﻿<?xml version="1.0" encoding="UTF-8"?><rss version="2.0"
	xmlns:content="http://purl.org/rss/1.0/modules/content/"
	xmlns:dc="http://purl.org/dc/elements/1.1/"
	xmlns:atom="http://www.w3.org/2005/Atom"
	xmlns:sy="http://purl.org/rss/1.0/modules/syndication/"
		>
<channel>
	<title>Comments on: Catalytic RNA An Unworthy Catalyst For A Serious &#8216;Origins&#8217; Discussion</title>
	<atom:link href="http://www.uncommondescent.com/intelligent-design/catalytic-rna-an-unworthy-catalyst-for-a-serious-origins-discussion/feed/" rel="self" type="application/rss+xml" />
	<link>http://www.uncommondescent.com/intelligent-design/catalytic-rna-an-unworthy-catalyst-for-a-serious-origins-discussion/</link>
	<description>Serving The Intelligent Design Community</description>
	<lastBuildDate>Mon, 13 Feb 2012 20:01:59 +0000</lastBuildDate>
	<sy:updatePeriod>hourly</sy:updatePeriod>
	<sy:updateFrequency>1</sy:updateFrequency>
	
	<item>
		<title>By: Strasbourg</title>
		<link>http://www.uncommondescent.com/intelligent-design/catalytic-rna-an-unworthy-catalyst-for-a-serious-origins-discussion/comment-page-1/#comment-340946</link>
		<dc:creator>Strasbourg</dc:creator>
		<pubDate>Tue, 24 Nov 2009 18:25:19 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=9812#comment-340946</guid>
		<description>@ Robert Deyes:
just some short comments on some of the flaws.Your argumentation is indeed an argumentation from ignorance. In addition you cherrypick and cite outdated literature:

&lt;cite&gt;Perhaps to the disappointment of ‘RNA Worlders’, Duke University chemist David Deamer and others convincingly discredited such a message on the grounds that those processes necessary for the formation of RNA polymers would have been highly inefficient on a lifeless earth. Their conclusions were profound: “It is now clear that an RNA world (or even its molecular precursor, pre-RNA) would be difficult to achieve directly from simple organic molecules dissolved in a global ocean (Joyce, 1991). Even if it were possible to generate chemically activated nucleotides capable of polymerizing into RNA in solution, in the absence of some concentrating mechanism these would be greatly diluted, and no further reactions could occur…[Such] inherent inefficiencies would seem to be inconsistent with moving beyond the initial stages of generating monomers and perhaps random polymers.” (13) 

Actually, there are possible concentration mechanisms for nucleotides as building blocks for nucleic acids:

&quot;Extreme accumulation of nucleotides in simulated hydrothermal pore systems&quot;; Baaske P., et al (2007)
www.pnas.org/cgi/doi/10.1073/pnas.0609592104

In addition a paper is coming out this week in JBC, which demonstrates that the generation of long RNAs without an additional catalyst is possible from nucleotides (cGMP):

&quot;Generation of Long RNA Chains in Water&quot; Constanzo G., et al.(2009)


&lt;/cite&gt;&lt;cite&gt;Moreover, achieving such activities in the laboratory is only possible through the directed guidance of random RNA molecules towards pre-determined functional end points (19, 20).

That is called SELEX/Systematic Evolution of Ligands by Exponential Enrichment, (did you notice the word EVOLUTION?)
The selective pressure in the test tube is determined by the `breeder` of the molecules...(Not an intelligent designer)

Michael


P.S. 
&lt;/cite&gt;&lt;cite&gt;&quot;Surely the strength of my arguments comes from the fact that I have actually been in the lab and run my own experiments (designed RNAs, set up reactions, run gels, calculated reaction rates etc…..).&quot;

