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	<title>Comments on: A de novo&#8211;&#8217;Out of Nowhere&#8217; &#8212; Gene</title>
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		<title>By: Trikke</title>
		<link>http://www.uncommondescent.com/biology/a-de-novo-out-of-nowhere-gene/comment-page-1/#comment-304988</link>
		<dc:creator>Trikke</dc:creator>
		<pubDate>Wed, 18 Feb 2009 18:25:42 +0000</pubDate>
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		<description>&lt;strong&gt;Heya...&lt;/strong&gt;

Very nice site. All the best....</description>
		<content:encoded><![CDATA[<p><strong>Heya&#8230;</strong></p>
<p>Very nice site. All the best&#8230;.</p>
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		<title>By: peter borger</title>
		<link>http://www.uncommondescent.com/biology/a-de-novo-out-of-nowhere-gene/comment-page-1/#comment-129891</link>
		<dc:creator>peter borger</dc:creator>
		<pubDate>Mon, 30 Jul 2007 13:06:06 +0000</pubDate>
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		<description>VIGE is an abbreviation from GUToB (a general and universal theory of biological variation).

GUToB is the alternative biological theory that accounts for all biological observations. 

It is known that microsatellite DNA and the elements currently known as retroelements (or transposable elements, transposons, IS, or the like) can swap DNA strands and influence gene expression. These elements were specially designed genetic elements to delibrately induce variation in a controlled way in ancient multipurpose genomes. The elements themselves and the genetic mechanisms that made them transpose qualify as genetic redundancy and will therefore whither away rapidly (because selection does not act on these elements). 
It is no surprise that more and more evo-biologist claim that viruses contributes extensively to evolution. That is because what they believe are the remnants of viruses are NOT what they think they are. Rather these elements have been specially created to induce rapid adaptations and speciation events. Selection is irrelevant. That is what GUToB holds.</description>
		<content:encoded><![CDATA[<p>VIGE is an abbreviation from GUToB (a general and universal theory of biological variation).</p>
<p>GUToB is the alternative biological theory that accounts for all biological observations. </p>
<p>It is known that microsatellite DNA and the elements currently known as retroelements (or transposable elements, transposons, IS, or the like) can swap DNA strands and influence gene expression. These elements were specially designed genetic elements to delibrately induce variation in a controlled way in ancient multipurpose genomes. The elements themselves and the genetic mechanisms that made them transpose qualify as genetic redundancy and will therefore whither away rapidly (because selection does not act on these elements).<br />
It is no surprise that more and more evo-biologist claim that viruses contributes extensively to evolution. That is because what they believe are the remnants of viruses are NOT what they think they are. Rather these elements have been specially created to induce rapid adaptations and speciation events. Selection is irrelevant. That is what GUToB holds.</p>
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		<title>By: PaV</title>
		<link>http://www.uncommondescent.com/biology/a-de-novo-out-of-nowhere-gene/comment-page-1/#comment-129471</link>
		<dc:creator>PaV</dc:creator>
		<pubDate>Fri, 27 Jul 2007 22:35:35 +0000</pubDate>
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		<description>Here&#039;s the link: http://www.genetics.org/cgi/reprint/170/4/1945.pdf</description>
		<content:encoded><![CDATA[<p>Here&#8217;s the link: <a href="http://www.genetics.org/cgi/reprint/170/4/1945.pdf" rel="nofollow">http://www.genetics.org/cgi/reprint/170/4/1945.pdf</a></p>
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		<title>By: PaV</title>
		<link>http://www.uncommondescent.com/biology/a-de-novo-out-of-nowhere-gene/comment-page-1/#comment-129470</link>
		<dc:creator>PaV</dc:creator>
		<pubDate>Fri, 27 Jul 2007 22:35:07 +0000</pubDate>
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		<description>Peter: could you give us some more information on these VIGE&#039;s?

