2108 Physics Nobel

In light of the 2018 Physics Nobel Prize that was announced today, I recall a story I did for The Scientist in 2005 about the development of optical tweezers by Art Ashkin and Steve Chu when both were at Bell Labs (I decline to link to the institution currently bearing that name). Some people at the time felt that the 1997 prize that Steve Chu shared should have included Ashkin, although the 1997 prize dealt with trapping atoms rather than beads and bacteria. If so, this recognition could be seen as correcting that.

September 25, 2002

Ten years ago today, Lucent Technologies released the Final Report of our committee on possible misconduct by J. Hendrik Schön. The conclusion was clear: that there had been extensive misrepresentation and, by implication, that the entire body of work was suspect. Actually, the report had been largely finished for a while, but Lucent wanted a chance to have their lawyers and management check things over. This was a small price to pay to have the report publicly released in full. Remember that they had no legal obligation to release anything, but they released everything. The response to the report was very gratifying. Although there had been until then some holdouts who felt that the investigation might be some kind of witch-hunt, the extensive documentation that we provided of the many instances of misconduct assured that virtually no one maintained that belief afterwards. In spite of this sense of satisfaction and closure, however, we took no joy in delivering that verdict.

June 26, 2002: When did it start?

The second question most people ask with respect to Hendrik Schön is "When did he start faking data?"

(The first question is either "Why did he do it?" or "How could he possibly think he could get away with it?" Neither of these questions can be answered without a Vulcan mind meld.)

In our investigation committee, we did not seek to answer this question, only to pursue allegations that were brought to our attention, either directly or through Bell Labs. In fact, as the number of papers under suspicion grew from five to 25 or so, we realized we needed to close the door to new allegations, and we set an arbitrary cutoff date of June 20, 2002. We had plenty of material to work with for our report.

It turns out that a few days later we got another allegation that gave a strong hint that the faking began when Hendrik was in graduate school at the University of Konstanz, before anyone at Bell Labs knew anything about him.

To be honest, we were somewhat relieved that the new information came in after the cutoff, because investigating it would have involved us in a completely new class of materials and measurements, as well as new co-authors (obviously none from Bell Labs). We also did not have access to the digital data that was so useful for the other papers, and our authority to investigate this work would have been somewhat questionable, since we had been invited in by Bell Labs.

As we would later be told, Hendrik's thesis was rather unexceptional: lots of slow experimental work trying to accomplish a rather mundane task of introducing electrically active dopants into potential solar-cell materials. Reportedly, he was not having much success despite stead efforts, but at some point he suddenly reported dramatic success in doping the materials.

There were several different experiments on different materials with different dopants. Three figures from the papers are overlaid in this animated gif:

.

At least in the context of the other clear cases of copying, this looks pretty clear. Obviously not all the curves are the same, but some are, and the three figures are represented as coming from three different materials. However, the committee never examined this case in detail, so there may be important caveats.

The University of Konstanz decided in 2004 to rescind Hendrik's doctorate, deeming him "unworthy." This retroactive action struck me as rather odd. A court concluded in 2010 (amusing translation here; follow either link for a relatively recent picture) that the revocation was inappropriate, but in 2011 that decision was reversed.

In 2003, Jennifer Couzin reported in Science that "a committee at the University of Konstanz examining the work of disgraced physicist Jan Hendrik Schön found inconsistencies in several papers Schön published during his studies there, but no proof that he had deliberately manipulated data."

But I think we know he had already started down the path.

Confirming Expectations

A good experiment definitively distinguishes between alternative hypotheses. But things get tricky when a well established standard view is pitted against ill-defined alternatives.

My Focus story today describes measurements of density fluctuations in ultra-cold gases. Several experimental groups have been capturing and cooling bunches of about a thousand atoms above "atom chips" to study such things as Bose-Einstein condensates. In this case, Julien Armijo, a former member of a group at the Insitute d'Optique in Palaiseau, attributes some of the density fluctuation to quantum zero-point excitation of sound waves in the atomic cloud.

For an isolated oscillator, the signature of zero-point motion is conceptually straightforward: below a certain temperature the motions no longer decrease with temperature. What's left are the intrinsic quantum-mechanical oscillations, and the freezing temperature corresponds to the minimum quantum of energy needed to excite the oscillator. The obvious "null hypothesis" to be excluded would therefore be that the fluctuations continue to decrease toward zero with further cooling.

For the atomic cloud, however, the situation is much more subtle, because the sound waves have a continuous spectrum that extends to zero energy. This means that there are always some waves--the ones with the longest wavelength--that are excited no matter how low the temperature.

A further complication is that different wavelengths vary in their effect on the density fluctuations. A sophisticated theory says that the quantum contribution from the longest wavelengths does not add to the density fluctuations at all. In fact, this theory says that, at very long wavelengths, the fluctuations go away at zero temperature--exactly what one would expect if there were no quantum fluctuations!

As it turns out, though, the experiment measures fluctuations in individual pixels that are a few microns on a side, which corresponds to including waves with wavelengths on the same scale. The theory says that these waves will cause a measurable density fluctuation even at zero temperature.

But the same theory says that at nonzero temperatures, including shorter wavelengths will decrease the contribution of thermal excitations by exactly the same amount. The two terms get bigger as the pixels get smaller, but since they cancel anyway that doesn't affect the prediction.

This is messier than just looking for fluctuations that don't freeze out, isn't it?

It's rather difficult to choose a good null hypothesis where there are no zero-point motions. After all, everyone believes that, physically, the quantum fluctuations should be there, although different theoretical treatments may make slightly different predictions. So there is no particularly obvious way to choose a model where the quantum fluctuations are absent.

