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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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October 9, 2013

The 2013 Nobel Prize in Chemistry

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Posted by Derek

The 2013 Nobel Prize in Chemistry has gone to Martin Karplus of Harvard, Michael Levitt of Stanford, and Arieh Warshel of USC. This year's prize is one of those that covers a field by recognizing some of its most prominent developers, and this one (for computational methods) has been anticipated for some time. It's good to see it come along, though, since Karplus is now 83, and his name has been on the "Could easily win a Nobel" lists for some years now. (Anyone who's interpreted an NMR spectrum of an organic molecule will know him for a contribution that he's not even cited for by the Nobel committee, the relationship between coupling constants and dihedral angles).

Here's the Nobel Foundation's information on this year's subject matter, and it's a good overview, as usual. This one has to cover a lot of ground, though, because the topic is a large one. The writeup emphasizes (properly) the split between classical and quantum-mechanical approaches to chemical modeling. The former is easier to accomplish (relatively!), but the latter is much more relevant (crucial, in fact) as you get down towards the scale of individual atoms and bonds. Computationally, though, it's a beast. This year's laureates pioneered some very useful techniques to try to have it both ways.

This started to come together in the 1970s, and the methods used were products of necessity. The computing power available wouldn't let you just brute-force your way past many problems, so a lot of work had to go into figuring out where best to deploy the resources you had. What approximations could you get away with? How did you use your quantum-mechanical calculations to give you classical potentials to work with? Where should be boundaries between the two be drawn? Even with today's greater computational power these are still key questions, because molecular dynamics calculations can still eat up all the processor time you can throw at them.

That's especially true when you apply these methods to biomolecules like proteins and DNA, and one thing you'll notice about all three of the prize winners is that they went after these problems very early. That took a lot of nerve, given the resources available, but that's what distinguishes really first-rate scientists: they go after hard, important problems, and if the tools to tackle such things don't exist, they invent them. How hard these problems are can be seen by what we can (and still can't) do by computational simulations here in 2013. How does a protein fold, and how does it end up in the shape it has? What parts of it move around, and by how much? What forces drive the countless interactions between proteins and ligands, other proteins, DNA and RNA molecules, and all the rest? What can we simulate, and what can we predict?

I've said some critical things about molecular modeling over the years, but those have mostly been directed at people who oversell it or don't understand its limitations. People like Karplus, Levitt, and Warshel, though, know those limitations in great detail, and they've devoted their careers to pushing them back, year after year. Congratulations to them all!

More coverage: Curious Wavefunction and C&E News. The popular press coverage of this award will surely be even worse than usual, because not many people charged with writing the headlines are going to understand what it's about.

Addendum: for almost every Nobel awarded in the sciences, there are people that miss out due to the "three laureate" rule. This year, I'd say that it was Norman Allinger, whose work bears very much on the subject of this year's prize. Another prominent computational chemist whose name comes up in Nobel discussions is Ken Houk, whose work is directed more towards mechanisms of organic reactions, and who might well be recognized the next time computational chemistry comes around in Sweden.

Second addendum: for a very dissenting view of my "Kumbaya" take on today's news, see this comment, and scroll down for reactions to it. I think its take is worth splitting out into a post of its own shortly!

Comments (103) + TrackBacks (0) | Category: Chemical News


COMMENTS

1. KC Nicolaou on October 9, 2013 7:57 AM writes...

Damnit.

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2. Rafael Najmanovich on October 9, 2013 8:23 AM writes...

Another name that should be remember here is that of Harold Scheraga...

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3. RegularReader on October 9, 2013 8:23 AM writes...

As a former computational chemistry TA, this is exciting news! Congratulations to the winners!

FYI: One of the winners is known for coma-inducing seminars...

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4. Curious Wavefunction on October 9, 2013 8:24 AM writes...

Always nice to wake up and see your own field recognized. Well-deserved, although I would have included Norman Allinger one way or another. Also definitely an award recognizing a field rather than just individuals.

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5. Bob Sacamano on October 9, 2013 8:29 AM writes...

The Nobel proof-readers let one get by in the linked document.

Page 5: 'Praiser-Parr-Pople' should read 'Pariser-Parr-Pople.'

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6. Anonymous on October 9, 2013 8:33 AM writes...

Bob - you need to get out more

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7. JTA on October 9, 2013 8:35 AM writes...

