Monthly Archives: December 2010

YouCut Citizen Review of the National Science Foundation

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Eric Cantor (R-VA), who’ll become House majority leader when the next US Congress convenes in January, is launching an experiment. Called YouCut Citizen Review, Cantor’s web-based initiative seeks the public’s advice in cutting federally funded projects. Perhaps because NSF’s awards database is online and open to the public, Cantor and his colleagues picked America’s science agency for its first target.

Adrian Smith (R-NE) introduces the NSF campaign with a short video. His arguments seem neither unreasonable nor extreme. He’s in favor of NSF funding for the “hard sciences,” which, he says, has led to 150 American Nobel Prizes. It’s the soft science he doesn’t like. To quote from the YouCut website,

Recently, however NSF has funded some more questionable projects—$750 000 to develop computer models to analyze the on-field contributions of soccer players and $1.2 million to model the sound of objects breaking for use by the video game industry. Help us identify grants that are wasteful or that you don’t think are a good use of taxpayer dollars.

It’s tempting to attack YouCut as a cynical ploy to shrink government and cut taxes by exploiting the public’s limited understanding of cutting-edge science. To the uninitiated, quark soup, WIMPs, Sonic hedgehog, and the hairy ball theorem might sound silly, questionable, and dispensable.

It’s tempting, too, to attack Cantor and Smith, neither of whom has a background in science. Although Smith currently serves on the House Science Committee and its technology and innovation subcommittee, he attended Liberty University, which was founded in 1971 by TV evangelist Jerry Falwell. The university’s Doctrinal Statement includes the paragraph:

We affirm that the Bible, both Old and New Testaments, though written by men, was supernaturally inspired by God so that all its words are the written true revelation of God; it is therefore inerrant in the originals and authoritative in all matters. It is to be understood by all through the illumination of the Holy Spirit, its meaning determined by the historical, grammatical, and literary use of the author’s language, comparing Scripture with Scripture.

Liberty University teaches young Earth creationism.

However, as a proponent of free speech, open government, and science education, I don’t object to YouCut. NSF spends millions trying to interest the public in the research it funds. Those projects should be able to withstand the scrutiny of the public who ultimately pays for them.

As for Smith’s computer-modeled soccer players, I couldn’t find the corresponding application on NSF’s awards database. Searching for “soccer” yielded 34 successful applications, some of which had to do with fullerenes. Fortunately, USA Today‘s science reporter Dan Vergano had rooted out the offending application and linked to it on his blog.

Far from being wasteful or frivolous, the soccer study turned out to be directed toward understanding virtual collaborations. Moreover, the grant application—in common with the ones I found with my “soccer” search—had a compelling, easy-to-understand abstract. Even the soft-seeming “2007 RoboCup International Symposium” made a strong case:

The RoboCup International Symposium is the premier meeting for presentation and discussion of scientific advances in diverse areas inspired by the RoboCup Initiative, including: robot soccer, rescue robotics, and robots and people. The Symposium’s scope encompasses research and education activities in the fields of computer vision, artificial intelligence, human robot interaction, multi-agent systems, robot mechanisms, and robot locomotion. The 11th annual RoboCup International Symposium will be held in conjunction with RoboCup 2007 in Atlanta, July 9-10, 2007.

If members of the public trawl NSF’s awards database for questionable science, they could be surprised, relieved, and intrigued—but not outraged. YouCut’s campaign against NSF could backfire. I hope so.

Charles Day

Femtosecond electron diffraction

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“Snapshots of cooperative atomic motions in the optical suppression of charge density waves” might not seem like an exciting title. But the paper, which appeared in last Thursday’s Nature was my favorite of last week.

Charge density waves are periodic distortions in crystals that consist of stacked chains or planes of atoms. Above a critical temperature, the valence electrons are free to move about the crystal. Below that temperature, the atoms shift positions slightly, moving closer to some neighbors than to others. The shift has the effect of marooning the electrons in puddles around the atoms, like fish trapped in rockpools at low tide. The crystal becomes an insulator and acquires an additional periodicity.

Rudolf Peierls worked out the basic physics of charge density waves in a 1934 paper. One-dimensional crystals, Peierls pointed out, are intrinsically unstable and inevitably buckle. Charge density waves are manifestations of the Peierls distortion in bulk materials. Neutron scattering experiments confirmed the waves’ existence in the 1950s.