I found, very quickly, this paper.  Is this along the lines your describing?</description>
		<content:encoded><![CDATA[<p>Peter: could you give us some more information on these VIGE&#8217;s?</p>
<p>I found, very quickly, this paper.  Is this along the lines your describing?</p>
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		<title>By: peter borger</title>
		<link>http://www.uncommondescent.com/biology/a-de-novo-out-of-nowhere-gene/comment-page-1/#comment-129392</link>
		<dc:creator>peter borger</dc:creator>
		<pubDate>Fri, 27 Jul 2007 07:53:47 +0000</pubDate>
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		<description>it is known to virologists.</description>
		<content:encoded><![CDATA[<p>it is known to virologists.</p>
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		<title>By: Jehu</title>
		<link>http://www.uncommondescent.com/biology/a-de-novo-out-of-nowhere-gene/comment-page-1/#comment-129252</link>
		<dc:creator>Jehu</dc:creator>
		<pubDate>Thu, 26 Jul 2007 17:01:00 +0000</pubDate>
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		<description>Peter,

I already point to recent published research that found less homology between ORFans and viruses than non-ORFAn genes.  So there is no evidence that viruses are a significant source of ORFans.  

Now you are saying that you have found homologs to ORFans in more complex organisms? How did you do this? Did you perform your own BLAST search?</description>
		<content:encoded><![CDATA[<p>Peter,</p>
<p>I already point to recent published research that found less homology between ORFans and viruses than non-ORFAn genes.  So there is no evidence that viruses are a significant source of ORFans.  </p>
<p>Now you are saying that you have found homologs to ORFans in more complex organisms? How did you do this? Did you perform your own BLAST search?</p>
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		<title>By: peter borger</title>
		<link>http://www.uncommondescent.com/biology/a-de-novo-out-of-nowhere-gene/comment-page-1/#comment-129177</link>
		<dc:creator>peter borger</dc:creator>
		<pubDate>Thu, 26 Jul 2007 08:17:32 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/darwinism/a-de-novo-out-of-nowhere-gene/#comment-129177</guid>
		<description>&quot;ORFans are defined as ORFs (Open Reading Frames) having no sequence homologs in other genomes.&quot;

This is how it has been defined. Many orfan genes are found in viruses. Since I don&#039;t believe viruses just drop out of the sky, I started to check whether ORFans are really orfans. 
They are not. Many ORFans are lokated in retroelements or other jumping genetic material found in higher genomes (but that does not count, apparently). It should thus be noted that ORFans are not really orfan genes, but that viruses have their origin in jumping genetic elements. In fact, these elements are not remnants of viruses, but rather ar variation inducing genetic elements (VIGE). Viruses have their origin in VIGEs, not the other way around. Darwinians tend to mix thing up. It&#039;s their worldview.
It is a bit like the 1% difference between chimp an human. &quot;Everybody&quot; in the field knew it wasn&#039;t true. &quot;Everybody&quot; in the field knows ORFans are not really ORFans.</description>
		<content:encoded><![CDATA[<p>&#8220;ORFans are defined as ORFs (Open Reading Frames) having no sequence homologs in other genomes.&#8221;</p>
<p>This is how it has been defined. Many orfan genes are found in viruses. Since I don&#8217;t believe viruses just drop out of the sky, I started to check whether ORFans are really orfans.<br />
They are not. Many ORFans are lokated in retroelements or other jumping genetic material found in higher genomes (but that does not count, apparently). It should thus be noted that ORFans are not really orfan genes, but that viruses have their origin in jumping genetic elements. In fact, these elements are not remnants of viruses, but rather ar variation inducing genetic elements (VIGE). Viruses have their origin in VIGEs, not the other way around. Darwinians tend to mix thing up. It&#8217;s their worldview.<br />
It is a bit like the 1% difference between chimp an human. &#8220;Everybody&#8221; in the field knew it wasn&#8217;t true. &#8220;Everybody&#8221; in the field knows ORFans are not really ORFans.</p>
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		<title>By: Jehu</title>
		<link>http://www.uncommondescent.com/biology/a-de-novo-out-of-nowhere-gene/comment-page-1/#comment-129169</link>
		<dc:creator>Jehu</dc:creator>
		<pubDate>Thu, 26 Jul 2007 07:08:41 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/darwinism/a-de-novo-out-of-nowhere-gene/#comment-129169</guid>
		<description>I disagree.  I don&#039;t see how genes that appear out of nowhere are a problem for ID.  On the other hand, they are not predicted for Darwinism.  Remember, Darwinism works only by small gradual changes.  Darwinism cannot explain large chunks of information that come out of nowhere.</description>
		<content:encoded><![CDATA[<p>I disagree.  I don&#8217;t see how genes that appear out of nowhere are a problem for ID.  On the other hand, they are not predicted for Darwinism.  Remember, Darwinism works only by small gradual changes.  Darwinism cannot explain large chunks of information that come out of nowhere.</p>
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		<title>By: Patrick</title>
		<link>http://www.uncommondescent.com/biology/a-de-novo-out-of-nowhere-gene/comment-page-1/#comment-129099</link>
		<dc:creator>Patrick</dc:creator>
		<pubDate>Wed, 25 Jul 2007 18:47:31 +0000</pubDate>
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		<description>Sounds like this is a data point that needs further research before it can be connected to either ID or Darwinism as evidence for either.</description>
		<content:encoded><![CDATA[<p>Sounds like this is a data point that needs further research before it can be connected to either ID or Darwinism as evidence for either.</p>
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		<title>By: Jehu</title>
		<link>http://www.uncommondescent.com/biology/a-de-novo-out-of-nowhere-gene/comment-page-1/#comment-128971</link>
		<dc:creator>Jehu</dc:creator>
		<pubDate>Tue, 24 Jul 2007 17:52:07 +0000</pubDate>
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		<description>ORFans are defined as ORFs (Open Reading Frames) having no sequence homologs in other genomes.  Thus there is no evidence of possible evolution of the ORFan gene.  Darwinists, desperate to have an explanation, claimed the future sequencing of genomes would find homologous genes.  This did turn out to be the case in many instances but additional sequencing also uncovered more ORFan genes, so that &lt;a href=&quot;http://mic.sgmjournals.org/cgi/content/full/151/8/2499?view=long&amp;pmid=16079329&quot; rel=&quot;nofollow&quot;&gt; the number of ORFans has continued to increase&lt;/a&gt;.

