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Posted by on Jul 20, 2013 in Book Review, Creationism, Evolution, Genetics, Research, Science | 31 comments

Darwin’s Doubt -Prologue – Part I

So begins our epic journey through a book. I may not be the best person to undertake this journey, but then the author probably wasn’t the best person to write this book either.

Why do I say that? This book is about “The explosive origin of animal life and the case for intelligent design”. Stephen C Meyer is one of the founders of the Discovery Institute’s Center for Science and Culture. He is currently the director of said center and a ‘senior fellow’ at the Discovery Institute.

He has a bachelor’s degree in earth science and physics and a Ph.D. In history and philosophy of science. He has written 5 books (including Darwin’s Doubt) on the subject of intelligent design, but has not written (as much as my research allows) any peer-reviewed articles on any subject.

Please note that Meyer had one paper published. That paper was subsequently retracted by the journal, because it did not meet their standards, it was not peer-reviewed, and it was on a subject that was not relevant to the journal. You can look that up more here.

So what about Darwin’s Doubt?

Our story opens with a brief mention of Watson and Crick who “first illuminated the chemical structure and information bearing properties of DNA”.  And right there, on page one, we have a problem. Now, I freely admit that I am hyper sensitive to this book and may be biased.

So, with that being said, I’ll point out that Watson and Crick did not “illuminate” the structure of DNA. That work was actually done by Rosalind Franklin. She was the one who actually created the images (via X-Ray diffraction) that Watson and Crick used to formulate the hypothesis about the structure of DNA.

While the nucleotide pairing structure of DNA was developed in the 50s (as stated by Meyer), the actual knowledge of how DNA transfer information to ribozomes (via nucleic acid triples) wasn’t discovered until the 60s.

My problem isn’t so much that Meyer got it wrong, most people get it wrong. Almost no one outside of molecular biology circles knows about Rosalind Franklin. But Meyer should know about her. To me, this continues the shoddy research that Meyer had major problems with in Signature in the Cell.

But we continue.

On page two (of the Kindle edition) I see another concern. Meyer has apparently ignored the entire scope of evolutionary developmental biology. He says:

Scientists now know that building a living organism requires information, and building a fundamentally new form of life from a simpler form requires an immense amount of new information. Thus, wherever the fossil record testifies to the origin of a completely new form of animal life – a pulse of biological innovation – it also testifies to a significant increase in the information content of the biosphere.

(emphasis in original)

This is a major claim. Indeed, this is the fundamental premise on which intelligent design is based. And there’s not a single citation to support this claim. Nothing. When he says “scientists”, I’m assuming here that he means more than fellow ID proponents Michael Behe, Douglas Axe, and Ann Gauger.

Let me be perfectly clear, I don’t buy this claim. I think he’s wrong. The scientific field of evo-devo (evolutionary developmental biology) is the reason why. This field shows us that simple changes to an organism’s genome can result in massive changes to the organism itself. I would recommend Endless Forms Most Beautiful: The New Science of Evo Devo by Sean Carroll as an introduction to evo-devo.

Indeed, when looking at the variety of life, we don’t see these massive changes to the genome that we would expect. To quote Gerhart and Kirschner Cells, Embryos and Evolution

where we most expect to find variation, we find conservation, a lack of change

What developmental biologists have found is that it’s not so much massive changes to the genome that creates diversity, but small changes to the regulation of genes.

For example, in this paper Sean Carroll shows that to go from the wild Mexican grass teosinte to maize (image below) is not a change in gene function (specifically the tb1 gene), but a change in how that gene is turned on and off.

CELL1162.f2.4C

Selection for Plant Morphology Acts upon Variation in Developmental Gene RegulationThe domestication of maize (right) from teosinte (left) selected for ear and plant morphology. Genetic analyses have revealed that selection acted upon regulatory elements of the tb1 gene. (Photos courtesy John Doebley.)

 

It really is that simple. And here’s where the problem with intelligent design’s application to biology is most prevalent.

