Shapiro’s anti-Darwinian book gets panned

By way of introducing today’s post, I’ll put above the fold a comment I got last night from a reader:

themayan commented on Jim Shapiro continues his misguided attack on neo-Darwinism

Lets stop the BS! The Neo-Darwinian synthesis/ the modern synthesis is dead and has been dead for a long time. It’s an out dated theory which has which has ran its course and found lacking in light of 21st century data. He are holding up a rotting corpse of a theory which is reminiscent of the movie A Weekend at Bernies. I say hooray for Shapiro and other dissenters who are stirring the waters and forcing people to either put up or shut up, or unfortunately in Coynes case, attack the messenger. I’m with Suzan Mazur on this one when she broke the story on the Altenberg 16 summit a few years ago and when she asked the question “Will the Real Theory of Evolution Please Stand up?”

Why are comments like this invariably accompanied by bad spelling, grammar and punctuation?  More important, they’re never accompanied by evidence.  Why, exactly, is neo-Darwinism dead? What is wrong with the idea that randomly produced genetic variation, fuelling the processes of natural selection and genetic drift, is responsible for both the diversity of life and (in the case of natural selection) the remarkable “design” of creatures that used to be imputed to God? (Suzan Mazur, by the way, is a gonzo journalist who has spent an unsuccessful career trying to attack neo-Darwinism on obscure websites. You can find one example here.)

At any rate, this is germane to the discussion we’ve been having about biologist James Shapiro’s attacks on neo-Darwinism in HuffPo (Shapiro works here at the University of Chicago). In February I did a post on Shapiro’s new book, Evolution: A View from the 21st Century. I didn’t read the book, but simply criticized a HuffPo piece that Shapiro wrote summarizing his thesis, which was that modern discoveries about cell biology showed that two tenets of modern evolutionary theory—gradualism and the efficacy of natural selection as the cause of adaptive “design”—were wrong. He responded in a comment on my website, and also in a defensive column at HuffPo. Yesterday I pointed out what was wrong with Shapiro’s response.

Now Anthony M. Dean, who works on the molecular evolution of microbes at the University of Minnesota, has bitten the bullet, read Shapiro’s book, and reviewed it in the latest issue of Microbe. I admit to a frisson of pleasure in seeing that Dean’s critique of Shapiro is nearly identical to mine, and in noting that, unlike Shapiro, Dean doesn’t see the edifice of modern evolutionary theory as about to crumble. I excerpt Dean’s take on Shapiro’s anti-Darwinian claims, which may be of interest mainly to readers who study evolution:

It is one thing to establish that certain cellular subsystems do not conform to received dogma. It is quite another to establish that a paradigm shift in thinking is necessary. Every evolutionary biologist knows the field is littered with the corpses of those who once heralded the arrival of the next Kuhnian Messiah. At the end of Part II Shapiro too has failed to convince that the many fascinating molecular phenomena he describes requires a wholesale jettisoning of Darwinian doctrine. Indeed, throwing out basic Darwinian principles (random mutation, heritable variation, and the sieve of natural selection) would seem folly, as they surely predate the evolution of such highly evolved nonconformist subsystems as CRISPR-Cas.

In Part III Shapiro seriously overreaches. He argues that horizontal gene transfer, symbiogenesis, whole genome doubling, and the modular and duplicative nature of protein evolution are non-Darwinian because they do not conform to strict vertical inheritance and Darwin’s advocacy of “numerous, successive, slight variations.” Shapiro asserts “The data are overwhelmingly in favor of the saltationist school that postulated major genomic changes at key moments in evolution . . . Only by restricting their analyses to certain classes of genomic DNA, such as homologous protein coding sequences, can conventional evolutionists apply their gradualist models.”

His stance is patently unfair. Thomas Huxley famously criticized Darwin for championing too gradualist a view of phenotypic evolution. Today’s Darwinists accept Huxley’s criticism. Many evolutionary studies focus on gradually evolving homologous coding sequences precisely because these are best for establishing phylogenetic relationships among species-a matter of some importance to biologists. Horizontal gene transfer, symbiotic genome fusions, massive genome restructuring (to remarkably little phenotypic effect in day lilies and muntjac deer), and dramatic phenotypic changes based on only a few amino acid replacements are just some of the supposedly non-Darwinian phenomena routinely studied by Darwinists. Shapiro’s implication that gene duplication and functional divergence is somehow non-Darwinian is also wrong. New uses for old parts has long been a staple of the Darwinian diet. In a spectacular example of cognitive dissonance Shapiro first describes, with fanfare, how Woese identified the Archaea as a distinct group of prokaryotes using phylogenetic analyses of rRNA sequences-analyses that assume “the slow accumulation of random gradual changes transmitted by restricted patterns of vertical descent”—only to later assert that “The DNA record definitely does not support the slow accumulation of random gradual changes transmitted by restricted patterns of vertical descent.”

If, as Shapiro argued in his HuffPo response, I “misunderstood [his] point completely,” then I guess Dean did, too.  My rule is that when two or more biologists independently tell you the same problem with your idea or experiment, you should pay more than twice the attention that you do to a single critic.

h/t: Eli

27 Comments

  1. Chris aka Happy Cat
    Posted April 8, 2012 at 5:37 am | Permalink

    Jerry,

    Seems like, among other laymen at least, the “Neo-Darwinism is dead” meme is itself alive and well. I’ve encountered it in the NY Times comments and in places like Youtube. The impression I come away with is people believing this are uncomfortable with science not having 100% of the answers. The unanswered questions and new discoveries seem to gnaw at some people’s insecurities.