Darwinists then argued that the ORFan genes were the product of horizontal gene transfer from a virus.  So a BLAST search was done comparing the homology of proteins in ORFan genes to virus genes.  It was found that &lt;a href=&quot;http://www.biomedcentral.com/1471-2148/6/63&quot; rel=&quot;nofollow&quot;&gt;only 2.8%&lt;/a&gt; of all microbial ORFans have detectable homologs in viruses, while the percentage of non-ORFans with detectable homologs in viruses is 7.9%, a significantly higher figure.  So ORFans are actually less likely to derive from a virus than a non-ORFan.

The take away point here is that the assumption that this novel gene in a fruit fly came from a virus can&#039;t be taken for granted.  Horizontal gene transfer from a virus has not shown to be the source of ORFans in other organisms.</description>
		<content:encoded><![CDATA[<p>ORFans are defined as ORFs (Open Reading Frames) having no sequence homologs in other genomes.  Thus there is no evidence of possible evolution of the ORFan gene.  Darwinists, desperate to have an explanation, claimed the future sequencing of genomes would find homologous genes.  This did turn out to be the case in many instances but additional sequencing also uncovered more ORFan genes, so that <a href="http://mic.sgmjournals.org/cgi/content/full/151/8/2499?view=long&amp;pmid=16079329" rel="nofollow"> the number of ORFans has continued to increase</a>.</p>
<p>Darwinists then argued that the ORFan genes were the product of horizontal gene transfer from a virus.  So a BLAST search was done comparing the homology of proteins in ORFan genes to virus genes.  It was found that <a href="http://www.biomedcentral.com/1471-2148/6/63" rel="nofollow">only 2.8%</a> of all microbial ORFans have detectable homologs in viruses, while the percentage of non-ORFans with detectable homologs in viruses is 7.9%, a significantly higher figure.  So ORFans are actually less likely to derive from a virus than a non-ORFan.</p>
<p>The take away point here is that the assumption that this novel gene in a fruit fly came from a virus can&#8217;t be taken for granted.  Horizontal gene transfer from a virus has not shown to be the source of ORFans in other organisms.</p>
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