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<title>AgnosticWeb.com - Complexity of gene codes</title>
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<description>An Agnostic&#039;s Brief Guide to the Universe</description>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>An award to the discoverers of miRNA, a  very active sublayer of gene function:-http://www.pauljanssenaward.com/sites/default/files/pdf/DPJA_Winner_Announcement_Press_Release-Final_Approved_6_19_12.pdf</p>
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<link>https://agnosticweb.com/index.php?id=10741</link>
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<pubDate>Mon, 02 Jul 2012 17:16:41 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>A new repair enzyme has been found for DNA repair. Each discovery makes the genome more complex, and makes the question of &amp;apos;chance development&amp;apos; more problematic:-http://www.physorg.com/news/2011-09-biochemists-genetic-code-tool.html</p>
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<link>https://agnosticweb.com/index.php?id=7328</link>
<guid>https://agnosticweb.com/index.php?id=7328</guid>
<pubDate>Wed, 28 Sep 2011 15:02:11 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>An article discusses using bacteria for codes messages. The key sentences is in the second paragraph, in which the researchers suggest that they can use bacterial DNA for the coding. Life is a living computer!-http://www.physorg.com/news/2011-09-chemists-bacteria-encode-secret-messages.html</p>
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<link>https://agnosticweb.com/index.php?id=7326</link>
<guid>https://agnosticweb.com/index.php?id=7326</guid>
<pubDate>Tue, 27 Sep 2011 14:40:16 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>Complexer and complexer. Now the discovery of an RNA mechanism that appears to act on its own to change DNA instructions. It is stop and change:-http://www.sciencenews.org/view/generic/id/331345/title/Loophole_found_in_genetic_traffic_laws</p>
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<link>https://agnosticweb.com/index.php?id=6572</link>
<guid>https://agnosticweb.com/index.php?id=6572</guid>
<pubDate>Sat, 18 Jun 2011 01:45:06 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>Look at how this monster mechanism works. Made by chance, huh?-http://www.physorg.com/news/2011-03-rna-exporting-machine-deciphered.html</p>
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<link>https://agnosticweb.com/index.php?id=6237</link>
<guid>https://agnosticweb.com/index.php?id=6237</guid>
<pubDate>Tue, 29 Mar 2011 14:23:22 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>Here we go again. Another thoughtful article about epigenetic research and how complicated it is, because epigenetic controls are extremely complex:-http://www.the-scientist.com/article/display/58005/</p>
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<link>https://agnosticweb.com/index.php?id=6234</link>
<guid>https://agnosticweb.com/index.php?id=6234</guid>
<pubDate>Mon, 28 Mar 2011 19:36:08 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>Once again, many thanks to David for alerting us to new findings concerning the makeup of cells:-http://www.physorg.com/news/2011-03-molecular-cell-identity.html-&amp;quot;<strong><em>If a big bunch of your brain cells suddenly went rogue and decided to become fat cells, it could cloud your decision-making capacity a bit. Fortunately, early in an organism&amp;apos;s development, cells make firm and more-or-less permanent decisions about whether they will live their lives as, say, skin cells, brain cells or, well, fat cells</em>.</strong> -<em>Those decisions essentially boil down to which proteins, among all the possible candidates encoded in a cell&amp;apos;s genes, the cell will tend to make under ordinary circumstances. But exactly how a cell chooses its default protein selections from an overwhelmingly diverse genetic menu is somewhat mysterious.-A new study from the Stanford University School of Medicine may help solve the mystery. The researchers discovered how a particular variety of the biomolecule RNA that had been thought to be largely irrelevant to cellular processes plays a dynamic regulatory role in protein selection</em>.