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	<title>Comments on: Viruses and the tree of life</title>
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	<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/</link>
	<description>About viruses and viral disease</description>
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		<title>By: Ramsy</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-30950</link>
		<dc:creator>Ramsy</dc:creator>
		<pubDate>Thu, 09 Feb 2012 09:37:00 +0000</pubDate>
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		<description>I personally think that viruses are non-living and living, because of the fact that they sought of become alive when they enter a living cell. Another thing that boggles me is how do viruses know how to do their thing, how do they find a cell......?</description>
		<content:encoded><![CDATA[<p>I personally think that viruses are non-living and living, because of the fact that they sought of become alive when they enter a living cell. Another thing that boggles me is how do viruses know how to do their thing, how do they find a cell&#8230;&#8230;?</p>
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		<title>By: Dan, Tx</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-30937</link>
		<dc:creator>Dan, Tx</dc:creator>
		<pubDate>Tue, 07 Feb 2012 21:43:00 +0000</pubDate>
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		<description>I consider viruses to be alive, they have a genome, they use the genome to direct transcription, translation, and protein synthesis (except for viroids).  But even naked RNA strands of viroids are capable of replication in the correct environment (host cell).  What living organism can reproduce in the absence of nutrients? None. Viruses are no different, they require a very special set of nutrients. They are obligate parasites - many organisms are known that can not grow or replicate outside of their hosts, but can survive in a resting state. So, I see viruses as living. The flu is not cause by a toxin, it is caused by a pathogen that replicates and causes symptoms in its host.  Viruses probably have arisen many times as degenerated bits from other living forms and have been cobbled together from bits picked up along the way. So, they are very different from organisms that we think of in the tree (usually). However, over short periods of time populations clearly can evolve.  You seem hung up on the fact that the virus only is actively living when it inhabits a host cell. This is quite a prejudice.  Perhaps the earth could view us as viruses? After all, we don&#039;t make our own planets, we just live off of ones that are already there.  Prions are the example of a non-living infectious agent.  I do draw the line at prions, because they do not possess a genome and are simply proteins that are unable to specify their own.</description>
		<content:encoded><![CDATA[<p>I consider viruses to be alive, they have a genome, they use the genome to direct transcription, translation, and protein synthesis (except for viroids).  But even naked RNA strands of viroids are capable of replication in the correct environment (host cell).  What living organism can reproduce in the absence of nutrients? None. Viruses are no different, they require a very special set of nutrients. They are obligate parasites &#8211; many organisms are known that can not grow or replicate outside of their hosts, but can survive in a resting state. So, I see viruses as living. The flu is not cause by a toxin, it is caused by a pathogen that replicates and causes symptoms in its host.  Viruses probably have arisen many times as degenerated bits from other living forms and have been cobbled together from bits picked up along the way. So, they are very different from organisms that we think of in the tree (usually). However, over short periods of time populations clearly can evolve.  You seem hung up on the fact that the virus only is actively living when it inhabits a host cell. This is quite a prejudice.  Perhaps the earth could view us as viruses? After all, we don&#8217;t make our own planets, we just live off of ones that are already there.  Prions are the example of a non-living infectious agent.  I do draw the line at prions, because they do not possess a genome and are simply proteins that are unable to specify their own.</p>
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		<title>By: Chris Stacy</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-26078</link>
		<dc:creator>Chris Stacy</dc:creator>
		<pubDate>Fri, 25 Mar 2011 14:21:00 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-26078</guid>
		<description>Someone already answered you generally about proteins vs. DNA, but you ought to google these terms for more information on a tangent you would be interested in:  &quot;epigenetics&quot; and &quot;RNA world&quot;.  There are probably decent Wikipedia articles to get you started.