DNA is not just an information storage system. It is an active part of the control of the genes. Even when a new organism is only a collection of 16 cells, the DNA begins to regulate each cell differently. One cell begins to produce a certain hormone. Every cell in the organism will respond in a very specific way. The cell that produced that hormone becomes the front of the organism. The cells that receive the least amount of the hormone become the tail.

Different genes are turned on or off at different times of the organism’s development based on these hormonal signals. A genetic mutation (as in the maize above) not in the gene that controls seed production, but in the gene that controls the gene for seed production results in a wildly different structure.

This is the most fundamental misunderstanding that ID proponents have. It is a critical flaw in their notions. Basically, their notions don’t match with reality.

Now, I’ve gone on for bit and we’re on 60 or 12,555 of the Kindle edition of Darwin’s Doubt.

This is going to be a long slog.

 

  • RexTugwell

    A long slog this will be indeed … for me, if only to keep you honest in your “reviews” of the book. Dr. Meyer doesn’t deserve this kind of treatment. It’s one thing to disagree with an idea, even adamantly. It’s another matter to be so opposed to it that you’re willing to be blinded by even the simplest facts and end up looking like a fool. It’s becoming increasingly clear that atheists must suffer from some kind of inferiority complex. How else to explain their constant attempts to ruin the reputations of good people while at the same time showing the world that they themselves deserve no respect but only pity?

    I have to agree with you that you may not be the best person to undertake this journey. It’s best left to persons willing to avail themselves of ALL the facts. I’m afraid the only shoddy research around here is your own. “Facts” regarding Meyer only merit a quick lookup on Wikipedia while to support your own position, you refer to sciencedirect.com. Let’s start with Rosalind Franklin. First, you need to be quoted in full:

    “My problem isn’t so much that Meyer got it wrong, most people get it wrong. Almost no one outside of molecular biology circles knows about Rosalind Franklin. But Meyer should know about her. To me, this continues the shoddy research that Meyer had major problems with in Signature in the Cell.”

    I thought you said you read Signature in the Cell. In SITC, Dr. Meyer tells the story of the time leading up to the discovery of the structure of DNA. In that account, along with Watson and Crick, Rosalind Franklin is an major character across 10 pages in the story. Meyer is clear that she was essential in the discovery due to her X-ray imaging of DNA as well as her molecular knowledge – especially with respect to the properties of DNA in the presence or absence of water. Meyer is correct that Watson and Crick “first illuminated the chemical structure” of DNA because while Franklin created the X-ray images of DNA, she did not believe the molecule to be helical. Watson and Crick did.

    As for the Meyer / Sternberg episode, that’s covered later in the book; if you get that far. I won’t include a spoiler here. The rest of your piece prematurely criticizes the book’s treatment of evo-devo as well as other theories and fields that try to explain new body plans and phyla. Be advised, Meyer’s research for the book is thorough and he’s anticipated the objections you’re likely to come up with. Your observation that changes in an organism is controlled by changes in how a gene is turned on and off is a major thesis of the book and is mainly covered in chapter 14 – The Epigenetic Revolution. This chapter, curiously enough, was NOT covered in Nick Matzke’s “review”. We’ll see whose notions don’t match reality.

    • SmilodonsRetreat

      We’ll see.

      Isn’t it interesting that I, at least, admit that I may be biased, but Meyer never does, when he most assuredly is biased. Oh well. Doesn’t much matter.

      Until Meyer and the others actually do some research and until they develop a comprehensive, testable hypothesis, then ID is still dead in the water. This blog report isn’t a comprehensive take-down of ID. There’s nothing to take down. ID is meaningless.

      This book, so far, is just a whine that evolution can’t explain something. It’s not positive supporting evidence of ID. So far… that may change.

      But you know what. In the 15 years that I’ve been following the ID story line, they still haven’t done anything to support their own work. And they never will. ID is a socio-political philosophy. That’s all. And you and others have bought in to it hook-line-and-sinker. Why? I don’t know. I have my suspicions though.