Armijo measures fluctuations that don't change with effective pixel size, just as the complete theory predicts. Of course, the measurements also agree with a theory that omits the size dependence of both the quantum and the thermal contributions. What they don't agree with, he emphasizes, is a model that includes only the thermal corrections, since these are no longer cancelled by the quantum term. It's not clear that anyone thinks this would be a credible model that needs to be excluded. (Setting Plank's constant to zero, a common way to "turn off" quantum effects, seems to make both corrections go away.)

What is clear is that the claim that this is a "direct observation of quantum phonon fluctuations" needs to be parsed quite carefully.

May 28, 2002: First look at internal Schön investigations

Just after Memorial Day in 2002, our committee finally received the records of multiple internal Bell Labs investigations of the work of Hendrik Schön. The frustrating delay of several weeks in getting these documents was caused in part by the need to be sure that we had legal indemnification from Lucent for our activities. That being accomplished, we were ready to begin in earnest, and the documentation was weighty and troubling.

We received a large three-ring binder with a dozen or so sections dealing with various issues. In addition, we got copies of email correspondence with and about Hendrik, including management discussions about various issues. (There was no easy way to verify how complete the email collection was, but there was a lot there.)

Since these documents, including internal company communications, were made available as part of our official committee activities, I can't share them in detail, even now. But they illustrated serious concern among the Bell Labs managers, going back at least to the summer of 2001. Hendrik was strongly encouraged, for example, to help other researchers to reproduce his extraordinary dielectric films, and was told that it was more important to solidify his existing work than to demonstrate new breakthroughs.

This concern was not in evidence, however, in various public statements about the work, notably the "self-aligned monolayer field-effect transistor," or SAMFET, described in the fall of 2001. For example, a Business Week article quoted his recently appointed immediate manager John Rogers as if he had witnessed the assembly: "The whole thing just happens in a beaker at a chemistry bench." A Lucent press release included endorsements of the profound potential from his then third-level manager Cherry Murray ("Although there may be no practical applications for a decade, it could lead to a new paradigm in electronics") and second-level manager Federico Capasso ("The molecular-scale transistors that we have developed may very well serve as the historical 'bookend' to the transistor legacy started by Bell Labs in 1947." Ironically the word "bookend" was more appropriate than he seemed to realize.). Capasso is also reported to have told an internal Bell Labs meeting that it was OK if the work was not completely correct because it was so exciting that it would stimulate further work that would clarify what was going on.

During the same period, Hendrik's original mentor, Bertram Batlogg, continued to extol the earlier experiments on single-crystal organic semiconductors, even as he strongly questioned Hendrik's description in an unpublished document of the way the insulating film had been optimized.

There is a profound lesson in the fact that all of these fine scientists were willing to put aside their own misgivings and to publicly endorse Hendrik's results. I can't seriously entertain the idea that any of them the knew the results were faked and were deliberately misleading people. Instead, I have to believe that they had managed to deceive themselves that the problems were mistakes or misunderstandings, and that the groundbreaking work would stand the test of time even after these problems were resolved.

They were all wrong. The scientific world would have been better served if they had been more willing to openly question the honesty of their sincere young colleague.

May 24, 2002: What got the Schön investigation going?

Leading into the spring of 2002, there had been increasing discomfort with Hendrik Schön's stunning body of scientific results. The official investigation into his possible misconduct, however, only began when a group of nano-physicists noticed duplicated data in five papers. As described nicely in Eugenie Reich's book Plastic Fantastic, Lydia Sohn (then at Princeton), Paul McEuen, Leo Kouwenhoven, and Charleses Marcus and Lieber sent their findings to the Bell Labs management and to the journals where the articles were published at the beginning of May. It is interesting to speculate whether and how the investigation would have proceeded if it had been communicated less publicly.

During this period, a PowerPoint version of the slides was widely circulating in the nano community. The usual technique was to print out the graphs on transparencies and line them up, but I include them here as animated gifs for a change of pace. The figures show very similar curves, even though the data are represented as being taken from completely different samples. In principle this could happen once through gross negligence, by sending the wrong figure (with the wrong label!). In addition, however, the axes are sometimes differ in sign or by an integer multiplier, or they have some curves missing, which are much harder to understand. But the most damning evidence is that the small deviations from the curves are often very similar in different plots, even though this "noise" should vary each time the measurement is repeated.

For many researchers, seeing these images was all the evidence they needed that Schön had fabricated at least some of his data. Others held out hope that there was some innocent explanation, and looked to our "blue-ribbon panel" to resolve the issue. We on the committee felt a lot of pressure to get it right. But by this time ten years ago, we still hadn't yet gotten any detailed documentation from Lucent.

May 21, 2002: Investigating the Schön Affair

Ten years ago this week, Lucent Technologies announced that it had convened a panel to investigate possible scientific misconduct at Bell Labs. Interestingly, the story in the New York Times by Kenneth Chang featured the role of Bertram Batlogg, mentioning Hendrik Schön only in the final paragraph.

At the time, I thought this story missed the point, since it seemed clear that Schön was at the center of the problems. (Batlogg wasn't even an author on some of the papers in question.) But as Chang told me later, Batlogg had been highly visible when the spectacular "breakthroughs" were being announced. For this reason, Chang (who had covered the earlier work) thought that Batlogg's was the name that readers would be most likely to recognize, and not highlighting it would be a disservice to readers.

One of the biggest challenges to the committee (which I served on) was figuring out how to deal with Batlogg's role, neither assigning him primary responsibility nor minimizing his role.

Free to Choose

Today's New York Times features a bizarre op-ed by Charles Murray of the American Enterprise Institute, a think tank that describes its scholars as "committed to expanding liberty, increasing individual opportunity, and strengthening free enterprise."