Moreover,everything about DNA is subject to what is broadly called &quot;regulation&quot;.  The story that DNA ultimately codes for proteins is an extraordinarily simplistic explanation. There is so much more to it, most of which we do not understand. </description>
		<content:encoded><![CDATA[<p>Someone already answered you generally about proteins vs. DNA, but you ought to google these terms for more information on a tangent you would be interested in:  &#8220;epigenetics&#8221; and &#8220;RNA world&#8221;.  There are probably decent Wikipedia articles to get you started.</p>
<p>Moreover,everything about DNA is subject to what is broadly called &#8220;regulation&#8221;.  The story that DNA ultimately codes for proteins is an extraordinarily simplistic explanation. There is so much more to it, most of which we do not understand.</p>
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		<title>By: Liz</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-24801</link>
		<dc:creator>Liz</dc:creator>
		<pubDate>Mon, 10 Jan 2011 15:51:00 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-24801</guid>
		<description>It is just plain scary that people like you, who have no clue about this stuff are making vaccines.</description>
		<content:encoded><![CDATA[<p>It is just plain scary that people like you, who have no clue about this stuff are making vaccines.</p>
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		<title>By: ductub</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-21552</link>
		<dc:creator>ductub</dc:creator>
		<pubDate>Sat, 24 Apr 2010 18:51:43 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-21552</guid>
		<description>Prof. Racaniello,&lt;br&gt;1. If your view is that viruses are not alive, are they dead? Or do you think they are neither alive or dead?&lt;br&gt;2. If viruses are not alive, why some viral vaccines contain live viruses?&lt;br&gt;3. Do you think that obligate intracellular bacteria are not alive either? They can&#039;t replicate without host cells, same as viruses.&lt;br&gt;4. I disagree with the view that viruses cannot adapt and evolve, in fact as a professor of virology, you should know this better than anyone. If they can, they should be considered as a living thing, despite lacking the &quot;organismic&quot; structure and ability to metabolize. This is as opposed to inert structures, which can be considered as dead.&lt;br&gt;Sincerely</description>
		<content:encoded><![CDATA[<p>Prof. Racaniello,<br />1. If your view is that viruses are not alive, are they dead? Or do you think they are neither alive or dead?<br />2. If viruses are not alive, why some viral vaccines contain live viruses?<br />3. Do you think that obligate intracellular bacteria are not alive either? They can&#39;t replicate without host cells, same as viruses.<br />4. I disagree with the view that viruses cannot adapt and evolve, in fact as a professor of virology, you should know this better than anyone. If they can, they should be considered as a living thing, despite lacking the &#8220;organismic&#8221; structure and ability to metabolize. This is as opposed to inert structures, which can be considered as dead.<br />Sincerely</p>
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		<title>By: ductub</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-21438</link>
		<dc:creator>ductub</dc:creator>
		<pubDate>Sat, 24 Apr 2010 11:51:43 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-21438</guid>
		<description>Prof. Racaniello,&lt;br&gt;1. If your view is that viruses are not alive, are they dead? Or do you think they are neither alive or dead?&lt;br&gt;2. If viruses are not alive, why some viral vaccines contain live viruses?&lt;br&gt;3. Do you think that obligate intracellular bacteria are not alive either? They can&#039;t replicate without host cells, same as viruses.&lt;br&gt;4. I disagree with the view that viruses cannot adapt and evolve, in fact as a professor of virology, you should know this better than anyone. If they can, they should be considered as a living thing, despite lacking the &quot;organismic&quot; structure and ability to metabolize. This is as opposed to inert structures, which can be considered as dead.&lt;br&gt;Sincerely</description>
		<content:encoded><![CDATA[<p>Prof. Racaniello,<br />1. If your view is that viruses are not alive, are they dead? Or do you think they are neither alive or dead?<br />2. If viruses are not alive, why some viral vaccines contain live viruses?<br />3. Do you think that obligate intracellular bacteria are not alive either? They can&#39;t replicate without host cells, same as viruses.<br />4. I disagree with the view that viruses cannot adapt and evolve, in fact as a professor of virology, you should know this better than anyone. If they can, they should be considered as a living thing, despite lacking the &#8220;organismic&#8221; structure and ability to metabolize. This is as opposed to inert structures, which can be considered as dead.<br />Sincerely</p>
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		<title>By: E.I. </title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-20091</link>
