Field of Science

A potentially revolutionary new technique for chemical structure determination


I am a big believer in science as a tool-driven rather than an idea-driven revolution, and nowhere do you see this view of science exemplified better than in the development of instrumental techniques in chemistry - most notably NMR and x-ray diffraction. NMR and crystallography were not just better ways to see molecules, but in their scope, their throughput, their cost and their speed, they opened up whole new fields of science like genomics and nanomaterials up to investigation that their developers couldn't even have imagined.

So it is with some interest that I saw a paper from the Nelson, Gonen and Rodriguez labs at UCLA and the Stoltz lab at Caltech that describes a new way to rapidly determine the structures of organic molecules. And I have to say: very few papers in recent times have made me sit up and do a double take, but this one did. At one point in the paper the authors say they were "astounded" by the ease of the technique, and I don't think that word is out of place here at all.

Until now, crystallography has been the gold standard for all kinds of structure determination; it gives you as direct a view of molecules at the atomic level as possible. But the very name "crystallography" implies that you need to get your sample into a crystalline state, and as any chemist who has worked with a headache-inducing list of assorted powders, gels, oils and tars knows, being crystalline is not the natural state of most molecules. In most cases your samples are thus simply not in a convenient form for crystallography.

That's why NMR has been the primary technique for routine organic structure determination. But NMR is still relatively slow and depends on having a machine that's expensive and sometimes breaks down. You also cannot do NMR on a benchtop, and getting the sample in a pure enough condition in the right solvent is also key to good structure determination. Then there are all the problems attendant with shimming, water suppression and other artifacts that NMR presents, although sophisticated software can now take care of most of these. Nonetheless, as powerful as NMR is and will continue to be, it's not exactly a rapid, plug-and-play system.

That's why this recent paper is so promising. It describes a crystallographic technique that uses cryo-EM and micro-electron diffraction (micro ED) for efficiently finding out the structure of organic molecules. Electron diffraction itself is an old technique, pioneered for instance by Linus Pauling in the 1930s, but this is not any old ED, it's micro ED. Cryo-EM already won the Nobel Prize two years ago for determining the structures of complex proteins, but it has never been routinely applied to small molecule structure determination. This new technique could change that landscape in a jiffy. And I mean in a jiffy - the examples they have shown take a few minutes each. The first molecule - progesterone - went from powder to pattern in less than 30 mins, which is quite stunning. And the resolution was 1 Å, and you can't ask for more. Up to twelve samples were investigated in a single experiment.

But what really made me sit up was the variety of starting points that could be investigated. From amorphous powders to samples straight out of flash chromatography to mixtures of compounds, the method made quick work out of everything. As mentioned above, amorphous powders and mixtures are the rule rather than the exception in standard organic synthesis, so one can see this technique being applied to almost every chemical purification and synthetic manipulation done in routine synthesis or structure determination. For me the most amazing application however was the determination of a mixture of four different molecules: no other technique in organic chemistry which I know can do mixtures in a few minutes with such high resolution with such little material.

There are undoubtedly still limitations. For one thing, cryo-electron microscopes are still not cheap, and while sample preparation is getting better, it's also not instantaneous in every case. I also noticed that most of the compounds this study looked at were rather rigid, with lots of fused and other rings; floppy molecules will likely cause some trouble, and although thiostrepton is an impressive-looking molecule, it would be interesting to see how this works for beasts like rapamycin or oligopeptides. In general, as with other promising techniques, we will have to see what the domain of applicability of this method is. 

Nonetheless, this is the kind of technique that promises to take a scientific field in very novel directions. It could accelerate the everyday practice of organic chemistry in multiple fields - natural products, chemical biology, materials science - many fold; and at some point, quantity has a quality of its own. It could allow the investigation of the vast majority of compounds that cannot be easily coaxed into a crystal or an NMR tube. And it could perhaps even allow us to study conformational behavior of floppy compounds, which from first-hand experience I know is pretty hard to do.

