Monday, June 25, 2007

Amazing Natural Phenomena – Columnar Joints

Columnar joints is the name geologists give to these column like rock formations found in many parts of the world. Apparently, the first one that got talked about a lot was the Giant’s causeway (the first image) somewhere of the coast of northern Ireland. There are apparently a whole bunch of them around the world. The only one I have seen (just yesterday) is the Devil’s postpile (the second image). I as always asked Wikipedia to see what was known about them. As will all natural structures that appear too ordered or too functional to be “natural”, there is a story that people invented to explain their origin. For example, Wikipedia has this story for the Giant’s Causeway

“Legend has it that the Irish giant Fionn mac Cumhaill (Finn McCool) built the causeway to walk to Scotland to fight his Scottish counterpart Benandonner. One version of the legend tells that Finn McCool fell asleep before he got to Scotland. When he did not arrive, the much larger Benandonner crossed the bridge looking for him. To protect Fionn, his wife Oonagh laid a blanket over Fionn and pretended he was actually Fionn's baby son (in a variation, Fionn fled after seeing Benandonner's great bulk, and asked his wife to disguise him as the baby.) In both versions, when Benandonner saw the size of the 'infant', he assumed the alleged father, Fionn, must be gigantic indeed. Therefore, Benandonner fled home in terror, ripping up the Causeway in case he was followed by Fionn. Another variation is that Oonagh painted a rock shaped like a steak and gave it to Benandonner, whilst giving the baby (Fionn) a normal steak. When Benandonner saw that the baby was able to eat it so easily, he ran away, tearing up the causeway...”

Cool huh?! Next question to ask is do we have a physical explanation for how these apparently ubiquitous structures form. Well, volcanologists have been thinking about these for a number of years and a lot is known. The physics as such is too complicated and I don’t understand it well enough to tell you clearly what is going on. But, loosely speaking, the structures are a result of two things. One is the fact that hot lava cools from outside. So, there is a temperature gradient in the material when going from out to inside. This produces a stress instability in the system. The second thing is that ground water is being boiled off by the lava continuously and there is come kind of a capillary effect associated with this. These two things together give rise to the structures we see. If you want to know more, you should go to the webpage of this guy, who is reproducing these structures in his lab using cornstarch and trying to sort out the exact details of the hydrodynamic and elastic instabilities that drive this particular pattern. And even if you are not up to further reading on this, check out this video from Discovery Channel, where the investigator talks about his experiments.
So, even though I still don’t understand the details of what is going on, I went to bed peacefully convinced that there were no giants or giant’s cunning wives required to explain the phenomena :)).

Wednesday, June 20, 2007

Come one come all

Just in case you missed it, there is a comments party on here. Please, don’t feel left out…join in! Let us all strive to give confused the all time record for number of comments to a blog post!

Sunday, June 17, 2007

On Understanding

I promised not to wax philosophical for a while. But I have been having these discussions on Evolution and the role of thermodynamics in cosmology with all manners of people and as a consequence I have realized that many people don’t stop to think what they mean when they say they understand something. So, I want to use this post to address the question “What is understanding?” Let us start with the dictionary definition of the word. Merriam-Webster’s says the following:

Etymology: Middle English, from Old English understandan, from under + standan to stand
transitive verb
1 a : to grasp the meaning of (understand Russian) b : to grasp the reasonableness of (his behavior is hard to understand) c : to have thorough or technical acquaintance with or expertness in the practice of (understand finance) d : to be thoroughly familiar with the character and propensities of (understands children)
2 : to accept as a fact or truth or regard as plausible without utter certainty (understand that he is returning from abroad)
3 : to interpret in one of a number of possible ways
4 : to supply in thought as though expressed ("to be married" is commonly understood after the word engaged)

Well, that does not help much because understanding is a complicated combination of 1a-d. Let me try and explain what I mean. Suppose I know 10 facts. I try to understand these facts by trying to find relationships among them, i.e., look for the one underlying fact, usually called an assumption or faith depending on your taste, from which the ten other facts I know can be derived from purely logic. Now, you can ask, “What is the use of this? Why can’t I just keep the ten facts in my mind?” Well, there are two uses. The first one is that this reduction simplifies the world around us. The second is that it allows for a phenomenon called predictability. If I used my logic correctly to deduce the primary fact from which the other 10 facts are derivable, then I can use the same logic to conclude that 10 other things must be true as well, and these 10 things I did not know when I started this exercise. Then, I watch the world around me for the verification of the ten new things I now think must be true. If they are, then my assumption is right and it becomes a part of my understanding of the world. If they are not, then I take the new set of things that I now know to be true and apply logic again to ask how my assumption must be modified so as to account for all the facts I know at this time.

