Friday, December 21, 2007

Confessions and other things

a) I ran away from the department yesterday ridiculously early so as to avoid running into my paymaster and having to explain to him why he still has not got the first draft of a paper we are writing together.

b) The reason I am not able to write the paper is because I have a “Yeah, so what?” reaction to the results in the paper. He is excited about them though.

c) This tells me that I am unable to get excited by inherently non-mechanistic theories (the ones where the mathematics does not really reveal why something is happening and you have to answer the why part with words). This is a very disturbing revelation for a theoretical physicist primarily interested in emergent phenomena.

d) I got a new comment on my post on elastomers at SC. To be able to respond to the comment, I reread the post as I had forgotten what I had said in it. I realized I like rereading what I have written. So I went and read “the hugely popular for mysterious reasons “Micelles and Vesicles post””. Is this normal? To like rereading one’s own posts?

e) Also, blogging break coming up. Going to NYC for a few days of what is hoped will be fun.

And on a completely different note, I came across this “gives you unjustifiable patriotic goose bumps” video from Lead India. Also gives me an opportunity to test iShare (trying to be the youtube of India?) Do complain if it does not work here or in your feedreader so I will know if there are problems.

[via]

Monday, December 17, 2007

Dark Energy again

A short while ago I said a little something about dark energy over at the SC blog. Today I discovered this at the hubblesite. I did not like it too much, but it has more info than my post did on some aspects, but less info on others. Further reading available here as well. Also, Cosmic Variance has something to say on the presentation here.

Sunday, December 16, 2007

Jai Hind

Even I begin to feel a little patriotic when I see these BharatBala videos…[via]


You can watch a whole bunch of their videos here (requires you to register though).

Wednesday, December 12, 2007

Random stuff 5

I spent part of this weekend watching Quentin Tarantino's grind house flicks (not by choice, I assure you), involving flying off of appendages, cutting off of unmentionables, smashing of faces and lots of squirting of blood and goo. So this post on Death and Tombstones did not put me off at all. I thought it was a cute compilation (I know, I am crazy, but you get numb beyond a point).

On a different note, have you seen these new videos from Delta airlines? People appear to like Kidtastrophe best. Here is my favorite though…I am always praying just like the couple in this one, for exactly the same miracle especially on my semi annual transatlantic flights.

And this last video, music video, “12 days of Christmas” by boymongoose I am sure you have already seen. But for some reason I am not able to get the song out of my head since I heard it! I have no idea why.

Monday, December 10, 2007

The second law

A while back, I had written this post on irreversibility. But I was just talking text book thermodynamics and stat mech. Here, Sean Carroll is putting the arrow of time in a cosmological perspective. Do check it out. Also, while you are at it, stop by SC and read my post on elastomers and tell me what you think.

Friday, December 7, 2007

Biochemistry of booze

Just came across this. It is a cool little applet that tells you the biochemistry of various drugs. Does not sound bad at all. So my question now is…why is this stuff bad for us exactly?

Wednesday, December 5, 2007

Winter is here

That is me in front of my department just now...darth wader no less.

Tuesday, December 4, 2007

The blue-white divide?

I was out having beer with some of the grad students in the department. We were talking about this and that and in the course of it I realized that the guy I was talking to, a second year grad student, was actually older than I was. When I asked him about it, he said he had worked as a car mechanic for a few years out of high school before he decided to go to college. That reminded me of the fact that this was in no way unique. In my grad class, I had friends that had been furniture movers, construction workers and picture framers before they decided to go to college or go back to college as was the case with a couple of these guys. And the one striking thing about this is that not one of the dudes in question was desi, they were Korean, Chinese, American or European in each case. I mean, in India, the blue-collar white-collar divide is complete is n’t it? The only case of older desi grad students we come across are usually people that took an unambiguously white-collar job right out of college and then changed their mind for some reason or the other and came back to school. Strange.

Wednesday, November 28, 2007

Random funny things

Did you check out Krish Ashok’s inverse square law of taxi fares yet? Do take a look…I associate his factor S with service and attention given by wait-staff in an Indian Restaurant in the US!

And for those of you that have not seen Om Shanti Om either because you lacked the time/opportunity, or made a conscious intellectual choice to avoid “junk” of that kind, please do check out Akshay Kumar in “The Return of Khiladi”. You might loose a synapse or two in your brain because of watching it, but it will be compensated by the aerobic exercise of rolling on the floor laughing!

And finally, here is the ICL ad for the Chennai superstars? I know, it is all over the internet, but it is too…funny I think (I so hate the pink we have been stuck with, it dampens my enthusiasm some)….for me to pass up ot it.

Tuesday, November 27, 2007

Changing Chennai

No, no, I am not trying to change Chennai, I am saying it is changing. Apparently there are people in madras that crave waffles for breakfast and there seem to be a whole bunch of places you can get those too. And the linked post mentions so many meats... if I had still been living in Madras, I sure as hell would not know the difference between salami and sausage! Terrible or wonderful? Yet to make up my mind. (dyed in the wool tam-brahminism preventing me from making the "right" choice, i.e., wonderful...the baggage of conditioning dammit!:))

Theory of Everything?

