Saturday, 12 June 2010

Johnald's Fantastical Daily Link Splurge

Johnald's Fantastical Daily Link Splurge

Random Guy Allegedly Steals Astronaut Sally Ride’s Flight Suit

Posted: 10 Jun 2010 03:24 PM PDT

A Texas man was indicted for stealing one of famed astronaut Sally Ride's flight suits.

Calvin Dale Smith kept the one-piece garment in a suitcase for an unknown number of years, federal investigators allege. He is believed to have obtained the suit during a stint working for the Boeing division that was tasked with caring for the NASA flight suits. Smith pleaded not guilty on May 27, and the case has a July 12 court date. He faces up to 10 years in prison.

Smith's estranged wife turned him in to the police after discovering the suitcase. Smith was in prison following an incident of domestic violence with a firearm. The suit could be worth more than $2,500, according to Robert Pearlman, a space collectible expert who authenticated the flight suit for the FBI NASA Office of the Inspector General. There is a substantial market for space program objects, but no serious collector would have touched a suit without proper documentation of its provenance.

"When collectors purchase valid items, they learn the chain of ownership, so they can show it off and not have questions asked about it," Pearlman said.

But Smith's motives may not have been financial. According to KHOU TV, the CBS affiliate in Houston, Smith's daughter said he had "a crush" on Ride.

As the first American woman in space, Ride became a 1980s icon. She entered near-earth orbit on June 18, 1983, 20 years after the first woman in space, cosmonaut Valentina Tereshkova.

The U.S. actually had female astronauts way back in the late 1950s, but the Woman in Space Program was canceled in 1961, despite the excellent, and in some cases, superior performance of the women on NASA's grueling physical tests.

While Smith awaits trial, media outlets and collectors alike are wondering how a random Boeing employee walked out with not just the space suit but a host of valuable space program items without being detected. According to court documents, "Among the assorted items [Smith's wife] had gathered was an Omega watch, various specialized machined parts used in the NASA space program, to include an 'ERCM Safety Tether Assembly' and three 'airlock parts' (similar to couplers), as well as other items of NASA property."

Pearlman offered one suggestion: Given the number of shuttle missions, there were simply a lot of things to keep track of.

"At one point, it was probably one suit of hundreds. If you were maintaining back-up and flown suits and educational and display suits, you would have a very large closet of light blue flight suits hanging around," Pearlman said. "In that regard, if one suit were to go missing, and you had no reason to access that area, I would suspect that it wouldn't be the first thing to pop up on the radar."

Even Ride undoubtedly owned at least a handful of suits, although the exact number is unknown. What we do know, Pearlman said, was that the allegedly pilfered light-blue get-up never flew in space.

Image: NASA. Sally Ride and the crew of STS-7, an early shuttle mission.

Via CollectSpace

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Oil Disaster Shows Need for Endangered Species Act Overhaul

Posted: 10 Jun 2010 11:56 AM PDT

Of the many regulatory problems that helped make the Gulf of Mexico oil disaster possible, the Endangered Species Act's shortcomings have received little attention — but fixing its flaws and loopholes could help prevent future catastrophes.

Oil companies never considered the impacts of a massive spill on the Gulf's sperm whales or five sea turtle species. They didn't have to, because the law doesn't require it.

"We need to include disaster planning in the Endangered Species Act consultation process," said environmental lawyer Keith Rizzardi. "We can learn from experience."

So far, critics have focused on the Minerals Management Service's evasion of National Environmental Policy Act, which requires federal agencies to evaluate environmental impacts when making decisions. The MMS essentially operated in collusion with the oil industry in what one federal investigator called "a culture of ethical failure," allowing drilling to proceed without NEPA review. Those approvals have continued, with at least 19 environmental waivers granted since the April 20 explosion.

The MMS also ignored the Endangered Species Act, which demands consideration of impacts on endangered species. Since January 2009, the MMS has approved 346 drilling plans without getting required permits — but even if they'd followed the Act's letter, it probably wouldn't have mattered.

