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	<title>Comments on: To Stop Evolution: New Way Of Fighting Antibiotic Resistance Demonstrated By Scripps Scientists</title>
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	<link>http://www.uncommondescent.com/evolution/to-stop-evolution-new-way-of-fighting-antibiotic-resistance-demonstrated-by-scripps-scientists/</link>
	<description>Serving The Intelligent Design Community</description>
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		<title>By: Lenski&#8217;s et al. E. Coli Paper &#171; The Deeps of Time</title>
		<link>http://www.uncommondescent.com/evolution/to-stop-evolution-new-way-of-fighting-antibiotic-resistance-demonstrated-by-scripps-scientists/comment-page-1/#comment-291590</link>
		<dc:creator>Lenski&#8217;s et al. E. Coli Paper &#171; The Deeps of Time</dc:creator>
		<pubDate>Sat, 28 Jun 2008 00:14:34 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/index.php/archives/85#comment-291590</guid>
		<description>[...] et al. E. Coli&#160;Paper  As I noted before, you can read Lenski’s et al. paper on evolution (PDF) in an experimental population of bacteria here. This paper has been touted as the first [...]</description>
		<content:encoded><![CDATA[<p>[...] et al. E. Coli&nbsp;Paper  As I noted before, you can read Lenski’s et al. paper on evolution (PDF) in an experimental population of bacteria here. This paper has been touted as the first [...]</p>
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		<title>By: DaveScot</title>
		<link>http://www.uncommondescent.com/evolution/to-stop-evolution-new-way-of-fighting-antibiotic-resistance-demonstrated-by-scripps-scientists/comment-page-1/#comment-554</link>
		<dc:creator>DaveScot</dc:creator>
		<pubDate>Thu, 02 Jun 2005 19:05:55 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/index.php/archives/85#comment-554</guid>
		<description>Give hard sci-fi novel &quot;Darwin&#039;s Radio&quot; by Greg Bear a read for an intriguing and entertaining view of saltation driven by computational capability in the DNA molecule.  I really liked the first book (Radio).  The second book in the series, &quot;Darwin&#039;s Children&quot;, was a little slow for me and had far less hard science driving the plot.

Here&#039;s a review of it by biologist Michael Goldman that appeared in NATURE

http://www.gregbear.com/A55885/Bear.nsf/pages/300040</description>
		<content:encoded><![CDATA[<p>Give hard sci-fi novel &#8220;Darwin&#8217;s Radio&#8221; by Greg Bear a read for an intriguing and entertaining view of saltation driven by computational capability in the DNA molecule.  I really liked the first book (Radio).  The second book in the series, &#8220;Darwin&#8217;s Children&#8221;, was a little slow for me and had far less hard science driving the plot.</p>
<p>Here&#8217;s a review of it by biologist Michael Goldman that appeared in NATURE</p>
<p><a href="http://www.gregbear.com/A55885/Bear.nsf/pages/300040" rel="nofollow">http://www.gregbear.com/A55885.....ges/300040</a></p>
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		<title>By: Markus Rammerstorfer</title>
		<link>http://www.uncommondescent.com/evolution/to-stop-evolution-new-way-of-fighting-antibiotic-resistance-demonstrated-by-scripps-scientists/comment-page-1/#comment-511</link>
		<dc:creator>Markus Rammerstorfer</dc:creator>
		<pubDate>Sun, 29 May 2005 06:32:31 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/index.php/archives/85#comment-511</guid>
		<description>Thank you for your thoughts! I&#039;m reading at the moment Wallace Arthur&#039;s &quot;Biased Embryos and Evolution&quot; and as far as I can see is the &quot;EvoDevo&quot;-approach kindly in the direction of Goldschmidt. It seems to me as the right time to read Goldschmidt in original.       </description>
		<content:encoded><![CDATA[<p>Thank you for your thoughts! I&#8217;m reading at the moment Wallace Arthur&#8217;s &#8220;Biased Embryos and Evolution&#8221; and as far as I can see is the &#8220;EvoDevo&#8221;-approach kindly in the direction of Goldschmidt. It seems to me as the right time to read Goldschmidt in original.</p>
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		<title>By: PaV</title>
		<link>http://www.uncommondescent.com/evolution/to-stop-evolution-new-way-of-fighting-antibiotic-resistance-demonstrated-by-scripps-scientists/comment-page-1/#comment-476</link>
		<dc:creator>PaV</dc:creator>
		<pubDate>Thu, 26 May 2005 18:57:35 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/index.php/archives/85#comment-476</guid>
		<description>Markus, here are two quotes I picked out of the paper:  
&quot;Reznick and his colleagues studied guppy-like fish in the genus Poeciliopsis. They report that placentas have evolved independently three times in closely related Poeciliopsis species. Other species in the genus lack placentas, and some have partial maternal provisioning via tissues that may be precursors of placentas.&quot; 
AND:
&quot;In the Science paper, the researchers show that: 1) Fish in the genus Poeciliopsis have placentas in various stages of evolution, and 2) There are clusters of closely related species that either have highly evolved placentas, placentas in intermediate stages of evolution, or no placentas at all. These provide ideal material for studying how such complexity evolves.&quot; 

