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	<title>Comments on: Carl Zimmer on Irreducible Complexity</title>
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		<title>By: Patrick</title>
		<link>http://www.uncommondescent.com/intelligent-design/carl-zimmer-on-irreducible-complexity/comment-page-3/#comment-301499</link>
		<dc:creator>Patrick</dc:creator>
		<pubDate>Wed, 07 Jan 2009 17:53:29 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4336#comment-301499</guid>
		<description>#61

I&#039;d add to this that the testable hypothesis must not consist of pathways less than 100 informational bits and only several beneficial and/or neutral steps, which we all agreed should be feasible for non-foresighted processes. I say this because that&#039;s all Darwinists keep hyping while they ignore the real problems.</description>
		<content:encoded><![CDATA[<p>#61</p>
<p>I&#8217;d add to this that the testable hypothesis must not consist of pathways less than 100 informational bits and only several beneficial and/or neutral steps, which we all agreed should be feasible for non-foresighted processes. I say this because that&#8217;s all Darwinists keep hyping while they ignore the real problems.</p>
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		<title>By: Joseph</title>
		<link>http://www.uncommondescent.com/intelligent-design/carl-zimmer-on-irreducible-complexity/comment-page-3/#comment-301301</link>
		<dc:creator>Joseph</dc:creator>
		<pubDate>Sun, 04 Jan 2009 14:22:59 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4336#comment-301301</guid>
		<description>The YellowShark,

Can you please provide a testable hypothesis pertaining to blind, undirected processes?

I believe by attempting to do so you wil see the scientific vacuity of the anti-ID position.</description>
		<content:encoded><![CDATA[<p>The YellowShark,</p>
<p>Can you please provide a testable hypothesis pertaining to blind, undirected processes?</p>
<p>I believe by attempting to do so you wil see the scientific vacuity of the anti-ID position.</p>
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		<title>By: Patrick</title>
		<link>http://www.uncommondescent.com/intelligent-design/carl-zimmer-on-irreducible-complexity/comment-page-2/#comment-301286</link>
		<dc:creator>Patrick</dc:creator>
		<pubDate>Sat, 03 Jan 2009 22:25:31 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4336#comment-301286</guid>
		<description>Ugh, I just reread what I wrote. My poorly worded point was that &quot;most mutations are neutral&quot; would need to apply uniformly (in general) and thus specifically to pathways relevant to the problems at hand. As in, it does no good if 80% of ALL mutations as a whole are largely irrelevant to the scenarios/barriers facing Darwinism. More on this later when I have time. I&#039;ll quickly note Futuyma&#039;s early estimates were limited mostly to inferences from phylogenetic analyses of sequence data, inferences that are only as good as the assumptions they make about population demography and the neutrality of synonymous mutations. The data from experimental observations is limited at this time. It&#039;s also not quite clear from experimental observations whether percentile distributions hold steady from virus to eukaryotes to all other higher creatures, never mind specific categories and pathways.

EDIT:

I&#039;d also like to add that many amino acids at different parts of a protein are interchangeable and thus functionality remains unchanged for some nucleotide changes in a sequence. If that&#039;s where the majority of neutral mutations are limited to then how does that help Neutral Theory?</description>
		<content:encoded><![CDATA[<p>Ugh, I just reread what I wrote. My poorly worded point was that &#8220;most mutations are neutral&#8221; would need to apply uniformly (in general) and thus specifically to pathways relevant to the problems at hand. As in, it does no good if 80% of ALL mutations as a whole are largely irrelevant to the scenarios/barriers facing Darwinism. More on this later when I have time. I&#8217;ll quickly note Futuyma&#8217;s early estimates were limited mostly to inferences from phylogenetic analyses of sequence data, inferences that are only as good as the assumptions they make about population demography and the neutrality of synonymous mutations. The data from experimental observations is limited at this time. It&#8217;s also not quite clear from experimental observations whether percentile distributions hold steady from virus to eukaryotes to all other higher creatures, never mind specific categories and pathways.</p>
<p>EDIT:</p>
<p>I&#8217;d also like to add that many amino acids at different parts of a protein are interchangeable and thus functionality remains unchanged for some nucleotide changes in a sequence. If that&#8217;s where the majority of neutral mutations are limited to then how does that help Neutral Theory?</p>
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		<title>By: TheYellowShark</title>
		<link>http://www.uncommondescent.com/intelligent-design/carl-zimmer-on-irreducible-complexity/comment-page-2/#comment-301270</link>
		<dc:creator>TheYellowShark</dc:creator>
		<pubDate>Sat, 03 Jan 2009 15:44:21 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4336#comment-301270</guid>
		<description>&lt;blockquote&gt;If you are saying that in order for a long stepwise pathway to be viable that the majority of steps/mutations must be neutral or beneficial (weakly, strongly, destructively, constructively; doesn’t matter), then I’d agree with you. But if you’re talking in general, then I have to wonder what you are speaking of.  Most of the estimates I’ve seen [link here] for deleterious mutations are generally in the range of 90 to 99 percent...&lt;/blockquote&gt;
This is not at all what your link says.  Your link states, quite clearly: &quot;Our analysis suggests that ?95% of all nonsynonymous mutations that could contribute to polymorphism or divergence are deleterious&quot;.