If validated, this technique also exemplifies something I have talked about before, which is how scientific tools and discoveries build on each other; in other words, how scientific convergence is a key driving force in science. When cryogenics was invented, nobody foresaw cryo-electron microscopy, and when cryo-EM was invented, nobody foresaw its application to routine organic synthesis. And so it goes on, science and technology piggybacking in ever-expanding spirals.

Lessons from Tom Steitz, surveyor of molecular empires (1940-2018)



The ribosome is one of the most important and complicated molecular machines ever devised by evolution. Functioning as the factory and assembler for making proteins from RNA, it is as important as DNA itself and is found in every life form on planet Earth. If we find life on another planet, along with some form of DNA, it is almost certain to contain some kind of ribosome.

Tom Steitz, Venki Ramakrishnan and Ada Yonath won the Nobel Prize for chemistry in 2009 for cracking the structure of the ribosome. I was saddened to hear that Steitz passed away a few days ago. Incidentally, his demise comes after Venki Ramakrishnan published his memoir on his ribosome odyssey, a journey that both starred and owed a lot to Tom Steitz.

Over more than two decades, Steitz, Ramakrishnan, Yonath and others used laborious techniques to carefully obtain more complicated and better structures of this beast of a molecule. And a beast it certainly was; the 40S subunit of a eukaryotic ribosome contains 1900 nucleotides and 33 proteins. While protein crystallography is now routine, solving the structure of a multiprotein assembly like the ribosome is incredibly daunting even now, and is a tribute to both the perseverance and the creativity of these scientists. Crystallography is the ultimate example of marathon running in science, something that at its highest levels can easily take a decade and long hours in the lab. Even before he attacked the ribosome, Steitz had already established a reputation as one of the world's top crystallographers, doing a detailed study of the enzyme hexokinase for instance. Among other findings, his work revealed that the ribosome is composed mainly of RNA rather than proteins; another boost for the RNA world theory for the origins of life.

I have fond memories of Steitz from my time as a postdoc at the University of North Carolina, Chapel Hill. In 2010, a year after he won the prize, he was a visiting lecturer at UNC. Four or five of us had a chance to sign up for a private breakfast with him in a small room at the faculty club. There wasn't a trace of ego in Steitz's interactions with us, but what I remember best was his unending curiosity regarding each of our research projects (not surprisingly, he was particularly interested in some cryo-EM work a colleague of mine was doing). It was clear that Seitz was no prima donna, but a scientist's scientist who was not resting on his laurels but seeking new adventures.

The New York Times has a good obituary of Steitz that showcases many of his qualities. After his PhD he trained at the famed MRC Laboratory of Molecular Biology, an institution started by Watson, Crick, Perutz and others that has produced more than fifteen Nobel Laureates. The article talks about the atmosphere in the institute, where Nobel laureates sat next to graduate students during tea and lunch in the cafeteria and constantly talked science. One thing that struck Steitz was how much time they spent talking about experiments rather than doing them; later he realized that they were basically enforcing a process of ruthless elimination on the experiments by discussing them beforehand, so that they would pursue only the most promising ones. That's a good lesson.

I remember another MRC-related anecdote that Steitz told us during our breakfast eight years ago; he was constantly surprised how the famous scientists at the MRC asked seemingly stupid or simple questions whose answers were not as obvious as we think. For instance, he remembers Max Perutz asking everyone what a eukaryote was; the question led to an unexpectedly fascinating discussion about the molecular differences between eukaryotes and prokaryotes. Steitz emphasized to us how important it is to keep on asking simple questions and setting our egos aside, a lesson that many of us sadly don't imbibe.

Steitz's wife Joan is an equally eminent biologist in her own regard. She was awarded a Lasker Prize this year and has done much to advance RNA science in addition to serving as a role model for women in science. When Steitz was looking for a faculty position he was offered one at Berkeley, but they declined to offer Joan - a protégé of James Watson - one, so Steitz turned down the job, and the couple moved to Yale where both of them acquired prestigious positions.

Tom Steitz was a scientist's scientist and an honorable man who did much to advance progress in molecular biology and the cause of honest, sound science. He will be missed.