Charge density waves, then are well established. What got me excited about the new paper are the words “snapshot” and “cooperative atomic motions” in its title. The nine-author team from universities in Canada, Germany, and Slovenia has succeeded in observing a Peierls distortion on the few-hundred-femtosecond timescale over which it occurs.

To pull off that coup de recherche, the team took a thin crystal of one of the best-studied charge-density-wave materials, 1T-TaS2, and chilled it below the temperature at which charge density waves appear. Next, the team zapped the crystal—first with a brief pulse of light and then, after a precisely controlled and adjustable delay, with a brief pulse of electrons.

As an electron pulse passed through the crystal, it diffracted off the regular array of atoms to form a pattern that embodied the crystal’s instantaneous structure. From those patterns collected at different delays, the team could track how charge density waves form.

The light pulse gave the valence electrons enough energy to flow freely. Responding to the electrons’ liberation, the more sluggish atoms started to shift back to their undistorted positions. However, even as the atoms were shifting, the electrons began to cool and sank back into confinement around the atoms. The atoms, too, regained their original, Peierls-distorted configuration.

In the schematic, which depicts the process, the atoms are red and the electron distribution is purple: light for low density; dark for high density. The whole process took less than 4 picoseconds to play out.

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The paper’s implications go beyond charge density waves. As the authors point out at the very beginning of the abstract:

Macroscopic quantum phenomena such as high-temperature superconductivity, colossal magnetoresistance, ferrimagnetism and ferromagnetism arise from a delicate balance of different interactions among electrons, phonons and spins on the nanoscale. The study of the interplay among these various degrees of freedom in strongly coupled electron–lattice systems is thus crucial to their understanding and for optimizing their properties.

Femtosecond electron diffraction, as the technique is called, should yield a host of interesting results in the future. It could even prove decisive in solving one of the hardest problems in physics: explaining high-Tc superconductivity.

Charles Day

Wearing my rowing and physicist hats

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Sometimes, when I’m working out at my gym, I wear my Capital Rowing Club baseball cap. The club’s logo identifies me as a rower, which, as I found out last week, isn’t a bad thing.

Lifting weights alongside me was a newcomer to Washington. He saw my hat and we chatted about rowing. I told him about the club and encouraged him to join.

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I don’t habitually wear anything that identifies me as an astronomer (my former research area), a physicist (my current field of operations), or an editor (my current job). Still, when I encounter members of the general public, I’m aware that in a modest, indirect way, I represent the physics community.

For the most part, the questions I get from the general public at parties, on airplanes, or at other social encounters spring from pure curiosity. To answer “What’s new in physics?” I might reply about advances in medical physics, particle physics, or other areas that I suspect my interlocutor might not have heard of.

Occasionally, however, I’m asked about climate change by people who are skeptical of its manmade component. Not being a climatologist, I don’t attempt to refute their views. Rather, I point out that the evidence that Earth’s troposphere has warmed is undeniable. Spacecraft have reliably measured the mean global sea-level rise (about 2 mm/y). Spring, as measured by the greening of remotely sensed vegetation, is arriving a week earlier in the Northern Hemisphere than it used to. The controversy, I say, is about what will happen in the future and what we should do about it.

My conciliatory approach is aimed not just at avoiding a dispute that I doubt I could win. I lack the specialist knowledge to make a compelling case for anthropogenic climate change. Rather, I’d like to leave my climate-skeptic interlocutors with the idea that experiment is the final arbiter in climatology and other sciences.

That said, I can’t bring myself to say anything conciliatory about astrology.

Charles Day

Moebius soap films

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For May’s issue of Physics Today I wrote a news story about a clever biophysical experiment by Aurélien Roux of the Curie Institute in Paris and his collaborators.

Roux wanted to find out how the protein dynamin forms a pouch of cell membrane that projects into the cell during a process called endocytosis. At the start of endocytosis, the pouch—termed a vesicle—is open to the cell’s exterior. In the final step, the neck of the vesicle, which is squeezed by a collar of polymerized dynamin, is pinched off, trapping the vesicle and its contents inside the cell.

