• Darwin’s Doubt – Chapter 13 – Part 1

    As specifically requested by a commenter, I am continuing with Darwin’s Doubt. Apparently Chapter 13 has arguments devastating to evolution and/or evidence to support Intelligent Design.

    The chapter (entitled The Origin of Body Plans) begins with a research experiment. But not just any research experiment (PDF), this one resulted in a Nobel Prize in Physiology or Medicine (1995).

    Basically, the researchers heavily mutated fruit flies, then observed their development. By doing so, they were able to identify places in the genome that, when mutated, changed the shape of the organism.

    Meyer tells us an interesting quote here:

    “The problem is, we think we’ve hit all the genes required to specify the body plan of Drosophila,” he said, “and yet these results are obviously not promising as raw materials for macroevolution. The next question then, I guess, is what are—or what would be—the right mutations for major evolutionary change? And we don’t know the answer to that.”4  (Darwin’s Doubt pg 257)

    That footnote 4? Well, here’s the footnote comment:

    Quotes recorded in contemporaneous notes taken by philosopher of biology Paul Nelson, who was in attendance at this lecture.

    So, there is no possible way we can verify what was actually said in this discussion or the context in which this comment was made. Since it’s from someone else’s notes, Meyer wouldn’t even need ellipses to generate a confusing message.

    But who is this Paul Nelson? Meyer calls him a “philosopher of biology”. I’m not sure what that means, but Paul A. Nelson is a creationist. He’s a Young Earth Creationist and fellow of the Discovery Institute (where Meyer is currently the director of the Center for Science and Culture).

    I personally find it rather interesting that Meyer fails to inform us of these details. It’s a known fact that creationists misrepresent material and fabricate or take out of context quotes from scientists. Again, since it’s been a while since I’ve talked about this. We have dozens of examples from right here in Meyer’s own book (from the first few chapters) and an entire project dedicated to pointing out such quotemines at the talk.origins archive.

    Here’s an article calling out Paul Nelson for quotemining. And another one where Nelson makes claims about scientists without them knowing about it. Or this article which also shows a Nelson quotemine. Or this one which also accuses him of quotemining.  It’s actually amazing to me that Nelson would take comments of evolutionary biologists and try to interpret them as support for intelligent design.

    Given this, I think we must question the accuracy of Paul Nelson’s report here.

    So, chapter 13 (as I predicted) hasn’t started out that well. At the top of the third page (and the bottom of the second page) are quotes from a scientist that no one has any possible way of confirming. Notes written by a creationist who is a known advocate of intelligent design, that the Earth is only 6,000 years old, and who is also known for taking quotes out of context.

    I honestly don’t understand how anyone, at this point, can think that Meyer’s book is anything but scientific fiction*.

    But I’d also like to comment specifically on this part of the quote

    The next question then, I guess, is what are—or what would be—the right mutations for major evolutionary change? And we don’t know the answer to that.

    To this question Meyer says

    Thirty years later, developmental and evolutionary biologists still don’t know the answer to that question.

    Umm… that’s simply not true. Here’s a list of how changes appearing during development can result in new forms.

    Dr. Sewall Wright is one of the founders of population genetics. He was describing why small changes over time are much more effective that drastic changes all at once. His work was being done in the 1930s.

    So scientists have known for four score of years how evolution actually works. Not by massive changes in one generation, but by millions of successive changes over millions of years. Meyer, if you recall, seems to think that the Cambrian explosion of 40 million years, isn’t enough time to generate new body plans, even tking into account the research that shows that the genes leading up to these new body plans were present in the populations at the time well before the Cambrian explosion began.

    Meyer has, once again, set up a strawman and demolished it with a powerful kick. The experiments described at the beginning of the chapter was massively mutational and few of the fruit flies survived the experience. But that wasn’t the point of the exercise. The experiment was see what happened during development when certain mutations happened. To ensure that the researchers got the right mutations, they had to ensure that large numbers of mutations happened. This was in the late 1970s, scientists didn’t have the technology that we take for granted now.

    Once again, I will refer everyone to my article about mutations and my article about how new taxonomic groups are formed. These two articles continue to show that creationists (including Meyer) either don’t understand how evolution actually works or they purposefully misrepresent it to people who don’t know how evolution works.

    Just a cursory search of the literature reveals many articles that relate to development of body plans and/or the Cambrian explosion. I’ll have to go into these much later, but here are a few examples.

    Maxwell, E., Furrer, H. & Sánchez-Villagra, M. Exceptional fossil preservation demonstrates a new mode of axial skeleton elongation in early ray-finned fishes. Nature communications 4, 2570 (2012).

