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	<title>Comments for The Secret Microbe</title>
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	<link>http://secretmicrobe.org</link>
	<description>Webial home of Aaron Darling, Ph.D. \\ Stories from a computational genomics geek</description>
	<lastBuildDate>Sun, 01 Apr 2012 13:11:42 +0000</lastBuildDate>
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		<title>Comment on Who owns your review? by Vencio</title>
		<link>http://secretmicrobe.org/who-owns-your-review/comment-page-1#comment-1484</link>
		<dc:creator>Vencio</dc:creator>
		<pubDate>Sun, 01 Apr 2012 13:11:42 +0000</pubDate>
		<guid isPermaLink="false">http://secretmicrobe.org/?p=97#comment-1484</guid>
		<description>Nice discussion! I believe that review disclosure would help readers to think critically about the work they are reading. The issue of &quot;credit to good reviewers&quot; is also important too, I agree, but could be treated independently from the &quot;copyright&quot; issue. If let to author decide, I guess that people wouldn&#039;t publish alongside their papers bad reviews. Therefore, if we are going in this direction, it would be necessary to be something mandatory not optional, right? Thanks.</description>
		<content:encoded><![CDATA[<p>Nice discussion! I believe that review disclosure would help readers to think critically about the work they are reading. The issue of &#8220;credit to good reviewers&#8221; is also important too, I agree, but could be treated independently from the &#8220;copyright&#8221; issue. If let to author decide, I guess that people wouldn&#8217;t publish alongside their papers bad reviews. Therefore, if we are going in this direction, it would be necessary to be something mandatory not optional, right? Thanks.</p>
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		<title>Comment on KDE 4.1: Open the menu with the windows key by sujendra</title>
		<link>http://secretmicrobe.org/kde-41-open-the-menu-with-the-windows-key/comment-page-1#comment-1145</link>
		<dc:creator>sujendra</dc:creator>
		<pubDate>Sun, 15 May 2011 13:07:41 +0000</pubDate>
		<guid isPermaLink="false">http://secretmicrobe.org/?p=9#comment-1145</guid>
		<description>Hi,
Thanks for mentioning this point; works out of the box for Kubuntu 11(2.6.38-8-generic) as well..!!</description>
		<content:encoded><![CDATA[<p>Hi,<br />
Thanks for mentioning this point; works out of the box for Kubuntu 11(2.6.38-8-generic) as well..!!</p>
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		<title>Comment on KDE 4.1: Open the menu with the windows key by Ben</title>
		<link>http://secretmicrobe.org/kde-41-open-the-menu-with-the-windows-key/comment-page-1#comment-1094</link>
		<dc:creator>Ben</dc:creator>
		<pubDate>Sun, 19 Dec 2010 19:56:17 +0000</pubDate>
		<guid isPermaLink="false">http://secretmicrobe.org/?p=9#comment-1094</guid>
		<description>Hi guys - if you screw up and xmodmap reports errors, simply type &#039;xkbmap&#039; to reset things. Then try again.</description>
		<content:encoded><![CDATA[<p>Hi guys &#8211; if you screw up and xmodmap reports errors, simply type &#8216;xkbmap&#8217; to reset things. Then try again.</p>
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		<title>Comment on Who owns your review? by Quick Links &#124; A Blog Around The Clock</title>
		<link>http://secretmicrobe.org/who-owns-your-review/comment-page-1#comment-672</link>
		<dc:creator>Quick Links &#124; A Blog Around The Clock</dc:creator>
		<pubDate>Fri, 15 Oct 2010 16:15:42 +0000</pubDate>
		<guid isPermaLink="false">http://secretmicrobe.org/?p=97#comment-672</guid>
		<description>[...] Who owns your review? [...]</description>
