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	<title>Comments on: What can medical research learn from the open source software movement?</title>
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	<link>http://bacteriality.com/2007/12/11/opensource/</link>
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		<title>By: Paul Albert</title>
		<link>http://bacteriality.com/2007/12/11/opensource/comment-page-1/#comment-17790</link>
		<dc:creator>Paul Albert</dc:creator>
		<pubDate>Thu, 23 Jul 2009 16:00:12 +0000</pubDate>
		<guid isPermaLink="false">http://bacteriality.com/2007/12/11/opensource/#comment-17790</guid>
		<description>Hi Alex,

You&#039;re right to be confused. As it turns out, we cited the right cohort and right author but the wrong study. 

Here&#039;s the study we should have cited:
http://www.ncbi.nlm.nih.gov/pubmed/16481636

You know, we try to be very careful with our sources, but this mistake made it into the paper. Frankly, it&#039;s really disappointing, but there&#039;s not much I can do at this point. 

Anyway, thanks for pointing out the error!

thanks,
Paul</description>
		<content:encoded><![CDATA[<p>Hi Alex,</p>
<p>You&#8217;re right to be confused. As it turns out, we cited the right cohort and right author but the wrong study. </p>
<p>Here&#8217;s the study we should have cited:<br />
<a href="http://www.ncbi.nlm.nih.gov/pubmed/16481636" rel="nofollow">http://www.ncbi.nlm.nih.gov/pubmed/16481636</a></p>
<p>You know, we try to be very careful with our sources, but this mistake made it into the paper. Frankly, it&#8217;s really disappointing, but there&#8217;s not much I can do at this point. </p>
<p>Anyway, thanks for pointing out the error!</p>
<p>thanks,<br />
Paul</p>
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		<title>By: Alex</title>
		<link>http://bacteriality.com/2007/12/11/opensource/comment-page-1/#comment-17789</link>
		<dc:creator>Alex</dc:creator>
		<pubDate>Thu, 23 Jul 2009 15:15:52 +0000</pubDate>
		<guid isPermaLink="false">http://bacteriality.com/2007/12/11/opensource/#comment-17789</guid>
		<description>I have a question regarding your paper &quot;Vitamin D: the alternative Hypothesis&quot; related to Lappe et al. You wrote:
&quot; In a similar study looking at a larger cohort
and over a longer period of time, Rossouw et al´found no such effect&quot;.

However, looking for the Rossouw et al abstract no Vitamin D Supplementation is mentioned, only Estrogen + Progrestin intake.

I do not have the full paper, only the abstract. May be you can clarify this point, it would be appreciated!

best regards,

Alex</description>
		<content:encoded><![CDATA[<p>I have a question regarding your paper &#8220;Vitamin D: the alternative Hypothesis&#8221; related to Lappe et al. You wrote:<br />
&#8221; In a similar study looking at a larger cohort<br />
and over a longer period of time, Rossouw et al´found no such effect&#8221;.</p>
<p>However, looking for the Rossouw et al abstract no Vitamin D Supplementation is mentioned, only Estrogen + Progrestin intake.</p>
<p>I do not have the full paper, only the abstract. May be you can clarify this point, it would be appreciated!</p>
<p>best regards,</p>
<p>Alex</p>
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		<title>By: Amy Proal</title>
		<link>http://bacteriality.com/2007/12/11/opensource/comment-page-1/#comment-15986</link>
		<dc:creator>Amy Proal</dc:creator>
		<pubDate>Wed, 04 Feb 2009 00:07:08 +0000</pubDate>
		<guid isPermaLink="false">http://bacteriality.com/2007/12/11/opensource/#comment-15986</guid>
		<description>Hi Carol,

Oooh that conversation would have made me perk up as well!  It&#039;s amazing how changing a few data points can alter the results of a study.  There&#039;s a study by Lappe et al. on vitamin D and cancer.  Everything looks shiny and happy for cancer patients who are taking vitamin D in the abstract.  But if one reads the actual paper, the researchers discarded data of subjects who developed cancer during the first year of the study on grounds that &quot;cancers during the first year would have been present but undiagnosed at entry.&quot;  That excuse doesn&#039;t really hold IMO, and those exact subjects were the ones who would have had the most VDR blockage and been most susceptible to the negative effects of vitamin D.  Very misleading.

