brdgt | Science Tuesday - Tetrahedrons, Wine, Lizards, Exercise, and Climate Change

Researchers have been using Dungeons & Dragons dice to learn how to pack tetrahedrons. The record density recently hit 85.63 percent.

Packing Tetrahedrons, and Closing in on a Perfect Fit
By KENNETH CHANG, The New York Times, January 5, 2010

More than 2,300 years ago, Aristotle was wrong.

Now, in the past year, a flurry of academic activity is suddenly zooming in on an answer to a problem akin to wondering how many people can fit into a Volkswagen Beetle or a phone booth. Except here mathematicians have been thinking not about the packing of people, but of geometric solids known as tetrahedrons.

“It’s pretty remarkable how many papers have been written on this in the past year,” said Henry Cohn, a mathematician at Microsoft Research New England.

A tetrahedron is a simple construct — four sides, each a triangle. For the packing problem, researchers are looking at so-called regular tetrahedrons, where each side is an identical equilateral triangle. Players of Dungeons & Dragons recognize the triangular pyramid shape as that of some dice used in the game.

Aristotle mistakenly thought that identical regular tetrahedrons packed together perfectly, as identical cubes do, leaving no gaps in between and filling 100 percent of the available space. They do not, and 1,800 years passed before someone pointed out that he was wrong. Even after that, the packing of tetrahedrons garnered little interest. More centuries passed.

A similar conundrum for how to best pack identical spheres has a more storied history. There, the answer was obvious. They should be stacked like oranges at a supermarket (with a packing density of 74 percent), and that is what Johannes Kepler conjectured in 1611. But proving the obvious took almost four centuries until Thomas C. Hales, a mathematician at the University of Pittsburgh, succeeded in 1998 with the help of a computer.

With tetrahedrons, the best packing arrangement is not obvious, and after it was pointed out that tetrahedrons did not pack perfectly, it seemed that they did not pack very well at all. In 2006, two Princeton University researchers, Salvatore Torquato, a chemist, and John H. Conway, a mathematician, reported that the best packing they could find filled less than 72 percent of the space — packing more loosely than spheres. That ran counter to a mathematical conjecture that, among so-called convex objects (those without dimples, holes or hollows), spheres should have the loosest ideal packing.

The Princeton paper prompted Paul M. Chaikin, a professor of physics at New York University, to buy tetrahedral dice by the hundreds and have a high school student stuff them into fish bowls and other containers. “We immediately found you could do better than 72 percent,” said Dr. Chaikin, who had earlier worked with Dr. Torquato on the packing of squashed spheres, or ellipsoids. (It turned out that squashed spheres pack more densely than spheres.)

The Princeton paper also led Jeffrey C. Lagarias, a mathematics professor at the University of Michigan, to ask Elizabeth Chen, one of his graduate students, to look at tetrahedron packing. Ms. Chen recalled his telling her: “You’ve got to beat them. If you can beat them, it’ll be very good for you.”

Ms. Chen examined several hundred arrangements over the next few weeks, and, she said, “there happened to be several that stood out as very dense.” Her best packing easily eclipsed what Dr. Conway and Dr. Torquato had found, with a packing density of almost 78 percent, surpassing spheres.

“In fact, my adviser totally did not believe me,” Ms. Chen recalled.

After making physical models of tetrahedrons and demonstrating the packing patterns, she convinced Dr. Lagarias that her packings were as dense as she had said they were, and finally published her findings a year ago.

Meanwhile, Sharon C. Glotzer, a professor of chemical engineering also at the University of Michigan, was interested to see whether the tetrahedrons might line up as liquid crystals do. “We got into it, because we are trying to design new materials for the Air Force that have interesting optical properties,” she said.

Dr. Glotzer and her colleagues wrote a computer program that simulated the jostling of tetrahedrons and how they arranged themselves when pushed together. They found not liquid crystals but complex quasicrystal structures with patterns almost repeated yet not quite. “That is the most astonishing crazy thing,” Dr. Glotzer said.

Examining the quasicrystals, they did find a periodic structure that represented another leap in packing density: over 85 percent. Just as that finding was prepared for publication last month in the journal Nature, a group at Cornell, using a different search method, found yet another packing that was just as dense.

But while Dr. Glotzer’s structure was surprisingly complex — the repeat pattern consists of 82 tetrahedrons — the Cornell crystal was surprisingly simple, with just four. It is also puzzling to researchers why the tetrahedrons in Dr. Glotzer’s simulations tend to the complex quasicrystal structures if the best packing is actually a much simpler structure.

“That’s part of what’s so surprising about this,” said Dr. Cohn, of Microsoft Research. “Each of these packings feels very different.”

A few days before Christmas, Dr. Torquato and Yang Jiao, a graduate student, reported that they had tweaked the Cornell structure to bump up the packing density by a fraction, to 85.55 percent.

“I’d be shocked if what we have right now is the densest,” Dr. Torquato said in an interview last week. “It just happens to be the densest known right now.”

Dr. Torquato need not be shocked.

On Monday, Ms. Chen, the University of Michigan graduate student, posted a new preprint, which describes a family of packings that include the latest Cornell and Princeton structures. But it also includes a better packing. The calculation was verified by simulations from Dr. Glotzer’s group.

