Stephen Goldup/Univ. of Edinburgh

TAMING CHANCE. This molecule acts like the microscopic demons James Clerk Maxwell envisaged in the 19th century. Thermal or Brownian motion moves a ring-shaped molecule (blue) from one side to another of a dumbbell-shaped molecule (yellow). But a “gate” molecule (green) is designed to lock the ring molecule to just one side of the dumbbell. Brownian motion provides energy to move the ring, but the gate molecule steers it.

Occasionally, scientists stumble upon what seems to be a free lunch. But they’re not concerned about possibly violating the laws of economics. It would be much more shocking to break the laws of physics.

To physicists, the no-free-lunch rule is precious. One form of it is the first law of thermodynamics, which says that energy cannot be created from nothing. The second law of thermodynamics goes even further, declaring not only that lunches are never free but also that they come at some minimum price.

Nonetheless, some natural phenomena seem, at first glance, to violate the spirit, if not the letter, of those laws. Take living cells. In recent years, scientists have found that some molecular machines—proteins that perform crucial tasks of life, from shuttling molecules through membranes to reading information off of DNA—seem to move spontaneously. These machines are likely powered by the random motion of water molecules in their environment, the “thermal noise” that thermodynamics insists is not available for doing work.

While some researchers debate how such machines work without breaking physical laws, other scientists have begun to exploit similar phenomena to create artificial molecular motors—nanomachines that imitate nature by putting randomness to work. “The idea is, let’s take advantage of thermal noise, rather than fight against it,” says Dean Astumian, a theoretical chemist at the University of Maine in Orono.

Researchers have just begun to build artificial nanomachines that perform simple tasks, such as moving molecules, by steering random motion in one direction rather than another. In the Feb. 13 Journal of the American Chemical Society, a team led by David Leigh, a chemist at the University of Edinburgh in Scotland, describes the first molecule designed to use chemical energy to open or close a gate and allow one of its parts to randomly cross the gate in one direction, but not the other.

It’s very much like the task assigned to a hypothetical “demon” by the 19th-century Scottish physicist James Clerk Maxwell. His thought experiment was an early attempt to show how the second law defines group behavior and thus applies only to large numbers of particles.

Maxwell’s angel

The second law requires that in any given activity, some of the expended energy will end up as waste heat.

For example, even an efficient power plant can lose half or more of its fuel’s energy to waste heat. This waste heat cannot be recovered without expending more energy—and producing more waste heat—in the attempt.

Ultimately, waste heat manifests as random molecular motion, like the incessant hailstorm of water molecules buffeting proteins in a cell’s watery guts.

“It’s sort of like you’re riding a bicycle and there’s a Richter-12 earthquake going on all the time,” says George Oster, a molecular biology theorist at the University of California, Berkeley.

It’s hard to see how the molecular movements (called Brownian motion) produced by such violence could accomplish anything useful. Every second, a typical molecular motor will exchange millions of times as much energy with the environment through these random collisions as it will in the performance of its actual task, Astumian explains. But beginning in the early 1990s, scientists began to suspect that certain protein motors can perform their tasks not despite Brownian motion, but thanks to it.

One example is RNA polymerase (RNAP), an enzyme responsible for reading genetic information from DNA. RNAP latches on to a DNA double strand at the beginning of a gene, cleaves the two strands apart, and clamps around one of them. It then moves along DNA’s bases—the A’s, C’s, G’s, and T’s that constitute the genetic code’s alphabet—and assembles a corresponding molecular chain of RNA. The RNA molecule then acts as a template for producing proteins.

RNAP, however, does not always move forward. Brownian motion can push it either way. “It’s like a zipper—it slides back and forth,” says Evgeny Nudler, a biochemist at New York University.

Roger Kornberg, a structural biologist at Stanford University, and his collaborators first decoded the structure of RNAP in 2001, earning him the 2006 Nobel Prize in Chemistry. In the same award-winning papers, the team suggested that RNAP may be able to select the Brownian fluctuations that propel it forward and discard those that would set it back. That sounds suspiciously like a free lunch, but in fact, the laws of physics do not prevent it.

RNAP’s secret lies in the fact that the second law is statistical in nature. At the scales of molecules, random fluctuations can temporarily create small amounts of seemingly “free” energy. Cells can take energy out of Brownian motion by selecting the favorable fluctuations and rejecting the others—very much in the spirit of Maxwell’s demon.

Maxwell asked whether the random differences among the energies of particles could somehow be harnessed. He imagined a box filled with a gas and divided into two parts by a wall that didn’t conduct heat. The wall had a tiny door, and standing by it, “a being whose faculties are so sharpened that he can follow every molecule in its course,” Maxwell wrote in Theory of Heat (1871). This “demon” could open or close the door whenever a gas molecule approached, in such a way as to let the faster molecules cross in one direction only, and the slower ones in the opposite direction. After a while, the faster molecules would make one side of the box hotter than the other. Heat would flow in the “wrong” direction.

For decades, physicists argued whether such a demonic being could actually violate the second law. Ultimately, modern thinking goes, the energy that the demon’s brain spends on processing (and erasing) information about the particles would offset any recovery of waste heat, and thereby preserve the second law’s validity.

So, molecular motors such as RNAP could work like microscopic Maxwell demons, using energy to select favorable fluctuations of energy when opportunities arise. In fact, RNA polymerase is so far the best-established example of a biological Maxwell demon, says Steven Block, a biophysicist at Stanford University.

But that doesn’t mean it gets a free lunch.

When they decoded RNAP’s structure, Kornberg and his team discovered that RNAP includes a system of two moving parts, located next to the site within RNAP where new RNA bases bind to the DNA template. When this two-part system folds, it falls onto the binding site like a trigger onto a bullet casing. Perhaps, some researchers thought, such a trigger pushes the newly formed DNA-RNA double strand forward by one step.

Indeed, in 2005, Nudler and his collaborators showed that mutations altering the trigger structure rendered the RNAP unable to move preferentially forward.