    D. Murdock, S. Bengtson, F. Marone, J. Greenwood, P. Donoghue, Evaluating scenarios for the evolutionary assembly of the brachiopod body plan.Evolution & development 16, 13–24 (2013).

    Stöger, I. et al. The continuing debate on deep molluscan phylogeny: evidence for Serialia (Mollusca, Monoplacophora + Polyplacophora). BioMed research international 2013, 407072 (2012).

    Either way, Meyer continues to be an unreliable reporter. I’ll continue with Chapter 13 as I have time, since it’s somehow important. 

    The rest of the series.

    * I use this phrase instead of science fiction, which has a specific meaning. I take the idea from historical fiction where an author uses history as a source for a fictional story. In this case, Meyer is using science as a source for a fictional philosophy.

    Category: Book ReviewCreationismEvolutionfeaturedGeneticsScience


    Article by: Smilodon's Retreat

    • Doc Bill

      Marshall said it best when he referred to Meyer’s “systematic failure of scholarship.” None of these Disco Tute guys just fell off the turnip truck. They have been misrepresenting biological science for decades with surgical precision. The quote mining is very carefully done and they just don’t care if they get exposed. Meyer was busted by Marshall for quote mining Marshall and Meyer still didn’t care; kept on going.

      Poor old Nelson lives in a world all his own. A young universe world, to be sure, but the poor guy has no job and who knows how he spends his day. Married well, I guess. Good work if you can get it! What’s pathetic about Meyer is how he references his own Disco Tute fellows as if they are real scientists and not just a bunch of propagandists referencing each other. The “scholarship” is not just unreliable or failed, it’s non-existant.

    • RexTugwell

      Good luck, Smilodon. I’ve got my popcorn ready.

      • Christine Janis

        Hey Rex

        Are you as high on the words of Dan Graur when he shreds the findings of the Encode team?


        • RexTugwell

          Hey Dr. Janis, I believe the current topic is molecular clocks and their veracity, not ENCODE. You’ve got a copy of Darwin’s Doubt. What’s your professional opinion of chapter 5 and where has Meyer gone wrong?

          • Christine Janis

            Irrelevant. You want to quote Graur in favor of creationist screeds? You won’t quote him when it comes to Encode. Chose your people to quote mine with care.

            My professional opinion of Chapter 5? I’d like to ask Meyer: “Hey, we have 4 different New Testament Gospels that all have slightly different versions of the same story. Does this prove that Jesus never existed?”

          • Doc Bill

            Meyer isn’t just wrong, he’s deliberately misrepresenting science wrong. He’s lying wrong. He didn’t make a mistake, rather he deliberately distorted, and contorted published science to meet his ideological ends.

            Refute that with facts, Rexy-wexy, otherwise STFU.

    • http://www.facebook.com/people/John-Pieret/100000023960330 John Pieret

      either don’t understand how evolution actually works or they purposefully misrepresent it

      I don’t think that ‘either … or’ is necessary. It can be (and I think is) ‘both’.

    • RexTugwell

      Well, Smilodon, you’re off to a predictable start. My estimation of you increased somewhat when I saw you were going to tackle chapter 13 and then you spent half of this article poisoning the well with quote-mining accusations, ad hominems and irrelevancies.

      The only two points worth commenting on are:

      So scientists have known for four score
      of years how evolution actually works. Not by massive changes in one generation, but by millions of successive changes over millions of years.

      How is this different from what Darwin wrote? This is the assertion isn’t it? However, as before with your net zero energy explanation of the universe, your above claim is merely descriptive and does nothing to provide an explanation of the mechanism.

      … the research that shows that the genes
      leading up to these new body plans were present in the populations at the time well before the Cambrian explosion began.

      Based on what? Molecular clocks? Extrapolations based on
      known mutation rates? In silico models generated by software that was written assuming common descent? I think this was covered in chapter 5 of DD. Oh…never mind. Chapters 3 to 12…that’s flyover country to you.

      You started out your review of Darwin’s Doubt grousing about
      how Meyer gave short shrift to Rosalind Franklin. I hope it won’t be more of the same.

      • SmilodonsRetreat

        Let’s see. We have a liar, quoting another liar about something that someone said that can’t be checked. Why don’t we focus on why you think that Meyer is still a reliable source for anything?

        As far as the rest. What you are saying is that in every single post, you expect me to describe the entirety of knowledge about evolution because you can’t be bothered to remember what I’ve said before and/or look up references for yourself. Whatever.