		<dc:creator>E.I. </dc:creator>
		<pubDate>Sun, 31 Jan 2010 04:16:03 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-20091</guid>
		<description>Yes, it is true that viruses do not fit into the cellular tree of life, but viruses are capable of forming phylogenetic trees of their own.  These trees show relatedness among viruses of a particular domain (eukaryotic viruses, archaeal viruses, etc.) and do suggest a common viral ancestor.  The fact that we know so little about viruses  complicates these phylogenetic comparisons.&lt;br&gt;&lt;br&gt;As for the argument that viruses don&#039;t share a common structure...  Viruses rapidly evolve; it&#039;s one of the major reasons for their tremendous success.  This rapid evolution makes it difficult to say that viruses don&#039;t share things in common.  We have little idea what the early earth was like, but it is obvious that conditions have changed since the origin of &quot;life.&quot;  As viruses adapted to new hosts they altered their genetic makeup to make them better equipped for a certain host.&lt;br&gt;&lt;br&gt;The fact that there is not a common ancestor does not mean that it never existed.  That is just illogical and  completely unsupported.  Cellular life leaves fossilized evidence.  We are learning that viruses do as well, but it is much (MUCH) more difficult to collect this data (viruses are much smaller than cells).</description>
		<content:encoded><![CDATA[<p>Yes, it is true that viruses do not fit into the cellular tree of life, but viruses are capable of forming phylogenetic trees of their own.  These trees show relatedness among viruses of a particular domain (eukaryotic viruses, archaeal viruses, etc.) and do suggest a common viral ancestor.  The fact that we know so little about viruses  complicates these phylogenetic comparisons.</p>
<p>As for the argument that viruses don&#39;t share a common structure&#8230;  Viruses rapidly evolve; it&#39;s one of the major reasons for their tremendous success.  This rapid evolution makes it difficult to say that viruses don&#39;t share things in common.  We have little idea what the early earth was like, but it is obvious that conditions have changed since the origin of &#8220;life.&#8221;  As viruses adapted to new hosts they altered their genetic makeup to make them better equipped for a certain host.</p>
<p>The fact that there is not a common ancestor does not mean that it never existed.  That is just illogical and  completely unsupported.  Cellular life leaves fossilized evidence.  We are learning that viruses do as well, but it is much (MUCH) more difficult to collect this data (viruses are much smaller than cells).</p>
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		<title>By: tumblemark</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-19355</link>
		<dc:creator>tumblemark</dc:creator>
		<pubDate>Thu, 17 Dec 2009 13:01:45 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-19355</guid>
		<description>On the matter of virus monophylogeny, consider that their origin in the three kingdom tree of life has been established in the computational biology paper:&lt;br&gt;&lt;br&gt;Sun F-J, Caetano-Anolle´s G (2008) Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses. PLoS&lt;br&gt;Comput Biol 4(3): e1000018. doi:10.1371/journal.pcbi.1000018</description>
		<content:encoded><![CDATA[<p>On the matter of virus monophylogeny, consider that their origin in the three kingdom tree of life has been established in the computational biology paper:</p>
<p>Sun F-J, Caetano-Anolle´s G (2008) Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses. PLoS<br />Comput Biol 4(3): e1000018. doi:10.1371/journal.pcbi.1000018</p>
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		<title>By: yoyo123a</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-17754</link>
		<dc:creator>yoyo123a</dc:creator>
		<pubDate>Thu, 08 Oct 2009 03:20:46 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-17754</guid>
		<description>Your blog is nice,i like it.&lt;br&gt;&lt;br&gt;&lt;a href=&quot;http://www.360huoyuan.com&quot; rel=&quot;nofollow&quot;&gt;http://www.360huoyuan.com&lt;/a&gt;</description>
		<content:encoded><![CDATA[<p>Your blog is nice,i like it.</p>
<p><a href="http://www.360huoyuan.com" rel="nofollow">http://www.360huoyuan.com</a></p>
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		<title>By: ALVAC-HIV and AIDSVAX B/E</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-17548</link>
		<dc:creator>ALVAC-HIV and AIDSVAX B/E</dc:creator>
		<pubDate>Sun, 27 Sep 2009 15:32:21 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-17548</guid>
		<description>[...] the disease and the virus) Rotavirus seasonality (thanks Didier!) Viruses and the tree of life at virology blog Big brains have evolved twice (thanks [...]</description>
		<content:encoded><![CDATA[<p>[...] the disease and the virus) Rotavirus seasonality (thanks Didier!) Viruses and the tree of life at virology blog Big brains have evolved twice (thanks [...]</p>