However, Kornberg suggests, the trigger may not be what pushes the zipper forward. Instead, the trigger’s role could be to test the strength of the binding in the latest DNA-RNA base pair. If the wrong, noncomplementary RNA base had gotten there by mistake, it would not be bonded as strongly as a complementary base would be, and the trigger would dislodge it, correcting the transcription error. The trigger’s “principal role would not be in motion, but in recognition,” he says.

Here is where the Maxwell-demon analogy could be useful, Kornberg adds. Once a correct complementary base pair has formed, Brownian motion would allow the zipper to move forward. The trigger would prevent a backward step.

Block’s team measured the pull exerted by single RNAP molecules during the transcription process. Those measurements seem consistent with this picture, Kornberg says.

So, Brownian motion would provide the energy for RNAP to crawl along DNA. The higher chemical affinity of complementary pairs—and the larger amounts of energy they release when they bind—would do the demon’s work. And pay for lunch.

Geography as destiny

No matter what the details of its machinery are, RNAP is an example of how evolution has invented ways of doing complex tasks in the forbidding environment of Brownian motion. Researchers who are trying to build artificial machines at the molecular scale—one of the promises of nanotechnology—would very much like to do the same, says Astumian.

The molecule described by Leigh’s team at Edinburgh is a step in that direction, operating just like a Maxwell demon by opening and closing its gate to let molecules through.

“We made a molecule that works with the process that Maxwell envisaged,” says Leigh, who proudly remarks that his house is just around the corner from the place where Maxwell once lived.

Leigh’s molecule is really three molecules. Two form a type of rotaxane, which is a dumbbell-shaped molecule plus a ring molecule around the dumbbell’s axle. Because of Brownian motion, this ring is generally free to bounce between the dumbbell’s ends, where it can loosely bind. Left alone, the ring will keep randomly jumping between the two sides.

The researchers put their rotaxanes in water and added to the solution the third molecule, which is designed to bind to the middle of the axle. This third molecule would act as a gate, blocking the ring to one side and holding it there.

The ring’s two sides have different shapes. When the ring is on one side of the dumbbell, the gate can bind to the axle. When the ring is on the other side, its shape will prevent the gate from binding.

The researchers demonstrated that in 70 percent of the molecules, the rings ended up sticking to the preferred side of the dumbbell, trapped into position by the gate.

The team described a similar molecule for the first time a year ago in Nature—although in that case, the gates were controlled by shining ultraviolet light on the solution rather than by the presence of molecules in the solution itself.

In both cases, the energy moving the ring comes from Brownian motion, but the molecules determine where the ring ends up. “It’s a chemical way of implementing Maxwell’s demon,” says Astumian, who in 1998 envisaged a similar working principle with Imre Derényi, now at Eötvös University in Budapest.

Leigh says that one could imagine stringing together many rotaxanes. The rings would still move mostly at random, but on average the gates would tend to push them in a specific direction, from one rotaxane to the next.

Einstein rules

Meanwhile, physicists, inspired in part by the discoveries about protein motors, have found renewed interest in the small fluctuations that characterize thermodynamics at microscopic scales.

“On average, the second law will never be violated,” says Christopher Jarzynski, a theoretical physicist at the University of Maryland in College Park.

But, as Maxwell suggested, the second law may apply more to macroscopic thermodynamics. It thus is not always helpful for understanding phenomena such as the spontaneous folding of newly minted proteins, which take place in the cell’s thermal bath.

In the 1990s, Jarzynski and others developed new theoretical tools to predict how much energy the Brownian bath can spontaneously make available, for example, to help out a molecular motor.

In 2002, Berkeley biochemist Carlos Bustamante and his collaborators tested Jarzynski’s hypothesis for the first time on a biological molecule. They took single RNA molecules in a folded state and repeatedly pulled them apart to unfold them, while measuring the force exerted during the process. In accordance with Jarzynski’s predictions, Brownian fluctuations would sometimes impede the process, and sometimes help it by providing a bit of free energy. In such cases, says Bustamante, “the work is being done by the bath, in a sense.”

Last year, another team performed similar measurements by unfolding proteins (Science News: 7/14/07, p 22). Experiments such as these can help researchers understand why biological molecules fold in one way rather than another—knowledge that may help them understand diseases caused by protein folding gone wrong.

In any case, it seems that the free lunches of molecular motors do always carry some sort of cost. Consequently, most scientists today would still agree with the sentiment Einstein expressed about thermodynamics in 1949: “It is the only physical theory of universal content which I am convinced that, within the framework of the applicability of its basic concepts, will never be overthrown.”

The Archimedes Codex: How a Medieval Prayer Book Is Revealing the True Genius of Antiquity’s Greatest Scientist — Reviel Netz and William Noel

Some of the works of Archimedes—the Greek thinker and tinkerer who lived in 3rd-century B.C. Sicily and discovered the principle of buoyancy—survive only in a single 8th-century copy. As Netz and Noel recount, the manuscript was lost and found multiple times, erased and recycled into a prayer book by a 13th-century monk, and lived through fire, mold, and forgers who covered some of its pages with fake medieval paintings. In 1998, a collector bought the manuscript for $2 million and entrusted it to Noel, a curator at the Walters Art Museum in Baltimore. Using pioneering technology, researchers have managed to read most of the book’s content, allowing historians—including Netz—new glimpses into Archimedes’ genius. Da Capo, 2007, 320 p., color photos and b&w illus., hardcover, $27.50. [Also see: The 'Jurassic Park' of Manuscripts.]

ISBN: 030681580X

Apollo’s Fire: Igniting America’s Clean Energy Economy — Jay Inslee and Bracken Hendricks

The authors present a manifesto for the Apollo Alliance, a clean-energy advocacy organization that Inslee, a [democratic] congressman from Washington state, helped found and where Hendricks is a senior fellow. Greening the U.S. economy is not only necessary to save the environment and wean us off Middle Eastern oil, the authors write. It will also create millions of “green-collar” jobs, which will be held by everyone from engineers developing better solar panels to the workers who will install them. The book evokes the national focus on reaching the moon in the 1960s to advocate a comprehensive array of policy and technological solutions. It also aims to allay fears of losing jobs to new regulations and to defuse tensions between trade unions and environmentalists, two traditionally Democratic constituencies. Island Press, 2007, 416 p., b&w photos, hardcover, $25.95.

