Saturday, June 30, 2007


I have written about Sam Harris's gripe with Noam Chomsky in a previous post, and indicated that I believe in a middle ground and consider both their arguments as valid ones; Harris's that hatred of the US springs from faith, Chomsky's that hatred of the US springs as a repurcussion to a long tradition of US imperialism. I am reading Harris's magnificent "The End of Faith" currently, and got a chance to consider his critique of Chomsky in detail.

I in fact find myself agreeing with Harris on many counts. I agree that to consider the Clinton administration's 1998 bombing of the Al Shifa pharmaceutical plant in Sudan as being "morally equivalent" to 9/11 is absurd, even if the act was not justified. The US has blood on its hands, no doubt a whole bloodbath, but Harris says that in very few cases have US intentions been to maim innocent civilians, and this is true. Maybe its aims were misguided, and operations certainly were sloppily carried out, but unlike attacks by terrorists, it is rarely that the US has intentionally aimed to cause the deaths of innocent civilians.

I think Harris is largely right, and that's why I have always written about taking Chomsky with a healthy dose of salt. That's why I have also on numerous occasions said that in the historical book of atrocities, the US would still be way down in the list. But at the same time I think it's important to note that one cannot always put a high premium on noble intentions. For example, the intention of toppling Saddam's Hussein's regime was no doubt a valid and even noble one, especially when we consider it in a sanitized, isolated context; after all, there's no doubt that he was a repressive monster. But does that mean that what Bush did was right, even assuming that he had the truly good intention of getting rid of a murderous tyrant?

No, and of course there are a variety of reasons, but especially one important reason, that intentions put into effect without thinking about consequences can still constitute immoral acts. In case of Bush, apart from the fact that he lied, he also did not think about the bloody and far-reaching consequences of his actions. Sometimes good intentions can have violent consequences, and carrying out those intentions without thinking about those consequences is as bad and irresponsible as having malevolent intentions.

The problem with putting such a high premium on good intentions also is that one can then justify many acts that are carried out under that rubric. In short, it can lead to the ends justifying the means. Many events in World War 2 are good examples; most notably the civilian bombing of Hamburg, Dresden and Tokyo, and the bombing of Hiroshima and Nagasaki. Many historians now judge these acts as unnecessary and immoral. But one can always justify them by saying that the intention was to defeat Hitler or Imperial Japan, which was a good one. No doubt it was a good one, but that did not mean that any and every action in support of that intention was justified.

Intentions can be sterling, but actions carried out in their support cannot be justified and are irresponsible if one simply fails to neglect the devastating consequences that follow.

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Friday, June 29, 2007


It's obvious that both global warming and evolution are supported by reams of evidence, yet why are people so loathe to accept this? There are of course many many reasons and answers to this question, some of which I have discussed on this blog. But on a public basis, what I think is quite key is the simple fact that it's easy to dissent, but relatively difficult to justify. By "difficult" I certainly don't mean that it's actually difficult to justify the evidence for global warming or evolution. In fact that's extremely simple because the evidence is right there in front of us.

But what's dificult is to justify and explain viewpoints from a public debate standpoint. Consider a global warming debate in which a dissenter throws around a 10 second general objection, for example, "Computer models can be unpredictable because they are built on assumptions". This statement is much easier for the lay public to understand because it represents a pretty general fact that is true in many cases. Now it's the climatologist's turn to defend himself. This is going to take much more time because he or she would have to explain how it's true that computer models can be unpredictable, but how researchers take this uncertainty into account, run multiple simulations, weed out fudge factors, do statistical analyses coming up with multiple scenarios, and assign degree of confidence to predictions. This knowledge is surely out there, but it's quite obvious that the climatologist is going to take more than the 10 minutes alloted response time to explain this. And with good reason; although the punchlines of science can be simple, actually explaining science often takes time, and that too with good reason, since science wants to do as thorough a job of analysing the data and drawing conclusions as it can.
But the lay public often does not see this. What they think is that the climatologist is unable to answer the dissenter's objections in 10 minutes. They take this to mean that he cannot defend himself. In the public's eyes, the dissenter has scored points.