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		<title>By: Prophage</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-17145</link>
		<dc:creator>Prophage</dc:creator>
		<pubDate>Sat, 22 Aug 2009 20:37:44 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-17145</guid>
		<description>Virses are living entities!  They are obligate parasites which means that  they need a host to replicate, otherwise they are dormant.&lt;br&gt;&lt;br&gt;They discovery of Sputnik- a virus that infects a virus also adds weight to this argument.&lt;br&gt;&lt;br&gt;Any genetic material capable of replicating can be considered &quot;living&quot;. It will only be a matter of time, loss of old dogma and a broader view of life sciences that will result in this idea becoming universal...</description>
		<content:encoded><![CDATA[<p>Virses are living entities!  They are obligate parasites which means that  they need a host to replicate, otherwise they are dormant.</p>
<p>They discovery of Sputnik- a virus that infects a virus also adds weight to this argument.</p>
<p>Any genetic material capable of replicating can be considered &#8220;living&#8221;. It will only be a matter of time, loss of old dogma and a broader view of life sciences that will result in this idea becoming universal&#8230;</p>
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		<title>By: Traveller</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-23426</link>
		<dc:creator>Traveller</dc:creator>
		<pubDate>Sun, 02 Aug 2009 04:39:00 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-23426</guid>
		<description>This is quite impressive, I am pleased to read this post, keep posts like this coming, you totally rock!Cheers,&lt;a href=&quot;http://sain-web.com&quot; rel=&quot;nofollow&quot;&gt;Blog Review&lt;/a&gt;</description>
		<content:encoded><![CDATA[<p>This is quite impressive, I am pleased to read this post, keep posts like this coming, you totally rock!Cheers,<a href="http://sain-web.com" rel="nofollow">Blog Review</a></p>
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		<title>By: Chelsea</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-23421</link>
		<dc:creator>Chelsea</dc:creator>
		<pubDate>Sun, 05 Jul 2009 03:53:00 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-23421</guid>
		<description>YES YES YES!!!!!!!!!</description>
		<content:encoded><![CDATA[<p>YES YES YES!!!!!!!!!</p>
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		<title>By: Chelsea</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-5346</link>
		<dc:creator>Chelsea</dc:creator>
		<pubDate>Sun, 05 Jul 2009 02:01:31 +0000</pubDate>
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		<description>my mother is greatly against vaccine use, and i have never once been vaccinated and have many health benefits due so..&lt;br&gt;&lt;br&gt;our race is so hideously fixated on saving EVERYONE that we do not take in account the future&lt;br&gt;&lt;br&gt;we are AFRAID of natural selection.</description>
		<content:encoded><![CDATA[<p>my mother is greatly against vaccine use, and i have never once been vaccinated and have many health benefits due so..</p>
<p>our race is so hideously fixated on saving EVERYONE that we do not take in account the future</p>
<p>we are AFRAID of natural selection.</p>
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		<title>By: Chelsea</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-5337</link>
		<dc:creator>Chelsea</dc:creator>
		<pubDate>Sun, 05 Jul 2009 01:51:52 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-5337</guid>
		<description>i was pondering about all of this and is it possible that the reason, in #9, &quot;This conclusion is paradoxical because viral genomes are the most abundant on earth.&quot; is because all life could have been created from different &#039;viruses&#039;?</description>
		<content:encoded><![CDATA[<p>i was pondering about all of this and is it possible that the reason, in #9, &#8220;This conclusion is paradoxical because viral genomes are the most abundant on earth.&#8221; is because all life could have been created from different &#39;viruses&#39;?</p>
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		<title>By: Xelo</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-1561</link>
		<dc:creator>Xelo</dc:creator>
		<pubDate>Sun, 21 Jun 2009 17:39:49 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-1561</guid>
		<description>I will agree that when outside a cell that the virion is not living or more aptly put dormant. However every organism is built to reproduce and pass on its genetic material from one generation to another.  Once in side a host cell viruses reproduce and can use cellular energy to create more of themselves. Also they evolve, they respond to pressures from their biotic environment. Simply put, viruses evolve and reproduce, two characteristics that inanimate matter, should not posses.</description>
