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	<title>Comments on: HGT and evolution</title>
	<atom:link href="http://telicthoughts.com/hgt-and-evolution/feed/" rel="self" type="application/rss+xml" />
	<link>http://telicthoughts.com/hgt-and-evolution/</link>
	<description>An independent blog about intelligent design</description>
	<pubDate>Mon, 06 Oct 2008 18:36:37 +0000</pubDate>
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		<title>By: Rock</title>
		<link>http://telicthoughts.com/hgt-and-evolution/#comment-63138</link>
		<dc:creator>Rock</dc:creator>
		<pubDate>Thu, 01 Feb 2007 21:07:07 +0000</pubDate>
		<guid isPermaLink="false">http://telicthoughts.com/hgt-and-evolution/#comment-63138</guid>
		<description>"Contra Neo-Darwinism where the very concept is alien."

Uh, "alien," not to be taken literally, Mike Gene. LOL</description>
		<content:encoded><![CDATA[<p>&#034;Contra Neo-Darwinism where the very concept is alien.&#034;</p>
<p>Uh, &#034;alien,&#034; not to be taken literally, Mike Gene. LOL</p>
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		<title>By: Rock</title>
		<link>http://telicthoughts.com/hgt-and-evolution/#comment-63137</link>
		<dc:creator>Rock</dc:creator>
		<pubDate>Thu, 01 Feb 2007 20:52:15 +0000</pubDate>
		<guid isPermaLink="false">http://telicthoughts.com/hgt-and-evolution/#comment-63137</guid>
		<description>"From the Holstein's pov"¦"

And I truly appreciate the Holstein's sense of humor in these matters and I appreciate the fact that you share the Holstein's perspective, Aagcob, because in this context a lot of people can't maintain their sense of perspective and proportion, which is basically the source of humor. Sometimes these subjects are like arguing about women's fashions with a Wahhabi. 

""¦I need to know about the nature of this "evidence" they demand of me. And after over six years of asking, I have been consistently disappointed by the answers.""”Mike Gene

In this context"”It seems natural enough to me to identify "module" with "gene," as Deem seems to do. But there is no basis for such a comparison in the formal theory of Neo-Darwinism. The "genes," Fisher, Wright, and Haldane described are &lt;em&gt;no&lt;/em&gt;t modules. So when biologists start think of genes as modules they are departing from the neo-classical theory of evolution (not "Darwinism," but MET or Neo-Darwinism, as formally stated) and departing in what direction?

Von Dassow &#38; Munro (1999) argued that the concept of modularity occurs naturally to biologists. And it should. They're right. But the word and the concept itself was borrowed from design science and the biologists (who bother to define the word) define it and use it the same way the engineers do.

Contra Neo-Darwinism where the very concept is alien.

Obviously design science and biology engage in a useful, productive, and theoretically significant exchange of ideas. The Neo-Darwinists did the same! 
But not in this case of modularity.

Mike Gene is always asking what his critics require of him, what they require as "evidence." (And I've always advised him and the other IDers to choose their critics like they choose their friends--well. Because some "critics" don't have 'standards.") Which is the same as asking what is required of a theory. Now, if your requirements are pretty lax, then Neo-Darwinian theory should suffice for you. My requirements are different. And they change.

Is this a case of "double-standards"? Do we require more of IDers like Mike Gene then we require of Neo-Darwinists like Fisher, Wright, and Haldane?

But there really is no comparison, as Mike Gene repeats, its not a theory or a science, it's a "hobby." Like collecting stamps, building ships in a bottle, and gardening. 

A way to occupy idle time. 

To be fair to Mike Gene that explains my continuing interest as well. I am particularly interested, as he is, in how the scientific community reacts to such challenges. Mostly they don't. Even when they do, e.g., http://telicthoughts.com/may-i-suggest-idiots/#more-1256
they seem to be intent on nothing else but demonstrating that even scientists can have shit-for-brains.

