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	<title>Comments on: Computer gamers solve problem in AIDS research that puzzled scientists for years</title>
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	<link>http://blogs.discovermagazine.com/notrocketscience/2011/09/18/computer-gamers-solve-problem-in-aids-research-that-puzzled-scientists-for-years/</link>
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		<title>By: Ed Yong</title>
		<link>http://blogs.discovermagazine.com/notrocketscience/2011/09/18/computer-gamers-solve-problem-in-aids-research-that-puzzled-scientists-for-years/#comment-13154</link>
		<dc:creator>Ed Yong</dc:creator>
		<pubDate>Thu, 27 Oct 2011 17:58:52 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/notrocketscience/?p=5384#comment-13154</guid>
		<description>Here&#039;s a comment from Firas Khatib:


As one of the authors on the NSMB paper (which you can read for free right now as it was NSMB&#039;s Article of the Month: http://www.nature.com/doifinder/10.1038/nsmb.2119) I wanted to address Stephen Curry&#039;s great point that a lot more information about the actual M-PMV protein would have made for a more complete paper.

All those details can be found in this paper (where we paid the open access fees so that anyone can read it for free): http://journals.iucr.org/d/issues/2011/11/00/lv5014/index.html

You can see that the structure of HIV-1 protease DIMER has been known for 23 years now.  But there was no accurate structure of retroviral protease in the MONOMERIC form: before the protein actually assembles as an enzymatically competent dimer. The crystal structure that the Foldit players helped solve fills this long-time gap. Hopefully now, with the knowledge of the structure of the M-PMV protease monomeric target, we can prevent dimerization and we&#039;ll have an excellent new avenue to new-generation AIDS drugs. (And obviously we have deposited this result in the publicly-accessible Protein Data Bank, so that anyone can access it: http://www.pdb.org/pdb/explore/explore.do?structureId=3SQF)

I also wanted to point out that (in terms of the players getting proper credit on the Nature Structural and Molecular Biology paper) we actually asked the 3 individual players to be co-authors on the paper but they refused, instead asking for their entire team to get the credit.

You can see &#039;mimi&#039; mentioning this in the cosmiclog piece (https://bitly.com/foldit1): &quot;You may be aware that we asked for accreditation for the Foldit Contenders Team within the article, rather than being named individually.&quot;