First I saw this. Then, I went to the physics archive, the democratic forum where anyone can post and found this. I printed it, skimmed it and formed a minimal impression (to the effect that it is a good idea but ways to go before it can be a theory of everything). But, I am not well versed in the relevant jargon, so I need to spend some time and talk to people who are well versed (and that is the advantage of being in a physics department, all kind of help is just a stroll down the corridor away!) before I can tell you about it. But, in the mean time do go and check out this post, and scroll through the comment thread, we have Garret Lisi in there trying to explain this stuff himself.

PS: The pretty picture is the polytope with E8 symmetry, the group that has that nice property that the fuss is all about. I know, I know, I just put it in because it is pretty :)

Thursday, November 22, 2007

Happy Birthday!

To cc (my blog persona) and the Curiosity Shop. We have been in existence for a year and we had fun! When I started blogging, I said “I don't know why I am doing this”. I still don’t. But it has turned out to be a lot of fun. In the year that was, I have made friends and foes, I have laughed and cried, even awarded titles and been asked to “kneel down and beg forgiveness”, pretty much the whole spectrum you would go through if you had a real life (I clearly don’t).

And I found one side benefit. The blog has become a compendium of odds and ends that catch my attention (not comprehensive though, for, whole months went by when I noticed things and thought about them but did not blog about them). For example, the other day, I was looking for a Scientific American article on creationism I had read a while back to revisit something. I did what I always do, go to the filing cabinet and reach for the folder “This and that: Colloquium”. It was not there. This usually means I was reading the said paper in a plane or a train and did not bring it back. Under normal circumstances, the next step would have been to google. But now, I have a blog and I know I said something about it here and so I went to the Shop and looked and there it was! So, just for that reason, the Shop should become a more complete and better organized filing cabinet for the junk in my head!

Anyways, thank you to my readers who stop by here to say things to me and help me keep up the necessary illusion that other people read this stuff as well. Now wish me well for the future (most of you are my seniors in the blog world, right? So this is asking for “aashirwaad”). And do come back to read some more.

Tuesday, November 20, 2007

Ideas and such

This past week, I have been watching a TED video a day to keep boredom away. Just thought will share some of them with you. But, if you have not seen them already, be warned, each video is 20 minutes long. It is totally worth the 20 minutes, so only click on it if you have the time.

1) Larry Lessig : This is the Creative Commons License guy. I only know of him slightly, due to press surrounding the Microsoft law suit and he is not saying anything that gives me goose bumps. But his talk is, for me, representative of how to build an argument using analogies. Fantastic, for just that one reason.

2) Dan Dennett: In his talk, he is essentially making the point that “ideas” take the role of genes in social evolution. We know this. But he articulates this beautifully. And towards the end, he says things that did give me goose bumps.

3) Richard Dawkins: We all know this guy. Who has not read the Selfish Gene right? In this talk he talks about the fact that our so called “intuition” is evolutionary conditioning associated with the length and time scales we are able to probe with our senses (a point I had made earlier in a different context), and this is the reason we find fundamental physics on small scales and large scales counterintuitive. But he does this beautifully, or at least I thought so, because it resonated with the thoughts in my head.

Friday, November 16, 2007

Terrible stuff…

I just saw this…it upsets me, to the extent that I am not able to articulate what I want to say just now.

Never thought of it…

“Fairness" is often described in terms of equality of outcomes. But in a game, the “fairest” rules are often those that make the ablest players mostly likely to win, instead of those that distribute wins most evenly among players.

Even outside of games, a wide range of otherwise puzzling common intuitions about fairness can be understood if the fundamental "game" of life is seen as wooing, i.e., attracting mates by showing that you have fit genes. The fairest social institutions are then those in which success correlates as much as possible with genetic fitness.

For example, it can seem fair that the most attractive witty athletic folks get more mates and money, but seem unfair that the rich can buy better education for their children. Makeup can seem fair, while breast implants seem unfair.

Totally cool essay…some of the logic as applied to policy implications I am unable to buy just yet, but still…

Link [via]

Wednesday, November 14, 2007

Random stuff again

I pissed off more than my normal share of people today, among them, one of my paymasters. Foot constantly in my mouth kind of day. So, I thought I will take refuge in my feed reader (which contains now even the feed from the physics archive) and came across the following video on SepiaMutiny. If anybody says Shah Rukh Khan cannot act, they should take a look at this, where he says some outrageous things with a straight face!

Wednesday, November 7, 2007

Journal club – Immunization and terrorists

I was whiling away some time yesterday when I read this paper [1]. What the paper is about is “effective immunization strategy for scale free networks”. First let me tell you what each of these words mean. If you already know or are not interested, skip to the last two paragraphs.

What is a network? It is a collection of points (nodes) that are connected to each other in some way (links), so that you can get from one point to another though some path along these links. What are the real world systems a network can represent ? The Internet (each computer is a node and each hard wired connection is a link), the world wide web (each website is a node and each link is a link…), social networks of people, biological networks of chemical reactions, epidemiological networks that map out how a disease spreads through a social network of people in physical contact and so on and so forth. In fact, I think there is a subset of mathematicians and physicists who would have you believe that any problem in the world that is worth solving is actually reducible to a question about some property of some network!