I'm just curious, what are examples of scientific problems that the recipients have solved using "multiscale models"? Or woud you say that this prize was given rather for laying the theoretical framework (force fields, etc) for methods that may deliver new science today or in the near future?

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8. Anonymous on October 9, 2013 8:39 AM writes...

From the Yahoo News version of the story:

"The Nobel jury said the tool is "universal", helping pharmaceutical engineers to design new drugs or engineers to make cleaner energy sources or smarter manufactured products."

http://news.yahoo.com/karplus-levitt-warshel-win-nobel-chemistry-prize-101235340.html

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9. a on October 9, 2013 8:47 AM writes...

Also, Bill Goddard might be feeling ticked too.

Warshel, how can I put it, his reputation for, putting it mildly, 'prickliness' precedes him..........

I guess the chip on his shoulder will be lifted somewhat.

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10. Anonymous on October 9, 2013 9:05 AM writes...

@7: The specific problem they solved is: How to model complex molecular dynamics accurately and efficiently given limited computing power.

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11. DAD on October 9, 2013 9:14 AM writes...

Agree with post 9...Goddard was there very early and has made enormous contributions at all levels from analytical theory to computational methods and frameworks to software applications to full application across a variety of academic efforts and industries. The winners all have a biology bent to their work, so maybe Sweden will one day recognize multi-scale computational work in non-biological systems like materials and reaction chemistry....(Houck/Goddard?)...

Also agree that the three chosen here have not oversold their craft (even if the Nobel committee has in their write-up...;)

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12. annon on October 9, 2013 9:38 AM writes...

Nobel prize for an area that is oversold and often badly used. Sad, sad, sad.

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13. Anonymous on October 9, 2013 9:48 AM writes...

Seems to be a big year for theory vs experiment & discovery, given this and the Physics prize.

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14. Anon on October 9, 2013 9:55 AM writes...

@1 Ha!

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15. luysii on October 9, 2013 10:02 AM writes...

Amazing! He's the 7th Nobelist present in the Harvard Chemistry department from 60 - 62 when I was a grad student there. Even better these guys weren't sitting there resting on their laurels, but in the process of actively creating them.

They are Woodward, Corey, Bloch, Lipscomb, Hoffmann, Gilbert and now Karplus. It should be noted that 3 of them were Hitler's gift to the USA -- Bloch, Hoffmann, Karplus -- all of whose parents fled the Nazi's because of they were Jews.

The place was full of European expats back then, and Don Voet (whose parents also got out of Europe for the same reason) used to say that the universal scientific language was broken English.

I wonder if 30 or so years hence we'll have all sorts of muslim nobelists, given the carnage going on there presently. Hopefully, we will.

P. S. Even though Gilbert was a physics prof, he was hanging around the chemistry department a lot of the time back than, and his Nobel work was definitely chemical.

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16. leftscienceawhileago on October 9, 2013 10:04 AM writes...

"Scientists who took chemistry into cyberspace win Nobel Prize"

...

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17. JTA on October 9, 2013 10:20 AM writes...

@10: What is an example of a complex molecular dynamics problem that has been addressed accurately? For example in the simulation of protein dynamics the consensus is that the models are not accurate enough and the simulations are not exhaustive (ie, efficient) enough.

To me, merely implementing "complex molecular dynamics" is not an achievement of such fundamental nature that it would warrant a NP of its own. The prize would of course be warranted if the technique is useful in answering real chemical or biological questions. But to my understanding QM/MM is not there yet. Maybe the NP committee has faith that QM/MM will become more useful in the future, and is giving the prize now for the theory behind it?

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18. anthony nicholls on October 9, 2013 10:34 AM writes...

Oh, please, Derek. I'm disappointed in you. Yes, perhaps Karplus deserved one for his many contributions, but MD? Really? Science is about making predictions that experiment confirms, not finding systems that sometimes agree with simulations, which is what MD does. It's a technique of essentially zero utility in pharma and almost no use outside pharma, which damages attempts to do real science by its patina of being 'real', i.e. heaven forbid you don't actually move atoms around and still get thermodynamic averages. It is not well-deserved, it's a disaster for those of us who would like to see computational chemistry be a predictive science. Finally, on your comment about Levitt and others tackling proteins because they were such good scientists- what rot! They did that because it was sexy and they could make movies that got grant money. One thing is was not was good science.

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19. coupled cluster on October 9, 2013 10:41 AM writes...