We were amazed by this display of camaraderie!</description>
		<content:encoded><![CDATA[<p>Here&#8217;s a comment from Firas Khatib:</p>
<p>As one of the authors on the NSMB paper (which you can read for free right now as it was NSMB&#8217;s Article of the Month: <a href="http://www.nature.com/doifinder/10.1038/nsmb.2119" rel="nofollow">http://www.nature.com/doifinder/10.1038/nsmb.2119</a>) I wanted to address Stephen Curry&#8217;s great point that a lot more information about the actual M-PMV protein would have made for a more complete paper.</p>
<p>All those details can be found in this paper (where we paid the open access fees so that anyone can read it for free): <a href="http://journals.iucr.org/d/issues/2011/11/00/lv5014/index.html" rel="nofollow">http://journals.iucr.org/d/issues/2011/11/00/lv5014/index.html</a></p>
<p>You can see that the structure of HIV-1 protease DIMER has been known for 23 years now.  But there was no accurate structure of retroviral protease in the MONOMERIC form: before the protein actually assembles as an enzymatically competent dimer. The crystal structure that the Foldit players helped solve fills this long-time gap. Hopefully now, with the knowledge of the structure of the M-PMV protease monomeric target, we can prevent dimerization and we&#8217;ll have an excellent new avenue to new-generation AIDS drugs. (And obviously we have deposited this result in the publicly-accessible Protein Data Bank, so that anyone can access it: <a href="http://www.pdb.org/pdb/explore/explore.do?structureId=3SQF" rel="nofollow">http://www.pdb.org/pdb/explore/explore.do?structureId=3SQF</a>)</p>
<p>I also wanted to point out that (in terms of the players getting proper credit on the Nature Structural and Molecular Biology paper) we actually asked the 3 individual players to be co-authors on the paper but they refused, instead asking for their entire team to get the credit.</p>
<p>You can see &#8216;mimi&#8217; mentioning this in the cosmiclog piece (<a href="https://bitly.com/foldit1" rel="nofollow">https://bitly.com/foldit1</a>): &#8220;You may be aware that we asked for accreditation for the Foldit Contenders Team within the article, rather than being named individually.&#8221;</p>
<p>We were amazed by this display of camaraderie!</p>
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		<title>By: Jar Games</title>
		<link>http://blogs.discovermagazine.com/notrocketscience/2011/09/18/computer-gamers-solve-problem-in-aids-research-that-puzzled-scientists-for-years/#comment-13153</link>
		<dc:creator>Jar Games</dc:creator>
		<pubDate>Thu, 13 Oct 2011 23:40:47 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/notrocketscience/?p=5384#comment-13153</guid>
		<description>Thus, this could be a god sign that everything has a solution and this game could be a basis in solving scientific problems. Thanks for bringing this wonderful ideas.</description>
		<content:encoded><![CDATA[<p>Thus, this could be a god sign that everything has a solution and this game could be a basis in solving scientific problems. Thanks for bringing this wonderful ideas.</p>
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		<title>By: Fortisimo</title>
		<link>http://blogs.discovermagazine.com/notrocketscience/2011/09/18/computer-gamers-solve-problem-in-aids-research-that-puzzled-scientists-for-years/#comment-13152</link>
		<dc:creator>Fortisimo</dc:creator>
		<pubDate>Tue, 11 Oct 2011 21:03:21 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/notrocketscience/?p=5384#comment-13152</guid>
		<description>Whether or not the structure had already been solved using NMR, this is an interesting method for finding solutions to a fairly complex problem.  I appreciate the novelty of its approach, and in fact I feel the full implications have not even been brought to light.  Consider this; in order to convince people to work on this problem, a dedicated game had to be created that provided adequate gratification to each player (whether they had the slightest interest in the scientific implications or not), a series of tutorials to train the player how to make modifications to the proteins structure in a way that would yield stable final products, and then unleash the newly trained user on some already solved, more complicated problems to verify that they had properly learned to solve this type of problem.  From there, they finally got the opportunity to work on new problems which had not been fully solved previously.  This procedure is remarkably similar to another type of problem solving strategy--- one that is neither a brute force computational method, nor a sheep herding exercise for gamers.  What I&#039;m talking about is using neural networks (which require some sort of fitness function for feedback on their solutions, training data to use so they can adjust to create the proper outputs, and then can be finally used to solve complicated non-linear problems such as these) instead of a collection of gamers with some free time on their hands.  Neural networks can be trained specifically for one task, do not need to be convinced of the importance of a problem (or gimmicked into being involved with video game tropes).  Furthermore, they can work 24 hours a day, 7 days a week and only at the cost of computing power.    So, I suppose the main question is what size and depth of a neural network is needed to solve such complicated protein folding problems and therefore how much computational resources would each network require.  It&#039;s possible though that such problems could more efficiently be solved by a mass of such networks than by the methods described in this paper.