      • RexTugwell

        I’d love to hear your suspicions of why I drink the ID Kool Aid.

        • Viktor Shakapopolous

          So, you’ve admitted to drinking the Kool aid. That is a start.

    • Hrafn

      It is hilarious to see Rexie put scare quotes around Matzke’s review. This review has sent the ID echo chamber into a complete tizzy, and has led them to dispatch their two star supercilious scientifically-illiterate talking heads, the Two Daves of the Apocalypse, David ‘the self-confessed crank’ Berlinski and David “The Kingdom of Priests” Klinghoffer to sneer at it.

      Their ignorant sneers simply puts greater focus on the fact that Matzke, unlike Meyer and his Boy Blunder research assistant Casey Luskin, is an actual scientist, and actually working in a relevant field (Evolutionary Biology).

      May I return the compliment and put scare quotes around Meyer’s (and ID’s) “science”, his “information” claims, his “credibility”, and the “accuracy” of his reporting of the state of scientific research.

  • Wayne Robinson

    I agree with your comment about Meyer’s assertion of the Cambrian involving a large injection of new genetic information. No reference to back up the assertion. Although, Meyer’s use of references is highly suspect, with a link to an endnote, giving ‘author, article name, pages’ – and then you have to hunt through the bibliography to find the source, which you have to do, because Meyer often gets his references wrong.

    It’s part of the reason why he later gets ENCODE wrong, claiming that it showed that at least 80% of the human genome is ‘functional’ whereas it was 20-80% – wanting there to be little junk DNA in all species.

    The large injection of new genetic information comes from his assertion that a single cell eukaryote had a genome size of around 1 million base pairs. And a typical metazoan such as a fruit fly such as Drosophila melanogaster has one of 140 million base pairs.

    What does Meyer think happened? The Cambrian explosion involved single celled organisms going to metazoans in less than 6 million years?

    He also asserts that the development of a gut involves the simultaneous development of digestive enzymes, such as lipases and proteinases. Bacteria had done that billions of years earlier.

    In another place he claims that evolutionists can’t explain the origin of eukaryotes by ‘random mutation and natural selection’. He’s right. They don’t. Eukaryotes arose from a symbiotic fusion of a eubacterium and an Archaea bacterium about 2 billion years ago.

    • SmilodonsRetreat

      That’s one of the things I’m going to try to do as I read through this book. Actually find the references and read them to find out what they said and what Meyer said they said. Very often, the two aren’t even close.

  • Guest

    Why do you state that Meyer’s paper was not peer reviewed, doesn’t that mis-represent the wikipedia article you reference? It appears that the paper had been peer reviewed and approved for publication.

    That
    paper was subsequently retracted by the journal, because it did not
    meet their standards, it was not peer-reviewed, and it was on a subject
    that was not relevant to the journal. – See more at:
    http://www.skepticink.com/smilodonsretreat/2013/07/20/darwins-doubt-prologue-part-i/#sthash.iUvrVKBF.dpuf
    That
    paper was subsequently retracted by the journal, because it did not
    meet their standards, it was not peer-reviewed, and it was on a subject
    that was not relevant to the journal. – See more at:
    http://www.skepticink.com/smilodonsretreat/2013/07/20/darwins-doubt-prologue-part-i/#sthash.iUvrVKBF.dpuf
    That
    paper was subsequently retracted by the journal, because it did not
    meet their standards, it was not peer-reviewed, and it was on a subject
    that was not relevant to the journal. – See more at:
    http://www.skepticink.com/smilodonsretreat/2013/07/20/darwins-doubt-prologue-part-i/#sthash.iUvrVKBF.dpuf
    Please
    note that Meyer had one paper published. That paper was subsequently
    retracted by the journal, because it did not meet their standards, it
    was not peer-reviewed, and it was on a subject that was not relevant to
    the journal. – See more at:
    http://www.skepticink.com/smilodonsretreat/2013/07/20/darwins-doubt-prologue-part-i/#sthash.iUvrVKBF.dpuf

    • SmilodonsRetreat

      The only “reviewer” of the paper was Sternberg. No one knows what his review process was.