That concludes my definition of understanding. Now, there are some important things associated with this definition that we need to keep in mind. First, note that in the above sense, understanding is a dynamic thing. It evolves as the number of things we know increases. Also note that this understanding requires an active application of the intellect to sort out the various things we know. The first point above is the reason why it is important to be “open minded” in order to understand, that is, one must be willing at all times to re examine one’s assumptions regarding the world every time a new fact makes itself available to us. Questioning our open mindedness at all times is a prerequisite for understanding

The second point above is associated with a common mistake people make. They confuse familiarity with understanding. You see, there is another way to have predictability in our world. If I drop a ball ten times and every time it falls to the ground instead of going up, by the eleventh time I know it is going to fall down. But this is because I am familiar with this fact, i.e., I have seen it before and remember it, not because I understand it. I did not use my intellect actively to integrate the fact that the ball falls down with other things I know, for example an apparently unrelated one like the fact that the earth revolves around the sun. I am able to predict the outcome only because I have seen it before. I am finding that many people do not distinguish between these two origins of predictability and hence mistake familiarity with something for understanding the same thing. This is a trap we must all be aware of, otherwise we will surely fall into it.

Do you see what I am saying? Do you agree? And, in spite of my choice of examples, this applies to understanding all things, not just the physical world, but society, the mind, or anything else you can think of.

Sunday, June 10, 2007

Random stuff

Being slow on the uptake on most things I did not hear of image macros until recently and the whole LOLcat thing until today. There are a whole bunch of images here. The one below is one that I liked a lot.

Also, I watched Shrek the third and it sucks. I hope this is the last movie out of the franchise as the writers seem to have run out of witty ways to implement their whole anti fairy tale thing. Falstaff has an eloquent rant on this you might want to read.

And just in case you did not read this, here is a hilarious take by J. A. P on the whole MS university, nude art controversy. I went back there yesterday to look at the comment thread and found a statement by J.A.P that resonated with me enough that I will now have to make a post out of it…He said “I'm not an advocate of democracy, really - I believe in benevolent despotism. Preferably mine”. More on that later.

Thursday, June 7, 2007

Free Will

As you might have noticed in the sequence of posts showing up on this blog, I have been thinking about evolution, intelligent design, life, god and consciousness (sounds like a long winded way of saying life universe and everything, doesn’t it?:)). I have come to realize that all these questions are hopelessly entwined and I cannot isolate and formulate any one of these concepts separately at a given time. And every time I try and put them all together in my mind, I find myself carrying out the logical exercise that is called “chasing one’s own tail”. Therefore I have decided to take a break from these thoughts and let them simmer in my subconscious as a manner of speaking.

But before I do that, one final thought. I had said in an earlier post, that the thing that we cannot yet accept and hence bring into the realm of natural science is the fact that our consciousness is nothing but chemistry. But, this is a vague statement and I would like to dwell on this for a moment. Some aspects of our thought process we are readily able to associate with chemistry. For example, the thought that I am hungry or I am sleepy or I like a sunny day or I hate rainy days, I can accept are originating from the chemistry of my body. So, one needs to identify those thoughts in our conscious mind that we under any circumstance cannot believe come from chemistry. If you think about it you will be able to see that those are the thoughts that originate from our free will.

Every hour of every day we find ourselves making choices. And if we examine the choices we make, we find that we cannot always explain it by chemistry (or biology if you prefer) as some of them are clearly the opposite of what chemistry or biology would have made. A simple example would be that I have the ability to starve myself if I chose to. That is my free will. My stomach can tell me it is hungry as much as it wants. But I can always choose not to eat. And this is the aspect of our minds we do not understand. And this lack of understanding is the root of all existential angst that we feel.

Once I had this thought, i.e., our inability to understand the apparent existence of our free will is the root of all of our problems, I also realized that this is not something new I have come up with. All of us already know this. And the best example that demonstrates this is the ubiquitous expression of this thought found in our pop culture. Find below a few instances that came to my mind.

1) The Architect telling Neo, “As you so adequately put, the problem is choice”, in my favorite sci-fi trilogy of all times, The Matrix movies. A clip of this movie is below.

2) Next, Bruce Almighty. Morgan Freeman playing God tells Jim Carrey playing Bruce Nolan that he can do anything, but he cannot mess with free will. A clip from the movie below. (Ok, I should confess. The creator of this clip cut out the part about free will when he made this. But it is 10 minutes of Jim Carrey and he is always fun to watch, so I am embedding it anyway!:))

3) And last but definitely not the least, my all time favorite writer Douglas Adams in his book “Restaurant at the end of the universe” tells us about the intelligent elevators found in the technologically advanced civilization in the Sirius star system.

