• Darwin’s Doubt – A Review

    A pro-ID reader has graciously sent me a copy of Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design by Stephen Meyer with the understanding that I will read and report on it.  I’ll remind everyone that I made several predictions about the book. Since I made my predictions, my understanding of the book has changed.  It is, apparently, almost purely about the Cambrian Explosion and why this is evidence of special creation.  Make no mistake about it, ID is special creation with “certain features of the universe and of living things are best explained by an intelligent cause.”

    Now this review will take a while.  First, I’m traveling for the next two weeks.   A week in Denver, unfortunately not for fun, but for work.  Then a week in Cedar Rapids, Iowa. My ability to review the book will be limited due to this (sorry).  Unfortunately, I can’t read (or do much of anything) on aircraft.  I have vertigo and a airplane trip puts me out for a while.

    The second part is that I fully intend to (somehow) acquire the references (if any) used by Meyer.  I’ll review them to see if Meyer reports them accurately and if the same conclusion is drawn.  It’s not that I don’t trust Meyer… well… OK… it’s that I don’t trust Meyer.  The people from the Discovery Institute are consummate charlatans. I’ll be perfectly honest, there isn’t anything in this book that shows evolution is wrong or that ID has any supporting evidence.  If there was, they would publish and then they wouldn’t shut up about it.

    This is just  book to lead the lay-person to the conclusion that science can’t explain everything. I may sound biased, and I am, a bit.  The DI doesn’t do science.  Meyer doesn’t do science.  Behe has tried to redefine science.  Dembski doesn’t do science.  How can one refute science when one does not do science? That all being said, I will try my best to be scrupulously fair.  I will let you, my readers, decide if I’m being fair or biased. I will also ask that anyone willing to help me acquire research papers send me a message from my contact page.  I would be grateful.

    Prologue (part I, part II, part III, part IV )

    Part I  The Mystery of the Missing Fossils

    1. Darwin’s Nemesis (part 1, part 2, part 3, part 4, part 5, part 6, part 7, part 8 )
    2. The Burgess Bestiary (part 1, part 2, part 3, part 4, part 5, part 6)
    3. Soft Bodies and Hard Facts
    4. The Not Missing Fossils?
    5. The Genes Tell the Story?
    6. The Animal Tree of Life
    7. Punk Eek!

    Part II – How to Build an Animal

    1. The Cambrian Information Explosion
    2. Combinatorial Inflation
    3. The Origin of Genes and Proteins
    4. Assume a Gene (part 1, part 2, part 3, part 4, part 5)
    5. Complex Adaptations and the Neo-Darwinian Math (guest post)
    6. The Origin of Body Plans (part 1, part 2)
    7. The Epigenetic Revolution

    Part III – After Darwin, What?

    1. The Post-Darwinian World and Self-Organization
    2. Other Post-Neo-Darwinian Models
    3. The Possibility of Intelligent Design (part 1, part2, part 3)
    4. Signs of Design in the Cambrian Explosion (part 1)
    5. The Rules of Science
    6. What’s at Stake

    As an aside, here are two additional articles of relevance to this text.

    This article is a review of another Meyer quotemine in Darwin’s Doubt.

    This article is an explanation of why Meyer misunderstands evolution and higher taxonomic orders.

    This article is the closing of the reviews and why. If you have specific questions about specific pages (not whole chapters), then let me know and I’ll see what I can do.

    Category: Book ReviewCreationismEvolutionResearchScience


    Article by: Smilodon's Retreat

    9 Pingbacks/Trackbacks

    • Read review: lacked any evidence that the book was even read by you.
      There is no scientific explanation for the evolution of the mechanism upon which genetic mutation does its magic. The mistakes in nucleic acid replication requires the super complex system of nuclear acid replication to be already up and running.

      • PS. I am a Neurologist and not someone you might dismiss as a “bitter clinger”.

        • SmilodonsRetreat

          I don’t dismiss anyone unless they are extremely rude or constantly ignore the evidence. Your job doesn’t mean anything… it’s the quality of the argument. And the argument you present is flawed.

        • Viktor Shakapopolous

          Your rantings are far more similar to what one would see from a creationist paint salesman than from someone pretending to be a neurologist.

      • SmilodonsRetreat

        If you had read the review, you would know that I’m on page 60 of 12,500+ (the Kindle numbering system).

        As far as the rest, you left out something. It’s called natural selection. And you are right, but the part II reviews shows that the “supercomplexity” wasn’t required in the beginning as RNA can be both the information storage system AND the information processing system.

