Gamers Piece Together Retrovirus Enzyme Structure 149
An anonymous reader writes "Gamers have solved the structure of a retrovirus enzyme whose configuration had stumped scientists for more than a decade. The gamers achieved their discovery by playing Foldit, an online game that allows players to collaborate and compete in predicting the structure of protein molecules. After scientists repeatedly failed to piece together the structure of a protein-cutting enzyme from an AIDS-like virus, they called in the Foldit players. The scientists challenged the gamers to produce an accurate model of the enzyme. They did it in only three weeks."
Avoid SGC (Score:1, Offtopic)
If Stargate Command comes to your door recruiting, best bet is to politely turn them down.
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That didn't work so well for Eli Wallas [wikipedia.org], did it?
Comment removed (Score:4, Insightful)
Re:Avoid SGC (Score:4, Interesting)
You've obviously never heard about Wikipedia's Poke'mon problem. At one stage, there was more about Poke'mon (as in, a ludicrously large amount more) on Wikipedia than there was about World War II.
Hence the creation of Bulbapedia. The Poke'mon Problem probably still holds though.
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Alt-0233, at least on a standard US Windows installation, yields "é". ...Yeeeah, I actually know that offhand.
Just a hunch, but I'm willing to bet there's a lot more people technologically-capable people interested in Pokémon than WWII though.
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I prefer Alt-130, myself. :)
Re:Avoid SGC (Score:4, Insightful)
Re:Avoid SGC (Score:5, Insightful)
Which isn't really a problem, in my opinion.
Wikipedia isn't limited by space and volunteer driven. If somebody currently wants to write about Pokemon, then they will try to write about Pokemon. If you insist on interferring with that attempt, then you're likely to seriously cause a bad impression to somebody who's trying to make a honest, if not very important contribution.
As a result, they get fed up and leave, maybe for Bulbapedia, instead of sticking around, and maybe writing on something a bit more important next time. After all, Wikipedia isn't a job, and you can't command people like that there.
The mentality of that some not very important articles are too long is IMO a big problem. Because there has to be something silly and harmless to get a new contributor started. Pokemon is probably one of the best first starting subjects, because it's easy to contribute on it: there's lots of info that can be contributed, and it's well documented outside on WP.
In comparison starting from trying to contribute on the page of Pasteur will be like walking into a battlefield. You'll quickly need to start discussing medical literature, and that's not really easy for most people. Somebody with a real interest might get into that, but most likely only after getting practice on something else, just like coders don't get started by contributing to the Linux kernel.
IMO that's why Wikipedia is losing contributors. If you actively reject attempts to contribute in the easiest places, then smack people in the face with huge amounts of WP: regulation in other places, then very few people are going to be willing to stick around.
Re:Avoid SGC (Score:4, Insightful)
Oh well, clearly they are doing just fine without me - won't even miss it if they disappeared tommorow. Seriously.
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You're misguided then. If your edits were reverted by a bot that's not because someone decided that the topic was not worth to appear at Wikipedia, it was because they were of such low quality that a Bayesian network decided that they looked like spam or random vandalism.
WP bots don't revert based on the subject; they look for misspellings, short incoherent babbling, unexplainded short edits and deletion of whole paragraphs. If your edits did belong to one of those classes, any human reviewer would have del
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I gave up on wikipedia, there is no way to make it into a truly useful tool.
Here is history of a comment I was making as an example, [wikipedia.org] this is more of a public announcement about a pump and dump scheme that is in process. SEC is notified, they are doing absolutely nothing about it, they don't care.
You think SEC cares about retail investors who are being destroyed by pump and dumps schemes? You think SEC cared about Madoff?
But you can't leave a comment on wikipedia, where it could REALLY be useful to people, w
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Attention: SEC is ignoring all signs of Jonathan Lebed pumping and dumping Agria Corp (GRO) and Mega Precious Metals (MGP:CN) stock, which has been going on since May of 2011 and is still continuing in September of 2011 through his current company 'NIA' (National Inflation Association), even though SEC was given this information. The pump and dump is in progress and has been for a number of months right now. NIA touts penny stock Mega Precious Metals based solely on its "inferred" 1.2 million ounces of gold. (See external links).
you need to use your own blog, or something like dailykos.