        I’ve talked about all of this, in detail, previously, with links to and descriptions of the relevant peer-reviewed literature. Indeed, I listed three publications in this very post. But you aren’t interested in that… just in the stuff you think will somehow win points. When are you going to understand that they only points are won through evidence and so far, Meyer hasn’t presented any.

        I’ll say this again, because it hasn’t seemed to have sunked in the last dozen times I’ve said it. Even if Meyer somehow disproves evolution (which he doesn’t) in this book, it doesn’t mean that ID is correct. Only positive supporting evidence can do that. And after multiple requests by me to you, you still have not given me a page number where that evidence can be found.

        Whether you like how I write about Darwin’s Doubt or not, I’m merely writing about what is written. Meyer has made some fundamental errors in his statements, his quotes, and his assumptions. I’m pointing out where all of those are wrong. If you don’t like me doing that, then I would encourage you to contact Meyer and have him correct those problems.

      • Doc Bill

        Oh, joy, Rexy said “ad hominems!”

        Please, Rexy-wexy, list the ad hominems that so offended your sensibilities. And do show your work. Quote the argument and declare why it is ad hominem.

        • http://www.facebook.com/people/John-Pieret/100000023960330 John Pieret


          I’m guessing that calling someone (who Rex agrees with) a liar and/or an incompetent amount to “ad hominems” in Rex’s world. As if we had to take what anyone says as [cough] gospel. Despite all the evidence, Bernie Madoff was just trying to help his suckers … er … clients make money.

          What Smilodon has done is demonstrate, in great detail, that Meyer is a liar and/or an incompetent. He has not argued that, just because Meyer is a theist, he is untrustworthy, which would be an ad hominem; he has shown his work that Meyer, in particular, is a liar and/or an incompetent. It is not an ad hominem, it is a conclusion based on empiric evidence.

          • Doc Bill

            Shhhhhhhh, I know! I want Rexy-wexy to admit his mistake and that he like all creationists is a clueless twit. What are my chances?

    • RexTugwell

      Do me a favor, will you Smilodon? Add the following paper to your list of references above, please. It’s a real science paper, published by a real science journal, written by real scientists working in a real science lab about real science. It clearly calls into question “the research that shows that the genes leading up to these new body plans were present in the populations at the time well before the Cambrian explosion began.”

      Graur, D. & Martin, W. (2004) Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision. TRENDS in Genetics 20:80-86 PDF

      Among other sources (like Darwin’s Doubt ch. 5), this link is provided by none other than your own Larry Moran, the one whom I believe coined the term IDiot – no friend of ID he. Larry’s a is a big fan of Graur and Martin’s paper. Here are a few quotes from his Aug 23, 2013 blog page praising Graur and Martin and panning molecular clocks:

      Dan Graur and Bill Martin—a formidable team that you want on your side because the alternative can be very embarrassing. You really, really don’t want to mess with these guys.

      We need more papers like this one.

      The Graur & Martin paper attacks molecular clock calibrations, pointing out that there are very few solid time points in the fossil record that can be used to calibrate the rate of molecular changes (in years).

      Like it or not, there’s still disagreement between the fossil data and molecular clock estimates.

      The abstract itself is worth the read. Cherry-picking your sources; that’s just shoddy research. Contrary to what Smiley would have us believe, what we have here is the fossil record not behaving itself; so the “real” scientists needed to conjure up some ancient genes to tell a fictional story.

      • SmilodonsRetreat

        And you think think that means that evolution is all wrong?

        The fact that any of this can be done at all means that evolution is right.

        Molecular biologists know that the time scales are ‘tentative’. That’s why we match it to fossil evidence. Or at least try to.

        Rex, why do you continue to try to cast doubt on evolution and science? You must know that even if you totally disprove evolution, right here, right now, it doesn’t mean that ID is right. Only positive supporting evidence will do that. So step up. Where’s the evidence.

        Give me a page number where Meyer lists the evidence and the links to the papers that support said evidence.

        Oh, and cherry picking, is when you take one paper that you think supports your claims and ignore the MILLIONS of others that refute your claims. Thanks for demonstrating that for us.

        • RexTugwell

          …and thanks again for demonstrating your DDS. For future reference,
          I’ll take your non-answer to be a refusal to include the paper. Exclude
          the Graur & Marin paper if you like; just don’t pretend “the research that shows that the genes leading up to these new body
          plans were present in the populations at the time well before the
          Cambrian explosion began.”
          It’s not true and there’s no evidence to support it.