I am very disappointed in us. (And myself. LOL)</description>
		<content:encoded><![CDATA[<p>&#034;From the Holstein&#039;s pov&#034;¦&#034;</p>
<p>And I truly appreciate the Holstein&#039;s sense of humor in these matters and I appreciate the fact that you share the Holstein&#039;s perspective, Aagcob, because in this context a lot of people can&#039;t maintain their sense of perspective and proportion, which is basically the source of humor. Sometimes these subjects are like arguing about women&#039;s fashions with a Wahhabi. </p>
<p>&#034;&#034;¦I need to know about the nature of this &#034;evidence&#034; they demand of me. And after over six years of asking, I have been consistently disappointed by the answers.&#034;"”Mike Gene</p>
<p>In this context&#034;”It seems natural enough to me to identify &#034;module&#034; with &#034;gene,&#034; as Deem seems to do. But there is no basis for such a comparison in the formal theory of Neo-Darwinism. The &#034;genes,&#034; Fisher, Wright, and Haldane described are <em>no</em>t modules. So when biologists start think of genes as modules they are departing from the neo-classical theory of evolution (not &#034;Darwinism,&#034; but MET or Neo-Darwinism, as formally stated) and departing in what direction?</p>
<p>Von Dassow &amp; Munro (1999) argued that the concept of modularity occurs naturally to biologists. And it should. They&#039;re right. But the word and the concept itself was borrowed from design science and the biologists (who bother to define the word) define it and use it the same way the engineers do.</p>
<p>Contra Neo-Darwinism where the very concept is alien.</p>
<p>Obviously design science and biology engage in a useful, productive, and theoretically significant exchange of ideas. The Neo-Darwinists did the same!<br />
But not in this case of modularity.</p>
<p>Mike Gene is always asking what his critics require of him, what they require as &#034;evidence.&#034; (And I&#039;ve always advised him and the other IDers to choose their critics like they choose their friends&#8211;well. Because some &#034;critics&#034; don&#039;t have &#039;standards.&#034;) Which is the same as asking what is required of a theory. Now, if your requirements are pretty lax, then Neo-Darwinian theory should suffice for you. My requirements are different. And they change.</p>
<p>Is this a case of &#034;double-standards&#034;? Do we require more of IDers like Mike Gene then we require of Neo-Darwinists like Fisher, Wright, and Haldane?</p>
<p>But there really is no comparison, as Mike Gene repeats, its not a theory or a science, it&#039;s a &#034;hobby.&#034; Like collecting stamps, building ships in a bottle, and gardening. </p>
<p>A way to occupy idle time. </p>
<p>To be fair to Mike Gene that explains my continuing interest as well. I am particularly interested, as he is, in how the scientific community reacts to such challenges. Mostly they don&#039;t. Even when they do, e.g., <a href="http://telicthoughts.com/may-i-suggest-idiots/#more-1256" rel="nofollow"></a><a href='http://telicthoughts.com/may-i-suggest-idiots/#more-1256'>http://telicthoughts.com/may-i...</a><br />
they seem to be intent on nothing else but demonstrating that even scientists can have shit-for-brains.</p>
<p>I am very disappointed in us. (And myself. LOL)</p>
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		<title>By: Aagcobb</title>
		<link>http://telicthoughts.com/hgt-and-evolution/#comment-63134</link>
		<dc:creator>Aagcobb</dc:creator>
		<pubDate>Thu, 01 Feb 2007 19:46:45 +0000</pubDate>
		<guid isPermaLink="false">http://telicthoughts.com/hgt-and-evolution/#comment-63134</guid>
		<description>Hi, Mike
&lt;blockquote&gt;It's when they start insisting that we are all supposed to adopt their non-teleological perspective that I need to know about the nature of this "evidence" they demand of me. And after over six years of asking, I have been consistently disappointed by the answers.&lt;/blockquote&gt;