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In addition to your points, it also raises the issue of what is "important." Pokemon for better or worse is a big part of our culture, as are celebrities, The Simpsons, and Seinfeld. Wikipedia's job shouldn't be to rewrite what we think we should be.... it should be to document what we are. And there shouldn't be a limit to the amount of information, only that information is as factual as we can get it. But that's just my opinion.
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It was only a couple of years ago that the anime fans lost their last stand, and the "crucifixion in anime" section was removed from the "crucifixion" article. I did a whole long post detailing the event but I can't find it now :-(
(actually searching back in my emails, I found myself saying I can't find it again, around March this year. D'oh! )
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If I want detailed information on WWII there are books and real encyclopedias that have it covered.
If I want detailed information on "popular culture" items, I used to look to wikipedia, specifically because there was a page for every pokemon and other obscure things.
Up until The Great Webcomic Purge I though WP was a cool project, now it's just a faster information source than google.
Bart Simpson has a bigger page (Score:2)
so eat my shorts!
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Once you've put 40 meaningful words into my wikipedia entry, I'll tell you all you want to know about the worth of a wikipedia article.
Re:Avoid SGC (Score:5, Insightful)
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So? In more important news, most celebrities (including many that are famous for being stupid, mean, drug addicts etc.) are better paid and better known than most (all?) prominent scientists. Not to mention other worthwhile people.
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Seems like you're proving WP's point.
Re:Avoid SGC (Score:4, Insightful)
Because
1- the lives of real people, including scientists, are private, whereas that of a fictional character are all open to anybody to summarize, analyze and discuss
2- the achievements of real people are sometimes controversial. Who could say with certainty that Cooley and Tukey invented the FFT, while it was used by Gauss in his astronomy work to speed up his calculation, but thought it unimportant enough to report compared to his number theory work? That itself may be controversial. Science is littered with misappropriated credit. For instance George Dantzig did not invent the first solution the the LP problem. Fourier knew about it ; people in the Soviet Union were using it before WWII. Hence writing about real people, particularly scientists, is hard.
3- There are far far far fewer people interested in the life of non-glamorous people than even minor fictional characters.
4- Who cares? People write about what they want in wikipedia. Someone writing on stargate does not prevent someone else writing on Paul Dirac.
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2- the achievements of real people are sometimes controversial. Who could say with certainty that Cooley and Tukey invented the FFT, while it was used by Gauss in his astronomy work to speed up his calculation, but thought it unimportant enough to report compared to his number theory work? That itself may be controversial. Science is littered with misappropriated credit. For instance George Dantzig did not invent the first solution the the LP problem. Fourier knew about it ; people in the Soviet Union were using it before WWII. Hence writing about real people, particularly scientists, is hard.
This also applies to fictional people. Did Han shoot Greedo in cold blood or was it self defense? ;)
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Everything about the TV character is public knowledge.
Actual scientists, not so much. In fact, if someone posted a bio containing that kind of detail about, say, me, on Wikipedia, and I hadn't published it in an autobiography or something, I'd be downright creeped the fuck out.
Thanks a lot (Score:2)
Well, I guess I can throw away the DVDs of Stargate Universe I was saving up for Christmas vacation.
Next time, how 'bout a little spoiler alert, yeah?
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The first blurb on the wikipedia article spoils about the first 20 minutes of the pilot. That is all.....
Hardly a spoiler for a 2-season show :p
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Just re-watch SG1... don't torment yourself with SGU.
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. The only way to beat the buggers was to have a kid think he was playing a game. I thought it was pretty obvious conclusion, and wasn't the least bit surprised by the ending. Anyway, I think that this just signifies that we aren't anywhere close to AI yet, and that we don't even understand how smart we really are, compared to machines.
