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Energy in Motion: How the nanomachines of life harvest randomness to do the cells’ work

Saturday, March 22nd, 2008
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gated molecule 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.

(more…)

Some Book Reviews

Tuesday, January 8th, 2008

In the past few months, I have occasionally collaborated to Science News’ Book Reviews page. Here are the mini-reviews I’ve written so far.

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

Tied Up in Knots

Sunday, December 30th, 2007

Call it Murphy’s Law of knots: If something can get tangled up, it will. “Anything that’s long and flexible seems to somehow end up knotted,” says Andrew Belmonte, an applied mathematician at Pennsylvania State University in University Park. Belmonte has plenty of alarming anecdotal evidence. “It certainly happens in my house, with the cords of the venetian blind.” But the knot scourge is a global one, as anyone who owns a desktop computer can confirm after peeking at the mess of connection cables and power cords behind the desk.

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.

(more…)

Freakotonics

Tuesday, December 18th, 2007

Slightly noisy signals can turn into rare large spikes in an optical fiber’s output, in much the same way as unpredictable weather conditions occasionally create monstrous, isolated oceanic waves, researchers have found.

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))

Shadow World

Saturday, November 17th, 2007

AdS/CFTCover 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.

(more…)


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