ISBN: 1597261750

Four Laws That Drive the Universe — Peter Atkins

Although it deals with seemingly familiar concepts such as temperature, thermodynamics ranks among the most conceptually treacherous branches of physics. Many students, for example, have puzzled over the definition of entropy, a measure of disorder. Atkins, a chemistry professor at the University of Oxford in England, guides the reader through the basics of thermodynamics in just over 120 pages by keeping a steady focus on the subject’s four fundamental laws. The book contains a modicum of formulas. And although it’s tersely written and titled like a popular-science book, Four Laws is a textbook both in essence and in structure. Atkins’ elegant exposition will appeal to the lay reader with a serious interest in physics. Oxford Univ. Press, 2007, 128 p., b&w illus., hardcover, $19.95.

ISBN: 0199232369

Auto Mania: Cars, Consumers, and the Environment — Tom McCarthy

As crude oil approaches $100 per barrel, wallet pain, more than any fears of global warming, may eventually lead Americans to reconsider their thirst for ever-heavier and ever-faster cars and trucks. Since Henry Ford’s invention of the mass-produced car, consumers have chosen what to drive based less on the environmental consequences—which include not just tailpipe emissions but the full product cycle, from mining to disposal—than on the allure of the car as a status symbol, McCarthy argues. He tells the story of a nation’s affair with four wheels and of how the car’s role as cultural icon has influenced its evolution. When considering the car’s impact on the environment, it is simplistic to blame it all on Detroit’s “big three” or the inadequacy of government regulations. One case in point, McCarthy writes, is the astonishing rise of the SUV, which took even car manufacturers by surprise. Yale Univ. Press, 2007, 368 p., b&w illus. and photos, hardcover, $32.50.

ISBN: 0300110383

Now, scientists think they may have found out how and why things find their way into knotty arrangements. By tumbling a string of rope inside a box, biophysicists Dorian Raymer and Douglas Smith have discovered that knots—even complex knots—form surprisingly fast and often. The string first coils up, and then its free ends swivel around the other coils, tracing a random path among them. That essentially makes the coils into a braid, producing knots, the scientists say.

The results’ relevance may go well beyond explaining the epidemic of tangled venetian blind cords. That’s because spontaneous knots seem to be prevalent in nature, especially in biological molecules. For example, knottiness may be crucial to the workings of certain proteins (see “Knots in Proteins”). And knots can randomly form in DNA, hampering duplication or gene expression—so much so that living cells deploy special knot-chopping enzymes.

Raymer’s interest in knots began as an answer waiting for a question. Two years ago, he was an undergraduate student working in Smith’s lab at the University of California, San Diego (UCSD). Raymer fancied taking a class about the abstract theory of knots, offered by UCSD’s math department. Smith told him that he should take it only if he could find a practical use for it—some kind of knot experiment.

Raymer never took the class, but he and Smith did come up with a simple idea for an experiment. They put a string in a cubic container the size of a box of tissue. By tumbling the box 10 times “like a laundry dryer,” as Raymer puts it, the researchers hoped to observe knots forming spontaneously on occasion. They didn’t have to wait for long: Knots formed right away. “The first couple of times, it was pretty amazing,” Raymer says.

The researchers repeated the procedure more than 3,000 times, and knots formed about every other time. Longer strings, or more-flexible strings, tended to knot more often.

The researchers took pictures, planning to gather precise statistics of the types of knots that were forming. Raymer soon realized that, to make sense of the mess, he’d need to teach himself the mathematics of knots after all.

Ready-made tools

The theory of knots began in earnest in the 1860s, under the stimulus of the British physicist William Thomson, later known as Lord Kelvin. Kelvin suggested that atoms of different elements were really different kinds of knotted vortices in the ether. So to lay the foundations of chemistry, he believed, it was imperative to classify knots. Ultimately, physicists discovered that the ether didn’t exist. But mathematicians took an interest in knots for knots’ sake, as part of the young branch of mathematics called topology.

Topology studies shapes. Specifically, it studies shapes’ properties that are not affected by stretching, moving, twisting, or pulling—anything that doesn’t break up the object or fuse some of its parts. The proverbial example is that, to a topologist, a coffee mug is the same as a doughnut. In your imagination, you can squash the mug into a doughnut shape, and it will retain the property of having a hole, namely its handle.

A sphere is different. You can stretch a sphere into a stick and bend the stick so its ends touch. But turning that open ring into a doughnut will involve fusing the ends, and that’s forbidden.

In topology, a knot is any curved line that closes up on itself, possibly after a circuitous path in three dimensions. A circle is regarded as the “trivial” knot. Two loops are considered to be the same knot if you can turn one into the other by topological manipulation, which in this case means anything that does not break the curve or force it to run through itself.

Topologically, a knotted string is not a real knot, as long as its ends are free. That’s because either of the ends can always thread back through any entanglement and undo the knot. An open string, no matter how garbled, is the same as a straight segment. (Mathematicians usually think of strings as being stretchable and infinitesimally thin, so in topology there is no issue of a knot being tight.)

Strictly speaking, then, the string in Raymer and Smith’s box was never knotted. But it was still a mess. When the researchers joined the string’s ends, they made it into a closed loop, often something that even a mathematician would call a knot.

Raymer soon realized that telling different knots apart, or recognizing when two knots are the same is a tricky business. Topologists usually work with two-dimensional drawings of knots called knot projections. From different points of view, the same curve will look different and so will its projections. Topologists’ best tools for distinguishing knots are algebraic expressions called knot polynomials. These are sums of multiples of a variable, such as x, raised to different powers. The variable has no meaning per se, and all the information is in the numbers by which it’s multiplied. But the x’s make it easier to calculate a knot polynomial starting from a knot projection.

James Alexander, a Princeton University mathematician, invented the first knot polynomial in the 1920s. Two topologically equivalent knots always will give the same Alexander polynomial, no matter how different their projections look. So if two knots have different polynomials, they’re certainly nonequivalent. The converse, however, is not true: Some distinct knots have the same Alexander polynomial. That means that the Alexander polynomial is not a fail-safe way of distinguishing knots.

