Category: California Institute of Technology

Online Video Game Plugs Players Into Real Biochemistry Lab

On By A.P.In Adrien Treuille, biochemistry, California Institute of Technology, Cloud biochemistry, Crowdsourcing, David Baker, Dr. Rajadhyaksha, Erik Winfree, EteRNA, Foldit, Jeehyung Lee, Proceedings of the National Academy of Sciences, Rhiju Das, Science, Shawn Douglas, video game, virtual lab, Zoran PopovićLeave a comment

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Crowdsourcing is the latest research rage—Kickstarter to raise funding, screen savers that number-crunch, and games to find patterns in data—but most efforts have been confined to the virtual lab of the Internet. In a new twist, researchers have now crowdsourced their experiments by connecting players of a video game to an actual biochemistry lab. The game, called EteRNA, allows players to remotely carry out real experiments to verify their predictions of how RNA molecules fold. The first big result: a study published this week in the Proceedings of the National Academy of Sciences, bearing the names of more than 37,000 authors—only 10 of them professional scientists. “It’s pretty amazing stuff,” says Erik Winfree, a biophysicist at the California Institute of Technology in Pasadena.

Some see EteRNA as a sign of the future for science, not only for crowdsourcing citizen scientists but also for giving them remote access to a real lab. “Cloud biochemistry,” as some call it, isn’t just inevitable, Winfree says: It’s already here. DNA sequencing, gene expression testing, and many biochemical assays are already outsourced to remote companies, and any “wet lab” experiment that can be automated will be automated, he says. “Then the scientists can focus on the non-boring part of their work.”

EteRNA grew out of an online video game called Foldit. Created in 2008 by a team led by David Baker and Zoran Popović, a molecular biologist and computer scientist, respectively, at the University of Washington, Seattle, Foldit focuses on predicting the shape into which a string of amino acids will fold. By tweaking virtual strings, Foldit players can surpass the accuracy of the fastest computers in the world at predicting the structure of certain proteins. Two members of the Foldit team, Adrien Treuille and Rhiju Das, conceived of EteRNA back in 2009. “The idea was to make a version of Foldit for RNA,” says Treuille, who is now based at Carnegie Mellon University in Pittsburgh, Pennsylvania. Treuille’s doctoral student Jeehyung Lee developed the needed software, but then Das persuaded them to take it a giant step further: hooking players up directly to a real-world, robot-controlled biochemistry lab. After all, RNA can be synthesized and its folded-up structure determined far more cheaply and rapidly than protein can.

Lee went back to the drawing board, redesigning the game so that it had not only a molecular design interface like Foldit, but also a laboratory interface for designing RNA sequences for synthesis, keeping track of hypotheses for RNA folding rules, and analyzing data to revise those hypotheses. By 2010, Lee had a prototype game ready for testing. Das had the RNA wet lab ready to go at Stanford University in Palo Alto, California, where he is now a professor. All they lacked were players.

A message to the Foldit community attracted a few hundred players. Then in early 2011, The New York Times wrote about EteRNA and tens of thousands of players flooded in.

The game comes with a detailed tutorial and a series of puzzles involving known RNA structures. Only after winning 10,000 points do you unlock the ability to join EteRNA’s research team. There the goal is to design RNA sequences that will fold into a target structure. Each week, eight sequences are chosen by vote and sent to Stanford for synthesis and structure determination. The data that come back reveal how well the sequences’ true structures matched their targets. That way, Treuille says, “reality keeps score.” The players use that feedback to tweak a set of hypotheses: design rules for determining how an RNA sequence will fold.

Two years and hundreds of RNA structures later, the players of EteRNA have proven themselves to be a potent research team. Of the 37,000 who played, about 1000 graduated to participating in the lab for the study published today. (EteRNA now has 133,000 players, 4000 of them doing research.) They generated 40 new rules for RNA folding. For example, at the junctions between different parts of the RNA structure—such as between a loop and an arm—the players discovered that it is far more stable if enriched with guanines and cytosines, the strongest bonding of the RNA base pairs. To see how well those rules describe reality, the humans then competed toe to toe against computers in a new series of RNA structure challenges. The researchers distilled the humans’ 40 rules into an algorithm called EteRNA Bot.

The human players still came out on top, solving structures more accurately than the standard software 99% of the time. The algorithmic version of their rules also outperformed the standard software, but only 95% of the time, showing that the crowdsourced human RNA-folding know-how has not been completely captured yet. The next step, Lee says, is to make the wet lab completely robotic. It still requires humans to operate some of the steps between the input of player RNA sequences and the data output.

EteRNA won’t work for every kind of science, says Shawn Douglas, a biomolecular engineer at the University of California, San Francisco, because a problem has to be “amenable to game-ification.” But he’s optimistic that there will be many more to come. “Many areas of biological research have reached a level of complexity that the mental bandwidth of the individual researcher has become a bottleneck,” Douglas says. EteRNA proves that “there are tens of thousands of people around the world with surplus mental bandwidth and the desire to participate in scientific problem solving.” The trick is to design a good game.

http://news.sciencemag.org/biology/2014/01/online-video-game-plugs-players-real-biochemistry-lab

Thanks to Dr. Rajadhyaksha for bringing this to the It’s Interesting community.

If The Sun Went Out, How Long Could Life On Earth Survive?

On By A.P.In California, California Institute of Technology, David Stevenson, Eric Blackman, Space and Time, The Sun, University of Rochester1 Comment

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If you put a steamy cup of coffee in the refrigerator, it wouldn’t immediately turn cold. Likewise, if the sun simply “turned off” (which is actually physically impossible), the Earth would stay warm—at least compared with the space surrounding it—for a few million years. But we surface dwellers would feel the chill much sooner than that.