      A normal peer-review process involves several experts in the field and not only the editor of the journal.

      So, Sternberg who was the person who both sent papers out for review AND made publishing decisions was the only person involved with Meyer’s paper. That’s not a peer-review… that’s one creationist helping another creationist by publishing a paper that would never be accepted without that help.

      • Martin Lewitt

        What you describe is different than a statement that the paper wasn’t peer reviewed. Why weren’t you satisfied with just a supportable statement that the paper was retracted. Many papers are published that never should have been published. It is quite common in climate science for papers reporting climate model results to have no discussion of the diagnostic literature for the models and the implications for the the error ranges of the models. What is unusual in the Meyers case is not that it should have been retracted, but that it was retracted.

        • SmilodonsRetreat

          Who were the peer-reviewers?

          • Martin Lewitt

            They are anonymous, who were the reviewers for other papers in that journal? What evidence is there that papers in the journal that have not been retracted have been subjected to any more thorough review. Laziness can easily explain the lapse that let this paper through. I just find it strange that you aren’t careful to avoid the criticism of misrepresenting a source that you are intent on pinning on Meyer if you can.

          • SmilodonsRetreat

            So you have no clue if this paper was properly peer-reviewed or not. Thanks. I note that the Proceedings publishes it’s list of reviewers each year… except for 2004, the year this incident happened

            Again, the paper was “reviewed” by the editor (which is not done). This is what Sternberg said. Meyer’s paper was on the Cambrian fossils. A subject the Sternberg does not have relevant degrees in (yes, for peer-review purposes, this is important) and other members of the society did have proper credentials.

            Sternberg ignored proper procedure and made a mockery of the peer-review process. You say it was actually “peer-reviewed”, am I understanding you correctly?

            I am curious.. who was “lazy” in this case? The only person who saw Meyer’s paper was Sternberg. Sternberg is a creationist, as is Meyer. That is the only reason the paper was published. ID proponents have been trying to get a paper published for years. Instead of doing actual science, Meyer writes a “review paper” with no new information, just a new conclusion drawn from someone else’s work and his buddy, Sternberg, publishes it as his last act with the Proceedings.

            Argue as you will, Sternberg said that he “peer-reviewed” it and he doesn’t have the proper qualifications to do so. There is no evidence that others reviewed the paper… unlike other papers, anonymous reviewers or not.

          • Martin Lewitt

            I would be surprised if it was properly reviewed. Probably most peer reviewers are lazy judging by how many errors I find in published papers, especially when I check the supposed sources. It is really common when there are several authors, people seem to assume the papers were internally peer reviewed.

            However, having made my point, I’d like to suggest that if you are going to claim that Meyer’s is misrepresenting a source, that in all fairness, you should realize there is a difference between disagreeing with an authors results and disagreeing with an authors interpretation of those results. An author is entitled to well founded results but doesn’t get to control the interpretation. A usuful guide would be the discussion section where the authors are given some leeway. Claims in that section are not part of the results.

          • SmilodonsRetreat

            What are you talking about?

            I’ve shown that Meyer is misrepresenting sources. If he says that an author said x and the author really says not-x, then it’s not a “different conclusion”, it’s a misrepresentation.

            Meyer is free to draw “his” conclusion, but he’s not free to change other’s conclusions. And he does. We’ll see, keep reading.

  • Martin Lewitt

    Why did you claim that Meyer’s paper was not peer reviewed, when the wikipedia article you reference describes a much more complex situation, including evidence that it had been peer reviewed, and statements from a critic just doubting that the reviewers were scientists in the field, implicitly accepting that there might have been reviewers?

