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	<title>Comments for Scientific B-sides</title>
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	<link>http://scientificbsides.wordpress.com</link>
	<description>The flipside of the A-side: bonus after-hour ramblings on life, the universe and everything</description>
	<lastBuildDate>Sat, 30 Mar 2013 18:49:33 +0000</lastBuildDate>
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		<title>Comment on The cancer of Henrietta Lacks: more telomerase, less angels please! by jshoyer</title>
		<link>http://scientificbsides.wordpress.com/2013/03/29/the-cancer-of-henrietta-lacks-more-telomerase-less-angels-please/#comment-419</link>
		<dc:creator><![CDATA[jshoyer]]></dc:creator>
		<pubDate>Sat, 30 Mar 2013 18:49:33 +0000</pubDate>
		<guid isPermaLink="false">http://scientificbsides.wordpress.com/?p=3980#comment-419</guid>
		<description><![CDATA[My enthusiasm for the book has also waned, because I find it depressing. I find it sad that some consider Gey a monster; for me, his most regrettable act was the way he labelled the HeLa cell line, instead of just giving it a number. Jones&#039;s and McKusick&#039;s original attempt to honor Henrietta by revealing her identity seems to have caused mostly pain for her descendents, by bringing them unwanted public attention and confusion.

I have no idea how human cells are propagated, but I really hope they haven&#039;t been continuously passaged for 60 years. Don&#039;t labs and companies use frozen stocks for starting large scale cultures? In any case, I agree that there have probably been very interesting adaptive changes in the cells since they were originally collected.

Here&#039;s hoping that the living Lacks family members allow researchers to sequence their genomes (with proper privacy and security control), and that they (and cervical cancer patients) can get some health benefits from the resulting data!]]></description>
		<content:encoded><![CDATA[<p>My enthusiasm for the book has also waned, because I find it depressing. I find it sad that some consider Gey a monster; for me, his most regrettable act was the way he labelled the HeLa cell line, instead of just giving it a number. Jones&#8217;s and McKusick&#8217;s original attempt to honor Henrietta by revealing her identity seems to have caused mostly pain for her descendents, by bringing them unwanted public attention and confusion.</p>
<p>I have no idea how human cells are propagated, but I really hope they haven&#8217;t been continuously passaged for 60 years. Don&#8217;t labs and companies use frozen stocks for starting large scale cultures? In any case, I agree that there have probably been very interesting adaptive changes in the cells since they were originally collected.</p>
<p>Here&#8217;s hoping that the living Lacks family members allow researchers to sequence their genomes (with proper privacy and security control), and that they (and cervical cancer patients) can get some health benefits from the resulting data!</p>
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		<title>Comment on The Immortal Life of Henrietta Lacks, the Sequel by Florian Markowetz</title>
		<link>http://scientificbsides.wordpress.com/2013/03/24/the-immortal-life-of-henrietta-lacks-the-sequel/#comment-418</link>
		<dc:creator><![CDATA[Florian Markowetz]]></dc:creator>
		<pubDate>Fri, 29 Mar 2013 12:55:28 +0000</pubDate>
		<guid isPermaLink="false">http://scientificbsides.wordpress.com/?p=3939#comment-418</guid>
		<description><![CDATA[Thanks for that. I wrote an update on the telomeres: http://wp.me/p1WV42-12c

Actually I hadn&#039;t see the original press release, but found a link to a copy now. Just answering &#039;No&#039; is indeed making it very (too!) simple. But the reasons they give seem valid to me: &quot;Without any genetic information from the original tumour or from Henrietta Lacks, it is impossible to distinguish which parts of the genome sequenced here originate from Mrs. Lacks, her tumour, or laboratory adaptation.&quot;

Security: I don&#039;t work with HeLa cells but with large sample collections where we have SNP information (not complete genomes). They are stored at the European Genome-Phenome Archive (https://www.ebi.ac.uk/ega/) behind a &#039;firewall&#039;. You need to write an application and specify why you need this information for your project to get the genetic data. How secure that is in practice, I don&#039;t know.  