Well, what would you expect?  You have to place their responses in context.  The last six years was the heyday of the period when creationists were aggressively pushing ID as a valid alternative theory to evolution which ought to be taught in public schools.  In that context, the evidenciary bar should be set very high indeed.  In the context of a hobby which isn't science and shouldn't be taught in public schools, anything and everything can be considered "evidence" of design.</description>
		<content:encoded><![CDATA[<p>Hi, Mike</p>
<blockquote><p>It&#039;s when they start insisting that we are all supposed to adopt their non-teleological perspective that I need to know about the nature of this &#034;evidence&#034; they demand of me. And after over six years of asking, I have been consistently disappointed by the answers.</p></blockquote>
<p>Well, what would you expect?  You have to place their responses in context.  The last six years was the heyday of the period when creationists were aggressively pushing ID as a valid alternative theory to evolution which ought to be taught in public schools.  In that context, the evidenciary bar should be set very high indeed.  In the context of a hobby which isn&#039;t science and shouldn&#039;t be taught in public schools, anything and everything can be considered &#034;evidence&#034; of design.</p>
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		<title>By: MikeGene</title>
		<link>http://telicthoughts.com/hgt-and-evolution/#comment-63075</link>
		<dc:creator>MikeGene</dc:creator>
		<pubDate>Thu, 01 Feb 2007 04:00:48 +0000</pubDate>
		<guid isPermaLink="false">http://telicthoughts.com/hgt-and-evolution/#comment-63075</guid>
		<description>Hi Aagcobb,

&lt;blockquote&gt;Are you talking about abiogenesis. I thought, if I had understood correctly, that you hypothesized that eukaryotes were designed to have added complexity in order to evolve. Now, unless I'm misunderstanding you, you seem to be suggesting that dna was designed in the very beginning. Are you envisioning multiple intervening events, or am I misunderstanding you?&lt;/blockquote&gt;

Rather than trying to envision where I am going, it would be better to focus on where I am at.  Deem stated, "Life clearly evolved to store genetic information in a modular form, and to accept useful modules of genetic information from other species."  It is clear that life stores genetic information in modular form and that this has made life susceptible to HGT (Shapiro calls this "natural genetic engineering").  All I am doing here is noting that any attempt to attribute these two universal features to evolution is simply a non-teleological perspective.  A teleological perspective notes the same two observations yet ponders if they are part of a larger design (for that, the President Of The Geological Society Of London would lash out at me and &lt;a href="http://telicthoughts.com/may-i-suggest-idiots/" rel="nofollow"&gt;label me an IDiot&lt;/a&gt;). 

&lt;blockquote&gt; IMO, which is insignificant, anything which makes a design theory at least as, or more probable than, evolutionary theories.&lt;/blockquote&gt;

