Caught behind but not out!

Sunday, January 21, 2007

Moving

The waters were rough and I decided to steer my ship to calmer shores. I have moved to http://scientificbellows.wordpress.com. I have no idea why i moved but reason begets reason and I'd rather not have one!

Friday, July 07, 2006

Irreversible

Irreversible. A movie that I picked up with fear. It is a movie who's IMDB trivia would may you wary of watching it.

"The first 30 minutes of the film has a background noise with a frequency of 28Hz (low frequency, almost inaudible), similar to the noise produced by an earthquake. In humans, it causes nausea, sickness and vertigo. It was the main cause of people walking out of the theaters during the first part of the film in places like Cannes and San Sebastian. In fact, it was added with the purpose of getting this reaction." (IMDB trivia)

I think the director Gaspard Noe will be pretty pleased if I called the movie shocking or used adjectives like ugly. He would sleep in his grave knowing that his soul has served its purpose. However, that is what Irreversible is. The use of any other adjective would not only be flawed but would be far away from the truth. The movie proceeds in reverse chronological order just like others in its genre such as Memento. Its nice to note that it simply isnt a gimmick exploited to make viewers curious to watch the movie.

The movie starts of with a killing. Murder in its most brutal form and is best watched with eyes closed. Actually no, the movie starts off with Les temps detruit tout- Time destroys everything. As one watches it is inevitable that you try to question the murder. What prompted so much hatred? Rage? Anger? As a viewer, you are left in despair. The answer to 'why' is slowly unwrapped.

To go into the details of what the movie is about is superfluous considering some reviewers who have written about the movie (having been paid to write!)- Roger Ebert's review


What starts as a movie that is absolutely brutal evolves into something that provides reason for it and ends in happiness where you leave with a smile. Consider the same in proper time sequence....the end would be sheer disgust.
Time destroys everything. When the movie describes the events that lead up to the fateful moment you wonder how things would be if time were static. How would lives change if you could peek a few hours into the future? Time changes everything.

I made an interesting observation on Rotten tomatoes. The movie has an unfortunate 56% rating from critics. But that is something I would expect.

To me, it seems like the kind of movie that no one can be grey about. Unfortunately this movie does not give any more options than a chess board.

Sunday, June 25, 2006

The petit problems of the world

I look at the skies and imagine that the world is a beautiful place to live in. I enjoy the view I get of the stars, my morning coffee and the ability to read and understand the world around me. I do not have real problems. A fairly bold statement I think that rests on how one defines real problems. I think it is fair to say that I live an extraordinarily happy life compared to many millions who don't. I'm not sure if these are blessings or luck but perhaps a mere game of probability where the dice was rolled and landed on the side with two sixes.

I think hard, the questions turn up in millions, answers, a few. An important reason why a lot of people fail to maintain a decent standard of living is because of two main reasons- access and opportunity. For most part due to biased sympathies towards child labour this article will deal with opinions that surround this issue. Here are links to two articles that I have read which have prompted this piece.

Child labour in the South Indian matchstick industry (link)

Child labour in coal mines in Congo (link)

Of course, its easy to say that you have heard of these issues before but I think its important we constantly remind ourselves of the harsh realities of the world. I don't think they are issues to be pitied upon on one occasion and end up drawing the curtains on them.

It is interesting that the problems are more or less the same in different parts of the world and the reasons are also somewhat similair. Again access and opportunity are staggering blocks to development.

The road to change has also been a standard route taken. It involves freeing children by legal means or by convincing parents about its dangers. Unfortunately these solutions lack foresight. Most of these children are back to square one after a while. The real solution involves solving the two main problems I have stated earlier which are unfortunately not trivial problems with straightforward solutions. So in some sense we are stuck in a vicious cycle where the solution is of utopian scales.

The skeptical reader would wonder if I have provided solutions but the goal of this article was never to provide solutions but to ask the same 'boring' questions. What do we do?

I strongly urge you to take a look at these links to understand the kind of problems that many children in the world face and some steps towards healing them.

Protecting children's rights (link)



Saturday, June 24, 2006

PMS a.k.a. Post movie watching syndrome

Coming to the US, I have developed this insurmountable urge to watch at least four movies a week. I must pat my back to the commendable job that I have done so far. I have managed to meander my way past tons of crap that loom in the background of some great movies that I have watched. My most recent movie is Garden State. A sweet, feel good, coming of age movie. I wonder if the following post has ideas inspired by PMS (post movie watching syndrome). I think I should make this term official. Copyright it! Perhaps.

