tag:blogger.com,1999:blog-4948885059517209129.post623286729435200080..comments2023-10-29T08:04:00.488-07:00Comments on Quintessence of Dust: Exploring the protein universe: a response to Doug AxeStephen Mathesonhttp://www.blogger.com/profile/05057004085073574659noreply@blogger.comBlogger13125tag:blogger.com,1999:blog-4948885059517209129.post-51293119521895999122011-05-19T11:32:17.381-07:002011-05-19T11:32:17.381-07:00Steve, what do you make of the long list on their ...Steve, what do you make of the long list on their editorial board?<br /><br />http://bio-complexity.org/ojs/index.php/main/about/editorialTeam<br /><br />Are they all pro-ID types? (I mean, besides the usual suspects.)<br /> John Farrellhttp://profiles.yahoo.com/u/5X452YIVEN2SURO73GB4U7OTWQnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-82104262081393369132011-05-18T15:19:30.437-07:002011-05-18T15:19:30.437-07:00 Oh and while I'm on the subject of Michael Ly... Oh and while I'm on the subject of Michael Lynch, he has a fascinating looking paper in press at Nature:<br /><br />"Non-adaptive origins of interactome complexity"<br /><br />http://www.nature.com/nature/journal/vaop/ncurrent/full/nature09992.html<br /><br />Bit of a press release and also a write up:<br /><br />http://www.sciencedaily.com/releases/2011/05/110518131425.htm<br /><br />http://www.nature.com/news/2011/110518/full/news.2011.294.htmlSteveFnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-90841752267235316312011-05-18T13:35:50.627-07:002011-05-18T13:35:50.627-07:00Steve, it's not really worth your time, except...Steve, it's not really worth your time, except as an exercise in spotting the errors. Axe's model is based on sequential arising and fixation of multiple novel variations in a population where the variants are neutral or slightly deleterious. The obvious issue is that waiting for alleles to arise and go to fixation greatly increases the time required - but that is not a realistic roadblock. Many significant changes in the Lenski long-term E Coli experiment have occurred without fixation of the needed changes. Dennisnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-45349724519264835642011-05-18T07:32:07.935-07:002011-05-18T07:32:07.935-07:00 From what I remember of the Gauger and Axe paper,... From what I remember of the Gauger and Axe paper, they experimentally estimated the number of mutations required to go from one to another. The evolution is impossible bit came from Axe's population model arguing that that number of mutations couldn't realistically occur. That's what I recall anyway, could be wrong. But if not, it's a pretty central part of the argument. Anyway, it was largely an attack on this recent paper from Michael Lynch:<br /><br />"The rate of establishment of complex adaptations"<br /><br />http://www.indiana.edu/~lynchlab/PDF/Lynch182.pdf<br /><br />As I said, I would side with Michael Lynch pretty much any day of the week (and not just against creationists, I really like his evolutionary biology work in general) but it would be interesting to see an evaluation of the Axe paper. It's kind of along similar lines to Behe's EoE type stuff and got the DI very excited when it came out:<br /><br />http://www.evolutionnews.org/2011/01/bio-complexity_paper_shows_man042611.htmlSteveFnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-50061931664709091132011-05-17T19:03:27.077-07:002011-05-17T19:03:27.077-07:00Steve, no I haven't read that one. I doubt it ...Steve, no I haven't read that one. I doubt it is of any value. I just read one of Lynch's recent papers in <a href="http://dx.doi.org/10.1073/pnas.1010836107" rel="nofollow">PNAS</a> and found it very interesting and informative and I guess I'm having a hard time picturing Axe (with his very simplistic views of adaptation) mounting a credible challenge to Lynch. But I'll have a look sometime. SteveMathesonhttp://sfmatheson.blogspot.comnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-34650091479566478662011-05-17T18:56:14.121-07:002011-05-17T18:56:14.121-07:00Charley, while I understand your frustration, I kn...Charley, while I understand your frustration, I know you to be wrong about the behavior of Calvin profs back then. They did show respect for creationists, meaning that they did not use harsh rhetoric (the way I have been known to do). And they did, in several prominent publications in the 1980s, address creationist errors in print.<br /><br />My attempt to be charitable to Gauger and Axe is my choice, intended to show approval for experimental work. It has nothing to do with any feeling of "obligation" coming from Calvin. Thanks for the comment, though, and I do see your point. SteveMathesonhttp://sfmatheson.blogspot.comnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-18592191702994876982011-05-17T18:32:14.941-07:002011-05-17T18:32:14.941-07:00Biologic Institute:
