Uncommon Descent Serving The Intelligent Design Community

Jerry Coyne responds to Behe

William Dembski
July 4, 2007
Darwinism, Evolution
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Coyne contra Behe in The New Republic; Behe contra Coyne at Amazon; and now Coyne contra Behe at TalkReason. The following comment by Coyne caught my eye:

Both Richard Dawkins (in his review of The Edge of Evolution in The New York Times) and myself have noted Behe’s remarkable reluctance to submit his claims to peer-reviewed scientific journals. If Behe’s theory is so world-shaking, and so indubitably correct, why doesn’t he submit it to some scientific journals? (The reason is obvious, of course: his theory is flat wrong.)

Let me suggest another reason: Coyne is wrong and doesn’t want Behe upsetting his applecart.

Comments
pav the survey would have to include every individual animal of the other breeds to prove its complete absence in them take albinism for example - only 1 in 70 humans is heterozygous for it and 1 in 17,000 homozygous for it - now say we suspected it was entirely absent in some sub-population of humans that had been reproductively isolated for a long time with no albinism observed - how many individuals would need to be dna tested for the allele to confirm its complete absence versus just more rare than 1 in 70? you'd have to test every single individual - what if its there but in one in 700 individuals? you'd have to test on average 700 individuals before you found a copy!DaveScot
July 15, 2007
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Also, contra PaV, (from the Nature press release): Mosher et al. did not detect this mutation in 14 other heavy-muscled breeds of dog, suggesting that it might be unique to whippets.-------Patrick Caldon I just now noticed this post. Since I don't have access to the paper (only the abstract), I'm wondering how they determined that MSTN is not present in other heavily-muscled dog breeds: was it through protein assays, or was it through complete genome analysis. I suspect the former. This, then, would simply mean that MSTN is not expressed in those other heavily-muscled breeds. Artifical selection may have simply resulted in a genome that gives expression to the already present MSTN in the whippets. Nonetheless, this remains extraneous to the main point, which is that a two base-pair deletion is the cause of the phenotype.PaV
July 14, 2007
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Jon You asked for a field that studies, among other things, the scientific method itself. That precludes Science Studies as defined in your link.DaveScot
July 6, 2007
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Jon Jackson, There has always been debate over the implications of scientific findings as scientists protect their pet theories and some of it can be very nasty. I taught for 8 years in two different universities and faculty meeting were frequently contentious. That is why there is always a push to find new theories/experiments to look at the data from different perspectives. It is part of the quality control. However, when the issues of science have political implications the analysis of data process is very suspect and even more contentious. The people who discuss evolution seem to have major personal self identity stakes in which theory is correct and the discourse is seldom civil. Their self identity determines their position, not the evidence. This site tries to maintain civil discourse but self identity still seems to affect a lot of the discussion. Also, I think a lot of posts here are inappropriate. Political concerns in general seem to trump truth concerns in many areas which is why there is often a series of people talking past each other as they try to defend their point of view. Also for issues like evolution that go further than the science involved the contention is much more visible to the public. Most science debates rarely get further than the narrow fields of the particular discipline. From my perspective, evolution and things like global warming are not about science but political control of the society and when that happens truth is the first thing sacrificed. But most science does not have these wide political considerations and as such the quality control process is rarely visible.jerry
July 6, 2007
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Actually Dave, I'm thinking Science Studies was a little more along the lines of what I was thinking of. But thanks for the tip.Jon Jackson
July 6, 2007
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Jon Jackson I was wondering if anyone knows of a branch of science that studies science and the scientific method itself It's Philosophy of Science. Professor Dembski has a PhD in it along with a PhD in math.DaveScot
July 6, 2007
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@ Patrick: A lot of our disagreement has to do with the fact that we have different concepts about terms like "new" "variation" "potential". This would require a long extra discussion. None of the processes and changes you describe are surprising to me. But I judge them always against the big open questions of evolutionary biology: The origin of novelty and all aspects connected with that, often filed under the term "macroevolution". And I see dog-breeding and other microevolutionary processes as interesting by itself but not essentially contributing to this "big" question.Markus Rammerstorfer
July 5, 2007
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jerry, "The one issue that seems to come up at various times is falsification of the data and just about every novel finding is subject to others performing the same experiment. So there is a constant quality control process going on that monitors other’s work." I'm not sure the second sentence follows from the first. The whole raison d'etre for this blog is that both you and the most rabid of Darwinists look at the same data and come to different conclusions. So wouldn't it be reasonable to say that it isn't data but interpretation that is at issue? Yet one of the cornerstones of science (as I understand it) is advancing knowledge by casting aside our weight of preconceptions and interpreting data without prejudice. What does it say at the beginning of this blog? "Materialistic ideology has subverted the study of biological and cosmological origins so that the actual content of these sciences has become corrupted." Wouldn't a systematic study science itself help to eliminate this? jerry, "It is unlikely that a scientist would become a master of some abstract field without learning the methodology of science along the way." I'm thinking they call it consensus science. Though most likely you are right that they did learn it and have just grown sloppy at it. As to the Goldman videos at the Teaching Company, I found them interesting and look forward to seeing them. Thank you.Jon Jackson
July 5, 2007
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Sorry - accidentally hit post; to finish, Atom, IGF-1 variation is a SNP. Also, contra PaV, (from the Nature press release): Mosher et al. did not detect this mutation in 14 other heavy-muscled breeds of dog, suggesting that it might be unique to whippets.Patrick Caldon
July 5, 2007
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Markus, You say these things do not represent novel capability, but the expression of some kind of underlying capability in the wolf-design, I say it does. This is quibbling over the semantics of "novel" or "capability". On greyhounds, it's not hard to verify that they accelerate better than wolves, and shepherd dogs can guard and herd sheep in a way which wolves cannot. But since you're not happy with this, let's give another example; it's not hard to verify that Jack-Russell terriers (which are small) will be far superior at hunting game in burrows underground than wolves. To me "superior is as superior does"; if you get a pack of wolves outside a fox burrow and they can't get at the fox, but a single Jack Russell terrier can get the fox, then you need to provide some detailed technical argument to say that wolves and JRTs have the same capability for hunting foxes. Incidentally there are alleles present in JRTs (and many small dog breeds) which are not present in wolves, called IGF-1; in this case it is a single base pair substitution (a SNP). This was published a couple of months ago. This allele (probably among others) ultimately gives JRTs an ability to hunt foxes which wolves do not have. Also no "Darwinist" argues that variation is without borders. You could view the whole study of population genetics as an attept to get a handle on these borders. Get a copy of a good text on evolution (e.g. Mark Ridley's text) and you'll see chapter after chapter describing borders and getting a handle on the precise mechanisms of variation and the borders which do exist. A lot of the reason that people like Haldane and RA Fisher are famous is that they got a pretty good handle on how variation works, and described mathematically/statistically what the borders are. Seriously, if you want to argue about this, a good undergraduate text on population genetics would make excellent reading. I'm happy to hear an argument that the wolf has the same underlying capability to hunt foxes in burrows that JRTs have, but given that a wolf could never fit in a fox burrow you'll have to precisely define the word capability, since you're clearly using it in a non-standard sense. Atom, MSTN is a double deletion event. IGF-1 is aPatrick Caldon
July 5, 2007
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@Patrick: "There are dog breeds with capabilities that wolves do not have. Greyhounds accelerate faster, and according to wiki are the second-fastest accelerating land animal, pipped only by cheetahs." To my knowldege wolves accelerate also (and they do pretty well at it...). Even better: They do it by means of the same locomotion system as Greyhounds. Greyhounds are just selected to have higher speeds and represent a specialization of the traits connected with a high ability to acclerate. No proof for the creative power of evolution but for the potential of the original wolve-design and the eagerness of breeders. "Many herding dogs can be taught to herd cattle and sheep." Well, they have nice brains and suitable instincts to be taught by intelligent agents. You as a breeder can adapt their complex instincts and social behavior for your own purpose. Try the same with a cat... etc. Variation is rich (especially within dogs) but there is no reason to believe that it is without borders. Breeders know this well. Today we know many reasons for this variations. Mutations have little to do with it. Breeding = No food for DarwinistsMarkus Rammerstorfer
July 5, 2007
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It all comes from a two-pair deletion. That’s well within the constraints of Behe’s EOE.
Exactly my point PaV. I had a feeling it was something like that, which is why I wanted details.Atom
July 5, 2007
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Here's this from a paper that was published this year: A Mutation in the Myostatin Gene Increases Muscle Mass and Enhances Racing Performance in Heterozygote Dogs Dana S Mosher,1 Pascale Quignon,1 Carlos D Bustamante,2 Nathan B Sutter,1 Cathryn S Mellersh,3 Heidi G Parker,1 and Elaine A Ostrander1* ABSTRACT: Double muscling is a trait previously described in several mammalian species including cattle and sheep and is caused by mutations in the myostatin (MSTN) gene (previously referred to as GDF8). Here we describe a new mutation in MSTN found in the whippet dog breed that results in a double-muscled phenotype known as the “bully” whippet. Individuals with this phenotype carry two copies of a two-base-pair deletion in the third exon of MSTN leading to a premature stop codon at amino acid 313. Individuals carrying only one copy of the mutation are, on average, more muscular than wild-type individuals (p = 7.43 × 10−6; Kruskal-Wallis Test) and are significantly faster than individuals carrying the wild-type genotype in competitive racing events (Kendall's nonparametric measure, τ = 0.3619; p ≈ 0.00028). These results highlight the utility of performance-enhancing polymorphisms, marking the first time a mutation in MSTN has been quantitatively linked to increased athletic performance." It all comes from a two-pair deletion. That's well within the constraints of Behe's EOE. Also, note that MSTN is present in sheep and cattle. There's no indication that the MSTN gene is not found in other breeds, only that this mutation is only found in the whippets.PaV
July 5, 2007
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Hey Patrick Caldon,
There are genes in some dog breeds which do not exist in others nor in wolves. For instance there is a variant MSTN gene in some whippets which causes whippets having the gene to run faster. This is a gain in function on account of the change. This gene was not put there by genetic engineering, it appears to have arisen out of a (random) mutation.
Thanks for the input. Do you know what changes were made in the amino acid sequence, namely how many amino acids were substituted/added and what it did on the biomolecular level? The point of contention in Behe's book (which is germane due to the thread) is that Darwinian/unguided processes only produce simple changes of a CCC level or less. There is a level of complexity (measured by Behe in the book) past which unguided mechanisms cannot produce, unless each step to that outcome confers selective advantage. I would be interested to know exactly what new molecular machines were produced by those new genes, or whether or not the changes were simply to break control mechanisms or allow more of a certain protein to be produced (in other words, if they are simple changes or not.) Everyone agrees that simple changes (new genes) can be generated, but unguided mechanisms cannot be expected to produce new molecular machines (composed of three or more different protein complexes) in the lifespan of earth.Atom
July 5, 2007
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Jon Jackson, Every scientific journal article has a section on how the work was performed, including the instruments, timing of procedures etc so that other scientists can theoretically reproduce the exact same experiment. All scientists are trained in the methodology of science and theoretically go through a lot of training on performing experiment before they are let loose. They are also observed by other scientists in the process. Obviously some are better at it than others. The one issue that seems to come up at various times is falsification of the data and just about every novel finding is subject to others performing the same experiment. So there is a constant quality control process going on that monitors other's work. It is unlikely that a scientist would become a master of some abstract field without learning the methodology of science along the way. That does not mean he/she could not be a sloppy scientist in terms of procedures but is not too likely to happen without scrutiny by other scientists. I recommended Philosophy of Science and History of Science because each will examine in detail the methodologies and basic patterns of research that scientists have used over time and how it has influenced the types of experiments they do. Einstein made some fantastic leaps in theory but it took hundreds of scientists to observe some solar eclipses to verify it.jerry
July 5, 2007
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bfast, "This would be intriguing study, however the results of such a study could not be published on any “active” topic. Rather, someone needs to study a topic while it is active, then publish the findings when the prevailing opinion proves false." This would seem to be somewhat of a non sequitur, unless of course you intent was to showcase bad science. What I'm wondering is, who watches the watchman? If one of the purposes of science is to advance human understanding through observation, then observing the observer (science and scientists) would seem to be a good thing in and of itself. So as well as studying bad science you could study good science. As to the philosophy of science part (jerry) I'm not sure how much of that depends on direct observation of scientists at work as opposed to, say, reading peer reviewed conclusions. If the former then the philosopher in question would seem to be in a much better position to observe any possible bias or error on the part of the scientist in question. But if the latter then how would he know if, say, the scientist in question at a given step of his reasoning simply assumed something that did not necessarily follow from a previous step and then managed to hide it? Consider teachers, for example: Having taken some education courses I can tell you that most teachers have the equivalent of a minor in the course they are preparing to teach and a major in education itself. So we could say that teachers know a little about what they're going to teach but a lot about how to teach. But if no one is studying science itself then how can a scientist even begin to learn about how to conduct science? It would seem to be the ultimate insulation from reality: A scientist who knows much about his own abstract field but next to nothing about how to actually go about systematically finding things out without introducing his own biases into the picture. Or think about it this way: Postmodernist thought teaches us that the messenger becomes part of the message. But who is watching how the scientist observes and then transmits his message about nature? Forget confirmation bias, the real wonder is that we're not prostrating ourselves every time a scientist walks by. But, like I said, I'm no scientist.Jon Jackson
July 4, 2007
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Markus, There are genes in some dog breeds which do not exist in others nor in wolves. For instance there is a variant MSTN gene in some whippets which causes whippets having the gene to run faster. This is a gain in function on account of the change. This gene was not put there by genetic engineering, it appears to have arisen out of a (random) mutation. There are dog breeds with capabilities that wolves do not have. Greyhounds accelerate faster, and according to wiki are the second-fastest accelerating land animal, pipped only by cheetahs. Many herding dogs can be taught to herd cattle and sheep. Danes, newfoundlands and various mastiffs are larger or heavier. Pointers and similar gun dogs can indicate to a human hunter where prey is without killing it. I would hazard to guess that bloodhounds are superior trackers. Most of this variation has arisen in the last few thousand years. I do not know if these additional abilities represent "complexity" as you see it, but they certainly represent novel capability. Perhaps if you defined complexity more precisely and showed me in a step-by-step manner how to attach a numerical value for complexity to the now-being-sequenced dog genomes and wolf genomes, I could understand how you say that dogs have greater complexity than wolves. As it is I can't really follow your argument.Patrick Caldon
July 4, 2007
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Jon Jackson, You may want to look at those who study Philosophy of Science and the History of Science. The Teaching Company has a few excellent courses on these topics especially by Stephen Goldman (who is not ID friendly). They might not answer your question specifically because ID is such a charged topic that just admitting it sounds reasonable some times is enough to get one ostracized. Goldman discusses in detail how assumptions about how science should be practiced has changed over time especially in the 20th century.jerry
July 4, 2007
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Jon Jackson, "I was wondering if anyone knows of a branch of science that studies science and the scientific method itself" This would be intriguing study, however the results of such a study could not be published on any "active" topic. Rather, someone needs to study a topic while it is active, then publish the findings when the prevailing opinion proves false. This, of course, may require studying a dozen different topics -- in addition to evolution, global warming comes to mind -- before one gets a scientific hobby-horse that is finally rejected by science so that findings about it can be published.bFast
July 4, 2007
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If Behe’s theory is so world-shaking, and so indubitably correct, why doesn’t he submit it to some scientific journals? (The reason is obvious, of course: his theory is flat wrong.) Wow. They've completely lost it. Not to take them by the hand and lead them through a process in reasoning as one would a very stupid child but one shouldn't say the "reason is obvious" when reasonable alternatives can easily be provided i.e. he has given up on major scientific journals because they have become intellectually corrupt, and feels it would be a waste of time and perhaps even be counter-productive. And(cough cough) is Coyne 100 percent certain Behe hasn't submitted his theory to a mainstream scientific journal with a peer review process? I guess it should be fair to note that if Behe did submit his theory Coyne would lose any credibility in discussing this matter.tribune7
July 4, 2007
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Wouldn’t a stack of rejections serve as evidence of bias?
Review the case of Richard Sternberg at www.rsternberg.net, or Guillermo Gonzalez at www.evolutionnews.org. "Evidence of bias" is not exactly in short supply. You might even say there is "overwhelming evidence".russ
July 4, 2007
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Before you can get rejected by a journal you have to submit a paper. Wouldn't a stack of rejections serve as evidence of bias?charlessandwalk
July 4, 2007
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because the journals are run by peer-reviewers like Coyne, Dawkins, Miller, and Carroll, running the journals. DUH! --Sal And what is utterably laughable about all of this is the fact that Coyne knows full well that he qualifies as a "peer reviewer". Well, then, if "peer reviewers", like Coyne, would reject Behe's paper in an instant, then, pray tell Dr. Coyne, give us the grounds for said rejection. I'm getting the impression that neither Coyne, nor any of the other evo-biologists out there, want to touch Behe's logic with a ten-foot pole. IMO, Behe, in EOE, is simply following up on the groundwork he laid in the paper he co-wrote with David Snoke. He's now simply fleshed out, in a well-researched area of biology, what the numbers were already telling him in Snoke and Behe.* PT couldn't deal with the numbers. There weren't any substantive criticisms. My feeling is that their failure to raise such criticisms encouraged Behe to continue on with his arguments. As I was reading the first 120 pages and so of EOE, I was thinking: game, set, match! * PS: If one follows the testimony at the Dover trial, you will note that plaintiff's lawyers attacked Behe's testimony regarding Snoke and Behe, wherein Behe testified that you couldn't get two a.a. changes occurring next to one another unless you had a population of 10^20 organisms acting over a billion years (I'm writing strictly from memory---and I have a poor one!), by introducing the fact that there are 10^30 bacteria in the entire world, so that, statistically, one would suppose dual a.a. substitutions were happening all the time. No problem, eh? Of course, while this is true---Behe (and all of us would have) had to concede this. BUT!!!!!!! What about much smaller populations that don't reproduce as quickly. Even in Dover, the "edge of evolution" could already be seen by clear-thinking individuals. Alas, for the Darwinists, it's now time for Behe's revenge!PaV
July 4, 2007
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I have to wonder if all of these reviewers are suffering from some sort of 'aconfimation' bias? It's as if, while reading Behe, their minds become unable to grasp and hold on to his arguments. I've noted that when I read something I truly disagree with my mind plays tricks on me. I skip large segments of the content so as not 'waste' time on 'nonsense' and my memory seems almost to reject the arguments made. Perhaps (to get a truly thoughtful review) it might help to get someone who doesn't harbor so much anger at ID. Then again the editors at these publications might share this anger. On a side note, I was wondering if anyone knows of a branch of science that studies science and the scientific method itself and if someone might have written something along these lines for the lay reader? You know, not being a scientist myself and all.Jon Jackson
July 4, 2007
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Some peer-reviewed work (partly done by ID-proponents) concerning the limits of variation and power of microevolutionary processes: Lönnig, W.-E. (2006): "Mutations: The Law of Recurrent Variation." IN: Texeira Da Silva J.A. (ed.): "Floriculture, Ornamental and Plant Biotechnology" Global Science Books, London, Vol 1. p.601-607 Lönig, W.-E.; Stüber, K.; Saedler, H.; Kim, J.H. (2007): "Biodiversity and Dollo’s Law: To What Extent can the Phenotypic Differences between Misopates orontium and Antirrhinum majus be Bridged by Mutagenesis?" IN: "Bioremediation, Biodiversity and Bioavailability" 1(1), p. 1-30, Global Science BooksMarkus Rammerstorfer
July 4, 2007
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I think Sal's veiw "because the journals are run by peer-reviewers like Coyne, Dawkins, Miller, and Carroll, running the journals. DUH!" corresponds more closely to the evidence as it seems journals will not accept work that challenges the reigning evolutionary assumptions and biases.Lord Timothy
July 4, 2007
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Markus Rammerstorfer (1,2) Well said and I agree completely about the limits of breeding. I did a little research on this in another forum (ID the Future). Recombination seems to be the basic variational mechanism exploited by plant and animal breeders, and many longterm programs and experiments have shown strict limits to how far the phenotypical modification due to recombination can progress for a given species using artificial selection. Even a Darwinian evolutionist in the debate referred to recombination as mostly doing a Mr. Potato Head routine of reshuffling combinations of variations generated by previous mutations. Another reason genetic recombination couldn't be unlimited is because if it were, we would expect extremely high rates of birth defects and infant mortality. It obviously is strictly regulated. If recombination were the almost unlimited source of variation in addition to mutation that is supposed by