Murray summarizes the results of head-to-head comparison of standardized-test performance for students in public and charter schools. The charter-school students, he admits, "generally had 'achievement growth rates that are comparable' to similar Milwaukee public-school students. This is just one of several evaluations of school choice programs that have failed to show major improvements in test scores, but the size and age of the Milwaukee program, combined with the rigor of the study, make these results hard to explain away."

"So let's not try to explain them away," Murray says.

This makes good sense. This kind of experiment has been done many times, as described by Diane Ravitch in her thought-provoking 2010 book, The Death and Life of the Great American School System: How Testing and Choice Are Undermining Education. The results are clear in their lack of clarity: some charter schools are excellent, others are terrible. The data don't support the vision that non-public schools are automatically superior, although some no doubt are. In addition, the data show no indication that public schools faced with competition respond by cleaning up their act, another frequent argument for school choice.

So do these conclusions shake the confidence of a school-choice advocate like Murray? Hardly: "Why not instead finally acknowledge that standardized test scores are a terrible way to decide whether one school is better than another?" he says.

Murray is correct, of course, that tests scores have serious flaws. Ravitch, who admits that she was once a strong proponent of both choice and testing, spends much of her book describing the problems with standardized tests. Especially troublesome are the tests that states devise to show that they are meeting the goals of the "No Child Left Behind" act. Ravitch laments both the limited range of skills being tested--essentially basic math and reading--as well as the distortions that inevitably occur when tools meant to monitor progress start to be used to enforce it.

Ravitch forcefully argues that school improvement is a hard slog, not achieved by silver bullets like charter schools or by extensive data collection like that promoted by the Obama administration's "Race to the Top." Instead of statistical analyses modeled on business practices, she advocates a rigorous (voluntary) national curriculum and on-the-ground assessments by professional educators, not business managers.

Murray acknowledges the failures of previous silver bullets: "whether the reform in question is vouchers, charter schools, increased school accountability, smaller class sizes, better pay for all teachers, bonuses for good teachers, firing of bad teachers — measured by changes in test scores, each has failed to live up to its hype." But he concludes is that the problem lies with testing, and that choice is still a social good, because it allows parents to choose schools whose teaching styles the parents find appropriate.

It will be interesting to see whether Murray's fellow school-choice advocates follow his recommendation to admit that there is no measurable benefit of charter schools, but policy should support them anyway on ideological grounds. Somehow I doubt it.

 

Changing the Rules

Is the Large Hadron Collider a time machine?

Although I usually like Dennis Overbye's physics writing for the New York Times, I thought he misfired in answering this question yesterday, in the general-audience "Week in Review" section.

In a Q&A entitled A Primer on the Great Proton Smashup that discussed the scientific ideas that underlie research at the LHC, Overbye addressed the question:

"What does it mean to say that the collider will allow physicists to go back to the Big Bang? Is the collider a time machine?"

It may seem silly, but it's actually a good question, since I'd bet a lot of people get confused by the metaphors that writers use to motivate the research. These metaphors get repeated often enough that they are almost cliché, but, as with all metaphors, it's important to know which parts to take seriously and which parts are more poetic or even misleading. Not everybody will know which is which, and it's good to explain it every so often.

Here's Overbye's complete answer:

"Physicists suspect that the laws of physics evolved as the universe cooled from billions or trillions of degrees in the first moments of the Big Bang to superfrigid temperatures today (3 degrees Kelvin) — the way water changes from steam to liquid to ice as temperatures decline. As the universe cooled, physicists suspect, everything became more complicated. Particles and forces once indistinguishable developed their own identities, the way Spanish, French and Italian diverged from the original Latin.

By crashing together subatomic particles — protons — physicists create little fireballs that revisit the conditions of these earlier times and see what might have gone on back then, sort of like the scientists in Jurassic Park reincarnating dinosaurs."

I'll discuss in a moment what I think Overbye means by "the laws of physics evolved," but this notion is awfully subtle for a general reader. More importantly, it completely undercuts the whole thrust of the question: physicists believe they are learning about the early universe in high-energy particle collisions precisely because the laws of physics are the same. If the laws are the same, we can create the same conditions (mostly temperature) to learn about what might have happened in the early universe. (He eventually does say that.)

The confusion comes because the phrase "the laws of physics" can be mean quite different things.

In the context of LHC, it seems clear to me that we refer to the behavior at the deepest levels of the universe. These rules don't get repealed overnight.

In fact, as I understand the phrase, it refers not to the current human description of events, which changes as we learn more, but to the "truth," which doesn't. Otherwise, it wouldn't make sense to say that we want to learn about the laws of physics from the collider (since we already know the laws, even if they're wrong).

Still, we often say the laws of physics say that something is impossible. In that context, the phrase can only refer to our current understanding of the laws, as best as we can discern them.

In fact, when we talk about the laws of physics we're frequently not talking about the deep levels probed by the LHC. Instead, we're referring to laws that describe the more mundane behavior of objects in our cold everyday reality.

In one sense, these "laws" are just a manifestation of the deeper laws. Describing the world in terms of protons, or nuclei, or atoms, or molecules, or cells, or organs, or organisms, or societies, is often vastly more useful than describing it with quarks or strings.

In some cases, the higher-level description can be mathematically related to the deeper description, for example by "coarse graining" the description to smooth out fine details.

This is the sense in which we can say that the "laws of physics" evolve: when the universe was very hot, the description had to include a lot of ingredients that are no longer important now that the universe is much cooler. We can now accurately describe things using a simplified description that doesn't have to include the messier details. The "laws" are different now.

This is Overbye's answer. But I think it will confuse people, since the goal of the LHC is to learn about the immutable laws, not the simpler descriptions or approximations.

