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Joined: 10/27/2008
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Big article on Science games and distributed computing in this week's New Scientist (8th Nov 08, pg 36-39, http://www.newscientist.com/channel/being-human/mg20026811.700-how-online-games-are-solving-uncomputable-problems.html). Couldn't see it anywhere, sorry if its been mentioned already.

Aside from bringing fame to Cheese hehe, its got a couple of interesting paragraphs on the future of Foldit:

Some stuff about CASP for which it says "Initial analysis of results from Foldit are very promising".

Then Zoran Popovic says "We've already seen solutions from these volunteers that are very competitive to massive computational efforts, and at times even outperform them. I expect people to do much better once we refine the tools to better fit the gameplay and human puzzle-solving process".

Then another paragraph which says that starting from this month Foldit will be expanded with a new protein design game to create synthetic proteins, and in December puzzles for growing and moulding sythetic proteins that bind specifically to a virus will go live.

Joined: 05/24/2008
AWESOME !!!

Thanks for that.

MJ.

Joined: 05/24/2008
- Copyrights 2008 - new scientist.

ARISTIDES is a typical 13-year-old boy. He plays basketball after school, is learning the clarinet, and in the evening sits in front of his computer playing games. There is one game that he is especially keen on, however, which marks him out from his peers. Every day he logs on to www.fold.it, where, under the nickname "Cheese", he plays a game that involves twisting, pulling and wiggling a 3D structure that looks a bit like a tree's root system. He manipulates different lengths of these snaking green tubes until they fit into the smallest volume possible. It may sound like a rather bizarre game - a distant 3D relative of Tetris, perhaps - but it is in fact a brilliant disguise for one of the toughest conundrums facing biologists today: how do proteins fold?

The structures Aristides plays with are computer representations of real proteins such as collagen. Without understanding the first thing about molecular biology, he is contributing to one of the knottiest problems of modern science. "Predicting exactly how a long protein chain curls up as compactly as possible, amongst all the myriad possibilities, is a very hard problem to solve with computers," says David Baker at the University of Washington in Seattle, who invented the game.

As the length of a protein chain increases, the number of possible ways it can be folded increases exponentially. Even for the simplest chains, it would take a typical desktop computer several centuries to predict the optimum way a protein would fold. Yet with the help of 60,000 amateur players like Aristides, in the six months it has been running Foldit has already calculated how scores of proteins would fold.

Foldit's success is largely down to a clever new twist on an old idea. The last decade has seen a rise in "distributed computing" projects, in which massive computational problems are chopped up into smaller parts and supplied via the internet to millions of desktop computers around the globe to do the number crunching in parallel. The oldest and most popular of these ventures was set up as part of the Search for Extraterrestrial Intelligence project. In SETI@home, signals received by several radio telescopes are analysed by otherwise-idle computers for signs of a message from aliens. Distributed computing has since been applied to many other areas, including protein folding, cracking encryption codes and climate prediction.
Calling all brains

But there are limits to what even a million computers can do. "Despite computers being very quick and accurate at certain problems, for many tasks they are still far surpassed by the human brain, such as in visual processing, spatial reasoning or problem solving," says Aaron Sloman, who studies artificial intelligence at the University of Birmingham, UK. So now the idea of distributed computing is being turned on its head. Instead of harnessing idle machines, researchers are inventing ways of using the processing power inside the brains of "idle" computer owners.

There seems to be no shortage of this intellectual power going begging. Clay Shirky at New York University has calculated that every weekend in the US alone, 100 million person hours are spent watching TV adverts - the same amount of time it took to create and edit the 2.5 million encyclopedia entries on Wikipedia. If only a fraction of this spare brainpower could instead be channelled into simple online tasks that help science, the contribution would be enormous.

One of the earliest attempts to elicit help from people online was NASA's Clickworkers website. The project, launched in 2000, asked volunteers to mark the position and size of craters in photographs of the Martian surface snapped by the Viking probes in the 1970s. More recently, volunteers have been classifying different landforms in the ultra-high-resolution images beamed back by the Mars Reconnaissance Orbiter. NASA is also hoping to bring this workforce to bear on images returned by the Dawn spacecraft when it explores Vesta and Ceres, the two most massive objects in the asteroid belt between Mars and Jupiter.

There is a significant problem with the Clickworkers approach, however - it is a solitary experience that simply isn't much fun. It is hard to see what motivates the home volunteers, beyond a rewarding sense of contributing to an important cause. This highlights a problem key to all efforts at human processing: how do you keep the volunteering brains interested long enough to keep them coming back?

Luis von Ahn, a computer scientist at Carnegie Mellon University in Pittsburgh, Pennsylvania, says he has the answer. Since 2002, he has been pushing the use of volunteers, or "human computers", far beyond the early efforts of Clickworkers. His secret is to transform complex problems into simple, addictive games.