Reviews would only have considered the physical footprints of wells, ship traffic and other relatively small impacts. That's because the Endangered Species Act only requires consideration of events that are "reasonably certain to occur." That a wellhead would blow — as happened 36 times in the Gulf between 1992 and 2006 — and release a steady stream of oil was not so far-fetched as the industry insisted, but it wasn't reasonably certain.

Rizzardi intends to discuss changes to the Act at the next meeting of the National Oceanic and Atmospheric Administration's Marine Fisheries Advisory Committee, of which he is a member. Congress has the ultimate responsibility for changing the law, which would be relatively easy, requiring little more than amendments to its wording. "It's more a matter of politics than law," said Penn State environmental law professor Jamison Colburn.

Environmental law specialist J.B. Ruhl of Florida State University said that planning for every conceivable disaster would be difficult, and that far-fetched possibilities might discourage legitimate development. But he agreed that considering catastrophic risk is "a valid question," and Rizzardi said that amendments needn't paralyze development, but would simply require foresight and planning.

In the event of disaster, agencies and companies could say, "We can't guarantee that it won't cause extinction — but we can do everything possible to mitigate the disaster," said Rizzardi. "We don't do any of that now." The lack of planning has been painfully evident in the Gulf, where deployment of obvious, first-line relief measures — oil skimmers, containment structures, chemical dispersants — were logistically delayed and poorly understood. Had the Endangered Species Act demanded it, those plans might have been made.

In addition to considering catastrophes, the Endangered Species Act also needs to restrict what's called segmented consultation, in which impacts are evaluated only in incremental blocks — over, say, the first few years of a project, rather than its expected lifetime. That makes it easy to avoid thinking about long-term problems.

"Incremental step consultation is most appropriate for long-term, multi-staged activities for which agency actions occur in discrete steps, such as the development of oil and gas resources on the Outer Continental Shelf," reads the ESA now. "Segmentation into oblivion goes on all the time," said Colburn.

But Colburn warned that amendments are only a first step. Endangered Species Act enforcement is woefully underfunded. Total federal spending on endangered species amounts to about $562 million, including what's given to NOAA and the Fish and Wildlife Service, who are responsible for protecting the animals and evaluating plans submitted by other federal agencies.

Both NOAA and FWS are barely able to handle what's already asked of them, and have more incentive to complete reviews and reduce backlog than to do their jobs right, said Colburn.

"Americans don't want to spend more money for environmental protection, but they have to," said Colburn. "If you want to have a market economy with agents like BP out there, you need to have well-funded environmental enforcement."

Image: International Bird Rescue Research Center/Flickr.

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Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecological tipping points.

Exoplanet Hunters Finally Catch One in a Star’s Debris Disk

Posted: 10 Jun 2010 11:08 AM PDT

A giant planet lurks in the dust and debris surrounding a young, nearby star — and astronomers have finally seen it in action.

Using the Very Large Telescope in Chile, astronomers took infrared images of the planet in two different positions around its star in 2003 and late 2009.

"It's so exciting that we can see it," said astronomer Paul Kalas of the University of California, Berkeley, who was not involved in the new work. "We've been looking a long time."

The discovery, announced June 10 in Science, proves that giant planets can form quickly around young stars and suggests that dust disks are signposts for stars hosting giant planets.

Beta Pictoris, a star almost twice the mass of the sun and located 63 light-years away, has been a celebrity among planet hunters since the 1984 discovery of a wide halo of dust and rocky debris that could eventually coalesce into planets. Later observations showed that the disk was oddly warped, and that it had a big hole near the center.

Theoretical models predicted that a planet around five to 10 times the mass of Jupiter could make both the warp and the hole. But when Anne-Marie Lagrange of the Grenoble Observatory in France, first author of the new paper, and her colleagues observed the star in 2003, they saw nothing.

"The tools we had in 2003 were not precise enough," she said.

