• Darwin’s Doubt – Chapter 11 – Part 2

    Continuing from Part 1 about Meyer’s retracted paper that he claims was peer-reviewed (but no one can verify), Meyer says this:

    Despite the intense furor, there was no formal scientific response to my article: neither the Proceedings nor any other scientific journal published a scientific refutation.

    Seriously? No one refutes this either, but that doesn’t mean it’s correct. If lack of refutation was the only requirement for being right, then we would be in serious trouble. No, the requirement for being right is that you have to actually be right and have evidence to back up your claim. Meyer doesn’t do that.

    Meyer, curiously, then goes on to admit that there were refutations of his paper (long one here by Alan Gishlick, Nick Matzke, and Wesley R. Elsberry ). Indeed, Meyer’s article was published on August 4th. The review he mentions by Gishlick, Matzke, and Elsberry (hereafter referred to as Meyer’s Hopeless Monster) was published on August 24th at Panda’s Thumb.

    I think it amusing that Meyer relies on no one publishing a peer-reviewed refutation to support his case. By doing this Meyer says that peer-review is somehow important to his case. Of course, then one must ask where are the peer-reviewed papers supporting Intelligent Design? Why does Meyer choose to ignore the hundreds of thousands of peer-reviewed papers on evolution, when he desperately attempted to get ID into peer-review.

    Let me quote from Meyer’s Hopeless Monster:

    There is nothing wrong with challenging conventional wisdom – continuing challenge is a core feature of science. But challengers should at least be aware of, read, cite, and specifically rebut the actual data that supports conventional wisdom, not merely construct a rhetorical edifice out of omission of relevant facts, selective quoting, bad analogies, knocking down strawmen, and tendentious interpretations. Unless and until the “intelligent design” movement does this, they are not seriously in the game. They’re not even playing the same sport.

    Where have we seen this before?  Oh yeah, in this very detailed review of Meyer’s latest book where he misrepresents scientists, doesn’t cite all evidence, and ignores relevant facts. Not to mention poor analogies and an utter disregard for the actual science.

    Scientists have to play in and respect reality. Creationists live in a fantasy world where facts and reality are not welcome.

    So what is the big argument about? Well, it’s simple really. Where do new genes come from?

    Meyer asserts in his paper (and in this book) that

    • the Cambrian required a massive amount of new information
    • that the higher orders of life are real things and not artifacts of fossilization and our classification scheme
    • that these organisms required new proteins and new body plans that never before existed
    • that these new proteins and new body plans are extremely complex and highly specified
    • These complex and specified things are highly improbable therefore evolution can’t have done it

    That long response I linked to has very detailed explanations of why these claims are all wrong. I’ll be happy to talk about it, but the authors already have. That response includes 49 citations (including three by Axe). There’s a lot to wade through there.

    That’s the thing I’ve noticed over the years (and especially, this review). Creationists, even the ones like Meyer and Axe aren’t really interested in learning. They aren’t interested in doing the research. They aren’t interested in finding things that don’t support their claims, understanding them, and doing the kind of work required to support their own claims and refute their detractors.

    Meyer shows that to a ‘t’ here. He simply ignores the papers that contradict his claims. That’s not how research is done. That’s not how science books are written.

    Meyer, indeed, chooses to reject science. Saying:

    Elsewhere Matzke, along with biologist Paul Gross, stated that the paper by Long “reviews all the mutational processes involved in the origin of new genes and then lists dozens of examples in which research groups have reconstructed the genes’ origins.”9 In their view, “Competent scientists know how new genetic information arises.”10
    But do evolutionary biologists really know this?
    Let’s take a closer look at the article that allegedly shows “how new genetic information arises.”11

    What’s very curious is that all three of those references (9, 10, and 11) in the chapter refer to the same article. But it’s not the Long paper referred to in the text… or, for that matter, in the Elsberry response.

    Here, I must admit some confusion. Meyer is either a poor researcher or a poor writer (or both). At the bottom of page 210 he refers to the response

    Gishlick, Matzke, and Elsberry’s response, which they titled “Meyer’s Hopeless Monster.”

    He then says that these three authors refer to a paper in their work:

    “The Origin of New Genes: Glimpses from the Young and Old,” had appeared in Nature Reviews Genetics in 2003. Gishlick, Matzke, and Elsberry asserted that this paper—coauthored by Manyuan Long, an evolutionary biologist at the University of Chicago, and several colleagues—was representative of an extensive “scientific literature documenting the origin of new genes.”7

    I am confused by this slightly. The reason is (after talking with two of the authors of Meyer’s Hopeless Monster) that the article Meyer is talking about was only referenced as an article that Meyer ignored. Along with 13 other articles that Meyer ignored.