&amp;quot;-May I make two brief comments on this? Firstly, it seems to be happening more and more frequently that what had previously been thought to be x is now thought to be y. At the risk of being a bore, let me say yet again that even though it&amp;apos;s heartening to see science constantly correcting itself, every correction should sound a warning signal that we can take nothing for granted when the &amp;quot;experts&amp;quot; make their pronouncements.&amp;#13;&amp;#10; &amp;#13;&amp;#10;Secondly, it&amp;apos;s striking that the article talks of cells making decisions and choosing. Once again, I feel there&amp;apos;s a parallel here between bodies and societies. Ants and bees and other social organisms also make decisions and choose. Our cells are not under our control, and if it&amp;apos;s the biomolecule RNA taking the decisions, the question still remains as to what kind of  &amp;quot;thoughts&amp;quot; govern the process, and where they come from. David thinks it&amp;apos;s all been pre-programmed by a universal intelligence. I suggested earlier that all living things including cells may be endowed with some sort of intelligence and even inventiveness - hence new combinations leading to innovations leading to new organs and new species. Just as great-grandpa termite and colleagues invented and built the first hill, maybe great-great-grandpa Geniucell and colleagues (cooperation is essential in all contexts) invented and built the first leg, wing, eye etc. The net outcome would be the same, but my scenario leaves open the origin of the mechanism. Fantasy? Is it any more fantastic than a universal and eternal intelligence, or unthinking blobs of matter just happening by chance to create all these amazing machines?</p>
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<link>https://agnosticweb.com/index.php?id=6232</link>
<guid>https://agnosticweb.com/index.php?id=6232</guid>
<pubDate>Thu, 24 Mar 2011 13:27:25 +0000</pubDate>
<category>Introduction</category><dc:creator>dhw</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>How do cell types stay the same if they all have the same DNA? There are 200 different cell types in humans. It&amp;apos;s RNA to the rescue:-http://www.physorg.com/news/2011-03-molecular-cell-identity.html</p>
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<link>https://agnosticweb.com/index.php?id=6223</link>
<guid>https://agnosticweb.com/index.php?id=6223</guid>
<pubDate>Mon, 21 Mar 2011 20:07:01 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>How DNA is protected from mistakes in replication. There are two paths. Acetylation is a key component.-http://www.physorg.com/news/2011-03-scientists-key-dna.html</p>
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<link>https://agnosticweb.com/index.php?id=6206</link>
<guid>https://agnosticweb.com/index.php?id=6206</guid>
<pubDate>Fri, 18 Mar 2011 15:40:47 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>How one riboswitch can can respond to more than one energy protein, turning genes on and off. Note the three-dimensional changes of the Riboswitch. It is as though the molecule has a brain, or at least carries control information: -http://www.physorg.com/news/2011-02-rna-onoff.html</p>
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<link>https://agnosticweb.com/index.php?id=5936</link>
<guid>https://agnosticweb.com/index.php?id=5936</guid>
<pubDate>Mon, 14 Feb 2011 01:14:35 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>There is confusion among scientists about the importance of a gene regulation mechanism, which is the extent of  the influence of &amp;apos;Alu&amp;apos; segments:- <a href="http://sandwalk.blogspot.com/">http://sandwalk.blogspot.com/</a>  look for Feb. 12th.-Review by Science Daily:    -http://www.sciencedaily.com/releases/2011/02/110209131828.htm</p>
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<link>https://agnosticweb.com/index.php?id=5925</link>
<guid>https://agnosticweb.com/index.php?id=5925</guid>
<pubDate>Sat, 12 Feb 2011 16:43:17 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>Daphnia pulex, the water flea, is a crustacian used to study water contamination. In 200 million bases it has 31,000 genes, apparently developed for protection against toxic chemicals in water. My guess is that this is the penultimate example of epigenetics in action. 50% more genes than we have! And many not like ours.-&amp;#13;&amp;#10;http://www.sciencedaily.com/releases/2011/02/110203141822.htm-http://www.physorg.com/news/2011-02-crustacean-genome-sequenced.html</p>