Within a week, the average global surface temperature would drop below 0°F. In a year, it would dip to –100°. The top layers of the oceans would freeze over, but in an apocalyptic irony, that ice would insulate the deep water below and prevent the oceans from freezing solid for hundreds of thousands of years. Millions of years after that, our planet would reach a stable –400°, the temperature at which the heat radiating from the planet’s core would equal the heat that the Earth radiates into space, explains David Stevenson, a professor of planetary science at the California Institute of Technology.

Although some microorganisms living in the Earth’s crust would survive, the majority of life would enjoy only a brief post-sun existence. Photosynthesis would halt immediately, and most plants would die in a few weeks. Large trees, however, could survive for several decades, thanks to slow metabolism and substantial sugar stores. With the food chain’s bottom tier knocked out, most animals would die off quickly, but scavengers picking over the dead remains could last until the cold killed them.

Humans could live in submarines in the deepest and warmest parts of the ocean, but a more attractive option might be nuclear- or geothermal-powered habitats. One good place to camp out: Iceland. The island nation already heats 87 percent of its homes using geothermal energy, and, says astronomy professor Eric Blackman of the University of Rochester, people could continue harnessing volcanic heat for hundreds of years.

Of course, the sun doesn’t merely heat the Earth; it also keeps the planet in orbit. If its mass suddenly disappeared (this is equally impossible, by the way), the planet would fly off, like a ball swung on a string and suddenly let go.

http://www.popsci.com/science/article/2013-07/if-sun-went-out-how-long-could-life-earth-survive?cmpid=obinsite

Drugs to enhance massage

On By A.P.In C-tactile fibres, California, California Institute of Technology, David Anderson, Francis McGlone, Liverpool John Moores University, massage, Nature, Neuroscience, ScienceLeave a comment

massage

Nerves dedicated to creating these feelings have been identified and artificially stimulated in mice, leading to hope that the work could aid the development of drugs that relieve pain or stress.

Some nerves rapidly transmit sensations of touch or pain to the brain, but others work much more slowly. These C-tactile fibres, as they are known in humans, are found under hairy skin and respond to stroking.

David Anderson at the California Institute of Technology in Pasadena and colleagues used calcium imaging to identify similar bundles of nerves in mice.

When the mice were in a special chamber, the team injected them with a chemical that activated these nerves. Afterwards, the mice visited the chamber almost twice as often as they had before, suggesting that they enjoyed the experience and wanted more (Nature, DOI: 10.1038/nature11810).

A drug that evokes a similar response in humans could boost the beneficial effects of skin-to-skin contact such as massage in rehabilitation or for psychiatric conditions, says Johan Wessberg at the University of Gothenburg in Sweden.

Interactions involving stroking are common among many mammals, particularly in nurturing, and removing this contact can impair development. “For the first time we are getting a neurological basis for these phenomena,” says Francis McGlone at Liverpool John Moores University in the UK.

http://www.newscientist.com/article/mg21729025.200-think-that-massage-feels-good-try-adding-drugs.html

Shot Away from Its Companion, Giant Star Makes Waves: Spitzer Captures Infrared Portrait

On By A.P.In astronomy, bow shock, California, California Institute of Technology, Infrared Science Archive, Jet Propulsion Laboratory, NASA, Pasadena, Science, Science Mission Directorate, Space and Time, Spitzer Space Telescope, Wide-field Infrared Survey Explorer, WISE, Zeta OphiuchiLeave a comment

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Like a ship plowing through still waters, the giant star Zeta Ophiuchi is speeding through space, making waves in the dust ahead. NASA’s Spitzer Space Telescope has captured a dramatic, infrared portrait of these glowing waves, also known as a bow shock.

Astronomers theorize that this star was once sitting pretty next to a companion star even heftier than itself. But when that star died in a fiery explosion, Zeta Ophiuchi was kicked away and sent flying. Zeta Ophiuchi, which is 20 times more massive and 80,000 times brighter than our sun, is racing along at about 54,000 mph (24 kilometers per second).

In this view, infrared light that we can’t see with our eyes has been assigned visible colors. Zeta Ophiuchi appears as the bright blue star at center. As it charges through the dust, which appears green, fierce stellar winds push the material into waves. Where the waves are the most compressed, and the warmest, they appear red. This bow shock is analogous to the ripples that precede the bow of a ship as it moves through the water, or the pileup of air ahead of a supersonic airplane that results in a sonic boom.

NASA’s Wide-field Infrared Survey Explorer, or WISE, released a similar picture of the same object in 2011. WISE sees infrared light as does Spitzer, but WISE was an all-sky survey designed to take snapshots of the entire sky. Spitzer, by contrast, observes less of the sky, but in more detail. The WISE image can be seen at: http://www.jpl.nasa.gov/news/news.php?release=2011-026 .

NASA’s Jet Propulsion Laboratory, Pasadena, Calif., manages the Spitzer Space Telescope mission for NASA’s Science Mission Directorate, Washington. Science operations are conducted at the Spitzer Science Center at the California Institute of Technology in Pasadena. Data are archived at the Infrared Science Archive housed at the Infrared Processing and Analysis Center at Caltech. Caltech manages JPL for NASA. For more information about Spitzer, visit: http://spitzer.caltech.edu and http://www.nasa.gov/spitzer .

http://www.sciencedaily.com/releases/2012/12/121218153330.htm