What is immunization? It is exactly the same as in English. I give a vaccine to a node (person) so that it cannot be infected by a disease and hence cannot spread it. What is an immunization strategy? Given a network that you do not know much about (only the fact that it is a network) what scheme should I use to immunize nodes so that with least possible immunization I can guarantee that I will not have an epidemic?

And finally, what is a scale free network? You can find some info here, but in my mind, when somebody says scale free network, I imagine airports as nodes and flights that emanate from them as links. Supposing I draw this, it looks like the image alongside [2]. The first thing you notice is that there are hubs. Suppose you close your eyes and pick one point on the network, like as not, that point will be connected to one other point and that point will be a hub, i.e., connected to a whole bunch of other points. You can do this exercise in your mind with airports if you like and you will see the same thing. Mathematically, such networks turn out to have some nice properties, but for the purpose at hand let us leave it at that.

Alright, so much for preliminaries. What is this paper about? Well, it turns out that if you used a “random immunization” strategy, i.e., if you randomly chose a fraction of people that are connected by such a network and immunized them and asked “Is my population now protected from an epidemic?”, you find that you basically have to immunize everybody before you can be sure there is no epidemic. So this is no good as a strategy. So, what is a better strategy? The authors of this paper say that instead of randomly picking people and immunizing them, you do the following. You randomly pick a person, then randomly pick one of his/her acquaintances (a node that is linked to the node you picked) and immunize them instead. In this way, your network becomes protected from epidemics way sooner. This is their primary result [3].

Now if you think about it, it is easy to see why this is true in scale free networks, again using the airports analogy from earlier. Suppose I wanted to shut down air traffic in the USA. I have a list of airports. The way I want to accomplish my mission is by randomly picking airports to shut down. Now suppose I randomly picked an airport and shut down the airport that I picked, it will take me forever to do this for I will choose the hubs with the same probability as I would choose the hundreds of other itty-bitty airports around. Instead if I said I will pick an airport at random and shut down one of the airports it is connected to, I am way more likely to shut down hubs than in my first route. And hence the strategy described in this paper is indeed better for scale free networks.

But what made this paper priceless in terms of amusement obtained for the time spent was the following sentence…”As a final remark, we note that our approach may be relevant to other networks, such as ecological networks of predator prey [32,33], metabolic networks [34], networks of cellular proteins [35], and terrorist networks. For terrorist networks, our findings suggest that an efficient way to disintegrate the network is to focus more on removing individuals whose name is obtained from another member of the network.” Homeland security…are you listening?

Caveats and Disclaimers

[1] I know squat about networks theory, so if you are an expert, correct me and if you are not, do not trust me entirely.

[2] It is actually an image of stock trades in the new york stock exchange stolen from here…thanks to google’s image search, but same difference.

[3] As far as the mathematics go, there are other assumptions in here…the network must a) have a tree structure, b) be undirected, c) uncorrelated, d) unweighted. But for the resolution I have of such things…same difference.

Tuesday, November 6, 2007

Politics of the blogsphere?

Apparently people either love Amit Varma or just plain hate him…strange. No wonder comments are off on his numero uno blog. As I said, strange…

Monday, November 5, 2007

Hindus and Atheism

Patrix got me thinking this morning when I read this post on his blog. Rather than take up his comment space, as I will probably end up being verbose and not clear at all, I thought I will express the thoughts that came flooding into my head here. The question that started this flood of thoughts was “Are Hindus more likely to be Atheists?” And the first sound in my head is a resounding and joyous “YES”! Now why is that? Let me try and explain.

First, some caveats. This is a theoretical physicist’s answer in the sense that it is correct in the context of the ideal system and may not be valid in the more complex real world. The reason I need this “ideal system” assumption is that Hinduism is really a social construct rather than a religion. And the society is complicated. The simplifying assumption I am making here is that I am visualizing a Hindu society where there is no caste. Caste is just a designation of your profession and comes with no associated mental stigma or physical discrimination.

Given all that, why do I think Hindus are more likely to become atheist? To understand this, I need to first say what an atheist is. Conventionally, an atheist is thought to be a person who says “there is no god”. This is not quite right in my mind. It should really be a person that says “I have no god”, in exactly the same tone of voice as one would say “I have no washing machine”. Hinduism has this freedom inherently built in. In the Hindu environment, gods come in all colors and flavors. There is the “goody-goody” Rama, there is the incorrigible flirt and master of cunning, Krishna, the manifestation of wrath and lust, Shiva and so on and so forth. This allows a mindset that necessarily separates the “religious” aspects as those associated with fables and the “social” aspect that is associated with conformity, morals ethics and so on. And the “spiritual” aspect of this religion is inherently personal, in that, rightly, there is no given path, there are guidelines to choose possible paths but that is it. All this makes it an easy step up to do away with the religious aspect altogether in our minds. Thank God for the absence of “Jesus this and Jesus that” to quote lieutenant Dan from Forrest Gump!

Do you think you agree?

Guruvaayoor

I just saw this (via India Uncut). I did not know that they allowed women in in Salwar Kameez there. The last time I went there (12 years ago perhaps?), women had to be in Sarees or long skirts (the south Indian kind) and men had to be in Dhothis. I remember distinctly because my brother and a cousin usually wore short pants and had to buy dhotis in Guruvayoor just for the occasion and they were so pissed. I also remember thinking at the time that the required attire seems to be for the purpose of guraranteeing quick access for excretory purposes…Now, I am inclined to think more dirty things…

Thursday, November 1, 2007

Ode to my darling

I love you. We had a good thing going. But you know I had to give you up. Had to move on ....It hurts me to do this, but I must. Surely, I will remember our time together with fondness.