Most of Ken Houk's work uses other people's functionals such as Becke's B3LYP or Truhlar's M06 and little else. That's like using Heck or Suzuki coupling to make blablablamycins and demanding a Nobel prize for it.

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20. JH on October 9, 2013 10:41 AM writes...

I just hope that they give a prize to Carl Djerassi while they still can. He pioneered some computational tools and algorithms for chemical structure prediction AND he's done a mountain of fundamental research on dozens of other topics. I think that it would be nice if he were in the running.

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21. DAD on October 9, 2013 10:55 AM writes...

@Anthony...agree with your criticism of my post. I should have prefaced my whole post with "if Sweden is going to award a prize for this area..." I was looking at this a bit more optimistically...the award is not not a disaster as long as it's viewed as important early contributions that only barely started the path toward computational chemistry as a predictive science. You have more wisdom than I to judge that perception, and you may have stronger feelings that some of the work actually derailed the path toward a truly predictive science (there a predictive exceptions, so it's hard to state the case that it's all worthless). Synonymous with your take, one could easily argue that with modeling being so decisively predictive in other fields, such as Aeronautical Engineering, that the "meso-scale" modeling in our field has not cracked the nut it was was designed to crack...and hence should not be considered Prizeworthy.

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22. Anonymous academic on October 9, 2013 11:00 AM writes...

@9: I've never even met Warshel, but just reading some of his papers was enough to give me the same impression. I'm not an expert in the field, but I could have sworn that some of them amounted to "our simulations prove these experiments wrong".

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23. Myma on October 9, 2013 11:10 AM writes...

For those not familiar, the winners directly (or indirectly) (or with their groups) created the theory and the actual code behind CHARMm, which is used as a basis for computational chemistry on many many other software platforms as well as used by itself.
Interestingly, since I looked it up this morning, there _is_ a wikipedia page for CHARMm, which lists the Nobel winners as well as the other shoulda/coulda/woulda's people mention in other comments. If anyone is a wikipedia author/editor (which I am not), that page could perhaps be updated to mention the Nobel prize.

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24. Curious Wavefunction on October 9, 2013 11:14 AM writes...

Anthony, you have a point but I don't quite share your cynicism. Science is not just about prediction, it's about explanation (David Deutsch says this very well in his latest book). MD simulations can often point the way toward other experiments that need to be done by shedding light on plausible operating factors. Perhaps they can suggest conformational flexibility of certain side-chains affecting ligand binding which can be tested by mutagenesis, perhaps they can point to loop movements which might affect crystal packing and hamper crystallization. In one of my own projects I have used them to rationalize differences between in vitro and cell activity. Maybe they don't always help in a big way, but they can certainly help in many little ways.

I don't always see MD simulations as predictive tools, I see them as suggestive tools which point to a new experimental direction or constrain the number of known possible explanations. In any case, I think the Nobel Prize this year was more of a lifetime achievement award for the general field of computational chemistry than for any specific technique. It really makes a statement that the field as a whole is being widely employed in diverse fields of chemistry.

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25. Anonymous on October 9, 2013 11:24 AM writes...

I'd rather see a Nobel awarded for masturbation, because it's just as useless, but at least more interesting/enjoyable.

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26. RC on October 9, 2013 11:27 AM writes...

@1 is an LOL.

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27. Per-Ola Norrby on October 9, 2013 11:35 AM writes...

To answer some who say that QM/MM hasn't acomplished anything yet; I'm competing with the technique, using another method, but I still admire the results, the answers we can get about the reasons for reaction selectivity (one of humanities toughest challenges if we want to build a sustainable society). An example I know well is Maseras explaining why the AD (2001 Nobel) can reach such extreme selectivities, and when. Plenty of examples in enzyme mechanisms also. If we don't learn the underlying causes, how can we ever make rational improvements? And build a less wasteful society? And many of these problems have a size and complexity that makes QM/MM a preferred method

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28. Anonymous on October 9, 2013 11:47 AM writes...

@24,27: Any fool or tool can explain things retrospectively, but that's not science (nor useful) unless it makes testable predictions that prove to be correct.

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29. Per-Ola Norrby on October 9, 2013 12:02 PM writes...

@28 So go into for example the Maseras papers on AD and look at the predictions and results. I was impressed. You can't just say it hasn't been done, because there are examples. But we're usually not allowed to publish predictions unless the experimental verification is in the same paper. I can give additional examples from my own work if you wish, but only QM or MM, not QM/MM. I only ever used that for rationalization myself (still science, I'd say, new understanding)

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30. Anonymous on October 9, 2013 12:17 PM writes...

