The price of global warming science is eternal vigilance

John Tierney of the NYT weighs in on the hacked emails and accurately nails it

I’ve long thought that the biggest danger in climate research is the temptation for scientists to lose their skepticism and go along with the “consensus” about global warming. That’s partly because it’s easy for everyone to get caught up in “informational cascades”, and partly because there are so many psychic and financial rewards rewards for working on a problem that seems to be a crisis. We all like to think that our work is vitally useful in solving a major social problem — and the more major the problem seems, the more money society is liable to spend on it.

I’m not trying to suggest that climate change isn’t a real threat, or that scientists are deliberately hyping it. But when they look at evidence of the threat, they may be subject to the confirmation bias — seeing trends that accord with their preconceptions and desires. Given the huge stakes in this debate — the trillions of dollars that might be spent to reduce greenhouse emissions — it’s important to keep taking skeptical looks at the data. How open do you think climate scientists are to skeptical views, and to letting outsiders double-check their data and calculations?

We are all subject to the confirmation bias, and I can say from experience that we have to battle it in our research every single day as fallible human beings. But as Tierney says, when the stakes are so incredibly high, when governments and international budgets and debts and the fate of billions is going to be affected by what you say, you better fight the conformation bias ten times as much as usual.

Listen to Capt. Ramsey, son:

"Mr. Hunter, we have rules that are not open to interpretation, personal intuition, gut feelings, hairs on the back of your neck, little devils or angels sitting on your shoulders..."

The damning global warming emails; when science becomes the casualty

By now everyone and his grandmother must have heard about the hacked emails of the prestigious University of East Anglia Climate Research Unit (CRU). The emails were sent by leading climate change scientists to each other and seem to express doubts and uncertainty. More importantly they also seem to display some troubling signs of rather dishonest discourse, with scientists trying to hold dangerously unfavorable opinions of journal editors who seem to be open to publishing papers that don't seem to agree with their views, and asking each other to delete emails which might signal doubt.

There is at least one example of bad science revealed in the emails. It seems that one set of data from tree ring proxies did not show the expected rise in temperatures for a particular period and showed a decline. What was done was that just for that period, a different set of data from another method which did show the rise was grafted on to this piece of data. John Tierney of the NYT has the two graphs on his blog. Does this change the general conclusion? Probably not. Is this bad science and enough to justify a flurry of indignant questions in the minds of outsiders? Certainly so. Good science would have meant revealing all the pieces of data including those which showed a decline.

Now what is remarkable (or perhaps not remarkable at all) is the vociferous political- not scientific- reaction that has erupted in blogs all over the internet. I would point readers to my fellow blogger Derek Lowe's succinct summary of the matter. While I am not as skeptical about climate change as he is, it is disconcerting to see how much political, personal and social baggage the whole issue is carrying. Whenever a scientific issue starts carrying so much non-scientific baggage, one can be assured that we are in trouble.

The comments on most blogs range across the spectrum. There are the outright deniers who claim that the emails "disprove global warming"; they don't, and I can't see how any set of personal exchanges could say almost anything definitive about a system as complex as the climate. Phrases like "hide the decline" (in the case of the above tree ring proxy data) and "trick" have been taken out of their technical context to indicate subversion and deception. And then there are the proponents who want to act like nothing has happened. I like George Monbiot's take on it where he says that even if the science of climate change has certainly not come crashing down, the public image of climate change has been dealt a serious blow, and denying this would simply mean burying your head in the sand. After all, we are supposed to be the good guys, the ones who are supposed to honestly admit to our limitations and failings, and we are not doing this. What ramifications this will have for the important Copenhagen climate summit this month is uncertain.

However, the very fact that we have to worry as much about the public image of climate science as the science itself plainly speaks to the degree of politicization of the issue. I think the liability of this entire matter has basically become infinite and I think scientists working in the field are facing an unprecedented dilemma which few scientists have ever faced. Here's the problem; we are dealing with an extremely complex system and it is hardly surprising if the science of this system (which after all is only a hundred years or so old) keeps getting revised, reshuffled and reiterated even if the basics remain intact. That would be perfectly normal for a vast, multidisciplinary field like this. That is the way science works. One finds such revision and vigorous debate even in highly specific and recondite areas like the choice of atomic partial charges in the calculation of intermolecular energies. The climate is orders of magnitude more complicated. If the usual rules of scientific discourse were to be followed, making such debates and disagreements open would not be a problem.