After Kalas's group and another team released images of planets around the stars Fomalhaut and HR 8799 in November 2008, Lagrange and colleagues tried again. They used newer techniques to cancel out the light from the star, allowing the planet to shine through.

The image showed a bright object next to Beta Pictoris, but whether it was a planet or another star in the background was unclear.

"Frankly, if I had a bet on whether or not they'd actually seen a planet back in 2003 … I would definitely bet it was not a planet," said astronomer Ben Zuckerman of the University of California, Los Angeles, who was involved in imaging the planets around HR 8799.

Follow-up observations in late 2008 and early 2009 also came up empty. Finally, in October 2009, the planet re-emerged on the other side of the star. Lagrange and colleagues kept taking images until March 2010 to confirm that the object was a planet.

"We spent a really long time, nights and days, to check it," she said. "It really shows that when we see disks, we have to look at every detail, because they can indicate the presence of a planet."

Because Beta Pictoris is such a young star — about 10 million years old, or two thousandths the age of the solar system — studying its planetary system can help astronomers decide between competing models of planet formation. For instance, earlier theoretical work showed that debris disks around stars broke up fairly quickly, within a few million years. Some theorists worried that massive planets wouldn't be able to form fast enough, but the planet around Beta Pictoris is proof that they can.

"It's taking a snapshot of another solar system right after it's born," Kalas said. "The other alternative is to invent a time machine and go back 4.5 billion years and look at our own Jupiter when it just formed. But obviously we can't do that."

The planet weighs in between six and 12 times the mass of Jupiter, similar to the models' predictions. It orbits its star at about the orbit of Saturn, between eight and 13 times the distance from the Earth to the sun, making it the closest planet to a star ever imaged. It also means the planet makes a complete circuit around its star every 17 to 30 Earth years, well within human lifetimes.

"Eventually, we'll have a movie of this planet going around Beta Pic," Kalas said. By contrast, the planets around HR 8799 and Fomalhaut take between 100 and 870 years to complete an orbit.

The next step is to observe the planet in more wavelengths to get an idea of what its atmosphere is made of, Lagrange said. And with new instruments like the Gemini Planet Imager coming online, the next few years should see even more direct images of extrasolar planets.

"The future is really bright," said astronomer Christian Marois of the National Research Council of Canada's Herzberg Institute of Astrophysics. "It'll be a really interesting field in the next two or three years."

Image: ESO/A.-M. Lagrange. This image shows the dust disk around the star (blue light at edges), and the observed position of beta Pictoris b in 2003 and autumn 2009. The light from the star has been blocked out to make the planet visible.

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No Progress on Better Chemicals for Oil Disaster Cleanup

Posted: 10 Jun 2010 10:24 AM PDT

Almost three weeks after federal orders to find less toxic chemicals to break up oil in the Gulf of Mexico, no progress has been made.

The same dispersant chemicals are still being used. BP barely tried to test an alternative, and the EPA's own testing results on the toxicity and effectiveness of alternatives are slow in coming. Experts say the tests will only provide a bare minimum of data, far less than they'd like for managing the unprecedented use of dispersants. Nothing is clear, except that too little is known.

"At the end of the day, you're asked to look at alternatives. Then you find that you don't know enough about alternatives to make that decision," said Carys Mitchelmore, a University of Maryland biologist who co-authored a 2005 National Academy of Sciences dispersant report and has testified to Congress about their use during the Deepwater Horizon disaster.

Dispersants separate oil into smaller droplets that should biodegrade quickly. They were applied to surface oil in the gulf soon after the disaster began. Their use was unfortunate but arguably necessary: If oil broke down at sea, rather than near shore, damage to prized coastal ecosystems could be reduced. Deep-sea animals would be sacrificed, but the shorelines would be saved.

Many questions surround dispersant use. They're toxins on their own, their effects on sea life are largely unquantified, and whether they'd work in the gulf as elsewhere is unknown. Nor had dispersants been previously deployed in the volumes needed in the gulf. Their injection directly into the wellhead, a mile beneath the sea, is also unprecedented. Depth and pressure and temperature might alter the interaction of dispersant and oil in unanticipated ways.