Note the word &quot;nonsynonymous&quot;, and that they restrict themselves to &quot;mutations that could contribute to polymorphism or divergence&quot;.

The fact that &quot;most mutations are neutral&quot; was one of the most important &amp; surprising findings of biology in the last 50 years.  It is the reason that genetic drift of neutral mutations forms the null hypothesis for molecular biology.

Estimates sourced in Futuyma&#039;s &quot;Evolutionary Biology&quot;, which I don&#039;t have on me at the moment (I&#039;m at Winnipeg Station) give approximately 80% of all mutations being neutral, 15% being deleterious and 5% being beneficial.</description>
		<content:encoded><![CDATA[<blockquote><p>If you are saying that in order for a long stepwise pathway to be viable that the majority of steps/mutations must be neutral or beneficial (weakly, strongly, destructively, constructively; doesn’t matter), then I’d agree with you. But if you’re talking in general, then I have to wonder what you are speaking of.  Most of the estimates I’ve seen [link here] for deleterious mutations are generally in the range of 90 to 99 percent&#8230;</p></blockquote>
<p>This is not at all what your link says.  Your link states, quite clearly: &#8220;Our analysis suggests that ?95% of all nonsynonymous mutations that could contribute to polymorphism or divergence are deleterious&#8221;.</p>
<p>Note the word &#8220;nonsynonymous&#8221;, and that they restrict themselves to &#8220;mutations that could contribute to polymorphism or divergence&#8221;.</p>
<p>The fact that &#8220;most mutations are neutral&#8221; was one of the most important &amp; surprising findings of biology in the last 50 years.  It is the reason that genetic drift of neutral mutations forms the null hypothesis for molecular biology.</p>
<p>Estimates sourced in Futuyma&#8217;s &#8220;Evolutionary Biology&#8221;, which I don&#8217;t have on me at the moment (I&#8217;m at Winnipeg Station) give approximately 80% of all mutations being neutral, 15% being deleterious and 5% being beneficial.</p>
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		<title>By: TheYellowShark</title>
		<link>http://www.uncommondescent.com/intelligent-design/carl-zimmer-on-irreducible-complexity/comment-page-2/#comment-301268</link>
		<dc:creator>TheYellowShark</dc:creator>
		<pubDate>Sat, 03 Jan 2009 15:27:55 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4336#comment-301268</guid>
		<description>Patrick@44:

Ken Miller&#039;s reponse is up at the Loom.

http://blogs.discovermagazine.com/loom/2009/01/02/smoke-and-mirrors-whales-and-lampreys-a-guest-post-by-ken-miller/</description>
		<content:encoded><![CDATA[<p><a href="mailto:Patrick@44:">Patrick@44:</a></p>
<p>Ken Miller&#8217;s reponse is up at the Loom.</p>
<p><a href="http://blogs.discovermagazine.com/loom/2009/01/02/smoke-and-mirrors-whales-and-lampreys-a-guest-post-by-ken-miller/" rel="nofollow">http://blogs.discovermagazine......en-miller/</a></p>
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		<title>By: Patrick</title>
		<link>http://www.uncommondescent.com/intelligent-design/carl-zimmer-on-irreducible-complexity/comment-page-2/#comment-301229</link>
		<dc:creator>Patrick</dc:creator>
		<pubDate>Fri, 02 Jan 2009 21:14:08 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4336#comment-301229</guid>
		<description>Short on time so I&#039;ll only focus on one topic and ignore the unsubstantiated assertions:

&lt;blockquote&gt;The “majority of mutations” are NEUTRAL.&lt;/blockquote&gt;

If you are saying that in order for a long stepwise pathway to be viable that the majority of steps/mutations must be neutral or beneficial (weakly, strongly, destructively, constructively; doesn&#039;t matter), then I&#039;d agree with you. But if you&#039;re talking in general, then I have to wonder what you are speaking of.