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Really has to do with what you mean by AI. If you mean general reasoning machine, no we're not anywhere close.
If you are talking about solving certain domains of knowledge, AI is around us every day and doing very well! Jeopardy playing, chess solving, spam classifying, robot vacuuming, voice recognition, etc., are all some of the more visible expressions of AI.
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Like I said, it completely depends on what your expectation of AI is.
I also think you're completely wrong in your characterizations of some of these technologies. If, for example, Roombas and the Roomba AI are just a "highschool science project" it just goes to show how far along robotics has come and what we take for granted in terms of autonomous capabilities. Voice recognition is hugely improved and a common features on cars and cell phones. Plenty of people fail at basic things like what country is XYZ
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If Stargate Command comes to your door recruiting, best bet is to politely turn them down.
(This comment is in regards to the first episode of Stargate Universe, in the event that you're curious.)
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Showing my age, but The Last Starfighter [imdb.com] also came to mind. Can anyone think of an earlier instance of video game talent scouting in sci-fi?
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Re:if Centauri comes recruiting... (Score:2)
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If Stargate Command comes to your door recruiting, best bet is to politely turn them down.
Might be a better idea to accept with the proviso that you're allowed to pack several changes of clothes.
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But the gamers won't get any of the royalties (Score:2, Interesting)
I'm sure that, despite figuring out the protein structure, that the gamers won't receive any of the patent royalties that the patent will likely generate.
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Yep. Unfortunately for the researchers, I've already patented the business model of
1) Create mapping of task to game
2) Get suckers to play game
3) Map winning game solutions to task solutions
4) Profit
This is distinguished from "Ender's Game" by the presence of Step 3. It is distinguished from the standard slashdot business plan by the lack of "???".
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I'm sure that, despite figuring out the protein structure, that the gamers won't receive any of the patent royalties that the patent will likely generate.
You do realize that the structure on its own doesn't generate royalties, right? Knowing the structure is just one step towards developing new treatments. The gamers didn't do the simulations for ligand binding and enzymatic activity; they just did the work for the static structure.
What you're calling for is like saying we should name planets after the first people who looked at them, because they knew they were there even though they didn't know anything else about them.
Crappy analogy (Score:2)
What you're calling for is like saying we should name planets after the first people who looked at them, because they knew they were there even though they didn't know anything else about them.
I take that back, that was a crappy analogy. After all, in this situation all the gamers did was offer up CPU time towards solving the protein folding problem for this specific enzyme. They didn't even look at anything, really. They didn't even necessarily have any idea what they were actually doing with their spare CPU cycles in the grand scheme of things.
Really, the notion that they should be compensated for what they voluntarily donated is worse than suggesting that any Nobel Prize for which an acc
Re:Crappy analogy (Score:5, Informative)
Your understanding of it is rather mistaken, please download the game and try it for yourself.
FoldIt is not a distributed number crunching @Home variant where a screensaver uses your CPU cycles to help with a massive parallel calculation because the upstream researchers can't afford a personal super computer.
FoldIt is an interactive 3D puzzle game (like what Bill the Cat's version of a Rubic's Cube would be like) where many human brains attack a problem, not their computers. The scientists already have super computers but they aren't much help in this class of problem, where human reasoning really shines.
According to TFA, the gamers are named as co-authors on the write-up in a highly prestigious journal, which is very nice kudos indeed.
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According to TFA, the gamers are named as co-authors on the write-up in a highly prestigious journal, which is very nice kudos indeed.
Yes, I suspect F@H players are like OSS contributors at heart, they enjoy a puzzle and just want a bit of recognition when they're the first to solve it.
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When was the last time you read a patent for a chemical or biological agent? The substance itself is just a valid a claim under the patent as the process that created it. US Classification 200/157.68 (definition) [uspto.gov] is one of the classes the resulting patent could land in if the process involves microwave energy.
If the person(s) who solved this challenge realize this, a landmark legal battle over crowd-sourcing for patent-eligible materials could be on the verge of happening.