None of these questions could be answered. The specific choice of dispersant, however, seemed a more tractable matter, and generated controversy from the start. BP chose two formulations of Corexit, one used during the Exxon Valdez oil spill and another developed in its aftermath. According to EPA data on other dispersants approved for emergency use, 12 were better than Corexit at breaking down gulf oil, at least in laboratory tests. BP argued that Corexit was far better studied than the alternatives, which is true — but the role of former BP executive Rodney Chase as a director of Nalco, Corexit's manufacturer, raised suspicions.

With public concern growing and the amount of Corexit used approaching one million gallons — it now stands at 1.21 million gallons — the EPA changed course May 20. Agency officials said no damage had been seen, but the massive quantities and many uncertainties justified finding an alternative. They gave BP 72 hours to find a less-toxic, equally effective alternative to Corexit.

Three days later, BP reported that no suitable alternatives existed. EPA chief Lisa Jackson called their response "insufficient," and accused the company of being "more focused on defending your initial decisions than on analyzing possible better options." She also announced that the EPA would assess dispersants on its own, and subsequently ordered BP to cease surface dispersant use and cut subsurface use dramatically.

"We said, we are going to do our own science, and also directed BP to conduct more in-depth science of their own. That's where we are at this point," said EPA deputy press secretary Brendan Gilfillan.

With Coast Guard help, BP conducted tests of some alternative dispersants — including Dispersit, which ultimately didn't meet the EPA's toxicity requirements — early in May, but the results were neither released nor shared with the EPA.

Joannie Docter, president of Globemark Resources, the manufacturer of JD 2000 — one of five dispersants that met the EPA's toxicity standard — said she was told by BP on May 18 that only Corexit would be used in the gulf. At the time, BP hadn't even tested JD 2000, which happened only after the EPA's request. BP's rejection letter "says there's not enough information," said Sinclair. "They did the testing after the fact."

But though BP appears to have malingered, consideration of alternatives is tricky. Analysis so far has been based on publicly available benchmark tests submitted to the EPA by companies seeking approval for their dispersants. Effectiveness ratings in those tests represented laboratory reference points rather than real-world evaluation. Toxicity measures are equally unreliable.

"The data presented in the tables is a one-time toxicity test. These should be redone," said Mitchelmore. "The tests will be much more scientifically robust if they're repeated, which is what the EPA is doing, then expanding on that and doing further chronic toxicity tests."

Only a smattering of such information exists for dispersants other than Corexit. "There have been way more toxicity studies done on Corexit than anything else, because it's the dispersant of choice," said Mitchelmore. "I did all my studies on Corexit 9500. There's such limited funding out there to do this research. Would I would have liked to screen six dispersants? Yes, but there wasn't money."

Meanwhile, as BP pointed out in its response to the EPA, simple tests could miss subtle but important details. For example, some of the ingredients in a seemingly acceptable dispersant called Sea Brat #4 may degrade into nonylphenol, an endocrine disrupter that could bioaccumulate in ever-higher concentrations up the food chain.

While BP knew the ingredients in Sea Brat #4, most dispersant formulations have been kept secret by their manufacturers. Indeed, Nalco kept Corexit's formulation under wraps and only revealed it to the EPA after extensive negotiations. The ingredients were revealed by the EPA on June 8. Perhaps not coincidentally, on May 28 the agency changed the Toxic Substances Control Act, giving itself power to suspend industry confidentiality claims on chemical compounds. Knowing the identity of each chemical used should help the EPA better characterize each dispersant.

According to Mitchelmore, acute toxicity tests take several days, and chronic toxicity tests between one and three weeks. According to Gilfillan, "We don't have a hard timeline" on when test results will be obtained. "It looks like sometime in coming days or weeks."