And as it comes in writing, its time to intersperse the random thought that projects out of my mind. I think about story telling and about how as little kids we used to listen to stories being told. Some of them happy, some of them sad. It really mattered who told us the story. Its not so different when we grow up. We still listen to stories, we read them and we watch them. And it still matters as to how the story is being told. I maintain the belief that there are very few stories in the world and in some way or the other we have watched everyone of them. What really matters is how the story was told. We carry, if I may use a word as harsh as this, the scars of childhood in many aspects of our life. I wonder then how people grow up. As Johnny Depp, who plays the writer J.M. Barrie in the fabulous movie Finding Neverland, remarks, "You are grown up now". The story of Peter Pan written by J.M. Barrie is said to have marks of being autobiographical. I take Barrie's side and wonder what it is to be grown up. Is it something you realize when it happens? Sounds a lot to me like sex.

Somehow I have always felt that people take the act of growing up too seriously. When you grow older the one thing that happens is that your toys get a lot more expensive! We still quarrel, of course we do so within the legal framework we draw up for ourselves. Have strong opinions, likes and dislikes. I truly wonder if life carries a very limited set of patterns much like the very few stories that exist in Hollywood. Perhaps it would be a lot less complicated if we all thought of ourselves as little children.

Thursday, June 22, 2006

The rants of a Ph.D student- part one

The rants of a Ph.D student is hopefully a long series of write ups that I hope to give on what life as a Ph.D student is. I had refrained from writing about this for quite a while but then I think there does come a point where you end up pondering about life, the universe and everything. This point is when you have one of those days when the sun rises in the west, little puppies are no longer cute and you rather eat stale food from three days ago then cook afresh. And this is also when Doctorate meets philosophy.

A series of unfortunate incidents that took place yesterday leave me in this strange predicament. I had not one, but two failed experiments due to sheer incompetence. And when such incidents happen it is best to find solace in reason than in rage. I think about the day and I learn my lesson. I think this is key to several more of these kind of days I will have. Never do an experiment when you don't feel like doing it. I can see the eyebrows raised and wondering about all the exceptions to this rule that my dear reader conjures up. But yes, they are exceptions. There will be days when you wont have a choice and have to stick around in the lab until you start hallucinating. I can only offer my deep felt condolences to such days. But then the lesson is that when you can postpone the experiment, do so with no guilt. (This of course doesnt apply if you feel like this everytime you wake up!) There will be other days and longer hours in the night when you can make it up. At least for me what happened was that I pursued my experiments in spite of being brain dead and all of them failed miserably. The nature of my present work is such that it might mean losing the entire week. All for want of a nail.........

I reached the point where the voice in my head screamed for me to stop. I closed shop and headed to the nearest Chinese eat out and then followed it up with a super Banana split. Its hard to forget the disaster which was yesterday but then the fact is that it is important to forget and move on. Today seems a lot more hopeful. It was raining for a bit but then its back to being bright and sunny - as metaphorical as it may sound, I live in a place where climate change is real (An Inconvenient truth- Al Gore)

I'm quite sure it wont be long before my next rant and well, a new lesson well learnt.

P.S.

Other interesting rants I have read:

Suhasni's rants about her research (link)


Tuesday, June 20, 2006

Run Kaushik Run!!!@!@$$$$$%E%&&

Today was the day that i decided to conquer all. Conquer the overwhelming power of sleep and the wills of procrastination that prevented me from even trying! I decided to wake up at 5.30 in the morning and run. The alarm rang at 5.30. But having set the clock 10 minutes fast, it was actually 5.20. I cursed my stars for losing out on 10 minutes of sleep (stars are useful especially when u have no one else to curse) The next was warm up session while I brushed my teeth. I found multi tasking as a useful way to save time. I was fighting a battle against the rising sun. I had to complete my conquest before the sun showed up. Damn the socks. I couldn't find them.Perhaps for the reason that they were neatly tucked away in some vague drawer. I wish my mom had told me where they were before she left. Earlier they were strewn all over the place which made it quite convenient for me to pick them up and wear.