In case you are wondering, I was talking to my jeans, my jeans of 6 and a half years that I had to retire from active service this past month. We were together almost everyday during that time. The only exceptions were days with weddings, funerals and thesis defense occurring during their course and hot summer days in Florida spent close to some water body and far away from air-conditioners (the Atlantic Ocean, the Gulf of Mexico, Lake Wauberg, Ichetucknee river etc). As you can imagine, these were few and far between.

This pair of jeans was not the first one I ever had. But this is the first time I am bidding an emotional farewell to one. Now, why is that? It is because this is my “grad student jeans”. Before this, I had had a pair in high school and a pair in college. But then, it was not the same thing. In India, I had really cheap ones that I would now not call jeans at all, I wore them infrequently and then committed what I would now consider a crime of sorts, I washed and ironed them between wears! How na├»ve I was then!

And then, one day I went to grad school. I discovered that I had no time to do laundry. That was now designated a once in three weeks or even once in a month activity that you undertook only when your entire closet was in your hamper and you had no choice but to do it. I discovered that jeans are extraordinarily comfortable things if you just “broke them in”, something which takes you a week of wearing everyday to achieve, after every wash. And so I got hooked, to the pleasure of living in my pair of unwashed jeans. Once you discover this pleasure, you feel awkward wearing anything else. That is the beginning of the bonding. If you have felt it, you know what I am talking about.

And so I wore my jeans day in and day out. It began to fray in various places. This did not bother me. It almost completely lost color in parts. I did not even notice. A belt loop broke. I ran all the way to Ada’s tailoring the day this happened, paid what must have been close to 50% of the jeans’ original price and got it fixed. It was a given in my life that otherwise consists of what is known as the “Apartment, Department, Advisor, Budweiser” Routine. My jeans, my darling jeans.

And then, one day, a couple of months ago, it tore open right above the knee where the cloth had been worn down to mere threads. I was depressed. A deep inexpressible fear caused my stomach to knot up. But, I decided to set this aside. I continued to wear it torn, and planned to get the hole darned before winter came and I could not wear pants with a hole it. And I got it darned the first day I landed in India. And felt so good wearing it after more than a week’s hiatus (I could not wear torn jeans during the previous week for I was traveling for work in Europe, and Europeans tend to frown if you show up to give your seminar in torn jeans).

I thought all was well. I would go back to New York State without worrying about me getting cold in my torn jeans. I was happy. But then, the next day I squatted down on the floor to get something out of my back pack. And “trrrrrrrrrrrrr”. The death knell sounded. The jeans tore open right above where I had gotten it darned. The problem was that there was no cloth, just threads in the vicinity of the first hole, so the darning threads had nothing to hold on to. My heart broke just then, for I realized that our time together had come to an end. I HAD TO GIVE MY JEANS UP! A part of my world came to an end then. I was inconsolable for a time.

Of course, as with all things, time heals and I have moved on now. I have broken in my new pair, a Levi’s that fits like heaven even now…I can only imagine how well it will fit once we get acquainted to each other. It has been on me for two and a half weeks now. I am steeling myself to subjecting it to a first wash this weekend, as it is still reeking blue on my white sock when I walk through the rain. So, I am able to look back on my first love with nostalgia instead of pain and I hope it rests in peace in my mother’s closet where I left it with the promise of wenting my wrath on anyone responsible for trying to throw it away. And wish me luck with my new relationship that I hope lasts at least as long as my first one.

Tuesday, October 30, 2007

Can it get more WTF ?

Apparently Dumbledore is gay. If I had heard just that, I would have said, “OK, whatever” and forgotten about this, but then I read this. And so I have to go…WTF?

Tuesday, October 23, 2007

Back at the desk

After almost a month of traveling and almost a month before that of nearly complete chaos, I am back at my desk for what I hope is an uninterrupted stint of atleast a few months (the next anticipated travel and craziness as things stand now is in March). I had fun. Paris was hectic and might as well have been in the States or anywhere else in the world for all the Parisian things I got to do. Spain was fun. It was hectic there too, but atleast I got to do a few things, like eat the world’s best chocolate cake at Habanita’s, a little natural foods eatery in Sevilla, while having interesting conversations with old friends and some new ones as well. And then I went home. To Madras Nalla Madras.

I went back with apprehension. The place must have changed, I clearly have changed. Will I still have the euphoric sensation I used to have in days past whenever I had been away for any stretch (short trips of a week or so when I was a kid to a few months at a time when I was in college) and I saw the first signpost, either on the road or on the train station, proclaiming I was in Madras? You know what? I did! And it was not an illusion in that the subsequent two weeks I had so much fun and fitted right in!

Lots of things have changed. I was completely unable to make my way around madras, what with all the roads being one-way now and most right turns that used to be there eliminated. My only consolation was that my dad and almost every autowallah I talked to said they had the same problem as the whole system was apparently still dynamic and evolving! The former cool places have now moved to second rung with other new places taking the forefront. An instance of the magnitude of change is the picture here of the Madras Bangalore highway, where the toll booths are now open and only a few miles of the road is still “under construction” and they appear to be actually constructing in the said patches.