@29: What protein structures has QM/MM predicted to fold from just its primary sequence? Or what is the most complex reaction or rearrangement it has predicted, except for basic local energy minimization?

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31. pipeline_junkie on October 9, 2013 12:23 PM writes...

I recall a comment by Harry Gray at a lecture... something like... "years ago, we would ask the computational chemists their predictions then go with the complete opposite. Back then, that was a sure win. Nowadays, you ask them and their right 50% of the time. That's how much better computational chemistry is getting."

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32. luysii on October 9, 2013 12:33 PM writes...

Well if Houk ever gets the Nobel, he'd be #8 -- see comment #15. Although an undergraduate in '60 - '62, he participated in the Woodward seminars, and was already quite impressive

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33. MarcelSwart on October 9, 2013 12:55 PM writes...

Note, the prize is for QM/MM, not for MD!
How to effectively separate this into meaningful portions in an efficient way is what they received the prize for. How to get to the geometries (either through MM geometry optimization, Monte Carlo or Molecular Dynamics) used for it is explicitly left out:
"The importance of the work of the laureates is independent of what strategy is used for the choice of studied configuration(s). The prize focuses on how to evaluate the variation in the energy of the real system in a accurate and efficient way for systems where relatively large geometry changes or changes in electronic configuration in a smaller part of the studied system is strongly coupled to a surrounding that is only weakly perturbed."
http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2013/advanced-chemistryprize2013.pdf

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34. anon the II on October 9, 2013 1:06 PM writes...

As an organic chemist, I, like Derek, have known about Karplus from his famous equation since I was an undergraduate 38 years ago. Oddly enough, I've never heard of the other two. How did that happen? I also would have thought Allinger would have been in there. It was good to see Scheraga get a mention, though a mention in the Pipeline comments isn't quite a Nobel. Maybe one day.

As for #18 Anthony's comments on MD. I tend to agree. MD has largely been a distraction and has probably hindered implementation of better methods of conformational searching.

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35. dearieme on October 9, 2013 1:10 PM writes...

"@24,27: Any fool or tool can explain things retrospectively, but that's not science ...": maybe not, but it seemed to be a large part of chemistry when I was an undergraduate.

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36. Anonymous on October 9, 2013 1:10 PM writes...

Interesting to read your first sentence, Derek.

The official NobelPrize.org site mentions:

Martin Karplus Université de Strasbourg, France and Harvard University, Cambridge, MA, USA.

The usual bias...;-)

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37. Sili on October 9, 2013 1:13 PM writes...

I just hope that they give a prize to Carl Djerassi while they still can. He pioneered some computational tools and algorithms for chemical structure prediction AND he's done a mountain of fundamental research on dozens of other topics. I think that it would be nice if he were in the running.
To Hell with that. He deserves the Peace Prize for The Pill. But of course noöne will dare give him it.

Just look what junk they gave the Medicine/Physiology prize for last year. Who needs more babies?

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38. Anonymous on October 9, 2013 1:13 PM writes...

The closest I ever came to a Nobel Prize, was renting an apartment from John Pople's (1998 Chemistry Prize) brother back in my graduate school days (Bristol, UK)!

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39. Curious Wavefunction on October 9, 2013 1:19 PM writes...

#28: If you think explanation is not an important part of science then I am afraid you don't have a very good idea of what science is. Before prediction comes explanation: Einstein had to explain known facts about gravity before he could predict the perihelion of Mercury. Darwin had to explain known facts about species before he could predict how new ones are formed. If you think only fools do explanation then surely you must think that Einstein and Darwin were fools. And of course, explanation is still better than no explanation at all.

The example I cited above was in fact a predictive example. MD predicted the kinds of functional groups - including linker lengths - that would stabilize the loop. The predictions were validated by synthesis and the synthetic chemists appreciated it. The main problem with computational chemistry in my experience comes from both computational and non-computational chemists who overstate the utility of the methods and then complain when reality does not meet their unrealistic expectations. Computational chemistry is a tool, just like any other tool in chemistry, and you cannot blame a tool if its practitioners don't use it judiciously.

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40. Anonymous on October 9, 2013 1:31 PM writes...

@39: Then I say everything works by act of God, or magic. They explain everything. Is that good enough "science" for you?

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41. Anonymous on October 9, 2013 1:38 PM writes...