		<content:encoded><![CDATA[<p>I will agree that when outside a cell that the virion is not living or more aptly put dormant. However every organism is built to reproduce and pass on its genetic material from one generation to another.  Once in side a host cell viruses reproduce and can use cellular energy to create more of themselves. Also they evolve, they respond to pressures from their biotic environment. Simply put, viruses evolve and reproduce, two characteristics that inanimate matter, should not posses.</p>
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		<title>By: Anonymous</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-23418</link>
		<dc:creator>Anonymous</dc:creator>
		<pubDate>Mon, 08 Jun 2009 16:29:00 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-23418</guid>
		<description>I do continue to have questions about point 4, and if anyone can assist in clarifying I would be much appreciated. The ODE is very serious about keeping the editorial control of the paper out of the publishers hands, but Steve Smith’s recommendation and (this is the point I need clarification on) proposed contract had language that separated editorial control of the paper &lt;a href=&quot;http://www.chasereviews.com/chasecom.php&quot; rel=&quot;nofollow&quot;&gt;chase.com&lt;/a&gt; from the publisher and, as far as I can tell, give the publisher a higher rank in business matters only.</description>
		<content:encoded><![CDATA[<p>I do continue to have questions about point 4, and if anyone can assist in clarifying I would be much appreciated. The ODE is very serious about keeping the editorial control of the paper out of the publishers hands, but Steve Smith’s recommendation and (this is the point I need clarification on) proposed contract had language that separated editorial control of the paper <a href="http://www.chasereviews.com/chasecom.php" rel="nofollow">chase.com</a> from the publisher and, as far as I can tell, give the publisher a higher rank in business matters only.</p>
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		<title>By: jerryclatham28</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-1424</link>
		<dc:creator>jerryclatham28</dc:creator>
		<pubDate>Mon, 08 Jun 2009 05:09:38 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-1424</guid>
		<description>Viral translation genes originate from cells The mimivirus genome harbors genes encoding elements of the protein synthesis machinery. This observation has been interpreted to mean that viruses did not always rely on cells for translation. However, sequence analysis indicates that these genes are derived from cells by horizontal gene transfer.Viruses steal genes from cells Viral genomes encode many genes that have no homologues in cells. It has been suggested that viruses influence evolution of cells &lt;a href=&quot;http://www.chasereviews.com&quot; rel=&quot;nofollow&quot;&gt;www.chase.com&lt;/a&gt; by donating new genes. Sequence analysis has failed to provide support for this hypothesis. Viruses are ‘gene robbers, not gene inventors and massive gene suppliers’.</description>
		<content:encoded><![CDATA[<p>Viral translation genes originate from cells The mimivirus genome harbors genes encoding elements of the protein synthesis machinery. This observation has been interpreted to mean that viruses did not always rely on cells for translation. However, sequence analysis indicates that these genes are derived from cells by horizontal gene transfer.Viruses steal genes from cells Viral genomes encode many genes that have no homologues in cells. It has been suggested that viruses influence evolution of cells <a href="http://www.chasereviews.com" rel="nofollow">http://www.chase.com</a> by donating new genes. Sequence analysis has failed to provide support for this hypothesis. Viruses are ‘gene robbers, not gene inventors and massive gene suppliers’.</p>
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		<title>By: MicrobiologyBytes &#187; Blog Archive &#187; Are viruses alive?</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-582</link>
		<dc:creator>MicrobiologyBytes &#187; Blog Archive &#187; Are viruses alive?</dc:creator>
		<pubDate>Thu, 23 Apr 2009 13:43:32 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-582</guid>
		<description>[...] Virology Blog: Viruses and the tree of life [...]</description>
		<content:encoded><![CDATA[<p>[...] Virology Blog: Viruses and the tree of life [...]</p>
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		<title>By: profvrr</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-452</link>
		<dc:creator>profvrr</dc:creator>
		<pubDate>Wed, 01 Apr 2009 15:55:53 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-452</guid>