But with an issue that is so exquisitely fraught with political and economic liabilities and where the stakes are so enormously high, I believe that the normal process of scientific debate, discourse and progress has broken down and is being bypassed. Scientists who would otherwise engage in lively debate and disagreements have become extremely loathe to make their doubts public. These scientists fear that they would essentially be condemned by both sides. The right wing extremists would seize upon any honest disclosure of debate as the kick that brings the entire edifice crumbling down. They would predictably try to discredit even reasonable conclusions drawn by climate change scientists. At the same time, left wing extremists would essentially disown such scientists and either declare them an anomaly or more predictably declare them to be political and corporate shills. A scientist who honestly voices his doubts would become a man without a country.

This is of course in addition to the ample scorn that establishment upholders like climate blogger Joe Romm would heap on them. Thus, if you are a scientist working in climate change today, it would be rather difficult for you to make even the normal process of science transparent. Plus, most scientists are genuinely scared that all the momentum they have built over the years would fizzle out if their right wing opponents pounce on their private doubts. Think about it. The Copenhagen summit is going to be held in a month. Scientists have faced enormous obstacles in convincing the public and governments about climate change. Your work has been crowned by grudging acknowledgement even by George W Bush and the Nobel Peace Prize for Al Gore. Would you be ready to throw away all this rightly hard-earned and hard-fought consensus for the sake of a few dissenting opinions? The simple laws of human nature dictate that you probably would not.

In my opinion, that is what seems to have happened with the scientists at the CRU. They have been so afraid of not only expressing their doubts (many of which as noted above would be valid given the science involved) but also entertaining other dissenting opinions that they have unfortunately picked the option of trying to silence open debate in a way that would be unacceptable in science in general. One can understand their motivation, but their actions still seem deplorable.

I think these emails point to a much more serious structural problem in the scientific enterprise of climate change. For good reasons and bad, whether to stand up to political hacks or ironically to defend good science, this enterprise has accumulated so much political baggage that it is now virtually impossible for it to compromise, to change, to maneuver even in the face of cogent reasons. The science of climate change has essentially bound itself into a straitjacket. My prediction is that important decisions about this science will in the future be mainly politically motivated. Public consensus not completely backed by good science will be the driving force for major decisions. The consequences of those decisions, just like the climate, are uncertain. We will have to wait and see.

But as usual, the casualty is ultimately science itself. What was good science and ineffective politics before is becoming effective politics and bad science. Whatever else happens, science never wins when it gets so overtly politicized. And hopefully about this there will be universal consensus.

More model perils; parametrize this

Now here's a very interesting review article that puts some of the pitfalls of models that I have mentioned on these pages in perspective. The article is by Jack Dunitz and his long-time colleague Angelo Gavezzotti. Dunitz is in my opinion one of the finest chemists and technical writers of the last half century and I have learnt a lot from his articles. Two that are on my "top 10" list are his article showing the entropic gain accrued by displacing water molecules in crystals and proteins (a maximum of 2 kcal/mol for strongly bound water) and his paper demonstrating that organic fluorine rarely, if ever, forms hydrogen bonds.

In any case, in this article he talks about an area in which he is the world's acknowledged expert; organic crystal structures. Understanding and predicting (the horror!) crystal structures essentially boils down to understanding the forces that makes molecules stick to each other. Dunitz and Gavezzotti describe theoretical and historical attempts to model forces between molecules, and many of their statements about the inherent limitations of modeling these forces rang as loudly in my mind as the bell in Sainte-Mère-Église during the Battle of Normandy.

Dunitz has a lot to say about atom-atom potentials that are the most popular framework for modeling inter and intramolecular interactions. Basically such potentials assume simple functional forms that model the attractive and repulsive interactions between nuclei which are treated as rigid balls. This is also of course the fundamental approximation in molecular mechanics and force fields. The interactions are basically Coulombic interactions (relatively simple to model) and more complicated dispersion interactions which are essentially quantum mechanical in nature. The real and continuing challenge is to model these weak dispersive interactions.

