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	<title>Comments on: &#8220;The tree of life is being politely buried&#8221;</title>
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		<title>By: jerry</title>
		<link>http://www.uncommondescent.com/biology/the-tree-of-life-is-being-politely-buried/comment-page-2/#comment-303141</link>
		<dc:creator>jerry</dc:creator>
		<pubDate>Thu, 29 Jan 2009 02:38:32 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4696#comment-303141</guid>
		<description>Platonist said,

&quot;what is now being proposed is several different trees of life?&quot;

I believe that this is all  that can definitely be concluded at the moment.  At present I think the term common ancestry is more appropriate than common descent.  But this is me personally.

Maybe as I read more of the Darwinian literature, I will learn more and change my mind.  That is the best place to find the information.  Right now SINEs, LINES, pseudo-genes, ERVs and other homologies indicate some commonalities and if one assumes a gene pool of a population that is much larger than what exist today for any species, genera, family, order or class, micro evolution would explain a lot of what we see in the world.  But no naturalistic process can explain where all the variation came from.  Allen MacNeill shows up periodically and has told us at least 47 times about his 47 engines of variation but as you can see I asked him above for data on what each produced and as of yet have not had an answer.

This speculation about an original gene pool is all conjecture but fits the data as far as I know.  The origin of these large gene pools is what is truly a mystery.  The creation of variation is the issue not natural selection or common elements in various species.  It will always be the main issue.</description>
		<content:encoded><![CDATA[<p>Platonist said,</p>
<p>&#8220;what is now being proposed is several different trees of life?&#8221;</p>
<p>I believe that this is all  that can definitely be concluded at the moment.  At present I think the term common ancestry is more appropriate than common descent.  But this is me personally.</p>
<p>Maybe as I read more of the Darwinian literature, I will learn more and change my mind.  That is the best place to find the information.  Right now SINEs, LINES, pseudo-genes, ERVs and other homologies indicate some commonalities and if one assumes a gene pool of a population that is much larger than what exist today for any species, genera, family, order or class, micro evolution would explain a lot of what we see in the world.  But no naturalistic process can explain where all the variation came from.  Allen MacNeill shows up periodically and has told us at least 47 times about his 47 engines of variation but as you can see I asked him above for data on what each produced and as of yet have not had an answer.</p>
<p>This speculation about an original gene pool is all conjecture but fits the data as far as I know.  The origin of these large gene pools is what is truly a mystery.  The creation of variation is the issue not natural selection or common elements in various species.  It will always be the main issue.</p>
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		<title>By: Platonist</title>
		<link>http://www.uncommondescent.com/biology/the-tree-of-life-is-being-politely-buried/comment-page-2/#comment-303113</link>
		<dc:creator>Platonist</dc:creator>
		<pubDate>Wed, 28 Jan 2009 21:12:39 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4696#comment-303113</guid>
		<description>So rather than a universal common ancestor and a tree of life, what is now being proposed is several different trees of life? 

That mammals and reptiles, birds and dinosaurs have no connection to one another?</description>
		<content:encoded><![CDATA[<p>So rather than a universal common ancestor and a tree of life, what is now being proposed is several different trees of life? </p>
<p>That mammals and reptiles, birds and dinosaurs have no connection to one another?</p>
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		<title>By: jerry</title>
		<link>http://www.uncommondescent.com/biology/the-tree-of-life-is-being-politely-buried/comment-page-1/#comment-302943</link>
		<dc:creator>jerry</dc:creator>
		<pubDate>Mon, 26 Jan 2009 23:11:56 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4696#comment-302943</guid>
		<description>Allen,

We have seen your list before and use it constantly as a reference.  But is it the source for the original gene pool?  How much research is there that these sources which you list really had an effect of the genomes and produced the variety that we see.  No one doubts that each has happened.   One of the things about human nature is to crow when you are proven correct and I see no crowing about the changes that have been made to separated populations through your laundry list of variation change processes.  If such a list exist then we can eat some crow.

Another thing that is becoming evident is that many of the so called species are really just variants or slight modifications of each other and represent restrictions on a previously larger gene pool.  As populations drift off for whatever reason and face new environments and loose the diversity that existed in their previous population they thus exhibit less variation.  How much new variation is being introduced into these separate populations to compensate this lost variation?