		<description>Hi Bill,&lt;br&gt;&lt;br&gt;Don&#039;t apologize for questions - here at virology blog there aren&#039;t any bad questions. We want to teach virology so all inquiries are welcome. In fact your questions are excellent.&lt;br&gt;&lt;br&gt;Having a discussion board is a great idea. I&#039;ll look into the software to run it. As for your questions:&lt;br&gt;&lt;br&gt;1. Chromosomes were known for many years to be composed of both protein and DNA, and scientists didn&#039;t know which was the genetic material. A key experiment was done in 1944 when Avery, McLeod and McCarty showed that DNA could induce a change in bacterial phenotype. In 1952 Hershey and Chase provided further support for DNA as genetic material, by showing that the DNA, and not protein, enters cells during a viral infection.&lt;br&gt;&lt;br&gt;2. Vaccines mimic (although not always perfectly) what happens in a natural infection - the production of immunity to the virus. This immune response clearly exerts selective pressure on the virus. A perfect example is the yearly antigenic change of influenza virus that is selected each year by population immunity. Some viruses, like poliovirus, are not antigenically variable and probably not subject to such selective forces.</description>
		<content:encoded><![CDATA[<p>Hi Bill,</p>
<p>Don&#39;t apologize for questions &#8211; here at virology blog there aren&#39;t any bad questions. We want to teach virology so all inquiries are welcome. In fact your questions are excellent.</p>
<p>Having a discussion board is a great idea. I&#39;ll look into the software to run it. As for your questions:</p>
<p>1. Chromosomes were known for many years to be composed of both protein and DNA, and scientists didn&#39;t know which was the genetic material. A key experiment was done in 1944 when Avery, McLeod and McCarty showed that DNA could induce a change in bacterial phenotype. In 1952 Hershey and Chase provided further support for DNA as genetic material, by showing that the DNA, and not protein, enters cells during a viral infection.</p>
<p>2. Vaccines mimic (although not always perfectly) what happens in a natural infection &#8211; the production of immunity to the virus. This immune response clearly exerts selective pressure on the virus. A perfect example is the yearly antigenic change of influenza virus that is selected each year by population immunity. Some viruses, like poliovirus, are not antigenically variable and probably not subject to such selective forces.</p>
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		<title>By: bill_mcculley</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-445</link>
		<dc:creator>bill_mcculley</dc:creator>
		<pubDate>Mon, 30 Mar 2009 13:34:37 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-445</guid>
		<description>Hello Dr. Racaniello,&lt;br&gt;&lt;br&gt;Great questions for discuss.  I hope you don&#039;t mind laypersons (electrical engineers like myself) in asking a few questions I&#039;ve been thinking about!  One recommendation is perhaps a you can setup a general discussion area on this website for oddball questions like mine or others that aren&#039;t easily catagorized.&lt;br&gt;&lt;br&gt;This thread is about as broad as any other, so here are a couple of unconventional ideas I&#039;ve had -&lt;br&gt;&lt;br&gt;1.  Did you ever think, at a more primary fundamental level, perhaps proteins/amino acids themselves were the actual &quot;intelligence&quot; rather than DNA &quot;driving the show&quot;.  Perhaps DNA is merely just a scoffolding which the amino acids decide to hang their hats.  Perhaps there is something beyond the interaction between amino acids - beyond mere biochemstry?  (Perhaps it sounds really strange)&lt;br&gt;&lt;br&gt;2.  Did you ever wonder if, by the broad use of vaccines, we are exerting an artificial stress on the ecology of a virus, thereby essentially resulting in a stronger virus to be selected down the road?  Sort of like the National forest park policy of preventing fires for for so many decades, thus creating conditions in which much larger, horrendous forest fires can now occur.  &lt;br&gt;&lt;br&gt;Like I said, I&#039;m interested about learning more.  So I hope you don&#039;t mind my lack of exact terminology or my understanding in terms of the basic concepts of virology&lt;br&gt;&lt;br&gt;- Bill</description>
		<content:encoded><![CDATA[<p>Hello Dr. Racaniello,</p>
<p>Great questions for discuss.  I hope you don&#39;t mind laypersons (electrical engineers like myself) in asking a few questions I&#39;ve been thinking about!  One recommendation is perhaps a you can setup a general discussion area on this website for oddball questions like mine or others that aren&#39;t easily catagorized.</p>
<p>This thread is about as broad as any other, so here are a couple of unconventional ideas I&#39;ve had -</p>
<p>1.  Did you ever think, at a more primary fundamental level, perhaps proteins/amino acids themselves were the actual &#8220;intelligence&#8221; rather than DNA &#8220;driving the show&#8221;.  Perhaps DNA is merely just a scoffolding which the amino acids decide to hang their hats.  Perhaps there is something beyond the interaction between amino acids &#8211; beyond mere biochemstry?  (Perhaps it sounds really strange)</p>
<p>2.  Did you ever wonder if, by the broad use of vaccines, we are exerting an artificial stress on the ecology of a virus, thereby essentially resulting in a stronger virus to be selected down the road?  Sort of like the National forest park policy of preventing fires for for so many decades, thus creating conditions in which much larger, horrendous forest fires can now occur.  </p>