Florian]]></description>
		<content:encoded><![CDATA[<p>Thanks for that. I wrote an update on the telomeres: <a href="http://wp.me/p1WV42-12c" rel="nofollow">http://wp.me/p1WV42-12c</a></p>
<p>Actually I hadn&#8217;t see the original press release, but found a link to a copy now. Just answering &#8216;No&#8217; is indeed making it very (too!) simple. But the reasons they give seem valid to me: &#8220;Without any genetic information from the original tumour or from Henrietta Lacks, it is impossible to distinguish which parts of the genome sequenced here originate from Mrs. Lacks, her tumour, or laboratory adaptation.&#8221;</p>
<p>Security: I don&#8217;t work with HeLa cells but with large sample collections where we have SNP information (not complete genomes). They are stored at the European Genome-Phenome Archive (<a href="https://www.ebi.ac.uk/ega/" rel="nofollow">https://www.ebi.ac.uk/ega/</a>) behind a &#8216;firewall&#8217;. You need to write an application and specify why you need this information for your project to get the genetic data. How secure that is in practice, I don&#8217;t know.  </p>
<p>Florian</p>
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		<title>Comment on &#8220;The fame she so richly deserves&#8221; &#8212; Rebecca Skloot: The immortal life of Henrietta Lacks by The cancer of Henrietta Lacks: more telomerase, less angels please! &#124; Scientific B-sides</title>
		<link>http://scientificbsides.wordpress.com/2012/01/30/the-immortal-life-of-henrietta-lacks/#comment-417</link>
		<dc:creator><![CDATA[The cancer of Henrietta Lacks: more telomerase, less angels please! &#124; Scientific B-sides]]></dc:creator>
		<pubDate>Fri, 29 Mar 2013 12:46:22 +0000</pubDate>
		<guid isPermaLink="false">http://scientificbsides.wordpress.com/?p=1652#comment-417</guid>
		<description><![CDATA[[...] are making headlines again. I had been very impressed when I read it first (as you can see from my review in early 2012), but I am less enthusiastic now that I had some time to think about [...]]]></description>
		<content:encoded><![CDATA[<p>[...] are making headlines again. I had been very impressed when I read it first (as you can see from my review in early 2012), but I am less enthusiastic now that I had some time to think about [...]</p>
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		<title>Comment on The Immortal Life of Henrietta Lacks, the Sequel by The cancer of Henrietta Lacks: more telomerase, less angels please! &#124; Scientific B-sides</title>
		<link>http://scientificbsides.wordpress.com/2013/03/24/the-immortal-life-of-henrietta-lacks-the-sequel/#comment-416</link>
		<dc:creator><![CDATA[The cancer of Henrietta Lacks: more telomerase, less angels please! &#124; Scientific B-sides]]></dc:creator>
		<pubDate>Fri, 29 Mar 2013 12:46:18 +0000</pubDate>
		<guid isPermaLink="false">http://scientificbsides.wordpress.com/?p=3939#comment-416</guid>
		<description><![CDATA[[...] all the clamor over sequencing the HeLa genome, Rebecca Skloot and her book &#8216;The immortal life of Henrietta Lacks&#8216; are making [...]]]></description>
		<content:encoded><![CDATA[<p>[...] all the clamor over sequencing the HeLa genome, Rebecca Skloot and her book &#8216;The immortal life of Henrietta Lacks&#8216; are making [...]</p>
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		<title>Comment on The Immortal Life of Henrietta Lacks, the Sequel by jshoyer</title>
		<link>http://scientificbsides.wordpress.com/2013/03/24/the-immortal-life-of-henrietta-lacks-the-sequel/#comment-415</link>
		<dc:creator><![CDATA[jshoyer]]></dc:creator>
		<pubDate>Tue, 26 Mar 2013 21:55:49 +0000</pubDate>
		<guid isPermaLink="false">http://scientificbsides.wordpress.com/?p=3939#comment-415</guid>
		<description><![CDATA[Activated telomerase is in fact mentioned in the book. &#039;Telomere&#039; is right there in the index.