A similar example exists for evolution, where actually the argument should be much simpler, but unfortunately it's not. Some dissenter (or god forbid, ID guy) will say something like "The bacterial flagellum is too complex to have arisen through chance". Not withstanding the fact that this statement is just plain wrong ("change" is not operating here), we have to admit that the bacterial flagellum does at least look complicated for the layman. But now, when the biologist has to answer this objection, he needs to demonstrate how each part of the flagellum has counterparts in other organisms, how even "half a flagellum" can actually work, and how the flagellum has actually arisen as a result of a mix-and-match kind of strategy adopted by natural selection. He would also have to explain the experiments leading to these conclusions. The explanation is elegant and extremely persuasive, but naturally it will take more than the allocated 10 minutes, leading laypeople to believe that perhaps the disssenter has a point.

The reason why this situation is unfortunate is because the burden of proof is always put on the scientist, when it is actually on the dissenter who has to prove his point. But the public often does not understand this, because they don't understand the weight of scientific evidence that strengthens the scientist's positions. Understanding this evidence itself will take some reading and exploring, but what they want is a 10 minute (or less) answer. Unfortunately for the public, the very fact that something can take more time to explain means that it may be dubious. Needless to say, this is absurd for obvious reasons.

In addition to this problem, such dissenters also are usually good at rhetoric, since unlike scientists, they have spent most of their time practising it in the absence of actual evidence to support their claims. Scientists are often not very good at rhetoric since don't feel a need to be a good at that, and rightly let the evidence speak for itself. But that means that in public debates, where the public is unfortunately more easily swayed by rhetoric, they are inherently pitted on the hard side.

A similar situation also exists for people in non-scientific fields. Noam Chomsky has made the good point that he is always on the losing side in a short television debate, because the objection of the dissenter is a 10 second statement which reflects what's expressed by the conventional media. Since it's already there in the papers and on TV, people already know this, so all he has to do is to state it. On the other hand, when Chomsky needs to counter his point, he needs to reference and cite non-conventional and minority sources that the public has not heard of. Clearly, this is a more time-consuming task. Unfortunately, Chomsky has only 10 minutes to respond, so he cannot do this convincingly in those few minutes. The result is that the public goes away with a false impression that Chomsky is wrong and the dissenter is right.

This situation is rife throughout the media. It is inherent in every interview that TV channels do and every talk show where guests are invited to present their views. In each and every one of these cases, there is a potential and many times actual risk of the public getting the wrong impressions simply because someone does not have enough time to make their views clear.

There is no clear-cut solution to these problems except to educate the public through means other than the 10 minute segment shows. In that respect, the books written by Chomsky or climatologists or evolutionists and many others serve an absolutely essential and admirable function. But the public also should be informed about this very point; that they should not trust debates held in a studio that last for 30 minutes, with 10 minutes alloted to each speaker. Because in such a case, they are almost always going to get a biased impression, no matter how convincing it seems.

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Thursday, June 28, 2007


Michael Behe the "biochemist" once again plunges into sophistry with his advocacy of intelligent design in his new book. But Kenneth Miller in a review shows that not only is Behe wrong, but he is also ignorant, and as ignorant as before. The one thing I fail to understand is how Behe can constantly embarrass himself in spite of being soundly proven wrong on multiple occasions. This inevitably points again to the fact that ID has nothing to do with science, and everything to do with partisan politics and religion...

...Read the rest of the entry on Desipundit...

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Wednesday, June 27, 2007


A Mighty Heart is a good movie. I am a little puzzled by some of the reception, including that from Asra Nomani, in whose home Daniel and Mariane Pearl were staying and who also went through the heartbreaking trauma of waiting to hear about Pearl until the unfortunate day when the news finally came about his murder. I am puzzled because while Nomani criticises the portrayal of Daniel Pearl in the movie as unrealistic, I thought that the movie was not really about him; it was about his wife Mariane who was a pillar of quiet strength and unwavering conviction after he was abducted. She is really the focus of the movie, and Angelina Jolie does put on one of her best performances ever, and after movies like Mr. and Mrs. Smith, gives us the renewed hope that she can actually act well.

I actually think it is prudent that the movie does not focus on Daniel Pearl. That's because it is presented in semi-documentary form, strictly focusing on what happened. It begins on the day when Daniel was kidnapped, and if it is going to portray events realistically, it is logical that he is not a big part of the movie because nobody after that really knew what was exactly happening to him. It also does not want to portray Daniel Pearl as some kind of hero, because after all he was just doing his job when he was abducted. I think that he actually behaved heroically after he was kidnapped, but even then, the real focus is on his wife, who showed exceptional equanimity and great restraint when appearing on television. She did not lash out against the kidnappers, realising that that could make matters worse. Most of all, she did not really care about them and only cared about her husband's safety, which makes what happened later even more tragic.