      • Viktor Shakapopolous

        “There is no scientific explanation for the evolution of the mechanism upon which genetic mutation does its magic.”

        Why on earth would a rational person expect something like that in a BOOK REVIEW?

        Of course, from what I have read, the book offers NO evidence for the way in which this unidentified, evidence-free “designer” operated. Are you asking Meyer for those specifics, as well?

      • Tim Tian

        the theory of evolution isn’t a theory about the creation of life. What you’re looking for is the theory of abiogenisis.

    • BornRight

      You rock! I greatly appreciate the time and effort you’re putting in to expose the stupidity in Meyer’s book “Darwin’s Doubt”. Nick Matzke and Don Prothero have written great reviews, but your effort is the most comprehensive, dismantling the book chapter by chapter. Kudos! I can’t wait to read the remainder of the series.

    • Eric Collier

      Fantastic review! So what are the chances of a Smilodon-Meyer debate?

      • SmilodonsRetreat

        Slim at best. Meyer wouldn’t want to and I’m not very good in a live debate. I get too emotional and lose track of the points I need to make. I’ll happily do a written debate with him.

    • mrheuss

      Thanks for this – I am learning a lot. Your efforts are appreciated.

    • FormAndFunction

      Thanks for your work on this review, and thanks in particular for the table of contents you’ve got started. 🙂 I’ve got it bookmarked!

    • Pingback: A Journey through Darwin's Doubt - Page 22 - Parapsychology and alternative medicine forums of mind-energy.net()

    • Joe_Buddha

      Any possibility of linking these parts in a chain so I don’t have to come back here and try to remember what’s next?

    • Engr3454, BS, MS, MDiv, PE

      1. I HAVE slogged through the whole book (although I make no claim to have chased through any of the footnotes or bibliography).
      2. I AGREE with most of your judgments about it, although—
      3. I strongly suggest you suspend further review articles until you have at least also slogged through at least the rest of the text. That will save you, and the rest of us reading your review, the time wasted wondering whether Meyer later addresses the questions raised in the earlier sections. In most cases, he does attempt to do so, and I am sure you will find ample opportunity to question the results of his attempts.
      4. I have only the usual layman’s smattering of training in evolutionary biology and biochemistry, but did study thrology and philosphy of religion (through PhD course work, “all but dissertation,”) and agree that it is really Meyer’s theology that it is lacking: Despite his denials, his version of ID is “God of the gaps,” whereever convenient gaps may be found..

    • Engr3454, BS, MS, MDiv, PE

      Sorry for the typo in my previous post. I studied theology, not “thrology.”
      Though I suggested you suspend further review articles until you have read the whole book, please do not abandon the effort, which is much appreciated.

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    • Smilodon — FYI: I think many of the comments in my two preliminary posts about Meyer’s earlier book also apply to this one, since they concern the logical structure of his arguments. See here and here.

    • Jeff Johnson

      You critiqued some of the book but not all of it? What about an evolutionists response to chapter 9 (IMO Meyer’s and ID’s strongest argument).

      • SmilodonsRetreat

        I was told three times that I hadn’t reviewe’d Meyer’s strongest argument. All three times I found quotemines, lies, and misrepresentationa of science. Summarize the argument for me.

        • Jeff Johnson

          Much of the technical jargon goes over my head. My understanding of that chapter is that proteins and DNA are specific in what they do. B/c they are specific, the amino acids that form proteins as well and genes cannot randomly mutate to form functional proteins or other useful genes. According to the math (Combinatorial Inflation) it’s not possible. Macro evolution hinges on this.

          • SmilodonsRetreat

            If this were true, you might have a point. It still wouldn’t help the ID case because it’s only an argument against evolution… if it were true… which it is not.

            First, you assume that all modern proteins must appear as they are. That’s not true. Every protein in every cell in every organism on Earth has a 4 billion year history. What you expect is Henry Ford to create a modern F1 car. Which is clearly silly.

            Second, genes CAN randomly mutate to form functional proteins and useful genes. This blog has a dozen or more examples of this, straight from peer-reviewed research… that’s why Meyer is either a liar or the worst researcher in history. He ignores all the evidence that goes against what he thinks is true. (Here’s just one example: http://www.skepticink.com/smilodonsretreat/2014/02/06/can-mutation-cause-changes-part-2/)

            Third, specificity is not an argument against evolution (http://www.skepticink.com/smilodonsretreat/2015/02/23/specificity/) because, as that link will show, random protein sequences do not have one and only one protein that can do a specific task. Indeed, the solution space of proteins for a specific task is effectively infinite. Out of a trillion random protein sequences, about 6% of them had the ability to bind with ATP (the energy of the cell). That doesn’t sound like much, but it’s still 60 billion proteins. After evolutionarily looking for high affinity proteins, they found 24 really good candidates in four unique families. So specificity that you and Meyer say exists actually doesn’t, not in the real world.

            Fourth, specificity is wrong in another way as well. You (and all ID proponents) assume that there is one and only one “best” sequence. Here’s why that is incorrect. http://www.skepticink.com/smilodonsretreat/2014/12/29/why-specificity-in-intelligent-design-is-useless/

            Fifth. Macroevolution, at the population level doesn’t exist. Macroevolution is an artifact of the fossil record. Here’s an explanation of that. http://www.skepticink.com/smilodonsretreat/2013/09/16/where-higher-orders-of-life-come-from/

            In short, the argument for specificity is flawed in a number of ways. Anyone one of which is sufficient to kill the idea of ID. And one of which shows how dishonest creationists are.

            • Jeff Johnson

              After reading and rereading, the problem is the improbability of mutation to produce needed new proteins and new proteins are what is needed to change an organism give it new abilities.
              The study that Axe did makes it clear that evolution is not only implausible, it’s impossible.
              From what I saw, the examples you propose only modified existing proteins and did not create anything new. The other example is guess work. Not actual documented observations.

            • SmilodonsRetreat

              Define “Something New” in terms of proteins. How do you determine what “something new” is and why? In detail please.

              Once you realize that there is almost nothing “new” in biology, then you will understand that the beliefs of creationists are wrong. There are almost NEVER massive changes between one generation and the next (I can still think of a few cases). Instead, it is very small changes over a long time frame.

              Axe assumes that an organism must appear, exactly as it is, from a random mix of amino acids and DNA. That is most assuredly not how organisms are formed. Of course it’s nearly impossible to generate a human HBB allele from a random mix of nucleotides. Of course, the modern HBB alleles didn’t come from a random mix of nucleotides did they? They came from the organisms parents, maybe with slight changes. And those came from the parents parents, etc. etc. etc. etc. for billions of years.

              Let me ask you this. What is the explanation? What process produces those new genes? What is the evidence that such a process exists? (evolution can’t do it, is not evidence that any other process can).

            • Jeff Johnson

              Something new is a new organ, or appendage. It’s something that is completely different than anything else that previously existed.
              I’m not talking about massive changes either. What we’re discussing is the basic building blocks, the very beginning of what would cause and show that evolution is possible. In his book, Meyer’s argues mostly about what it would take for Cambrian explosion to have occurred by means of evolution. He demonstrated clearly that the universe has not existed long enough for evolution to have happened even for the Cambrian animals never mind what diversity we have today.

              You mention how the HBB alleles didn’t come from a random mix of nucleotides, but how did arise in the first place? It had to have an origin. And that’s where the difficulty for evolution lies. In explaining origins.

            • SmilodonsRetreat

              Did you read the articles that I wrote about Meyer’s specific claims?

              Turns out he ignored a lot of research that actually describes (in some detail) where those things come from. That’s a scholarly failure of the highest order. Whether he accepts the dozens of papers or not, he still should have referenced them.

              There is no difficultly in explaining origins. I don’t know maybe type “evolution of HBB” into a search engine. This was on the first page: http://perspectivesinmedicine.cshlp.org/content/2/12/a011627.full

              For some reason I’m reminded of Michael Behe (paraphrasing)
              “No one knows how the immune system evolved.”
              “Have you read these 75 papers and 24 books, three of which are titled “evolution of the immune system”?”
              “No, but even if I did, they couldn’t explain it.”


            • Jeff Johnson

              Of course I haven’t had a chance to read everything in the link you referenced but in doing a quick scan I noticed the phrase under figure 2, “inferred gene arrangements in the last common ancestor to jawed vertebrates are diagrammed at the bottom”. The common ancestor is inferred. It’s all guesswork. Educated guesswork but still guesswork.
              Also, there is no description of the origin of the gene.

              Also in the concluding remarks: “Exploration of these genes in many different species continues to illuminate some and challenge other evolutionary models”.
              There is not consensus within the evolution community themselves as to how genes and proteins evolved. So why would I put my believe that the theory?

            • SmilodonsRetreat

              Inferences of design are good enough for Meyer… why not evolution?

              Indeed, if you read actual ID books, they all talk about the INFERENCE OF DESIGN.