    These articles were not specifically mentioned in the text of Meyer’s Hopeless Monster… again, except for as part of a list of articles that Meyer ignored. Meyer also  ignores the articles that are directly discussed in Meyer’s Hopeless Monster, choosing to focus on this one.  I wonder why.

    To continue with Meyer’s confusion, reference 7 (in the quote above) as well as 8,9, and 10 (third quote above) all reference, not Meyer’s Hopeless Monster, but a chapter out of a book called Not in Our Classrooms: Why Intelligent Design Is Wrong for Our Schools. Paul Gross and Nick Matzke wrote the chapter called “Analyzing Critical Analysis: The Fallback Antievolutionist Strategy”.

    So, what did Gross and Matzke actually say. Sorry for the wall of text, but I think it relevant.

    It would be no exaggeration to say that this argument is at the heart of the ID movement. The only problem is that it is scandalously wrong. Competent scientists know how new genetic information arises: a variety of will-understood mutational mechanisms copy and modify the DNA latter sequence that makes up a gene. If the new sequence is advantageous to the organism, natural selection spreads the new gene through the population by way of well-understood process of population genetics. This shows where new genetic information comes from, and it fully explains, as a bonus, the otherwise puzzling fact that most genes belong to large families and superfamilies of similar composition.

    One particularly useful paper was published in Nature Reviews Genetics in 2003; written by Manyuan Long of the University of Chicago, it reviews all the mutational processes involved in the origin of new genes and then lists dozens of examples in which research groups have reconstructed the genes’ origins. The paper lists 122 references, virtually all of them published in the last ten years. None has ever been mentioned by the ID movement, let along rebutted. Dr. Long has devoted his whole career to studying the origin of new genes; his online resume lists some two dozen recent publications on the topic.

    So what does this tell us. First, the paper that Meyer seems to think is the basis of the origin of new genes is just a review paper. The real studies involved are those 122 (slightly fewer) papers that detail how we know that those mechanisms produce new genes.

    Meyer does not address or acknowledge those papers. Indeed, as we shall see, Meyer gets confused about science again and unwittingly causes the entire structure of ID to fail.

    It’s about to get very interesting, as our own commenter has made clear. Stay tuned.

     The rest of the series. 

    Category: Uncategorized

    Article by: Smilodon's Retreat

    • Doc Bill

      Meyer’s position is totally absurd. Otherwise the only way to rebut Walt Brown’s “hydroplate” theory, or Baumgardner’s “run-away subduction” or Hovind’s “vapor canopy” or Austin’s “catastrophic flood” theory would be by publishing “rebuttals” in peer-reviewed scientific journals. However, all of these crazy, crackpot ideas are offered with no supporting evidence, no testable theory, and can be disproved on the back of an envelope.

      No, it is not the function of science journals to “disprove” every crackpot, stupid, idiotic notion that comes along.

      So, where’s the meat in the Bankruptcy Chapter 11? Lots of soft fluff so far. Come on, Tuggy, give us a clue. (Find a clue, first, then give us one.)

    • Nicholas J. Matzke

      This has links to most of the major discussions of the Meyer 2004 kerfluffle: http://pandasthumb.org/archives/2004/09/the-meyer-2004.html

      The PT critique was referenced by, among other places, Nature…

      • SmilodonsRetreat

        Thanks Nick.

      • Robert

        Almost all the links on that page seem to throw 404 errors for me…

        • RexTugwell

          Robert, curiously enough, the links to the DI responses are broken on the PT site. Try these corrected links for the response dated 2004/09/28:

          One Long Bluff

          Neo-Darwinisms’s Unsolved Problems

          • SmilodonsRetreat

            Because I’m sure that a creationist website will present all the information just as a science site would… man I can’t even keep that up.

            This ought to be good. Looking forward to what you think of the rest of Chapter 11… but don’t fret… more to come.

    • Christine Janis

      Pleased to announce that I have used the “hopeless monster” meme in a paper just submitted. It’s about extinct kangaroos that walked rather than hopped —- now termed “hop-less monsters”.

      • SmilodonsRetreat

        You win the internet for the rest of today and 8 hours tomorrow!

      • Doc Bill

        I believe the researchers for that were Dr. Robert Keeshan and Dr. Jean Green with assistance from M.R. Rabbit.

    • Christine Janis

      from that “Panda’s Thumb” link

      Meyer cites some papers by University of Chicago reasearcher Mike Foote.
      However, of the two papers by Foote cited by Meyer, ——the Mesozoic
      record of mammal clade divergence”

      I’m *so* embarrassed that Meyer used my paper in support of his bogus argument.

    • Void Walker

      Where’s little Rexy? I miss the cute lil’ fella….zero substance, zero decent arguments, zero brains. Just like a puppy, but not nearly as cute.