All the actors in the movie have put on good performances. The movie is really a narration of events. If we believe that it tries to accurately convey reality, then we must also praise the few outstanding officers in Pakistani intelligence who worked day and night to pursue leads and root out coconspirators. Reactions by some Pakistani officials claiming that Indian intelligence is behind the kidnapping are absurd as expected.

In the end, Mariane Pearl rightly says that she also grieves for those Pakistani families whose sons, fathers, and brothers are also killed by terrorists everyday. Especially for those of us in the US, such stories while indisputably tragic, are given outstanding publicity and attention by the media. They threaten to dwarf the equally tragic stories of hundreds of other journalists and common people in other countries.

Finally, this is not just an American tragedy because of an even more fundamental reason; it is a product of conflict and hatred inspired mainly by religious faith. Let's say Daniel Pearl was not Jewish. Would that have prevented his abduction? Likely not. But if Islamic fundamentalists had not seen Americans as orchestrating a Christian crusade to invade and conquer their lands and their 'culture', would that have prevented such an event? It is much more likely that it would have. That's why the issue is not an American issue. It is an issue about faith.

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Tuesday, June 19, 2007


Among all the (rather predicted) stupidity over Rushdie's being knighted, there is something the contradiction of which immediately underscored itself when I read it.

Iran's parliament:
"Salman Rushdie has turned into a hated corpse which cannot be resurrected by any action," First Deputy Speaker Mohammad Reza Bahonar told Iran's parliament.The action by the British Queen in knighting Salman Rushdie, the apostate, is an unwise one," he said to loud applause from MPs.

"The British monarch lives under this illusion that Britain is still a 19th Century superpower and that bestowing titles is something still deemed important."

So, if this bloke thinks that nobody should give a diatom for British knighthoods, why does he himself give so many diatoms? Won't the best way of underscoring his conviction about the insignificance of knighthoods be to simply ignore them? From his outrage, one can immediately understand how important knighthoods for 'apostates' are for him really.

Of course, this is Iran, and so it should not be surprising. But this is something I really fail to realise; if people's faith is so firm and profound, how on earth can it constantly be shaken by such happenings? The only sensible interpretation here is that they have ingrained teachings from their holy book that have apparently instructed them to react violently almost as a reflex action over every small and sundry thing such as this one.



On its website, PLOS printed an opinion about its content published by the Deccan Herald. Either PLOS randomly crawls the web in search of reviews and picks them up willy nilly, or I am unaware of an unusually well-informed, untapped minority source of scientific opinions that needs to be introduced to the world. Or probably both. In either case, it's revealing.

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Monday, June 18, 2007


For many people of faith, science seems like just another reality generating enterprise, and scientists as just another community of people with their own core set of beliefs. However, this belief, just like religious beliefs, is illusory. It neglects the fact that science is actually anything that constrains us to trust something on the basis of evidence, something that we conform to in our daily lives, and a scientist is anyone who does this. In this regard, many people in the world who don't have a scientific degree are nonetheless scientists.

Read the rest of the entry on Desipundit...

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Desipundit has been gracious to offer me writing space on their Wordpress powered domain, and I am happy to be a part of their enterprise. My blog there is From so simple a beginning. From now on, posts related to science and its many manifestations in society will be on Desipundit, and will be excerpted and linked to here. Naturally, feel free to comment there as you do here.

Wednesday, June 13, 2007


I mentioned in the last post how the transition time between academic science---->industrial technology needs to be accelerated, and it struck me that there were so many things in the conference which were being talked about by pharma scientists, which originally came from academia. Ketki has also mentioned the increasing collaboration between academia and industry, and I cannot help but think of technologies that people in pharma currently rave about, all of which were developed in academic laboratories.