<p>Like I said, I&#39;m interested about learning more.  So I hope you don&#39;t mind my lack of exact terminology or my understanding in terms of the basic concepts of virology</p>
<p>- Bill</p>
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		<title>By: Are viruses alive? &#171; MicrobiologyBytes</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-421</link>
		<dc:creator>Are viruses alive? &#171; MicrobiologyBytes</dc:creator>
		<pubDate>Wed, 25 Mar 2009 09:02:18 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-421</guid>
		<description>[...] Virology Blog: Viruses and the tree of life [...]</description>
		<content:encoded><![CDATA[<p>[...] Virology Blog: Viruses and the tree of life [...]</p>
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		<title>By: Pages tagged "five ancestors"</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-378</link>
		<dc:creator>Pages tagged "five ancestors"</dc:creator>
		<pubDate>Sat, 21 Mar 2009 07:36:57 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-378</guid>
		<description>[...] bookmarks tagged five ancestors Viruses and the tree of life&#160;saved by 13 others  &#160;&#160;&#160;&#160;TNAwrestling bookmarked on 03/21/09 &#124; [...]</description>
		<content:encoded><![CDATA[<p>[...] bookmarks tagged five ancestors Viruses and the tree of life&nbsp;saved by 13 others  &nbsp;&nbsp;&nbsp;&nbsp;TNAwrestling bookmarked on 03/21/09 | [...]</p>
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		<title>By: foop</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-371</link>
		<dc:creator>foop</dc:creator>
		<pubDate>Thu, 19 Mar 2009 19:06:06 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-371</guid>
		<description>Seems to me that they can become alive in the right environments.</description>
		<content:encoded><![CDATA[<p>Seems to me that they can become alive in the right environments.</p>
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		<title>By: discarded lies - hyperlinkopotamus</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-366</link>
		<dc:creator>discarded lies - hyperlinkopotamus</dc:creator>
		<pubDate>Thu, 19 Mar 2009 18:56:46 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-366</guid>
		<description>&lt;strong&gt;Viruses and the tree of life...&lt;/strong&gt;

Viruses and the tree of life...</description>
		<content:encoded><![CDATA[<p><strong>Viruses and the tree of life&#8230;</strong></p>
<p>Viruses and the tree of life&#8230;</p>
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		<title>By: Dave UH</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-368</link>
		<dc:creator>Dave UH</dc:creator>
		<pubDate>Thu, 19 Mar 2009 17:55:16 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-368</guid>
		<description>I thought that the line of reasoning was very cogently presented.  I, as a supporter of viruses being alive and having a deep root in evolutionary history will have to rethink my previously held hypothesis, in light of recent discoveries.  I believe that at this time there is not enough evidence to assert the view that viruses are remnants from the &quot;RNA World&quot;.</description>
		<content:encoded><![CDATA[<p>I thought that the line of reasoning was very cogently presented.  I, as a supporter of viruses being alive and having a deep root in evolutionary history will have to rethink my previously held hypothesis, in light of recent discoveries.  I believe that at this time there is not enough evidence to assert the view that viruses are remnants from the &#8220;RNA World&#8221;.</p>
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		<title>By: PaperHand</title>
		<link>http://www.virology.ws/2009/03/19/viruses-and-the-tree-of-life/comment-page-1/#comment-364</link>
		<dc:creator>PaperHand</dc:creator>
		<pubDate>Thu, 19 Mar 2009 13:29:06 +0000</pubDate>
		<guid isPermaLink="false">http://www.virology.ws/?p=942#comment-364</guid>
		<description>I&#039;ve never really understood the &quot;are viruses alive or not?&quot; debate.  Life isn&#039;t a simple binary function.  Whether you count viruses as alive or not depends on your definition of life, it seems to me.  So, really, isn&#039;t the debate more &quot;Is a definition of life that includes viruses useful or not?&quot;?  Framing the debate as &quot;are viruses alive or not?&quot; implies that there is an already-established definition of &quot;life&quot; allowing a debate over whether viruses fall in that established category.</description>
		<content:encoded><![CDATA[<p>I&#39;ve never really understood the &#8220;are viruses alive or not?&#8221; debate.  Life isn&#39;t a simple binary function.  Whether you count viruses as alive or not depends on your definition of life, it seems to me.  So, really, isn&#39;t the debate more &#8220;Is a definition of life that includes viruses useful or not?&#8221;?  Framing the debate as &#8220;are viruses alive or not?&#8221; implies that there is an already-established definition of &#8220;life&#8221; allowing a debate over whether viruses fall in that established category.</p>
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