But that is much too vague and doesn't help me.  I'm not worried about making a "design theory" more "probable" than "evolutionary theories."  That's a long, long way down the road as far as I am concerned.  I'm  more interested in whether a design perspective can help us better understand life, evolution, and how they interface.  Non-teleologists, as usual, are free to ignore me as you won't find me chasing after them in an attempt to get their attention.  It's when they start insisting that we are &lt;strong&gt;all&lt;/strong&gt; supposed to adopt their non-teleological perspective that I need to know about the nature of this "evidence" they demand of me.  And after over six years of asking, I have been consistently disappointed by the answers.</description>
		<content:encoded><![CDATA[<p>Hi Aagcobb,</p>
<blockquote><p>Are you talking about abiogenesis. I thought, if I had understood correctly, that you hypothesized that eukaryotes were designed to have added complexity in order to evolve. Now, unless I&#039;m misunderstanding you, you seem to be suggesting that dna was designed in the very beginning. Are you envisioning multiple intervening events, or am I misunderstanding you?</p></blockquote>
<p>Rather than trying to envision where I am going, it would be better to focus on where I am at.  Deem stated, &#034;Life clearly evolved to store genetic information in a modular form, and to accept useful modules of genetic information from other species.&#034;  It is clear that life stores genetic information in modular form and that this has made life susceptible to HGT (Shapiro calls this &#034;natural genetic engineering&#034;).  All I am doing here is noting that any attempt to attribute these two universal features to evolution is simply a non-teleological perspective.  A teleological perspective notes the same two observations yet ponders if they are part of a larger design (for that, the President Of The Geological Society Of London would lash out at me and <a href="http://telicthoughts.com/may-i-suggest-idiots/" rel="nofollow">label me an IDiot</a>). </p>
<blockquote><p> IMO, which is insignificant, anything which makes a design theory at least as, or more probable than, evolutionary theories.</p></blockquote>
<p>But that is much too vague and doesn&#039;t help me.  I&#039;m not worried about making a &#034;design theory&#034; more &#034;probable&#034; than &#034;evolutionary theories.&#034;  That&#039;s a long, long way down the road as far as I am concerned.  I&#039;m  more interested in whether a design perspective can help us better understand life, evolution, and how they interface.  Non-teleologists, as usual, are free to ignore me as you won&#039;t find me chasing after them in an attempt to get their attention.  It&#039;s when they start insisting that we are <strong>all</strong> supposed to adopt their non-teleological perspective that I need to know about the nature of this &#034;evidence&#034; they demand of me.  And after over six years of asking, I have been consistently disappointed by the answers.</p>
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		<title>By: Aagcobb</title>
		<link>http://telicthoughts.com/hgt-and-evolution/#comment-63065</link>
		<dc:creator>Aagcobb</dc:creator>
		<pubDate>Wed, 31 Jan 2007 22:58:59 +0000</pubDate>
		<guid isPermaLink="false">http://telicthoughts.com/hgt-and-evolution/#comment-63065</guid>
		<description>Hi Rock,
&lt;blockquote&gt;No. I intervened (me personally, LOL) to redirect a naturally occuring evolutionary process to make a cow that produces a lot of milk"“my objective. (Actually, I'm, lactose-intolerant and wonder why any adult mammal, which I assume is weaned, would have such an objective"“but they do.) Which, btw, falsifies a a direct statement of Darwin's: No creature exists whose "sole purpose" (did he say it that way) is to serve another creature. Sorry, charlie"“Holstein.&lt;/blockquote&gt;

I have to disagree there, Rock.  From the Holstein's pov, they bred lactose-tolerant humans to feed and shelter them and protect them from predators!</description>
		<content:encoded><![CDATA[<p>Hi Rock,</p>
<blockquote><p>No. I intervened (me personally, LOL) to redirect a naturally occuring evolutionary process to make a cow that produces a lot of milk&#034;“my objective. (Actually, I&#039;m, lactose-intolerant and wonder why any adult mammal, which I assume is weaned, would have such an objective&#034;“but they do.) Which, btw, falsifies a a direct statement of Darwin&#039;s: No creature exists whose &#034;sole purpose&#034; (did he say it that way) is to serve another creature. Sorry, charlie&#034;“Holstein.</p></blockquote>
<p>I have to disagree there, Rock.  From the Holstein&#039;s pov, they bred lactose-tolerant humans to feed and shelter them and protect them from predators!</p>
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		<title>By: Rock</title>
		<link>http://telicthoughts.com/hgt-and-evolution/#comment-63052</link>
		<dc:creator>Rock</dc:creator>
		<pubDate>Wed, 31 Jan 2007 22:17:14 +0000</pubDate>
		<guid isPermaLink="false">http://telicthoughts.com/hgt-and-evolution/#comment-63052</guid>
		<description>Sorry, Bilbo, I was responding to Aagcobb, who responded with what I can only presume is a "rhetorical" question. 

I am a &lt;em&gt;designer&lt;/em&gt;, which means that I &lt;em&gt;intervene&lt;/em&gt; in natural processes to control them to obtain my own objectives.

As people say, natural processes do not occur according to a plan, do not have an objective, a goal, a direction, etc.

But guess what?--I, like every other life form, do! I have all of those, none of which is subserved by natural processes (by definition), which is exactly why I intervene in such processes.