As you&#039;ve probably seen, the original press release was the most egregious example of &#039;dumbing down&#039;, implying that absolutely nothing could be inferred about current Lacks family members.

Any thoughts on how sequence data like this could be distributed to labs that pledge to keep them secure private? It&#039;s way too late for anonymity, but it seems like security is a higher priority here than open science. Especially if someone attempts to current Lacks family members for comparison...]]></description>
		<content:encoded><![CDATA[<p>Activated telomerase is in fact mentioned in the book. &#8216;Telomere&#8217; is right there in the index.</p>
<p>As you&#8217;ve probably seen, the original press release was the most egregious example of &#8216;dumbing down&#8217;, implying that absolutely nothing could be inferred about current Lacks family members.</p>
<p>Any thoughts on how sequence data like this could be distributed to labs that pledge to keep them secure private? It&#8217;s way too late for anonymity, but it seems like security is a higher priority here than open science. Especially if someone attempts to current Lacks family members for comparison&#8230;</p>
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		<title>Comment on &#8220;The fame she so richly deserves&#8221; &#8212; Rebecca Skloot: The immortal life of Henrietta Lacks by The Immortal Life of Henrietta Lacks, the Sequel &#124; Scientific B-sides</title>
		<link>http://scientificbsides.wordpress.com/2012/01/30/the-immortal-life-of-henrietta-lacks/#comment-413</link>
		<dc:creator><![CDATA[The Immortal Life of Henrietta Lacks, the Sequel &#124; Scientific B-sides]]></dc:creator>
		<pubDate>Sun, 24 Mar 2013 13:32:58 +0000</pubDate>
		<guid isPermaLink="false">http://scientificbsides.wordpress.com/?p=1652#comment-413</guid>
		<description><![CDATA[[...] Skloot, author of The immortal life of Henrietta Lacks reports in the New York Times [...]]]></description>
		<content:encoded><![CDATA[<p>[...] Skloot, author of The immortal life of Henrietta Lacks reports in the New York Times [...]</p>
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		<title>Comment on Mix Tape #1: Best Songs About Science by Dan Gareau</title>
		<link>http://scientificbsides.wordpress.com/2012/01/13/mix-tape-best-songs-about-science/#comment-411</link>
		<dc:creator><![CDATA[Dan Gareau]]></dc:creator>
		<pubDate>Thu, 07 Mar 2013 20:50:47 +0000</pubDate>
		<guid isPermaLink="false">http://scientificbsides.wordpress.com/?p=1576#comment-411</guid>
		<description><![CDATA[here&#039;s two more that didn&#039;t make it onto the first comment:
http://youtu.be/nmxAzkM3fhw
http://youtu.be/jsUd0oJ5LrY]]></description>
		<content:encoded><![CDATA[<p>here&#8217;s two more that didn&#8217;t make it onto the first comment:<br />
<span class='embed-youtube' style='text-align:center; display: block;'><iframe class='youtube-player' type='text/html' width='580' height='357' src='http://www.youtube.com/embed/nmxAzkM3fhw?version=3&#038;rel=1&#038;fs=1&#038;showsearch=0&#038;showinfo=1&#038;iv_load_policy=1&#038;wmode=transparent' frameborder='0'></iframe></span><br />
<a href="http://youtu.be/jsUd0oJ5LrY" rel="nofollow">http://youtu.be/jsUd0oJ5LrY</a></p>
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		<title>Comment on Mix Tape #1: Best Songs About Science by Dan Gareau</title>
		<link>http://scientificbsides.wordpress.com/2012/01/13/mix-tape-best-songs-about-science/#comment-410</link>
		<dc:creator><![CDATA[Dan Gareau]]></dc:creator>
		<pubDate>Thu, 07 Mar 2013 20:43:58 +0000</pubDate>