“Modern elevators are strange and complex entities. The ancient electric winch and “maximum-capacity-eight-persons” jobs bear as much relation to a Sirius Cybernetics Happy Vertical People Transporter as a packet of mixed nuts does to the entire west wing of the Sirian State Mental Hospital.

This is because they operate on the curious principle of “defocused temporal perception”. In other words they have the capacity to see dimly into the immediate future, which enables the elevator to be on the right floor to pick you up even before you knew you wanted it, thus eliminating all the tedious chatting, relaxing and making friends that people wee previously forced to do while waiting for elevators.

Not unnaturally, many elevators imbued with intelligence and precognition became terribly frustrated with the mindless business of going up and down, up and down, experimented briefly with the notion of going sideways, as a sort of existential protest, demanded participation in the decision-making process and finally took to squatting in basements sulking.

An impoverished hitchhiker visiting any planets in the Sirius star system these days can pick up easy money working as counselor for neurotic elevators.”

Ok, that is it for all this deep stuff (I wanted to say s*$@#, but my mom brought me up well:)). I am now going to spend what time I have in the next two weeks catching up on my movie watching. Spiderman 3, Pirates of the Caribbean 3 and Shrek 3.

Monday, June 4, 2007

On Micelles, Vesicles and Artificial Cells

-The magic of directed self assembly

This post is a collection of thoughts on the principles of entropy, energy and equilibrium expressed in the context of self assembly of surfactant molecules [1]. Let us begin by asking what a surfactant is. For the purposes at hand, a surfactant is a molecule with a small head that likes water and a long tail that hates water as shown in the cartoon alongside. What “loves” means in the following is that the entity can lower its energy by being in contact with water and what “hates” means is that it costs the system a lot of energy when it is in contact with water [2]. Now, we put a bunch of these surfactant molecules in water and allow them to come to “equilibrium”. What do they do?

To understand this question, we have to first clarify what a system will like to do. The equilibrium state of the system will be one where it can do the maximum number of things it likes. The first thing the system likes to do is lower its energy as much as it can. On the other hand, the system likes to have as much disorder as possible, technically speaking, “maximize its entropy”. If I call the energy of the system E and the entropy of the system S, then the system likes to have a minimum value for the quantity F = E – TS, and this is called the free energy of the system. Don’t let this little jargon scare you. What follows is simple enough even if you don’t remember this. Also, before we can guess what the system will like to do, we need to know one more thing about the surfactant molecules. If two surfactant molecules come close to each other, what would they do? The tails of these molecules are such that they are happiest when they are as close to each other as they can get, for they lower their energy by reducing their interaction with water and increase their entropy as well [3]. The heads of these molecules are such that they want to stay as far away from each other, because these heads are usually charged and like charges repel right? So they lower their energy by staying away from each other.

With that, we have all the ingredients we need to answer the question we asked. It is now all about a competition between love and hate. Suppose the heads love water way more than the tails hate it. Then the equilibrium state of the system will be a solution of the surfactant molecules in water, with all the molecules well separated from each other and doing their own thing [4]. Next, suppose the circumstances are that the hate of the tail wins. Also, suppose that the heads are wide objects so that the overall shape of the surfactant molecule is a cone (see figure). Then, the molecules are happiest when they form micelles. Micelles are objects that are spheres, with the polar heads outside near the water and the tails inside, talking only to each other and protected from the water by the polar heads. Note that, in order to form micelles, you need a given amount of surfactant in the water (If you have fewer surfactant molecules, entropy wins and they stay in the form of the solution). The everyday situation under which micelles are formed is when you wash your clothes with soap. The dirt on the clothes form nucleating centers for the micelles and the micelle itself being water soluble, dissolves in the water when you rinse your clothes.

The more interesting case is when the heads are not fat, i.e., the surfactant molecule is a cylinder rather than a cone (see figure) and still the hate of the tails wins. In this case, the system forms what are called “lipid bilayers”. This is just two layers of surfactant molecules assembled such that the tails of each layer face each other (effectively, it is like having a layer of oil trapped between two layers of polar heads). Now, in this structure, the tails in the middle are clearly happy for all their neighbors are fellow hydrocarbons. But, just as clearly, the tails at the edge of the structure are unhappy because they have to talk to the surrounding water. One way to eliminate this is for this bilayer to fold on itself to form a spherical shell (see figure, which displays a cross section of such a structure). This way, there is no surface of tails talking to the water. But the trade off comes at the cost of forcing the heads in the inner layer to be more close to each other than they like. But, if the hate of the tails for water is large enough, this happens and the resulting stable structure is now a vesicle!