		<content:encoded><![CDATA[<p>[...] Who owns your review? [...]</p>
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		<title>Comment on Who owns your review? by Steve Koch</title>
		<link>http://secretmicrobe.org/who-owns-your-review/comment-page-1#comment-664</link>
		<dc:creator>Steve Koch</dc:creator>
		<pubDate>Fri, 15 Oct 2010 03:16:12 +0000</pubDate>
		<guid isPermaLink="false">http://secretmicrobe.org/?p=97#comment-664</guid>
		<description>@Aaron, yeah that is a problem with rejected papers.  One other thing I&#039;d had in mind is that referees would have an option &quot;decline to review&quot; after seeing the manuscript.  This &quot;declined to review&quot; would also be published, if they choose to see the MS.  So, at least if upon looking it&#039;s a total mess or obviously not suited for the journal, you could choose that option.  But I agree, it&#039;s a problem.  When I&#039;m in the PLoS ONE frame of mind, it&#039;s less of a problem, because at least you know the paper won&#039;t be declined due to impact assessment.  But even there, it&#039;s still a problem.  It&#039;d be cool if the original manuscript were automatically posted, but then I think we&#039;ve reached the point of completely post-publication review.  Not that that is bad, but I think people are less ready for it at this point.  BTW:  I&#039;m going to forget to come back here at some point, so you can either holler at me on the friendfeed thread http://friendfeed.com/treeoflife/b26b8131/i-love-this-idea-from-aaron-darling-who-works-in or email</description>
		<content:encoded><![CDATA[<p>@Aaron, yeah that is a problem with rejected papers.  One other thing I&#8217;d had in mind is that referees would have an option &#8220;decline to review&#8221; after seeing the manuscript.  This &#8220;declined to review&#8221; would also be published, if they choose to see the MS.  So, at least if upon looking it&#8217;s a total mess or obviously not suited for the journal, you could choose that option.  But I agree, it&#8217;s a problem.  When I&#8217;m in the PLoS ONE frame of mind, it&#8217;s less of a problem, because at least you know the paper won&#8217;t be declined due to impact assessment.  But even there, it&#8217;s still a problem.  It&#8217;d be cool if the original manuscript were automatically posted, but then I think we&#8217;ve reached the point of completely post-publication review.  Not that that is bad, but I think people are less ready for it at this point.  BTW:  I&#8217;m going to forget to come back here at some point, so you can either holler at me on the friendfeed thread <a href="http://friendfeed.com/treeoflife/b26b8131/i-love-this-idea-from-aaron-darling-who-works-in" rel="nofollow">http://friendfeed.com/treeoflife/b26b8131/i-love-this-idea-from-aaron-darling-who-works-in</a> or email</p>
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		<title>Comment on Who owns your review? by koadman</title>
		<link>http://secretmicrobe.org/who-owns-your-review/comment-page-1#comment-663</link>
		<dc:creator>koadman</dc:creator>
		<pubDate>Fri, 15 Oct 2010 02:39:19 +0000</pubDate>
		<guid isPermaLink="false">http://secretmicrobe.org/?p=97#comment-663</guid>
		<description>@Steve,
Your suggestion about publishing reviewers comments alongside the article is actually already done in some form by the folks at the journal Biology Direct, http://www.biology-direct.com/
I&#039;ve never published there but as far as I can tell it&#039;s a very limited form of what we&#039;re discussing because reviews generally come from the editorial board members and of course it&#039;s just one of the many thousands of journals out there.  Are there other examples?