In the early 1980s, Vaughan Jones of the University of California, Berkeley rekindled mathematicians’ interest in knots when he defined a new kind of knot polynomial, a discovery that earned him the Fields Medal, the most coveted prize in mathematics. The Jones polynomials distinguish knots with greater, if not complete, accuracy than the Alexander polynomials. That made the Jones polynomials Raymer’s choice to catalog his knots.

Tie land

Raymer wrote a computer program to calculate Jones polynomials from the pictures he had taken each time he opened the box. The program found that the humble box had produced at least 120 distinct types of knots. Some were pretty complex.

The most basic measure of knot complexity is the minimal crossing number, the number of overpasses needed to draw the simplest possible projection of the knot. For the trivial knot, that number is zero. The simplest true knot, the trefoil requires that just three crossings be drawn. A few of the knots from the tumbling box required as many as 11, Raymer and Smith report in the Oct. 16 Proceedings of the National Academy of Sciences

Raymer says he and Smith were surprised, because previous knot experiments—physicists have tried a few in recent years—had seen only some of the simplest knots. For example, in 2001 Belmonte and his collaborators showed that a hanging chain (not from Belmonte’s venetian blinds) tended to knot up when shaken. In 2006, a team led by physicist Jens Eggers of the University of Bristol in England got a ball chain to form knots by setting it on a vibrating dish.

De Witt Sumners, an applied mathematician at Florida State University in Tallahassee, says he was not surprised that knots would form in a box. In computer simulations, mathematicians have found that random motion creates paths that almost always tie themselves up. Together with Stu Whittington of the University of Toronto, Sumners demonstrated mathematically in 1988 that if you wait long enough, these random walks will get knotted virtually 100 percent of the time.

Sumners suspects that with longer tumbling, Raymer and Smith would have gotten knots almost always, instead of just every other time. “They should have spun longer,” to see the full effects, Sumners says.

In their paper, on the other hand, Raymer and Smith propose a theoretical explanation for the mess in their box that differs from the most general type of random walk. Because their string tended to coil up whether or not it formed knots, they created a mathematical model of a bundle of coils as a series of parallel, horizontal strands. In a computer simulation, Raymer and Smith allowed one of the strands—representing one of the free ends of the string—to cross over or under one of the others in the bundle. After several such steps, the strands had braided, which often meant that the string as a whole was now knotted.

This simplified model didn’t reproduce the exact results of their experiment, but it did predict that specific knots had about the right odds of forming within the allowed time.

Jam-packed

Belmonte calls the braid model “very obvious, but maybe not universal,” meaning that different physical phenomena probably tie knots in different ways. In bacterial DNA, for example, one way that knots can form is by genetic recombination. That’s when, to facilitate the reshuffling of genes, enzymes cut DNA at two places and reattach the ends in a different order. Bacterial genomes are circular, so recombination can produce veritable knotted loops.

In the late 1990s, biochemists discovered enzymes that seem able to detect when DNA has a knot. The enzymes then undo the knot by brute-force cut and paste.

Keeping DNA tidy may be crucial to some of the cell’s most important functions. That’s because copying DNA and reading out the information it contains are performed by other enzymes, called polymerases, which walk along DNA. “When [a polymerase] comes to a knotted area, it will be stuck,” Belmonte says.

Scientists have discovered similar knot-busting enzymes in cells that have open-string chromosomes, such as in humans. The presence of such enzymes suggests that knotting may be an issue for human chromosomes as well. And scientists have also found knots in mitochondria, cellular organelles that contain loop DNA.

Another place where DNA knots can form is inside viruses, says Andrzej Stasiak, a structural biologist at the University of Lausanne in Switzerland. Viruses build containers called capsids in which the viruses tightly pack their DNA for traveling from one host cell to the next. In some viruses, the capsid keeps DNA at a pressure of more than 60 atmospheres.

Stasiak says that the packing process probably produces coiling similar to that seen by Raymer and Smith. Their coil-and-braid model could help explain why the DNA of some viruses often ends up being knotted.

But even if Raymer and Smith’s results don’t prove to be directly relevant to the molecules of life, they are “a very good beginning” for a general study of physical knots, according to Belmonte. “Now we can at least ask these questions: Are there universal laws of knots?”

The new technique for creating such “rogue waves” in the lab might help physicists understand them as a general phenomenon, in the hope of predicting the risks for vessels at sea.

A rogue wave will appear “at a random location, at a random time,” says Bahram Jalali, an electrical engineer at the University of California, Los Angeles (UCLA), who developed an interest in rogue waves while spending time on his 36-foot sailboat.

(Read the rest of my article on the Science News web site (password required))

Cover illustration by Anders Sandberg

This artist’s impression represents a view of a hyperbolic plane — the kind of beast that M. C. Escher loved to paint — projected on the surface of a sphere. Maldacena’s concept of the holographic universe translates a string theory living in hyperbolic space (the 3-D analogue of hyperbolic plane) into a theory of particles living on the surface of a sphere.

In a school of thought that teaches the existence of extra dimensions, Juan Maldacena may at first sound a little out of place.

String theory is physicists’ still-tentative strategy for reconciling Einstein’s theory of gravitation with quantum physics. Its premise is that the subatomic particles that roam our three-dimensional world are really infinitesimally thin strings vibrating in nine dimensions. According to Maldacena, however, the key to understanding string theory is not to add more dimensions but to cut their number down.

In his vision, the mathematical machinery of strings completely translates into a more ordinary quantum theory of particles, but one whose particles would live in a universe without gravity. Gravity would be replaced by forces similar to the nuclear forces that prevailed in the universe’s first instants. And this would be a universe with fewer dimensions than the realm inhabited by strings.

Just as a hologram creates the illusion of the third dimension by scattering light off a 2-D surface, gravity and the however many dimensions of space could be a higher-dimensional projection of a drama playing out in a flatter world.

In physics parlance, the two theories would be dual to each other—two mathematically equivalent languages for describing the same reality. Physicists could study each phenomenon using whichever language that makes it easier to understand.