Conventional wisdom is also called
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Not necessarily. It's more or less inevitable. The more education one has, the more difficulty one typically has in seeing solutions that don't come from that view of the world.
Somebody that's studied statistics and probability theory is probably not going to do very well playing poker for long periods of time because the knowledge from those areas tell that person that the odds don't change over time. The problem is that ultimately they do, the human component of the game does get tired, does make mistakes
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However, if the players are figuring out how to use the results, that would be incredibly embarrassing.
The players would have to be molecular biochemists (or similar) to figure out how to use the resulting structure, and the researchers have already started figuring out how to use it. They may identify a site on the surface for which they can create a compound that will attach and block the enzyme.
This is all very difficult, and that would be an astounding achievement, but there is nothing embarrassing abou
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The problem was solved within the context of a university driven research project (Foldit) which was geared towards finding out if humans could be more efficient then computer algorithms in finding protein folding solutions. Gamification in action but this isn't breaking any research paradigms.
This just goes to confirm what that project already discovered though: that humans are still somewhat better at this type of problem solving then computers, with the postulated reason being that we're much more resist
OT (Score:1)
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The problem was solved within the context of a university driven research project (Foldit) which was geared towards finding out if humans could be more efficient then computer algorithms in finding protein folding solutions. Gamification in action but this isn't breaking any research paradigms.
Correct. Also, the reason why researchers didn't figure out the structure entirely on their own is not because they're dumb or closed-minded, but because manually fiddling with protein structures like this is very ti
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If I was one of those gamers and I got patent royalties I'd feel awful about myself.
Solving this problem was a one-time effort. Would I accept a nice one-time reward for it? Yes. Would I want sick people around the world to have to pay me a little money every time they use the drug? No.
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I don't even understand patent law in the first place. Between patent laws and corporations that patent shit someone else worked on I think the whole system has gone off the rails. You shouldn't even be able to patent things that already exist in nature. You didn't invent it, you just figured out how it worked. In this case, the company that got the patent didn't even do the figuring out.
I believe in projects like foldit - the more people working on a problem, the better chances we have of solving it, b
Excellent use of crowd-sourcing (Score:5, Insightful)
There is no substitute for human ingenuity, which is captured by crowd sourcing. Kudos to whoever managed to make folding protein structures entertaining enough to capture the interest of enough people to make it feasible. :)
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Perhaps this approach would bring about the next few waves of major advancements in other fields , such as videogames...
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That would recursively loop until it collapsed society. We better not do that.
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They have this already, it's called "being a human being in real life."
The only problem is all these fucking noobs and griefers. Kicking them from the game is a bannable offense, for some reason.
Re:Excellent use of crowd-sourcing (Score:4, Interesting)
Several items to note on this:
- kudos to researchers for bringing in gamers to gain some understanding on solving tghis problem
- kudos to the FoldIt programmers for making this 3D structure puzzle a solvable problem. They also constantly refined the puzzle based on feedback from the gamers.
- Not mentioned so far is the incredible importance of finding a workable structure to the retroviral protease enzyme, and that the researchers noted the structure may provide the opportunity to be blocked. If so that would appear to this layman of a nearly universal cure for viruses that insert DNA into chromosomes. I may be overstating that but I don't think it's limited to AIDS.
- There are many other puzzles to be solved for cellular components from what I read. This is clearly one of utmost importance, but I imagine there are others to solve now.
- This reminds me from what I read of the widespread efforts of laymen participation in solving important mathematical puzzles in the 1500's to 1800's.
- I don't know about this having a real useful impact to primary education, other than wow interest factor, but seems to be something that could be ongoing challenges, real "games" to solve if you will, for some time to come. There are innumerable puzzles to be solved at this level.
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I wonder why the article said they were looking at the retroviral protease structure to see if they could find a way to block it? That was purported to be the importance of solving this structural problem. That and understanding how it works.
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Thanks. I'll take another look at that.
Adding to the Wow factor (Score:3)
According to Popovic, “Foldit shows that a game can turn novices into domain experts capable of producing first-class scientific discoveries. We are currently applying the same approach to change the way math and science are taught in school.”