His first game, called ESP, was designed to create a list of words people would associate with each image in a database in order to help train artificial intelligence systems. To do this, the game pairs up anonymous players and presents them with identical photographs. The players must try to guess the word their partner would use to describe the object pictured in the fastest time, gaining points for doing so. Once agreement is reached, a new image is displayed and the pair continue racing the clock for maximum points.

The game is now available on the "Games with a Purpose" website (www.gwap.com), which has so far attracted 120,000 members and had some significant successes. ESP, for example, has labelled more than 50 million photos, and last year was licensed by Google to help improve its image search engine. "People love playing this game, and report feeling a strong bond with the faceless stranger they collaborate with," von Ahn says.
“People love playing this game,and feel a strong bond with thestranger they collaborate with”

His latest scheme is the reCAPTCHA project. CAPTCHAs are computer-generated images in which a word is distorted and presented against a distracting background to make recognition impossible for a computer system, but simple for a person. These are now used on sites such as Facebook and Twitter to confirm a new user is indeed human, and so prevent hackers from using software bots to set up hundreds of accounts automatically, to use for generating spam emails or for other nefarious purposes.

ReCAPTCHA exploits people's ability to identify distorted images. It uses text from an old manuscript that needs to be converted into digital form, but which optical character-recognition software has failed to classify. The unknown word is presented to the user in addition to a known word, which acts as the real test of humanness. By correctly deciphering the text of both words, users confirm themselves to be human and are allowed to sign up to the online account, while at the same time helping to digitise and preserve an ageing text (see diagram).

The system has already helped to transcribe more than a billion words, and is now being used to digitise the 130-year back catalogue of The New York Times. In the future, von Ahn hopes to use a similar trick to create transcripts of historical audio recordings.

Using people to process images is not a foolproof method, however. There have been some unexpected consequences, as the scientists who run Galaxy Zoo discovered. This project, launched in 2007, has involved 160,000 volunteers helping to identify about a million galaxies in images collected by the Sloan Digital Sky Survey. Volunteers are asked to classify the structure of galaxies as either spiral or elliptical, and to record the rotation direction of the spiral galaxies. No expertise is needed, so newcomers can immediately begin contributing to the project.

One of the things Galaxy Zoo researchers wanted to know was whether there is any bias in the direction of spin in spiral galaxies. A previous study had found that the odds of a galaxy rotating clockwise or anticlockwise depended on where you looked in the sky, suggesting an unexpected organisation in the universe at large scales. However, the massive data set produced by Galaxy Zoo's volunteers confirmed that there is no such bias in the observable universe.

Galaxy Zoo did detect a curious bias in the way that different people were classifying the same galaxies, though. For some reason, people turn out to be more likely to classify a spiral galaxy as spinning anticlockwise than clockwise, although the researchers believe that this did not taint the results overall; the effect is subtle and only became apparent because the number of volunteers contributing to Galaxy Zoo was so large.

Nevertheless, it highlights an interesting concern with human processing - how can you be sure unconscious preferences or quirks of human psychology are not colouring your results? The source of the bias in Galaxy Zoo is unclear. "Personally, I suspect it might simply be because 'anticlockwise' is the middle button," says Kate Land who conducted the study into Galaxy Zoo's results.

Galaxy Zoo has produced another surprising result. Last year, Dutch school teacher Hanny van Arkel spotted a bizarre astronomical entity in one image. The object looks likes a wisp of bright green smoke, contains no stars and is unlike any celestial phenomenon ever seen. If it hadn't been for van Arkel's keen eye, it is unlikely this new object would have been detected. "The human brain is incredibly good at identifying the unusual, something that is difficult to program into the search parameters of an automated visual cataloguing system," says Chris Lintott, an astrophysicist at University of Oxford and one of the Galaxy Zoo team leaders. In recognition of van Arkel's shrewd observation, it has been named Hanny's Voorwerp (Dutch for "object").

While Galaxy Zoo relies largely on astronomy enthusiasts, and von Ahn's reCAPTCHAs are used at points where the web user has no choice but to solve the puzzle, a new generation of projects hopes to entice the general public to donate their spare time purely for fun. Foldit is at the forefront of these efforts.

Foldit grew out of a distributed computing project called Rosetta@home, also run by Baker. In a similar way to the SETI@home project, Rosetta@home uses spare computer time on PCs around the world to search through all the possible configurations to find the most compact form a protein can fold into. Using the results from the project, Baker's research team has published a string of papers over the past year in Nature and Science on protein-structure prediction and design. Baker and his team found, however, that the raw results from Rosetta@home had to be tweaked by hand to be scientifically useful. He now wants to watch how Foldit users play to improve the computer programs behind Rosetta@home.