Maldacena first presented his conjecture in November 1997, and it quickly became a leading theme in string theory research. Ten years later, physicists still don’t have proof of it, though many have tried and thousands of papers have been written. But hints have been accumulating, and recently experts have found “very strong evidence” that the conjecture is true, says Maldacena, now at the Institute for Advanced Study in Princeton, N.J.

Meanwhile, the work by Maldacena and others has helped clarify a nagging paradox about black holes, gravity’s most extreme phenomena, by translating the problem into ordinary quantum theory. Physicists have also used the dictionary in reverse, turning problems about real-world particles such as quarks into questions about how seismic waves shake black holes. Surprisingly, the black hole calculations have often turned out to be more manageable than the original form of the problem.

But the most important fallout from Maldacena’s intuition has probably been on the field of string theory itself. His work has offered physicists hope that they can make the string idea rigorous by tracing its roots to ordinary quantum physics. Maldacena’s conjecture has energized string theory advocates, occupying the center of a confluence of ideas coming from several branches of physics. “It’s the most incredible discovery in theoretical physics in the last 20 years,” says Harvard University’s Nima Arkani-Hamed.

Stone-cold genius

In 1997, Maldacena was contemplating a stubborn paradox having to do with black holes. Stephen Hawking of the University of Cambridge in England had long ago calculated that black holes would slowly evaporate, eventually disappearing in a burst of gamma rays. Apparently, no record would survive of the shape, size, or history of all the stuff that had fallen into a black hole.

But quantum mechanics does not allow information to be erased from the universe. Physical processes leave traces that could in principle be reversed to reconstruct the past, if accepted principles of quantum theory are correct. But perhaps, Hawking and others suggested, ordinary quantum theory breaks down inside a black hole.

Maldacena attacked the paradox using string theory. But instead of using the extra elbow room afforded by six additional dimensions, he took the opposite approach, suggesting that gravitational phenomena in a stringy universe—including black holes—can have a representation in terms of particles.

So if the quantum physics of particles—where nothing can destroy information—can completely encapsulate the physics of black holes, then a black hole cannot destroy information either. There would have to be some other explanation for Hawking’s paradox, but at least the foundations of quantum theory should be safe.

In 2004 , spurred in part by Maldacena’s work, Hawking admitted that he had changed his mind, and stated that black holes probably don’t destroy information after all (Science News: 9/25/04, p. 202).

Maldacena first posted his proposal online in November 1997, barely a year after earning his Ph.D. degree at Princeton University. Within a few weeks, some of the leading string theory experts, including Edward Witten of the Institute for Advanced Study and Igor Klebanov of Princeton University, helped write a more explicit dictionary for Maldacena’s duality. By the following June, when physicists met for a string theory conference in Santa Barbara, Calif., many were already unraveling the implications of Maldacena’s idea.

At the meeting’s banquet, physicists sang and danced to a song entitled “The Maldacena,” a spoof of the then-popular “Macarena.” “In some ways, it really took over the field,” Klebanov says of the conjecture, which another leading researcher calls the work of a “stone-cold genius.”

The sky’s the limit

Since 1997, physicists have proposed countless variations on Maldacena’s theme, all of which interpret a string as a swarm of particles living in a small number of dimensions. Perhaps the easiest case to visualize is when that number is two. In such a scenario, anything that takes place in your many-dimensional, stringy universe has a sort of shadow representation in terms of particles moving on that universe’s “sphere at infinity.” This esoteric-sounding concept is actually similar to the familiar celestial sphere of the night sky as seen from Earth: It’s the two-dimensional surface spanning all possible directions one can point to infinitely far in space.

But on the face of it, neither of the universes involved in the duality has anything even remotely to do with the actual physical world. At one end of the duality are particles living in, say, two dimensions. The physics they obey, called conformal field theory, is vaguely similar to the physics of quarks, but not quite the same. The strong nuclear force between real quarks actually gets relatively weak when the quarks get extremely close to each other. But in conformal field theory, forces are the same at any distance.

At the other end is a stringy universe that has an eternal tendency to contract (even though it doesn’t get any smaller because it’s infinitely large to begin with). That’s quite the opposite from the universe in which we live, which seems to contain a sort of antigravity called dark energy that makes the universe expand at an accelerating pace (Science News: 1/3/98, p. 4).

Unfortunately, the equations of conformal field theory seem a good match only for the mathematics of strings living in a contracting universe. Still, many physicists remain hopeful that they will find an appropriate version of the duality that will do the trick for a universe like ours. If proved true, such a correspondence would offer a road map for building a complete string theory for the laws of nature.

Aside from the need to find a way of testing their ideas with experiments, string theorists’ ultimate goal is to reconcile Einstein’s theory of gravity with quantum physics. Gravity is the only fundamental force of nature that hasn’t been “quantized,” or subjected to the weird rules of quantum theory. As Arkani-Hamed puts it, if we lived in an eternally contracting universe, “the problem of quantizing gravity would have been solved.”

Soon after Maldacena’s first proposal, physicists realized that his duality could already shed light on the real world. For example, physicists believe that Maldacena’s arguments on black holes, while formulated for the black holes of a contracting universe, are probably also relevant to black holes living in a universe like ours. In that case, a problem that seemed intractable on the strings side became much easier on the particles side. But the converse can also happen.

Black hole near New York!

When physicists smash heavy atomic nuclei together with sufficient energy, the atoms’ protons and neutrons break up. For less than a sextillion of a second they melt into a blob called a quark-gluon plasma. It’s similar to the state of all matter in the first microseconds after the big bang.

Beginning in 2000, Dam Son, now at the University of Washington in Seattle, and his collaborators wanted to calculate a quark-gluon plasma’s viscosity—roughly speaking, a measure of how quickly the plasma will dampen turbulence within it. In principle, one should be able to do such calculations using the known equations of particle physics. When quarks are not bound together, though, those equations become extremely hard to solve.

But in a quark-gluon plasma, quarks will experience extremely intense forces, whose strength does not vary appreciably as the particles move. That makes the plasma’s behavior a good approximation of the conformal field theory that rules Maldacena’s sphere at infinity. Starting from that assumption, Son showed that Maldacena’s duality translates the physics of plasma turbulence into that of black hole earthquakes.