One further, mind-blowing complication. Many cosmologists are exploring the possibility that our universe is just one of an infinite number of universes that formed, like bubbles, out of a larger multiverse. According to this view, the "laws of physics" --perhaps even the dimension of space--may be entirely different in each of these universes.

Even if we will always see the laws of physics as unchanging, they may be not be the same everywhere.

 

 

Picturing Quantum Mechanics

They say a picture is worth a thousand words. But what if those words are wrong?

Very cool recent experiments demonstrated a chemical reaction between molecules below a millionth of a degree (in Science, subscription required). My latest story for Physical Review Focus describes theoretical modeling of this reaction. We accompanied the story with this picture from the news release issued by the Joint Quantum Institute (a partnership between the National Institute of Standards and Technology and the University of Maryland), where the work was done.

It's a pretty picture, with its superhero color scheme and all, and it satisfies our need to avoid a solid block of text. But although it might not be a bad illustration of a room-temperature chemical reaction, it distorts much of what makes these ultra-low-temperature reactions special.

It's clear in the picture that two diatomic molecules are approaching each other, with dramatic consequences in store. The details of how the artist represents the bonds connecting a potassium and a rubidium atom in each molecule don't bother me too much. It doesn't match either of the customary representations, which are ball-and-stick models and the more accurate space-filling models, but there's no perfect way to represent something that can never be seen with visible light. Of course everyone knows that potassium atoms are green, but we'll let that slide, too.

The really problematic part of this picture is very difficult to avoid: the molecules really aren't anywhere, in the sense the picture conveys.

As first shown by experiments at Bell Labs in 1927, matter acts as waves as well as particles. At temperatures below a millionth of a degree, the relevant wavelength for these molecules is hundreds of nanometers, which is much, much larger than the separation of molecules shown in the experiment. There is no meaning to saying that these molecules are separated by such a short distance. They are simultaneously close and far away.

One way to think about this is to invoke Heisenberg's uncertainty principle. According to this principle, if you know an object's momentum with very high precision, you can't, even in principle, know its position very accurately. For these ultracold molecules, the momentum is almost zero, with very high precision, so you can only know where it is to the nearest hundreds of nanometers.

There's a second problem, too. The picture shows the molecules with particular orientations in space. That may not seem strange, but the molecules in the experiment were prepared in the rotational "ground state," with the lowest possible energy. Like the s-orbitals of electrons in a hydrogen atom, this state is spherically symmetrical. This means that the molecule is equally likely to be pointing in any direction. This isn't the same thing as saying we don't know what direction it's pointing (even though it does). Quantum mechanics says that it has no direction, at least until an experiment requires it to.

So the reacting molecules really aren't at any particular distance from one another, and they don't have any particular orientation relative to each other. That's one of the things that makes this chemical reaction--and the theoretical description of it--so interesting.

But good luck drawing that.

 

Flyfire

When I was an undergraduate at MIT in the late 1970s, one of the most impressive people I knew was my roommate Walter.

Walter was a mechanical engineer, and knew an incredible amount of just-plain-practical stuff about how to make things work, from types of stainless steel to the ins and outs of convective cooling.

The rest of us vicariously enjoyed his entry in Woodie Flowers' design completion, the 2.70 contest (named for the number of the design course). The idea was to take a box of stuff--tongue depressors, rubber bands, and so forth--and turn it into a machine that would beat other students in a glorified "king-of-the-hill" like task. This was way before I heard the phrase KISS, "Keep It Simple, Stupid," but we all learned that successful designs took this minimalist idea as a core principle.

This sort of contest has been picked up by others, even bringing high-school teams into the game, for example in the FIRST competitions. It's a great way to inspire imaginative people in ways that go way beyond the ordinary classroom experience. And it's a hands-on demonstration of the creativity that underlies true design.

Walter also worked with Otto Piene, the artist who headed MIT's Center for Advanced Visual Studies. Among other things Walter helped sew enormous inflatable anemones for Piene's Centerbeam project on the mall in Washington, D.C., as well as designing and building beam-steering mechanisms for an early laser show.

I'd forgotten all of this until reporting my latest story for CACM on a new project from MIT, which brings together two teams. One group comes from the Department of Urban Studies and Planning, which is exploring ways that distributed technology can illuminate or improve urban life, such as tracking trash disposal or using cell phones to monitor commuting. The second group is from the "Aero and Astro" department, where researchers have been exploring autonomous vehicles for military and other applications.

The Flyfire project aims to do something even stranger: to use LED-bearing helicopters to make a giant display. Although there may be some practical need for such a display, the most compelling vision for now is to create giant public art projects, of the kind pioneered by Piene and others.

Maybe it will never be particularly useful. Maybe it will never even work. But these grand visions tap into something essential in the human spirit.

Mining Evolution

Can a worm get breast cancer? And how would you know if it did (since it doesn't have breasts)?

Biomedical research has made great use of "disease models": conditions in lab organisms that resemble the human diseases that the researchers really want to learn about. By seeing how a model condition develops and how it responds to drugs or other changes, researchers can make better guesses about what might help people. But finding such disease models usually requires some obvious similarity between the outward manifestations of the disease in humans and the animal subjects.

In the Proceedings of the National Academy of Sciences, a team from the University of Texas in Austin led by Edward Marcotte use the underlying molecular relationships to find connections between disorders with no such obvious relationship. In addition to a worm analog of breast cancer, they found an amazing connection between plant and human disorders. The analysis of plants' failure to respond to gravity led them to human genes related to Waardenburg syndrome. This syndrome includes an odd constellation of syndromes resulting from defects in the development of neural crest cells.

I saw Marcotte speak about this fascinating work at the conference I attended last December in Cambridge, Massachusetts. My writeup should be posted soon by the New York Academy of Sciences.