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<link>https://agnosticweb.com/index.php?id=5863</link>
<guid>https://agnosticweb.com/index.php?id=5863</guid>
<pubDate>Sun, 06 Feb 2011 16:48:25 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>We have no idea why a Japonese plant has 50 times the base pairs of human DNA:-http://www.the-scientist.com/article/display/57932/</p>
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<link>https://agnosticweb.com/index.php?id=5845</link>
<guid>https://agnosticweb.com/index.php?id=5845</guid>
<pubDate>Fri, 04 Feb 2011 19:37:40 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>A new article in Nature describes plant genes ramping up defenses against pathogens according to their circadian rhythms for light and dark:-http://www.the-scientist.com/news/display/57972/</p>
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<link>https://agnosticweb.com/index.php?id=5829</link>
<guid>https://agnosticweb.com/index.php?id=5829</guid>
<pubDate>Wed, 02 Feb 2011 19:42:09 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>The latest article in Nature on gene codes finds that certain base pairs can be reversed by DNA in an &amp;apos;excited state&amp;apos;creating an even broader code mechanism. Look at this abstract:- <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09775.html-Hoogsteen">http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09775.html-Hoogsteen</a> base pairs expand the information available. In life it is information all the way down! And here, in a sense, the DNA can call up its own mutations when necessary. Fit this into Neo-Darwinism, if you can.</p>
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<link>https://agnosticweb.com/index.php?id=5827</link>
<guid>https://agnosticweb.com/index.php?id=5827</guid>
<pubDate>Wed, 02 Feb 2011 01:19:30 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<blockquote><p>My thanks to David for his comprehensive answers to my questions concerning horizontal gene transfer, and especially about Steve Talbott&amp;apos;s article on the genome ... with its intriguing reference to &amp;quot;<em>the misbegotten hope for a non-lifelike foundation of life</em>&amp;quot;. &amp;#13;&amp;#10;&gt; &amp;#13;&amp;#10;&gt; You remark at the end: &amp;quot;<em>We need to follow this fellow </em>[Talbott ... he has two Ts]. <em>I&amp;apos;ll bet he discusses design in future articles</em>.&amp;quot;&amp;#13;&amp;#10;&gt; &amp;#13;&amp;#10;&gt; I think you&amp;apos;re right ... in which case, the &amp;quot;non-lifelike foundation&amp;quot; may yet turn out to be a metaphorical shot in the theological foot!-I insist that his metaphore refers to the &amp;apos;hope&amp;apos; of atheist scientists. His article refutes them all the way down. Life is the foundation of life in life&amp;apos;s chemistry. The scientists have wounded feet!</p>
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<link>https://agnosticweb.com/index.php?id=5810</link>
<guid>https://agnosticweb.com/index.php?id=5810</guid>
<pubDate>Mon, 31 Jan 2011 14:33:34 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>My thanks to David for his comprehensive answers to my questions concerning horizontal gene transfer, and especially about Steve Talbott&amp;apos;s article on the genome ... with its intriguing reference to &amp;quot;<em>the misbegotten hope for a non-lifelike foundation of life</em>&amp;quot;. -You remark at the end: &amp;quot;<em>We need to follow this fellow </em>[Talbott ... he has two Ts]. <em>I&amp;apos;ll bet he discusses design in future articles</em>.&amp;quot;-I think you&amp;apos;re right ... in which case, the &amp;quot;non-lifelike foundation&amp;quot; may yet turn out to be a metaphorical shot in the theological foot!</p>
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<link>https://agnosticweb.com/index.php?id=5807</link>
<guid>https://agnosticweb.com/index.php?id=5807</guid>
<pubDate>Mon, 31 Jan 2011 11:13:09 +0000</pubDate>