A gravitational disturbance, Son says, will alter a black hole’s shape, which is otherwise that of a perfect sphere. In response, the black hole will “oscillate, radiate energy, and settle down to be spherical again.” Son and his collaborators calculated how quickly the seismic waves on the black hole’s surface will dampen down. Translated back, the calculation suggested that the viscosity of a quark-gluon plasma could be much smaller than physicists thought possible.

Initially, some nuclear physicists were nonplussed, to say the least, about the idea of doing nuclear physics using black holes. “The first time I heard about it, I literally thought it was crazy,” says William Zajc of Columbia University in New York City.

In 2005, however, physicists at the Relativistic Heavy Ion Collider (RHIC) at Brookhaven National Laboratory in Upton, N.Y., announced the results of an experiment that collided nuclei of gold atoms, melting them into a quark-gluon plasma (Science News: 4/23/05, p. 259). The stuff’s viscosity seemed close to Son’s prediction, says Larry McLerran, a RHIC (pronounced “rick”) theorist.

Many physicists working at RHIC—Zajc being one of them—changed their minds about Son’s calculation. “It’s far more useful than we ever imagined,” he says. “The fact that it was done in some higher-dimensional space and it involved black holes—well, that just added to the intrigue.”

Since then, some of the RHIC physicists have revisited certain theoretical assumptions used to interpret the experiment’s data. As a result, some say it’s no longer so clear that the viscosity is as low as Son claimed it could be. Not everyone buys the black hole model of a quark-gluon plasma. “It’s certainly interesting, but you have to be very skeptical about it,” he says.

More recently, Subir Sachdev of Harvard University and his team have extended Son’s ideas to study transitions between certain exotic—but real—states of matter. As Sachdev and coauthors describe in the October Physical Review B, the team applied its new methods to the motion of electrons inside a superconductor when the temperature goes up just enough that the material becomes an electrical insulator. Instead of estimating viscosity, as Son did, the researchers calculated how long it will take for vortices of electrons to stop whirling. In their case, Sachdev says, the relevant dual phenomenon was the damping of electromagnetic disturbances that ensue when a photon falls into a black hole.

Ariadne’s thread

The power of the string—particle duality, Maldacena says, lies in the fact that one can frame a problem in whichever mathematical language makes it easier to solve.

Calculations about particles are more manageable when the particles interact weakly. But the duality translates strongly interacting particles into weakly interacting strings. “When one of the descriptions becomes hard, the other one becomes easy, and vice versa,” Maldacena says.

At least that is the prevailing belief, even though it has not been rigorously proved. In all cases in which physicists have been able to calculate two dual quantities independently, they got the same result, which is encouraging. But until recently, in all those examples the interaction strengths were at the extremes—infinitesimally small or infinitely large.

In the past 2 years, Niklas Beisert, now at the Max Planck Institute for Gravitational Physics (Albert Einstein Institute) in Potsdam, Germany, and his collaborators have found the first examples that work at all possible interaction strengths. “If this was the theory of the real world, we would in some sense describe the mass of the proton and of all other composite particles,” he says. What they found is that the two theories make the same predictions for those values. The calculations have created a kind of Ariadne’s thread that can be followed from one theory to the other.

“The work they did is really wonderful,” Maldacena says. “It’s an incredible test” for Maldacena’s conjecture, says Klebanov, who recently helped corroborate the results with numerical calculations. Still, the conjecture “certainly hasn’t been proven in mathematical terms,” Beisert warns. However, most experts now say they are virtually sure that it eventually will be.

But even if Maldacena’s conjecture is true, does it mean that string theory is correct? Most string theorists would bet on it. It would be too much of a coincidence, they say, if such a seemingly miraculous mathematical duality were to apply to a particular kind of abstract universe but not to our own. “I believe that nature uses the same small set of ideas over and over,” says Joseph Polchinski of the Kavli Institute for Theoretical Physics at the University of California, Santa Barbara.

Others are not so sure, and point out that there have been times in history when physicists have promoted hypotheses on the basis of their aesthetic appeal, only to be contradicted by the experimental evidence. A classic example, says Abhay Ashtekar of Pennsylvania State University in University Park, is Lord Kelvin’s idea of vortices. In the 1860s, Kelvin pointed out that many of the known properties of chemical elements could arise naturally if atoms were knotted vortices in the fabric of the ether. The uncanny coincidence went away once physicists demonstrated that the ether probably didn’t exist.

For now, Maldacena’s duality ideas have become an engine for motivating and inspiring string theory research. “It’s been a very good run,” Klebanov says. “But we’re still just kind of scratching the surface.”

In many ecosystems, several competing species coexist because none is best at everything. Tobias Reichenbach of the Ludwig Maximilian University in Munich and his colleagues ran computer simulations of three virtual bacteria species fighting a sort of rock-paper-scissors game.

One species produces a toxin. A second is immune to the toxin and outcompetes the first. A third species is sensitive to the toxin but can overtake the second species because it’s unburdened by the metabolic cost of producing an antidote. Each virtual population, shown here in a different color, propagates in waves as it pushes aside its weaker competitor while being chased by the stronger one, the researchers explain in an upcoming Physical Review Letters. Scientists have observed similar patterns among certain marine organisms.

Tobias Reichenbach

(From Science News, Nov. 3, 2007.)

Now, astrophysicists may have to rethink their models of how supernovae create heavier elements. On the other hand, they may also be able to explain anomalous X-ray flashes coming from neutron stars. When matter falls onto a neutron star and starts sinking into its crust, pressures 10 trillion times as high as those at the sun’s center force electrons and protons to merge, forming neutrons. Aluminum-42 and magnesium-40 may be among the elements that form temporarily during that process.

Read my article from this week’s Science News

Washed away

Last year, physicists reported seeing tantalizing experimental traces of the axion, a hypothetical subatomic particle that’s been mentioned as a possible constituent of cosmic dark matter. But the axion was showing up where theory said it shouldn’t be. It now looks as if it wasn’t there after all.

The particle sprang from an attempt to explain certain differences between the strong and weak nuclear forces. Cosmologists seized on the axion because its properties made it a plausible component of dark matter, the unseen material that far outweighs ordinary matter in the universe.