              Please explain in detail why that’s OK, but not for science… or admit that it’s just a bias on your part.

              So again, please tell us, in detail, the correct way all these things came about. No inferences allowed, provide evidence.

              Oh, and that’s just one paper… why not look up the subject on your own and see how much there is?

            • Jeff Johnson

              And for good reason. Good science goes where the evidence leads, and the evidence does not lead a reasonable person to believe in evolution.

              I was looking to see if there was a reasoned and logical response to evolution’s problem of Combinatorial Inflation. I have my answer.


            • SmilodonsRetreat

              Yes you do. It’s a shame you don’t accept it like every scientist who understands evolution does.

            • Doc Bill

              Seriously, Jeffy, do you even bother to read the nonsense you write? I didn’t think so. Sadly, this word salad of yours isn’t even mockworthy! Where’s old Rexy when we need him??

              You wrote

              Something new is a new organ, or appendage. It’s something that is completely different than anything else that previously existed. I’m not talking about massive changes either.

              You’re fucking kidding me, right? No massive change, just a new organ or appendage. Since clearly you don’t have a clue about science and particularly evolution and especially chemistry of any kind, what you wrote after that can be totally ignored. You don’t have the first, foggiest clue what Meyer wrote, and the only thing that he “demonstrated clearly” was that he is a shameless liar or as Charles Marshall put it more politely, “Meyer’s work suffers from a systematic failure of scholarship.”

              But, hey, I’m feeling generous so here’s a pop quiz easy enough for you to earn a few points. Consider a polypeptide sequence in a functioning protein that undergoes a point mutation, say, replacing an alanine with a guanine. Is the resulting sequence new? Explain your reasoning.

              Bonus question! Suppose the point mutation described above reduces the efficiency of a catalytic reaction (we’ll assume the protein is an enzyme) by 5%. Is the mutation considered harmful, beneficial, neutral or something else? Explain your reasoning.

              Good luck! I’ll make some popcorn.

            • Doc Bill

              Oh, please, describe in your own words, in one sentence if possible, exactly what Axe did and its significance to the theory of evolution.

              Please. I’ll make some popcorn.

            • Jeff Johnson

              He demonstrated how incredibly high the odds are against folded proteins being able to be formed just by mutations.

            • SmilodonsRetreat

              So you think that proteins don’t fold?

              I’m sorry, your statement makes no sense.

            • Jeff Johnson

              LOL, folded from being randomly sequenced by an evolved gene

            • SmilodonsRetreat

              Do you think folds are somehow random?

              Just out of curiosity, have you read the papers I linked to for you?

            • Doc Bill

              No, that’s not what Axe did. Let me simplify what Axe did. Axe took a dog and tried to evolve it into a cat. The experiment didn’t work (no, duh!) and he declared that evolution was impossible.

              Only instead of a dog and a cat he took to “similar” proteins, proteins from two different families of proteins that had a common ancestor perhaps hundreds of millions of years ago. The experiment didn’t work (for the same “no, duh!” reason) and he declared that evolution was impossible.

              Finally, Jeffy, let me suggest that you take a course or four in statistics, probability and numerical analysis. Then you can come back here and apologize for your shamefully dishonest use of the word “odds.”

      • Doc Bill

        If Chapter 9, Combinatorial Inflation, is (IYO) Meyer’s and ID’s “strongest argument” then clearly ID has no argument whatsoever. First of all, the nonsense about “random assembling of amino acids into proteins” can be dismissed altogether because that’s not how proteins are constructed and evolve, and secondly, it’s not a random process, so the entire “thesis” collapses at that point. There’s no point in continuing because Meyer is simply building on thin air. His basis has no merit therefore his conclusion has no substance.

        Simply put, he’s wrong. Meyer equates coin flipping to chemistry and that analogy simply does not survive the translation. Proteins, for example, can be grouped into similar collections or families and those families have a traceable genetic history. They don’t appear out of thin air – ever. And, yes, ancestral proteins that no longer exist in nature have been synthesized and shown to have the expected response to what an ancestral protein was predicted to do. This is based on genetic analysis and chemistry, not voodoo as Meyer would have you believe.

        Does he discuss that in his book. No. Why? Because he’s trying to pull the alpha-keratin (wool) over your eyes.

        Therefore, (IYO) Meyer’s and ID’s “best” argument is a lie. Well, on that point you have my full agreement!

        • Jeff Johnson

          Do you have a reference for your point about proteins and their responses after being synthesized? What about genes?
          You say that’s not how proteins evolve. Then how do they evolve???