It&#039;s not a problem confined to the US.  I recently read an article in SEED magazine about the medical culture in China.  The Chinese Medical Association recently passed a law allowing researchers to report negative results and not lose funding or their jobs.  The culture values success so much that according to the article researchers are afraid to take risks because they might fail.  The hope is that the new law will help change the current mentality yet many believe that researchers are still afraid to admit failure.   I think that&#039;s a universal problem, but one that needs to change as new paradigms for chronic disease begin to take hold.

Thanks for your comments,
Amy</description>
		<content:encoded><![CDATA[<p>Hi Carol,</p>
<p>Oooh that conversation would have made me perk up as well!  It&#8217;s amazing how changing a few data points can alter the results of a study.  There&#8217;s a study by Lappe et al. on vitamin D and cancer.  Everything looks shiny and happy for cancer patients who are taking vitamin D in the abstract.  But if one reads the actual paper, the researchers discarded data of subjects who developed cancer during the first year of the study on grounds that &#8220;cancers during the first year would have been present but undiagnosed at entry.&#8221;  That excuse doesn&#8217;t really hold IMO, and those exact subjects were the ones who would have had the most VDR blockage and been most susceptible to the negative effects of vitamin D.  Very misleading.</p>
<p>It&#8217;s not a problem confined to the US.  I recently read an article in SEED magazine about the medical culture in China.  The Chinese Medical Association recently passed a law allowing researchers to report negative results and not lose funding or their jobs.  The culture values success so much that according to the article researchers are afraid to take risks because they might fail.  The hope is that the new law will help change the current mentality yet many believe that researchers are still afraid to admit failure.   I think that&#8217;s a universal problem, but one that needs to change as new paradigms for chronic disease begin to take hold.</p>
<p>Thanks for your comments,<br />
Amy</p>
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		<title>By: Carol</title>
		<link>http://bacteriality.com/2007/12/11/opensource/comment-page-1/#comment-15980</link>
		<dc:creator>Carol</dc:creator>
		<pubDate>Tue, 03 Feb 2009 05:43:30 +0000</pubDate>
		<guid isPermaLink="false">http://bacteriality.com/2007/12/11/opensource/#comment-15980</guid>
		<description>Amy,  Quoted from your essay 
&quot;If a negative result is based on good science, why confine it to obscurity? Why would we want to, in essence, encourage researchers to produce positive results even if those results make no significant contribution? You get what you ask for, and our system is, in essence, asking for such results.&quot;