On the "just kidding" track: if that could happen, I wonder how the exams will look like? Will they resemble a FPS [wikipedia.org]?
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I'd say the first step would be a more realistic gravity pull in Tank Command.
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I thought we were trying to eliminate the FPS aspect of schooling and make it more of a RPG or possibly puzzle game.
Pocoyo (Score:2)
make it more of a RPG or possibly puzzle game.
Oh, so that's why Pocoyo is playing with tetrominoes at the start of each episode: Tetris is his preschool homework.
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Yeah; there are too many complaints of students camping at a drop point. Work is in place to help them increase their INT and DEX, and to complete class projects as parties with varied strengths. Of course, there's a large debate about how to increase WIS and how Mana should be used.
Personally, I remember school being a puzzle game... attempting to put all the pieces in the right place before the time ran out.
Apply This Methodology Elsewhere (Score:3)
RTS Crowdsourcing - Solve the whole 'nationalism and dick waving' contest one civ game at a time!
Racing Games Crowdsourcing - Design better robot drivers and automate all vehicles, lower traffic fatalities!
Angry Birds Crowdsourcing - Design better projectile systems for the military!
Farmville Crowdsourcing - Make the people that partake in this one play until they die from starvation, eliminating half the 1st world population and donating their wealth to people who are actually starving!!!! (Reverse logic on this one)
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Farmville Crowdsourcing - Make the people that partake in this one play until they die from starvation, eliminating half the 1st world population and donating their wealth to people who are actually starving!!!! (Reverse logic on this one)
WIN!!! - That Reverse logic pure genius. Almost as good as the foldit game
Have they fixed the awful music yet? (Score:4, Interesting)
Re:Have they fixed the awful music yet? (Score:4, Informative)
They have. There's a general options button and within that you can turn off the music and/or sound effects
When they fix something they should tell people (Score:2)
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Quit your whining. They have X number of people, and I'd rather they develop software for protein folding than email back individual people who complained about things probably already on a to-do list. For most software projects I'd consider my response a little harsh, but you're advocating an approach where resources used to CURE AIDS are being diverted to "not offending trovingslosh". The least you can do is forgive them, discard your own pettiness, and re-harness your natural ability to spend your gaming
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Wow. Just stop and listen to yourself. You are a hypocritical asshole.
Re:When they fix something they should tell people (Score:4, Insightful)
Wow, "quit your whining". You think they should treat their users any way they please because they are trying to cure Aids. I'm surprised that you didn't throw in a "think of the children" line too
My point isn't about "not offending trovingslosh", but rather about developers who set up feedback systems but can't be bothered to even give a courtesy response when sincere suggestions, even pleas, are made. If I had received even a simple "yea, we will add a choice to disable the "music" when we can get to it, I would have tried to wait it out, or at least checked occasionally to see if they got around to making the fix and I could go back to folding without the torture. I should mention that I did stick it out for over a month, maybe three, with less use and eventually just checking in to see if things were fixed, before I decided that what should have been a very simple UI change wasn't likely to happen. There were many other changes and updates in that time. So you see it as a waste of their time to bother to respond to the feedback system that they created. I see it as a waste of volunteer manpower to ignore the feedback that they solicited, and arrogance on the part of the developers to think that everyone should have to listen to the developer's own choice of "music" when freely giving their time to a scientific application that really had no good reason to insist on playing music in the first place. I doubt very much if I'm the only one that was offended and driven away, both by the sound and by the apathy of the developers for the input of the volunteer users contributing their time.
Thanks, you've helped me make up my mind. I wasn't thrilled about restarting and trying to work up in rank past a quarter million users, but I realize now that it isn't just that, it's having volunteered my time and work for a group that didn't have the common courtesy to respond to very valid feedback. I feel good now about deciding not to go back.
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And this is why courting gamers to do good for humanity is always going to be a flaky prospect.
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It sounds like you mix up 'not treating you' with 'treating you any way they please'.
