• Darwin’s Doubt – Chapter 11 – Part 4

    Now Meyer begins a short section called “Common Ancestor Genes?” He start these three paragraphs by saying:

    Nearly all of the scenarios developed in the papers that Long cites start with an inferred common ancestral gene from which two or more modern genes diverged and developed. (page 214)

    That’s a pretty stout claim. I intend to review that claim in detail. It’s not because I don’t believe him… OK, yes, it’s because I don’t believe him.

    The first article in Long’s paper[1] is: Evolution of the intron-exon structure of eukaryotic genes.[2] What do the authors have to say about their work?

    To study the origins o f exon shuffling, we identified in our database those regions of genes which were homologous to prokaryotic genes. These are ancient conserved regions (AC1L) [58] which represent complete genes or portions of genes that descended in a relatively unchanged manner from a common ancestor. These regions have no introns in the prokaryotes, but they have introns in the eukaryotic versions.


    Phylogenetic analysis o f eukaryotic genes that exist in both nuclear and organellar versions revealed that these genes are products of ancient duplications, which probably antedate the prokaryote/eukaryote divergence. If introns are in identical positions in such genes, they are good candidates for ancient introns.

    So the authors did not assume that the genes were from a common ancestor, but determined that through careful analysis. The authors point out several examples of evidence that support the idea that genes are common between wildly different organisms. For example, this paper [3] points out that five introns are in identical positions in both nuclear and chloroplast GADPH. This is evidence that GADPH evolved in the ancestor of prokaryotes and eukaryotes.

    Let’s take a second or two here and reiterate the problem with Meyer (and most creationists). Meyer makes a claim here. It probably took him 10-12 seconds to write that sentence. I am fairly confident that he did not actually read the articles. So far, it’s take me 40 minutes to find the paper, download it, read it, reread for details, then write the few short paragraphs that I have.

    By extension (and assuming I can even get all these articles), it’ll take me 81 hours to do this for all the papers. The Gish Gallop is alive and well in the creationist playbook.  An unsupported claim that must be thoroughly debunked and requires something on the 4 orders of magnitude more effort to debunk than it took to write (292,800 seconds vs 12 seconds).

    Sorry, but my time is worth more than that.

    I’ve shown here that at least one paper does not assume an ancestral gene. Indeed, I would very much like a creationist to find ONE paper in this list that assumes an ancestral gene. I very much think that the vast majority (75% or more) instead describes the evidence which leads to the conclusion that ancestral genes exist.

    Meyer then comes along and says why those things are not actual evidence for common ancestry.

    As I noted in Chapters 5 and 6, standard methods of phylogenetic reconstruction presuppose, rather than demonstrate, that biological similarity results from shared ancestry.

    I very much disagree with this. Because the phylogentic sequences are not the ONLY piece of evidence that supports common ancestry. All the actual evidence that exists supports common ancestry and none of it supports instantaneous design of organisms like intelligent design does.[4]

    Here’s a long discussion of the evidence for common ancestry. Now, when creationists talk about it, then will (as Meyer is doing) pick at one part and pretend that none of the rest of it exists. Meyer, for example, says that we assume that common ancestry is true because of the arrangement of certain patterns in DNA.

    But is that really an assumption? Instead, is it evidence to support a claim?

    The latter is correct. Consider that molecular evidence (gene sequences such as mentioned above) match many of the predictions made about common ancestry before molecular techniques were possible. For example, Thomas Huxley proposed that birds were descendants of dinosaurs in the 1870s. He was just looking at the anatomy. And here, over 100 years later, is the molecular evidence that supports that idea.

    We think that common ancestry is true not because we assume it to be true, but because there is a large amount of evidence to support it. When creationists talk about common ancestry they do not mention all of the evidence, they mention one piece and then claim it is a circular argument.

    What creationists have to deal with is the fact that common ancestry exists. This isn’t a wild fantasy, it’s real and their notions absolutely cannot deal with it.

    Once again, I will ask that someone, anyone, tell me the page numbers in Darwin’s Doubt where Meyer supports Intelligent Design?  The entire book is not evidence for Intelligent Design. The entire book, so far, is a poorly written and researched attempt to discredit evolution. Since the majority of the claims that Meyer has made so far are totally wrong, this isn’t a book against evolution. It’s a fantasy.