Most of the estimates I&#039;ve &lt;a href=&quot;http://www.pnas.org/content/104/16/6504&quot; rel=&quot;nofollow&quot;&gt;seen&lt;/a&gt; for deleterious mutations are generally in the range of 90 to 99 percent, with the remaining percentage comprising weakly beneficial yet often destructive mutations, and then rarely beneficial constructive mutations. But if you&#039;re only considering &quot;beneficial&quot; mutations in general, the ratio of deleterious-to-beneficial mutations is very roughly estimated to be one in one million by Gerrish and Lenski.

I&#039;ll also quickly comment on the &lt;a href=&quot;http://www.amazon.com/gp/blog/A3DGRQ0IO7KYQ2?_encoding=UTF8&amp;cursor=1194890141.703&amp;cursorType=after&quot; rel=&quot;nofollow&quot;&gt;Behe vs Smith disagreement&lt;/a&gt;. Honestly I wonder why Darwinists choose to highlight this viral examples, especially since it only confirms Behe&#039;s own hypothesis. There&#039;s better examples in vertebrates, which have far less resources to work with compared those fast replicators. Even then there&#039;s not much to excited about. For example, I was reading about a change that required 3 amino acids which were encoded by 9 nucleotides each. So that&#039;s a pathway with only 54 informational bits involved. Where exactly do examples like this cause a problem for ID when it&#039;s all within previously stated expectations?

&lt;blockquote&gt;so basically what you’re saying is that IC is a worthless concept in ID. If IC can evolve, then it cannot be used as a form of design detection.&lt;/blockquote&gt;

I&#039;ll just quote myself from this very thread:


&quot;Being IC does NOT equate to “X-structure cannot evolve in principle”. IC primarily deals with DIRECT Darwinian Pathways and always has. Behe has always stated that INDIRECT Darwinian pathways are another matter.&quot; The key is whether there exists indirect pathways for everything. For example, if a system is composed of 3 parts there&#039;s a good chance that there is a viable indirect pathway.</description>
		<content:encoded><![CDATA[<p>Short on time so I&#8217;ll only focus on one topic and ignore the unsubstantiated assertions:</p>
<blockquote><p>The “majority of mutations” are NEUTRAL.</p></blockquote>
<p>If you are saying that in order for a long stepwise pathway to be viable that the majority of steps/mutations must be neutral or beneficial (weakly, strongly, destructively, constructively; doesn&#8217;t matter), then I&#8217;d agree with you. But if you&#8217;re talking in general, then I have to wonder what you are speaking of.</p>
<p>Most of the estimates I&#8217;ve <a href="http://www.pnas.org/content/104/16/6504" rel="nofollow">seen</a> for deleterious mutations are generally in the range of 90 to 99 percent, with the remaining percentage comprising weakly beneficial yet often destructive mutations, and then rarely beneficial constructive mutations. But if you&#8217;re only considering &#8220;beneficial&#8221; mutations in general, the ratio of deleterious-to-beneficial mutations is very roughly estimated to be one in one million by Gerrish and Lenski.</p>
<p>I&#8217;ll also quickly comment on the <a href="http://www.amazon.com/gp/blog/A3DGRQ0IO7KYQ2?_encoding=UTF8&#038;cursor=1194890141.703&#038;cursorType=after" rel="nofollow">Behe vs Smith disagreement</a>. Honestly I wonder why Darwinists choose to highlight this viral examples, especially since it only confirms Behe&#8217;s own hypothesis. There&#8217;s better examples in vertebrates, which have far less resources to work with compared those fast replicators. Even then there&#8217;s not much to excited about. For example, I was reading about a change that required 3 amino acids which were encoded by 9 nucleotides each. So that&#8217;s a pathway with only 54 informational bits involved. Where exactly do examples like this cause a problem for ID when it&#8217;s all within previously stated expectations?</p>
<blockquote><p>so basically what you’re saying is that IC is a worthless concept in ID. If IC can evolve, then it cannot be used as a form of design detection.</p></blockquote>
<p>I&#8217;ll just quote myself from this very thread:</p>
<p>&#8220;Being IC does NOT equate to “X-structure cannot evolve in principle”. IC primarily deals with DIRECT Darwinian Pathways and always has. Behe has always stated that INDIRECT Darwinian pathways are another matter.&#8221; The key is whether there exists indirect pathways for everything. For example, if a system is composed of 3 parts there&#8217;s a good chance that there is a viable indirect pathway.</p>
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		<title>By: jerry</title>
		<link>http://www.uncommondescent.com/intelligent-design/carl-zimmer-on-irreducible-complexity/comment-page-2/#comment-301219</link>
		<dc:creator>jerry</dc:creator>
		<pubDate>Fri, 02 Jan 2009 16:49:06 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4336#comment-301219</guid>
		<description>TheYellowShark,