If you want to get ID&#039;s attention such research would do it.  Does it exist?  Or is is just conjecture?  If it does exist, give us the significant results in laymen&#039;s terms so all can appreciate it.</description>
		<content:encoded><![CDATA[<p>Allen,</p>
<p>We have seen your list before and use it constantly as a reference.  But is it the source for the original gene pool?  How much research is there that these sources which you list really had an effect of the genomes and produced the variety that we see.  No one doubts that each has happened.   One of the things about human nature is to crow when you are proven correct and I see no crowing about the changes that have been made to separated populations through your laundry list of variation change processes.  If such a list exist then we can eat some crow.</p>
<p>Another thing that is becoming evident is that many of the so called species are really just variants or slight modifications of each other and represent restrictions on a previously larger gene pool.  As populations drift off for whatever reason and face new environments and loose the diversity that existed in their previous population they thus exhibit less variation.  How much new variation is being introduced into these separate populations to compensate this lost variation?</p>
<p>If you want to get ID&#8217;s attention such research would do it.  Does it exist?  Or is is just conjecture?  If it does exist, give us the significant results in laymen&#8217;s terms so all can appreciate it.</p>
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		<title>By: tribune7</title>
		<link>http://www.uncommondescent.com/biology/the-tree-of-life-is-being-politely-buried/comment-page-1/#comment-302941</link>
		<dc:creator>tribune7</dc:creator>
		<pubDate>Mon, 26 Jan 2009 22:31:47 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4696#comment-302941</guid>
		<description>Allen,

How reasonable do you think it is that there have been multiple origins of fundamentally different life forms?</description>
		<content:encoded><![CDATA[<p>Allen,</p>
<p>How reasonable do you think it is that there have been multiple origins of fundamentally different life forms?</p>
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		<title>By: Allen_MacNeill</title>
		<link>http://www.uncommondescent.com/biology/the-tree-of-life-is-being-politely-buried/comment-page-1/#comment-302921</link>
		<dc:creator>Allen_MacNeill</dc:creator>
		<pubDate>Mon, 26 Jan 2009 16:58:26 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4696#comment-302921</guid>
		<description>In #26 jerry asks:

&quot;Where did all the variety in a population originate from?&quot;

Here&#039;s a list:

http://evolutionlist.blogspot.com/2007/10/rm-ns-creationist-and-id-strawman.html</description>
		<content:encoded><![CDATA[<p>In #26 jerry asks:</p>
<p>&#8220;Where did all the variety in a population originate from?&#8221;</p>
<p>Here&#8217;s a list:</p>
<p><a href="http://evolutionlist.blogspot.com/2007/10/rm-ns-creationist-and-id-strawman.html" rel="nofollow">http://evolutionlist.blogspot......awman.html</a></p>
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		<title>By: jerry</title>
		<link>http://www.uncommondescent.com/biology/the-tree-of-life-is-being-politely-buried/comment-page-1/#comment-302918</link>
		<dc:creator>jerry</dc:creator>
		<pubDate>Mon, 26 Jan 2009 16:47:47 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4696#comment-302918</guid>
		<description>Allen,

Your reading comprehension skills are lacking and you are starting to sound like the American press.  Can you read what I said and not someone else&#039;s interpretation of it.  Now I admit I am not the best writer and there are others here who are much more precise than I am but I believe the average person should get what I said and not put there own personal spin on it.  Which is why I said for you to come here more often to be able to represent ID more accurately and not put your own bias on it.

I am not a Deist but a traditional Christian.  I believe that life on this earth was created by an intelligent being 3.5-3.8  billion years ago and unlike some ID people who believe in front loading, believe that the evidence points to one or more interventions since that time.  Multi-celled animals would be one.

Do you give your student the Mike Sherman article to read and to speculate on how the Cambrian Explosion occurred and how a preceding organism must of had all those genes that were not being used but which were necessary for the variety of multi-celled organisms that then unfolded?  What process led to that.

Any way to clear up your misunderstanding.  I am referring to micro evolution alone and that the genome might have been designed to allow small variations to occur and this with the help of the natural selection process (yes, I insist it is a process but it is not an issue but just semantics) allow small variations to arise that adapt to changing environments.  But the limits on these changes are such that no novel complex capabilities occur naturally.  I say the last because the empirical evidence supports this and neither you, Will Provine, or any other evolutionary biologist has ever been able to demonstrate otherwise.  The logic is it can not happen in the time observed.  Even if the universe was infinitely old as thought by many till recent and still assumed by some, the sequence of events for life are time bound and the time is not enough for all the parent gene pools to have arisen naturally.