		<guid isPermaLink="false">http://scientificbsides.wordpress.com/?p=1576#comment-410</guid>
		<description><![CDATA[Here are some songs of science by me:
http://youtu.be/jq0dQx7RWv8
http://youtu.be/nmxAzkM3fhw
http://youtu.be/fG_OzU1pzlA
http://youtu.be/jsUd0oJ5LrY
http://youtu.be/BF-oplD5jrk]]></description>
		<content:encoded><![CDATA[<p>Here are some songs of science by me:<br />
<span class='embed-youtube' style='text-align:center; display: block;'><iframe class='youtube-player' type='text/html' width='580' height='357' src='http://www.youtube.com/embed/jq0dQx7RWv8?version=3&#038;rel=1&#038;fs=1&#038;showsearch=0&#038;showinfo=1&#038;iv_load_policy=1&#038;wmode=transparent' frameborder='0'></iframe></span><br />
<a href="http://youtu.be/nmxAzkM3fhw" rel="nofollow">http://youtu.be/nmxAzkM3fhw</a><br />
<span class='embed-youtube' style='text-align:center; display: block;'><iframe class='youtube-player' type='text/html' width='580' height='357' src='http://www.youtube.com/embed/fG_OzU1pzlA?version=3&#038;rel=1&#038;fs=1&#038;showsearch=0&#038;showinfo=1&#038;iv_load_policy=1&#038;wmode=transparent' frameborder='0'></iframe></span><br />
<a href="http://youtu.be/jsUd0oJ5LrY" rel="nofollow">http://youtu.be/jsUd0oJ5LrY</a><br />
<span class='embed-youtube' style='text-align:center; display: block;'><iframe class='youtube-player' type='text/html' width='580' height='357' src='http://www.youtube.com/embed/BF-oplD5jrk?version=3&#038;rel=1&#038;fs=1&#038;showsearch=0&#038;showinfo=1&#038;iv_load_policy=1&#038;wmode=transparent' frameborder='0'></iframe></span></p>
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		<title>Comment on Mix Tape #1: Best Songs About Science by geluid verhuur amsterdam</title>
		<link>http://scientificbsides.wordpress.com/2012/01/13/mix-tape-best-songs-about-science/#comment-405</link>
		<dc:creator><![CDATA[geluid verhuur amsterdam]]></dc:creator>
		<pubDate>Thu, 14 Feb 2013 09:26:10 +0000</pubDate>
		<guid isPermaLink="false">http://scientificbsides.wordpress.com/?p=1576#comment-405</guid>
		<description><![CDATA[A few songs I already forgotten how great they are.Especially Thomas Dolby.]]></description>
		<content:encoded><![CDATA[<p>A few songs I already forgotten how great they are.Especially Thomas Dolby.</p>
]]></content:encoded>
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		<title>Comment on &#8220;Detecting Novel Associations in Large Data Sets&#8221; &#8212; let the giants battle it out! by Maximal Information Coefficient &#8211; just a messed-up estimate of mutual information? &#124; Scientific B-sides</title>
		<link>http://scientificbsides.wordpress.com/2012/01/23/detecting-novel-associations-in-large-data-sets-let-the-giants-battle-it-out/#comment-400</link>
		<dc:creator><![CDATA[Maximal Information Coefficient &#8211; just a messed-up estimate of mutual information? &#124; Scientific B-sides]]></dc:creator>
		<pubDate>Sun, 10 Feb 2013 20:19:41 +0000</pubDate>
		<guid isPermaLink="false">http://scientificbsides.wordpress.com/?p=2399#comment-400</guid>
		<description><![CDATA[[...] Novel Associations in Large Data Sets&#8217; in Science by Reshef et al before (here and here). The reception in the statistics community was mixed and while Terry Speed seemed to love it, Rob [...]]]></description>
		<content:encoded><![CDATA[<p>[...] Novel Associations in Large Data Sets&#8217; in Science by Reshef et al before (here and here). The reception in the statistics community was mixed and while Terry Speed seemed to love it, Rob [...]</p>
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