But the problem is fuzzy. As Dunitz says, atom-atom potentials are popular mainly because they are simple in form and easy to calculate. However, they have scant, if any, connection to "reality". This point cannot be stressed enough again. As this blog has noted several times before, we use models because they work, not because they are real. The coefficients in the functional forms of the atom-atom potentials are essentially varied to minimize the potential energy of the system and there are several ways to skin this cat. For instance, atomic point charges are rather arbitrary (and definitely not "real") and can be calculated and assigned by a variety of theoretical approaches. In the end, nobody knows if the final values or even the functional forms have much to do with the real forces inside crystals. It's all a question of parameterization which gives you the answer, and while parameterization may seem like a magic wand which may give you anything that you want, that's precisely the problem with it...that it may give you anything that you want without reproducing the underlying reality. Overfitting is also a constant headache and one of the biggest problems with any modeling in my opinion; whether in chemistry, quantitative finance or atmospheric science. More on that later.

An accurate treatment of intermolecular forces will have to take electron delocalization into consideration. The part which is the hardest to deal with is the part close to the bottom of the famous Van der Waals energy curve, where there is an extremely delicate balance between repulsion and attraction. Naturally one thinks of quantum mechanics to handle such fine details. A host of sophisticated methods have been developed to calculate molecular energies and forces. But those who think QM will take them to heaven may be mistaken; it may in fact take them to hell.

Let's start with the basics. In any QM calculation one uses a certain theoretical framework and a certain basis set to represent atomic and molecular orbitals. One then adds terms to the basis set to improve accuracy. Consider Hartree-Fock theory. As Dunitz says, it is essentially useless for dealing with electron delocalization because it does not take electron correlation into account, no matter how large a basis set you use. More sophisticated methods have names like "Moller-Plesset perturbation theory with second order corrections" (MP2) but these may greatly overestimate the interaction energy, and more importantly the calculations become hideously computer intensive for anything more than the simplest molecules.

True, there are "model systems" like the benzene dimer (which has been productively beaten to death) for which extremely high levels of theory have been developed that approach experimental accuracy within a hairsbreadth. But firstly, model systems are just that, model systems; the benzene dimer is not exactly a molecular arrangement which real life chemists deal with all the time. Secondly, a practical chemist would rather have an accuracy of 1 kcal/mol for a large system than an accuracy of 0.1 kcal/mole for a simple system like the benzene dimer. Thus, while MP2 and other methods may give you unprecedented accuracy for some model systems, they are usually very expensive for most systems of biological interest and not very useful.

DFT still seems to be one of the best techniques around to deal with intermolecular forces. But "classical" DFT suffers from a well-known inability to treat dispersion. "Parameterized DFT" in which an inverse sixth power term is added to the basic equations can work well and promises to be a very useful addition to the theoretical chemist's arsenal. More parameterization though.

And yet, as Dunitz points out, problems remain. Even if one can accurately calculate the interaction energy of the benzene dimer, it is not really possible to know how much of it comes from dispersion and how much of it comes from higher order terms. Atom-atom potentials are happiest calculating interaction energies at large distances, where the Coulomb term is pretty much the only one which survives, but at small interatomic distances which are the distances most of interest for the chemist and the crystallographer, a complex dance between attraction and repulsion, monopoles, dipoles and multipoles and overlapping electron clouds manifests itself. The devil himself would have a hard time calculating interactions in these regions.

The theoretical physicist turned Wall Street quant Emanuel Derman (author of the excellent book ("My Life as a Quant: Reflections on Physics and Finance") says that one of the problems with the financial modelers on Wall Street is that they suffer from "physics envy". Just like in physics, they want to discover three laws that govern 99% of the financial world. More predictably as Derman says, they end up discovering 99 laws that seem to govern 3% of the financial world with varying error margins. I would go a step further and say that even physics is accurate only in the limit of ideal cases and this deviation from absolute accuracy distinctly shows in theoretical chemistry. Just consider that the Schrodinger equation can be solved exactly only for the hydrogen atom, which is where chemistry only begins. Anything more complicated that, and even the most austere physicist cannot help but approximate, parametrize, and constantly struggle with errors and noise. As much as the theoretical physicist would like to tout the platonic purity of his theories, their practical applications would without exception involve much approximation. There is a reason why that pinnacle of twentieth century physics is called the Standard Model.

I would say that computational modelers in virtually every field from finance to climate change to biology and chemistry suffer from what Freeman Dyson has called "technical arrogance". We have made enormous progress in understanding complex systems in the last fifty years and yet when it comes to modeling the stock market, the climate or protein folding, we seem to think that we know it all. But we don't. Far from it. Until we do all we can do is parametrize, and try to avoid the fallacy of equating our models with reality.