I&#039;m all for putting together a small movement of reviewers who demand publication of their reviews.  Even if there aren&#039;t enough of us to create any real pressure on journal editorial boards we would at least raise awareness about the issue.  That will create momentum.  Snowball effect.  yeah!  I propose we start with a website and a short and simple manifesto that supporters can reference.  Maybe also gather a set of founding members for the idea and maintain a registration list for supporters.

But one thing still nags me...  What to do about the work that goes into reviewing papers that ultimately never get published?  Should the reviews be published anyway?  And the paper published along with a public REJECTED designation?</description>
		<content:encoded><![CDATA[<p>@Steve,<br />
Your suggestion about publishing reviewers comments alongside the article is actually already done in some form by the folks at the journal Biology Direct, <a href="http://www.biology-direct.com/" rel="nofollow">http://www.biology-direct.com/</a><br />
I&#8217;ve never published there but as far as I can tell it&#8217;s a very limited form of what we&#8217;re discussing because reviews generally come from the editorial board members and of course it&#8217;s just one of the many thousands of journals out there.  Are there other examples?</p>
<p>I&#8217;m all for putting together a small movement of reviewers who demand publication of their reviews.  Even if there aren&#8217;t enough of us to create any real pressure on journal editorial boards we would at least raise awareness about the issue.  That will create momentum.  Snowball effect.  yeah!  I propose we start with a website and a short and simple manifesto that supporters can reference.  Maybe also gather a set of founding members for the idea and maintain a registration list for supporters.</p>
<p>But one thing still nags me&#8230;  What to do about the work that goes into reviewing papers that ultimately never get published?  Should the reviews be published anyway?  And the paper published along with a public REJECTED designation?</p>
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		<title>Comment on Who owns your review? by Steve Koch</title>
		<link>http://secretmicrobe.org/who-owns-your-review/comment-page-1#comment-662</link>
		<dc:creator>Steve Koch</dc:creator>
		<pubDate>Fri, 15 Oct 2010 01:59:26 +0000</pubDate>
		<guid isPermaLink="false">http://secretmicrobe.org/?p=97#comment-662</guid>
		<description>Great post and I totally agree.  I&#039;ve thought for more than 6 years now that anonymous peer-review is a waste.  Basically ever since my first paper in graduate school.  The first draft received very thoughtful reviews with a lot of negative comments.  Most of those negatives won arguments for me with my advisor (zing!) and one reviewer came up with an experiment idea that worked out very well.  They made my first paper a lot better.  I still regret that I don&#039;t know who those people are and that they don&#039;t get any credit from readers.

I&#039;d go one step further in peer review reform: I&#039;d require publication of referee comments _alongside_ the originally submitted manuscript.  For one thing, this would make referee comments more understandable (presuming the final manuscript fixed the problems).  But more importantly, I think it would stop people from submitting unfinished work.  Unlike you, I frequently end up thinking that the authors rushed to submission, figuring they&#039;d get a chance to revise and do the work in the meantime.  Or they just submit unrefined junk hoping it will slip by.  I think they&#039;d stop doing this if they knew their original work would be published.

It seems to me that reasoned arguments like yours to overhaul or abolish pre-publication peer review are ramping up quickly over the past couple years.  Maybe it&#039;s time to form a coalition of referees and make demands.  This would actually be easy.  For example, we get a group of people to agree on some condition, such as: we will only serve as referee if our signed comments are published along side the final manuscript (that&#039;s a weaker demand than I want).  of course, most publishers won&#039;t agree to this, but if we stick to our guns: hey, less work for us!  Eventually, people will see the wisdom of our way and join us and force change.  OK, maybe I&#039;m dreaming, but it seems nice.  Actually, what&#039;s preventing me from making that my own ultimatum?  Nothing really, my tenure committee would never find out that I was refusing all my referee requests, except for PLoS ONE.

OK, thanks for the great post!</description>
		<content:encoded><![CDATA[<p>Great post and I totally agree.  I&#8217;ve thought for more than 6 years now that anonymous peer-review is a waste.  Basically ever since my first paper in graduate school.  The first draft received very thoughtful reviews with a lot of negative comments.  Most of those negatives won arguments for me with my advisor (zing!) and one reviewer came up with an experiment idea that worked out very well.  They made my first paper a lot better.  I still regret that I don&#8217;t know who those people are and that they don&#8217;t get any credit from readers.</p>
<p>I&#8217;d go one step further in peer review reform: I&#8217;d require publication of referee comments _alongside_ the originally submitted manuscript.  For one thing, this would make referee comments more understandable (presuming the final manuscript fixed the problems).  But more importantly, I think it would stop people from submitting unfinished work.  Unlike you, I frequently end up thinking that the authors rushed to submission, figuring they&#8217;d get a chance to revise and do the work in the meantime.  Or they just submit unrefined junk hoping it will slip by.  I think they&#8217;d stop doing this if they knew their original work would be published.</p>
<p>It seems to me that reasoned arguments like yours to overhaul or abolish pre-publication peer review are ramping up quickly over the past couple years.  Maybe it&#8217;s time to form a coalition of referees and make demands.  This would actually be easy.  For example, we get a group of people to agree on some condition, such as: we will only serve as referee if our signed comments are published along side the final manuscript (that&#8217;s a weaker demand than I want).  of course, most publishers won&#8217;t agree to this, but if we stick to our guns: hey, less work for us!  Eventually, people will see the wisdom of our way and join us and force change.  OK, maybe I&#8217;m dreaming, but it seems nice.  Actually, what&#8217;s preventing me from making that my own ultimatum?  Nothing really, my tenure committee would never find out that I was refusing all my referee requests, except for PLoS ONE.</p>
<p>OK, thanks for the great post!</p>
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		<title>Comment on Who owns your review? by koadman</title>
		<link>http://secretmicrobe.org/who-owns-your-review/comment-page-1#comment-661</link>
		<dc:creator>koadman</dc:creator>
		<pubDate>Thu, 14 Oct 2010 21:52:10 +0000</pubDate>
		<guid isPermaLink="false">http://secretmicrobe.org/?p=97#comment-661</guid>
		<description>Anonymity aside, I still think the issue of review copyright and permissions is very ambiguous.  I would love to be able to publish anonymous reviews of my papers, and so it would be great if all reviewers (anonymous or named) would indicate their willingness to have the reviews published with a copyright statement.