So that is my position and except for the possible design of the genome to allow change, is the general position of ID.  So most of what you teach in your evolutionary biology course is accepted by ID and it is only when you go off the reservation and allow speculation to become dogma that we disagree.  ID are the ones on firm scientific grounds and evolutionary biology for part of its paradigm is ascribing to magic for explanations.</description>
		<content:encoded><![CDATA[<p>Allen,</p>
<p>Your reading comprehension skills are lacking and you are starting to sound like the American press.  Can you read what I said and not someone else&#8217;s interpretation of it.  Now I admit I am not the best writer and there are others here who are much more precise than I am but I believe the average person should get what I said and not put there own personal spin on it.  Which is why I said for you to come here more often to be able to represent ID more accurately and not put your own bias on it.</p>
<p>I am not a Deist but a traditional Christian.  I believe that life on this earth was created by an intelligent being 3.5-3.8  billion years ago and unlike some ID people who believe in front loading, believe that the evidence points to one or more interventions since that time.  Multi-celled animals would be one.</p>
<p>Do you give your student the Mike Sherman article to read and to speculate on how the Cambrian Explosion occurred and how a preceding organism must of had all those genes that were not being used but which were necessary for the variety of multi-celled organisms that then unfolded?  What process led to that.</p>
<p>Any way to clear up your misunderstanding.  I am referring to micro evolution alone and that the genome might have been designed to allow small variations to occur and this with the help of the natural selection process (yes, I insist it is a process but it is not an issue but just semantics) allow small variations to arise that adapt to changing environments.  But the limits on these changes are such that no novel complex capabilities occur naturally.  I say the last because the empirical evidence supports this and neither you, Will Provine, or any other evolutionary biologist has ever been able to demonstrate otherwise.  The logic is it can not happen in the time observed.  Even if the universe was infinitely old as thought by many till recent and still assumed by some, the sequence of events for life are time bound and the time is not enough for all the parent gene pools to have arisen naturally.</p>
<p>So that is my position and except for the possible design of the genome to allow change, is the general position of ID.  So most of what you teach in your evolutionary biology course is accepted by ID and it is only when you go off the reservation and allow speculation to become dogma that we disagree.  ID are the ones on firm scientific grounds and evolutionary biology for part of its paradigm is ascribing to magic for explanations.</p>
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		<title>By: jerry</title>
		<link>http://www.uncommondescent.com/biology/the-tree-of-life-is-being-politely-buried/comment-page-1/#comment-302917</link>
		<dc:creator>jerry</dc:creator>
		<pubDate>Mon, 26 Jan 2009 16:22:59 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4696#comment-302917</guid>
		<description>JayM said,

&quot;Just to be clear, Jerry, are you proposing an ID variant here? It seems that you’re saying that the universe is designed to produce life but that the mechanisms by which that life arises require no intelligent intervention.&quot;


No,  No, No.  All I am saying is that the design of the cell and the organism itself allows for variation to occur and that this makes good design.  Once the cell is available and once a multi cell gene pool is available by means unknown  but probably due to an intelligent input, a lot of the variants of life play out through naturalistic processes.  This is entirely consistent with Behe&#039;s Edge of Evolution.


&quot;If I understand you correctly, that’s an interesting alternative to traditional ID theory. How would we scientifically demonstrate that intelligence was involved in the those “processes and structures”? Is there a CSI equivalent?&quot; 


This is my speculation but is entirely consistent with ID and may prove nonsense in the long run.  But I wanted to tweak Allen MacNeill who lost his reading comprehension skills when he read my answer.  Allen operates under a template that we are dumb here and has to show it with his patronizing answers.  I will answer Allen next.

I think the evidence points to micro evolution as a major force in providing variety in the world.  Look around you and you will see an amazing variety that varies by environment.  Most of this can can be explained by micro evolution without producing much new FCSI in the animal world.  Apparently the plant world is more likely to combine genomes but I know little of it.  

The animal world looks like it is more a result of devolution or a narrowing of the original gene pool over time to various sub-populations and these are what we see as the variety.  Just plain old micro evolution working to create variety as a population adapts to a different environment.  Sort of a vanilla type of evolution but evolution it is.  And these types of examples are what the Darwinist exult in to show their theories work.  

Whoopie Doo.  ID accepts all of this and it is trivial but the Darwinists do not realize by using these examples they are undermining their theory which is really the creation of new FCSI.  Or in other words where did the original gene pool come from?  Where did all the variety in a population originate from?  This I do not believe arose through naturalistic means.