That's right Dorothy. Everything is a model. Let's start with the benzene dimer.

Dunitz, J., & Gavezzotti, A. (2009). How molecules stick together in organic crystals: weak intermolecular interactions Chemical Society Reviews, 38 (9) DOI: 10.1039/b822963p

California axes science

From the NYT

As the University of California struggles to absorb its sharpest drop in state financing since the Great Depression, every professor, administrator and clerical worker has been put on furlough amounting to an average pay cut of 8 percent.

In chemistry laboratories that have produced Nobel Prize-winning research, wastebaskets are stuffed to the brim on the new reduced cleaning schedule. Many students are frozen out of required classes as course sections are trimmed.

And on Thursday, to top it all off, the Board of Regents voted to increase undergraduate fees — the equivalent of tuition — by 32 percent next fall, to more than $10,000. The university will cost about three times as much as it did a decade ago, and what was once an educational bargain will be one of the nation’s higher-priced public universities.

There was a time when people used to go to Berkeley for the lower tuition. Seems the last refuges of education are gradually eroding away.

What did you say the error was??

I was looking at some experimental data for drug molecules binding to a pharmaceutically relevant protein.

The numbers reported were as percentages of binding relative to a standard which was defined to be 100%. Here's how they looked:

97.3 + - (plus or minus) 68.4
79.4 + - 96.1
59.5 + - 55.3
1.4 + - 2.5

Seriously, how did the reviewers allow this to go through?

A new look, with hair combed and shoes brushed

As you may have noticed, I have transitioned to a spanking new look at Field of Science (FoS), thanks to Edward's invitation and am loving it. I also join a super team of fellow bloggers whom I hope to regularly read. You won't have to update your bookmarks since you will be automatically directed here when you click on the old link.

I have to admit that after exercising my primitive blog management skills for the last five years, this feels like warp speed and spinach combined.

A hermitian operator in self-imposed exile

Perfect Rigor: A Genius and the Mathematical Breakthrough of the Century
Masha Gessen (Houghton Mifflin Harcourt, 2009)

Pure mathematicians have the reputation of being otherworldly and divorced from practical matters. Grisha or Grigory Perelman, the Russian mathematician who at the turn of this century solved one of the great unsolved problems in mathematics, the Poincare Conjecture, is sadly or perhaps appropriately an almost perfect specimen of this belief. For Perelman, even the rudiments of any kind of monetary, professional or material rewards resulting from his theorem were not just unnecessary but downright abhorrent. He has turned down professorships at the best universities in the world, declined the Fields Medal, and will probably not accept the 1 million dollar prize awarded by the Clay Mathematics Institute for the solution of the some of the most daunting mathematical problems of all time. He has cut himself off from the world after seeing the publicity that his work received and has become a recluse, living with his mother in St. Petersburg. For Perelman, mathematics should purely and strictly be done for its own sake, and could never be tainted with any kind of worldly stigma. Perelman is truly a mathematical hermit, or what a professor of mine would call using mathematical jargon, a "hermitian operator".

In "Perfect Rigor", Masha Gessen tells us the story of this remarkable individual, but even more importantly tells us the story of the Russian mathematical system that produced this genius. The inside details of Russian mathematics were cut off from the world until the fall of the Soviet Union. Russian mathematics was nurtured by a small group of extraordinary mathematicians including Andrey Kolmogorov, the greatest Russian mathematician of the twentieth century. Kolmogorov and others who followed him believed in taking latent, outstanding talent in the form of young children and single-mindedly transforming them into great problem solvers and thinkers. Interestingly in the early Soviet Union under Stalin's brutal rule, mathematics flourished where other sciences languished partly because Stalin and others simply could not understand abstract mathematical concepts and thus did not think they posed any danger to communist ideology. Soviet mathematics also got a boost when its great value was recognized during the Great Patriotic War in building aircraft and later in work on the atomic bomb. Mathematicians and physicists thus became unusually valued assets to the Soviet system.