Two and one-half months into the MP, my (teen) daughter was on a flight, seated within ear-shot of a &#039;researcher&#039; who was discussing by phone, just how to document the results of a clinical study, in which some patients had died.  She was &#039;tuned-in&#039; to the topic, because together we ourselves had already analyzed (critiqued) one clinical study that pertained to the meds she had been offered by the rheumatologist.  This site and the MP site have been an excellent education.  Thanks, Amy</description>
		<content:encoded><![CDATA[<p>Amy,  Quoted from your essay<br />
&#8220;If a negative result is based on good science, why confine it to obscurity? Why would we want to, in essence, encourage researchers to produce positive results even if those results make no significant contribution? You get what you ask for, and our system is, in essence, asking for such results.&#8221;</p>
<p>Two and one-half months into the MP, my (teen) daughter was on a flight, seated within ear-shot of a &#8216;researcher&#8217; who was discussing by phone, just how to document the results of a clinical study, in which some patients had died.  She was &#8216;tuned-in&#8217; to the topic, because together we ourselves had already analyzed (critiqued) one clinical study that pertained to the meds she had been offered by the rheumatologist.  This site and the MP site have been an excellent education.  Thanks, Amy</p>
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		<title>By: Tim</title>
		<link>http://bacteriality.com/2007/12/11/opensource/comment-page-1/#comment-1619</link>
		<dc:creator>Tim</dc:creator>
		<pubDate>Mon, 04 Feb 2008 21:44:03 +0000</pubDate>
		<guid isPermaLink="false">http://bacteriality.com/2007/12/11/opensource/#comment-1619</guid>
		<description>While the Open Source analogy is not without merit, I think what is being called for here is real science; a process similar to evolution itself. Trial hypotheses are tested and those that best explain some phenomenon are retained while those lacking in explanatory power are discarded. If science were conducted like that, then the infection hypothesis would be given an opportunity to fail like any other hypothesis.</description>
		<content:encoded><![CDATA[<p>While the Open Source analogy is not without merit, I think what is being called for here is real science; a process similar to evolution itself. Trial hypotheses are tested and those that best explain some phenomenon are retained while those lacking in explanatory power are discarded. If science were conducted like that, then the infection hypothesis would be given an opportunity to fail like any other hypothesis.</p>
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		<title>By: Joy</title>
		<link>http://bacteriality.com/2007/12/11/opensource/comment-page-1/#comment-1370</link>
		<dc:creator>Joy</dc:creator>
		<pubDate>Fri, 18 Jan 2008 01:11:04 +0000</pubDate>
		<guid isPermaLink="false">http://bacteriality.com/2007/12/11/opensource/#comment-1370</guid>
		<description>I can&#039;t understand why this amazingly good piece of work by Paul Albert hasn&#039;t been picked up for publication in other venues yet! 

After 20+ years in the software development business, my greatest lesson learned is that nobody cares to learn lessons from their own recent tendencies to make the same coding errors over and over, let alone learn lessons from the errors of others. 

Most developers fail to take the time to procure and study classic textbooks, such as Brooks&#039; &quot;The Mythical Man-Month,&quot; Summerville&#039;s &quot;Software Engineering,&quot; or some of Gerald M. Weinberg&#039;s works on code review, the psychology of computer programming, or organic problem solving.

What little I know of the medical field comes from personal interaction with my own doctors. And they all have been too busy to actively stay &quot;current&quot;  in their reading. Perhaps we shouldn&#039;t blame the doctors. Perhaps what they are reading has been so unhelpful, that they have made the right choice to not make the time for it? 

And as Mr. Albert points out, perhaps if it was their own condition, or the condition of their own child, they would suddenly find ways to get around this meaningless information logjam and find out what is really working and/or not working. 

In this “Internet Age” the “gatekeepers” have lost their power to control the flow of information. It is only a matter of time before more cutting-edge researchers begin to dare to prove it.</description>
		<content:encoded><![CDATA[<p>I can&#8217;t understand why this amazingly good piece of work by Paul Albert hasn&#8217;t been picked up for publication in other venues yet! </p>
<p>After 20+ years in the software development business, my greatest lesson learned is that nobody cares to learn lessons from their own recent tendencies to make the same coding errors over and over, let alone learn lessons from the errors of others. </p>
<p>Most developers fail to take the time to procure and study classic textbooks, such as Brooks&#8217; &#8220;The Mythical Man-Month,&#8221; Summerville&#8217;s &#8220;Software Engineering,&#8221; or some of Gerald M. Weinberg&#8217;s works on code review, the psychology of computer programming, or organic problem solving.</p>
<p>What little I know of the medical field comes from personal interaction with my own doctors. And they all have been too busy to actively stay &#8220;current&#8221;  in their reading. Perhaps we shouldn&#8217;t blame the doctors. Perhaps what they are reading has been so unhelpful, that they have made the right choice to not make the time for it? </p>
<p>And as Mr. Albert points out, perhaps if it was their own condition, or the condition of their own child, they would suddenly find ways to get around this meaningless information logjam and find out what is really working and/or not working. </p>
<p>In this “Internet Age” the “gatekeepers” have lost their power to control the flow of information. It is only a matter of time before more cutting-edge researchers begin to dare to prove it.</p>
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		<title>By: Phil Schoner</title>
		<link>http://bacteriality.com/2007/12/11/opensource/comment-page-1/#comment-638</link>
		<dc:creator>Phil Schoner</dc:creator>
		<pubDate>Fri, 21 Dec 2007 16:07:09 +0000</pubDate>
		<guid isPermaLink="false">http://bacteriality.com/2007/12/11/opensource/#comment-638</guid>
		<description>In keeping with the spirit of the season &quot;Although its been said many times, many ways&quot;, money and profits figure prominently in the failure of our current medical research system.  What would all those drug companies do if it became known that Benicar and cheap pulsed AB&#039;s could cure such a wide range of chronic diseases.  Diseases which currently provide them with such huge sources of revenue.