Based on these two quotes, I would say the evidence fits almost perfectly with what Goldschmidt proposes.  His interpretation would likely be something along the lines of this:  Over the life history of this particular form a &#039;systemic mutation&#039; has occurred, that is, a &#039;repatterning&#039; of the chromosomal material.  The net affect of this change is to disturb the rates of reaction within the developmental pattern of poecilioppus.  When the inducer for the placenta rises above its threshold value while the embryo is still developing, then the full placenta appears.  If it reaches its threshold value later on, then the placenta will be partially formed, and, if very late, then it will not appear at all.&quot;  In other words, he would see this as being hormonally based (or through other potent chemicals) and directly related to chemicals manufactured by germ plasm material  (Yes, even back in 1940, Goldschmidt already realized the chemical producing power of germ plasm (DNA))



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		<content:encoded><![CDATA[<p>Markus, here are two quotes I picked out of the paper:<br />
&#8220;Reznick and his colleagues studied guppy-like fish in the genus Poeciliopsis. They report that placentas have evolved independently three times in closely related Poeciliopsis species. Other species in the genus lack placentas, and some have partial maternal provisioning via tissues that may be precursors of placentas.&#8221;<br />
AND:<br />
&#8220;In the Science paper, the researchers show that: 1) Fish in the genus Poeciliopsis have placentas in various stages of evolution, and 2) There are clusters of closely related species that either have highly evolved placentas, placentas in intermediate stages of evolution, or no placentas at all. These provide ideal material for studying how such complexity evolves.&#8221; </p>
<p>Based on these two quotes, I would say the evidence fits almost perfectly with what Goldschmidt proposes.  His interpretation would likely be something along the lines of this:  Over the life history of this particular form a &#8216;systemic mutation&#8217; has occurred, that is, a &#8216;repatterning&#8217; of the chromosomal material.  The net affect of this change is to disturb the rates of reaction within the developmental pattern of poecilioppus.  When the inducer for the placenta rises above its threshold value while the embryo is still developing, then the full placenta appears.  If it reaches its threshold value later on, then the placenta will be partially formed, and, if very late, then it will not appear at all.&#8221;  In other words, he would see this as being hormonally based (or through other potent chemicals) and directly related to chemicals manufactured by germ plasm material  (Yes, even back in 1940, Goldschmidt already realized the chemical producing power of germ plasm (DNA))</p>
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		<title>By: PaV</title>
		<link>http://www.uncommondescent.com/evolution/to-stop-evolution-new-way-of-fighting-antibiotic-resistance-demonstrated-by-scripps-scientists/comment-page-1/#comment-475</link>
		<dc:creator>PaV</dc:creator>
		<pubDate>Thu, 26 May 2005 18:33:17 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/index.php/archives/85#comment-475</guid>
		<description>Markus:

Not having time at the moment to look at the article you cite, let me quickly tell you that Goldschmidt&#039;s view was that macroevolution came about by a shifting in the patterns of the chromosomal material.  If this reshifting was on a large scale, then it would be (1) much more difficult for the organism to be viable, but (2)if it did become viable, then we would see organismal change at least at the genus level, if not at the Class level (or higher).

Goldschmidt also implied through this chromosomal view that the &quot;genotype&quot; of most organisms is contained in, using his terms (from the 1940&#039;s), in the germ plasm of living cells.  He doesn&#039;t elaborate it much in his famous book of 1940, but this is the impression he gives.