Kolmogorov and a select band of others took advantage of the state's appreciation of math and created small, elite schools for students to train them for the mathematical olympiads. Foremost among the teachers was a man named Sergei Rukshin who Gessen talks about at length. Rukshin believed in completely enveloping his students in his world. In his schools the students entered a different universe, forged by intense thought and mathematical camaraderie. They were largely shielded from outside influences and coddled. The exceptions were women and Jews. Gessen tells us about the rampant anti-Semitism in the Soviet Union which lasted until its end and prevented many bright Jewish students from showcasing their talents. Perelman was one of the very few Jews who made it, and only because he achieved a perfect score in the International Mathematical Olympiad.

Perelman's extreme qualities were partly a result of this system, which had kept him from knowing about politics and the vagaries of human existence and insulated him from a capricious world where compromise is necessary. For him, everything had to be logical and utterly honest. There was no room for things such as diplomacy, white lies, nationalism and manipulation to achieve one's personal ends. If a mathematical theorem was proven to be true, then any further acknowledgment of its existence in the form of monetary or practical benefits was almost vulgar. This was manifested in his peculiar behavior in the United States. For instance, when he visited the US in the 90s as a postdoctoral researcher he had already made a name for himself. Princeton offered the twenty nine year old an assistant professorship, a rare and privileged opportunity. However Perelman would settle for nothing less than a full professorship and was repulsed even by the request that he officially interview for the position (which would have been simply a formality) and submit his CV. Rudimentary formalities which would be normal for almost everyone were abhorrent for Perelman.

After being disillusioned with what he saw as an excessively materialistic academic food chain in the US, Perelman returned to Russia. For five years after that he virtually cut himself off from his colleagues. But it was then that he worked on the Poincare Conjecture and created his lasting achievement. Sadly, his time spent intensely working alone in Russia seemed to have made him even more sensitive to real and perceived slights. However, he did publicly put up his proofs on the internet in 2002 and then visited the US. For a brief period he even seemed to enjoy the reception he received in the country, with mathematicians everywhere vying to secure his services for their universities. He was unusually patient in giving several talks and patiently explaining his proof to mathematicians. Yet it was clear he was indulging in this exercise only for the sake of clarifying the mathematical concepts, and not to be socially acceptable.

However, after this brief period of normalcy, a series of events made Perelman reject the world of human beings and even that of his beloved mathematics. He was appalled by the publicity he received in newspapers like the New York Times which could not understand his work. He found the rat race to recruit him, with universities climbing over each other and making him fantastic offers of salary and opportunity, utterly repulsive. After rejecting all these offers and even accusing some of his colleagues of being traitors who gave him undue publicity, he withdrew to Russia and definitively severed himself from the world. The final straw may have been two events; the awarding of the Fields Medal which, since his work was still being verified, could not explicitly state that he had proven the Poincare conjecture, and the publication of a paper by Chinese mathematicians which in hindsight clearly seems to have been written for stealing the limelight and the honors from Perelman. For Perelman, all this (including the sharing of the Fields with three other mathematicians) was a grave insult and unbecoming of the pursuit of pure mathematics.

Since then Perelman has been almost completely inaccessible. He does not answer emails, letters and phone calls. In an unprecedented move, the president of the International Mathematical Congress which awards the Fields Medals personally went to St. Petersburg to talk him out of declining the prize. Perelman was polite, but the conversation was to no avail. Neither is there any indication that he would accept the 1 million dollar Clay prize. Gessen himself could never interview him, and because of this the essence of Perelman remains vague and we don't really get to know him in the book. Since Gessen is trying to somewhat psychoanalyze her subject and depends on second-hand information to draw her own conclusions, her narrative sometimes lacks coherence and meanders off. As some other reviewers have noted, the discussion of the actual math is sparse and disappointing, but this book is not really about the math but about the man and his social milieu. The content remains intriguing and novel.

Of course, Perelman's behavior is bizarre and impenetrable only to us mere mortals. For Perelman it forms a subset of what has in his mind always been a perfectly internally consistent and logical set of postulates and conclusions. Mathematics has to be done for its own sake. Academic appointments, prizes, publicity and professional rivalries should have no place in the acknowledgement of a beautiful mathematical proof. While things like applying for interviews and negotiating job offers may seem to us to be perfectly reasonable components of the real world and may even seem to be necessary evils, for Perelman they are simply evils interfering with a system of pure thought and should be completely rejected. He is the epitome of the Platonic ideal; where pure ideas are concerned, any human association could only be a deeply unsettling imposition.