Did a lot of traveling as well, so as to reintroduce myself to the theoretical physics community in India to facilitate the job search that must start shortly. Even if I wished for it and I have not decided if I do or do not yet, I cannot stay a post doc for ever, can I? And Tangled, sorry I did not get to meet you in B’lore. I was only there for about 48 hours and two seminars I had to give and family took up every minute of it.

That’s it then. I am assiduously weeding through my feed reader to get caught up on what all of you guys have been talking about. I am down to 600 something posts now. Will be back to normal on all fronts in a week or so I hope and “pray”! :))

Thursday, October 4, 2007

Travel Snapshots 1

Air India : In spite of accumulating a very large number of transatlantic miles over the years, this was my first time flying Air India. Have not been able to make up my mind whether better food and more leg room is fair trade for the stewardesses treating you like ill behaved school children on a picnic.

South of spain : Beautiful! I had forgotten how much I liked Sevilla. Too much work and hence too little site seeing, but just walking around the crowded town was fun enough. And the town has changed some, and become cleaner and prettier. I like it better, even though you will be hard pressed to find a local that agrees with me.

Madras airport : Super cool! Much nicer immigration hall, and every phone, escalator and restroom I saw were in good shape. I was impressed. But I still had people cutting me in the lines, so that has not changed.

Food on the streets of Madras: American Sweet Corn at every corner, restaurants serving burgers and fish and chips and lasagna! Not that I ate any of this, I just saw them. The last time I was here, these were expensive places for the few, but now they are everywhere and only about as expensive as the 50 Rs cups of coffee everybody appears to be drinking here!

TV: Bol, India Bol…the catch line for the reliance mobile ad, my man ARR in the Airtel ad, the former MP getting the death sentence leading the news, the story about the bad wheat in the PDS on IBN, T.I.M.E Now dwelling on the Snehashish Ganguly story (with oh so many WTF comments)

Simple Pleasures so far : The Hindu and coffee at 6 am. Pani poori, uthappam, home cooked food I did not make.
Ok ...off to watch India vs Australia to the sound of hindi commentry on DD now.

Am back!

I have been gone so long from this world, I don’t know where to start my “re-entry program”! So, I will just begin what I hope will be a sequence of travel posts till I am back in New York and then resume more serious blogging/catching up. Let us see how this goes.

Wednesday, August 29, 2007

Busy busy busy

I am back here after a long time. My feed reader says I have 450 unread posts. So I think I am just going to go ahead and mark everything as read and try to start afresh. And in the real world, I have been traveling. The most interesting of my many trips turned out to be the one to Ottawa. For example, I was walking around downtown Ottawa practicing my favorite hobby, people watching, when an old man walks up to me and says “Gandhi has been assassinated!” as if that is the hottest news of the day. Turns out he was drunk and slightly crazy. We took the conversation from there and went on to other things like how many engineers India produces every year and so on till I walked him home. I did not find out his name or what he had done for a living when he was younger and he did not ask me anything either, but we talked all the way to his house as if we were long lost buddies or something! So, this gives me one more data point in the “Canadians are crazy” experiment.

Also, in the midst of all this, my dad popped up in the US of A and I had to go visit him as well. And more traveling coming up, Paris, Sevilla, Madras, Bangalore, Bombay and then back. So I am not sure if I will be able to blog or read your blogs until all of this craziness is done with. And just in case BaL stops by here, I am drafting a new post for SC that is about the physics of flocking behavior in animals and fish, but again, that keeps getting pushed down my list of things to do to make room for the more work-related things that keep popping up. Hope everyone is doing well and having fun!

Thursday, August 9, 2007

Where does the day go?

I have so much "unaccounted for" time this past couple of weeks, it makes me question my sanity at times. If I think about it, I have not done anything too bad except sleep eight or nine hours when I can most certainly not afford it. But I am way behind on my various projects and have a ton of travel coming up starting next week, one cannot help but wonder if I am going to survive. Anyways, the bottom line is I don't have a coherent thought in my head to share with anyone. So I am just going to say I have my first post up at scientific curiousity about rainbows that I suggest you go and read and leave a comment to tell me if I made sense and if I did not, ask me about it.

And here is a "musical genius" named Erik Mongrain for your entertainment (the words within quotes are for you bhup).



More coherent thoughts later.

Sunday, July 29, 2007

On Weddings

Yesterday, I went to the wedding of a friend and colleague. They had a cute little civic ceremony. The girl here is the theoretical physicist. The guy is a farmer. A real one, with his own orchard and fruit shop and tractor and everything. The ceremony was set in their orchard. The parents of the bride and groom spoke. Then the bride and the groom sang a song together. Then, they tossed a coin to decide who should say the wows first. The girl won the toss. They exchanged wows, a judge that was hanging around in the background in his robe, pronounced them husband and wife and said “You may now kiss the bride again” (for they had been hugging and kissing all through the ceremony so far, no pretence of virginal purity or any such hypocrisy any where in sight), and they got onto the tractor of the groom and drove away. Cool, huh?