Darwinian evolutionists, one would expect no such limits to be demonstrated, and nothing like the very low rates of birth defects actually observed. The limits of random recombination are shown in laboratory directed-evolution studies, at http://etd.caltech.edu/etd/available/etd-05262006-112358/unrestricted/ChapterI.pdf: ".... DNA shuffling experiments (using recombination) are still limited in the area of (protein) sequence space that they can explore. The variants produced are usually not significantly different than their parents, displaying more than 85% sequence identity to the closest parent". This sounds remarkably similar to the limited magnitude of change obtained through recombinational mechanisms in dog breeding. The authors then describe how these limitations can be overcome by "site-directed" recombination in which the recombination sites are chosen by the (intelligent) experimenters rather than being randomly determined. Though he fully covers recombination as a source of variation for selection in another place in his current online biology textbook, Harvard biologist John Kimball's description of mutation in evolution is remarkable for its relative honesty. This is at http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Mutation_and_Evolution.html, and deserves quoting. He clearly shows that he believes mutation is the limiting factor and the primary source of variation despite the process of sexual recombination. He states "Mutations are the raw materials of evolution. Evolution absolutely depends on mutations because this is the only way that new alleles are created. But this seems paradoxical because most mutations that we observe are harmful (e.g., many missense mutations) or, at best, neutral.....So how can the small changes in genes caused by mutations, especially single-base substitutions ("point mutations"), lead to the large changes that distinguish one species from another? These questions have, as yet, only tentative answers." To say "tentative" is the understatement of the year. He lists several "tentative answers" - gene duplication followed by subsequent mutation, mutations in regulatory regions, and mutations in "selector genes" high in developmental heirarchies. Note that he doesn't list recombination. None of these mechanisms can avoid the basic complex specified information problem. He just committed the political incorrectness of baring one of the private problems in MET that practitioners would rather not be aired publicly. So much for Dawkins and Coyne citing dog breeding. Another relevant reference, at London Natural History Museum site http://www-personal.umich.edu/~gingeric/PDFfiles/PDG450_Earlywhales_abs.pdf: "Variation is the raw material of evolution, but there is little understanding of how variation on a microevolutionary scale (presumably mainly recombination-based) relates to large-scale evolutionary patterns." One reference of many that explicitly describes the role of recombination as in principle working by allowing selection to accumulate advantageous mutations is an evolutionary genetics tutorial of the Swiss Institute for Experimental Cancer Research, at http://www.isrec.isb-sib.ch/~pbucher/bioinfo_1/ (course_09jan06_2.ppt): "Effects of recombination: Advantageous mutations arising in different individuals spread independently through the population, can be combined in one genome and eventually may become jointly fixed."magnan
July 4, 2007
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why doesn’t he submit it to some scientific journals? (The reason is obvious, of course: his theory is flat wrong.) Let me suggest another reason: Coyne is wrong and doesn’t want Behe upsetting his applecart
Behe doesn't submit his work to journals because Coyne doesn't want Behe upsetting his applecart? That sounds unlikely, but if true it seems very accomodating of professor Behe.Rob
July 4, 2007
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Umm, why is Coyne responding via an atheist site that says it's supporting 'faith vs reason'? It has sectionson rebutting religious apologetics. The conclusion I think most people would come away with is- Darwinism=atheism. Is Coyne on record as saying that science= atheism and that it proves there is no God? If not, why is he using this site to put out his attacks? Is this maybe the reason that the NCSE constantly tries to tell religious people that Darwinism is no challenge to their religious views? When you constantly bring a subject up, one soon wonders if you're only bringing it up to falsely comfort others that you're not out to get them, or that their ideas aren't hostile to you in any manner. Is this why the Berkley evolution site had the section on religion and the priest and scientist shaking hands in regards to Darwinism? It's quite obvious that Darwinism to many equals atheism, and they make a good argument. Why, then, do the Darwinists get a pass on this when they so often accuse IDers of being religiously motivated? It's ridiculous.JasonTheGreek
July 4, 2007
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What I find suprising about Behe's book is that it seems nobody before him has asked the fundamental question what can be expected from evolution? I think this question is really important especially to antibiotic research and for other fields as well.Innerbling
July 4, 2007
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