    I would like one more point, but it’s so stupid that it deserves it’s own post. Meyer is truly lost his mind.

    The rest of the series.


    [1] Long, M., Betrán, E., Thornton, K. & Wang, W. The origin of new genes: glimpses from the young and old. Nature reviews. Genetics4, 865–75 (2003).

    [2] M. Long, S. de Souza, W. Gilbert, Evolution of the intron-exon structure of eukaryotic genes.Current opinion in genetics & development 5, 774–8 (1995).

    [3] Kersanach R, Brinkmann H, Liaud M -F, Zhang D-X, Martin W, • • Cerff R: Five identical intron positions in ancient duplicated genes of eubacterial origin. Nature 1994, 367:387-389.

    [4] Intelligent design means that various forms of life began abruptly through an intelligent agency, with their distinctive features already intact – fish with fins and scales, birds with feathers, beaks, and wings, etc. (Pandas 1993, 2nd edition, published, pp. 99-100)

    Chunks of Pandas are currently on the Discovery Institute website. The authors of Pandas include DI fellows Stephen Meyer (VP of the DI, director of the DI’s Center for Science and Culture, organizational head of the ID movement), Michael Behe, Dean Kenyon (YEC), and Nancy Pearcey (YEC). Dembski and Wells coauthored a new edition. Phillip Johnson, Dembski, Behe, etc. all endorsed the old edition of Pandas in print, and Behe defended Pandas as “intelligent design” in court. – Nick Matzke

    Category: Book ReviewCreationismEvolutionScience


    Article by: Smilodon's Retreat

    • Nicholas J. Matzke

      Yeah, this was one of the most outrageous and silly parts of meyer’s book. The ID movement has basically been trying to pretend and gene duplication + divergence etc doesn’t exist since the moment they adopted the information in DNA = ID argument in the 1980s. They never did the necessary lit review to even make a respectable attempt at an intellectually responsible case, then or in the nearly 30 years since. It’s a damn shame Meyer chickened out of the kitzmiller case because it would have been fun to ask him about it.

      Anyway for more ranting on the new genes question see my original PT review- although this topic is one where they are so obviously wrong it’s rarely gotten sufficient attention from creationism fighters compared to IC etc

      • SmilodonsRetreat

        Just wait until the next installment, where I’ll discuss what is, probably, the dumbest thing I’ve ever heard a professional creationist say/write.

      • Cazimir

        Have you read the book? Where did he say gene duplication + divergence doesn’t exist?

        • SmilodonsRetreat

          Ah, the old semantic games. “I never said that…” just implied it heavily throughout the entire book.

        • Nicholas J. Matzke

          What do you think Meyer’s rhetoric about “assume a gene” means?? It means that Meyer thinks evolutionary biologists are just making stuff up when they conclude that two different genes with similar sequences descend from a common ancestral gene via gene duplication + mutational divergence. If he accepts that these processes are real, then his “assume a gene” rhetoric doesn’t make any sense.

          • Cazimir

            S Meyer DD:

            “At best, these scenarios trace the history of preexisting genes, rather then explain the origin of the original genes themselves.”

            “Duplication mutation and various other modes of random mutational changes along with natural selection clearly constitute causes now in operation. No one dispute that.”

            You should really read the book. Looks like you haven’t.

    • Where’s Rex? Oh, excuse me … he’s allergic to facts and will only show up to point you to some other chapter in DD … as if it will make a difference.

      • SmilodonsRetreat

        I’ve noticed this too. I was going to comment on it, but I wanted to give them a chance.

      • Doc Bill

        Hang on! Rex was all Lady GaGa about Chapter 11, the Bankruptcy Chapter. Darwin killer it was. Proof of ID it was.

        My bet is that the dishonest, pompous windbag named Rexy Wexy will chicken out on his previous claims, claim he never made those claims, instruct us to “read more closely,” a typical dodge tossed out by all dishonest creationists. (I know, oxymoron.) Or he’ll start something totally new and move on having claimed victory.

        I really don’t understand why the term “wanker” hasn’t become more popular in the US because it really applies nicely to the Rexys of the world.

      • RexTugwell

        Why is everyone wondering where I am? Is it because I was the one who had to drag Smiley kicking and screaming into this chapter and others like it? It’s pretty bad when you have to shame someone reviewing a book to actually review it. Then again, it’s exactly the behavior I expected; so really no surprises there.

