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Biotech Medicine Science

Foldit Player May Have Created a Useful Protein 144

Posted by kdawson
from the know-when-to-hold-'em dept.
An anonymous reader writes "The organizers of the game Foldit, where you fold proteins for scientific research, announced that a user has found a protein that may be able to bind influenza viruses. Researchers plan to test the protein in a lab over the next few weeks to see if it might be medically useful."
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Foldit Player May Have Created a Useful Protein

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  • by MartinSchou (1360093) on Wednesday May 19, 2010 @12:47AM (#32261106)

    And who gets the patent(s), money etc. for this particular protein?

    • by Anonymous Coward on Wednesday May 19, 2010 @12:49AM (#32261120)

      Hint: Not the player.

    • by dward90 (1813520)
      If anyone from Foldit ever even met a lawyer, or uses money to pay for food, then you sign away any rights to any IP you *might* create while playing.
    • by glwtta (532858) on Wednesday May 19, 2010 @01:04AM (#32261188) Homepage
      And who gets the patent(s), money etc. for this particular protein?

      I guess it's whoever spends the hundreds of millions of dollars to follow up on the infinitesimal chance that this will lead to something useful?
      • Re: (Score:3, Interesting)

        by poetmatt (793785)

        research isn't that expensive.

        When are people going to realize that pharmaceutical and medical research isn't that expensive?

        it's infinitely more complicated than most things, but we wouldn't have the industries we have today if they were magically prohibitively expensive.

        • by RyuuzakiTetsuya (195424) <taiki&cox,net> on Wednesday May 19, 2010 @01:12AM (#32261234)

          it's not expensive to run one trial.

          it's expensive to run lots of trials. Spread that cost to the CDC, NIH, the WHO, various teaching hospitals, universities, pharmacos, foreign medical systems... and yes, research gets cheap per study.

          • by Kitkoan (1719118) on Wednesday May 19, 2010 @01:33AM (#32261314)

            it's not expensive to run one trial.

            it's expensive to run lots of trials. Spread that cost to the CDC, NIH, the WHO, various teaching hospitals, universities, pharmacos, foreign medical systems... and yes, research gets cheap per study.

            Problem is, the companies spend even more money on ads then medical R&D. [sciencedaily.com]

            • Re: (Score:3, Interesting)

              by tehcyder (746570)

              Problem is, the companies spend even more money on ads then medical R&D.

              That is the reality of capitalism, so depending on your point of view it's either a necessary evil, or another reason to have some sort of socialist planned economy (at least in some areas).

              • by tthomas48 (180798) on Wednesday May 19, 2010 @11:19AM (#32265570) Homepage

                Huh, oddly enough I seem to remember that when drug companies were banned from advertising on TV their drugs still sold. So it's not really a necessary evil. Drug companies used to be hugely profitable and didn't have as large marketing budgets.

                • by sjames (1099)

                  Interestingly, when cigarette ads were banned from television, it had the perverse effect of increasing the profitability of tobacco companies. It's a sort of tragedy of the commons. Given a product that people already know exists if nobody advertises they all save money and they all get their share of the market for that class of product. If even one advertises, they must all either concede the market to that one or all advertise. If they all advertise, their market shares will remain about the same but no

          • by glwtta (532858) on Wednesday May 19, 2010 @01:52AM (#32261432) Homepage
            Spread that cost to the CDC, NIH, the WHO, various teaching hospitals, universities, pharmacos, foreign medical systems... and yes, research gets cheap per study.

            The CDC and WHO don't fund any significant amount of research (and even if they did, the CDC budget is only something like $8 billion, WHO is under a billion), the NIH is supposed to primarily support basic research, not development (not to mention funding those universities you mentioned).

            Look, it's a fairly complex industry, fixing it isn't quite as simple as "let's everyone pitch in now!".
            • in so far as I understand it, research is largely decentralized to avoid things like bias and conflicts of interest.

              • Re: (Score:3, Informative)

                by Trepidity (597)

                Partly yes, but partly for the opposite reason as well: lots of entities makes it possible to play shell games. There are a lot of biochem profs who have biotech companies on the side, and you might not be surprised that what often happens is that 90% of the research is done in academia on grant funding, and then the last 10% migrates to their startup, which patents the result.