<category>Introduction</category><dc:creator>dhw</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<blockquote><blockquote><p>David drew our attention to an article about the genome, one aspect of which I have queried, as its ramifications are enormous. &amp;#13;&amp;#10;&gt; &gt; &amp;#13;&amp;#10;&gt; &gt; DAVID: <em>I don&amp;apos;t think he ever said that life did not come from inorganic materials.</em>&amp;#13;&amp;#10;&gt; &gt; &amp;#13;&amp;#10;&gt; &gt; The symphonic image and the complexity of the genome are clear, but there are two passages that aren&amp;apos;t. You&amp;apos;ve repeated one of my quotes: &amp;quot;<em>things do not become simpler, less organic, less animate.</em>&amp;quot; The other quote ends: &amp;quot;[Molecular biologists] <em>are writing &amp;quot;finis&amp;quot; to the misbegotten hope for a non-lifelike foundation of life, even if the fact hasn&amp;apos;t yet been widely announced. It is, I think, time for the announcement</em>.&amp;quot;&amp;#13;&amp;#10;&gt; &amp;#13;&amp;#10;&gt; Your first quote is right on &amp;apos;his&amp;apos; mark. With the discovery of the triplet code in DNA, many atheistic scientists assumed they had found the Rosetta Stone of genetics. Far from it, the new research is revealing an enormous number of layers, and when the molecles are &amp;apos;watched&amp;apos; in their dance of coding and control, each type of molecule acts as if it has a life of its own. Not exactly true but it looks like it. Those molecules are under tight controls. But the choreography is at a level of a great ballet company doing Nutcracker. Nothing &amp;apos;looks&amp;apos; inorganic. Nothing is simple. And he expects that further research will only  make the schemata more and more complex. Quote 2 is a metaphor for giving up on Darwin from his the original suppositions: &amp;apos;misbegotten hope for a non-lifelike foundation of life&amp;apos;, parses as the foundation of life &amp;apos;is life&amp;apos;. (Parallels his comment on turtles all the way down) &amp;#13;&amp;#10;&gt; &gt;&amp;#13;&amp;#10;&gt;  What do you think is the announcement? &amp;#13;&amp;#10;&gt; &amp;#13;&amp;#10;&gt; Very simple: Life is alive in all the layers. It may have started from inorganic matter, but that matter has changed into an animate-like construction of extreme complexity in which the organization of the parts has resulted in an emergence of living matter, most highly developed in the human brain with so-far unexplained consciousness. Like Stuart Kauffman&amp;apos;s theories of emergence from complex systems. There is no simple explanation for this observation. The parts are so carefully intertwined chance construction is extremely unlikely. It looks &amp;apos;irreducably complex&amp;apos;. &amp;#13;&amp;#10;&gt; &amp;#13;&amp;#10;&gt; We need to follow this fellow (Talbot). I&amp;apos;ll bet he discusses design in future articles.&amp;#13;&amp;#10;&gt; &amp;#13;&amp;#10;&gt; &amp;#13;&amp;#10;&gt; &gt; Thank you for the latest posts about horizontal gene transfer. This appears to shed light on how prokaryotes adapt to changing conditions, but does it have any bearing on the emergence of totally new organs and species? (I&amp;apos;m asking because I&amp;apos;m not sure whether I&amp;apos;ve understood all the implications.)-Prokaryotes can have horizontal gene transfer. These are single-celled organisms. Eukaryotes are multicelled. They have organs, and there is some small evidence for gene transfer at this level of development. Prokaryotes can form new species with gene transfer, but the evidence of gene transfer forming new organs in eukaryotes does not exist. And I doubt we will find evidence for this.</p>
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<link>https://agnosticweb.com/index.php?id=5794</link>
<guid>https://agnosticweb.com/index.php?id=5794</guid>
<pubDate>Sat, 29 Jan 2011 16:30:17 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<blockquote><p>David drew our attention to an article about the genome, one aspect of which I have queried, as its ramifications are enormous. &amp;#13;&amp;#10;&gt; &amp;#13;&amp;#10;&gt; DAVID: <em>I don&amp;apos;t think he ever said that life did not come from inorganic materials.</em>&amp;#13;&amp;#10;&gt; &amp;#13;&amp;#10;&gt; The symphonic image and the complexity of the genome are clear, but there are two passages that aren&amp;apos;t. You&amp;apos;ve repeated one of my quotes: &amp;quot;<em>things do not become simpler, less organic, less animate.