Even when the EPA's tests are finished, however, circumstances will limit their value. There isn't time to study long-term effects on animals, do ecosystem analyses, or even conduct lab studies on the full range of species affected by dispersants and dispersed oil. That data will be gathered in coming years, as results roll in from the giant laboratory that is now the Gulf of Mexico.

"The EPA is taking some important steps, but a lot of this stuff should have been done years ago," said Natural Resources Defense Council senior scientist Gina Solomon. "It's a shame that we have to wait for a crisis before realizing the need to gather toxicity information."

Image: Dispersant is injected into oil at the wellhead.
Flickr/pppspics.

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Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecological tipping points.

Japanese Spacecraft Deploys First-Ever Solar Sail

Posted: 09 Jun 2010 12:58 PM PDT

The unfurling of a Japanese solar sail, the first demonstration of a new space propulsion technology, went exactly according to plan.

According toJAXA's blog posts and photos from the event, the IKAROS spacecraft's sail appears to be in place. It's a big step in its attempt to travel driven only by sunlight.

"This is the first sail ever deployed in space, and if they succeed in using it for solar-sail flight — it'll still be a few weeks before we know that — it'll be a milestone," said Louis Friedman, executive director of the Planetary Society, an organization dedicated to promoting space exploration, which is readying its own solar-sailing mission.

A solar sail uses the pressure from photons striking its surface to push the spacecraft through space. Materially, the 650 square-foot sail is made of incredibly thin, aluminized plastic that's only 0.0003 inches thick, a little thicker than spider silk, or about the diameter of a red blood cell. When a photon strikes its surface, it bounces off, imparting its momentum to the sail. Each photon might not deliver much thrust, but over time, all that light adds up.

"The actual force might be just a few millionths of a g, but because it acts continuously, it allows you to build up large velocity changes over time," Friedman said. "That's where a sail really does its work is long missions."

The Japanese sail also has thin-film solar cells built into it. They could be used to generate electricity to drive an engine that would work alongside the sail.

The key difficulty with such a thin and large object is that it's hard to deploy. "The things we're watching for are all their dynamical behaviors that you ultimately can't model and that might cause undue stress on the material," Friedman said.

In the IKAROS design, the sail was unfurled by using centrifugal force generated by spinning the craft.

Space-travel proponents are particularly interested in the technology because it doesn't require fuel, which makes it the leading (and basically) only candidate for very long-distance travel.

"It's the only way we know — that anybody knows — to ultimately do practical interstellar flight because you don't have to carry your propellant along with you," Friedman said. "Anything else you do, whether it's nuclear or advanced engines, you're always carrying propellant and the mass becomes too great."

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WiSci 2.0: Alexis Madrigal's Twitter, Tumblr, and forthcoming book on the history of green technology; Wired Science on Twitter and Facebook.

Sharks’ Hunting Strategies More Like Physics Than Biology

Posted: 09 Jun 2010 11:04 AM PDT

When sharks and other ocean predators can't find food, their movement patterns shift in surprising ways that are associated with particle physics rather than animal behavior.

They abandon Brownian motion, the random motion seen in swirling gas molecules, for what's known as Lévy flight — a mix of long trajectories and short, random movements found in turbulent fluids.

"It's fascinating that you get these patterns. Maybe there's more structure to things than we think, and these patterns occur not just in physics in how particles behave, but in how animals behave," said biologist Nicoloas Pade of the United Kingdom's Marine Biological Association.

Computer models suggest Lévy flight is the optimal search pattern for predators in low-prey areas, and maximizes the chance of a random encounter. But real-world studies have been inconclusive, with reports of Lévy flight countered by doubts about data gathering and interpretation.

The latest findings, published June 9 in Nature, represent the largest dataset yet gathered in search of Lévy flight in animals. The researchers analyzed 13,000,000 movements recorded over 5,700 days in 55 radio-tagged animals from 14 ocean predator species in the Atlantic and Pacific Oceans, including whale shark, blue marlin and swordfish.