          • by fishexe (168879)

            ...NIH, the WHO, various teaching hospitals...

            Does Pete Townshend know about this? To paraphrase his words, "hope I die before I get asked to fund research."

        • by Kirijini (214824)

          we wouldn't have the industries we have today if they were magically prohibitively expensive.

          Unless they were prohibitively expensive except for the profits gained from patents.

          The patent system as it exists now might be screwed up and inefficient. But that doesn't defeat the truth that a patent system can shape market behavior in a way that's beneficial to us in the long run.

          • by PitaBred (632671)

            You mean shape the market. We can't tell for sure that it's beneficial, but we can tell for sure that places with more lax "intellectual property" laws tend to have higher rates of innovation.

          • by poetmatt (793785)

            wait, so magically they couldn't do this research without patents?

            one might wonder how we did medical research in the 1900's or something! /facepalm

        • by glwtta (532858) on Wednesday May 19, 2010 @01:36AM (#32261336) Homepage
          Research isn't, research and development is. (research can be pretty expensive, too).

          And we do have exactly the industry that we do - that is, everybody chasing blockbusters, the glut of "me-too" drugs, the paltry number of drugs actually making it to market - because it is prohibitively expensive.

          The current model seems to be for giant pharma companies to more or less indiscriminately buy up small biotechs, hoping to randomly strike gold with one of them. This does not lead to a very efficient system: I think we are up to $100+ billion spent on research annually ($70B from industry, $30B from the NIH) for a grand total of 26 new drugs approved last year.

          So yeah, 'prohibitively' is exactly the right word.
          • by 7-Vodka (195504)
            Please now quote me the sum spent on advertising for the same year.

            Kthanks.

            • by AndersOSU (873247)

              It's possible for R&D to be phenomenally expensive, and yet be out stripped by advertising.

              You're not going to find anyone here defending pharma's ad budget, but that doesn't make research any less expensive.

              Lets say pharma reduced their ad budget by more than half and spent it on R&D (and we all know that the only thing you need to invent something is money...)

              That would add what, another dozen drugs, half of which would be viagra plus, and the other half would reduce cholesterol slightly, but not

              • by sjames (1099)

                Or they could just quit the ads and sell the drugs at a more affordable price.

            • by stdarg (456557)

              For the sake of argument, let's say the industry spent 10 times more on advertising than research. If we're taking gp's numbers as true, industry spent $70 billion on research, NIH spent $30 billion. Industry also spent $700 billion on advertising, per our argument assumption.

              Without that $700 billion being spent on advertising, the $70 billion wouldn't have been spent on research (you can't make money if you don't sell your product).

              That would also be $700 billion gone from the economy, which would have go

              • by jackbird (721605)
                You're falling for the false premise that marketing directly to consumers is a responsible way to market prescription drugs. In a perfect world, doctors would receive independently-produced information about the pros and cons of various new drugs, and then discuss possible courses of treatment with their patients. Even the old system of hiring recent grads to give doctors steak dinners, free pens, and the occasional blowjob is a lot cheaper than buying superbowl ads and puts an allegedly responsible party
                • by stdarg (456557)

                  I don't think it's a false premise though. It may be if you take your assumption of a perfect world, but I don't really. I don't see anything wrong with getting consumers to find out more about drugs and be the ones to bring them up with their doctors. In fact doctors were bitching for years that consumers are too shy.

                  • by jackbird (721605)
                    Sure, the "fill out this questionnaire and bring it to your doctor to talk" ads/websites are somewhat responsible. The cute girl and a puppy with a voiceover rattling off a litany of horrible side effects TV ads are not.
          • Re: (Score:3, Insightful)

            by jmv (93421)

            Try comparing R&D expenses to their marketing expenses. R&D doesn't look that expensive anymore.

            • by Rich0 (548339)

              I dunno. The point under debate was whether the cost of R&D justifies the award of patents.

              You seem to be suggesting that we can get rid of patents and then companies can fund R&D with their ad budgets.

              What would really happen is that companies would stop both advertising and R&D without the patents. They wouldn't be making much money selling drugs, so why would they spend much money on either?

              If anything you'd see an end to R&D long before an end to advertising without patents. How much

            • by geekoid (135745)

              Depends on the product.
              Something that sin't medical necessary, like Vaigra, gets a lot of advertising. Other medicines, less so. When was the last time you saw an add on TV for a specific Chemo drug?