... an other Isaak Newton ?....ouch... it is a pity that I can not post here some (in the context pointless) gels of mine&lt;/cite&gt;</description>
		<content:encoded><![CDATA[<p>@ Robert Deyes:<br />
just some short comments on some of the flaws.Your argumentation is indeed an argumentation from ignorance. In addition you cherrypick and cite outdated literature:</p>
<p><cite>Perhaps to the disappointment of ‘RNA Worlders’, Duke University chemist David Deamer and others convincingly discredited such a message on the grounds that those processes necessary for the formation of RNA polymers would have been highly inefficient on a lifeless earth. Their conclusions were profound: “It is now clear that an RNA world (or even its molecular precursor, pre-RNA) would be difficult to achieve directly from simple organic molecules dissolved in a global ocean (Joyce, 1991). Even if it were possible to generate chemically activated nucleotides capable of polymerizing into RNA in solution, in the absence of some concentrating mechanism these would be greatly diluted, and no further reactions could occur…[Such] inherent inefficiencies would seem to be inconsistent with moving beyond the initial stages of generating monomers and perhaps random polymers.” (13) </p>
<p>Actually, there are possible concentration mechanisms for nucleotides as building blocks for nucleic acids:</p>
<p>&#8220;Extreme accumulation of nucleotides in simulated hydrothermal pore systems&#8221;; Baaske P., et al (2007)<br />
<a href="http://www.pnas.org/cgi/doi/10.1073/pnas.0609592104" rel="nofollow">http://www.pnas.org/cgi/doi/10.....0609592104</a></p>
<p>In addition a paper is coming out this week in JBC, which demonstrates that the generation of long RNAs without an additional catalyst is possible from nucleotides (cGMP):</p>
<p>&#8220;Generation of Long RNA Chains in Water&#8221; Constanzo G., et al.(2009)</p>
<p></cite><cite>Moreover, achieving such activities in the laboratory is only possible through the directed guidance of random RNA molecules towards pre-determined functional end points (19, 20).</p>
<p>That is called SELEX/Systematic Evolution of Ligands by Exponential Enrichment, (did you notice the word EVOLUTION?)<br />
The selective pressure in the test tube is determined by the `breeder` of the molecules&#8230;(Not an intelligent designer)</p>
<p>Michael</p>
<p>P.S.<br />
</cite><cite>&#8220;Surely the strength of my arguments comes from the fact that I have actually been in the lab and run my own experiments (designed RNAs, set up reactions, run gels, calculated reaction rates etc…..).&#8221;</p>
<p>&#8230; an other Isaak Newton ?&#8230;.ouch&#8230; it is a pity that I can not post here some (in the context pointless) gels of mine</cite></p>
]]></content:encoded>
	</item>
	<item>
		<title>By: faded_Glory</title>
		<link>http://www.uncommondescent.com/intelligent-design/catalytic-rna-an-unworthy-catalyst-for-a-serious-origins-discussion/comment-page-1/#comment-340812</link>
		<dc:creator>faded_Glory</dc:creator>
		<pubDate>Mon, 23 Nov 2009 11:01:59 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=9812#comment-340812</guid>
		<description>I agree with Mung, and would suggest that also required is a rigorous definition of &#039;intelligence&#039;, in the sense this word is used in the ID discussion. There is currently far to much ambiguity around the term. 

The sidebar definition (from Wiki) is unhelpful - “capacities to reason, to plan, to solve problems, to think abstractly, to comprehend ideas, to use language, and to learn.” These are properties of the designer, something I have heard countless ID supporters vigorously affirm we can not know anything about. 

fG</description>
		<content:encoded><![CDATA[<p>I agree with Mung, and would suggest that also required is a rigorous definition of &#8216;intelligence&#8217;, in the sense this word is used in the ID discussion. There is currently far to much ambiguity around the term. </p>
<p>The sidebar definition (from Wiki) is unhelpful &#8211; “capacities to reason, to plan, to solve problems, to think abstractly, to comprehend ideas, to use language, and to learn.” These are properties of the designer, something I have heard countless ID supporters vigorously affirm we can not know anything about. </p>
<p>fG</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Mung</title>
		<link>http://www.uncommondescent.com/intelligent-design/catalytic-rna-an-unworthy-catalyst-for-a-serious-origins-discussion/comment-page-1/#comment-340794</link>
		<dc:creator>Mung</dc:creator>
		<pubDate>Mon, 23 Nov 2009 07:28:05 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=9812#comment-340794</guid>
		<description>&lt;blockquote&gt;I think OOL is the best place to focus on in the ID vs Evo debate.&lt;/blockquote&gt;
I disagree. Too little both is known, and can be known, about the OOL.

It&#039;s too easy to portray the ID side as being a &quot;designer-of-the-gaps&quot; argument.

