tag:blogger.com,1999:blog-37148773.post4762013408590675506..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Dan Dennett RepliesLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger10125tag:blogger.com,1999:blog-37148773.post-34759063068134693772011-02-21T19:41:26.719-05:002011-02-21T19:41:26.719-05:00is any mainstream modern biologists that is not a ...<i>is any mainstream modern biologists that is not a pluralist with respect to adaptation/neutral evolution?</i><br /><br />Most biochemists that I know don't even know what neutral evolution is.DKnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-76452530564954921002011-02-21T14:14:45.912-05:002011-02-21T14:14:45.912-05:00Um, is any mainstream modern biologists that is no...Um, is any mainstream modern biologists that is not a pluralist with respect to adaptation/neutral evolution? <br /><br />I think that regardless of the actual relative role of adaptation and neutral evolution in explaining the diversity of life, adaptation has a more intuitive story, which is, in part, why it so popular. It's currency is also matter that we humans are familiar: limbs, wings, feathers. Neutral theory deals with codons, amino acids, phenotype spaces, and other unfamiliar oddities.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-52716693059438220932011-02-20T19:01:44.490-05:002011-02-20T19:01:44.490-05:00@Anonymous:
The claim that was made is completel...@Anonymous: <br /><br />The claim that was made is completely wrong regardless of whether protein coding or non-coding sequence is considered.DKnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86826910762476945642011-02-20T15:10:44.829-05:002011-02-20T15:10:44.829-05:00DK: (re: duplication events) Wrong again. One of ...DK: (re: duplication events) <i>Wrong again. One of the easiest ways to see why is read Larry's posts on "Onion test".</i><br /><br />Dennett is referring to duplication of protein-coding genes, so the onion test isn't particularly relevant. DK, the discussion is fascinating... really, you should try giving both perspectives a careful re-reading.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10445568583963618282011-02-20T14:08:26.403-05:002011-02-20T14:08:26.403-05:00This seems to be a defense of adaptationism purely...This seems to be a defense of adaptationism purely on the grounds that nearly neutral evolution explains more than neutral evolution.<br /><br />This might be true, but I don't think it's legit to claim that nearly neutral evolution falls under adaptationism.<br /><br />Explaining something in terms of negative vs. positive selection often leads to very different predictions.<br /><br />For example, if we include nearly neutral evolution within adaptationism, then Michaeal Lynch-style explanations of genome size and "complexity" (low population sizes lead to large genome sizes and eukaryote-style genomic shambles) must be considered adaptationist.<br /><br />I'm pretty sure they aren't. (An adaptationist explanation of larger genome sizes might be that the extra materials are providing a selective benefit to the organisms that have them).<br /><br />The specific points raised are also a little funky. None of the assumptions mentioned are needed to build phylogenies. However, many models of evolution do incorporate e.g. different rates of change between different kinds of amino acids, which might be said to be assuming nearly neutral evolution. They generally allow change among chemically similar amino acids with reasonable probabilities. You wouldn't expect that under positive selection; you'd expect the opposite, if anything.<br /><br />Actually if positive selection was the most frequent kind of evolution, we wouldn't expect phylogenies to have much historical signal in them at all. Convergent evolution would be the dominant pattern.<br /><br />Evolutionary rate differences between human and bacteria don't seem to be because of differences in error repair (and to the extent they are, humans aren't necessarily better at repairing DNA), so not sure where that statement comes from. <br /><br />So I don't think it's correct to use Ohta's work to defend adaptationism...Low-hanging Fruithttps://www.blogger.com/profile/13985524372401133567noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-66548327460391962402011-02-20T11:36:09.463-05:002011-02-20T11:36:09.463-05:00... and many of them have read the Gould & Lew...<i>... and many of them have read the Gould & Lewontin essay (reputedly one of the most-cited papers in academia) as showing that (as Jerry Fodor once said to me, years ago) “adaptationism is completely bankrupt.”</i><br />One should distinguish between "adaptationism is bankrupt" and "adaptation is bankrupt." For myself, I see adaptationism as bankrupt, yet I see adaptation as important.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-81533494200158388962011-02-20T10:07:26.228-05:002011-02-20T10:07:26.228-05:00"Dr. Dennett needs to learn some biology befo..."Dr. Dennett needs to learn some biology before writing books about it."<br /><br />DK<br /><br />Your comment is so rude I'm surprised it passed moderation.Veronica Abbasshttps://www.blogger.com/profile/07037599323472646996noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10155972717408804742011-02-20T00:30:30.794-05:002011-02-20T00:30:30.794-05:00You already accept the centrality of adaptation, a...<i>You already accept the centrality of adaptation, as you say yourself in response to anonymous: "We agree that adaptation is a very important part of evolution and to ignore it completely would be ridiculous."</i><br /><br />Some reasoning... So if one admits that ignoring something is ridiculous then one accepts the centrality of that something? Really???<br /><br /><i>Nobody can reason about sequence-based phylogenetic trees without some assumptions about what historical processes created the data we now have available in the DNA of living and—in some cases—recently extinct species where DNA can be extracted. Those assumptions include, trivially, assumptions about the relative high fidelity of DNA replication and transmission, the role of DNA expression in (partially) determining phenotypic features, and the tendency of selection to weed out dysfunctional mutations and combinations.</i><br /><br />Wrong. One can (and many have) build and analyze sequence-based phylogenetic trees without *any* of the assumptions mentioned. <br /><br /><i>Duplication events just happen, of course, and not for any reason. The vast majority of them, we may safely suppose, disappear in a few generations or even sooner, but when they persist, it is because they get exploited and preserved for their functional roles.</i><br /><br />Wrong again. One of the easiest ways to see why is read Larry's posts on "Onion test". <br /><br />At this point I lost an interest in reading any further. I find absolutely nothing fascinating in this discussion. Disappointing, maybe. Dr. Dennett needs to learn some biology before writing books about it. It's as simple as that.DKnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-45798479895382722882011-02-19T22:35:56.605-05:002011-02-19T22:35:56.605-05:00This is a fascinating discussion. Thank you Larry ...This is a fascinating discussion. Thank you Larry and Daniel. The students are lucky to have it presented.NewEnglandBobhttps://www.blogger.com/profile/07190715223856189053noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80606680747892539392011-02-19T22:19:09.432-05:002011-02-19T22:19:09.432-05:00The very existence of this whole discussion seems ...The very existence of this whole discussion seems very odd to me. That so much of evolution is of non-adaptive nature had always seems like the much more philosophically interesting result than the role that adaptation plays. In fact, it happens to be one of the most profound insights into many of the questions philosophers have been pondering over the millenia that science has ever provided. So one would expect philosophers to be very interested in it, not to be sweeping it under the rug. Maybe there are such philosophers and I just haven't happened to hear about them (I don't claim to be familiar with the current trends in that field), but on the other side maybe there aren't any and that's actually why this discussions is happening...Georgi Marinovhttps://www.blogger.com/profile/12226357993389417752noreply@blogger.com