As the animals went from areas of high ecological abundance to low, the equations describing their movement switched from Brownian motion to Lévy flight.

"Our analysis provides the strongest evidence yet for Lévy behavior in diverse animals ranging across natural landscapes," wrote the researchers.

The findings raise the question of where Lévy flight comes from — whether it's an instinctive or learned behavior, a property of individuals or a function of spatial distributions governed by as-yet-unknown laws — and how it first evolved.

"Animals' behavior is much more plastic than previously thought," said Pade. "They have a huge repertoire of movement strategies and patterns."

Image: 1) Movement patterns of a shark in productive (left) and unproductive water./Nature. 2) Aggregate analyses of movement patterns./Nature.

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Citation: "Environmental context explains Lévy and Brownian movement patterns of marine predators." By Nicolas E. Humphries, Nuno Queiroz, Jennifer R. M. Dyer, Nicolas G. Pade, Michael K. Musyl, Kurt M. Schaefer, Daniel W. Fuller, Juerg M. Brunnschweiler, Thomas K. Doyle, Jonathan D. R. Houghton, Graeme C. Hays, Catherine S. Jones, Leslie R. Noble, Victoria J. Wearmouth, Emily J. Southall & David W. Sims. Nature, Vol. 465 No. 7299, June 10, 2010.

Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecological tipping points.

High-Speed Video: Bursting Bubbles Breed Ever-Smaller Bubbles

Posted: 09 Jun 2010 10:49 AM PDT

Popped bubbles leave rings of smaller bubbles, whether they're soap bubbles in the sink or saltwater bubbles on the open ocean, new high-speed videos show. The smaller bubbles make still-tinier bubbles when they pop, which could help transmit both nutrients and pollutants from the ocean to the atmosphere.

Scientists have known for decades that when a raindrop falls into a pool of water, it kicks up a ring of smaller droplets, which make still smaller droplets, and so on. But popped bubbles were supposed to simply disappear.

"What's really exciting about this work is that it's really fundamental, and yet there's still some new things that people haven't really ever talked about before," said Harvard graduate student James Bird, first author of a paper in the June 9 Nature.

Bird and a fellow grad student stumbled on the effect while trying to spread soap bubbles evenly on a surface for a different project. They found that not only would the bubbles not spread, but when they popped, they left a circle of smaller bubbles behind. The ring even appeared when they held the bubble upside-down. Furthermore, when the daughter bubbles popped, they left behind their own ring of even-smaller bubbles.

"Neither of us had any idea what was causing it," Bird said.

Bird and colleagues made a bubble from a glycerol and water solution on a glass slide. They then filmed the bubble from the bottom and the side between 10,000 and 50,000 frames per second — 300 to 1,600 times faster than a regular video camera.

These high-speed videos allowed them a more detailed view of the physics of bubble-popping than was ever seen before, Bird said. "That's why it hadn't been discussed or probed in the past, at least not nearly to the degree of what we've done in this paper."

The movies showed that when the curved film of the bubble ruptures, the lip of the bubble folds backward. In their video, the lip folded so far that it reconnected with the rest of the film, like a gymnast bending backward and grabbing her own ankles. This loop of film trapped some air. The loop then kept bending away from the rest of the bubble, so that when it finally met the solid surface, it trapped another ring of air.

All that happened in less than 3 milliseconds (see below). Over the next 50 milliseconds, the two rings of air coalesced into about 25 individual bubbles.

Bird thinks the lip folds over because the air pressure inside the bubble is greater than the pressure outside. When a hole forms in the bubble, the two pressures equilibrate almost immediately. The sudden decrease in pressure inside the bubble sucks in the sides of the bubble, similar to a person sucking in their cheeks. The lip of the bubble then extends beyond the rest of the film, ready to trap air and form baby bubbles.

To test this idea, Bird and his colleagues ran a computer simulation including only four or five variables to describe the bubble's characteristics.

"It did a remarkably good job," he said.