Its enough to drive you crazy.

Phil</description>
		<content:encoded><![CDATA[<p>In keeping with the spirit of the season &#8220;Although its been said many times, many ways&#8221;, money and profits figure prominently in the failure of our current medical research system.  What would all those drug companies do if it became known that Benicar and cheap pulsed AB&#8217;s could cure such a wide range of chronic diseases.  Diseases which currently provide them with such huge sources of revenue.</p>
<p>Its enough to drive you crazy.</p>
<p>Phil</p>
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		<title>By: Amy Proal</title>
		<link>http://bacteriality.com/2007/12/11/opensource/comment-page-1/#comment-459</link>
		<dc:creator>Amy Proal</dc:creator>
		<pubDate>Fri, 14 Dec 2007 04:04:57 +0000</pubDate>
		<guid isPermaLink="false">http://bacteriality.com/2007/12/11/opensource/#comment-459</guid>
		<description>Wow, it&#039;s a real pleasure to hear from you, Dr. Bradley. Let&#039;s hope there are still other scientists out there like yourself who are willing to rethink the way they do research.

Joao, it does appear that Dr. Sharma is the bad guy in this story, doesn&#039;t it? If you asked him, he would probably say that what he believes about the pathology of sarcoidosis is no different from what any number of other pulmonologists believe-- but that should be no excuse. Quite literally, lives are on the line.

Saj, thank you as always for your good feedback.

Amy</description>
		<content:encoded><![CDATA[<p>Wow, it&#8217;s a real pleasure to hear from you, Dr. Bradley. Let&#8217;s hope there are still other scientists out there like yourself who are willing to rethink the way they do research.</p>
<p>Joao, it does appear that Dr. Sharma is the bad guy in this story, doesn&#8217;t it? If you asked him, he would probably say that what he believes about the pathology of sarcoidosis is no different from what any number of other pulmonologists believe&#8211; but that should be no excuse. Quite literally, lives are on the line.</p>
<p>Saj, thank you as always for your good feedback.</p>
<p>Amy</p>
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		<title>By: Shirley J</title>
		<link>http://bacteriality.com/2007/12/11/opensource/comment-page-1/#comment-456</link>
		<dc:creator>Shirley J</dc:creator>
		<pubDate>Fri, 14 Dec 2007 01:48:30 +0000</pubDate>
		<guid isPermaLink="false">http://bacteriality.com/2007/12/11/opensource/#comment-456</guid>
		<description>Way to go!!  I am so proud you! This is a great article.  Very well versed.  Amazing! Saj</description>
		<content:encoded><![CDATA[<p>Way to go!!  I am so proud you! This is a great article.  Very well versed.  Amazing! Saj</p>
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	<item>
		<title>By: joao</title>
		<link>http://bacteriality.com/2007/12/11/opensource/comment-page-1/#comment-455</link>
		<dc:creator>joao</dc:creator>
		<pubDate>Fri, 14 Dec 2007 01:04:36 +0000</pubDate>
		<guid isPermaLink="false">http://bacteriality.com/2007/12/11/opensource/#comment-455</guid>
		<description>So Dr Om Sharma is purposefully hiding vital information from Sarcoidosis patients and allowing them to suffer and even die? The media has to get wind of this!</description>
		<content:encoded><![CDATA[<p>So Dr Om Sharma is purposefully hiding vital information from Sarcoidosis patients and allowing them to suffer and even die? The media has to get wind of this!</p>
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