Read the rest of my article, freely available on the Science News Web site.

As I recounted in my end-of-year special last year, MIT physicist Frank Wilczek called the particle after a brand of detergent, because it was supposed to wash away all of the problems of the so-called standard model of particle physics. The brand is not longer sold in the U.S., but it apparently still is in France.

In the latest experiment, researchers attempted to demonstrate the axion’s existence by looking for an effect known as photon regeneration, or, in Zenlike fashion, as “light shining through a wall.” As I write in this week’s Science News:

Researchers shoot a laser beam through a magnetic field toward a metal plate. The metal wall blocks photons, but any axions created in the field would pass through. On the other side of the wall lies a second magnetic field that would convert some of the axions back into photons, making it appear that some photons had passed through.

They detected no axions at all. However, physicists say other types of experiment might have a better chance at discovering the particle. The most intriguing one would look for “light shining through the sun.” As the sun passes in front of a source of gamma rays located far away in the universe, some of the source’s photons could turn into axions. Those would easily zip through the sun, and then perhaps convert back into gamma ray photons, wihch astrophysicists could then pick up.

Wilczek told me that he has kept a box of the U.S.-brand detergent in his basement. Perhaps, if one day the axion is discovered, he could make loads of money by selling it on eBay.

“Graphene has always been before our eyes, but no one ever tried to look,” says Andre Geim, a physicist at the University of Manchester in England. A single-atom-thick, chicken wire web of carbon atoms, graphene forms the layers that stack up to make the graphite found in pencil lead and carbon soot.

However mundane the stuff may be, physicists have long predicted that if it were possible to isolate single graphene sheets, they would be sturdier than diamond and would have almost preternatural abilities to manipulate electrons. That could make graphene a better material than silicon for making computer chips. Until recently, though, no one had been able to isolate graphene sheets, let alone do anything useful with them.

In 2004, Geim and his collaborators startled the physics community by announcing that they had peeled graphene layers off graphite using common adhesive tape. The discovery raised a buzz in physics circles reminiscent of the excitement that greeted carbon nanotubes a decade ago.

In fact, graphene is nothing but a large, unrolled carbon nanotube, and the two materials share many qualities, including strength and conductivity.

Though promising, nanotubes have proved devilishly difficult to assemble into circuits. Nanotubes don’t readily connect to one another, and attaching them to metal contacts creates spots where electrons tend to scatter, dissipating energy as heat.

Graphene, on the other hand, comes in sheets. It may be possible to etch graphene circuits, just as circuits are now etched into silicon wafers. Forming circuits from one sheet of graphene could be much easier than assembling them from nanotube pieces. “We want to be able to use the essential properties of carbon nanotubes in a material that can be patterned easily,” says Walt de Heer of the Georgia Institute of Technology in Atlanta. “It could realize the dream people had of carbon-nanotube electronics.”

Graphene circuits could in principle work efficiently even with components measuring only a few atoms across—scales that can’t be achieved with ordinary semiconductors. In recent months, scientists have learned how to make graphene-based transistors and diodes—the basic elements of computer chips. And they have begun trying to connect graphene to other materials, including carbon nanotubes.

But that’s only a beginning. If graphene is to replace silicon one day, scientists and engineers will have to figure out how to manufacture large numbers of circuits with nearly atomic precision.

Caught on tape

Geim’s adhesive tape stratagem could hardly be the basis for a new chip-fabrication plant, but it continues to be researchers’ favorite way of making graphene for experimentation.

Anyone who uses a pencil is likely to leave some single-layer graphene flakes scattered on paper, he says. The graphene sheets in graphite are bound to one another only by weak electrostatic forces. That’s why pencil lead is so soft.

After gently rubbing graphite on a silicon-oxide crystal, Geim stuck strips of tape on the carbon debris, hoping that when he peeled off the tape, thin stacks of a few graphene sheets would stick to it. To further pry apart the sheets, he repeatedly folded the pieces of tape, sticky sides together, and peeled them open again. Then, by dissolving the tape in a solution, he let the graphene flakes settle onto the surface of a silicon-oxide crystal.

Through an ordinary microscope, Geim spotted graphene stacks of varying thicknesses stuck to the crystal’s surface. The translucent flakes created rainbows of colors “like oil on the surface of a rain puddle,” he says. With a bit of experience, Geim learned how to recognize single sheets by their colors. “If it’s blue or red, you know it’s thick,” he says. To find single layers, “you look for another shade of purple” (Science News: 10/23/04, p. 259; and 8/13/05, p. 110).

To confirm that they had actually found single sheets of graphene, Geim and his collaborators tested how the flakes conducted currents. Measurements showed that electrons were able to travel microns—enormous distances by atomic-scale standards—without bumping into atoms.

These findings confirmed crucial predictions about single-layer graphene. In graphene sheets, as in carbon nanotubes, each carbon atom binds strongly to three neighboring atoms, creating a web of hexagons resembling chicken wire. In addition, the atoms form bonds by sharing electrons from barbell-shape orbitals that are perpendicular to the chicken wire plane. These sideways orbitals fuse with their neighbors, creating veritable electron superhighways above and below the graphene plane.

In 2005, Geim and his colleagues made another important discovery. Placing graphene samples in magnetic fields whose intensities the researchers ratcheted up, they saw the electrical resistance increasing in discrete steps, a phenomenon known as the quantum Hall effect. Around the same time, a group led by Philip Kim of Columbia University made the same discovery after learning of Geim’s tape-peeling technique.

Obscure as it may sound, the quantum Hall effect was what sparked the physics community’s interest in graphene. “It put an enormous spotlight on the field,” de Heer says. That’s because the resistance steps produced by the effect had a pattern peculiar to graphene, so it convinced scientists that the new material really had “quite unique physics,” Kim says (Science News: 11/12/05, p. 309).

The effect implied that the electrons move in graphene’s conduction superhighways unlike the way they move in any other conductor. In a piece of metal, electrons that carry current act like gas particles, jittering mostly at random and moving faster the more energy they have. In graphene, on the other hand, conduction electrons tend to move in lockstep as a single quantum entity. Like photons, the swarms of electrons move at the same speed, regardless of their energy.