I must say that it has crossed my mind--thinking now in terms of ID--that something along this line may be the actual case of evolution, since one is forced to answer the question as to &quot;where&quot; this added &quot;information&quot; comes from.  It simplifies things if, indeed, the &quot;germ plasm&quot; of all living cells contain the information for every type of combination possible, i.e., every life form present.  But that does represent an extravagant claim, and so I tend to dismiss it.  However, Goldschmidt, being a preeminent geneticist and embryologist, makes me want to reconsider this possibility.  If indeed Goldschmidt is correct about germ plasm, then we shouldn&#039;t be surprised by the sudden origin of a placenta in a fish line--the information is there already in the chromosomes, and if they can rearrange themselves into a new--and VIABLE--configuration, then, voilÃƒÂ , a fish with a placenta.  (Not having read the article, but along the lines of Goldschmidt, I rather suspect that the &quot;placenta&quot; was induced by some kind of chemical method. [That is, chemical induction of some kind of chromosomal change]  I&#039;ll have to go look and see.)

PaV
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		<content:encoded><![CDATA[<p>Markus:</p>
<p>Not having time at the moment to look at the article you cite, let me quickly tell you that Goldschmidt&#8217;s view was that macroevolution came about by a shifting in the patterns of the chromosomal material.  If this reshifting was on a large scale, then it would be (1) much more difficult for the organism to be viable, but (2)if it did become viable, then we would see organismal change at least at the genus level, if not at the Class level (or higher).</p>
<p>Goldschmidt also implied through this chromosomal view that the &#8220;genotype&#8221; of most organisms is contained in, using his terms (from the 1940&#8242;s), in the germ plasm of living cells.  He doesn&#8217;t elaborate it much in his famous book of 1940, but this is the impression he gives.</p>
<p>I must say that it has crossed my mind&#8211;thinking now in terms of ID&#8211;that something along this line may be the actual case of evolution, since one is forced to answer the question as to &#8220;where&#8221; this added &#8220;information&#8221; comes from.  It simplifies things if, indeed, the &#8220;germ plasm&#8221; of all living cells contain the information for every type of combination possible, i.e., every life form present.  But that does represent an extravagant claim, and so I tend to dismiss it.  However, Goldschmidt, being a preeminent geneticist and embryologist, makes me want to reconsider this possibility.  If indeed Goldschmidt is correct about germ plasm, then we shouldn&#8217;t be surprised by the sudden origin of a placenta in a fish line&#8211;the information is there already in the chromosomes, and if they can rearrange themselves into a new&#8211;and VIABLE&#8211;configuration, then, voilÃƒÂ , a fish with a placenta.  (Not having read the article, but along the lines of Goldschmidt, I rather suspect that the &#8220;placenta&#8221; was induced by some kind of chemical method. [That is, chemical induction of some kind of chromosomal change]  I&#8217;ll have to go look and see.)</p>
<p>PaV</p>
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		<title>By: Markus Rammerstorfer</title>
		<link>http://www.uncommondescent.com/evolution/to-stop-evolution-new-way-of-fighting-antibiotic-resistance-demonstrated-by-scripps-scientists/comment-page-1/#comment-450</link>
		<dc:creator>Markus Rammerstorfer</dc:creator>
		<pubDate>Tue, 24 May 2005 08:12:19 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/index.php/archives/85#comment-450</guid>