Big discoveries from little things


That's physicist Albert Michelson, at the University of Chicago in 1894, saying that fundamental physics was essentially finished. In the fifty years after Michelson's talk, physics discovered the following: special and general relativity, quantum theory, nuclear fission and the expansion of the universe. And it was just getting warmed up. The famously acerbic Wolfgang Pauli would have probably called Michelson's prediction as "not even wrong".

Michelson clearly was woefully wrong in saying that the main task of physics would henceforth simply be more accurate measurements. And yet it would be wrong to take him to task for a clearly mistaken view, for at least two reasons. Firstly, physics in 1894 explained an enormous range of phenomena. From Newtonian mechanics that explained everything from apples falling down to the motion of planets to thermodynamics which explained everything from the increase in disorder in physical systems to the practical workings of steam engines, physics clearly had proved itself to be a spectacularly successful science, so there was good reason to think that most of the fundamentals had been worked out. 

Secondly, the kinds of things physics was being unable to explain then could be seen as little more than annoying anomalies and exceptions; the behavior of glowing blackbodies, the slight anomaly in the motion of mercury around the Sun, the absence of the luminiferous ether. In fact, Michelson himself would perform an experiment just three years later, in 1887, that would lead to a very important negative result: the lack of detection of the ether that had been predicted as a medium for the propagation of light and other electromagnetic radiation which Maxwell had worked out.

Neither Michelson nor anyone else could have seen the profound new worlds hidden in these seemingly mundane anomalies. Problems with blackbody radiation led to the birth of Planck's quantum theory, and problems with the ether and with the anomalous orbit of Mercury led to Einstein's special and general theories of relativity. And at least in one sense Michelson's highlighting of more and more accurate measurements was spot on: the difference between the perihelion of Mercury predicted by Newton's theory of gravity and what was actually measured was tiny - Newton's prediction was off only by a millionth of one percent (which meant that Mercury would arrive at its perihelion only half a second later than what Newton predicted), but that little deviation hid a stunningly different and new view of nature that took Einstein's genius to uncover.

Rather than mocking Michelson's 1894 statement as a foolish failure of prediction or the product of tunnel vision, it's more important therefore to recognize what it implies. Firstly, it's clear that nobody and not just Michelson could have known how different the future of physics would be, giving currency to Niels Bohr's statement that prediction is difficult, especially about the future. But more importantly, it's enlightening to realize how seemingly mundane experimental anomalies can lead to completely new ways of looking at the world. 

In my view, the fifty years that followed Michelson's statement, although now rightly regarded as a triumph of theoretical physics, should be viewed as an even greater triumph of experimental physics. Both the old quantum theory invented by Planck and the new quantum theory invented by Heisenberg and others arose from small, anomalous observations in seemingly obscure and minor areas of physics. So did relativity. Without the exceedingly accurate measurement of the error in the predicted vs measured anomaly of Mercury's orbit, who knows how long it would have taken general relativity to come along.

The development of physics following Michelson's statement gives one hope that the biggest discoveries in science will continue to be hidden in some of the smallest discrepancies in experiment. This is especially true of biology where we are now in a position to detect very small differences in protein and gene expression. Experimentalists should keep on looking for minor anomalies in their observations; flies in the ointment; nagging little differences in numbers that should be explained by the existing theoretical framework but are not. Sometimes it will be nothing, often it will simply be a result of statistical error or random noise, but occasionally, just occasionally, it could be a glimpse of the crack of light from a door that opens on to a whole new world.

On Nobel Prizes, Diversity And Tool-Driven Scientific Revolutions

First published on 3 Quarks Daily.
The Nobel Prizes in science will be announced this week. For more than a century the prizes have recognized high achievement in physics, chemistry and medicine. Some scientists crave the prizes so much that they get obsessed with them. A prominent, world-famous chemist once had lunch with my graduate school advisor. After a few minutes he went off on a tirade against the Nobel committee, cursing them for not giving him the prize. He never got it, and he never got over it. The Nobel can bring fame and recognition, but it can also make the lives of those who live for them miserable.
A human prize created by a human committee based on the will of a human who established it to atone for a better method of killing people should not cause people such agony. And yet, in many ways, the prizes reflect all that is good and bad about human nature. The physicist Phillip Lenard later turned out to be a Nazi who denounced Einstein and his relativity. The celebrated Werner Heisenberg wasn’t a Nazi, but he controversially participated in work toward an atomic weapon in Germany during the war. Fritz Haber made an even more damning pact with the devil. Haber and his collaborator Carl Bosch kept alive, by one measure, one third of the world’s population by inventing a process to manufacture ammonia for fertilizers from nitrogen in the air. Haber won the Nobel Prize for chemistry in 1918, right after he had spent the First World War inventing chemical weapons that led to the deaths of tens of thousands. António Moniz who won the prize in medicine in 1949 pioneered the highly controversial procedure of lobotomy which, even though it seemed like a good idea then, incapacitated thousands. And William Shockley who co-invented the transistor and inaugurated Silicon Valley later became infamous for promoting racist theories of intelligence. The moral landscape of Nobelists even in science is unambiguous, so one can imagine how much worse it would be and in fact is in areas like peace and economics.
There are also all the other human problems which have been highlighted with the prizes. The ratio of those who deserved the award but did not get it to those who did must be at least a hundred to one, although it’s at least possible to make an honest argument that those who did get it largely deserved to. Some spurned candidates have taken it in their stride and jest about it. The astronomer Jocelyn Bell-Burnell should have received the prize for the discovery of pulsars – rotating neutron stars; instead only her PhD advisor Anthony Hewish shared it. But Bell-Burnell has taken the fifty-year controversy in good humor, joking that it’s better that people ask her why she didn’t win it than why she did. The fallout from the controversy might have affected more than just Bell-Burnell: the astrophysicist Fred Hoyle who deserved a share of the 1983 prize for his groundbreaking work deciphering the synthesis of the elements in stars was sidelined, and some think it might have been for his vigorous public advocacy of Bell-Burnell.
Most egregious is the three-person rule which prevents many other worthy individuals from getting the prize almost every year. In one case, just like the chemist who was complaining to my advisor, one bitter scientist who felt especially ignored for the lack of recognition of his work on MRI took out a full-page advertisement in the New York Times protesting the omission. Even otherwise world-renowned scientists are not immune to wanting even more recognition. Robert Burns Woodward, by a very broad consensus the greatest organic chemist of the 20th century, wrote a remarkable letter to the Nobel committee protesting the chemistry prize in 1973 which was published in The Times of London, telling them that they had committed a grievous error by not including him among the winners; Woodward in fact had already won the prize in 1965 for his seminal contributions to the synthesis of complex organic substances like chlorophyll, and he would have undoubtedly won another one in 1981 with Roald Hoffmann had he not died the year before.
There is also a pronounced lack of women winning the prizes, especially in physics which has not seen a woman win for fifty years. While disappointing, to some extent this is not surprising since women haven’t been represented in higher physics education and the physics workforce because of systematic barriers; Princeton University did not admit female physics students in its astronomy graduate programs until the 1960s; the problem really should be addressed at a much lower level. Fortunately there have been an increasing number of women in physics and other sciences in the last twenty years, so hopefully in a few years we should start seeing women represented in the list. The prizes have also been overwhelmingly won by scientists from the United States and Europe: this fact is even less surprising since these countries are where most pioneering scientific research after the Second World War has taken place. The only Asian country which has been well represented has been Japan, and the Japanese have progressed in science and technology after their virtual destruction in World War 2 at breakneck speed. Chinese, Indian and other scientists have won a few of the prizes, but it’s always been for work done in the United States or Europe. It’s noteworthy therefore that three years ago, Tu Youyou became the first Chinese scientist and woman who won a Nobel Prize for work done in China; she won for the discovery of the antimalarial drug artemisinin. If China, India and other countries pour money into their scientific institutions and train the next generation of scientists, if they bring the same spirit of adventure, risk-taking and perseverance that has animated scientists in the United States and Europe, it’s inevitable that they will start producing Nobel-quality research within a few decades.
The history of the Nobel Prizes also offers an interesting window on changing developments in science. For me, the most promising insight they offer is of science as a tool-driven rather than as an idea-driven revolution. If you ask most of the public who their favorite scientists are, they are likely to be theoretical scientists like Einstein, Newton, Galileo and Hawking. And yet, as brilliant as these scientists’ work is, the actual work of uncovering new facts is done by experimentalists and not theorists, and yet the popular conception of science is biased toward theorists. For instance, let’s consider Nobel Prizes in physics where the demarcation between theory and experiment is well defined. By my count, among the 73 prizes awarded since the end of the war, no less than 27 have been awarded for new techniques; these include bubble chambers, laser spectroscopy and scanning tunneling microscopy, all of which have revolutionized many branches of physics. Science develops through both new tools and both ideas, but the image of science in the public mind is rather skewed and consists of singular minds coming up with great ideas. The truth is both more mundane and more important; experimentalists are the ones who actually find new things, while theorists are the ones who predict or explain them. You seldom get a Nobel Prize for explanation. You can get one for prediction, but as Niels Bohr rightly said, prediction is very difficult, especially about the future, so there have been very few genuinely groundbreaking predictions even in physics that were later verified by experiments. Paul Dirac’s prediction of antiparticles stands out as being especially remarkable, although it might have exaggerated the role that beauty and elegance play in theoretical ideas and set up an entire generation in physics for believing that truth equals beauty. In chemistry and medicine it’s far easier to accept the idea of science as a tool-driven revolution, partly because most chemical and biological systems are too complex to be reduced to first-principles explanations the way they can be in physics.
The image of singular minds also leads to the other big misconception regarding Nobel Prizes and science in general; the belief that lone geniuses do most of what’s important in science. In a trivial sense this has always been false since nobody invents or discovers something from scratch and everybody stands on the shoulders of giants. But it’s also becoming false in a big way, and tool-driven revolutions in science are largely responsible for the increasingly gaping discrepancy. The Higgs boson which was recognized a few years ago came out of the minds of at least six people, but its discovery was enabled by hundreds working at the Large Hadron Collider (LHC) in Geneva. Similarly, the discovery of gravitational waves for which three physicists were rightly awarded the prize last year was made possible using giant detectors that were constructed, operated and maintained by hundreds of researchers. Research now also spans multiple disciplines, and many important discoveries will not fit cleanly within the categories of physics or chemistry unless the definition of the disciplines themselves is expanded. Clearly there was no way Alfred Nobel and his contemporaries could have seen this evolution of science into a highly interdisciplinary endeavor collectively practiced by hundreds of people from different countries. And yet even in 2018 the prizes seem to be stuck in Nobel’s time. To keep the prizes relevant, it is imperative that they be expanded to honor entire teams spread across many fields. Perhaps a compromise would be to go the way of the much maligned peace prize, where both individuals and entire groups are recognized in the same year; the prize awarded to Al Gore and the IPCC for climate change would be a good example.
At the same time, I am also troubled by some who seem to take the other extreme position of saying that individuals should never be awarded the prize. This seems to me to be a kind of postmodern position that is driven more by communal ideology than facts. One of the signature features of scientific research is its diversity. Science may be done by large teams, but it will continue equally to be done by lone individuals. Even though they may stand on the shoulders of giants, singular minds like Einstein and Pauling do occasionally come along who see much further than anyone before. I certainly do not think Peter Higgs shouldn’t have been awarded the prize; I simply think that the LHC collaboration of scientists, engineers and technicians should also have been recognized.
Ultimately the Nobel Prize is a human institution, and like Thomas Jefferson, it embodies both glory and folly. To some this may make it imperfect and unworthy of recognition, but to me, the fact that the prize embodies the same complexity that makes humans so human is exactly what makes it so special, and worth celebrating.