Also, in response to some people saying that the gamers should get more credit or that the gamers seem to be more skilled at solving problems than the scientists in charge, one thing to consider is the fact that someone had to figure out the rules for the game and then create it before the gamers could even touch it.  If all it took to be a researcher was to be skilled at solving brightly colored puzzles on a computer screen then it wouldn&#039;t require 4 years of bachelor work and 6 years of PhD work (plus post-doc and all that good stuff).  That&#039;s not to say they aren&#039;t skilled, it&#039;s just that there are many many other cogs that make this machine work than the final step of brute forcing solutions.</description>
		<content:encoded><![CDATA[<p>Whether or not the structure had already been solved using NMR, this is an interesting method for finding solutions to a fairly complex problem.  I appreciate the novelty of its approach, and in fact I feel the full implications have not even been brought to light.  Consider this; in order to convince people to work on this problem, a dedicated game had to be created that provided adequate gratification to each player (whether they had the slightest interest in the scientific implications or not), a series of tutorials to train the player how to make modifications to the proteins structure in a way that would yield stable final products, and then unleash the newly trained user on some already solved, more complicated problems to verify that they had properly learned to solve this type of problem.  From there, they finally got the opportunity to work on new problems which had not been fully solved previously.  This procedure is remarkably similar to another type of problem solving strategy&#8212; one that is neither a brute force computational method, nor a sheep herding exercise for gamers.  What I&#8217;m talking about is using neural networks (which require some sort of fitness function for feedback on their solutions, training data to use so they can adjust to create the proper outputs, and then can be finally used to solve complicated non-linear problems such as these) instead of a collection of gamers with some free time on their hands.  Neural networks can be trained specifically for one task, do not need to be convinced of the importance of a problem (or gimmicked into being involved with video game tropes).  Furthermore, they can work 24 hours a day, 7 days a week and only at the cost of computing power.    So, I suppose the main question is what size and depth of a neural network is needed to solve such complicated protein folding problems and therefore how much computational resources would each network require.  It&#8217;s possible though that such problems could more efficiently be solved by a mass of such networks than by the methods described in this paper.</p>
<p>Also, in response to some people saying that the gamers should get more credit or that the gamers seem to be more skilled at solving problems than the scientists in charge, one thing to consider is the fact that someone had to figure out the rules for the game and then create it before the gamers could even touch it.  If all it took to be a researcher was to be skilled at solving brightly colored puzzles on a computer screen then it wouldn&#8217;t require 4 years of bachelor work and 6 years of PhD work (plus post-doc and all that good stuff).  That&#8217;s not to say they aren&#8217;t skilled, it&#8217;s just that there are many many other cogs that make this machine work than the final step of brute forcing solutions.</p>
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		<title>By: dckomentator</title>
		<link>http://blogs.discovermagazine.com/notrocketscience/2011/09/18/computer-gamers-solve-problem-in-aids-research-that-puzzled-scientists-for-years/#comment-13151</link>
		<dc:creator>dckomentator</dc:creator>
		<pubDate>Sun, 25 Sep 2011 02:19:05 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/notrocketscience/?p=5384#comment-13151</guid>
		<description>well done! reminds me of an episode on south park. as for the naysayers, complainers and the like: perhaps they should use their time solving problems rather than critiquing those who already have.</description>
		<content:encoded><![CDATA[<p>well done! reminds me of an episode on south park. as for the naysayers, complainers and the like: perhaps they should use their time solving problems rather than critiquing those who already have.</p>
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		<title>By: Jonny</title>
		<link>http://blogs.discovermagazine.com/notrocketscience/2011/09/18/computer-gamers-solve-problem-in-aids-research-that-puzzled-scientists-for-years/#comment-13150</link>
		<dc:creator>Jonny</dc:creator>
		<pubDate>Fri, 23 Sep 2011 22:42:17 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/notrocketscience/?p=5384#comment-13150</guid>
		<description>I think if gamers want credit for contributing to science then gamers should go to school, get a degree, and do the hard work of becoming a scientist just as every other scientist does.  Nobody is stopping them from doing this.</description>
		<content:encoded><![CDATA[<p>I think if gamers want credit for contributing to science then gamers should go to school, get a degree, and do the hard work of becoming a scientist just as every other scientist does.  Nobody is stopping them from doing this.</p>
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		<title>By: Alyson</title>
		<link>http://blogs.discovermagazine.com/notrocketscience/2011/09/18/computer-gamers-solve-problem-in-aids-research-that-puzzled-scientists-for-years/#comment-13149</link>
		<dc:creator>Alyson</dc:creator>
		<pubDate>Fri, 23 Sep 2011 20:01:02 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/notrocketscience/?p=5384#comment-13149</guid>
		<description>@Kim, Im glad you brought up the issue of compensation and credit.  Even if it did end up getting dismissed.

It is something that needs to be addressed at some point.   We live in a society that believes that &quot;value creators&quot; have the right to profit from that, and this type of &quot;game&quot; does seem to be an exploit of that.  Perhaps it will need to be addressed with the gamers, not the people exploiting their gaming, but it should be addressed at some point in some way.

Our economic system is already one that favors heavily those who are adept at exploiting the talent, work, and innovation of others, rather than those who are talented, hard working or innovative, and as a species we do need to ask ourselves if its wise to set up systems that favor exploitation over talent.

