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Discussion and Debate
Discussion and Debate
Physical & Life Sciences
Creation & Evolution
Similarity of human and chimp DNA is down.
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<blockquote data-quote="Naraoia" data-source="post: 58852922" data-attributes="member: 202689"><p>I'm not sure I understand exactly what you are asking here...</p><p></p><p> The<em> abstract</em> of that paper is already a big helping of misrepresenting the field, seasoned with unsupported claims out of personal incredulity. Doesn't seem to get much better, from the looks I've had at the main text...</p><p></p><p>Plus I don't see how it is relevant to my question to you, but look how easy I am to derail...</p><p></p><p style="margin-left: 20px"></p><p>Like all "conserved" DNA, conserved non-coding elements are conserved to <em>highly variable</em> degrees.<a href="http://www.pnas.org/content/108/31/12782/F1.expansion.html" target="_blank">Here</a>'s a figure from another study on enhancer evolution that demonstrates this. CsB, the HoxD control element illustrated in the figure, has bits that are conserved all the way across jawed vertebrates, other parts only across the amniotes, and some that are specific to the mammals. Note also that even with the most highly conserved regions, we're not talking about 100% identity.</p><p></p><p style="margin-left: 20px"></p><p>Actually, it's becoming increasingly clear that regulatory regions AND protein coding sequences (and RNA genes, let's not forget those) are heavily involved in evolution (and <a href="http://en.wikipedia.org/wiki/Molecular_evolution" target="_blank">molecular evolution</a> means something slightly different). <em>Of course</em> you mainly (or at least often) alter protein expression by messing with the regulatory elements. (Other options include microRNAs, alternative splicing and even <a href="http://www.sciencedirect.com/science/article/pii/S0092867411003059" target="_blank">ribosomal proteins</a>.) </p><p></p><p>He says that like coding sequence evolution was thought to alter protein expression before. (Which, as a matter of fact, it can do. IIRC, bacteria make use of rare codons to slow down translation, and I'm sure there are other examples.)</p><p></p><p>But regulatory elements are very obviously not the only players.</p><p></p><p style="margin-left: 20px"></p><p>And here our author conveniently omits that NO ONE is proposing that CNEs alone explain everything. Presumably, he's never heard of gene duplication, domain shuffling, HGT, heck, <a href="http://www.nature.com/nrg/journal/v12/n10/full/nrg3053.html" target="_blank"><em>de novo</em> gene birth from non-coding DNA</a>! (The first is hard to believe given that he discusses it in the main body of the paper...)</p><p></p><p style="margin-left: 20px"></p><p>And here, he basically says that enhancer evolution does work. Since morphologically and genetically speaking, we're well within the "ape kind" (unless <a href="http://pandasthumb.org/archives/2010/07/intraspecific-m.html" target="_blank">domestic dogs</a> are several different kinds...), your "did you read???!!11!!!" source appears to be on my side <img src="/styles/default/xenforo/smilies/old/kawaii.gif" class="smilie" loading="lazy" alt="^_^" title="Kawaii ^_^" data-shortname="^_^" /></p><p></p><p>A choice quote from the paper itself, for what it's worth:</p><p></p><p style="margin-left: 20px"></p><p>It doesn't work that way. Transcription factors work in combinations to activate (or repress) a target gene. We've just seen from the <em>eve</em> study that quite different sets of TFBSs can sum up to the exact same expression pattern, using the exact same TFs to boot (all enhancers were tested in the same species). It's like 2x2 + 3x7 is the same as 1x5 + 5x4. Thus expecting raw divergence in TFBS content to match expression divergence is probably not a good idea. <em>What</em> the differences are appears to be more important than <em>how many</em> there are. Naturally, that's also a far more <em>difficult</em> situation to analyse.</p><p> </p><p> They obviously did, or there wouldn't be a paper about it. You do know what "divergence" means, right?</p><p></p><p>And don't come with that tired trope. Fruit flies happened to be morphologically conservative over that time span. Other things haven't. (Ironically, the "slow-breeding" apes may have changed more in appearance in the last 20 million years than the "fast-breeding" flies!) But that's not why I brought this up at all.</p><p></p><p>Of course, you didn't seem to get why I did bring it up, so let's have another go at explaining that...</p><p> </p><p></p><p> </p><p> If you were a designer with a thimble of sense, <strong>why would you change a perfectly functional design to something that produces the exact same result?</strong></p><p> </p><p> That question above.</p><p></p><p>And before you answer "'cuz I felt like it", think about what that implies for the testability of the design hypothesis.</p></blockquote><p></p>