              • by jmv (93421)

                You'll notice I said "marketing", not "advertising". Most of the budget is *not* spent on ads, it is spent on inviting doctors to luxurious places (all expenses paid) to teach them about their new drugs. That's why you don't hear too much about it.

            • by glwtta (532858)
              Try comparing R&D expenses to their marketing expenses. R&D doesn't look that expensive anymore.

              Most big pharma companies spend roughly twice as much on advertising as they do on R&D. What's your point though? Advertising is how they make the money that pays for the research, what exactly are you suggesting they should do differently?
        • Re: (Score:3, Interesting)

          by Arancaytar (966377)

          Someone in the industry told me that it consists of immense up-front investments before a new drug is approved, which may then pay of tenfold in the remaining years until the patent runs out - or turn out to be a complete loss, if the studies are inconclusive or the substance is not safe in humans.

          Supposedly it's like playing poker with the company deciding to invest hundreds of millions more or abandon the research they've done so far.

          (Which doesn't include the money the company loses on lawsuits if they *

          • Re: (Score:1, Redundant)

            by Jaysyn (203771)

            And yet they still manage to spend more on advertising than R&D.

            • by AndersOSU (873247)

              If your business plan consisted of making a series of long-shot bets, wouldn't you want people to know about the one that paid off?

              That may sound crass, but think of it this way. A company has 1000 novel active ingredients, 900 of which drop out after spending $10,000 on each, 50 more drop out after spending an additional $100,000 each. 30 more drop out after spending $1,000,000 each, 15 more after further investment of $5,000,000. Then you patent. Then you go to clinical trials. Then you take 5 years

              • by Rich0 (548339)

                Agreed. And if they didn't spend the money on marketing it isn't like they would spend it on R&D instead. Drug companies all have cash sitting around that they aren't spending on anything, or that they're returning to investors.

                There really isn't much innovation in the area of clinical trials, but there is a LOT of cost. That is why there are so few new drugs on the market, and why they are so expensive. It is also why so few serious clinical trials get done in the area of things like supplements, w

              • by sjames (1099)

                That's the problem, in the absence of a ban on advertising, each individual company's decision to advertise is rational, but it's a tragedy of the commons. They'd all be more profitable iff none of them advertised.

        • by ceoyoyo (59147)

          Depends on the research. If your medical research involves human subjects and imaging it's expensive. If it just involves human subjects it depends what you're doing to them.

          Note that we have lots of other industries that have a very high cost of entry, yet exist anyway. Communications satellites, for instance. Or microprocessor fabrication.

        • by geekoid (135745)

          It's not as expensive as the poster stated, but that does not make it cheap. It will cost about 30 million and if it is successful up to another 30 million in advertising.

          Of course, after they do the very first tests, it may turn out to be useless. IN that case they may have only spent 100K

          If ti was infinitely more complicated, the it would be infinitely more expensive.

      • I guess it's whoever spends the hundreds of millions of dollars to follow up on the infinitesimal chance that this will lead to something useful?

        This is an entirely sensible approach to patents in this case. Therefore we can be absolutely sure that will not happen, at least not for those reasons.

        Likelier answer: whoever spends the most on lawyers. May or may not be the same people who prove it's useful.

    • by gzipped_tar (1151931) on Wednesday May 19, 2010 @01:30AM (#32261304) Journal

      http://fold.it/portal/node/267249 [fold.it]

      """Foldit project was initiated with the goal of democratizing science, and we stand behind that. the process of discovery and the eventual results of game play will all be open domain.

      """

      Not sure if that claim is backed up by legal documents. The game is suspiciously vague in legal matters. No software license. No EULA. Nothing about patents.

      Or perhaps there is, but not released to the public.

      • by openfrog (897716)

        Foldit project was initiated with the goal of democratizing science, and we stand behind that. the process of discovery and the eventual results of game play will all be open domain.

        It is relevant to note that there is no document in precise legal language, but in the absence of such, the sentence you quote IS legally binding.

    • The user of the software didn't develop the software, they only run it. Do you deserve any patents related to Windows just for using Windows?
      • by WNight (23683)

        Considering that's about what Amazon has with the one-click patent, yeah sure.