  • Martin Lewitt

    You might have brought up the evolvability of life enabled by robustness, developmental homeostasis and internal homeostasis. A gene modification that results in a longer leg bone for instance does not have to wait for or coincide with genes for longer blood vessels or muscles and tendons. Essentially, life evolved evolvability and amazing coincidences or networks of new genes, were not needed.

  • ReasonableDoubt

    I navigated here because some guy over at Pandas’ thumb sold this series of reviews as the “most ambitious effort” to slice and dice that poor fool Meyer. And since I would actually love to read a thoughful, well reasoned critique of Meyer’s work, I thought I would check it out. (Full disclosure: I actually agree with the poor fool, but I also like to understand the best arguments of both sides of an issue.)
    As usual, the reviewer’s attempt to illuminate Meyer as a fool actually ends up reflecting only the reviewer’s lack of understanding. (I am sure that the reviewer will now object that he, in fact, did not attempt to shine light of any wavelength whatsoever on any part of Meyer’s person. “Indeed, I have never even met Meyer! Aha!” <— Reviewer being overly literal. See paragraph 7 of the review.)
    Without too much delay, the reviewer turns his flashlight of truth from the irrelevant to the relevant, focusing the beam on Meyer's unremarkable assertion that significant increase in biological diversity involves significant increase in information. The reviewer doesn't think this is true. The "simple" explanation, says the reviewer, is that "DNA is not just an information storage system. It is an active part of the control of genes," which is apparently something that IDiots are just too blissfuly unware of. First of all, is the reviewer actually ignorant enough to believe that Meyer doesn't know that DNA actively participates in the control of genes? Or is this just a smear of Meyer? That's an honest question. It really could be either.
    Secondly, how does the fact that DNA is not "just an information storage device" answer Meyer's assertion? The only idea that the reviewer seems to be supporting (whether he knows it or not) is the idea that DNA stores information in a more complicated way than simple digital code. In other words, there's more information stored in DNA than might be apparent if viewed as a simple digital code. (Okay. Noted. Uhhh. And?) And, apparently, all you need to do to evolve a duck is to turn off the fish genes and turn on the duck genes. (Ohhh, so that's how it works!) The reviewer seems to be trying to counter Meyer's argument that increased diversity conincides with increased information by asserting that, in fact, … (drum roll please) … the information was already there from the beginning! Whoa, ID totally refuted, dude! I mean if the information was already there … then that … wait. Say that again?
    Its galling to be ridiculed by a fool.

    • SmilodonsRetreat

      Yes it is.

      First of all, is the reviewer actually ignorant enough to believe that Meyer doesn’t know that DNA actively participates in the control of genes? Or is this just a smear of Meyer? That’s an honest question. It really could be either.

      Honest answer, I think that Meyer does know this and he’s hoping that all his readers don’t know it. He’s a con man. He says sciency things that support a certain point of view (that of creationism) and he knows that those with a built in boas towards creationism will use him as a source. Meyer, unfortunately, does not use all of the available material and quotemines other pieces of material to create a misleading view of science.

      It does not require an immense amount of information to generate a new form of life. It requires very little change to generate a speciation event. We see it all the time. And yes, speciation events NOW are what will become larger groups in the future.

      Meyer, BTW, did not say “diversity” as you did. He said “a fundamentally new form of life from a simpler form requires an immense amount of new information.” Now, what is a “fundamentally new” form of life? Is it a new species? Again, we know that happens. Is it a new genus? What is a new genus. but a group of closely related species? What about a new family? That’s nothing more than a group of closely related genera. Etc. etc. Given time, it’s inevitable… no intelligence required.

      As far as the duck/fish thing. I know you aren’t that dumb and that it is strawman argument. I didn’t say it. I didn’t imply it. And I know it’s not true. If you need to explain why I’ll be happy to.