[QUOTE="Naraoia, post: 58852922, member: 202689"] I'm not sure I understand exactly what you are asking here... The[I] abstract[/I] of that paper is already a big helping of misrepresenting the field, seasoned with unsupported claims out of personal incredulity. Doesn't seem to get much better, from the looks I've had at the main text... Plus I don't see how it is relevant to my question to you, but look how easy I am to derail... [INDENT][/INDENT] Like all "conserved" DNA, conserved non-coding elements are conserved to [I]highly variable[/I] degrees.[URL="http://www.pnas.org/content/108/31/12782/F1.expansion.html"]Here[/URL]'s a figure from another study on enhancer evolution that demonstrates this. CsB, the HoxD control element illustrated in the figure, has bits that are conserved all the way across jawed vertebrates, other parts only across the amniotes, and some that are specific to the mammals. Note also that even with the most highly conserved regions, we're not talking about 100% identity. [INDENT][/INDENT] Actually, it's becoming increasingly clear that regulatory regions AND protein coding sequences (and RNA genes, let's not forget those) are heavily involved in evolution (and [URL="http://en.wikipedia.org/wiki/Molecular_evolution"]molecular evolution[/URL] means something slightly different). [I]Of course[/I] you mainly (or at least often) alter protein expression by messing with the regulatory elements. (Other options include microRNAs, alternative splicing and even [URL="http://www.sciencedirect.com/science/article/pii/S0092867411003059"]ribosomal proteins[/URL].) He says that like coding sequence evolution was thought to alter protein expression before. (Which, as a matter of fact, it can do. IIRC, bacteria make use of rare codons to slow down translation, and I'm sure there are other examples.) But regulatory elements are very obviously not the only players. [INDENT][/INDENT] And here our author conveniently omits that NO ONE is proposing that CNEs alone explain everything. Presumably, he's never heard of gene duplication, domain shuffling, HGT, heck, [URL="http://www.nature.com/nrg/journal/v12/n10/full/nrg3053.html"][I]de novo[/I] gene birth from non-coding DNA[/URL]! (The first is hard to believe given that he discusses it in the main body of the paper...) [INDENT][/INDENT] And here, he basically says that enhancer evolution does work. Since morphologically and genetically speaking, we're well within the "ape kind" (unless [URL="http://pandasthumb.org/archives/2010/07/intraspecific-m.html"]domestic dogs[/URL] are several different kinds...), your "did you read???!!11!!!" source appears to be on my side ^_^ A choice quote from the paper itself, for what it's worth: [INDENT][/INDENT] It doesn't work that way. Transcription factors work in combinations to activate (or repress) a target gene. We've just seen from the [I]eve[/I] study that quite different sets of TFBSs can sum up to the exact same expression pattern, using the exact same TFs to boot (all enhancers were tested in the same species). It's like 2x2 + 3x7 is the same as 1x5 + 5x4. Thus expecting raw divergence in TFBS content to match expression divergence is probably not a good idea. [I]What[/I] the differences are appears to be more important than [I]how many[/I] there are. Naturally, that's also a far more [I]difficult[/I] situation to analyse. They obviously did, or there wouldn't be a paper about it. You do know what "divergence" means, right? And don't come with that tired trope. Fruit flies happened to be morphologically conservative over that time span. Other things haven't. (Ironically, the "slow-breeding" apes may have changed more in appearance in the last 20 million years than the "fast-breeding" flies!) But that's not why I brought this up at all. Of course, you didn't seem to get why I did bring it up, so let's have another go at explaining that... If you were a designer with a thimble of sense, [B]why would you change a perfectly functional design to something that produces the exact same result?[/B] That question above. And before you answer "'cuz I felt like it", think about what that implies for the testability of the design hypothesis. [/QUOTE]
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