        I’m not commenting every day because I have a life and because this blog is merely a pimple on the ass of the whole Darwin v. ID debate. I don’t sense an urgency to respond regularly. After all, I patiently gave Smilodon 6 weeks to finish chapter 13. Once again, he didn’t disappoint.

        • SmilodonsRetreat

          Tell you what. I’ll review the whole book right now.

          1) it’s crap.
          2) It’s wrong.
          3) It’s full of lies.
          4) It’s full of shoddy research… or lies (take your pick)

          What’s more to review? What more do you need to know?

          I continue to ask (and have to receive an answer) Why do you still consider Meyer to be a reliable source of information when I have documented dozens of pieces of evidence where he is wrong? And not just a little wrong, but “make up something that doesn’t exist” wrong.

          • Doc Bill

            Just like I predicted. Widdle Wexy came back with about 150 words containing nothing but pompous windbag whining. As for Chapter 11, it lives up to its name.

        • christine janis

          “this blog is merely a pimple on the ass of the whole Darwin v. ID debate”

          Um — there’s no “Darwin versus ID” debate, because Darwin died over a century ago.

          In theory, you should be claiming an “Evolutionary biology versus ID” debate: but that’s also wrong because there is no scientific debate, just a bunch of IDers whinging that science doesn’t take them seriously. And 99% of evolutionary biologists are completely unaware of such a “debate” (I know, because I poll my colleagues frequently).

          What is the actual debate, Rex? And who is engaged against whom?

    • Cazimir

      Darwin’s Doubt:

      “None of these papers demonstrate how mutations and natural selection could find truly novel genes or proteins in sequence space in the first place; nor do they show that it is reasonably probable (or plausible) that these mechanisms would do so in the time available. These papers assume the existence of significant amounts of preexisting genetic information (indeed , many whole and unique genes) and then suggest various mechanisms that might have slightly altered or fused these genes together into larger composites.

      At best, these scenarios trace the history of preexisting genes, rather then explain the origin of the original genes themselves.

      None of the scenarios that the Long paper cites demonstrate the mathematical or experimental plausibility of the mutational mechanisms they assert as explanations for the origin of genes.”

      It seems to me that you are misrepresenting him. He doesn’t say ancestral genes doesn’t exist on the contrary.

      • SmilodonsRetreat

        See, I’m having a hard time just parsing what Meyer is trying to get at. The fact that genes change over time is… well… a fact. Even the highly conserved genes are different now than 50 million or 500 million years ago.

        Even the alligator, which hasn’t changed very much morphologically in the last 100 million years has very different genes than the alligators of 100 million years ago.

        So Meyer is being rather disingenuous here. He’s either saying what everyone knows is true, but saying that there’s an alternate explanation (without giving one) or he’s saying that genes actually don’t change, which is wrong.

        Evolutionary mechanisms can and do make small changes all over the genome. Even between one generation and next. That’s the basis of evolution. Gene duplications are a fact. And the papers I mentioned describes how gene duplications can lead to new species.

      • Sam Harris

        Given your quote, it seems like Meyer – and since you quote it approvingly, you – thinks that evolution postulates that RMNS literally looks for a specific, already existing gene. Pardon my frankness, but that is plain stupid.

    • Cazimir

      S Meyer DD:
      “Sometimes similarity appears between species where it cannot be explained by inheritance from a common ancestor and at the very least there are other possible explanations for sequence similarity. In the first place similar gene sequences might have evolved independently on two parallel lines of decent starting with two different genes as the hypotheses of convergent evolution asserts.

      In addition it is possible that similar genes might have been separately designed to meet similar functional needs in different organismal contexts. (for more compelling reasons to consider intelligent design see chapter 17through 19)

      Sequence similarity does not necessarily indicate or derive from a common ancestral gene. ”

      “Duplication mutation and various other modes of random mutational changes along with natural selection clearly constitute causes now in operation. No one dispute that. But have these processes demonstrated the capacity to produce the effect in question namely the genetic information necessary to structural innovation in the history of life. There are several good reasons to think that they have not. ”

      For pertinent arguments I recommend reading chapter 10 also.