We are playing the game of natural selection, after all, and clearly, the exploitative are &quot;winning&quot; on a global scale.  Im not sure thats in humanitys best interests in the long run.</description>
		<content:encoded><![CDATA[<p>@Kim, Im glad you brought up the issue of compensation and credit.  Even if it did end up getting dismissed.</p>
<p>It is something that needs to be addressed at some point.   We live in a society that believes that &#8220;value creators&#8221; have the right to profit from that, and this type of &#8220;game&#8221; does seem to be an exploit of that.  Perhaps it will need to be addressed with the gamers, not the people exploiting their gaming, but it should be addressed at some point in some way.</p>
<p>Our economic system is already one that favors heavily those who are adept at exploiting the talent, work, and innovation of others, rather than those who are talented, hard working or innovative, and as a species we do need to ask ourselves if its wise to set up systems that favor exploitation over talent.</p>
<p>We are playing the game of natural selection, after all, and clearly, the exploitative are &#8220;winning&#8221; on a global scale.  Im not sure thats in humanitys best interests in the long run.</p>
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		<title>By: Latigo1026</title>
		<link>http://blogs.discovermagazine.com/notrocketscience/2011/09/18/computer-gamers-solve-problem-in-aids-research-that-puzzled-scientists-for-years/#comment-13148</link>
		<dc:creator>Latigo1026</dc:creator>
		<pubDate>Fri, 23 Sep 2011 19:14:29 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/notrocketscience/?p=5384#comment-13148</guid>
		<description>Hardly the place to attempt to disguise a right wing diatribe as gaming comment.  A more legitimate suggestion would be a game that incentivizes all three corners of our democratic system -- capitalism, government, and social justice, to obtain the best possible outcome for all three layers of society: the poor and homeless, the working class, and the wealthy.  Now that would be a game worth playing.</description>
		<content:encoded><![CDATA[<p>Hardly the place to attempt to disguise a right wing diatribe as gaming comment.  A more legitimate suggestion would be a game that incentivizes all three corners of our democratic system &#8212; capitalism, government, and social justice, to obtain the best possible outcome for all three layers of society: the poor and homeless, the working class, and the wealthy.  Now that would be a game worth playing.</p>
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		<title>By: Stan</title>
		<link>http://blogs.discovermagazine.com/notrocketscience/2011/09/18/computer-gamers-solve-problem-in-aids-research-that-puzzled-scientists-for-years/#comment-13147</link>
		<dc:creator>Stan</dc:creator>
		<pubDate>Fri, 23 Sep 2011 11:59:35 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/notrocketscience/?p=5384#comment-13147</guid>
		<description>@greg kellerman, &quot;Now if Firas Khatib from the University of Washington would suggest that the business and Polly-sci departments put together a game, Washington Tycoon, we could turn our country around based on citizen-wide, gamer-play.&quot;

We already have that framework in place. It&#039;s called &quot;Capitalism&quot;.

Unfortunately, the players in another group called &quot;Government&quot; has imposed so many restrictions, taxes and other disincentives on the &quot;Capitalism&quot; group that its citizen-wide creative activities have been stifled, with the economy suffering as a direct result.

