Archive for September 23rd, 2011

The Smell of Fall

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I love the fall.
I look forward to watching the leaves turn red, orange, and yellow. I look forward to watching them fall. I look forward to watching the wind caress them and blow them all over the yard. I look forward to raking them into giant piles.
Fall seems very peaceful to me, it seems wise.
I adore pumpkins of all colors and sizes. I can never have enough of them around the house.
I cant wait till David takes me to buy our hay bail.
I love the smell of fall. I love the way the the cold mornings nibble on my nose. The magic in the air. I take a deep breath. I want it to permeate my whole body. Every single cell even in the tips of my toes. It calms me.
I love going on walks in the fall and getting just cold enough that I can feel my cheeks and nose turning red. I love coming home to the warmth of the house and the smell of apple cider, pumpkin pie, hearty soup, and beef stew.
I live for the first time I open the storage containers of fall decorations and the smell of pumpkin, cinnamon, and cranberry candles that has been locked inside for 12 months rushes out. I just stand above the boxes sucking in the moment. I am so caught up in it. I want to stand there forever.
Decorating for Halloween and Thanksgiving is a sacred experience for me. Spiders and turkeys. Gosh, I love them.
I got married on the September 23–the first day of fall.

Gamers solve molecular puzzle that baffled scientists

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David: Imagine the mysteries Angry Birds could solve.
Sandy: Middle East Peace brought to you by Angry Birds.

Video-game players have solved a molecular puzzle that stumped scientists for years, and those scientists say the accomplishment could point the way to crowdsourced cures for AIDS and other diseases.
“This is one small piece of the puzzle in being able to help with AIDS,” Firas Khatib, a biochemist at the University of Washington, told me. Khatib is the lead author of a research paper on the project, published today by Nature Structural & Molecular Biology.
The feat, which was accomplished using a collaborative online game called Foldit, is also one giant leap for citizen science — a burgeoning field that enlists Internet users to look for alien planets, decipher ancient texts and do other scientific tasks that sheer computer power can’t accomplish as easily.
“People have spatial reasoning skills, something computers are not yet good at,” Seth Cooper, a UW computer scientist who is Foldit’s lead designer and developer, explained in a news release. “Games provide a framework for bringing together the strengths of computers and humans.”
Unraveling a retrovirus
For more than a decade, an international team of scientists has been trying to figure out the detailed molecular structure of a protein-cutting enzyme from an AIDS-like virus found in rhesus monkeys. Such enzymes, known as retroviral proteases, play a key role in the virus’ spread — and if medical researchers can figure out their structure, they could conceivably design drugs to stop the virus in its tracks. The strategy has been compared to designing a key to fit one of Mother Nature’s locks.
The problem is that enzymes are far tougher to crack than your typical lock. There are millions of ways that the bonds between the atoms in the enzyme’s molecules could twist and turn. To design the right chemical key, you have to figure out the most efficient, llowest-energy configuration for the molecule — the one that Mother Nature herself came up with.
That’s where Foldit plays a role. The game is designed so that players can manipulate virtual molecular structures that look like multicolored, curled-up Tinkertoy sets. The virtual molecules follow the same chemical rules that are obeyed by real molecules. When someone playing the game comes up with a more elegant structure that reflects a lower energy state for the molecule, his or her score goes up. If the structure requires more energy to maintain, or if it doesn’t reflect real-life chemistry, then the score is lower.
More than 236,000 players have registered for the game since its debut in 2008.
The monkey-virus puzzle was one of several unsolved molecular mysteries that a colleague of Khatib’s at the university, Frank DiMaio, recently tried to solve using a method that took advantage of a protein-folding computer program called Rosetta. “This was one of the cases where his method wasn’t able to solve it,” Khatib said.
Fortunately, the challenge fit the current capabilities of the Foldit game, so Khatib and his colleagues put the puzzle out there for Foldit’s teams to work on. “This was really kind of a last-ditch effort,” he recalled. “Can the Foldit players really solve it?”
They could. “They actually did it in less than 10 days,” Khatib said.