		<description>Hi PaV! Not really familiar(Goldschmidt, Schindewolf, hopeful monsters - i know not much more). I know one german author - Ferdinand Schmidt and his concept of &quot;cybernetic evolution&quot; - who has proposed a really directed evolution: Organisms should be capable with help of ominous &quot;Feedback-Loops&quot; (?&gt;&quot;Regelkreise&quot;) to change her genes and blueprints purposefully. It was Schmidt&#039;s answer to the classical evolution-problems concerning the orgin of the eye and other systems of complex  (syn)organization. And a real solution of this &quot;problems&quot; needs purpose, teleology (here was Schmidt right...) - but in Schmidts case was this a sort of evolution-directing-&quot;computer&quot; in organisms originated with the origin of life - through undirected mechanisms, eventually in a darwinian manner as he says;-).
Okay, I&#039;m not a advocate of &quot;directed evolution&quot; but I think this concept (in the sense of preprogrammed variation-potential and mechanisms) could apply to some of the observable evolutionary phenomena. Look for example  at the Paper *Reznick, David N. et al. 2002: &quot;Independent Origins and Rapid Evolution of the Placenta in the Fish Genus Poeciliopsis&quot; Science 298: 1018-1020* and the summary under http://www.sciencedaily.com/releases/2002/12/021226071202.htm Here is the independent origin of a complex system within a genus (!) described. Should we believe that this is the outcome of undirected mechanisms? Or should we look for a sort of &quot;program&quot; or control-mechanism?               </description>
		<content:encoded><![CDATA[<p>Hi PaV! Not really familiar(Goldschmidt, Schindewolf, hopeful monsters &#8211; i know not much more). I know one german author &#8211; Ferdinand Schmidt and his concept of &#8220;cybernetic evolution&#8221; &#8211; who has proposed a really directed evolution: Organisms should be capable with help of ominous &#8220;Feedback-Loops&#8221; (?&gt;&#8221;Regelkreise&#8221;) to change her genes and blueprints purposefully. It was Schmidt&#8217;s answer to the classical evolution-problems concerning the orgin of the eye and other systems of complex  (syn)organization. And a real solution of this &#8220;problems&#8221; needs purpose, teleology (here was Schmidt right&#8230;) &#8211; but in Schmidts case was this a sort of evolution-directing-&#8221;computer&#8221; in organisms originated with the origin of life &#8211; through undirected mechanisms, eventually in a darwinian manner as he says;-).<br />
Okay, I&#8217;m not a advocate of &#8220;directed evolution&#8221; but I think this concept (in the sense of preprogrammed variation-potential and mechanisms) could apply to some of the observable evolutionary phenomena. Look for example  at the Paper *Reznick, David N. et al. 2002: &#8220;Independent Origins and Rapid Evolution of the Placenta in the Fish Genus Poeciliopsis&#8221; Science 298: 1018-1020* and the summary under <a href="http://www.sciencedaily.com/releases/2002/12/021226071202.htm" rel="nofollow">http://www.sciencedaily.com/re.....071202.htm</a> Here is the independent origin of a complex system within a genus (!) described. Should we believe that this is the outcome of undirected mechanisms? Or should we look for a sort of &#8220;program&#8221; or control-mechanism?</p>
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		<title>By: minlay</title>
		<link>http://www.uncommondescent.com/evolution/to-stop-evolution-new-way-of-fighting-antibiotic-resistance-demonstrated-by-scripps-scientists/comment-page-1/#comment-449</link>
		<dc:creator>minlay</dc:creator>
		<pubDate>Tue, 24 May 2005 06:45:04 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/index.php/archives/85#comment-449</guid>
		<description>http://biology.plosjournals.org/perlserv/?request=get-document&amp;doi=10.1371/journal.pbio.0030176