      • ReasonableDoubt

        I just knew that you were going to get defensive about the duck/fish thing. It was not a strawman argument. I know you didn’t say, think, or imply it. And nobody reading what I wrote, besides an Asbergers patient, would have thought that I was implying that you believed it. IT WAS SARCASM. So yeah, I’ll pass on the explanation of why you don’t believe what I never said you believe.

        • SmilodonsRetreat

          Then why bring it up?

          If you have comments that can help, then be plain about them. If you have criticism, then be plain about. Sarcasm doesn’t translate well in text, especially when no one knows you.

      • ReasonableDoubt

        Furthermore, if Meyer is try to hide the fact that DNA participates in the control of genes, it’s odd that he would talk about it so damn much!

        • SmilodonsRetreat

          Well, if SitC is any indication, he either doesn’t understand it or he is just trying to confuse the issue. We’ll see… I’m only on chapter 2.

  • Eerik Salke

    Even if genes are more than just information, this still doesn’t explain how evolution has taken a single celled creature with a small genome to something more complex like human beings who have a significantly larger genome. At some stage evolution must account for the very existence and development of new genetic information, regardless of how it behaves. Meyer probably didn’t feel the need to go into details about dna functionality because it still doesn’t provide an answer to the vore problem, how did it get here and how is new genetic information made? Evolution has no answers for these questions.

    • SmilodonsRetreat

      You might want to skip to the section in Chapter 11.

      Meyer ignores about 120 papers that actually deal with this. I’m not going to describe them all, but there will enough to show that “information” (which curiously enough Meyer never defines) can be created by known genetic processes.

      What’s more is that this information has been known for well over 11 years now. I would encourage you to read actual science instead of creationist books and websites.

      • Eerik Salke

        Your review of chapter 11 doesn’t currently address the new genetic information dilemma, will it come later? If not, I assume that these ’120 papers’ cover something more than mutations and doubling? Even transplated virus DNA, transposons and pseudo genes ultimately don’t explain how no genome at all became a massive genome.

        • SmilodonsRetreat

          Yes it’s coming.

          Let me ask this. Why DOESN’T gene duplication and mutation create new information?

          Do you know what the smallest RNA with a metabolic function is?

          • Eerik Salke

            Why doesn’t it? It kind of feels a little like this might be one of those ‘you don’t have enough imagination’ to believe in evolution moments? Because mutations & duplications have two limits 1) they both require an existing genome to work with 2) even with an existing genome they can only copy and / or degrade it. Unless there actually is proof out that shows these processes creating actual fresh new DNA? Which I’ve never seen. Even RNA, as far as I understand it, only works with pre existing DNA, which it can regulate & edit, but which its never been shown to actually create.

          • SmilodonsRetreat

            As I said, that “actual proof” that you’ve never seen is in some 100+ papers that I’m reading right now.

            It’s been shown, in dozens of experiments that changes to the genome both increase the amount of information in the genome and can change the effects of the genome.

            You haven’t seen these because you aren’t looking for them. A duplication is a NEW gene. It may be the same as the old gene, but then mutations kick in. I’ve written at least two articles linking to peer-reviewed work that describes this.

            In fact, as we see the VAST majority of mutations are neutral and do not affect the gene at all. Again, I’ve written about this a few times.

          • Eerik Salke

            The difference between manipulating pre existing DNA, even when RNA is doing it, and creating actual fresh new DNA is a BIG difference. But, evolution absolutely requires the latter.

          • SmilodonsRetreat

            No doubt about it. And we see that.

            Again, I want you to supply the MECHANISM that prevents DNA from changing. You’ve already admitted that duplication happen. That’s a simple fact.

            You can find hundreds of examples of positive mutations (as well as negative mutations) in the literature… if you look. Those are facts.

            Combine the two and you get that exact thing that you think cannot happen.

            Indeed, look at the article I wrote about color blindness. We see the full spectrum of colors because of exactly a duplication of an opsin gene followed by mutations that changed the wavelength the opsin is sensitive too.

            That is exactly the thing that you say is impossible. It would be funny if it weren’t so sad.