The new world record for packing density of tetrahedrons: 85.63 percent.

OBSERVATORY: Much-Maligned Mother of Many Beloved Wines
By HENRY FOUNTAIN, The New York Times, January 5, 2010

About a decade ago, researchers had some startling news for wine lovers. Some of their beloved grape varieties, including chardonnay and gamay noir, were the offspring of a third-rate parent, gouais blanc. In fact, the research showed that at least a dozen varieties were a result of crosses, a long time ago, between pinot noir and gouais blanc, which had such a bad reputation that its cultivation was at times outlawed.

The news just got a bit more startling. Looking at the DNA in chloroplasts in the 12 varieties, Harriet V. Hunt and Matthew C. Lawes of the University of Cambridge in England and colleagues set out to determine which was the paternal parent (supplying the pollen) and which was the maternal one (supplying the egg cells). Gouais blanc, they write in Biology Letters, was the mother of nine of the varieties: aligoté, auxerrois, franc noir, melon, bachet, sacy and romorantin, in addition to chardonnay and gamay noir.

Chloroplasts are the parts of the cell where photosynthesis occurs, and in the wine grape, Vitis vinifera, as in many other plants, their DNA is inherited from the mother. In some plant species, chloroplast genes are thought to determine important characteristics like tolerance of cold. So the much-maligned gouais blanc may have been responsible for some grape varieties’ key qualities.

Several lizard species that are dark have developed white skin in the White Sands of New Mexico.

OBSERVATORY: White Lizards Evolve in New Mexico Dunes
By HENRY FOUNTAIN, The New York Times, January 5, 2010

The White Sands of New Mexico are a good place to study evolution in progress. One reason is that the terrain, gypsum dunes white as a sheet of paper, is so different from the surrounding area. Another is that the dunes formed only about 6,000 years ago.

“From an evolutionary perspective, that’s really the blink of an eye,” said Erica Bree Rosenblum, a professor at the University of Idaho who has been studying evolution at White Sands for much of the past decade. Her focus has been on three lizard species that elsewhere are dark skinned but in White Sands have each evolved a white-skinned variety that makes them hard to find. “It’s really obvious what’s happened,” Dr. Rosenblum said. “Everybody got white so that they could better escape from their predators.” It’s a great example of convergent evolution, of species independently acquiring the same traits.

One question about convergent evolution is the mechanism by which it happens. Sure, these three lizards all developed white skin, but did they do it in the same way? Dr. Rosenblum and her colleagues have provided answers to this question in a paper in The Proceedings of the National Academy of Sciences.

“At first blush it seems like the answer is yes,” she said. In at least two of the lizard species, the researchers found that mutations on the same gene, linked to the production of the skin pigment melanin, were responsible.

The second part of the story is more interesting, Dr. Rosenblum said. In the two species, the mutations are different, and the molecular mechanism by which less melanin is produced is different, too.

And, she said, the different mechanisms have had an effect on how the white-skinned trait has spread through the populations. In one, the mutation has made the white-skinned trait dominant; in the other, the mutation has made it recessive. So, according to basic Mendelian genetics, the trait spreads more quickly in the first lizard species than the second.

Q & A: Temperature and Exercise
By C. CLAIBORNE RAY, The New York Times, January 5, 2010

Q. Does a person tend to burn more fat exercising outdoors in colder weather or in hotter weather? I am leaning to the colder weather side, since the body has to work harder to keep the body temperature near normal.

A. “Contrary to conventional wisdom, the combination of exercise and cold exposure does not act synergistically to enhance metabolism of fats,” according to a study published in 1991 in the journal Sports Medicine.

The study, done at the Hyperbaric Environmental Adaptation Program of the Naval Medical Research Institute in Bethesda, Md., found that some of the bodily processes involved in fat metabolism were actually slowed down by the effects of relatively cold temperatures on human tissue.

The researchers suggested that the slowdown in metabolic processes might be linked to the constriction of blood vessels in the peripheral fatty tissues when exercise is done in the cold.

The study found that the volume of air inhaled and exhaled in one minute increases upon initial exposure to the cold but may return to rates comparable to those in warm-air exercise upon prolonged exertion.

The heart rate is often, but not always, lower during cold-weather exercise, the study found, while oxygen uptake may increase, something the researchers suggested could be at least in part the result of shivering.

A satellite image of the East Siberian Sea from 1999-2008. This image has been degraded to hide the satellite’s true capabilities.

C.I.A. Is Sharing Data With Climate Scientists
By William J. Broad, The New York Times, January 5, 2010

The nation’s top scientists and spies are collaborating on an effort to use the federal government’s intelligence assets — including spy satellites and other classified sensors — to assess the hidden complexities of environmental change. They seek insights from natural phenomena like clouds and glaciers, deserts and tropical forests.

The collaboration restarts an effort the Bush administration shut down and has the strong backing of the director of the Central Intelligence Agency. In the last year, as part of the effort, the collaborators have scrutinized images of Arctic sea ice from reconnaissance satellites in an effort to distinguish things like summer melts from climate trends, and they have had images of the ice pack declassified to speed the scientific analysis.