Roux’s experiment popped back into my mind this morning when I encountered a paper in the Proceedings of the National Academy of Sciences entitled “Soap-Film Möbius Strip Changes Topology with a Twist Singularity.” Roux had told me that the mechanism by which the cell membrane changes its topology as the vesicle closes is unknown. Curious, I wondered if the new Möbius strip paper was relevant to endocytosis.

The paper was written by Raymond Goldstein, Keith Moffatt, and Adriana Pesci of the University of Cambridge and Renzo Ricca of the University of Milano-Bicocca. Here’s how it begins:

In an elegant article in 1940, the mathematician R. Courant laid out a number of fundamental questions about surfaces of minimal area that could be visualized with soap films spanning wire frames of various shapes. He noted that when the frame is a double loop it can support a film with a Möbius strip topology. Pulling apart and untwisting the loop leads to an instability whereby the film jumps with change of topology to a two-sided solution.

Goldstein and his coauthors point out that despite progress made on Courant’s questions, one stands out unanswered: What is the process that takes a one-sided film to a two-sided one?

In fact, if Goldstein’s paper is correct, that question is no longer unanswered. With a combination of high-speed videography and mathematical analysis, the Cambridge–Milan team demonstrates that the topological transition proceeds via a twist instability at the boundary wire. Clicking on the image of the Möbius soap film will take you to a video of the transition—filmed at 5600 frames a second!


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I’m not sure whether the Cambridge–Milan team’s paper is directly relevant to Roux’s experiment. Still the team’s approach might be applicable to models of endocytosis. As a science writer, I found the possibiity of a link between the two papers intriguing enough to write what, I hope, is a not uninteresting blog post.

But if you’re a scientist, not a science writer, spotting possible links between diverse experiments and theories could be a source of inspiration and future projects. If you don’t already do so, read widely, attend seminars in topics outside your immediate field, and keep an open mind.

Charles Day

Arsenic and phosphorus in bugs and superconductors

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On Mondays I usually visit Science‘s press site, which contains links to papers that will appear in the journal four days later alongside enticing summaries of the most newsworthy papers. This Monday the paper listed first bore the title “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus.” Its summary read:

Living off Toxic Waste — Bacteria That Munch on Arsenic:

Can you imagine eating toxic waste for breakfast? Researchers have discovered a bacterium that can live and grow entirely off arsenic, reports a new study. The findings point for the first time to a microorganism that is able to use a toxic chemical (rather than the usual phosphate) to sustain growth and life. Arsenic is normally highly toxic to living organisms because it disrupts metabolic pathways, but chemically it behaves in a similar way to phosphate. Scientists have previously found organisms that can chemically alter arsenic; and these organisms have been implicated in ground water poisoning events in Bangladesh and other places in Asia when people have shifted to using borehole or well water to avoid cholera. Now, Felisa Wolfe-Simon and colleagues have found a bacterium able to completely swap arsenic for phosphorus to the extent that it can even incorporate arsenic into its DNA. The salt-loving bacteria, a member Halomonadaceae family of proteobacteria, came from the toxic and briny Mono Lake in California. In the lab, the researchers grew the bacteria in Petri dishes in which phosphate salt was gradually replaced by arsenic, until the bacteria could grow without needing phosphate, an essential building block for various macromolecules present in all cells, including nucleic acids, lipids and proteins. Using radio-tracers, the team closely followed the path of arsenic in the bacteria; from the chemical’s uptake to its incorporation into various cellular components. Arsenic had completely replaced phosphate in the molecules of the bacteria, right down its DNA.

I quote the summary in full so that you can remark for yourselves the utter absence of any hint of extraterrestrial life. On the other hand, the press release I received from NASA on Monday mentioned only the paper’s implications for extraterrestrial life:

NASA SETS NEWS CONFERENCE ON ASTROBIOLOGY DISCOVERY; SCIENCE JOURNAL HAS EMBARGOED DETAILS UNTIL 2 P.M. EST ON DEC. 2

WASHINGTON — NASA will hold a news conference at 2 p.m. EST on
Thursday, Dec. 2, to discuss an astrobiology finding that will impact
the search for evidence of extraterrestrial life. Astrobiology is the
study of the origin, evolution, distribution and future of life in
the universe.