Biologists have repeatedly found that the networks of interacting molecules are organized into modules. Over the course of evolution, these modules can be re-used, often for purposes quite different from their original function. This much is well known, although seeming the persistence of modules over the vast evolutionary separation of plants and people is very dramatic.

What the Austin team did was to devise a methodology to identify related molecular modules in different species even without relying on similar outward manifestations, or phenotypes. They combed the known molecular networks of different species for modules that had a lot of "orthologous" genes: those that had retained similarity--and similar relationships--through evolution. They call the particular traits associated with these genes "orthologous phenotypes," or "phenologs." "We're identifying ancient systems of genes that predate the split of these organisms, that in each case retain their functional coherence," Marcotte said at the conference.

The importance of this scheme is that many molecular networks are poorly mapped, especially in humans. But if a particular gene is part of the network underlying a phenotype in another species--such as poor response of a plant to gravity--it's a good guess that the corresponding gene may be active in the orthologous phenotype in people. The researchers in fact confirmed many of these predicted relationships. Some of these genes were previously known to relate to disease, while others were new. The researchers created a list of hundreds more that they still hope to check.

These genes could give researchers many potential new targets for drugs or other interventions in diseases. So evolution is not just helping us to understand the biologic world we live in, but helping us devise ways to improve human health.

The Language of Life

Ten years after the announcement of the draft human genome, the world of human health seems in many ways unchanged. But it is changing, in many profound ways, says Francis Collins, who led the government-funded part of the genome project and is now the director of the National Institutes of Health.

Collin's new book, The Language of Life: DNA and the Revolution in Personalized Medicine, aims to help the public to understand the changes so far, and those that are still to come. He covers a wide range of topics, but the guiding theme is the promise of "personalized medicine" that tailors treatment for each individual based on their genetic information.

As he shows in his occasional columns in Parade magazine, Collins is a skilled communicator of complex medical topics, including their ethical and personal dimensions. He steers authoritatively but caringly through challenging topics like race-based medicine. On the pros and cons of genetic screening, for example, he describes the desirability of genetic tests as a product of not just the relative and absolute changes in risk associate with a gene, but the seriousness of the disease and the availability of effective intervention.

I confess that I was worried that Collins might let his well-publicized Christian beliefs color this book (his previous book is called The Language of God). They did not. His beliefs arise a few times, for example in the context of stem cell research, but he deals with serious ethical questions with great respect for different points of view. In addition, as should be expected for any modern biomedical researcher, he repeatedly and matter-of-factly draws important insights from evolution.

On the whole, the writing is accessible to general readers, even as Collins discusses complex scientific topics. On occasion, however, he shows an academic's tolerance for complex, caveat-filled verbiage, as when he writes, "Therefore, at the time of this writing, the effort to utilize genetic analysis to optimize the treatment of depression has not yet reached the point of effective implementation." This stilted language is the exception, but he also slips into occasional jargon that might leave some readers temporarily stranded.

A trickier issue is Collins' frequent use of patient anecdotes to illustrate how genetic information can lead to better decisions. These human stories, drawn from his long research and clinical experience, certainly succeed at Collins' goal of inspiring hope for the potential of personalized medicine, as well as showing clearly what it mean to people. But the succession of optimistic stories begins to seem skewed to draw attention away from structural challenges in American medicine that could seriously undermine this potential. When Collins mentions these issues, it tends to be in careful euphemisms: "A recent study estimated that in the United States each year, more than 2 million hospitalized patients suffer serious adverse drug reactions, with more than 100,000 of those resulting in a fatal outcome."

In a similar vein, Collins describes the successful identifications of gene variants associated with macular degeneration. The fact that similar studies for other diseases have been rather disappointing doesn't seem to bother him much. Perhaps his decades in research, including the identification of the cystic fibrosis gene, have made him confident that these problems too will pass. But he comes across as a very optimistic person.

In spite of my quibbles, I think The Language of Life succeeds well at putting the omnipresent news stories about genetic advances in a useful context of individual medical choices. As a writer who covers these areas of science, I didn't learn an awful lot of new things from the book, but I think most people will, and will enjoy themselves in the process.

Mathophobia

In many fields of science and engineering, any technical argument must be formulated mathematically if it is to be taken seriously. In contrast, in popular writing--even about science and engineering--including a single equation is a known recipe for getting many readers to click on to the next story. Understanding this discordant reaction to math reveals a lot about how popular and technical writing differ.

Back in 2003, when I was thinking about morphing from a practicing scientist into a science writer, I seriously questioned how I could possible to explain scientific arguments without variables and equations. Without the precision of a mathematical description, I wondered, how could I really know whether readers interpreted ordinary English phrases the way I intended? Moreover, without a algebraic description, how could readers judge how well a model matches observations?

Interestingly, in the years since, I've almost never felt hobbled by not being able to explain things with equations.

A lot of the difference arises from the different goals of journal articles and popular stories, and their very different sources of authority.

In a journal article, the goal is to convince other experts. In other words, the article should ideally be self contained, assembling all the relevant details so that an independent observer can make up their own mind.

In contrast, a popular science story aims merely to describe the conclusions, not prove them. As David Ehrenstein, the editor at Physical Review Focus, once told me, the goal is to present a plausibility argument for the conclusions: to give enough context and explanation that readers can appreciate what's being claimed and who's claiming it.

The last point is also critical: by and large, popular writing gains its authority from the quoted judgments of experts, not directly from the model or observations. Indirectly, of course, this authority comes from the reputation of the writer and the publication (that is, the editors), because they are the ones who decide which commentators are worth quoting. (Of course, those commentators must also respond to emails or phone calls!)

Since the goal is plausibility and a qualitative understanding, the limited precision of ordinary writing is usually good enough to convey the message.