The trove of images is “really useful,” said Norbert Untersteiner, a professor at the University of Washington who specializes in polar ice and is a member of the team of spies and scientists behind the effort.

Scientists, Dr. Untersteiner said, “have no way to send out 500 people” across the top of the world to match the intelligence gains, adding that the new understandings might one day result in ice forecasts.

“That will be very important economically and logistically,” Dr. Untersteiner said, arguing that Arctic thaws will open new fisheries and sea lanes for shipping and spur the hunt for undersea oil and gas worth hundreds of billions of dollars.

The monitoring program has little or no impact on regular intelligence gathering, federal officials said, but instead releases secret information already collected or takes advantage of opportunities to record environmental data when classified sensors are otherwise idle or passing over wilderness.

Secrecy cloaks the monitoring effort, as well as the nation’s intelligence work, because the United States wants to keep foes and potential enemies in the dark about the abilities of its spy satellites and other sensors. The images that the scientific group has had declassified, for instance, have had their sharpness reduced to hide the abilities of the reconnaissance satellites.

Controversy has often dogged the use of federal intelligence gear for environmental monitoring. In October, days after the C.I.A. opened a small unit to assess the security implications of climate change, Senator John Barrasso, Republican of Wyoming, said the agency should be fighting terrorists, “not spying on sea lions.”

Now, with the intelligence world under fire after the attempted airliner bombing on Christmas Day, and with the monitoring program becoming more widely known, such criticism seems likely to grow.

A senior federal official, who spoke on the condition of anonymity, defended the scientific monitoring as exploiting the intelligence field quite adroitly.

Ralph J. Cicerone, president of the National Academy of Sciences and a member of the monitoring team, said the program was “basically free.”

“People who don’t know details are the ones who are complaining,” Dr. Cicerone said.

About 60 scientists — mainly from academia but including some from industry and federal agencies — run the effort’s scientific side. All have secret clearances. They obtain guidance from the National Academy of Sciences, an elite body that advises the federal government.

Dr. Cicerone said the monitoring effort offered an opportunity to gather environmental data that would otherwise be impossible to obtain, and to do so with the kind of regularity that can reveal the dynamics of environmental change.

“It’s probably silly to think it will last 50 years,” he said of the program in an interview. “On the other hand, there’s the potential for these collections to go on for a long time.”

The C.I.A. runs the program and arranges for the scientists to draw on federal surveillance equipment, including highly classified satellites of the National Reconnaissance Office.

Officials said the effort to restart the program originated on Capitol Hill in 2008 after former Vice President Al Gore argued for its importance with Senator Dianne Feinstein, Democrat of California, who was then a member of the Senate Intelligence Committee; she became its chairwoman in early 2009.

The Obama administration has said little about the effort publicly but has backed it internally, officials said. In November, the scientists met with Leon E. Panetta, the C.I.A. director.

“Director Panetta believes it is crucial to examine the potential national security implications of phenomena such as desertification, rising sea levels and population shifts,” Paula Weiss, an agency spokeswoman, said.

The program resurrects a scientific group that from 1992 to 2001 advised the federal government on environmental surveillance. Known as Medea, for Measurements of Earth Data for Environmental Analysis, the group sought to discover if intelligence archives and assets could shed light on issues of environmental stewardship.

It is unclear why Medea died in the early days of the Bush administration, but President George W. Bush developed a reputation for opposing many kinds of environmental initiatives. Officials said the new body was taking on the same mandate and activities, as well as the name.

“I’m extremely pleased with what’s been happening,” said Michael B. McElroy, an atmospheric scientist at Harvard University and a senior member of the group. “It’s really first-rate.”

Among the program’s first responsibilities has been to assess earlier Medea projects to see which, if any, produced valuable information and might be restarted or expanded.

Dr. Untersteiner of the University of Washington said that in June the government posted some imagery results from that assessment on the Web sites of the United States Geological Survey in an area known as the Global Fiducials Library, which advertises itself as an archive of intelligence images from scientifically important sites.

Among other things, the online library displays years of ice imagery from six sites inside the Arctic Circle, including the Fram Strait, the main route for icebergs moving from the Arctic basin into the North Atlantic.

Scientists consider the Arctic highly sensitive to global warming and are particularly interested in closely monitoring its changes as possible harbingers.

In July, the National Research Council of the National Academy of Sciences released a report that praised the monitoring.

“There are no other data available that show the melting and freezing processes,” the report said. “Their release will have a major impact on understanding effects of climate change.”

Dr. Untersteiner said the federal government had already adopted one of the report’s recommendations — have reconnaissance satellites follow particular ice floes as they drift through the Arctic basin rather than just monitoring static sites.

For this summer, Dr. Untersteiner said he had asked that the intelligence agencies start the process sooner, “so we still see the snow cover, maybe in early May.”

Such research, Dr. Untersteiner said, promised to promote understanding of the fundamental forces at work in global climate change, including the endless whorls and gyres of polar ice.

“We still have a problem with ice mechanics,” he said. “But the dynamics are very revealing.”