Consider the recent use of NMR spectroscopy in studying the interaction of drugs with proteins, a development that has really taken place in the last five to ten years. NMR is essentially an academic field which has been around for almost fifty years now, originally developed by physicists who worked on radar and the bomb, and then bequeathed to chemists. It is the humdrum tool that every chemist uses to determine the structure of molecules, and in the last twenty years it was also expanded into a powerful tool for studying biomolecules. What if pharma had actually gone to the doorstep of the NMR pioneers twenty years back, and asked them to develop NMR especially as a tool for drug discovery? What if pharma had funded a few students to focus on such an endeavor, and promised general funding for the lab? What if Kurt Wuthrich had been offered such a prospect in the early 90s? I don't think he would have been too averse to the idea. There could then have been substantial funding to specially focus on the application of NMR to drug-protein binding, and who knows, maybe we could have had NMR as a practical tool for drug discovery ten years ago, if not as sophisticated as it is now.

Or think of the recent computational advances used to study protein-ligand interaction. One of the most important advances in this area has been the protocol called docking, in which one calculates the interactions that a potential drug has with a target in the body, and then thinks of ways to improve those interactions based on the structure of the drug bound to the protein. These programs are not perfect, but they are getting better every day, and now are at a stage where they are realistically useful for many problems. These docking protocols are based on force fields, which are programs that calculate the energies and structures of molecules. The paradigm in which force fields are developed, called molecular mechanics, was developed by Norman Allinger at UGA, and then improved by many other academic scientists. Only one very effective force field was developed by an industrial scientist named Thomas Halgren at Merck. During the 80s and 90s, force fields were regularly used to calculate the energies of simple organic molecules. One can argue that at that point they simply lacked the sophistication to tackle problems in drug discovery. But what if pharmaceutical companies had then channeled millions of dollars into these academic laboratories for specifically trying to focus on adapting these force fields for drug-like molecules and biomolecules? It is very likely that academic scientists would have been more than eager to make use of those funding opportunities and dedicate some of their time to exploring this particular aspect of force fields. The knowledge from this specific application could have been used in a mutually beneficial and cyclic manner to improve basic characteristics of the force fields. And perhaps we could have had good docking programs based on force fields in the late 90s. Pharma could also fund computer scientists in academia to develop parallel processing platforms specifically for these applications, as much of the progress in the last ten years has been possible because of exponential rise in software and hardware technology.

There are many other such technologies; fabrication, microfluidics, single molecule spectroscopy, which can potentially revolutionize drug discovery. All these technologies are being pursued in universities at a basic level. As far as I know, pharma is not providing significant funding to universities for specifically trying to adapt these technologies to their benefit. There are of course a few very distinguished academic scientists who are focused on shortening the science--->technology timeframe; George Whitesides at Harvard and Robert Langer at MIT immediately come to mind. But not everybody is a Whitesides or Langer, both of whom have massive funding from every imaginable source. There are lesser known scientists in lesser known universities who may also be doing research that could be revolutionary for pharma. Whitesides recently agreed to license his lab's technologies to the company Nano-Terra. Nano-Terra would get the marketing rights, and Harvard would get the royalties. There are certainly a few such examples. But I don't know of many where pharma is pouring money into academic laboratories to accelerate the transformation of science into enabling technology.

In retrospect, it's actually not surprising that future technologies are being developed in universities. In fact it was almost always the case. Even now-ubiquitous industrial research tools like x-ray crystallography, sequencing, and nuclear technology were originally products of academic research. Their great utility immediately catapulted these technologies into industrial environs. But we are in a new age now, with the ability to suddenly solve many complex problems being manifested through our efforts and intellect. More than at any other time, we need to shorten the transition time between science and technology. For doing this, industry needs to draw up a checklist of promising academic scientists and labs who are doing promising research, and try to strike deals with them to channel their research acumen into specifically tweaking their pet projects to deliver tangible and practical results. There would of course be new problems that we would need to solve. But such an approach in general would be immensely and mutually satisfying, with pharma possibly getting products on their tables in five instead of ten years, and academia getting funded for doing this. It would keep pharma, professors, and their students reasonably happy. The transition time may not always be speeded up immensely. But in drug discovery, even saving five years can mean potentially saving millions of lives. And that's always a good cause isn't it.

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Tuesday, June 12, 2007


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(Above: The view across from the bridge at the World Trade Center and Below: The always scenic view across the Charles in front of MIT)

I am finally back from a trip that was both professionally and personally immensely satisfying, and if there's one place I was really sad to leave, it was this one. I can keep on talking about how great a place Boston is- the place where I stayed and the historic places cruise I took around the harbor were just fantastic- but my praise has also been somewhat tempered by two realisations. Firstly, the boss paid the tab which makes it a little easier to have a good time. Secondly, everybody says that it's only in these four months that Boston is the best place on earth. Anytime after that and the enjoyment quickly starts to dwindle because of the pretty nasty weather. So if I could get a part time dream job where I could work in Boston only for four months, that really would be it. Dream on.