I looked out. The streets were empty. I thought to myself that at the stroke of the morning hour, when the town was asleep, Kaushik would run to light and freedom. Nehru would have been proud of me for this. And then I ran. I ran.I ran. I ran. I had images of Forrest as I ran. I thought it might be worthwhile making a movie out of this. Run Kaushik Run- 'the story one man's determination against all odds' (suitable music in the background as this is being said would help) So where was I? ah, yes. I ran. I ran. I ran. For five minutes. Damn, I thought to myself. Einstein was right. TIme does slow down when you move at the speed of light. So while considering the possibilities of time dilation, I decided to take a short break for another 5 minutes. No more breaks. I had to run. And I ran.....for another two minutes by which time my silencer had broken down, so one could probably hear me puff and pant from two blocks away. I consoled myself with the thought that it was probably the body's way of showing its need for fresh air. A much needed break was again taken. I looked at the clock and decided I had enough for the day....but then I cant give up can I ? After all this is the inspirational story of one man's fight against all odds and so I ran again but this time I made sure I was home.

I refused to turn on the fan so that I would still have the beads of sweat trickling down my spine....down my forehead. I would still have with me, the scars of the run. I should stop now, after all it is time for coffee! Ah,and now it suddenly seemed like there was purpose to life itself!

Sunday, April 23, 2006

What happens when biologists take up photography for a hobby?

Image courtesy: UT Austin news feature page

Last year had a fantastic article in Nature (sorry for my bias to pick nature articles, I promise other journals in the future), published by a bunch of undergraduate students on E.coli photography. The title was "Engineering Escherichia coli to see light"

The trick to doing this lies in getting bacteria to sense light or rather specifically in this case, getting E.coli to sense light. This isnt a trivial task because it is important maintain a signalling cascade while enabling the organism to posess a different response element.

The choice of the signalling pathway was a two component pathway (two component signalling pathways are those pathways in which there is a signalling element and a response element and the system is regulated by a kinase) The two component pathway in this case was EnvZ- OmpR involved in porin expression in response to osmotic shock.

A chimera between EnvZ and Cph1 (a gene in Synechocystis; a cyanobacterium) was constructed by analyzing potential crossover points between the two genes. The idea is to change the response domain in EnvZ to one which is light sensitive. This is not really as trivial as it seems. To appreciate the difficulty, one must understand the number of potential crossover points possible and what kinds of crossovers actually produce functional chimaeric response elements.

These chimeras were on plasmids which were transformed into EnvZ chromosomal knockouts of E.coli. These E.coli also had an ompC promoter linked to a lacZ reporter. In the osmotic regualtion system, OmpR binds ompC and activates the expression of the downstream genes. In this case, OmpR will activate LacZ reporter expression.

Now the parts are in place, but the story still has some length to go. The light sensitive protein needs an element called phycocyanobilin. Where does this come from? E.coli does not have the ability to produce these compounds. The advantage of a well characterised genome/genetic system really comes to the forefront here. The necessary genes were again take from Synechocystis and inserted into E.coli.

Lets do a recap on what we have and how the means are going to be attained.

1. A chimaeric protein of EnvZ- Cph1 that responds to light
2. ompC promoter- lacZ fusion which responds to OmpR binding
3. a biosynthetic system that produces phycocyanobilin which is a component of the light sensor.

How does the system function?

The sensor system is turned off when exposed to redlight due to the inhibition of autophosphorylation. (Only when the protein is phosphorylated, the response system is active and lacZ expression occurs) We now have a switch system in place that responds to light by means of the two component system.

The art of photography:

When an image is projected onto an agar plate containing these modified E.coli, the regions where there is a shadow have a lacZ which is expressed. The lacZ converts S-gal into a black insoluble compound thus producing a contrast image on the plate.

The moral of the story:

Synthetic biology is a field that is in its nascent stage and this kind of work shows how far one can go with controlling microorganisms. Craig Venter for instance is making headway in trying to synthesise the first synthetic minimal microbe. The control that this allows us to exert on bacterial systems is truly awesome.

'Enginering Escherichia coli to see light' Levskaya, A et. al. Nature 438, 441- 442 (2005)

Other useful links:

EnvZ- OmpR two component signalling pathway
A U Texas news release containing comments by some of the authors
Nature news update (subscription required)