So if you awoke to news of poison-eating space aliens in California, credit NASA not Science. But how plausible is the link between the discovery of bacteria that can swap arsenic for phosphorus and extraterrestrial life?

Phosphorus is the ninth most abundant element in living organisms. Its compounds are found in teeth, bones, cell membranes, and a host of important biomolecules, including cells’ main source of chemical fuel, adenosine triphosphate. Phosphate groups also hold together the nucleotides in RNA and DNA.

Because arsenic belongs to the same group in the periodic table as phosphorus, it can readily replace phosphorus in biomolecules. But the arsenated compounds don’t work—hence the element’s toxicity. The newly discovered bacteria are remarkable in that they apparently possess a chemical means of mitigating the toxicity.

But before you start scanning the skies for arsenic-laced M-class planets, keep in mind that arsenic is cosmically rarer than its group V neighbor phosphorus. In Earth’s crust arsenic occurs at a concentration of about 1.5 parts per million. Phosphorus is 1000 times more abundant.

Life as we know it on Earth originated just once, a reflection of its low probability of getting started. I’m therefore skeptical that life forms based on a rare element such as arsenic evolved elsewhere.

I can’t resist ending this blog entry by pointing out another scientific substitution of arsenic for phosphorus. Three years ago in his quest to find semiconductors with interesting magnetic properties, Hideo Hosono and his team from the Tokyo Institute of Technology synthesized a compound with the chemical formula LaOFeP.

The material becomes superconducting at the unremarkably low temperature of 4 K. But the arsenic-substituted compound, when doped with fluorine, superconducts at 26 K, which is uncomfortably high for a normal superconductor. Hosono had discovered a new and exciting class of superconductor.

Despite spawning thousands of papers from excited physicists and chemists around the world, Hosono’s discovery barely registered in the mainstream media.

Charles Day

Waves, whales, and cosmic neutrinos

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Waves appear early in most university physics courses. Richard Feynman introduced them halfway through the first volume of his Lectures on Physics. And if I remember correctly, my first term at Imperial College, London, included a course on waves given by a plasma physicist named H. J. Pain.

The ubiquity and importance of wave phenomena account for their early pedagogical debut. Diffraction, interference, and other wave concepts help us understand the propagation not only of light and sound, but also of electrons in metals and plasma in the Sun’s corona.

But even though I’ve written many times about different kinds of waves, big and small, in solids, liquids, and gases, I was surprised to receive a press release from CERN linking neutrino oscillations and whale songs.

Neutrinos come in three flavors, which, in order of increasing mass, are electron, muon, and tau. In 1957 Bruno Pontecorvo predicted that neutrinos could spontaneously swap back and forth from one flavor to another. Neutrino oscillations were presumed to account for an apparent deficit of neutrinos from the Sun. In 2001 detectors housed deep in an old Canadian nickel mine confirmed that neutrinos do indeed oscillate.

It turns out that the wavelength of neutrino oscillations is about the same as the wavelength of whale songs. That fortunate cosmic coincidence has led to a collaboration between particle physicists and biophysicists. To quote the CERN press release:

European astroparticle physicists are developing together KM3NeT, a large undersea neutrino telescope in the Mediterranean, dedicated to tracking neutrinos from astronomical sources. The deployment of deep sea neutrino detection lines for current experiments such as AntarËs in France, Nemo in Italy and Nestor in Greece has opened up the possibility of also installing monitoring devices for the permanent study of the deep sea environment: studies of ocean currents, of bioluminescence, of fauna and of seismic activity.

The accompanying cartoon shows what the KM3NeT detectors look like.

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I couldn’t find any pictures of hydrophones, seismographs, and other instruments that will be deployed alongside the KM3NeT detectors, but hydrophones at a different undersea neutrino experiment have already made an interesting and unexpected discovery: That sperm whales currently live in the Mediterranean.

Wave phenomena are sufficiently rich and varied that professors who teach them don’t lack interesting, realworld examples. Still, it’s my recollection that Pain and most other lecturers relied on examples that were tried and true, rather than new and exciting. Now, 29 years after my freshman year, I know enough to find the connection between neutrinos and whales to be surprising. Then, back in Pain’s class, I’d have found it inspiring.

Charles Day