Compartments

The development of a single cell into a complex creature such as you or me is almost miraculous. Early scientists were so baffled by this process that some supposed that the fertilized egg might contain a complete specification of the final organism.

This is just silly.

Still, it has only been in the last few decades that researchers have worked out how a smooth starting pattern in the concentrations of a few molecules develops into a complex, highly structured pattern. These molecules act as transcription factors that modify the activity of genes making dozens of other transcription factors, which spontaneously form patterns that serve as the invisible framework driving all subsequent development. The essence of this understanding is described in the charming 2006 book Coming to Life: How Genes Drive Development by Christiane Nüsslein-Volhard, who shared a Nobel Prize for her germinal work on the development of the fruit fly, Drosophila melanogaster.

A central part of this view is that different regions of the developing embryo are uniquely identified by the particular combination of transcription factor concentrations they contain. Each combination (influenced in part by its neighbors) stimulates the cells in that local region, or "compartment," to develop toward a particular final structure, such as the hindmost edge of a wing. Mutated animals that are missing the genes for particular factors develop characteristic problems, like extra wings or legs sprouting where their antennae should be. Researchers have also learned how to label the molecules with fluorescent dies that directly reveals the invisible patterns of factors that drive later development.

In their book The Plausibility of Life, Marc Kirschner and John Gerhart include developmental compartments as one of the key elements, along with weakly-linked modules and exploratory behavior, of "facilitated variation": the ability of organisms to respond to small genetic changes with large but viable changes in their structure.

Compartmentalization is in some ways similar to exploratory behavior, in which developing body structures such as blood vessels respond to local stimuli such as chemicals emitted by oxygen-starved cells. In both cases, individual cells respond to nearby cues, without needing to refer to some master plan. In the case of compartmentalization, however, both the cues and responses are more general chemical changes, in contrast to the more apparent structural changes seen in exploratory development.

What the two processes have in common is that they allow development that is flexible enough to succeed in diverse situations, for example when nutrients are scarce or the embryo is damaged. This sort of robustness presents a clear evolutionary advantage, since it makes it more likely that a complex organism will grow up and survive to reproduce.

But in addition, robust development lets organisms deal with genetic changes. Although many mutations are fatal, some cause dramatic changes in body organization or other features, while the flexible development process adapts to the new situation. As a result of this facilitated variation, evolution is able to explore a wider variety of strategies and move quickly to new solutions.

For Kirschner and Gerhart, this flexibility is key to understanding the nature and rapidity of evolution. A population can explore the potential advantage of a longer hindlimb, for example, without the need to separately coordinate changes in bone, muscle, blood vessels, nerves, and so forth. Adaptive development takes care of all that.

In fact, the pattern of compartmentalization appears to have been much more stable over the course of evolution than the details of body structure have been. The appearance of compartmentalization and the other features that allow facilitated variation look like the crucial revolutionary events that made rapid evolutionary change possible.

Poles Apart

Over the past few months, scientists studying global warming have been rocked by a series of awkward revelations. In November, someone made public more than 1000 emails, many quite damning, from climate researchers at the University of East Anglia (UEA), in what skeptics successfully branded as "Climategate." December and January saw the authoritative Intergovernmental Panel on Climate Change (IPCC) admitting that their published claim that Himalayan Glaciers would disappear by 2035 was improperly sourced and wrong, even as critics pounced on other instances in which the panel violated their own procedures for insuring that science was properly represented in their influential reports. (The IPCC had shared the 2007 Nobel Peace Prize with Al Gore.)

Not surprisingly, different people responded completely differently to these events. Critics see the revelations as confirming that global warming, and especially its human source, is just a hoax. Others counter that the revelations that scientists are fallible human beings do not in the least affect the overwhelming evidence for man-made climate change. Unsurprisingly, both extremes find confirmation for what they already believed.

They are also both wrong.

First let's examine the hoax theory. Although we don't know who released the emails, they look to have been culled from more than a decade of exchanges and chosen to best incriminate the mainstream climate researchers, both those at UEA and their correspondents. What is striking is that the emails do not
reveal any serious evidence that the researchers are fabricating the global temperature rise.

To be sure, the emails show serious misbehavior, including a request from UEA researcher Phil Jones that others delete emails to avoid a freedom-of-information inquiry. Other emails suggest that the researchers hoped to tweak the IPCC process to exclude legitimate, peer-reviewed papers that they didn't regard as credible.

But if the emails showed evidence of a true hoax, the critics poring over them haven't found it--and not for lack of trying. Instead, they have highlighted examples of ambiguous or unfortunate wording, which are conveniently picked up by the likes of Sarah Palin. But although Palin may not know any better, the critics understand that when Jones referred in 1999 to Penn State researcher Michael Mann's "trick" to "hide the decline," he was describing a technique to de-emphasize the inconvenient truth that tree-ring data don't match measured temperatures, which were clearly rising.

This is a serious matter: if the tree-ring data are not good proxies for temperature in cases where we know the temperature, how can we trust them in cases where we don't know the temperature? But as far as I know, the published papers acknowledge this manipulation, which is an acceptable way to deal with omissions of questionable data. Nothing is being hidden. In fact, this whole issue was addressed by the U.S. National Academy of Sciences in 1996, who confirmed the unprecedented nature of the current warming trend.

The critics know this. Their use of this and similar examples shows that they are less interested in the overall truth than in scoring points and discrediting mainstream climate science.

But the disingenuous actions of the critics do not excuse the behavior of the mainstream scientists.