How do you explain the existence of a Holstein? It evolved right? LOL

No. I intervened (me personally, LOL) to redirect a naturally occuring evolutionary process to make a cow that produces a lot of milk--my objective. (Actually, I'm, lactose-intolerant and wonder why any adult mammal, which I assume is weaned, would have such an objective--but they do.) Which, btw, falsifies a a direct statement of Darwin's: No creature exists whose "sole purpose" (did he say it that way) is to serve another creature. Sorry, charlie--Holstein.

Serious question? Did you even understand the question? Shall I rephrase? What can I do to help you out here, Aagacobb?

Ya wanna argue about "divine intervention" Is that what you mean?

You don't have an argument with me then. Your argument is with God. LOL

(And good luck winning that argument!)</description>
		<content:encoded><![CDATA[<p>Sorry, Bilbo, I was responding to Aagcobb, who responded with what I can only presume is a &#034;rhetorical&#034; question. </p>
<p>I am a <em>designer</em>, which means that I <em>intervene</em> in natural processes to control them to obtain my own objectives.</p>
<p>As people say, natural processes do not occur according to a plan, do not have an objective, a goal, a direction, etc.</p>
<p>But guess what?&#8211;I, like every other life form, do! I have all of those, none of which is subserved by natural processes (by definition), which is exactly why I intervene in such processes.</p>
<p>How do you explain the existence of a Holstein? It evolved right? LOL</p>
<p>No. I intervened (me personally, LOL) to redirect a naturally occuring evolutionary process to make a cow that produces a lot of milk&#8211;my objective. (Actually, I&#039;m, lactose-intolerant and wonder why any adult mammal, which I assume is weaned, would have such an objective&#8211;but they do.) Which, btw, falsifies a a direct statement of Darwin&#039;s: No creature exists whose &#034;sole purpose&#034; (did he say it that way) is to serve another creature. Sorry, charlie&#8211;Holstein.</p>
<p>Serious question? Did you even understand the question? Shall I rephrase? What can I do to help you out here, Aagacobb?</p>
<p>Ya wanna argue about &#034;divine intervention&#034; Is that what you mean?</p>
<p>You don&#039;t have an argument with me then. Your argument is with God. LOL</p>
<p>(And good luck winning that argument!)</p>
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		<title>By: Guts</title>
		<link>http://telicthoughts.com/hgt-and-evolution/#comment-63038</link>
		<dc:creator>Guts</dc:creator>
		<pubDate>Wed, 31 Jan 2007 21:38:55 +0000</pubDate>
		<guid isPermaLink="false">http://telicthoughts.com/hgt-and-evolution/#comment-63038</guid>
		<description>Bilbo:
&lt;blockquote&gt;
Are they referring to the parts of the immune system that Behe referrences as being IC? 
&lt;/blockquote&gt;

In general it is believed that different mechanisms for horizontal DNA transfer in bacteria can operate also to eukaryotes with low efficiency and have played an important role in evolution. A couple of enzymes that are involved in antibody production are highly related to transposases so they most probably share a common origin (see works by Nancy L. Craig, for instance Nature. 2004 Transposition of hAT elements links transposable elements and V(D)J recombination.  Dec 23;432(7020):995-1001). An alternative hypothesis might be that the transposon arose through escape of a RAG gene rather than vice versa, although there is the difficulty of that they are widespread in insects, whose genomes do not have any RAG genes (AFAIK). 

HGT mechanisms themselves are rather interesting, the mechanisms for each process are totally different, and so are the essential components for each of them. For conjugation you need a complex transfer machinery, especially in gram-negative bacteria, involving 15-30 different genes plus cis-acting elements. Transformation is usually mediated by dedicated machineries too, especially in gram-positives, that are unrelated to the conjugative machineries. Transduction is mediated by the ordinary phage
machinery that packs by mistake bacterial DNA in place of its own viral genome.

Sorry for jumping in , this is one of my favorite topics.