Funded by 'ignorant',...Biologic Institute:<br /><br />Funded by 'ignorant', 'slothful', 'duplicitous', 'ludicrous', 'stupid', 'cadre's of attack dogs'. The 'confusion they purposefully generate' and the 'falsehoods they employ' in their 'misinformation effort' are 'horrific mistakes', 'intellectual tragedies', promulgated from a ''wholly corrupt' 'intellectual ghetto'. They are a 'dangerous cancer'. 'Mendacious'. 'Idiotic'. 'Creepy'. 'Silly'. 'Confused'. 'Lacking integrity'. 'Profoundly misleading'. 'Political propogandists'. 'Enemies of science.' 'Idiots'. 'Liars'. 'Bottomfeeders'. chunkdznoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-16809437016146833492011-05-15T20:34:55.205-07:002011-05-15T20:34:55.205-07:00Early in my Biology education at Calvin 32 years a...Early in my Biology education at Calvin 32 years ago, the two professors teaching my evolution class spent five minutes to explain that Creation Science (as it was then called) was hooey and its practitioners were charlatans. We wasted no more time on the subject in the following years. Time has proven that we missed nothing in doing so.<br /><br />What a shame that Calvin profs today feel obligated to show respect for "scientists" who go through the motions of scientific inquiry with their conclusions in place before they start, who tie themselves in knots to make the data fit those conclusions, and who protect their faulty reasoning and weak hypothesis by hiding out with like-minded individuals in the BioLogic Institute and publish in a journal whose very title betrays its agenda. <br /><br />What a joke.charleynoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-15091307430681540582011-05-15T12:45:10.920-07:002011-05-15T12:45:10.920-07:00The “EVOLUTION IS
IMPOSSIBLE” aspect of the Axe a...The “EVOLUTION IS <br />IMPOSSIBLE” aspect of the Axe and Gauger paper also seems to rely to some extent on the population model developed by Axe and published in the <br />same Biocomplexity. That paper was essentially an attack on Michael Lynch’s<br /> recent work. The arguments are largely above my pay grade. Personally I’d back Lynch over Axe but do you have any thoughts? <br /><br />Here’s the paper:<br /><br /><br /><br />“The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations”<br /><br /><br />http://bio-complexity.org/ojs/index[…]BIO-C.2010.4<br /><br /><br /><br /><br /><br /> <br /> <br />BTW, I agree that it's good to see the ID crowd (well some of them at least) getting their hands dirty and doing some actual science, as opposed to glorified literature reviews. I've always found YECs in some ways more admirable because they are actually proactive about trying to support their views. Floody geologists go out into the field and try to do flood geology. It's a fool's errand but at least they've been putting their money where their mouths are. IDists have been woefully inadequate in this regard, but maybe some of the smarter ones are starting to realise they need to actually try and do some science. Good luck to them.SteveFnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-88868290584695036662011-05-15T12:12:48.682-07:002011-05-15T12:12:48.682-07:00One of the things that really rubs me the wrong wa...One of the things that really rubs me the wrong way about the ID movement is how little time ID advocates seem to spend formulating and experimentally testing hypotheses about ID. It's a good thing, I think, that there are at least a few ID advocates actually working in the lab to explore their speculation.SWTnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-81182143808638509542011-05-14T09:04:39.184-07:002011-05-14T09:04:39.184-07:00It's a fair question. The data are surely publ...It's a fair question. The data are surely publishable; it's the discussion and conclusions that would preclude publication in a real journal. In my opinion, the paper could have been published elsewhere if it had discussed the findings in the context of evolutionary transitions. This would have required a frank admission that the "transition" in question is not relevant to evolution. Instead, perhaps, the discussion would focus on why neofunctionalization is not a guaranteed outcome after gene duplication (as discussed widely <a href="http://genome.cshlp.org/content/19/8/1404.full" rel="nofollow">elsewhere</a>). Even that would be pretty trivial, but it would be publishable.SteveMathesonhttp://sfmatheson.blogspot.comnoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-49839539133478449832011-05-14T08:41:32.401-07:002011-05-14T08:41:32.401-07:00 These two statements seem mutually contradictory:... These two statements seem mutually contradictory:<br /><br />"I am encouraged by the fact that Biologic Institute is doing good scientific work and generating publishable data."<br /><br /> "interesting technically but badly flawed in its theoretical approach and conclusions"<br /><br />Is the paper publishable. it was was, why wasn't it submitted to a peer reviewed journal, instead of some place that seems more like a propaganda organ?HelenaConstantinenoreply@blogger.comtag:blogger.com,1999:blog-4948885059517209129.post-28789936140922584262011-05-14T02:59:38.360-07:002011-05-14T02:59:38.360-07:00You, too, have done some serious work in this post...You, too, have done some serious work in this post, and done it in a courteous and respectful manner -- all too uncommon, unfortunately.Martin LaBarnoreply@blogger.com