One of the good things about this conference was that our patent on a new (potential) anti-cancer compound just got filed days before the conference. That made it possible for me to present the work. The work was well-received, although as is always the case, there's miles to go before we can possibly sleep.

The conference itself was great, and it was held in a scenic location- the World Trade Center by the side of the harbor (although almost everything in Boston seems to be harbor-side). It was the first time I got a preview of what it's like to work in industry. I was happy to see that a camarederie similar to that among academic scientists exists in the pharmaceutical industry too. However, I also got the feeling that that camaraderie is more guarded, and also a little more exclusive. I may possibly have been the only graduate student there among about a hundred participants. I was also surprised to see, perhaps not so surprisingly in retrospect, that folks in industry do almost exactly the same kind of work that we do, at least in the very initial stages of drug design. But where they really get a head start is in validating early models by having massive in-house facilities and personnel for things like pharmacokinetics (investigating the properties of the drug in the body) and x-ray crystallography (having a structure of the drug bound to the protein which it is supposed to inhibit). So they can decide relatively early on whether to pursue or drop a prospective candidate. We are now planning to put our own compounds in animals, and I would have given anything to have a crystal structure and pharmacokinetic data in the early stages when we had the lead. Pharma can do this, and they learn a lot from it.

The downside of working in pharma? You cannot talk! About 60% of the presentations in the conference did not have a single chemical structure in them. In most cases the only structure displayed was an already well-known one. It's really frustrating to be a chemist and not see what are the structural characteristics that are leading to all those tantalizing pieces of biological and clinical data. And it looks like it's only going to get more proprietary. That's the only thing that makes me a little wary of working in pharma, the fact that you often cannot talk to people outside even if you know that they could have the answers to your questions. Also, the fact is that many of the technologies that are now roaring in pharma have their origin in basic science developed in academic labs. I always keep on imagining how much the science--->technology transit time would have been reduced if there could have been collaboration between pharma and those academic labs in the initial stages. Of course there are IP issues, but one cannot help but think about this.

But all in all, a very fruitful experience. I look forward to attending more of this next year.

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Tuesday, June 05, 2007


This is Boston,
home of the carp and the cod,
where the Lowells talk to the Perkins,
and the Perkins talk only to God

(Old New England ditty, from The Color of Truth)

I am in Boston for a structure-based design conference, and already I am charmed, as is almost everybody else who has been to Boston who I talked to. I am staying in one of the historic parts of the city named Faneuil market, and there's much here that reminds one of classic old-world charm. For example, you are trotting along a cobbled road, when you suddenly see a depression in the ground way below sea level. What at first looks like the home of a giant mouse, turns out to be one of those tiny charming places that sells whimsical trinkets and mementoes. You come across such places in the Fort area of Mumbai, in Delhi, and in Philadelphia, all places whose historical roots run deep. Just outside this Faneuil Heritage Shop is Faneuil Hall, where everyone from Paul Revere to Susan B. Anthony to JFK seem to have given speeches, connected to tea partys, stamp acts, and presidential campaigns. The site of the Boston Massacre is also very close by.

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The cobbled stone and red brick roads in the quaint old North Market and Quincy Market also have a classic historic look, with just the right amount of wear and tear. Shops littered around these roads sell all kinds of curiosities- exotic sounding seafood dishes, dresses and skirts that seem designed to make one point or another, and homemade earings and jewelry that seem patched together with string and sealing wax.

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A couple dressed up in eighteenth century outfits looked as if they actually live in Paul Revere's house.

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One of the nicest and most interesting things about this place, is that it seems to divide the city into two very different parts which are nonetheless very close to each other. On one side is the busy Boston downtown (or at least it looks like downtown). But cross only two streets and you get to the other side, a lovely and expansive view of the sea, the Long Wharf, with whale watches and ferries that seem to be as varied as the people around them.

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Close to the pier, I saw jellyfish gently and lazily letting the waves carry them to miscellaneous places. This striking contrast between the two parts which are still very close apart enables one to partcipate in the hundrum of busy downtown life during the day and then relax on the pier with a splendid view and poignant thoughts in the head.

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