When it comes to complex problems like protein folding, though, not everyone is convinced human processing is going to deliver the goods. Vijay Pande, the lead researcher on another distributed computing project to simulate protein folding called Folding@home at Stanford University, is concerned that volunteers will produce results that are far poorer than those that can be calculated computationally. "Folding a protein is like learning to play chess well, but with far more pieces and much more complicated rules, and so an even greater combinatorial explosion in the number of possibilities that must be considered," he says. He doesn't believe people will be that good at taking advantage of all the degrees of freedom. While Pande accepts that Foldit is a great way to demonstrate the complexity of proteins to non-scientists, he says he would be very surprised if their results are as good as those produced by computers.

Unsurprisingly, Baker disagrees. The vast number of different ways proteins can fold is precisely what flummoxes computers, he says. Players like Aristides demonstrate how skilful humans can be in spotting how to tweak a protein to optimise the folding. Within just a few months of taking up the game, Aristides has already emerged as one of the top 10 players out of the 60,000 worldwide, and has been invited onto the top-ranked team in Foldit. He has shown such an intuitive grasp of the subtle mechanics of the problem that he has been described by one of the Foldit researchers as a "Foldit savant", and has recently been flown to Seattle to tell them exactly how he solves the protein puzzles.

The accuracy of the different human and computational approaches will be revealed later this year, when the results of a competition called the Critical Assessment of Techniques for Protein Structure Prediction (CASP) are announced. The competition compares experimentally-determined protein structures with predicted configurations of proteins submitted by different teams using either computers or people. Initial analysis of results from Foldit are very promising. "We've already seen solutions from these volunteers that are very competitive to massive computational efforts, and at times even outperform them," says Zoran Popovi´c at the University of Washington, a principal investigator on Foldit. "I expect people to do much better once we refine the tools to better fit the gameplay and human puzzle-solving process."

Starting this month, Foldit will be expanded with a new game that essentially challenges players to design new proteins from scratch. Players will be able to change side chains, effectively creating synthetic proteins, and the best ones will be synthesised and tested, Popovi´c says. And in December, puzzles for growing and moulding synthetic proteins that bind specifically to a virus will go live. This could ultimately help produce new drugs and vaccines. "It is here that I think people will really have an advantage over computers," says Baker.

Just as the number of distributed computing applications grew with the popularity of SETI@home, so it is likely that other areas of science will follow the example set by Foldit. Shirky goes even further: "In the future there will be so many human processing initiatives that we'll all feel fierce competition for our idle brain cycles," he says. Whoever said technology was supposed to give us more leisure time could not have been more wrong.

FYI.

Joined: 11/07/2008
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Guess how I learned of this game? ^^

Good press indeed ^^. A little background for ppl unfamiliar with popular scientific magazines: scientists are always enthusiasts, so their articles will always be inclined to be a bit more positive about things than they are*. They won't call bad or doubtful results good, as a rule, but they will call good results very good**.

That said, appearing in the NS is in itself no mean feat, so a big congratulations to David Baker and his team for setting up a project that can stand up to a peer review and getting it published ^^

*Of course there's also the fact that people who aren't into the whole science thing won't go excited at "we might be on to something" the way scientists do, while science could definitely do with some more attention(masses choose politicians, politicians set max funding per year).

** And in a way they are, the chances of getting something right first time you try are a lot smaller in science than in everyday life.

Ps. Of course, any or all of this could be wrong, I'm only a layman who regulary reads the NS, so please correct me if I understood something fundamentally wrong.

Joined: 11/08/2008
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That was how I found out

That was how I found out about this ^^ Don't you just love new scientist

Joined: 11/06/2008
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Me Too

I joined two days ago from new scientist. I really like it but I can't understand the controls. I'm 11

amyL's picture
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New SCientist is the

New SCientist is the shizzzzz!

Joined: 11/12/2008
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HELL YEAH

new scientist ocks. btw both cheese's parents play this game 2 and they r highly ranked. :P

Joined: 11/12/2008
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rocks" (doh)

my bad

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found out same way

I also joined after seeing the article in New Scientist

Joined: 11/19/2008
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^^

Same. I love the New Scientist.

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Found it a different way

I was looking on lifehacker when i found it. Sounded interesting so i gave it a shot, and i loved it! :D

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yay

Glad you all were intrigued enough to give it a try. :) Hope you enjoy your time in the game!

There also should be some more improvements and significant changes coming in the next few months, so be sure to check back again even if you didn't like it enough now. I'm sorry the controls were confusing hellobella - that's something that I noticed too and it's on my list of things to change. :)

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foldit galaxy zoo

How can i play foldit galaxy zoo

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons