tag:blogger.com,1999:blog-37148773.post8138976748438070429..comments2024-03-19T00:24:23.577-04:00Comments on <center>Sandwalk</center>: Historical contingency and the evolution of the glucocorticoid receptorLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger15125tag:blogger.com,1999:blog-37148773.post-38796292291648380192014-08-14T10:45:26.639-04:002014-08-14T10:45:26.639-04:00"According to Behe, all the multiple mutation..."According to Behe, all the multiple mutations have to take place at the same time because none of the intermediates are beneficial and most of them are detrimental. "<br /><br />you all missed the question. Where did Behe said that? I just quoted Behe to show that all you (professor Moran and Thornton inlcluded) say about is all wrong.<br /><br />RegardsUnknownhttps://www.blogger.com/profile/15048816306720334798noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-86485931825172437122014-08-12T12:56:48.194-04:002014-08-12T12:56:48.194-04:00It's just an Unknown Idiot quoting something w...It's just an Unknown Idiot quoting something written by Behe five years ago and unable to mark it as a quotation, provide a comment from him/her/it-self, or even a proper link:<br /><br />http://www.evolutionnews.org/2009/10/severe_limits_to_darwinian_evo027401.htmlPiotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-40077118504495424392014-08-12T12:39:11.295-04:002014-08-12T12:39:11.295-04:00Can't tell if this is actually a schizophrenic...Can't tell if this is actually a schizophrenic Behe or some creationist chatbot pasting together sentences into a ransom-note style argument.Sean Boylehttps://www.blogger.com/profile/14488615727581444079noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-52879466036953831752014-08-12T11:16:53.859-04:002014-08-12T11:16:53.859-04:00At several places in his post Thornton implies I’m...<i>At several places in his post Thornton implies I’m unaware of the possibilities opened up by genetic drift</i><br /><br />Who is this? It would appear to be Michael Behe talking about himself in the third person.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63061533802225167112014-08-12T07:19:41.772-04:002014-08-12T07:19:41.772-04:00Thank you for demonstrating that you are able to m...Thank you for demonstrating that you are able to mindlessly copy-paste Behe. Now do us a favor and quote individual passages from Thornton, and the accompanying "refutation" from Behe, so that we can see you understand what you're reading. Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15593275096578597152014-08-11T11:20:25.712-04:002014-08-11T11:20:25.712-04:00"According to Behe, all the multiple mutation..."According to Behe, all the multiple mutations have to take place at the same time because none of the intermediates are beneficial and most of them are detrimental. "<br /><br />where did Behe ever said that?<br /><br />http://behe.uncommondescent.com/page/2/<br /><br />Now back to Thornton’s first point, the role of neutral mutations (which he sometimes labels “permissive” mutations). At several places in his post Thornton implies I’m unaware of the possibilities opened up by genetic drift:<br /><br /> “Behe’s discussion of our 2009 paper in Nature is a gross misreading because it ignores the importance of neutral pathways in protein evolution…. Behe’s first error is to ignore the fact that adaptive combinations of mutations can and do evolve by pathways involving neutral intermediates…. As Fig. 4 in our paper shows, there are several pathways back to the ancestral sequence that pass only through steps that are neutral or beneficial with respect to the protein’s functions.”<br /><br />My interest in evolution by neutral mutation, however, is a matter of public record. It is an old idea that if a gene for a protein duplicates (3), then multiple mutations can accumulate in a neutral fashion in the “spare” gene copy, even if those mutations would be severely deleterious if they occurred in a single-copy gene. Four years ago David Snoke and I wrote a paper entitled “Simulating evolution by gene duplication of protein features that require multiple amino acid residues” (4) where we investigated aspects of that scenario. The bottom line is that, although by assumption of the model anything is possible, when evolution must pass through multiple neutral steps the wind goes out of Darwinian sails, and a drifting voyage can take a very, very long time indeed. But don’t just take my word for it — listen to Professor Thornton (1):<br /><br /> “To restore the ancestral conformation by reversing group X, the restrictive effect of the substitutions in group W must first be reversed, as must group Y. Reversal to w and y in the absence of x, however, does nothing to enhance the ancestral function; in most contexts, reversing these mutations substantially impairs both the ancestral and derived functions. Furthermore, the permissive effect of reversing four of the mutations in group W requires pairs of substitutions at interacting sites. Selection for the ancestral function would therefore not be sufficient to drive AncGR2 back to the ancestral states of w and x, because passage through deleterious and/or neutral intermediates would be required; the probability of each required substitution would be low, and the probability of all in combination would be virtually zero.” (my emphasis)<br /><br />Let’s quote that last sentence again, with emphasis: “Selection for the ancestral function would therefore not be sufficient … because passage through deleterious and/or neutral intermediates would be required; the probability of each required substitution would be low, and the probability of all in combination would be virtually zero.” If Thornton himself discounts the power of genetic drift when it suits him, why shouldn’t I?Unknownhttps://www.blogger.com/profile/15048816306720334798noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14212397794855335532014-08-10T09:13:53.668-04:002014-08-10T09:13:53.668-04:00Also interesting:
Your assumption about my dad...Also interesting:<br /><br /><i>Your assumption about my dad's book is pretty accurate. <b>He tends to laugh off opposing viewpoints pretty flippantly, and he also seems not to accept facts that have disproven arguments of his (such as his argument that a bacterial flagellum is 'irreducibly complex').</b> I think the reason many Christians love him so much is because he actually has studied science, <b>and actually does know a fair amount about science. The problem is he tries to bend it to suit his beliefs.</b> I saw a comic right here on /r/atheism a week or two ago which really describes him well. As I recall, the comic depicted a couple scientists examining their calculations and saying (not an exact quote), "Well, here are the facts. Let's see what conclusion we can draw from them." And in the next panel, there are a couple Christians examining their work and saying, "Well, here's the conclusion. Let's try to find some facts to support it." <b>That about sums it up. He knows science, but he went into it trying to prove a theory that he simply grew up with that had no basis in science. As all Christians do now, he must point to the ever-smaller list of questions that science has not answered (yet) and say "There's your proof of God!"</b></i><br /><br />That's a sane kid.Pedro A B Pereirahttps://www.blogger.com/profile/15195139833344839287noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-91403599525753748842014-08-10T02:48:10.478-04:002014-08-10T02:48:10.478-04:00There's an irony here, in that the fallacies B...There's an irony here, in that the fallacies Behe's falling into have actually (mostly) been solved in the latest formulation of Dembski's CSI (complex specified information) metric. The early versions of CSI had serious problems, but after Wesley Elsberry and Jeffrey Shallit's critique, Dembski revamped it significantly. The new version actually does a pretty good job (not perfect, but pretty good) of setting out what's needed to make a probabilistic case against a natural process:<br /><br />- When calculating the probability of some specified result (e.g. "cortisol binding glucocorticoid receptor"), you need to calculate the total probablility of <em>all</em> of the ways something meeting that criterion. If there are multiple paths to multiple variant receptors, you have to sum the probabilities.<br /><br />If you don't know all of the possibilities... then the best you can really do is a lower bound on the total probability. But you'd need an <em>upper bound</em> in order to make a case against natural processes. Oops.<br /><br />- The new version also takes into account the fact that there are many possible specifications, and adjusts based on the verbosity of the specification. Basically, it multiplies the probability of <em>that</em> specification being met by the number of specifications of equal-or-lower verbosity.<br /><br />- Finally, when calculating that probability, you must do it under the "chance hypothesis" you want to rule out. You calculated the probability of a tornado in a junkyard producing this result, and got a high CSI value from that? Congratulations, you've correctly ruled out tornadoes in junkyards as sources of new functions in glucocorticoid receptors. But if you want to rule out actual evolutionary processes producing it, you must calculate the probability of actual evolutionary processes (mutation, selection, drift, etc all acting & interacting in the same population at the same time) producing it. Oh, that's too complicated to model accurately? Then I guess you're not going to be able to rule that hypothesis out.<br /><br />Also, note that this requirement interrelates with my first point as well: in order to calculate CSI correctly (under an actually relevant chance hypothesis), you need to calculate the probability of outcomes you don't know of, under a computationally intractable model. Good luck...<br /><br />If the IDists actually understood & seriously used this method, it'd be immediately clear that they don't have the necessary prerequisites for building a real case. Which, of course, is why they avoid actually using it, instead preferring <a href="http://www.uncommondescent.com/intelligent-design/siding-with-mathgrrl-on-a-point-and-offering-an-alternative-to-csi-v2-0/" rel="nofollow">old versions of CSI</a>, completely different things (<a href="http://www.uncommondescent.com/computer-science/the-tragedy-of-two-csis/" rel="nofollow">that they nontheless call CSI</a>), or (most often) just claiming to have detected CSI without having any real idea what they're talking about. Or (as in Behe's case), ignoring CSI entirely and just going ahead and making the very errors it was designed to avoid.Gordon Davissonhttps://www.blogger.com/profile/12435453658654474069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43839659019413219932014-08-09T21:10:40.940-04:002014-08-09T21:10:40.940-04:00Well, that's very sad-- Behe's "shunn...Well, that's very sad-- Behe's "shunning" his son I mean. I had not seen that reddit thread before now. I know very few Catholics who are that extreme.Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54183823700989284342014-08-09T17:44:40.801-04:002014-08-09T17:44:40.801-04:00I expect Behe to be biased, but in the process of ...<i>I expect Behe to be biased, but in the process of teaching his audience creationism, he doesn't even teach them any science at all, not even as an accidental side effect.</i><br /><br />Did you really expect Behe to want to teach anything to anyone? Here's an excerpt of what his son told after coming out of the closet:<br /><br /><i> I certainly don't think it always turns out this way, but my stubbornness in maintaining and voicing my beliefs conflicted with <b>my parents' policy of keeping the rest of my family shielded from alternate viewpoints.</b> "Indoctrination", unfortunately, is really the word that describes it best, and I do believe that my younger brothers (the members of my family I am closest to) are truly being hurt by this. So my parents and I are in perpetual disagreement. I have, for the most part, stopped talking to my parents, <b>and I am not allowed to speak to my little brothers at all</b>. I don't want to complain, but this has been very painful for both them and I. Hoping to move out soon.</i><br /><br />It's kind of funny that Behe doesn't want to "teach the controversy" to his own kids, isn't it?<br /><br />http://www.reddit.com/r/IAmA/comments/dngag/iama_son_of_michael_behe_the_catholic_biochemist/?sort=confidencePedro A B Pereirahttps://www.blogger.com/profile/15195139833344839287noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32691063057685421422014-08-09T01:25:57.288-04:002014-08-09T01:25:57.288-04:00After reading Thornton's latest paper Behe con...After reading Thornton's latest paper Behe concluded that Thornton's claim that the historical path taken was just one of many has now been proven wrong by Thorton's own work. Thornton showed that the permissive mutation that occurred might be the only one that can lead to cortisol sensitivity. <br />Its strange. After having the flaw in his thinking pointed out with several examples he goes right ahead and makes the same mistake again. He assumes that the GR was <i>destined</i>to gain the function it did, so to pass through that mutational bottleneck required the help of the intelligent designer. He assumes there are no pathways to other functions that could have occurred but didn't. If he wants to continue his teleological thinking, fine. But he needs to shift his arguments and explain why that mode of thinking is justified.<br />Come to think of it, why would the designer, whom most IDers credit with making time, space and matter from scratch, not to mention the bacterial flagellum and Plasmodium parasite, go through this tortuous plodding route over millions of years to create this new receptor?? After all, some grad student in Thornton's lab made the same receptor in a week or 2.<br />Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28444237472363928222014-08-08T14:25:31.130-04:002014-08-08T14:25:31.130-04:00From the conclusion of Behe's essay:
The edge...From the conclusion of Behe's essay:<br /><br /><i>The edge of evolution lies where reasonably probable, random mutation-selection runs out of steam and "dumb luck" (or -- for those willing to consider it -- purposeful design) takes over.</i><br /><br />Leaving aside the complete and willing misrepresentation of how drift (Behe translation: "dumb luck") fits into modern evolutionary theory, he appears to be unintentionally admitting that contingency can take the place of design.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-90054534141124917552014-08-08T13:33:21.518-04:002014-08-08T13:33:21.518-04:00If you read Behe's abysmal essay on Thornton&#...If you read <a href="http://www.evolutionnews.org/2014/06/more_strong_exp087061.html" rel="nofollow">Behe's abysmal essay on Thornton's latest work</a>, it's so horribly short on detail that no reader can get a clear idea on what it is Thornton did, or does. Behe's writing isn't actually science writing. Even as an Op-Ed piece, it's so confusing that no reader could even determine what we're reading about. All Behe basically says is "Nyah nyah, evolution is impossible!" over and over again. <br /><br />I expect Behe to be biased, but in the process of teaching his audience creationism, he doesn't even teach them any science at all, not even as an accidental side effect. His writing is worse than the old "blood clotting cascade" days.Diogeneshttps://www.blogger.com/profile/15551943619872944637noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23335057784498023862014-08-08T13:20:56.472-04:002014-08-08T13:20:56.472-04:00Introduction to ID-creationist interpretations of ...<b>Introduction to ID-creationist interpretations of evolutionary biology papers.</b><br /><br />This handy little guide will help you how to become a superb ID proponent by educating you on how to interpret what you read about evolution from non-ID/creationist sources. <br /><br />It will also help you understand how creationists think when <i>they</i> read evolution-related material. <br /><br />Normal word - Cdesign proponentsist interpretation: <br /><br />Rare = never ever. <br />Ulikely/improbable = impossible. <br />Likely = rare. <br />Theory = guess. <br />Guess = biased wish/materialist faith/you have no idea - therefore god!<br />We don't know = and you never will - therefore god!<br />Not fully understood = not at all understood, impossible to understand, magic/miracles required - therefore god!<br />Unexpected result = all naturalistic explanations ever have been falsified. <br />Neutral mutation = not beneficial, therefore impossiblee/doesn't exist. <br />natural selection = Orthodox neo-Darwinistic "party line".<br />It has a chance of one in 10^16 = It has a chance of one in 10^77<br />Maybe = biased guess. <br />Could have = couldn't and didn't. <br />Beneficial mutation = loss of function/tradeoff and/or loss of information. <br />New function = loss of information/information was already there. <br />New information = no new function. <br />New information and function = still belongs to the same class of enzymes (ex. hydrolases)<br />Improved function = no new information, ability was already there. <br />Mutation = destroys information, always degrades. <br />Gene duplication = no new information/still same information. <br />Gene duplication + subsequent mutation = no new information/still same information/only modified function, not <b>new</b> function.<br />Millions of years = ad hoc excuse invented to explain why we don't see 20 million year macroevolutionary change in a few months of experimental evolution. <br />Took billions of years = same excuse as above, just worse. <br />Ancestral sequence reconstruction = *crickets*<br />Molecular phylogeny = phyloschmylo, it's more Darwinist math-tricks. <br />Observation/experiment = hoax and/or only creationists properly understand the result. <br />Demonstration = hoax. <br />Statistics = Wat?<br />Statistically significant = NOT!<br />complex = impossible to evolve, must be designed. <br />Complexity = praise the lord<br />Information = immaterial soul-stuff that refutes materialism and all naturalistic expanations ever. <br />Quantum = immaterial soul-stuff that refutes materialism and all naturalistic expanations ever. Cannot possibly evolve. <br />Experiment shows how mutations can... = It's still just a bacterium/fruitfly/dog-kind. <br />Ape = monkey<br />monkey = ape<br />evolutionist = ape-monkey<br />homosexuality = bestiality and rape<br />evolution = materialism/naturalism/scientism/darwinism/chance/fair coin<br />darwinism = materialist religious faith<br /><br />Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-69165176533152772592014-08-08T12:34:30.057-04:002014-08-08T12:34:30.057-04:00This is completely wonderful - loved it the first ...This is completely wonderful - loved it the first time, happy you decided to reprint it. I particularly like the various examples Thornton uses to illustrate that Behe's notion of how probability works is completely wrong. (This is sufficiently obvious that it's one of those subjects where you ask yourself whether he understands full well it's wrong and keeps flogging it to adherents anyway; or whether he's so determined to hang on to his beliefs that he's kept himself from comprehending the simple, evident, mathematical facts.)judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.com