And as always this got me thinking about Indian wedding ceremonies I have been to. I have only been to south Indian tam-bram weddings. And I haven’t been to one in a while as I had decided that I will not go to these “extended-family-no-alcohol-parties” unless I was friends with the bride or the groom and most of my friends got married at inconvenient times and in inconvenient places (in India when I was not able to travel for example). But of course I have distinct memories of the many weddings I went to before I left home for college. And I had an advantage, in that I sat through the ceremonial part of the wedding with my great-granddad, who explained to me the significance of the various aspects of the wedding. But again, his explanation always had a religious tilt to them and over the years I have come to associate social or sociological rationalizations to them as well.

As a consequence, I have categorized the bits and pieces of the ceremony into the adult and the child parts. For example, the “oonjal”, where the bride and groom sit on a swing and are rocked and fed sweet things and sung to, or when the they have the “nalangu”, which are essentially slapstick games of breaking stuff on each other and throwing things and being carried on the shoulder of relatives to see who can be lifted higher must all clearly belong to the “child” category, included to make 8 or 10 year old kids that used to be the bride and groom once upon a time comfortable with the whole process. Then there are the really cute things that broadly belong in the adult category, like the woman following the man when he takes her hand to signify her support for him, or the “ammi mithikkardhu” part, when the man takes the woman’s feet in his hands and puts on the “metti”, to say I am your slave as much as you are mine. If you are not able to see the cuteness, imagine it in the context of 16 year olds in love for the first time.

But in today’s day and age, when 30-somethings are the ones getting married, all of this takes a rather ridiculous bent, doesn’t it? I wonder if our ceremonial weddings have evolved to better fit the social context today. Do you know? And if they haven’t then here is to hoping that they will in very short order!

Sunday, July 22, 2007

Random stuff 2

I woke up early this morning to do some work. The work entailed going through the revised version of a paper I wrote that a collaborator sent back to me. And I got depressed. The paper is unrecognizable now as something I wrote and am not sure what to do about it. So I took the escapist route out, namely take a break and do other things. So I went to my feed reader to get caught up on my blog reading. On Born a Libran’s blog, in his response to a tag that is inspired by a sound of music song, I found the following cool videos. Could not resist embedding them here.

The first one is Toyota ad with the one and only Aamir.

The second one must qualify as the weirdest commercial I have seen in recent times.

And yesterday afternoon when I was similarly depressed about something else (another paper that I am writing and having the hardest time finding the right words) I decided to cook while watching some TV. So I made what must surely be the world’s best “Keeria Saambar” while watching Pulp Fiction on TV (with all the f*@#’s bleeped out of course). And so now I have a question for any fellow fans of the movie that stumble here. Do you remember the OD scene when they revive Mia? After the scene (which is in the video below), Mia tells Vincent the Ketchup Joke (not in the video). What is the point of the Joke here?

Hope you all had a better weekend than I did. More coherent posts later.

Friday, July 20, 2007

Biomechanics – Cool stuff!

The physics posts that have shown up until now on this blog have been on boring things (albeit, close to my heart boring things) such as the second law and equilibrium self assembly. So, I have been thinking for a while now that I should write something on a cooler topic, even though I might know a lot less about it. The topic kind of chose itself this last week when my idle reading on collective intelligence (more on that in a subsequent post) took an interesting tangent.

The tangent is Biomechanics. As a discipline, in the broadest terms, this is a quest to understand the locomotion of living things. Of course, this quest can be addressed at many levels. But for the purposes of this post, we are going to restrict ourselves to the following question. Clearly, living things have lots of stuff on their mind (read neural control circuit) apart from locomotion. So, they have evolved in such a way that they must have a minimal feedback-limited control circuit that governs locomotion. If we could figure out what this minimal model is, we could apply it to robotics and hence be able to design robots that walk easily and hence have room left in them to build in other functions. Why would we want to do that? A standing example could be what happened to the Mars Rover Opportunity. The video below is a time lapsed footage of the rover extricating itself from some loose sand. In real time, it was stuck for a month [1].

You see, the Mars rover belonged to the old robotics paradigm of control that was not feedback-limited and certainly not minimal. This idea of minimality is something we learnt from watching nature solve complicated problems with ease [2]. So, people started asking, how do living things walk/run? A successful minimal model that came out of this study is what I call the “foot-forward strategy”. This model essentially said that the organism put half its feet down and kept the other half in the air (3 feet if you are a hexapod and one if you are human). It measured the resistance that the surface gave each of its feet and decided how far ahead to land the feet that are in the air and then keep repeating the process [3,4]. This model, that has just two ingredients could successfully explain the locomotion of a wide range of living things in a wide range (not exhaustive as you will see below) of terrains.

This strategy was implemented with great success in a robot called the Rhex. See below a video of Rhex zipping through all kinds of terrain, in a direction given to it by a guy with a remote control [5].

This is all well and good and a success to the method of scientific enquiry. But this model works only when the terrain is solid. Consider for example the following video of a spider moving on some uneven substrate. This substrate has holes that are larger than the foot of the spider and deeper than the length of its leg, but it still manages to zip across it (the video is slowed down 20 times).

So the question now is how do we understand this kind of motion. In attempt to study this question systematically, researchers decided to take this motion into the lab. Find below a video of a cockroach running across a wide mesh. Again the video is slowed down 50 times. It is actually moving very fast [6].