      Or this nice post:


      “Climbing Mt. Improbable
      Which leaves us back where we started. The average time it takes to get from one functional island to the next closest island in sequence space is in fact affected, quite dramatically, by the exponential decline in the ratio of potentially beneficial vs. non-beneficial sequences in sequence space with each step up the ladder of functional complexity. ”Climbing Mt. Improbable” is not as easy on the “back side” of the mountain as those like Richard Dawkins seem to imagine. Why not? Because, the backside of the mountain is not comprised of small little uniform steps from the bottom to the top. Rather, the steps from the bottom to the top get exponentially larger and larger from the bottom to the top.”

      “What this means is that populations get stuck on the peaks of these mountain ranges at very low levels of functional complexity – because neutral gap distances, or otherwise non-beneficial gap distances, are simply too wide to be crossed, this side of trillions of years of time, beyond these very low levels of functional complexity.”

      • SmilodonsRetreat

        It’s funny how when scientists say “might” or “possible”, that creationists yell and scream that it’s a just-so story.

        I’ts also funny how this very claim is a rehash of a rehash of something Meyer wrote which was debunked long, long ago. And yet, he still keeps using it, even though he knows it’s wrong (or he’s the worst researcher ever).

        Why is that, do you think?

        Don’t worry, I’m working on it.

        Finally… Oh, it’s Chapter 10 NOW that’s the important chapter.

        Tell me, after all the times (so far) I’ve shown what Meyer says to be wrong, deliberately misquoted, and ignoring relevant work, why do you think he’s still a reliable source?

        • cazimir

          “It’s funny how when scientists say “might” or “possible”, that creationists yell and scream that it’s a just-so story.”

          Of course when evolutionists present stories as evidence. Meyer didn’t do that he presented possible alternatives.

          What was debunked long ago? where was debunked?

          “Tell me, after all the times (so far) I’ve shown what Meyer says to be wrong, deliberately misquoted, and ignoring relevant work, why do you think he’s still a reliable source?”

          You haven’t shown any relevant evidence of what mutations can do. Can you show a list of evidence that proves random mutations ability to achieve the effect in question and which Meyer ignored or misrepresented?

          It’s your 4th post on chapter 4 and you debunked nothing. You accused Meyer of not referencing any of those papers from the Long paper, which is not true.

          • SmilodonsRetreat

            Which paper did he reference?

          • SmilodonsRetreat

            Let me just comment on something here.

            Mutations and what they can do. So, what you are asking me here is to provide something that shows, every mutational step of the way, when an population changes from one genus or higher level or another genus or higher level.

            If that is correct, then I will require that you provide the same level of detailed about your preferred notion on how it happened. Whatever your notion is. If you can’t do so, then we are at an impasse and the notion that is predictive and explanatory wins. Which is evolution.

            If it is not correct, then please describe exactly what you are expecting.

            What I think you are expecting is detailed changes over a multi-million year period of time. Considering that we’ve only understood what mutations really are for a few decades, that’s asking an awful lot…. and yet, we can trace the mutations through a population. It results in a phylogenetic tree. But Meyer tries to discredit that too… or so I hear. He really can’t, since there’s nothing to discredit.

            The problem, of course, is that the phylogenetic trees that are developed by tracing mutations in hundreds of gene pools for hundreds of populations matches the morphology of the organisms AND it matches the fossil record AND it matches the developmental history of the organisms.

            All of which are independent systems that show the same results. Which ID cannot deal with.

      • Doc Bill

        That’s right, Caz, support creationist Meyer spouting rubbish by linking to a creationist website spouting rubbish. Not very smart, are you, Caz? At least that part is indisputable!

        • cazimir

          Is it my fault that evolutionists ignore the problems with their theory? Do you expect them to acknowledge them easily?

          They present trivial cases and claim that as evidence that mutations can create anything. As if you can walk from new york to new jersey is evidence that you can random walk to Honolulu

          • Christine Janis

            “Is it my fault that evolutionists ignore the problems with their theory?”

            Which evolutionary research journals do you subscribe to, Caz? There are several dozen specialist ones, as well as many other journals that publish evolutionary science (such as Nature, Science, PNAS, etc.)

            I would expect that someone so well-acquainted with the problems with evolutionary theory would be keeping up with the literature (at least 100 new papers published each week).

            Or perhaps you assume that you don’t need any real knowledge of a scientific topic to declare that it has “problems”? Congratulations, that makes you on par with almost every other creationist.

          • Sam Harris

            Curious – how do YOU know that the theory has “problems”? Because a creationist said so?