Graphene’s uniqueness makes it an intriguing playground for physicists and materials scientists. Researchers say that it could even inspire new ways to manipulate information. Meanwhile, several teams are working on shaping graphene into transistors and other traditional electronic components.

No assembly required

Because electrons in graphene move at high speeds, graphene-based transistors could in principle switch currents on and off faster than semiconductor-based transistors do. Like carbon nanotubes, graphene is an excellent conductor of heat, so graphene chips could stay cooler than silicon chips. But the feature that makes graphene most appealing to scientists is its toughness.

“The graphitic bond—the carbon-to-carbon bond—is the strongest in nature,” even stronger than the bonds between carbon atoms in diamond, says de Heer. That strength gives graphene its remarkable stability, and means that graphene circuits could in principle be miniaturized to sizes of a few nanometers without falling apart.

By contrast, molecular-scale circuits made of silicon or other materials would quickly fail. “All other materials oxidize, decompose, move around, or melt,” Geim says. Furthermore, conventional transistors are made from silicon or another semiconductor that has been “doped” to modify its electronic properties. In negative doping, addition of a small amount of another element increases the number of current-carrying electrons. In positive doping, addition of a different element creates gaps in the electron distribution, which move around like positively charged carriers of currents. At nanometer scales, it becomes almost impossible to dope a material uniformly because the dopant atoms are so few and far between.

These limitations mean that individual features in silicon chips, already as small as 65 nm and with 45-nm technology in the offing, will probably reach their smallest possible size within 10 to 15 years.

Future graphene-chip technologies, meanwhile, could borrow many of the methods already used for creating silicon chips. Chip production uses a top-down approach, which starts with large sheets of crystalline silicon and uses sophisticated lithography techniques to etch circuitry into them. “In principle, the processing technology could work exactly the same” for graphene, says Pablo Jarillo-Herrero, a physicist in Kim’s lab at Columbia.

Jarillo-Herrero is one of several scientists who are seeking ways of chiseling narrow strips, called nanoribbons, out of graphene sheets. He has made nanoribbons as narrow as 20 nm across but says that it could take years to bring their width down to less than 10 nm. Because the hexagonal rings are about 0.2 nm in diameter, it gets harder to control the shape of a nanoribbon’s edges as the structures become narrower. Irregular edges would “suppress part of the unique properties of graphene,” says Jarillo-Herrero.

A more immediate goal is to make a field-effect transistor (FET) from graphene. FETs are the bread and butter of silicon chips. In a typical FET, a slice of negatively doped silicon is sandwiched between two pieces of positively doped silicon. In the transistor’s off state, no current flows because the middle section acts as an insulator, but applying an electric field to the middle layer turns it into a conductor, switching the transistor to on.

For graphene, the equivalent of doping is applying an external field that increases the local concentration of charge carriers of one type or the other. In a prototype graphene FET, a nanoribbon links two graphene sheets. An insulating layer is deposited on the structure, and electrodes lying just above apply controlling fields. In an alternative design demonstrated this month by the Columbia team, the electrodes and the nanoribbon lie side by side, carved out of the same graphene sheet.

The narrowness of a nanoribbon alters its electronic properties so that its conductivity is normally low. Applying an electric field sharply increases its conductivity, a team of Jarillo-Herrero’s Columbia colleagues reported in the May 18 Physical Review Letters.

The nanoribbon thus acts as the middle layer of a conventional FET does, allowing the device to be turned on or off. In an upcoming Physical Review Letters, Jarillo-Herrero and his collaborators at Columbia and at the Massachusetts Institute of Technology describe their first steps toward making nanoribbon-graphene transistors. Charles Marcus of Harvard University and his collaborators independently describe a similar achievement in the Aug. 3 Science.

Still, graphene electronics is far from proved as a viable candidate for the postsilicon era. As yet, graphene transistors are slower than silicon ones and much slower than transistors made with competing materials such as carbon nanotubes.

Déjà vu again

The best way to control graphene at the molecular scale may be through chemistry. In de Heer’s vision, engineers might someday insert atomic-scale components into carbon-based electronics by synthesizing molecules and attaching them to an etched template. This would combine the top-down method used in silicon-chip technology with a bottom-up approach of assembling components piece by piece.

De Heer says that his team has already succeeded in connecting two sheets of graphene with a carbon nanotube. In addition to nanotubes, polycyclic aromatic hydrocarbons or other organic molecules also have orbital structures that could merge seamlessly with those of graphene, de Heer says, making them ideal molecules for integration into graphene circuits.

Most experts caution that graphene research remains in its early stages. No one is ready to make promises, especially in light of the experience with carbon nanotubes. “Carbon nanotubes promised so much and so far [have] delivered so little, and we should naturally be cautious about promising too much for graphene,” Geim says.

Cees Dekker of Delft University of Technology in the Netherlands, who a decade ago created the first nanotube transistor (Science News: 5/9/98, p. 294), says that scientists’ excitement about graphene gives him a feeling of déjà vu. “Sometimes, people are enthusiastically rediscovering the properties of graphene which were already heavily discussed 10 years ago in conjunction to nanotubes,” he says.

Geim observes, however, that basic research in graphene has made remarkable strides in just over 2 years. He says that the new research field is here to stay. “It’s not a blip on the screen.”

While calling NASA’s “manned” space flight programs (such as [the International] Space Station) worthless with regards to science, Steven Weinberg calls NASA’s “unmanned” space flight programs (such as Martian robots Spirit and Opportunity robots and Hubble Telescope) very important to the advancement of science.

Steven Weinberg stated at the Tuesday, September 18, 2007 Science Writers’ Workshop called “Dark Energy: A Decade of Discovery and Mystery” at the Space Telescope Science Institute [home of the Hubble Space Telescope] in Baltimore, Maryland, U.S.A., “The International Space Station is an orbital turkey. No important science has come out of it. I could almost say no science has come out of it. And I would go beyond that and say that the whole manned spaceflight program, which is so enormously expensive, has produced nothing of scientific value.”

(From Nobel Laureate Weinberg calls space station an “orbital turkey”)