It doesn&#039;t help that the &quot;Government&quot; group thinks that their function is not to promote the economy, but to support a third group, the &quot;Drones&quot;, whose members believe that they deserve life-long support simply for voting some of their more vocal members into the &quot;Government&quot; group, rather than participating in the &quot;Capitalism&quot; group.</description>
		<content:encoded><![CDATA[<p>@greg kellerman, &#8220;Now if Firas Khatib from the University of Washington would suggest that the business and Polly-sci departments put together a game, Washington Tycoon, we could turn our country around based on citizen-wide, gamer-play.&#8221;</p>
<p>We already have that framework in place. It&#8217;s called &#8220;Capitalism&#8221;.</p>
<p>Unfortunately, the players in another group called &#8220;Government&#8221; has imposed so many restrictions, taxes and other disincentives on the &#8220;Capitalism&#8221; group that its citizen-wide creative activities have been stifled, with the economy suffering as a direct result.</p>
<p>It doesn&#8217;t help that the &#8220;Government&#8221; group thinks that their function is not to promote the economy, but to support a third group, the &#8220;Drones&#8221;, whose members believe that they deserve life-long support simply for voting some of their more vocal members into the &#8220;Government&#8221; group, rather than participating in the &#8220;Capitalism&#8221; group.</p>
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		<title>By: Qurtan</title>
		<link>http://blogs.discovermagazine.com/notrocketscience/2011/09/18/computer-gamers-solve-problem-in-aids-research-that-puzzled-scientists-for-years/#comment-13146</link>
		<dc:creator>Qurtan</dc:creator>
		<pubDate>Thu, 22 Sep 2011 18:07:34 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/notrocketscience/?p=5384#comment-13146</guid>
		<description>Fascinating. I have imagined that game can use the computing power of the players&#039; computers but this is a new approach to solving scientific problems.</description>
		<content:encoded><![CDATA[<p>Fascinating. I have imagined that game can use the computing power of the players&#8217; computers but this is a new approach to solving scientific problems.</p>
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		<title>By: Tom</title>
		<link>http://blogs.discovermagazine.com/notrocketscience/2011/09/18/computer-gamers-solve-problem-in-aids-research-that-puzzled-scientists-for-years/#comment-13145</link>
		<dc:creator>Tom</dc:creator>
		<pubDate>Tue, 20 Sep 2011 18:57:05 +0000</pubDate>
		<guid isPermaLink="false">http://blogs.discovermagazine.com/notrocketscience/?p=5384#comment-13145</guid>
		<description>Too many people are simply writing this off to either &quot;online gaming&quot; or &quot;crowd sourcing.&quot; What you also might want to consider, is that this particular group of Foldit players are &quot;naturally talented puzzle/problem solvers&quot;, that are fascinated by science.  And in this case, this particular group of puzzle solvers seem to be fascinated by structural &amp; molecular biology - not just any science, but specifically, structural/molecular biology!BRAVO to Foldit and this group of puzzle solvers!!  What a GREAT story!!  Sadly however, it illustrates how many of us are in the wrong role!!  &quot;The experts&quot; have been working on this problem for a decade, and the &quot;puzzle solvers&quot; solved the puzzle in 3 WEEKS!!!While I&#039;m confident that &quot;the experts&quot; are very bright and talented, they are clearly NOT &quot;naturally talented puzzle solvers.&quot;  Either that,, or they&#039;re not naturally fascinated by structural/molecular biology...  Without knowing them, of course I have no idea if &quot;the experts&quot; should even be in this field, but one could argue that some of them certainly don&#039;t seem to be in the right role..  And what about these particular puzzle solvers...  What are they doing for work?  What fields are they in?  What are they naturally most fascinated by?  And, are they leveraging their natural talent every day to help solve similar problems?  My argument is; when you marry one&#039;s Top Natural Talent with their Greatest Natural Fascination, it can lead to great discoveries - In every area of endeavor!  Using Einstein as an example, he used his considerable math talent to answer his own most profound questions about space and time. All &quot;The Greats&quot; focused their Top Natural Talent on their Greatest Natural Fascination, to help change the world, and you can to!   So let&#039;s raise the bar for ourselves and one another; Get in the right role in the right industry to do YOUR BEST WORK!  Find your Top Natural Talent and put it to work on your Greatest Natural Fascination!</description>
		<content:encoded><![CDATA[<p>Too many people are simply writing this off to either &#8220;online gaming&#8221; or &#8220;crowd sourcing.&#8221; What you also might want to consider, is that this particular group of Foldit players are &#8220;naturally talented puzzle/problem solvers&#8221;, that are fascinated by science.  And in this case, this particular group of puzzle solvers seem to be fascinated by structural &amp; molecular biology &#8211; not just any science, but specifically, structural/molecular biology!BRAVO to Foldit and this group of puzzle solvers!!  What a GREAT story!!  Sadly however, it illustrates how many of us are in the wrong role!!  &#8220;The experts&#8221; have been working on this problem for a decade, and the &#8220;puzzle solvers&#8221; solved the puzzle in 3 WEEKS!!!While I&#8217;m confident that &#8220;the experts&#8221; are very bright and talented, they are clearly NOT &#8220;naturally talented puzzle solvers.&#8221;  Either that,, or they&#8217;re not naturally fascinated by structural/molecular biology&#8230;  Without knowing them, of course I have no idea if &#8220;the experts&#8221; should even be in this field, but one could argue that some of them certainly don&#8217;t seem to be in the right role..  And what about these particular puzzle solvers&#8230;  What are they doing for work?  What fields are they in?  What are they naturally most fascinated by?  And, are they leveraging their natural talent every day to help solve similar problems?  My argument is; when you marry one&#8217;s Top Natural Talent with their Greatest Natural Fascination, it can lead to great discoveries &#8211; In every area of endeavor!  Using Einstein as an example, he used his considerable math talent to answer his own most profound questions about space and time. All &#8220;The Greats&#8221; focused their Top Natural Talent on their Greatest Natural Fascination, to help change the world, and you can to!   So let&#8217;s raise the bar for ourselves and one another; Get in the right role in the right industry to do YOUR BEST WORK!  Find your Top Natural Talent and put it to work on your Greatest Natural Fascination!</p>
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