Now my speculative addition is that the genome itself was designed to allow these minor changes to take place.  The error correction eliminates most of the changes and if it didn&#039;t then there would be a lot less successful reproduction.  But it lets a small amount of variation to get through and this random process allows for some beneficial mutations to take place but never enough that a wholesale amount of FCSI takes place.  

So I again say this is purely speculative and I have no clue how you would research this but is the genome itself designed to allow this process to proceed.  But I will repeat this is pure speculation but even with saying this 10 times or even 20 times people will say I hold this or that ID holds this as gospel.  You know the process.</description>
		<content:encoded><![CDATA[<p>JayM said,</p>
<p>&#8220;Just to be clear, Jerry, are you proposing an ID variant here? It seems that you’re saying that the universe is designed to produce life but that the mechanisms by which that life arises require no intelligent intervention.&#8221;</p>
<p>No,  No, No.  All I am saying is that the design of the cell and the organism itself allows for variation to occur and that this makes good design.  Once the cell is available and once a multi cell gene pool is available by means unknown  but probably due to an intelligent input, a lot of the variants of life play out through naturalistic processes.  This is entirely consistent with Behe&#8217;s Edge of Evolution.</p>
<p>&#8220;If I understand you correctly, that’s an interesting alternative to traditional ID theory. How would we scientifically demonstrate that intelligence was involved in the those “processes and structures”? Is there a CSI equivalent?&#8221; </p>
<p>This is my speculation but is entirely consistent with ID and may prove nonsense in the long run.  But I wanted to tweak Allen MacNeill who lost his reading comprehension skills when he read my answer.  Allen operates under a template that we are dumb here and has to show it with his patronizing answers.  I will answer Allen next.</p>
<p>I think the evidence points to micro evolution as a major force in providing variety in the world.  Look around you and you will see an amazing variety that varies by environment.  Most of this can can be explained by micro evolution without producing much new FCSI in the animal world.  Apparently the plant world is more likely to combine genomes but I know little of it.  </p>
<p>The animal world looks like it is more a result of devolution or a narrowing of the original gene pool over time to various sub-populations and these are what we see as the variety.  Just plain old micro evolution working to create variety as a population adapts to a different environment.  Sort of a vanilla type of evolution but evolution it is.  And these types of examples are what the Darwinist exult in to show their theories work.  </p>
<p>Whoopie Doo.  ID accepts all of this and it is trivial but the Darwinists do not realize by using these examples they are undermining their theory which is really the creation of new FCSI.  Or in other words where did the original gene pool come from?  Where did all the variety in a population originate from?  This I do not believe arose through naturalistic means.</p>
<p>Now my speculative addition is that the genome itself was designed to allow these minor changes to take place.  The error correction eliminates most of the changes and if it didn&#8217;t then there would be a lot less successful reproduction.  But it lets a small amount of variation to get through and this random process allows for some beneficial mutations to take place but never enough that a wholesale amount of FCSI takes place.  </p>
<p>So I again say this is purely speculative and I have no clue how you would research this but is the genome itself designed to allow this process to proceed.  But I will repeat this is pure speculation but even with saying this 10 times or even 20 times people will say I hold this or that ID holds this as gospel.  You know the process.</p>
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		<title>By: Allen_MacNeill</title>
		<link>http://www.uncommondescent.com/biology/the-tree-of-life-is-being-politely-buried/comment-page-1/#comment-302911</link>
		<dc:creator>Allen_MacNeill</dc:creator>
		<pubDate>Mon, 26 Jan 2009 15:33:49 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4696#comment-302911</guid>
		<description>jerry #23 and JayM #24:

&lt;blockquote&gt;&quot;...you’re saying that the universe is designed to produce life but that the mechanisms by which that life arises require no intelligent intervention.&quot;&lt;/blockquote&gt;

It certainly seemed that way to me, too. If so, jerry, you have essentially adopted exactly the same position taken by Darwin at the conclusion of the &lt;i&gt;Origin of Species&lt;/i&gt;. If the universe itself (i.e. purely &quot;natural&quot; processes, such as those described by Darwin) can produce life and living organisms, then the entire purview of ID is limited to the creation of the universe and the natural laws by which it operates. This is, of course, a purview that most evolutionary biologists (myself included) have never aspired to (nor even addressed), and which I believe is completely beyond the scope of any conceivable science. How would one go about empirically validating or falsifying the idea that whatever it was that created the universe did so in such a way as to make possible the origin and evolution of life without the subsequent intervention of an &quot;intelligent designer&quot;, a position you seem to be advocating?

