To check, use any graphics tool you like, that green and blue are actually the same color.

Via Kottke

The key to how any protein works is its three-dimensional shape, determined by all the ways its atoms interact. Trying to push two atoms closer when they want to repel is like holding magnets together when they’re oriented the wrong way. You can force them, but nature prefers configurations that follow the path of least resistance. In a simple molecule, that path is pretty clear: Water—H₂O—is hydrogen-oxygen-hydrogen balanced perfectly in a V-shape at a 104.4-degree angle. This push and pull is inevitable. Physics is destiny.

The Challenge
The online game Foldit is designed to reveal the shortcuts nature uses to weave a tangle of amino acids, like the one shown here, into a protein. Players click to move pieces around until they fit.

But the bigger the molecule, the more complex these negotiations become. And proteins are colossal. Of course, there is another way to figure all this out: Shining x-rays through a crystallized lump of protein can help reveal the exact position of its folded-up atoms. But that takes time—just 50,000 protein structures have been cracked since the late 1950s, while the sequences of millions of protein-coding genes have been discovered in the past 10 years alone. To make headway in figuring out what all these proteins do, scientists need a faster approach.

Two of Baker’s PhD students, James Thompson and Robert Vernon, groggy from a sleepless night and months of relentless CASP work, finally arrived with the answer. After a brief wrestle with a laptop, they loaded their results. Of the 15 Foldit solutions that Baker submitted to CASP, seven had finished in the money—all of them folded by Poehlman and his teammates. One of their solutions even took first place. A band of gamer nonscientists had beaten the best biochemists.

Arguably, though, the real Foldit victory had come a few months earlier. The creators of the game invited the top players to Seattle, seeking their help in making the app better. Popović contacted Poehlman’s parents. The kid was shocked. ‘Aristides didn’t believe us until we showed him the email,’ his mother says. ‘The silent stare he gave us was priceless.’ Poehlman and his dad, Louis, flew into Seattle late; they played Foldit for hours in their hotel before going to bed—just like at home.

At UW’s computer lab, Popović and his grad students filmed the Poehlmans playing Foldit and interviewed them about their techniques. Louis was exacting in his analysis of how he approached each puzzle, supplying sophisticated justifications for his moves. But when they turned to Cheese and asked him how he knew the way to tweak the proteins—for example, by orienting hydrophobic sidechains toward the protein core—he shrugged and said, ‘It just looks right.’

And that is exactly what Baker was looking for. ‘When I said early on that I hoped Foldit would help me find protein-folding prodigies, it was hopeful speculation,’ he says. ‘It’s fantastic to see it come true.’

The next CASP is two years away, and Baker doesn’t want to lose Foldit‘s momentum. He and Popović have given the players a challenge: Design a new protein. Baker’s lab is developing targets for cancer, AIDS, and Alzheimer’s, and the folders’ task is to build a small protein drug with the right shape and binding properties. This isn’t just an intellectual exercise. Baker says he will synthesize the most promising structures and test them in his lab. These proteins could actually have therapeutic value in the real world, outside the game. And if they do, the Foldit players will share the credit. It might be the first time that a computer game’s high score is a Nobel Prize.

John Bohannon (gonzo@aaas.org) is a correspondent for Science based in Vienna, Austria.

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(Via Wired News.)

Solving the Biggest Natural Explosion in Modern History – 1908 Tunguska Event – Popular Mechanics: ”

When Comets Attack: Solving the Mystery of the Biggest Natural Explosion in Modern History
On the morning of June 30, 1908, the sky exploded over a remote region of central Siberia. A fireball as powerful as hundreds of Hiroshima atomic blasts scorched through the upper atmosphere, burning nearly 800 square miles of land. Scientists today think a small fragment of a comet or asteroid caused the ‘Tunguska event,’ so named for the Tunguska river nearby. Now, a controversial new scientific study suggests that a chunk of a comet caused the 5-10 megaton fireball, bouncing off the atmosphere and back into orbit around the sun. The scientists have even identified a candidate Tunguska object—now more than 100 million miles away—that will pass close to Earth again “

This map and the data behind it were compiled by Dr. Henry Niman, a biomedical researcher in Pittsburgh, Pennsylvania, using technology provided by Rhiza Labs and Google. The map was compiled using data from official sources, news reports and user-contributions.

Garrett Lisi’s Theory of Everything: “

You may remember reading the New Yorker article on Garrett Lisi, a surfer, physicist, and snowboarder who came out of nowhere in 2007 to present a plausible Theory of Everything, ‘a unifying idea that aims to incorporate all the universe’s forces in a single mathematical framework’. I do but I missed this visualization of Lisi’s theory posted by New Scientist in late 2007.

My intuition is that if we ever arrive at a TOE for the physical realm, part of the model will have to demand a strictly continuous space/time/matter/energy fabric. This arises from a felt belief that all is one. I could probably expand on the “all is one” phrase and fill an entire book yet not add much clarity to that simple phrase.

(Via Kottke.)

That said, his post is enjoyable to read in the same way as the Dr. Bronner’s soap label.

They calculated that, in this one hospital, the checklist had prevented forty-three infections and eight deaths, and saved two million dollars in costs.

Yup, adding a checklist.

In a stellar piece of research and storytelling, Atul Gawande tells the ongoing story of critical-care specialist Peter Pronovost at Johns Hopkins Hospital.

Included and completely in context is an amazing story of mammalian diving reflex as embodied in a young Austrian girl, the challenges involved in supporting people in modern Intensive Care Units, and a neat anecdote about how the U.S. military and aviation as a discipline discovered the need for checklists.

When I worked at US Testing in 1967-69 we put all our radioactive waste we used for quality control when testing produce grown at Hanford in metal barrels that were later buried….. I hate to think of all those metal barrels that are still buried in the desert.

Regarding the recent find at Hanford:

An old glass jar inside a beaten up old safe at the bottom of a waste pit may seem an unlikely place to find a pivotal piece of 20th century history. But that’s just where the first bulk batch of weapons-grade plutonium ever made has been found – abandoned at the world’s oldest nuclear processing site.

As a race we’ll probably be dealing with this persistent pollution for longer than the span of all recorded history, and some of this pollution is stored in glass jars, in rusty old safes.