PS. Or do you expect me to make testable predictions with those explanations?

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42. Curious Wavefunction on October 9, 2013 1:48 PM writes...

No, that is not science because science deals with material entities, not supernatural ones. By the way that is precisely the point that David Deutsch makes in his book; you can invoke black boxes ("God" for instance) and make apparently testable and fairly accurate predictions, but it does not lead you any closer to science, let alone understanding. That is why prediction, while important, is not the Holy Grail of science.

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43. H2L on October 9, 2013 1:50 PM writes...

Why are most people in this thread talking about molecular dynamics (MD)? This award is for the combination of molecular mechanics and quantum mechanics (QM/MM). There are plenty of examples where QM/MM has been used to predict reaction rates, enzyme mechanisms, etc. These predictions have been later validated experimentally. While QM/MM is not a panacea, it definitely has a predictive domain of applicability.

I tend to agree with the people that say MD has not been fully proven yet. That is to say, predicting things like protein folding pathways and kinetics of biological processes are very hard and the methods have to improve before they are reliable enough to truly impact drug discovery. But I digress...let's get back to the 2013 Nobel Prize in QM/MM.

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44. Anonymous on October 9, 2013 1:55 PM writes...

@42: Your definition of what is supernatural vs science seems a little subjective. Please could you explain the difference.

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45. Anonymous on October 9, 2013 2:01 PM writes...

PS. Surely evolution, relativity and quantum mechanics are all just constructs of the mind, just like religious faith, and magic, or little green men for that matter. The difference, and only difference between them is in their ability to make testable predictions!

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46. KG on October 9, 2013 2:04 PM writes...

I have been in the field for a long time, and I know, and have interacted with, all of these individuals. I think it's nice that the field of compchem is recognized outside of pure quantum mechanics. And, unlike some of the commenters here, I don't ascribe to the view that MD is nonsense only good for retrospective analysis. To take only the most obvious example, min/MD is part-and-parcel every xray and NMR structure determination done in the past ~two decades.

Obviously, there are plenty of studies that have used MD to prove, mostly, that you can use government research money and computer cycles to unfold proteins with bad force fields, or to make molecules jiggle around with no real predictive payoff. But there are also ample prospective studies now in the literature (and not in the literature when it comes to use in pharma) that demonstrate the usefulness of macromolecular simulations.


I agree that if the intent here is to give the prize for QM/MM calculations, then it's probably pretty premature. But though that's the stated purpose--because the Nobel committee doesn't like to give out "lifetime achievement" awards--the reality would seem to be different. In particular, Karplus' award would assuredly be more for a body of work, than for his specific contributions to QM/MM calculations.

As for individual unpleasantness: Well, I have to agree there. I've interacted and/or worked with most everyone from these early generations of comp chemists, and one of the three inducted here is, well, not the most generous or sweetest of their (or any) generation. The second has a prickly exterior, but a more generous interior. And the third seems to have a second Ph.D. in sitting in talks oblivious to the speaker while he taps away at his keyboard, but is otherwise fine.

To be honest, given the political nature of the Nobel Prize, I'm a little surprised that some of these individuals made it through the process. But I suppose the answer there lies in the fact that while they can be unnecessarily acidic and unpleasant, only one could possibly be accused of being a dreaded self-promoter, and even he is far from the worst of the breed.

And I agree with some of the other comments that mention others who have made huge, lasting, contributions to the field who somehow missed out here. What can you say?

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47. Anonymous on October 9, 2013 2:09 PM writes...

@46: Too much time spent talking to computers vs people?

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48. watcher on October 9, 2013 2:20 PM writes...

#46: What is said on this side really does not matter, now, does it?

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49. Pig Farmer on October 9, 2013 2:57 PM writes...

@38: the closest I ever got to a Nobel Prize was reading a book by Francis Crick.

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50. Nobel Fries on October 9, 2013 3:10 PM writes...

The closest I got to a Nobel Prize was by living in a country where Nobel Laureate Obama was president.

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51. sgcox on October 9, 2013 3:14 PM writes...

Ok, While I normally agree with Curious Wavefunction (~42), here I part the ways. MD is a BlackBox (God ?) with no predictive functions. Example: you run MD on protein A for N femtoseconds. Can you now predict what will happen to protein B after M femtoseconds of MD _BEFORE_ running MD of protein B for M femtoseconds.
No? So you are left no wiser after this hmm, exercise.. So how can you call it a science, howe