Essentially all you are doing is making assertions and assuming they are true.  You are welcome to your speculative interpretations of some isolated facts but that is all they are is speculations.  To come here and assert that your assertions are established is hubris.  We have seen it all before and none have stood up when scrutinized.

Also the natural selection is not random is a red  herring argument and not an issue.  It is a meaningless discussion.  ID accepts NS but NS is very limited so the answer to the assertion that NS is not random is &quot;So what!&quot;  We been down this path a hundred times at least.  There is a random component to NS but mainly what is in play is the population gene pool and the environment.  No big deal.  The random part comes from how something is added to the gene pool.  So let&#039;s move on to something non trivial.  The fact that you waste any time on this issue means you do not have anything of substance or else you would have trotted it out.

There are no examples of gradual transitions in the fossil record, none, nada, zero, zilch, zip.  We have yet to see one.  We have been given the forrest animal to whale scenario but there are no gradual transitions there, only fossils millions of years apart and variations of marine mammals.  There is also what is referred to the &quot;crown jewel&quot; of the fossil record and that is the reptile to mammal movement of three bones from the jaw to the ear.  Again interesting but not an example of gradualism and ignores all other problems with the differences between mammals and reptiles.  So have at it if you find this when you read again.  We are still waiting for an example and as for the natural selection red herring, we have been down this path hundreds of times.

I always looked at concepts such as scaffolding and co-option as things that were pulled out of one&#039;s back pocket when something got sticky and there was no answer for what happened or exists.  They are not quite all purpose tools but they often are handy to survive a debate.  I am surprised you did not resort to the all purpose concept of emergence and that one can solve everything.  Maybe you are waiting till things get tough to pull that one out.  So essentially your assertions here are all begging the question arguments.  You take what seems logical within a framework and then assert them without examining the assumptions upon which the framework is based.  You beg the question.

It will be interesting to see how long you stay once you come back because assertions don&#039;t cut it.  Just as heads up for you.  We accept all forms of micro evolution so any changes to gene pools through the typical genetic processes is all well accepted even if a lot of it is in fluctuation as new information is discovered.  The debate is over how novel complex functional capabilities arose in life given that the information to run such capabilities is immense and unlikely to happen by chance.  So stick to that.