By that I mean that what you see as 'poor treatment' could as well be seen as 'no capacity to respond'.
I was going to write something here on how 'real' game companies treat forums and tasks spawned from forums, but really. There is no point.
If a "quit your whining"-post was enough to prevent you from rejoining FoldIt, then I don't believe it was really ever an option. Maybe you were in it because of the social hooks and th
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I was also shocked by the 'Stop your whining' line you have been served with your previous comment. Your are making a valid point underlining the importance of users' feedback.
However, I feel that in your response, you get carried over perhaps more by your taking offense of the above line than by the behavior of the Fold-it team. I even read a pinch of regret in your choice of words. What you want to condemn after all is not the idea that brought about a brilliant scientific accomplishment, but the negligen
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If you're using windows, you can open up the volume mixer, and adjust the sound for every individual application there.
Mute the program from that menu, and you're golden.
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Yea, if it worked. i own Vista for the computer in question, which was marked as Vista ready when I bought it. I upgraded the memory from 1 gig to 4, put in a hard disk nearly 3x larger, but when I went to install Vista, Vista itself complained it wasn't a good idea. I tried anyway but it was right, so the computer is still on XP. And I'll be damned if I'm going to buy the fix for Vista for the same hardware that I already own a copy of Vista for So no 7 (or in the future 8) for this computer. It is on XP a
Good Work (Score:1)
Kudos to the gamers.
Pokemon enzyme (Score:1)
a good game for parents and their children (Score:1)
because it's a good bonding experience.
This is great news (Score:1)
When I first heard of Foldit I really hoped that something would come of it. I thought that if their models were correct that it could be a great tool, and it looks like it is.
old hat (Score:1)
Never underestimate the determination of gamers! (Score:1)
Harness the power of obsessive gamers around the world! Seriously, Starcraft 2 alone is already almost a national sport in some Asian countries.
Now the programmers have to take Foldit to the next level: Cancer Wars! Whomever creates the best omni-purpose cancer fighter that doesn't blow apart the landscape(human body) wins!
And after that? Virus Cataclysm -- the viruses are invading and YOU are your body's last hope!
Maybe even: Reconstructors -- the body is failing and it's up to the player to restore it as
There was a US economy/world simulator (Score:2)
There was a US economy/world simulator.
I forgot the name though.
The easiest way to make progress in the game was to forgo any military for 4 years or so, and invest the money in the economy. After that you could literally bribe Cuba and whatever small nation you wanted to make them like you.
Such an on and off control is unlikely to happen in real life.
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How do our brains do this? (Score:1)
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The human brain is absurdly faster/more powerful than even the largest computers today. Admittedly, we are getting closer to the point where the two will meet, but it is still decades away by most estimates.
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From Wikipedia: "Foldit is an experimental video game about protein folding, developed as a collaboration between the University of Washington's departments of Computer Science and Engineering and Biochemistry (many of the same people who created Rosetta@home)."
Most likely, there will be a scientific paper containing the results, and as far as I know, scientific research papers are public (or maybe require a fee to read). Now drug companies can use these results to try to come up with a drug to fight HIV, w
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Most likely, there will be a scientific paper containing the results, and as far as I know, scientific research papers are public (or maybe require a fee to read).
Yes, they require a fee to read - in this case, $32 - and yes, scientists are just as unhappy about this as everyone else, but we have no other way to prove our worth to prospective employers, funding agencies, and tenure committees other than prominent publications. However, the actual structure (including experimental data) is deposited in a pu
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Actually, I forgot to mention that since this research is almost certainly NIH-funded, the article is required to be made public in the near future by depositing the manuscript in PubMed Central [nih.gov]. I forget whether the requirement is six months or a year after publication - until then, it remains exclusive to Nature Publishing Group - but eventually it will be freely available.
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I forget whether the requirement is six months or a year after publication - until then, it remains exclusive to Nature Publishing Group - but eventually it will be freely available.
Sounds like a mini-copyright is present in scientific publications.