It is tricky to interpret what must have been seen as private correspondence between colleagues. Nonetheless, the emails seem to show that the East Anglia scientists did not really trust the processes of science, or at least the political decisions based on the science. The researchers in the emails are acutely aware of the political context of their results, and present the data to make their case. For example, UEA tree-ring expert Keith Briffa says "I know there is pressure to present a nice tidy story as regards 'apparent unprecedented warming in a thousand years or more in the proxy data' but in reality the situation is not quite so simple." Briffa, whose data contains the "decline," commendably goes on to argue for a more honest and nuanced description of the data.

It's not unusual for researchers to choose data to tell a particular story. And there really is no evidence that the researchers suspected the story they were telling--of unprecedented, industrially-caused warming--was wrong. But it is clear that the handful of teams around the world who evaluate historical climate trends displayed their data to support a clear end goal. Subsequent revelations show that this mindset also affected the choice of references in the IPCC report, especially with regard to the impacts of climate changes.

One of my correspondents, a biologist who uses complex biological models, likens the climate-science consensus to Lysenkoism--the Soviet era anti-Darwinist biological agenda. I take this person to mean that dissent from the reigning paradigm is not accepted in mainstream scientific circles: anyone questioning the "consensus" is quickly branded a "denier." This is not the way to do science, especially for something as important as climate change. And what it means is that the "overwhelming consensus" is not as convincing as it seemed a few months ago.

But it doesn't mean that the consensus is wrong.

 

Survival of the Most Entangled

Most people think quantum-mechanics affects only atomic-sized objects, but many experiments have shown that it applies over many miles. In an experiment last year, for example, researchers sent pairs of light particles, or photons, between two of the Canary Islands off the coast of Africa, a distance of 144 kilometers.

http://www.flickr.com/photos/tenerife/ / CC BY 2.0

This picture dimly shows La Palma, where the photons started, as seen from Tenerife, where they were detected.

Although the Austrian team, led by Anton Zeilinger, only detected one in a million of the pairs they sent, they found that these pairs retained the critical property of entanglement. This means that results of measurements on the two particles are related in ways that can't be explained if each particle responds to the measurement independently: the pair acts like a single quantum-mechanical entity. Such pairs can be used to securely transmit information over long distances.

My latest story at Physical Review Focus describes a theoretical analysis of this experiment by researchers in Ukraine and Germany. They suggest that the pairs that survive the half-millisecond trip must have had unusually smooth sailing through the turbulent atmosphere, and that this is part of the reason why they are still entangled. (The motion of the air, like the shimmering of a mirage in the desert, generally disrupts the light transmission, but there are short moments of clarity.) This is a pretty comprehensible idea, so in the story I was able to sidestep a lot of interesting issues about how the entanglement was measured and what it means.

For example, the experimenters delayed one photon by about 50 ns by passing it through a fiber before sending it after the other one. That's not a long time, so the atmospheric conditions probably looked pretty similar to the two photons. Since they were subjected to much the same conditions, it doesn't seem so surprising that they would remain entangled. In fact, the original experimenters were pretty pleased that it all worked, but clearly they were hoping it might or they wouldn't have gone to the trouble.

Sending the two photons on the same path certainly isn't the most demanding task, either. More impressive would be sending them on different routes to a final destination where they were compared. But sending an entangled pair is good enough for some quantum communication schemes.

What made the paper particularly interesting was the conclusion that the turbulent atmosphere would be better than, say, an optical fiber that had the same average loss, because the fiber's properties wouldn't change with time. Zeilinger expressed pleasant surprise that the rare moments of exceptional clarity would more than make up for the times when the atmosphere was worse than usual. Still, having no turbulence at all (or a very clear fiber) would be even better.

Exploiting quantum mechanics in secure long-distance communication, for example via satellites, looks more realistic than ever.

Targeting Cancer

Amy Harmon of The New York Times had an excellent three-part series this week called "Target Cancer." She follows one clinician/researcher as he pursues a "targeted" treatment for melanoma, which aims at the protein produced by a gene called B-Raf that is mutated more than half of the time in this skin cancer.

The series does a great job in following the emotional roller-coaster ride of the doctor, and of course his patients. One early targeted drug doesn't work at all, perhaps because it also attacks normal cells and the side effects become intolerable before the dose is high enough to affect the cancer. A new drug seems not to do anything, but then the team decides to wait for the drug company to reformulate it to deliver higher effective doses.

The results are spectacular: the new formulation causes a virtually unheard of remission in the cancer, and raises hopes in formerly hopeless patients and in the doctors. The excitement and the potential are palpable as some patients dare to hope and others can't bear to. But within a few months, the patients are dying again.

The new drug is an example of personalized medicine, since it is effective only for patients with a particular mutation. There are a few other examples of therapy tuned to patients with a particular genetic profile, such as the breast-cancer drug erbitux and the anticoagulant warfarin (Coumadin).

But this treatment is actually for cancers with a particular mutation--a mutation the normal cells of the patient don't have. Cancers cells generally have more and more of mutations as the disease progresses, because it disrupts the normal quality-control mechanisms in the cell. A study announced last week (registration required) showed that the specific pattern of mutations could be used to monitor the ebb and flow during treatment, although it doesn't look practical yet for tailoring treatment.

Unfortunately, as described in this series, even when a drug targets a mutation in a particular patient's cancer, cancers often develop alternate routes to proliferation. Harmon alludes to one approach to this problem: a multi-pronged "cocktail" that attacks many possible mutations at once. Such cocktails are standard, for example, in treating HIV/AIDS.

Without vilifying the drug companies, she explains some challenges for these profit-oriented companies in pursuing this approach. In particular, even if the cocktail may ultimately be more effective, getting approval might delay or threaten their profits from the drug they have in hand, even if it only extends life for a few months. This is especially true if other drugs in the cocktail are owned by competing companies. In any case, the difficulties in testing multiple drugs make it much harder to know what is effective and what side effects may appear.