The interesting things to note here are twofold. One, in spite of the language I am using, in the actual experiment, all I did was take a spoonful of surfactant molecules and put it in water. All the structures mentioned above self assembled! I did not have to do a thing. The second thing to note is that, the above vesicle is essentially a minimal cell membrane, the first step towards the process that converts an auto catalytic chemical reaction into what we call now as life!

So, if we can make this membrane functional, namely, make sure that the chemical machinery required for life is trapped inside the vesicle, make appropriate “holes” so the membrane is suitably permeable (i.e., it lets some stuff in (raw material for making food) and some other stuff out (waste products) and not vice versa), we would have made an artificial cell! Some first steps in this direction have already been taken. See for example, this PNAS article reporting the use of “directed self assembly” to make a bio reactor, which is to say it is not quite a cell yet, and this article entitled “Towards an artificial cell based on gene expression in vesicles” . We are not very far from making what can only be termed as artificial life, in a physics lab, in a test tube. And the reason I started thinking along these lines was to be able to ask the question – “Intelligent design anyone??” :) [5].

Caveats and disclaimers

[1] The aim is to try and keep things simple, focusing on the primary ideas and suppressing all but the bare essentials in terms of details and subtleties.

[2] The jargon is that the head of a surfactant molecule is a polar group like sodium sulfate and hence this ionizes in water and hence is hydrophilic. The tail is a covalently bonded hydrocarbon polymer and hence hates the high dielectric constant medium of water and is hydrophobic.

[3] The entropy of a polymer would be given by the number of configurations they have. They can fluctuate better and sample their accessible phase space better in the lypophilic environment of other tails, than in water, where any fluctuation will result in an energy cost.

[4] It is clearly an oversimplification. The question is truly one of entropy versus energy. So, this will be a strong function of the concentration of the surfactant and the temperature of the water. At low enough concentrations or high enough temperature this will always be the default state with no possibility of self assembled structures.

[5] This is actually a frivolous statement. The stumbling block that people have to overcome is the complexity of a real biological membrane, which has embedded proteins and is active and what not. But from a physicist’s point of view, it is but self assembly, but takes a lot of time. I say this in spite of the fact that from what knowledge we have of the primordial soup and pre-life conditions on earth, there appear to have been singular events that precipitated the emergence of life in nature and we do not know either way, the probability of such singular events occurring from random initial conditions.

Friday, June 1, 2007

Ode to the unknown reader

As I had said in an earlier post, I have not been here, in the blog sphere very long. So I don’t know anything about anything and am too lazy to educate myself. But, as a matter of routine I had created accounts on a couple of the free web stats services out there. And then promptly forgot about them. Yesterday, I was badly stuck on something and needed to kill some time to allow my subconscious to mull over my confusion (that is my excuse for browsing instead of working while in my office :)) So, I went to these websites to look at the stats for this blog. Now, my lack of knowledge on how these stats are acquired prevents me from really understanding what they mean (for example, if somebody reads me through their feed reader, as some of you do, how would this show up in the sitemeter stats?). But to the extent that I do understand them, it appears that I have more readers than I know of!

Everybody knows that we see things not as they are, but rather as we are. So, my model blog sphere inhabitant is based on me. And when I read someone’s post all the way through and like what I read, 9 out of 10 times, I leave a comment, even when I don’t have anything intelligent to contribute to the topic being discussed in the post. The exceptions to this being if the blog writer is one of the more famous ones like my reptile object of admiration Sunil or the master of logic with a really erudite audience (going by his comment threads) Falstaff just to name a couple, or there are already a number of comments to the post in question and I don’t wish to add to the already redundant thread. So, I assumed that this was true for everybody else as well.

But that is surely not the case according to my stats. For example, I appear to have a couple of regular readers from my alma mater, the school that is the defending NCAA football AND basketball champs this year. And I don’t think I know who they are! And another surprise I found was that people stumbled on some of the posts from google searches! It is a surprise in two ways, one, just the fact that a page shows up within the first few results of any search at all and the second, the reader actually spent five minutes on the page they landed!

I guess that just as in real life, not a day goes by without learning something new and hence finding one more piece of a puzzle that is just beginning to take shape. Anyways, just wish to say thank you for reading. One needs at least an illusion of an audience to force oneself to think clearly and if they have a real one, all the better!