For those interested in reading and interpreting the primary literature for themselves, here&#039;s the abstract to the actual article in question:

The emergence of drug-resistant bacteria poses a serious threat to human health. In the case of several antibiotics, including those of the quinolone and rifamycin classes, bacteria rapidly acquire resistance through mutation of chromosomal genes during therapy. In this work, we show that preventing induction of the SOS response by interfering with the activity of the protease LexA renders pathogenic Escherichia coli unable to evolve resistance in vivo to ciprofloxacin or rifampicin, important quinolone and rifamycin antibiotics. We show in vitro that LexA cleavage is induced during RecBC-mediated repair of ciprofloxacin-mediated DNA damage and that this results in the derepression of the SOS-regulated polymerases Pol II, Pol IV and Pol V, which collaborate to induce resistance-conferring mutations. Our findings indicate that the inhibition of mutation could serve as a novel therapeutic strategy to combat the evolution of antibiotic resistance.</description>
		<content:encoded><![CDATA[<p><a href="http://biology.plosjournals.org/perlserv/?request=get-document&#038;doi=10.1371/journal.pbio.0030176" rel="nofollow">http://biology.plosjournals.or.....io.0030176</a></p>
<p>For those interested in reading and interpreting the primary literature for themselves, here&#8217;s the abstract to the actual article in question:</p>
<p>The emergence of drug-resistant bacteria poses a serious threat to human health. In the case of several antibiotics, including those of the quinolone and rifamycin classes, bacteria rapidly acquire resistance through mutation of chromosomal genes during therapy. In this work, we show that preventing induction of the SOS response by interfering with the activity of the protease LexA renders pathogenic Escherichia coli unable to evolve resistance in vivo to ciprofloxacin or rifampicin, important quinolone and rifamycin antibiotics. We show in vitro that LexA cleavage is induced during RecBC-mediated repair of ciprofloxacin-mediated DNA damage and that this results in the derepression of the SOS-regulated polymerases Pol II, Pol IV and Pol V, which collaborate to induce resistance-conferring mutations. Our findings indicate that the inhibition of mutation could serve as a novel therapeutic strategy to combat the evolution of antibiotic resistance.</p>
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		<title>By: PaV</title>
		<link>http://www.uncommondescent.com/evolution/to-stop-evolution-new-way-of-fighting-antibiotic-resistance-demonstrated-by-scripps-scientists/comment-page-1/#comment-448</link>
		<dc:creator>PaV</dc:creator>
		<pubDate>Tue, 24 May 2005 01:34:10 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/index.php/archives/85#comment-448</guid>
		<description>Markus, are you familiar with the work of Richard Goldschmidt?  I&#039;m reading his &quot;Material Basis of Evolution&quot;.  He talks there of &quot;directed mechanisms.&quot;  Any good resources/references out there on this sort of stuff?</description>
		<content:encoded><![CDATA[<p>Markus, are you familiar with the work of Richard Goldschmidt?  I&#8217;m reading his &#8220;Material Basis of Evolution&#8221;.  He talks there of &#8220;directed mechanisms.&#8221;  Any good resources/references out there on this sort of stuff?</p>
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		<title>By: Markus Rammerstorfer</title>
		<link>http://www.uncommondescent.com/evolution/to-stop-evolution-new-way-of-fighting-antibiotic-resistance-demonstrated-by-scripps-scientists/comment-page-1/#comment-443</link>
		<dc:creator>Markus Rammerstorfer</dc:creator>
		<pubDate>Mon, 23 May 2005 10:14:28 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/index.php/archives/85#comment-443</guid>
		<description>Not all microevolutionary processes are &quot;undirected&quot;. There is evidence that some processes are the result of mechanisms instead of pure &quot;chance-mutations&quot;, natural selection and some other processes. And I think that this could become a future line of evidence for ID. I have outlined this concept together with a friend under the name &quot;Potentielle KomplexitÃƒÂ¤t als ID-Forschungsprogramm. UrsprÃƒÂ¼nge der VariabilitÃƒÂ¤t&quot; (&quot;Potential Complexity as ID-research program: Origins of variability&quot;). This paper is not online but the basic idea is (I hope my english is good enough to describe it): Organisms are equipped with more as it is necessary to their immediate survival, for example alternative phenotypes activated in response to special conditions(look  for example at the phenotypic realization of C3/C4-photosynth. Systems with Eleocharis vivipara). If we have &quot;preprogrammed&quot; Mechanisms of variation we have evidence for ID. As we know evolution is a blind process. As we know a intelligence is capable to look forward. Organisms who have some features in respect not to present but to potential challenges in the future show a form of telelogy. There are some basic objections (selection conditions in the past...) to that concept but I hope they are refutable with a close look  at the evidence.                            </description>
		<content:encoded><![CDATA[<p>Not all microevolutionary processes are &#8220;undirected&#8221;. There is evidence that some processes are the result of mechanisms instead of pure &#8220;chance-mutations&#8221;, natural selection and some other processes. And I think that this could become a future line of evidence for ID. I have outlined this concept together with a friend under the name &#8220;Potentielle KomplexitÃƒÂ¤t als ID-Forschungsprogramm. UrsprÃƒÂ¼nge der VariabilitÃƒÂ¤t&#8221; (&#8220;Potential Complexity as ID-research program: Origins of variability&#8221;). This paper is not online but the basic idea is (I hope my english is good enough to describe it): Organisms are equipped with more as it is necessary to their immediate survival, for example alternative phenotypes activated in response to special conditions(look  for example at the phenotypic realization of C3/C4-photosynth. Systems with Eleocharis vivipara). If we have &#8220;preprogrammed&#8221; Mechanisms of variation we have evidence for ID. As we know evolution is a blind process. As we know a intelligence is capable to look forward. Organisms who have some features in respect not to present but to potential challenges in the future show a form of telelogy. There are some basic objections (selection conditions in the past&#8230;) to that concept but I hope they are refutable with a close look  at the evidence.</p>
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		<title>By: Jedi Deist</title>
		<link>http://www.uncommondescent.com/evolution/to-stop-evolution-new-way-of-fighting-antibiotic-resistance-demonstrated-by-scripps-scientists/comment-page-1/#comment-442</link>
		<dc:creator>Jedi Deist</dc:creator>
		<pubDate>Mon, 23 May 2005 08:47:49 +0000</pubDate>
		<guid isPermaLink="false">http://www.uncommondescent.com/index.php/archives/85#comment-442</guid>
		<description>Hmm. This seems to suggest that mutations aren&#039;t as random as we thought. Could mutations be the result of a mechanism? And if so, how could that mechanism have evolved in the first place?</description>
		<content:encoded><![CDATA[<p>Hmm. This seems to suggest that mutations aren&#8217;t as random as we thought. Could mutations be the result of a mechanism? And if so, how could that mechanism have evolved in the first place?</p>
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