The team also filmed bubbles popping in water from the Charles River in Boston. The pressure inside the bubble forms a dimple on the water's surface, which is exposed when the bubble pops. Water rushes in to fill the dimple, forming a jet of water, like when a stone drops in a pond.

The same folded-lip effect as in the glycerol bubbles forms baby bubbles, which can also pop and shoot jets into the air at speeds greater than 11 miles per hour.

Scientists already knew these small bubbles could spray particles of liquid into the atmosphere. This is where sea spray comes from, and why you feel fizz on your nose when you put your face over a glass of soda. These spray particles can carry whatever was on the surface up into the air, from salt to viruses to oil.

"What we've done is we've linked the larger bubbles with the smaller ones," Bird says. "The larger ones were neglected. Rather than being negligible, it's an enormous effect, because you're getting dozens of these little bubbles that can then pop and become aerosols."

The researchers also blew bubbles in liquids of different thicknesses, and found that thick-enough liquids did not form daughter bubbles. This finding could be useful in industries like glass-making, where bubbles are harmful.

Bird next wants to look at bubbles in extremely thick, gloppy materials like molten rock or mud.

Jens Eggers, an expert in droplets from the University of Bristol, thinks the cascade of smaller and smaller bubbles is a beautiful demonstration of a standard effect in nature. "Nature is full of these things, but few are really well understood," he said. "It's wonderful to have an example where people are really able to take it apart, and look at it from different angles, and really demonstrate that it works."

Image and video: J.C. Bird/Harvard School of Engineering and Applied Sciences

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Complex Life Traced to Ancient Gene Parasites

Posted: 09 Jun 2010 09:41 AM PDT

Mysterious gene structures called introns that help make complex organisms possible are descended from DNA parasites that infested bacteria billions of years ago, according to a new study.

Researchers studying Thermosynechococcus elongatus, a heat-loving microbe teeming with so-called mobile group II introns — the contemporary version of those parasites — found that as temperatures rise, the introns infect genes more efficiently.

Published June 8 in PLoS Biology, the findings fit the notion that group II introns flourished in the early Earth's heat, and were ultimately co-opted into their hosts' genomes.

"The introns that currently exist in the genomes of humans and other higher organisms are thought to have evolved from these group II introns," said molecular biologist Georg Mohr of the University of Texas at Austin. "Over evolutionary time, they acquired function."

Introns were discovered in the 1970s, when scientists thought genes followed simple, linear rules: Cellular machinery would translate the DNA of each gene into an unbroken string of RNA molecules, which then instructed cells to produce a protein. Introns added a twist. They're stretches of DNA that are not translated into RNA. Instead of producing an unbroken RNA string, an intron-bearing gene makes several pieces of RNA that are then stitched together.

Introns proved common in multicellular organisms. Many genes have multiples. The same gene in different organisms, or even different tissue types in the same organism, can have different intron configurations. Scientists were initially perplexed, but now think that introns are vitally important to cell function.

When pieces of RNA are re-assembled, modifications are made to their protein-calling code. By forcing this to happen, introns allow the same gene to produce many different proteins. That variation underlies cell development, tissue differentiation and the diversity of higher organisms. But even as the role of introns becomes clearer, their origins remain murky.

Researchers like Mohr and study co-author Alan Lambowitz, also a University of Texas at Austin molecular biologist, point to mobile group II introns. These snippets of DNA have many structural similarities to introns but are free-floating, jumping between genes like fleas on animals. Mohrg and Lambowitz think group II introns infested early bacteria, and were incorporated into the genomes of later organisms — a DNA-level example of the sort of symbiosis seen with mitochondria, which started out as microbial invaders and are now part of every animal cell.

The intron narrative makes sense, but has one critical hole. Researchers have been unable to find bacteria with more than a few group II introns. If modern bacteria are barely infested, it's hard to imagine how ancient bacteria could have accumulated the many introns found in modern animal cells.