What ID needs is a rigorous theory of information, a project to show how it applies to the cell, and an argument that shows why &quot;intelligent design&quot; is the best explanation.</description>
		<content:encoded><![CDATA[<blockquote><p>I think OOL is the best place to focus on in the ID vs Evo debate.</p></blockquote>
<p>I disagree. Too little both is known, and can be known, about the OOL.</p>
<p>It&#8217;s too easy to portray the ID side as being a &#8220;designer-of-the-gaps&#8221; argument.</p>
<p>What ID needs is a rigorous theory of information, a project to show how it applies to the cell, and an argument that shows why &#8220;intelligent design&#8221; is the best explanation.</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Arthur Hunt</title>
		<link>http://www.uncommondescent.com/intelligent-design/catalytic-rna-an-unworthy-catalyst-for-a-serious-origins-discussion/comment-page-1/#comment-340783</link>
		<dc:creator>Arthur Hunt</dc:creator>
		<pubDate>Mon, 23 Nov 2009 04:04:45 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=9812#comment-340783</guid>
		<description>&lt;blockquote&gt;Even in a controled laboratory setting, this stuff doesn’t stick around for long. &lt;/blockquote&gt;

Try telling that to TMV, whose RNA genome can survive the tobacco curing process and can last for decades (or longer) in the fridge.

Or try using this excuse on farmers whose crop is decimated by a viroid-based disease.  These nifty RNA pathogens have no protein coat and are transmitted mechanically.  They have no protection whatsoever and survive just fine outside of &quot;controlled laboratory settings&quot;.

And what RobertC said.

Finally, Robert Deyes, I find it very odd to suggest that the very center of all life - the RNA enzyme that sits at the heart of it all - is not a worthy subject for serious origins discussion.  I would think that, if we are to understand the origin of life, we most certainly are going to have to consider the peptidyltransferase reaction and the RNA that catalyzes the reaction in the here-and-now.</description>
		<content:encoded><![CDATA[<blockquote><p>Even in a controled laboratory setting, this stuff doesn’t stick around for long. </p></blockquote>
<p>Try telling that to TMV, whose RNA genome can survive the tobacco curing process and can last for decades (or longer) in the fridge.</p>
<p>Or try using this excuse on farmers whose crop is decimated by a viroid-based disease.  These nifty RNA pathogens have no protein coat and are transmitted mechanically.  They have no protection whatsoever and survive just fine outside of &#8220;controlled laboratory settings&#8221;.</p>
<p>And what RobertC said.</p>
<p>Finally, Robert Deyes, I find it very odd to suggest that the very center of all life &#8211; the RNA enzyme that sits at the heart of it all &#8211; is not a worthy subject for serious origins discussion.  I would think that, if we are to understand the origin of life, we most certainly are going to have to consider the peptidyltransferase reaction and the RNA that catalyzes the reaction in the here-and-now.</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: RobertC</title>
		<link>http://www.uncommondescent.com/intelligent-design/catalytic-rna-an-unworthy-catalyst-for-a-serious-origins-discussion/comment-page-1/#comment-340767</link>
		<dc:creator>RobertC</dc:creator>
		<pubDate>Sun, 22 Nov 2009 22:13:18 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=9812#comment-340767</guid>
		<description>Deyes,

RNA is unstable in our environment, largely because you, I, and everything living secrete huge amounts of RNAse. Pure RNA in a slightly acidic environment (as the early oceans are predicted to be) should be indefinitely stable. 

So, 
We have suggestions of how ribonucleotides could be generated, and form catalytic polymers. Add some energy, and a membrane, and why not? Your particular lab conditions don&#039;t really relate to origin of life conditions. 

Life’s First Spark Re-Created in the Laboratory
http://www.wired.com/wiredscience/2009/05/ribonucleotides/

Self-Sustained Replication of an RNA Enzyme
http://www.sciencemag.org/cgi/content/abstract/1167856

