This is one cell chasing one bacterium and the primary thing at play here is chemotaxis, so what is collective about this?” The collective aspect lies in how the cell crawls, i.e., at the sub-cellular scale. The interplay between membrane fluctuations, the stresses in the actin-microtubule network that makes up the cytoskeleton of the cell, the interaction of this network stress with the medium that the cell is in and many other things go into understanding how the cell crawls. The mathematical paradigm and the physics aspects of this question are not so different from those one uses to address animal group behavior we considered earlier! But for now, this is just a teaser. A separate post on this to follow later.

[1] Actually the first instance in literature was in the context of an algorithm for computer graphics, available here.

[2] If we want to be careful, then clearly third law tells us that the swimmer must at least be a force dipole. Since there is no mathematics displayed here, I fudge this point.

Tuesday, February 12, 2008

Are you a Rahmaniac?

As regular readers of this blog would know, I am crazy about the music of A R Rahman [1]. A random phone conversation with a friend a few days ago revealed to me that I actually know too much trivia about the guy and his music. So, find below a few random facts from the early years of this musical superstar (early years being pre Rangeela and Bombay, after which he stopped being the exclusive property of us Tamil folks). Interspersed with these random facts are a few questions for you. If you can answer all of them, then you must be a fellow Rahmaniac as well! [2]

Let us start with a classic:

While you listen to it, let me tell you something about it. Legend has it that when Mani Ratnam first talked to Rahman about the possibility of them working together on Roja, this was the music that Rahman played for him, having composed this some time earlier.

Now to Question 1: Do you know the first movie that Rahman committed to as a music director?

Next, we all know that Rahman was doing ad jingles before he started his movie career. Here is an ad from his early days.

This was the first time Arvind Swamy was featured in a work that had music by ARR. Now Question 2: Can you name three other instances? Everybody can name two for sure. A not so helpful hint: The following song is one of the lesser known ones in a candidate for the third album, but I like it a lot. Do you?

Moving on, after very urban scores in Roja, his second tamil release Pudhiya Mugham, ARR came up with this album that was so ethnic Tamil that it surprised everyone. Here is one of the lesser known songs from this album. Question 3 : Can you name the album?

He has subsequently come up with a whole bunch of such songs of course; Karuthamma and Sangamam come to mind when thinking along these lines.

Next, here is one more lesser known song by my man. It is still on my all time favorite list after all these years.

Question 4 for you: Can you name the movie? Hint : The movie had Ajith in it and if I remember correctly, the thalai actually dies in the movie!

Finally, deviating from my early Rahman theme, this song, composed slightly later in his career is one of my really really favorite songs that somehow many people do not remember.

Do you think it is good? Question 5 for you: Can you name the movie? Hint : This album features one song in which Apache Indian is credited as co-composer, the video of which is below:

[1] Those reading by feed : a) This post is an anomaly. So feel free to ignore it. Also, there are music pieces embedded in the post that might not show up in your reader.

[1] Without the aid of google of course. With google, we are all experts in everything, are n’t we?

Saturday, February 9, 2008

Admiration and Jealousy

My buddy K has been skiing every Saturday since the December holiday break. He has never set foot on a ski slope before that. So, how many days of skiing does that make? Six, may be seven days. He can now negotiate black diamond slopes with ease. I on the other hand will never volunteer for any activity that calls for me to reduce the amount of traction between my feet and the ground. So I take assorted reading material with me, ranging from papers I need to catch up with over coffee in the early afternoon to Time and Newsweek to browse with beer as the evening draws out, and sit at the bar in the ski lodge, warm and cozy, while K is out having his adventures.

I know what you are thinking. You are saying “Wait a minute, why are you telling me this? And in any case why go at all if you are not going to ski?” The answer to the first question is coming later on in the narrative. So, to the second question first. As with any experience, you relish it fully only when you have somebody to talk to about it. This process allows you to relive the experience when it is still fresh, and you embellish it by magnifying the best parts, fading out the not so good parts, thereby storing this polished version for later access in your long term memory banks. And K is not able to find a suitable skiing buddy. So he drags me along, so that when he takes a break, he will have somebody to narrate his adventures to and so that I can go “Aaha, Oho, Ahaahaa” like in the bru coffee advertisement from a long time ago.

Ok, so what is the problem? The problem is with me saying “Aaha, Oho, Ahaahaa”. As the first two paragraphs of this narrative indicate, clearly I understand the need people have to narrate their experience. Also clearly, by any objective standard, K is adding rapidly to his skill set and hence ought to be admired. But, I find myself not even a little bit interested or awed. So, I asked myself, why is that? And when I think about it, I might use the word “admire” easily, but it is an emotion that I rarely feel. And this leads to me to ask a broader question namely, what is admiration really? And the following is the answer I came up with.

There is no such thing as “objective” admiration. The only way we feel admiration is if we imagine ourselves doing the thing we admire, i.e., the quality or skill has to be part of our “ideal” self image. By way of illustration, let me mention a few mundane things. I know many women who admire other beautiful (or well dressed, well made up if you like) women. But, since beauty is not part of my self image, either real or ideal, it does not evoke the emotion in me. Surprisingly, I admire people who dance well (I am thinking Madhuri or Hrithik or from my real life, some of my friends). Apparently, in my ideal self image, I wish dancing is a skill I possess (I sure as hell don’t in reality)! And the connotation to self image need not be direct, could be subtle. For example, it turns out I admire Jason Bourne (I recently saw Bourne Ultimatum and hence the thought). But is it because I wish I could kick people’s ass? No, it is because that character displays amazing presence of mind, albeit in a physical sense. And I sure as hell have presence of mind high up on my list of virtues. And if the hypothesis in the first line of the previous paragraph is indeed right (and among what data I have, I am not able to come up with a contradiction), then Jealousy and admiration are just a hair’s breadth apart from each other. If I think “Wish I could do that too”, that is admiration and if I think “Wish I could do that instead of him/her”, that is jealousy! Do you think what I am saying here holds water?

Friday, February 1, 2008

On the Torus

What is it ?
In layman’s terms the inner tube of a tire or if you prefer, a doughnut or a vadai. Technically, it is the surface of revolution of a circle about a coplanar axis outside itself (to put that in context, a sphere is a surface of revolution of a circle about one of its diameters, i.e., a coplanar axis through its center).

Why am I talking about it?
I always thought that a torus is a strange object, almost like a mobius strip or something. Mathematically it is a weird compact manifold. And so I imagined that a torus is as likely to occur in nature as a cube. But then, I found out today that certain dumbbell shaped surfactants self assemble into nanoscale tori [1]! Further digging and googling told me something I should have known, that people who make Carbon nanotubes have actually seen Carbon nanorings that form at the same time, that are essentially tori.

What does this mean?
So, the above facts tell us that self assembly can lead to tori. If it is easy to form and stays stable, then more likely than not, we will find it in nature. And indeed we do. They call it (rather unimaginatively) the torovirus.

Goes to show that one has to modify and augment one’s intuition with each new fact learnt!

[1] A Primer on self assembly of surfactants available here.