          • SmilodonsRetreat

            So, let me just check with you here. This paper is a GOOD paper and you fully support all of the material in it. Correct?

            • RexTugwell

              Wow! Talk about a loaded question. No doubt you’re going somewhere with this, so for entertainment purposes, I’ll say “yes I fully support all the material in it” – especially the last sentence which states “whenever you see a time estimate in the evolutionary literature, demand uncertainty!”

            • SmilodonsRetreat

              Excellent. Then we are agreed. I, unlike you apparently, actually made the effort to read the paper. It refers to one instance (here: Hedges, S.B. and Kumar, S. (2003) Genomic clocks and evolutionary
              timescales. Trends Genet. 19, 200–206) in which

              a team of molecular evolutionists has inferred ostensibly precise molecular-clock dates for speciation events ranging from the divergence between cats and dogs to the early diversification of prokaryotes

              No, I totally agree that, in that instance, the precision and accuracy of the claim was unwarranted. Indeed, according to your reference, said team was making several errors about the common ancestor date of mammals and birds (310 mya) without any evidence. And that date was critical to the estimation that Graur and Martin are taking to task. Indeed, it appears that several publications used this date without realizing that the date was not accurate, but actually highly questionable. There are 12 specifically referenced works that they take to task for this error.

              I fully agree with Dr. Moran, that we need more papers like this that show a systemic error in publication and even molecular dating schemes.

              Now, your challenge is to show that this same issue applies to ALL papers using molecular clocks and not just the 13 papers that Graur and Martin directly mention. Indeed, if you do some careful reading, I think that you will find that most of the molecular clock papers are fairly accurate with “uncertainty” listed and explained as is error and a variety of other concerns… none of which is in any way detrimental to the science of evolution.

              You, however, are making a generalization error. By applying a discovered problem with one paper, to every paper that possibly talks about molecular clocks… without evidence. So, go find the evidence that the papers I refer to have the same problem and then we can talk. Until such time as you do that (or I discover similar problems on my own), then I will consider them standing.

              BTW: Since you accept the veracity of this article, then I will assume that you accept the veracity of all scientific articles published unless and until, you cite specific objections to them (also in the peer-reviewed literature). You creationists can’t have it both ways. Either science is a valid source or it isn’t. Taking a article because you think it supports your case and ignoring the thousands that don’t is cherry picking.

            • SmilodonsRetreat

              For example: http://epidemic.bio.ed.ac.uk/coronavirus_analysis

              Here’s a great analysis that talks about the things that concern you about molecular clocks.

              So, is this an OK study, since it specifically mentions error ranges, has a large data set, and uses both strict and relaxed molecular clocks?

            • RexTugwell

              Thanks. I’ll read the analysis. In the meantime, I strongly suggest you read chapter 5 of DD. Meyer makes an excellent case for why molecular clocks are inherently unreliable for calculating divergence dates. Well referenced. Great quotes.

            • SmilodonsRetreat

              At this point, when you see Meyer quoting something, you shouldn’t be saying “great quotes”, you should be saying “what did he misrepresent this time”. That you aren’t tells a lot about you.

              I note that you didn’t comment on my reply to the article you posted. I guess we can accept that as agreement then?

            • RexTugwell

              How convenient to hide behind Meyer’s supposed lack of honesty. My comment on your reply to the article is “read chapter 5″. It’ll answer your questions & objections. If you decide not to read it, at least don’t mislead your readers by making it seem like genes for new body plans preceding the Cambrian has any foundation.

              Just read the whole book. Isn’t that what reviewers usually do. The fact that you won’t just confirms what I suspected would happen from the start.

            • SmilodonsRetreat

              And you know very well why I haven’t.

              Meyer is so wrong about everything he has said so far in the book, why would I waste time. I said I would do 13… and I will. But know we’re talking about something else.

              Let me ask you, is there any place in this book, where Meyer provides ANY evidence for ID? Does he do any calculations of any values that IDists seem to think are valuable?

            • Doc Bill

              So, Rex, which Cambrian animals possessed genes not derived from their ancestors?

            • Doc Bill

              Are we reading the same chapter 5, Rex? It’s only 15 pages long and so full of fluff you need a Swiffer to get through it. Meyer sets up a few straw men to knock down, but that’s about all. If there’s a “clincher” paragraph in that mess I sure couldn’t find it.

              Tell you what, be a good boy, Rexy, and simply clue us in on what Meyer said in Chapter 5 that YOU think is so important, and why.