</description>
		<content:encoded><![CDATA[<p>Bilbo:</p>
<blockquote><p>
Are they referring to the parts of the immune system that Behe referrences as being IC?
</p></blockquote>
<p>In general it is believed that different mechanisms for horizontal DNA transfer in bacteria can operate also to eukaryotes with low efficiency and have played an important role in evolution. A couple of enzymes that are involved in antibody production are highly related to transposases so they most probably share a common origin (see works by Nancy L. Craig, for instance Nature. 2004 Transposition of hAT elements links transposable elements and V(D)J recombination.  Dec 23;432(7020):995-1001). An alternative hypothesis might be that the transposon arose through escape of a RAG gene rather than vice versa, although there is the difficulty of that they are widespread in insects, whose genomes do not have any RAG genes (AFAIK). </p>
<p>HGT mechanisms themselves are rather interesting, the mechanisms for each process are totally different, and so are the essential components for each of them. For conjugation you need a complex transfer machinery, especially in gram-negative bacteria, involving 15-30 different genes plus cis-acting elements. Transformation is usually mediated by dedicated machineries too, especially in gram-positives, that are unrelated to the conjugative machineries. Transduction is mediated by the ordinary phage<br />
machinery that packs by mistake bacterial DNA in place of its own viral genome.</p>
<p>Sorry for jumping in , this is one of my favorite topics.</p>
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		<title>By: Aagcobb</title>
		<link>http://telicthoughts.com/hgt-and-evolution/#comment-63031</link>
		<dc:creator>Aagcobb</dc:creator>
		<pubDate>Wed, 31 Jan 2007 21:29:05 +0000</pubDate>
		<guid isPermaLink="false">http://telicthoughts.com/hgt-and-evolution/#comment-63031</guid>
		<description>Are you the intervenor, Rock? :eek:</description>
		<content:encoded><![CDATA[<p>Are you the intervenor, Rock? <img src='http://telicthoughts.com/wp-includes/images/smilies/icon_surprised.gif' alt=':eek:' class='wp-smiley' /></p>
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		<title>By: Bilbo</title>
		<link>http://telicthoughts.com/hgt-and-evolution/#comment-63028</link>
		<dc:creator>Bilbo</dc:creator>
		<pubDate>Wed, 31 Jan 2007 21:17:15 +0000</pubDate>
		<guid isPermaLink="false">http://telicthoughts.com/hgt-and-evolution/#comment-63028</guid>
		<description>Rock, were you talking to Aagcobb or to me?</description>
		<content:encoded><![CDATA[<p>Rock, were you talking to Aagcobb or to me?</p>
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		<title>By: Rock</title>
		<link>http://telicthoughts.com/hgt-and-evolution/#comment-63027</link>
		<dc:creator>Rock</dc:creator>
		<pubDate>Wed, 31 Jan 2007 21:10:17 +0000</pubDate>
		<guid isPermaLink="false">http://telicthoughts.com/hgt-and-evolution/#comment-63027</guid>
		<description>If I design an evolutionary mechanism (and let me assure you, it is a trivial design problem to solve), then the question you asked makes no sense whatsoever. In this case design is the most probable explanation of the evolutionary mechanism. And I should hope so because it is the only correct explanation for an evolutionary mechanism that I have designed. 

Or maybe that's "insignificant." 

Would that count as an "intervention" (I'm sure somehow, it wouldn't count as "suffcient evidence.") Darwin had an interesting theory about the "intervention" of life forms into the evolutionary process. He devoted most of a book to the subject?

Ever heard of it?</description>
		<content:encoded><![CDATA[<p>If I design an evolutionary mechanism (and let me assure you, it is a trivial design problem to solve), then the question you asked makes no sense whatsoever. In this case design is the most probable explanation of the evolutionary mechanism. And I should hope so because it is the only correct explanation for an evolutionary mechanism that I have designed. </p>
<p>Or maybe that&#039;s &#034;insignificant.&#034; </p>
<p>Would that count as an &#034;intervention&#034; (I&#039;m sure somehow, it wouldn&#039;t count as &#034;suffcient evidence.&#034;) Darwin had an interesting theory about the &#034;intervention&#034; of life forms into the evolutionary process. He devoted most of a book to the subject?</p>
<p>Ever heard of it?</p>
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