        But even MS though doesn't claim ownership of all patents developed on Windows, which is somewhat what this is would be like.

  • by Shag (3737) on Wednesday May 19, 2010 @12:48AM (#32261114) Homepage

    Just wondering. Is there a "prize?" Like getting the first dose of whatever-it-turns-into?

    • Re: (Score:3, Funny)

      by Anonymous Coward
      Coincidentally, that's also the punishment for the loser.
    • Congratulations! YOu have won the honor of testing our first dose of the medicine. What, you don't want the prize? Should have read the fine print...

  • Isn't this how the premise for I am legend [imdb.com] came about?

    • by QuantumG (50515) *

      What ever happened to zombie lust for brains? Lately it's been declared too camp for the horror genre. Kinda like vampires turning into bats was previously.

      BBBRAAAAAAIIIINNNSSSS!!!

    • No. That was a modified measles virus to eradicate cancer cells.
    • No, the premise was "let's see if we can stuff with The Omega Man like we did I, Robot".

  • *sigh* (Score:1, Insightful)

    by Anonymous Coward

    If it is a useful protein, the patent will go to whoever owns the lab. The player and discoverer will be quietly shooed away. You'll see a slashdot article titled "foldit player sues lab" in 8 months. Then you'll never hear about it again.

    • Re:*sigh* (Score:5, Insightful)

      by Garble Snarky (715674) on Wednesday May 19, 2010 @01:22AM (#32261280)
      So... you're saying the work of studying proteins for years, coming up with the game idea, creating and distributing the software, is all nothing, in comparison to the guy who downloaded a program and clicked some buttons? I think the notion of "discovery" is pretty fuzzy in a lot of cases, but you're crazy if you think the player deserves MORE credit than the software authors here.
      • Re:*sigh* (Score:5, Insightful)

        by sFurbo (1361249) on Wednesday May 19, 2010 @03:55AM (#32262010)
        Or the people who synthesize the protein, test that it folds the right way, test it in vitro, test it in animals, perform phase 0, 1, 2 and 3 human trials. You know, the actually finding out if it can be used as a drug. Coming up with a drug candidate is the easy and cheap part of making a new drug.
        • by openfrog (897716)

          So... you're saying the work of studying proteins for years, coming up with the game idea, creating and distributing the software, is all nothing, in comparison to the guy who downloaded a program and clicked some buttons? I think the notion of "discovery" is pretty fuzzy in a lot of cases, but you're crazy if you think the player deserves MORE credit than the software authors here.

          Or the people who synthesize the protein, test that it folds the right way, test it in vitro, test it in animals, perform phase 0, 1, 2 and 3 human trials. You know, the actually finding out if it can be used as a drug. Coming up with a drug candidate is the easy and cheap part of making a new drug.

          The authors developed the game so they could leverage public contributions in a manner that would not have been affordable otherwise. In this equation, you don't only have to take account of the individual successful contribution. The project initiators actually gave a thought to the question raised here:

          Foldit project was initiated with the goal of democratizing science, and we stand behind that. the process of discovery and the eventual results of game play will all be open domain.

      • So... you're saying mathematics, computer science, electrical and computer engineering, the development of the first and all subsequent operating systems leading up to the one used for the game, the development of all programming languages leading up to the development of the language used for the game , is all nothing, in comparison to the work of studying proteins for years, coming up with the game idea, creating and distributing the software? I think the notion of "discovery" is pretty fuzzy in a lot of cases, but you're crazy if you think the software authors deserve MORE credit than the platform developers here.

        There, twisted your meaning all around for you.

        • You didn't twist anything, you just extended further the same point that I made. Of course each of the involved parties deserves some credit. The point is that singling out ONE of them as the sole discoverer makes no sense, especially if you're saying the sole discoverer is the player, the one involved party who did not actually create anything. Giving recognition to the platform developers would probably be unduly difficult, since there are tens of thousands of them, including, say, Von Neumann and Turing.
      • by fishexe (168879)

        I think the notion of "discovery" is pretty fuzzy in a lot of cases, but you're crazy if you think the player deserves MORE credit than the software authors here.

        Why? The creators of the software developed a tool, and the player used that tool to discover something. We don't give the inventor of the computer credit for discovering fractals, or the inventor of the microscope credit for discovering bacteria, do we?