I have already blogged on the similarity between this position and deism here:
http://evolutionlist.blogspot.com/2006/04/is-intelligent-design-distinguishable.html
So, jerry, exactly how does your position differ from deism, if indeed it does?</description>
		<content:encoded><![CDATA[<p>jerry #23 and JayM #24:</p>
<blockquote><p>&#8220;&#8230;you’re saying that the universe is designed to produce life but that the mechanisms by which that life arises require no intelligent intervention.&#8221;</p></blockquote>
<p>It certainly seemed that way to me, too. If so, jerry, you have essentially adopted exactly the same position taken by Darwin at the conclusion of the <i>Origin of Species</i>. If the universe itself (i.e. purely &#8220;natural&#8221; processes, such as those described by Darwin) can produce life and living organisms, then the entire purview of ID is limited to the creation of the universe and the natural laws by which it operates. This is, of course, a purview that most evolutionary biologists (myself included) have never aspired to (nor even addressed), and which I believe is completely beyond the scope of any conceivable science. How would one go about empirically validating or falsifying the idea that whatever it was that created the universe did so in such a way as to make possible the origin and evolution of life without the subsequent intervention of an &#8220;intelligent designer&#8221;, a position you seem to be advocating?</p>
<p>I have already blogged on the similarity between this position and deism here:<br />
<a href="http://evolutionlist.blogspot.com/2006/04/is-intelligent-design-distinguishable.html" rel="nofollow">http://evolutionlist.blogspot......hable.html</a><br />
So, jerry, exactly how does your position differ from deism, if indeed it does?</p>
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		<title>By: JayM</title>
		<link>http://www.uncommondescent.com/biology/the-tree-of-life-is-being-politely-buried/comment-page-1/#comment-302903</link>
		<dc:creator>JayM</dc:creator>
		<pubDate>Mon, 26 Jan 2009 12:32:49 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4696#comment-302903</guid>
		<description>jerry @23
&lt;blockquote&gt;
No Allen, the designer is the intelligence that came up with the processes and structures of both the cell and organism and thus enables the population of an organism to adapt to many of the various environments it encounters.
&lt;/blockquote&gt;
Just to be clear, Jerry, are you proposing an ID variant here?  It seems that you&#039;re saying that the universe is designed to produce life but that the mechanisms by which that life arises require no intelligent intervention.

If I understand you correctly, that&#039;s an interesting alternative to traditional ID theory.  How would we scientifically demonstrate that intelligence was involved in the those &quot;processes and structures&quot;?  Is there a CSI equivalent?

JJ</description>
		<content:encoded><![CDATA[<p>jerry @23</p>
<blockquote><p>
No Allen, the designer is the intelligence that came up with the processes and structures of both the cell and organism and thus enables the population of an organism to adapt to many of the various environments it encounters.
</p></blockquote>
<p>Just to be clear, Jerry, are you proposing an ID variant here?  It seems that you&#8217;re saying that the universe is designed to produce life but that the mechanisms by which that life arises require no intelligent intervention.</p>
<p>If I understand you correctly, that&#8217;s an interesting alternative to traditional ID theory.  How would we scientifically demonstrate that intelligence was involved in the those &#8220;processes and structures&#8221;?  Is there a CSI equivalent?</p>
<p>JJ</p>
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		<title>By: jerry</title>
		<link>http://www.uncommondescent.com/biology/the-tree-of-life-is-being-politely-buried/comment-page-1/#comment-302898</link>
		<dc:creator>jerry</dc:creator>
		<pubDate>Mon, 26 Jan 2009 06:25:46 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4696#comment-302898</guid>
		<description>&quot;That “designer” is the environment in which those organisms have evolved.&quot;

No Allen, the designer is the intelligence that came up with the processes and structures of both the cell and organism and thus enables the population of an organism to adapt to many of the various environments it encounters.  In other words, natural selection whether you want to call it an outcome or I want to call it a process (three sub-processes make one long process), is great design by an intelligence.

Sometimes the population cannot adapt and then the party&#039;s over.</description>
		<content:encoded><![CDATA[<p>&#8220;That “designer” is the environment in which those organisms have evolved.&#8221;</p>
<p>No Allen, the designer is the intelligence that came up with the processes and structures of both the cell and organism and thus enables the population of an organism to adapt to many of the various environments it encounters.  In other words, natural selection whether you want to call it an outcome or I want to call it a process (three sub-processes make one long process), is great design by an intelligence.</p>
<p>Sometimes the population cannot adapt and then the party&#8217;s over.</p>
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