</em>&amp;quot; The other quote ends: &amp;quot;[Molecular biologists] <em>are writing &amp;quot;finis&amp;quot; to the misbegotten hope for a non-lifelike foundation of life, even if the fact hasn&amp;apos;t yet been widely announced. It is, I think, time for the announcement</em>.&amp;quot;-Your first quote is right on &amp;apos;his&amp;apos; mark. With the discovery of the triplet code in DNA, many atheistic scientists assumed they had found the Rosetta Stone of genetics. Far from it, the new research is revealing an enormous number of layers, and when the molecles are &amp;apos;watched&amp;apos; in their dance of coding and control, each type of molecule acts as if it has a life of its own. Not exactly true but it looks like it. Those molecules are under tight controls. But the choreography is at a level of a great ballet company doing Nutcracker. Nothing &amp;apos;looks&amp;apos; inorganic. Nothing is simple. And he expects that further research will only  make the schemata more and more complex. Quote 2 is a metaphor for giving up on Darwin from his the original suppositions: &amp;apos;misbegotten hope for a non-lifelike foundation of life&amp;apos;, parses as the foundation of life &amp;apos;is life&amp;apos;. (Parallels his comment on turtles all the way down) &amp;#13;&amp;#10;&gt;&amp;#13;&amp;#10; What do you think is the announcement? -Very simple: Life is alive in all the layers. It may have started from inorganic matter, but that matter has changed into an animate-like construction of extreme complexity in which the organization of the parts has resulted in an emergence of living matter, most highly developed in the human brain with so-far unexplained consciousness. Like Stuart Kauffman&amp;apos;s theories of emergence from complex systems. There is no simple explanation for this observation. The parts are so carefully intertwined chance construction is extremely unlikely. It looks &amp;apos;irreducably complex&amp;apos;. -We need to follow this fellow (Talbot). I&amp;apos;ll bet he discusses design in future articles.-&amp;#13;&amp;#10;&gt; Thank you for the latest posts about horizontal gene transfer. This appears to shed light on how prokaryotes adapt to changing conditions, but does it have any bearing on the emergence of totally new organs and species? (I&amp;apos;m asking because I&amp;apos;m not sure whether I&amp;apos;ve understood all the implications.)</p>
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<link>https://agnosticweb.com/index.php?id=5793</link>
<guid>https://agnosticweb.com/index.php?id=5793</guid>
<pubDate>Sat, 29 Jan 2011 16:24:56 +0000</pubDate>
<category>Introduction</category><dc:creator>David Turell</dc:creator>
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<title>Complexity of gene codes (reply)</title>
<content:encoded><![CDATA[<p>David drew our attention to an article about the genome, one aspect of which I have queried, as its ramifications are enormous. -DAVID: <em>I don&amp;apos;t think he ever said that life did not come from inorganic materials.</em>-The symphonic image and the complexity of the genome are clear, but there are two passages that aren&amp;apos;t. You&amp;apos;ve repeated one of my quotes: &amp;quot;<em>things do not become simpler, less organic, less animate.</em>&amp;quot; The other quote ends: &amp;quot;[Molecular biologists] <em>are writing &amp;quot;finis&amp;quot; to the misbegotten hope for a non-lifelike foundation of life, even if the fact hasn&amp;apos;t yet been widely announced. It is, I think, time for the announcement</em>.&amp;quot;-What do you think he means, then, by &amp;quot;<em>a non-lifelike foundation of life</em>&amp;quot;, in the context of things NOT becoming less organic, less animate? Who do you think is hoping for a non-lifelike foundation? What do you think is the announcement? -Sorry for the third degree!-Thank you for the latest posts about horizontal gene transfer. This appears to shed light on how prokaryotes adapt to changing conditions, but does it have any bearing on the emergence of totally new organs and species? (I&amp;apos;m asking because I&amp;apos;m not sure whether I&amp;apos;ve understood all the implications.)</p>
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<pubDate>Sat, 29 Jan 2011 14:50:39 +0000</pubDate>
<category>Introduction</category><dc:creator>dhw</dc:creator>
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