              While you’re at it, how about naming a few Cambrian critters whose gene set was modified by the Intelligent Designer and how he might have gone about doing that, and so forth.

              Failing that, just naming a single Cambrian critter that had no ancestors would be peachy keen.

          • Doc Bill

            Fascinating, Rex! Which Cambrian critter had no ancestor? Enlighten us, please.

    • l zoltan

      What are those evidence For darwinian evolution that Meyer missrepresented or lied about?
      No reviewer of Meyer’s book put forward a single piece of evidence. What would be a more powerfull rebuttal then to show the best evidence there is ?

      The fact is that there simply isn’t any. Its the only reason why the reviewers have to resort to arguments like hes an idiot he is lying, Its not science, has a religious agenda….he doesn’t understand evolution.

      No scientist understands evolution. Just because they tell nice stories doesn’t mean they know. And its all they have.

      • SmilodonsRetreat

        You can read each individual post I wrote (there’s a link to the list of all of them at the bottom of each page). You’ll note that if you had read my article, I actually posted a link to where I specifically describe why we see macroevolution, but why micro evolution does it.

        I also specifically listed a link in this article with many, many examples which refute Meyer’s claim.

        I love this new “no scientist understands evolution” meme that has popped up all of a sudden. Thanks Klinghoffer.

        I’m going to quote something that Doc Bill (a reader here) put on another blog

        This is a Common Whine from the Disco Tute that EVERYBODY misunderstands “intelligent design” creationism. Of course, we know, and they know, and they know we know, it’s not the case. The Tute knows the scam and we know the scam, so it’s all a game.

        However, consider this. With a group of bright high school students who have yet to take college-level chemistry, math, physics or biology I was able to discuss with them, in semi-detailed terms, the essence of cosmology, the general theory of relativity, the photoelectric effect as a demonstration of quantum mechanics, the theory of evolution, the history of atomic theory and descriptions of atomic structure, and the stellar synthesis of elements from hydrogen through iron (and beyond). These kids had no problems with any of these concepts.

        Yet, somehow, for some reason, the Disco Tute after 20 years still can’t articulate a theory of “intelligent design” creationism that can be understood by not only high school students but PhD level scientists. It’s really quite amazing when you think about it. Quite amazing.

        Yes it is quite amazing.

        ID proponents. Quit attacking evolution. It doesn’t work. It hasn’t worked for the last 100 years. WHy don’t you support your own notions?

        I remind you that I have a blog post to be given to any creationist who answers a few simple questions about ID.

        • RexTugwell

          The amazement continues. Judging from the immature and silly things I’ve seen Doc Bill write so far, I have a hard time believing he can understand the basics of science let alone explain them to high school students. That being said, it is essential to understand that there is a big difference between explaining the theory of Darwinian evolution and demonstrating macroevolution in the lab or in the wild. Anyone can articulate what was understood as alchemy; to give evidence for it is another matter. The same thing is true of Galen’s theory of blood circulation.

          All ID proponents understand the theory of evolution and accept it as able to accomplish certain things we see in nature. It can’t explain everything – wild imagination and just-so stories notwithstanding. Lenski’s lab has demonstrated beyond a doubt that evolution happens – evolving new abilities at the expense of others. Whether macroevoution can be demonstrated depends on how well you, Smilodon, cover chapter 13 in Darwin’s Doubt.

          • SmilodonsRetreat

            What I can’t understand is how ID proponents can’t understand that macro-evolution equals micro-evolution plus time.

            That’s ALL IT IS. I’ve even demonstrated that for you. Indeed, since you’re such an expert in science, you should know this already. Yet, you continue to think (or at least promote the idea) that they are somehow different.

            The thing that I find absolutely hilarious is that Rex thinks that if I can’t refute every single thing that Meyer says, then evolution is doomed and Intelligent Design is correct.

            How, I handle chapter 13?!?!? What about how Meyer handles chapter 13 by opening with an anecdote that cannot be verified in any way shape or form, then stating a claim that is patently false. (As I have shown.)

            You have yet to explain why you consider Meyer to be a reliable source when I’ve documented a dozen cases of quotemines and incorrect science.

            Actually, we both know why. Because Meyer says things you want to hear and you aren’t honest with all of us enough to admit that no matter what science says, you will side with religion every time.

          • Doc Bill

            Hey, Rexy, way to duck the question.

            You’re so smart, describe the “theory of ID” in a couple of paragraphs along with a few supporting examples.

            I’ll make some popcorn. Oh, and Rex, your shoe’s untied.