        Granted, the creators of the software deserve great credit for creating a useful tool, just like we separately recognize Galileo for developing the telescope and Herschel for using it to discover Uranus.

  • I heard about this when it was first announced and cannot believe it still exists/people are still playing this "game"

    Anyway this is probably more of a PR smoke then an actual discovery. Drug companies burn through lots of computer time to find potential drug targets most of which do not work. I would expect that a protein (much larger and more complicated then developed drugs) would make the likelihood of its synthesis and folding into the desired structure even less likely to work.

  • Influenza is a fickle virus, able to alter its hemagglutinin and neuraminidase proteins very quickly. Although the link is very light on details, it sounds like they're hoping for a hemagglutinin-binding protein. While this would be a "proof of concept" for the usefulness of Foldit, don't hold your breath on this being any sort of flu cure.
    • by aiht (1017790)

      ... don't hold your breath on this being any sort of flu cure.

      Instead, hold your breath because this isn't any sort of flu cure.
      And the guy next to you on the train just sneezed.

      • by Anomalyst (742352)

        the guy next to you on the train just sneezed.

        I aint sick, just allergic to diesel generated electrical fields, you insensitive clod.

  • FoldIT? Open IT! (Score:1, Informative)

    by Anonymous Coward

    FoldIT is not only closed source software, but also closed as an application. It's the best application to remodel and fix up protein structures out there; yet it is not available to use it on your own protein structures.

    The groups behind it are research groups and of course with it being their own 'product' they are not forced to sell it or give it away, but they are still sitting on it, although many molecular biologists could benefit from its availability as a professional remodeling tool. When emailing

    • Re: (Score:3, Informative)

      by goombah99 (560566)

      The source code for the scientific part of it is freely available from RosettaCommons.org for academic use.

  • by Xoc-S (645831) on Wednesday May 19, 2010 @05:10AM (#32262404)
    I played fold.it for a few months a year and half ago. I was better than most at it, but there was one guy who almost always got the best score on every protein he worked on. He was a mutant at it; the Michael Jordan of protein folding. I joked that it was like The Last Starfighter [imdb.com] , he was being selected for being taken off planet by the aliens who developed the game. He had a way of identifying parts of a protein that could be modified to improve it. By studying people like him...on what they see that nobody else does, can lead to improved automated algorithms, which can lead to significant improvements in medicines.

    Finding optimal folds of proteins is an NP-Hard [wikipedia.org] problem [springerlink.com], so having any heuristic algorithm improvements can vastly increase the chance of having automated tools find useful folds in reasonable amounts of time.
    • If you don't want to play the game but do want to help protein research then there are a couple of ways you can donate some of your unused computer time to researchers in this field. The newest way about to come on-line is a project by Dr. Charlie Strauss at Los Alamos National Lab. He is in the process of setting up a distributed grid of volunteer computers from folks who want to donate cycles on their (intel) mac computers to protein design. It's not online yet but you already have the software instal

  • ... and their username isn't sexkitten69.

  • The funniest part is people assuming this will end up being a cure. Big Pharma has no interest in cures, just mildly effective maintenance drugs one has to keep purchasing in perpetuity.
    • by lwsimon (724555)

      I hear this all the time, and it doesn't make sense.

      If I'm Pfizer, sure, I have no interest in curing erectile dysfunction - I make a killing on Viagra.

      If I'm GlaxoSmithKlein, I'm doing everything I can to cure it, because that would take away a profit center for my competitor.

    • by the gnat (153162)

      The funniest part is people assuming this will end up being a cure. Big Pharma has no interest in cures, just mildly effective maintenance drugs one has to keep purchasing in perpetuity.

      Put down the bong and learn a little about how the real world works. Big Pharma only has a very limited monopoly on selling drugs. If and when the FDA finally approves it, they've only got maybe a decade and a bit left on the patent to make as much money as possible before dozens of generics in Third World countries start

      • ... they've only got maybe a decade and a bit left on the patent to make as much money as possible ... How much more do you think a cure for influenza is worth than a "mildly effective maintenance drug"

        Additionally: Curing a diseased person means there's a disease-prone person able to earn money and buy their other products for decades to come - and a doctor who knows they sell stuff that works well.

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