In the new study paper, the researchers finally filled the hole. Mobile group II introns account for more than one percent of the genome of T. elongatus, a cyanobacteria living in a Japanese hot spring. Its living conditions echo early Earth's, and "some of the earliest bacteria were these free-living cyanobacteria," said Lambowitz.

When they transplanted T. elongatus' group II introns into Escherichia coli, the researchers found that fusion rates depended on temperature. "High temperatures melt the DNA strands, and that makes it easier for group II introns to insert themselves," said Lambowitz. A hot environment two billion years ago "could have contributed to the introns' proliferation in early eukaryotes."

Whether this happened is speculative, but the findings may have an immediate use. Clostridium thermocellum, a heat-loving bacteria being studied by Department of Energy researchers for use in breaking down cellulose during biofuel production, has proven difficult to manipulate.

"The tools for knocking out and inserting genes have not existed for many thermophilic organisms," said Lambowitz. "The mobile group II introns from T. elongatus are different from other introns, because they can work at high temperatures."

Images: 1. The hot springs in Beppu, Japan where T. elongatus was discovered./Flickr/Joka2000. 2. The structure of a T. elongatus type II intron./PLoS Biology. 3. T. elongatus./Georg Mohr.

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Citation: "Mechanisms Used for Genomic Proliferation by Thermophilic Group II Introns." By Georg Mohr, Eman Ghanem, Alan M. Lambowitz. Public Library of Science Biology, Vol. 8 Issue 6, June 8, 2010.

Brandon Keim's Twitter stream and reportorial outtakes; Wired Science on Twitter. Brandon is currently working on a book about ecological tipping points.

U.S. Leading Charge on Synthetic Biology Funding

Posted: 08 Jun 2010 01:09 PM PDT

Synthetic biology received about $430 million in U.S. government funding from 2005 to 2010, far outpacing European governments, which gave their synthetic biologists $160 million over the same period. The emerging field received nearly no funding before 2005, according to a new Woodrow Wilson Center report.

The numbers are the latest indication that synthetic biology has become a buzzword at the highest-levels of politics and policy. Last month, President Obama convened a special commission to study synthetic biology and the House held a special hearing on the topic. Both events were apparently prodded by the J. Craig Venter Institute's announcement that they implanted a genome that was once a text document filled with letters into a living cell.

Though synthetic biology support is growing, it's far from a major research area for any government. The U.S. government alone spends almost $150 billion on R&D, the majority of which goes to "defense," broadly construed. The largest part of the civilian science budget, about $30 billion, goes to "health," which includes biomedical research.

The new numbers on synthetic biology, while interesting, are not definitive, said Todd Kuiken, a research associate on the Synthetic Biology Project at the Wilson Center. Government agencies don't specifically track synthetic biology projects as a line-item, and even the definition of the field is squishy. For example, Stanford synthetic biologist Drew Endy says the field's long-term goal is to "help make biology easy to engineer." No government process exists that sorts out projects fitting Endy's definition, especially from the genetic engineering that scientists have long done.

Because of the difficulty categorizing what is and isn't synthetic biology as well as extracting the information from the agencies, Kuiken said he thinks the real amount of money being spent on synthetic biology is higher than the number in the initial research brief. But he hopes that putting a provisional number on it will cause the government to start tracking their investments.

"If you at least get a number out there that is public, it forces the agencies to look deeper at it," Kuiken said.

One interesting twist to the numbers is the lack of funds dedicated to evaluating any peculiar risks posed by synthetic biology techniques.

"There is no project that we've seen looking at the risk," Kuiken said.

That said, about 4 percent of the research money is going to study the "ethical, legal and social implications" of the technology, which is comparable to how much nanotechnology money is spent on those issues.

The Synthetic Biology Project also assembled a map of all the institutions working on synthetic biology problems, which you can see above.

See Also:

WiSci 2.0: Alexis Madrigal's Twitter, Tumblr, and forthcoming book on the history of green technology; Wired Science on Twitter and Facebook.
Posted by johnald at 13:14

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