          • Doc Bill

            Seriously, Jeff? Much of the technical jargon goes “over your head” and you’re asking me with a PhD in chemistry to explain it to you? Explain what, Jeff? How far back to I have to go? Freshman college chemistry? Physics? Biochemistry 101? Kinetics? Catalysis? Group theory? Quantum mechanics?

            No, Jeff, I’m not going to play. You have the entire Internet. Get off your lazy butt and figure it out for yourself.

            Or, you can just drink creationist drool. Your choice.

            • Jeff Johnson

              Well that seems like a cop out. I’m not expecting a lesson in quantum mechanics but I think a honest response to chapter 9 is reasonable. Meyer was able to present his argument in a logical easy to understand way. This critic responded to easier points in the book but did not respond to this one. I think I see why.

            • SmilodonsRetreat

              Interesting, I guess you choose ignore my 5 point response… I can see why. It’s totally devastating to Meyer and the ID claim.

            • Jeff Johnson

              No, I’m still researching it. The first link didn’t work so I googled it and I’m still looking it over.

            • SmilodonsRetreat

              The first link is to this very blog… you could just search for the link or ask me to give it to you again.

              OK, I fixed it. It works now.

            • Doc Bill

              Well, no, Jeff, it’s not a cop out at all. You’re the one who’s uneducated, not me. So, when I read the scientific literature, which I do and you don’t, I read the summary, the conclusions and if I’m more interested I’ll read the methods and analysis.

              Therefore, when I, every other biochemist in the world, Google, Wikipedia and every biochemistry textbook ever written tell you that proteins don’t form random assemblages like some kind of pop-bead toy, you can take that to the bank as true knowledge.

              And when a creationist propagandist and documented prevaricator like Meyer is called out for his documented lies, misrepresentation and non-scientific gobbldy-gook by those same people aboe, you can take that to the bank as true knowledge, too.

              Let me simplify this for you even more. What Meyer is proposing is that proteins form by waving a wand (ash with a strand of unicorn hair) while incanting, “Accio polypeptides!” Does one really need to explain why that is wrong? Does one really need to document that the “Accio” spell was created by a fiction author named JK Rowling? I should think not.

              So, don’t give me that cop out nonsense. Learn some science then come back here and we’ll have a nice discussion.

            • RexTugwell

              So tell us Bag Man, what did you do as a biochemist while working in the oil industry for 30 years?

            • Doc Bill

              Proprietary. Go fish.

            • RexTugwell

              Just as I thought. Thanks. An office pool has been started to see what you’ll be next. The options are an astronaut, a cowboy or a choo-choo train engineer.

            • Doc Bill

              Well, I’m coo-koo for Cocco Pops. Does that count?

        • Jeff Johnson

          Yes it IS a random process as dictated by the evolution theory. LOL
          Natural selection does not work until there is a functional protein and even then would most likely be harmful to most sequences b/c they are less fit.

          • SmilodonsRetreat

            Time to put away that old myth that most mutations are harmful. It’s not true, it’s never been true.


          • Doc Bill

            That makes no sense, Jeffy. You still don’t understand what Meyer wrote. Do you even have the book?? The only thing that is “LOL” is that first badly wrong sentence you wrote. “Evolution theory” doesn’t dictate anything. That’s just stupid, Jeff.

            Secondly, the only thing (well, for the most part, but to keep it simple …) that is “random” is the location and nature of the nucleic acid substitution (or perhaps “change” is a better word) leading to a different peptide sequence. All that is simplified further by the phrase “random mutation.” Generally put, natural selection operates on random mutation. Whether or not it operates on a “functional protein” is irrelevant. It doesn’t matter, so your statement is just plain wrong. Looks like you didn’t get the last LOL after all!

      • Doc Bill

        I see that Jeffy has flounced. Not a surprise since his ignorance was becoming embarrassing for him and his arguments dissolved into “LOL’s.” It is the mark of the defeated creationist when they start arguing LOL as if they had a clue.

        Who knows? Maybe Jeffy will get a clue, but I doubt it.

        • Jeff Johnson

          So Doc Bill and SmilodonsRetreat, what do you guys think of the convention at the Royal Society in London last year on November 7-9???
          Link in case you missed it…

          • SmilodonsRetreat

            Well, none of the talks discredit evolution in any way, if that’s what you’re wondering.

            It is interesting that a couple of talks are about information contained in DNA, but in an actual robust manner that includes all relevant factors (unlike what ID describes).

            I haven’t listened to all the talks, but they all seem relatively straightforward. Certainly nothing earth shattering.