      • RexTugwell

        Oh I’m here Void. I thought you may be wondering where I was. I’m having a crisis here at work so will respond in time. Love your lame attempts at condescension. Shows off your small mind.

        • Doc Bill

          “Crisis at work” means he stapled his hand to the desk … again.

          • RexTugwell

            and it really hurts! :(

        • Void Walker

          Awe…I struck a nerve. :)

          • RexTugwell

            Not even close

            • Void Walker


        • Doc Bill

          Hey, no condescension meant. I have a PhD and you have a GED. You’ll find the broom in the laundry room. Thanks.

      • Doc Bill

        Rex is a typical creationist blowhard coward. Socially inept and with a huge dose of self-loathing, our little Rexy thinks that pretending to be sciency will make him sciency. Alas, Rexy, only a little hard work will enable you to reach that goal. And, face it, Rexy, you’re a very, very lazy Rexy. You rely upon your science from book reviews fed to you second or third hand by creationist websites and that makes you an expert. Yeah, well, maybe at a moron convention, but not in real life.

        But, yes, I agree with Void that Rexy and his fellow travelers are cute little chew toys and I’m always entertained by their unoriginal content. Sort of like watching ’60’s sitcoms in B/W.

        As for Meyer, I think Doubt has bit the dust. Sales are zero. Memory is zero. Impact is zero.

    • cazimir

      “So what does this tell us. First, the paper that Meyer seems to think is the basis of the origin of new genes is just a review paper. The real studies involved are those 122 (slightly fewer) papers that detail how we know that those mechanisms produce new genes.
      Meyer does not address or acknowledge those papers.”

      Really? What is the whole chapter about? Isnt’t about all those supposed mechanisms with references to the respective papers?

    • cazimir

      S. Meyer
      “but in Darwin’s Doubt I addressed six new (that is, post neo-Darwinian) theories of evolution — theories that proposed new mechanisms to either supplement or replace the reliance upon mutation and natural selection in neo-Darwinian theory. Readers may refer to Chapters 15 and 16 of Darwin’s Doubt. Those chapters reflect ample awareness of the distinction between the different meanings of “evolution” and neo-Darwinian theory, and show that many leading evolutionary theorists agree, as Margulis did, that the natural selection and random mutation mechanism lacks the creative power that neo-Darwinists have long attributed to it.”

      L. Margulis:
      “But this Darwinian claim to explain all of evolution is a popular half-truth whose lack of explicative power is compensated for only by the religious ferocity of its rhetoric. Although random mutations influenced the course of evolution, their influence was mainly by loss, alteration, and refinement. One mutation confers resistance to malaria but also makes happy blood cells into the deficient oxygen carriers of sickle cell anemics. Another converts a gorgeous newborn into a cystic fibrosis patient or a victim of early onset diabetes. One mutation causes a flighty red-eyed fruit fly to fail to take wing. Never, however, did that one mutation make a wing, a fruit, a woody stem, or a claw appear. Mutations, in summary, tend to induce sickness, death, or deficiencies. No evidence in the vast literature of heredity changes shows unambiguous evidence that random mutation itself, even with geographical isolation of populations, leads to speciation. Then how do new species come into being? How do cauliflowers descend from tiny, wild Mediterranean cabbagelike plants, or pigs from wild boars?” (Lynn Margulis, Dorion Sagan, Acquiring Genomes: A Theory of the Origins of the Species, (Basic Books, 2003), p. 29.)”

      • SmilodonsRetreat

        Why do creationists always think that quoting someone is a valid argument? And further quoting from a creationist website that is owned by the same organization that Meyer is a director of… really?

        Tell you what, you do what Meyer doesn’t do. Provide evidence that these claims are correct.

        Not the quote, because these are just assertions with no evidence to support them. I have supported my claim that Meyer is a liar with dozens of pieces of evidence. You just keep repeating the same crap that makes Meyer a liar and assuming that it’s valid.

        The quote from Margulis just shows that you (and potentially she) doesn’t keep up with the literature. I’ve debunked her claims in my review of Darwin’s Doubt and other posts on this very blog. It’s been done already. That you don’t know that just shows you aren’t keeping up.

        Read something OTHER than creationist websites for once. You know, maybe like… science.

        And before you say anything about it… claims presented without evidence can be dismissed without evidence.

        • azportsider

          I think it has to do with the authoritarian nature of religion, Smilodon. Creationists have no objective evidence for their notions, but to them the sayings of someone they view as an authority figure carries more weight than actual evidence does.

          BTW, Lynn Margulis, developer of the endosymbiosis theory of the origin of eukaryotic cells and onetime spouse of Carl Sagan, passed away in 2011.