Now, there are several possible explanations for how the cockroach manages this. One possible explanation could be that this is an emergent (euphemism for “pleasantly unforeseen”?) consequence of the foot-forward strategy itself. But this the researchers can test readily, for they had the Rhex and we know for a fact that Rhex does not know anything other than the foot-forward strategy. So they did that and let Rhex run on the mesh to see what happens.

Oops! Rhex does not like the mesh! This tells us that there are two possibilities. The messier of the two is the possibility that the Cockroach has more than the simple foot forward strategy built into its neural circuit and we need to figure out what that is. But there is a simpler possibility. May be there is a physiological feature of the leg of the insect that we are missing. And this latter turns out to be the answer. Look at the cartoon along side of a cockroach. Its legs have spines or hairs or whatever you want to call them. These hairs have the property that they give easily in one direction (when pushed towards the leg) and are very stiff in the other direction, requiring loads greater than the weight of the insect in question to make them give. What the insect does when its foot lands ina hole is to use one of these pikes for leverage. You can go back to the video of the cockroach to see that this is indeed the case. So the claim now is the foot-forward strategy together with spikes or hairs are sufficient to negotiate terrain with gaps. The researchers tested this as well. They took Rhex and put spikes on his legs with the same properties as those on the legs of insects and put him back on the mesh. See the outcome in the video below.

It works! Rhex manages to get across, even though less elegantly than his real insect counterparts. The researchers of course performed other tests to verify the hypohesis. They took a cockroach and removed the hair from its legs and watched it stumble on the mesh. They took one of the fastest running creature on earth, the ghost crab (Ocypode quadrata) and let it run on the mesh. It struggled of course, because it runs on sand and hence has no spikes on its legs. And then they put spikes on its legs and watched it make it across the mesh successfully [7]. And so the researchers have successfully demonstrated that the foot forward strategy is enough even with holes in the terrain! This whole thread is a cool illustration of scientific methodology in general and that is one of the reasons I decided to write about it. The other of course are the cool videos. Are you as impressed by the coolness of it all as I am?

Asides, References and Disclaimers:


[1] I had the unique opportunity of watching the rover stuck on Mars live! I was at a NASA meeting at the Kennedy Space Center at the time and they were supposed to show us the rover in action live. But as it turned out, the Rover was stuck for the duration of the meeting.

[2] I looked for a reference on the control strategy for the rover, but could not find one. So, what I am saying here is hearsay. It must be classified or something. And the hearsay comes from a friend of mine that is Robotics researcher at UPenn, subject to my understanding of what he said.

[3] Notice that individual sensing gives an advantage to the multilegged creature. If the resistance on the front most leg is smaller than the hind ones, you know you are probably going onto softer terrain and step accordingly and keep your eyes, if you have them, on your food or predator or ipod or whatever.

[4] This of course is my minimal interpretation of the model. Find more details on this and other models in this Science review paper and the references there in.

[5] All the references on the development and implementation of the Rhex can be found in the website liked above. As an aside note that this project is funded by DARPA. So, unless we have secretly discovered an alien inhabited planet that the U.S is planning to invade, Rhex is more likely to be used in Iraq or whatever the next location for the war on terror is!

[6] This and all of the following is work done by Daniel Goldman and his collaborators. You can find all relevant references at his website. The videos are all stolen from there as well.

[7] The crab videos are on youtube as well. If you want to watch them, they are here and here.

PS: Apologies if this post showed up multiple times in your feed reader. Blogger screwed me over.

Wednesday, July 18, 2007

An Onion Headline

Just in case you have n't already seen this...just could not resist embedding it!:)

Monday, July 16, 2007

Monies, memes and such

As (the mostly imaginary) readers of this blog would have realized, I am a person that is obsessed with understanding, and this obsession extends to understanding human psychology as well. And the way to go about this task is to take a lot of data from the world around me and build models that explain this data. As with all things, I share this obsession with some of my friends. So, a few years ago, a couple of my friends and I came up with a strategy for collecting such data. We decided we would come up with a few questions that we thought were “penetrating” in some sense. It was decided that we will ask these questions to all the people we met and we will catalogue and keep the answers for analysis after we had accumulated statistically significant amounts of data (or rather as many of the people we met as possible, I mean, if we really liked them we would not want to risk scaring them away for ever, would we?). This process will help help us get a statistical grasp of the human psyche (paah!! day dreams realizable only in utopia as you will see). I had forgotten all about this for a while now, but recently Bongo tagged me with a meme and this caused all our idealistic planning to come rushing back to my mind! Ok, you are allowed at this point to decide I am crazy, but read on anyway, it might amuse you.

Quite early on in this endeavor of gathering data, we realized of course that the problem was the absence of any “right” questions. For example, one of the questions a buddy came up with was some slight variation of “What would you do if you got a million dollars tomorrow”. We got answers that ranged from “Retire and move back to India” to “Oh! After capital gains and state taxes, that would let me clear may be 600000$, I guess I would pay off my house and three cars and add the rest to my portfolio in the form of some blue chip security or the other”. Clearly the only things that the above two answers told us was that the person with the first answer thought a million dollars was a lot of money and the second one must have a really large income and hence thought of a million dollars as an “everyday sum”. It later turned out that the second guy had a yearly income that was a little more than half the amount, vindicating my earlier statement. This was not useful. We could have found that out by just asking them how much they made every month.