The idea of analyzing molecular networks and attacking them at many points simultaneously is a recurring theme in systems biology. But sometimes it seems very far in the future.

Stoner Magnetism

My latest story at Physical Review Focus describes experimental evidence that a missing atom in a chicken-wire-like sheet of carbon can hold a single extra electron.

Theorists have long expected this to be the case, and that unpaired electrons on such vacancies might join up to make an entire single-atom-thick graphene sheet magnetic at relatively high temperatures. Many researchers are excited about the rapid and unusual motion of electrons in these sheets, and IBM researchers recently described a graphene field-effect transistor, grown on silicon carbide, whose expected frequency (f_T) exceeds 100GHz. If the layers are also magnetic at normal temperatures, this material could be fun and potentially practical for spintronics, which manipulates both the charge and magnetic properties of electrons.

The actually experiment didn't directly show magnetism, though, just a state that looked like it should hold only one electron. The researchers used scanning-tunneling microscopy to look at a clean, cold graphite surface, which includes many stacked graphene-like layers. In fact, the authors suggest that magnetism may exist in graphite, but not in graphene, because in the latter the effects of two equivalent carbon positions for a vacancy may cancel each other out.

It turns out to be a little bit tricky to explain the connection between local spins, which naturally carry a magnetic moment, and magnetism in a bulk material.

The usual story is straightforward: some types of atoms (or vacancies) naturally have a magnetic moment, "like a tiny bar magnet." Nearby moments exert forces that tend to align their neighbors, either the same way or oppositely. If it's the same, then the moments on many different atoms can all line up to form a net magnetization in a large sample, if the temperature is not so high that they get jostled out of position.

This description is correct--but only for some magnets.

For other magnets, it's just not accurate to say that the atoms each have magnetic moments that line up with each other. In these so-called "itinerant" magnets, the magnetization comes from the metallic electrons washing over all of the atoms. In this case, preference for one direction or another at a particular atom develops only as a part of the magnetization of the whole sample.

Mathematically, itinerant magnetism takes the form of an instability, in which the energy benefit of aligning the moments of the electrons overcomes the energy cost of doing so. A simple description was developed back in the 1940s by Edmund Stoner at the University of Leeds, and his name is still used to convey the ideas. (I apologize to anyone who expected this post to be about the natural charisma of pot-smokers.)

Of course, the distinction between the "local-moment" and "itinerant" magnetism is often somewhat fuzzy, and for the purpose of explanation to the general public it may not seem that important. But to people who understand the issues, getting it wrong is unforgivable, as I found out to my chagrin after using the above simple local picture in my Focus story on the 2007 Physics Nobel on Giant Magnetoresistance (GMR).

GMR read heads in disc drives can be seen as a simple type of spintronics device. In more sophisticated devices that people dream about, electrons will carry their magnetization to new locations, so it's important to be clear on the nature of that magnetism.

Trailblazing

What a piece of work is a man! For that matter, what an awesomely complex apparatus is any large organism, from a dog to dogwood!

But as we learn more about biology, our awe shifts from the intricate cellular arrangements in mature multicellular life to the ways these structures arise during development from simpler (but not simple) rules. Even if we can accept simple examples of self-organization, like the spontaneous arrangement of wind-blown sand into regular dunes, the self-assembly of living creatures seems to be a different scale of miracle. But researchers have repeatedly found that simple rules, in which cells respond to local cues like chemical concentrations and mechanical stresses, suffice to describe how various aspects of our complex bodies develop.

In The Plausibility of Life, Marc Kirschner and John Gerhart describe this rule-based strategy, which they call "exploratory behavior," as a very effective way for organisms to develop dependably in the face of unpredictable changes in their environment. But they go further, stressing that flexible, adaptive development speeds evolution by letting small genetic changes give rise to vastly different--but still viable--organisms. Exploratory behavior is thus a critical component of their concept of "facilitated variation."

As an illustration of rule-based organization, Kirschner and Gerhart review the foraging of ants. Steven Johnson described this and other examples in his thought-provoking 2002 book, Emergence. Simply by following local rules and responding to the scent trails left behind by their predecessors, individual ants join to form major thoroughfares between a food source and their nest. No master planner guides their motions.

Similarly, in a developing animal, some cells may find themselves far from the nearest blood vessel. In response to the lack of oxygen, they secrete chemicals that encourage the growth of new capillaries nearby. And in the brain, the intricate wiring of nerve cells is guided in part by signals that they receive and transmit during certain periods of development.

It really has to be this way. Although it's true--and amazing--that the 558 cells of the roundworm C. elegans take up pre-ordained positions in the final creature, the cells in much bigger creatures like us simply can't all have designated roles in the final organism. For one thing, there's just not enough information in our 20,000 or so genes to tell every cell where to go on some genetic master plan. Instead, each cell has to have a degree of autonomy in dealing with new situations. For example, if one of your legs is stunted early on, the muscles, nerves, blood vessels, and skin will all adapt to its new size, rather than blindly proceeding with some idealized plan. Even in C. elegans, the fixed cellular arrangement mostly results from such adaptive behavior of individual cells.

If you're still not convinced, think of the offspring of a bulldog and a Great Dane, which will have a facial and body structure unlike either of its parents. But we are not even surprised that the blood vessels and muscles will successfully adapt themselves to this completely novel shape.

It makes perfect sense that creatures that use this adaptive process in their development would be more successful during evolution.

But the reverse is also true: this flexibility makes evolutionary innovations much easier. The repurposing of mammalian digits for a dolphin's flipper, a horse's hoof, or a bat's wing is much faster if only a few genes have to change to determine the new shape, and the others adapt in parallel. In concert with modular organization, development that is built on exploratory principles is critical to letting evolution explore radically new architectures in response to small genetic changes.