I hope you enjoy your train ride.</description>
		<content:encoded><![CDATA[<p>TheYellowShark,</p>
<p>Essentially all you are doing is making assertions and assuming they are true.  You are welcome to your speculative interpretations of some isolated facts but that is all they are is speculations.  To come here and assert that your assertions are established is hubris.  We have seen it all before and none have stood up when scrutinized.</p>
<p>Also the natural selection is not random is a red  herring argument and not an issue.  It is a meaningless discussion.  ID accepts NS but NS is very limited so the answer to the assertion that NS is not random is &#8220;So what!&#8221;  We been down this path a hundred times at least.  There is a random component to NS but mainly what is in play is the population gene pool and the environment.  No big deal.  The random part comes from how something is added to the gene pool.  So let&#8217;s move on to something non trivial.  The fact that you waste any time on this issue means you do not have anything of substance or else you would have trotted it out.</p>
<p>There are no examples of gradual transitions in the fossil record, none, nada, zero, zilch, zip.  We have yet to see one.  We have been given the forrest animal to whale scenario but there are no gradual transitions there, only fossils millions of years apart and variations of marine mammals.  There is also what is referred to the &#8220;crown jewel&#8221; of the fossil record and that is the reptile to mammal movement of three bones from the jaw to the ear.  Again interesting but not an example of gradualism and ignores all other problems with the differences between mammals and reptiles.  So have at it if you find this when you read again.  We are still waiting for an example and as for the natural selection red herring, we have been down this path hundreds of times.</p>
<p>I always looked at concepts such as scaffolding and co-option as things that were pulled out of one&#8217;s back pocket when something got sticky and there was no answer for what happened or exists.  They are not quite all purpose tools but they often are handy to survive a debate.  I am surprised you did not resort to the all purpose concept of emergence and that one can solve everything.  Maybe you are waiting till things get tough to pull that one out.  So essentially your assertions here are all begging the question arguments.  You take what seems logical within a framework and then assert them without examining the assumptions upon which the framework is based.  You beg the question.</p>
<p>It will be interesting to see how long you stay once you come back because assertions don&#8217;t cut it.  Just as heads up for you.  We accept all forms of micro evolution so any changes to gene pools through the typical genetic processes is all well accepted even if a lot of it is in fluctuation as new information is discovered.  The debate is over how novel complex functional capabilities arose in life given that the information to run such capabilities is immense and unlikely to happen by chance.  So stick to that.</p>
<p>I hope you enjoy your train ride.</p>
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		<title>By: Joseph</title>
		<link>http://www.uncommondescent.com/intelligent-design/carl-zimmer-on-irreducible-complexity/comment-page-2/#comment-301209</link>
		<dc:creator>Joseph</dc:creator>
		<pubDate>Fri, 02 Jan 2009 13:54:49 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4336#comment-301209</guid>
		<description>&lt;blockquote&gt;The evidence for evolution speaks for itself.&lt;/blockquote&gt;

&quot;Evolution&quot; is NOT being debated.

Please read the following for YOUR clue:

&lt;a href=&quot;http://intelligentreasoning.blogspot.com/2007/12/biological-evolution-what-is-being.html&quot; rel=&quot;nofollow&quot;&gt;&lt;b&gt;Biological Evolution: What is being debated&lt;/b&gt;&lt;/a&gt;

Hint- the debate is about A) Origins and B) Mechanisms</description>
		<content:encoded><![CDATA[<blockquote><p>The evidence for evolution speaks for itself.</p></blockquote>
<p>&#8220;Evolution&#8221; is NOT being debated.</p>
<p>Please read the following for YOUR clue:</p>
<p><a href="http://intelligentreasoning.blogspot.com/2007/12/biological-evolution-what-is-being.html" rel="nofollow"><b>Biological Evolution: What is being debated</b></a></p>
<p>Hint- the debate is about A) Origins and B) Mechanisms</p>
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		<title>By: Joseph</title>
		<link>http://www.uncommondescent.com/intelligent-design/carl-zimmer-on-irreducible-complexity/comment-page-2/#comment-301208</link>
		<dc:creator>Joseph</dc:creator>
		<pubDate>Fri, 02 Jan 2009 13:50:21 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4336#comment-301208</guid>
		<description>tribune7-

According to Hawking in &quot;A Briefer History of Time&quot; the laws &quot;Just are (the way they are)&quot;.

And that is about all you will ever get from those who oppose ID.</description>
		<content:encoded><![CDATA[<p>tribune7-</p>
<p>According to Hawking in &#8220;A Briefer History of Time&#8221; the laws &#8220;Just are (the way they are)&#8221;.</p>
<p>And that is about all you will ever get from those who oppose ID.</p>
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		<title>By: tribune7</title>
		<link>http://www.uncommondescent.com/intelligent-design/carl-zimmer-on-irreducible-complexity/comment-page-2/#comment-301180</link>
		<dc:creator>tribune7</dc:creator>
		<pubDate>Thu, 01 Jan 2009 21:43:20 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=4336#comment-301180</guid>
		<description>&lt;i&gt;And do you really think accident can explain everything? . . . No. See “natural selection”. It is not chance. It is not “accident”.&lt;/i&gt;

Natural selection is an observable event but it can&#039;t be shown that it does what proponents of evolution claim it does.

Anyway, if it is a law, how do laws come about without design?</description>
		<content:encoded><![CDATA[<p><i>And do you really think accident can explain everything? . . . No. See “natural selection”. It is not chance. It is not “accident”.</i></p>
<p>Natural selection is an observable event but it can&#8217;t be shown that it does what proponents of evolution claim it does.</p>
<p>Anyway, if it is a law, how do laws come about without design?</p>
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