We got some really “out there” answers as well such as : “I will buy a plane and live from October through March here (here being Gainesville Fl) and live March through October in a place of the same latitude in the southern hemisphere with all the same amenities, air conditioning, high speed internet and the VPN that will let me access all journals and such. This way I will have outdoor weather all year round”. May be you could infer from this that this geeky person is outdoorsy and is relatively happy with life as it is so that her biggest problem was the weather?

You see, the motivation behind asking the question was to see what people would change in their lives if money was not an object, but elicit the answer without explicitly stating the same. If you do explicitly state what you are asking, then their answer will be biased by what they think they can tell you about their pet peeves. You are more likely to see the truth if you can ask a clever indirect question from whose answer you could infer what you were looking for. And yes, you are right, what you infer will be biased by what you think about things and hence will not be a “one to one and onto map” that will be “invariant to changes in the reference frame” i.e., be the same irrespective of the mind of the person constructing it. So, after a very short while of trying to fine tune the questions we would ask and encountering the inevitable (in retrospect) frustration of not getting anything useful or trustworthy, we abandoned this scheme of ours.

Now what has this got to do with memes and tags and such? I have been away from the Blogsphere for a little more than a week, working too hard to have time left over to do anything other than check email. Then I try to reenter the world by reading the posts in my reader and find that there are such an overwhelming number of them that I was too lazy to even try. So, instead I clicked around to see the network created by the random facts meme. It lead me to the realization that this is such a rich hunting ground for psychological data! There are all manners of people being tagged, all manners of interpretations of any given tag and of course the value of the written word, where you can see what is being said without the burden of the real personality! So, now I have a new “holy grail” [1] goal for my blog life. After I become this famous blogger that everybody reads and people just love to get a link from me even if it is in the form of a tag because of the traffic I send their way, I will try and start memes with specific objectives and watch them propagate through the blogsphere and thereby acquire all the data I need!:))) . As the Thalaivar once said “How is it?”:))

[1] The “holy grail” idea comes from the lingo used in scientific proposals. You see, when you go asking for money for a project, you have three levels of possible results you predict will come out of it. The highest is the holy grail. This is a result you know you will not get, but if you do by some serendipity you will get the nobel prize as well. The second result, which is what you are really shooting for is called the “Nature” in that you would probably get a paper in that revered journal when you are done. And then there is the “fall back”, the minimum result that you are sure you will get irrespective of how badly things go.

Sunday, July 8, 2007

Janma Saabalyam adenchitein

Inikku Shivaji paathittein. Shivaji sumaara irundaalum MGR super aa irundaar. I had fun. Yaar enna sonnalum seri., aana vayasukku thalaivar super aa irukkar. Period. :))

Thursday, July 5, 2007

I’ve been tagged – random facts

Bongo, as of now being awarded the title of second gentleman of the blogsphere (the first gentleman of course is the ever polite Patrix) has tagged me with the random facts meme. And I award him this title in spite of the fact that he tagged me only because “those who I can force into responding to a tag have mostly been tagged already”, for as is true for most people in most social situations, even virtual ones, I feel insecure and invisible and being tagged helps, right?:))

And now on to the meme. There is no way for a person to write eight random facts about themselves as it is bound to be biased by what they want people to know. But, I am going to try by picking eight random aspects of a person and writing down one fact about that aspect.

1. Appearance: I wore my hair in a “boy cut” of some form for the first twenty years of my life. Then one fine day I stopped cutting it and by the time I was 24 I had hair that fell below my waist. So I guess the fact is that my body produces way too much keratin?

2. Food: I LOVE “thaiyir saadam” and “avakkaai oorugai”, even more so now that I am attempting to be a vegan and it is “forbidden”. So the fact is that I am a dyed in the wool tam-bram.

3. Drink: Good coffee in the morning and good alcohol in the evening (no girly martinis for me, whisky neat or brandy with water preferable :))) So the fact is I am not that much of a tam-bram after all.

4. Music: With apologies to all the erudite and esoteric folks out there, tamil film music in general and by ARR my man in particular.

5. School girlish wish : I want to have had the genes of my father and his sisters instead of what I have now, namely my mother and her sisters. They all became fat as they got older. I am not that fond of eating but I hate to have to exercise!

6. Ms Universe type wish : Everybody in the world should have enough to eat so that “where is my next meal coming from” is not a thought of significance in their minds.

7. Siddhartha/Vivekananda type wish : That I had more concentration, more presence of mind and more rational thinking capacity than I do.

8. WTF fact of the day: It is raining outside now.

Ok, that did not turn out to be that random after all. But am too lazy to go back and rethink it and I should be working and not blogging anyways. And finally, on the need to propagate the meme. I have so few readers I don’t want to risk scaring them away by tagging them. And what if I am imagining that they read me and they really don’t? Horror of all horrors! But, I don’t want to be a spoil sport either. So, I (with great trepidation and anxiety) tag vatsan and tangled.

Tuesday, July 3, 2007

Eating Animals

This is perhaps one more reason you would want to be a vegetarian like me!:))

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.