University of Washington
A screen shot shows how the Foldit program posed the monkey-virus molecular puzzle.
One floppy loop of the molecule, visible on the left side of this image, was particularly tricky to figure out. But players belonging to the Foldit Contenders Group worked as a tag team to come up with an incredibly elegant, low-energy model for the monkey-virus enzyme.
“Standard autobuilding and structure refinement methods showed within hours that the solution was almost certainly correct,” the researchers reported in the paper published today. “Using the Foldit solution, the final refined structure was completed a few days later.”
Khatib said the Seattle team’s collaborators in Poland were in such a celebratory mood that they insisted on organizing a simultaneous champagne toast, shared over a Skype video teleconference.
“Although much attention has recently been given to the potential of crowdsourcing and game playing, this is the first instance that we are aware of in which online gamers solved a longstanding scientific problem,” Khatib and his colleagues wrote.
The parts of the molecule that formed the floppy loop turned out to be of particular interest. “These features provide exciting opportunities for the design of retroviral drugs, including AIDS drugs,” the researchers said.
Looking for new problems to solve
The monkey-virus puzzle solution demonstrates that Foldit and other science-oriented video games could be used to address a wide range of other scientific challenges — ranging from drug development to genetic engineering for future biofuels. “My hope is that scientists will see this research and give us more of those cases,” Khatib said.
He’s not alone in that hope. “Foldit shows that a game can turn novices into domain experts capable of producing first-class scientific discoveries,” Zoran Popovic, director of University of Washington’s Center for Game Science, said in today’s news release. “We are currently applying the same approach to change the way math and science are taught in school.”
That’s something that Carter Kimsey, program director for the National Science Foundation’s Division of Biological Infrastructure, would love to see happen. “After this discovery, young people might not mind doing their science homework,” she quipped.
One caveat, though: Playing Foldit isn’t exactly like playing Bejeweled. “Let’s be honest, proteins aren’t the sexiest video game out there,” Khatib told me. Give the game a whirl, and let me know whether it’s addictive or a drag.
Tale of a Contender
The final decisive move in the Foldit Contender Group’s solution to the monkey-virus puzzle involved twisting around that floppy loop, or “flap,” in the structure of the enzyme. The paper published today notes that one of the Contenders, nicknamed “mimi,” built upon the work done by other gamers to make that move.

Speed-of-light experiments give baffling result at Cern

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Puzzling results from Cern, home of the Large Hadron Collider, have confounded physicists because subatomic particles seem to have beaten the speed of light.
Neutrinos sent through the ground from Cern toward the Gran Sasso laboratory 732km away in Italy seemed to show up a tiny fraction of a second early.
The results – which threatens to upend a century of physics – were put online for scrutiny by other scientists.
In the meantime, the group says it is being very cautious about its claims.
They will be discussing the result in detail in a conference at Cern on Friday afternoon, which can be viewed online.
“We tried to find all possible explanations for this,” said report author Antonio Ereditato of the Opera collaboration.
“We wanted to find a mistake – trivial mistakes, more complicated mistakes, or nasty effects – and we didn’t,” he told BBC News.
“When you don’t find anything, then you say ‘Well, now I’m forced to go out and ask the community to scrutinise this.’”
Caught speeding?
The speed of light is the Universe’s ultimate speed limit, and much of modern physics – as laid out in part by Albert Einstein in his theory of special relativity – depends on the idea that nothing can exceed it.
Thousands of experiments have been undertaken to measure it ever more precisely, and no result has ever spotted a particle breaking the limit.
But Dr Ereditato and his colleagues have been carrying out an experiment for the last three years that seems to suggest neutrinos have done just that.
Neutrinos come in a number of types, and have recently been seen to switch spontaneously from one type to another.
The team prepares a beam of just one type, muon neutrinos, sending them from Cern to an underground laboratory at Gran Sasso in Italy to see how many show up as a different type, tau neutrinos.
In the course of doing the experiments, the researchers noticed that the particles showed up 60 billionths of a second sooner than light would over the same distance.
This is a tiny fractional change, but one that occurs consistently.
The team measured the travel times of neutrino bunches some 15,000 times, and have reached a level of statistical significance that in scientific circles would count as a formal discovery.
But the group understands that what are known as “systematic errors” could easily make an erroneous result look like a breaking of the ultimate speed limit, and that has motivated them to publish their measurements.
“My dream would be that another, independent experiment finds the same thing – then I would be relieved,” Dr Ereditato said.
But for now, he explained, “we are not claiming things, we want just to be helped by the community in understanding our crazy result – because it is crazy”.
“And of course the consequences can be very serious.”

Article from: BBC