Was our oldest ancestor a proton-powered rock? 
http://www.newscientist.com/article/mg20427306.200-was-our-oldest-ancestor-a-protonpowered-rock.html</description>
		<content:encoded><![CDATA[<p>Deyes,</p>
<p>RNA is unstable in our environment, largely because you, I, and everything living secrete huge amounts of RNAse. Pure RNA in a slightly acidic environment (as the early oceans are predicted to be) should be indefinitely stable. </p>
<p>So,<br />
We have suggestions of how ribonucleotides could be generated, and form catalytic polymers. Add some energy, and a membrane, and why not? Your particular lab conditions don&#8217;t really relate to origin of life conditions. </p>
<p>Life’s First Spark Re-Created in the Laboratory<br />
<a href="http://www.wired.com/wiredscience/2009/05/ribonucleotides/" rel="nofollow">http://www.wired.com/wiredscie.....cleotides/</a></p>
<p>Self-Sustained Replication of an RNA Enzyme<br />
<a href="http://www.sciencemag.org/cgi/content/abstract/1167856" rel="nofollow">http://www.sciencemag.org/cgi/.....ct/1167856</a></p>
<p>Was our oldest ancestor a proton-powered rock?<br />
<a href="http://www.newscientist.com/article/mg20427306.200-was-our-oldest-ancestor-a-protonpowered-rock.html" rel="nofollow">http://www.newscientist.com/ar.....-rock.html</a></p>
]]></content:encoded>
	</item>
	<item>
		<title>By: jpark320</title>
		<link>http://www.uncommondescent.com/intelligent-design/catalytic-rna-an-unworthy-catalyst-for-a-serious-origins-discussion/comment-page-1/#comment-340666</link>
		<dc:creator>jpark320</dc:creator>
		<pubDate>Sat, 21 Nov 2009 14:18:06 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=9812#comment-340666</guid>
		<description>I &lt;3 this article.

I think OOL is the best place to focus on in the ID vs Evo debate.

Great article</description>
		<content:encoded><![CDATA[<p>I &lt;3 this article.</p>
<p>I think OOL is the best place to focus on in the ID vs Evo debate.</p>
<p>Great article</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Robert Deyes</title>
		<link>http://www.uncommondescent.com/intelligent-design/catalytic-rna-an-unworthy-catalyst-for-a-serious-origins-discussion/comment-page-1/#comment-340658</link>
		<dc:creator>Robert Deyes</dc:creator>
		<pubDate>Sat, 21 Nov 2009 12:59:40 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=9812#comment-340658</guid>
		<description>Thanks for the citation Nakashima although it really doesn&#039;t answer the question posed years ago on how it is that we move beyond random polymers.  

Surely the strength of my arguments comes from the fact that I have actually been in the lab and run my own experiments (designed RNAs, set up reactions, run gels, calculated reaction rates etc.....).

Nakashima, take a look at the gel image I provided above- see the laddering under each of the bands?  That is degraded RNA.  Even in a controled laboratory setting, this stuff doesn&#039;t stick around for long.  I am not convinced that Mulkidjanian&#039;s Zn world does much to answer this stability problem.</description>
		<content:encoded><![CDATA[<p>Thanks for the citation Nakashima although it really doesn&#8217;t answer the question posed years ago on how it is that we move beyond random polymers.  </p>
<p>Surely the strength of my arguments comes from the fact that I have actually been in the lab and run my own experiments (designed RNAs, set up reactions, run gels, calculated reaction rates etc&#8230;..).</p>
<p>Nakashima, take a look at the gel image I provided above- see the laddering under each of the bands?  That is degraded RNA.  Even in a controled laboratory setting, this stuff doesn&#8217;t stick around for long.  I am not convinced that Mulkidjanian&#8217;s Zn world does much to answer this stability problem.</p>
]]></content:encoded>
	</item>
	<item>
		<title>By: Nakashima</title>
		<link>http://www.uncommondescent.com/intelligent-design/catalytic-rna-an-unworthy-catalyst-for-a-serious-origins-discussion/comment-page-1/#comment-340627</link>
		<dc:creator>Nakashima</dc:creator>
		<pubDate>Sat, 21 Nov 2009 03:55:30 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/?p=9812#comment-340627</guid>
		<description>Mr Deyes,

Try &lt;a href=&quot;http://www.ncbi.nlm.nih.gov/pubmed/19703272&quot; rel=&quot;nofollow&quot;&gt;citing some more recent research&lt;/a&gt; if you want to make an effective argument.</description>
		<content:encoded><![CDATA[<p>Mr Deyes,</p>
<p>Try <a href="http://www.ncbi.nlm.nih.gov/pubmed/19703272" rel="nofollow">citing some more recent research</a> if you want to make an effective argument.</p>
]]></content:encoded>
	</item>
</channel>
</rss>