That said, people who have fear of writing something negative about a colleagues work need to grow a spine.  The several times so far that I&#039;ve signed a negative review it&#039;s turned out pretty well.  In one case the authors contacted me and we had a very positive discussion about why I came to the conclusions in the review.  If non-anonymous review were the norm most people would acclimate to having a beer with someone who provided a candid evaluation of their work without unleashing a drunken torrent of insults.</description>
		<content:encoded><![CDATA[<p>Anonymity aside, I still think the issue of review copyright and permissions is very ambiguous.  I would love to be able to publish anonymous reviews of my papers, and so it would be great if all reviewers (anonymous or named) would indicate their willingness to have the reviews published with a copyright statement.</p>
<p>That said, people who have fear of writing something negative about a colleagues work need to grow a spine.  The several times so far that I&#8217;ve signed a negative review it&#8217;s turned out pretty well.  In one case the authors contacted me and we had a very positive discussion about why I came to the conclusions in the review.  If non-anonymous review were the norm most people would acclimate to having a beer with someone who provided a candid evaluation of their work without unleashing a drunken torrent of insults.</p>
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		<title>Comment on Who owns your review? by Jani Kotakoski</title>
		<link>http://secretmicrobe.org/who-owns-your-review/comment-page-1#comment-656</link>
		<dc:creator>Jani Kotakoski</dc:creator>
		<pubDate>Thu, 14 Oct 2010 20:57:55 +0000</pubDate>
		<guid isPermaLink="false">http://secretmicrobe.org/?p=97#comment-656</guid>
		<description>My fear with open (non-anonymous) review is that people would be less likely to give negative feedback on - or even reject - manuscripts of people they know within the community.

Mostly we know at least superficially the others working in the field, and consider some as friends with whom we like to go out for a beer at conferences.

When giving anonymous reports, we can keep on going out for a beer or two occasionally and still provide honest criticism of each other&#039;s work.</description>
		<content:encoded><![CDATA[<p>My fear with open (non-anonymous) review is that people would be less likely to give negative feedback on &#8211; or even reject &#8211; manuscripts of people they know within the community.</p>
<p>Mostly we know at least superficially the others working in the field, and consider some as friends with whom we like to go out for a beer at conferences.</p>
<p>When giving anonymous reports, we can keep on going out for a beer or two occasionally and still provide honest criticism of each other&#8217;s work.</p>
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		<title>Comment on KDE 4.1: Open the menu with the windows key by Ty</title>
		<link>http://secretmicrobe.org/kde-41-open-the-menu-with-the-windows-key/comment-page-1#comment-551</link>
		<dc:creator>Ty</dc:creator>
		<pubDate>Wed, 06 Oct 2010 09:23:38 +0000</pubDate>
		<guid isPermaLink="false">http://secretmicrobe.org/?p=9#comment-551</guid>
		<description>Tried this for a bit; decided to switch back.  Can you tell me how to modify the code so that I can revert back to the original functionality?</description>
		<content:encoded><![CDATA[<p>Tried this for a bit; decided to switch back.  Can you tell me how to modify the code so that I can revert back to the original functionality?</p>
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