Processing for Science

"@Home" projects band together and proliferate
By Charles Q. Choi

TEMPERATURE MODELING of the earth by the computing project Climateprediction.net depends on data that are divvied up in chunks and crunched by home users. Fans of the spacetime continuum can now uncover gravitational ripples at their desks thanks to the February launch of Einstein@Home. The project is one of the latest of at least 60 "@home" projects now on the Internet, in which personal-computer users can donate spare processor power to help solve scientific problems. And no need to choose one mission over another: @home software can now multitask, and enough microchip muscle exists to handle many more distributed-computing projects.
Save for computationally intense tasks such as rendering graphics, typical modern PCs that perform at least one billion floating-point operations per second (that is, most home computers built since about 2000) almost never employ their full power. Distributed computing takes advantage of this spare capacity, dividing large tasks into tinier ones and sending them over the Internet for usually idle computers to work on. The result is unparalleled processing muscle: IBM's BlueGene/L, now the most powerful supercomputer, cranks out about 70 trillion flops; meanwhile SETI@home conservatively runs off roughly 500,000 PCs at more than 100 trillion flops, says SETI@home director David P. Anderson.

Since the first public distributed-computing project--the Great Internet Mersenne Prime Search--was launched in 1996 to look for large prime numbers, virtual supercomputing projects have emerged for the serious (testing potential drugs with FightAIDS@home) to the sublime (the Monkey Shakespeare Simulator). Anderson expects hundreds of @home projects to emerge in the next few years and the number of participating CPUs to reach 30 million from the roughly 1.3 million of today.
A key development in the surge is the formation of distributed-computing platforms that can host multiple projects. Among the biggest is the Berkeley Open Infrastructure for Network Computing (BOINC), which hosts SETI@home and Einstein@Home as well as the formerly independent Climateprediction.net, which joined in August. In coming months BOINC partners will include FightAIDS@home, PlanetQuest and Orbit@home. Other umbrella distributed-computing software platforms include Grid.org, which is running two projects to find compounds against cancer and predict three-dimensional protein structures from amino acid sequences, and Find-a-Drug.org, which currently has nine projects looking for drugs against various ailments, such as malaria and Creutzfeldt-Jakob disease, the human relative of mad cow disease.
Such @home hosts are also time-savers for scientists. BOINC, for instance, offers open-source infrastructure code so researchers do not have to write their own. It can take several person-years to develop the software, because it must perform unobtrusively on different operating systems in up to a million computers while protecting against erroneous results and malicious attacks. "We want to make it easy for scientists to get access to millions of computers' worth of processing power," says Anderson, who also directs BOINC.
Anderson estimates that, for a typical computer, the practical upper limit for the number of @home projects is roughly 12. At that point, its processing power is parceled so thin that projects consider it useless. A service that rotates a PC automatically between projects is possible in the future, he adds. Still, umbrella platforms might interfere with one another if operating simultaneously on the same computer. But with the roughly 200 million privately owned computers in the world, notes Ed Hubbard, president of United Devices in Austin, Tex., which runs Grid.org, "there's plenty of room for everybody."

New Dinosaur Documents Shift from Meat to Veggie Diet

A treasure trove of fossils uncovered in Utah is helping paleontologists understand why some meat-eating dinosaurs evolved into vegetarians. The bones represent a new species belonging to a group known as the therizinosaurs, plant-eating cousins of Jurassic Park's Velociraptor.
Scientists unearthed some 1,700 bones, which date to 125 million years ago, from the base of the Cedar Mountain rock formation in Utah. According to James Kirkland of the Utah Geological Survey, hundreds to thousands of individual dinosaurs could have perished at the two-acre dig site. The researchers recovered bones representing about 90 percent of the skeleton of the new species, Falcarius utahensis, which walked on two legs and stood over four feet tall. Although no feathers turned up, the team posits that the beast was covered in shaggy protofeathers because direct evidence for feathers has been discovered on fossils of its close relatives in China.

Indeed, most of the fossils of other known therizinosaurs have come from China and Mongolia, with just one 90-million-year-old specimen hailing from New Mexico. "Falcarius utahensis shows the beginning of features we associate with plant-eating dinosaurs, including a reduction in size of meat-cutting teeth to leaf-shredding teeth, the expansion of the gut to a size needed to ferment plants, and the early stages of changing the legs so they could carry a bulky body instead of running fast after prey," Kirkland explains. This discovery thus places the most primitive therizinosaurs in North America. Study co-author Scott Sampson of the University of Utah notes that the rise of plant-munching therizinosaurs in Utah "may have been directly linked to the spread of flowering plants about 125 million years ago." --Sarah Graham

RELATED LINKS:
Dinosaurs and Other Monsters

Mouse Research Bolsters Controversial Theory of Aging

Aging is a process we humans tend to fight every step of the way. The results of a mouse study underscore the potential of antioxidants as a weapon in that battle: animals genetically modified to produce more antioxidant enzymes lived longer than control animals did. They also exhibited fewer age-related health problems overall.
The free radical theory of aging posits that substances with unpaired electrons attack the body's molecules and cause the functional decline of organs over time. Thus, antioxidants, which neutralize free radicals, should slow this deterioration. But animal models of aging designed to test the hypothesis have so far shown contradictory results.

In the new work, Peter S. Rabinovitch of the University of Washington and his colleagues engineered mice to produce higher-than-normal amounts of the enzyme catalase. Within cells, catalase removes hydrogen peroxide, a waste product of metabolism that could otherwise lead to damaging oxygen free radicals. In a paper published online this week by Science, the team reports that animals with higher levels of catalase in their mitochondria--the cell's energy-producing organelles--lived 20 percent longer on average than control animals did. What is more, mice in this so-called MCAT group had healthier heart tissue than normal mice and showed fewer mutations in their mitochondrial DNA. "This study is very supportive of the free-radical theory of aging," Rabinovitch says. "It shows the significance of free radicals, and of reactive oxygen species in particular, in the aging process."
Animals that overexpressed catalase in other parts of the cell, such as the nucleus, also exhibited longer life spans than their normal counterparts did, but the gains were modest. As such, the scientists note, the results reinforce the importance of mitochondria as a supplier of free radicals. The researchers have no plans to modify humans to increase protein expression, but they point out that future drug development could focus on protecting the body from free radicals. --Sarah Graham

RELATED LINKS:
The Science of Staying Young
The Truth about Human Aging
The Serious Search for an Antiaging Pill