    When respected director Ridley Scott touts his eagerly awaited film by spouting this bit of word salad it gives me a sad. First hominids? (no) Atlantis?(no) Earth one billion years old? (wtf?)

    • Torbjörn Larsson, OM
      Posted April 8, 2012 at 7:00 am | Permalink

      Ouch! Stargate poked around all that, but they had fun with it. And had some hard scifi science interested actors grounding it.

      If he were Cameron, I would say Scott’s grounding seems to be found at the bottom of the Challenger deep. Now I have to settle with somewhere between Legends and Gladiator.

    • Chris
      Posted April 9, 2012 at 7:11 am | Permalink

      The film is unfortunately inspired by von Daniken’s ‘Chariots of the Gods’, according to Scott (at least in its mythology, which the Alien series has in any case already explored).

  2. Matt G
    Posted April 8, 2012 at 5:38 am | Permalink

    Wow, talk about a straw man. It’s kind of like saying that because people enter houses through doors, the burglar can’t actually be in the house because he came in through the window. What a rigid mind Shapiro has that he can’t see that other mechanisms fit in quite reasonably (and are supported by evidence!). He’s like George Bush – he doesn’t do nuance.

    So what is his game? Is he an IDiot?

    • BillyJoe
      Posted April 8, 2012 at 11:21 pm | Permalink

      He’s a microbiologist but not an evolutionary biologist. That is his basic problem.

  3. Pete Moulton
    Posted April 8, 2012 at 5:43 am | Permalink

    “Why are comments like this invariably accompanied by bad spelling, grammar and punctuation?”

    Ummm…could it be because they’re invariably accompanied by monumental ignorance?

  4. Grania Spingies
    Posted April 8, 2012 at 5:50 am | Permalink

    Attack the messenger?

    A long piece that lists the problems with Shapiro’s arguments is not attacking the messenger, Mr “themayan” Dude.

  5. Torbjörn Larsson, OM
    Posted April 8, 2012 at 6:52 am | Permalink

    I’ll add that a neo-creationist synthesis of Happy Cat and Grania Spinges observations would be that there is no verified message here but an unsubstantiated meme.

    the field is littered with the corpses of those who once heralded the arrival of the next Kuhnian Messiah.

    No!? Does that mean that philosophers of science can be wrong (as there seems to be evidence)? Does that mean they can possibly be harmful to other fields like science (though I doubt that we can find evidence either way)?

    As they say among atheists on Easter: “good luck!”

  6. Barbara
    Posted April 8, 2012 at 7:08 am | Permalink

    Here’s the link to Dean’s review, well summarized by the extensive quote in the present post.

    http://www.microbemagazine.org/index.php/02-2012-reviews/4664-evolution-a-view-from-the-21st-century

    • whyevolutionistrue
      Posted April 8, 2012 at 7:17 am | Permalink

      I added that link, thanks.

  7. John Harshman
    Posted April 8, 2012 at 7:11 am | Permalink

    Let me take issue with Dean on a peripheral point:

    Many evolutionary studies focus on gradually evolving homologous coding sequences precisely because these are best for establishing phylogenetic relationships among species-a matter of some importance to biologists.

    Not true. The perfect character for phylogenetic analysis is one that changes at the one time you’re interested in and never thereafter. We’ve recognized for some time that rare events like retroviral or transposon insertions are great for phylogenetics. We just look at ordinary sequence change because such sequences are easy to find and compare, while rare events aren’t as easy, precisely because they’re rare. (And of course because the data have many other uses than just phylogenetics.)

    Say, can anyone count how many times neodarwinism has died in the past 50 years alone? I can think of Gould’s famous declaration, but how many more?

    • SnowyOwl
      Posted April 8, 2012 at 7:38 am | Permalink

      “Say, can anyone count how many times neodarwinism has died in the past 50 years alone? I can think of Gould’s famous declaration, but how many more?”

      By my calculus, about as many times as Apple was reported to be going out of business!

    • Posted April 8, 2012 at 3:36 pm | Permalink

      “Neo-Darwinism is dead! Long live Neo-Darwinism!”

      /@

  8. Jim Jones
    Posted April 8, 2012 at 8:30 am | Permalink

    “Why are comments like this invariably accompanied by bad spelling and punctuation?”

    Because they are written by people who ‘believe’ that “Obama is a Muslim” (code for “Shriek: a negro”).

    • ploubere
      Posted April 8, 2012 at 7:28 pm | Permalink

      Along that line, here’s a chilling video. It’s long, but watch just the first 10 minutes:

      • Brygida Berse
        Posted April 9, 2012 at 7:34 am | Permalink

        It’s long, but watch just the first 10 minutes

        I watched the whole thing. Thank you for posting, it was quite enlightening, in a sad way. Living in Massachusetts one takes so many things for granted; it’s easy to forget the realities of the American South.

  9. Tim
    Posted April 8, 2012 at 9:26 am | Permalink

    The comments accompanied by bad spelling and bad grammar are also highly correlated with Dunning-Krugeritis. In science, the topics are among the ‘usual suspects': evolution, climate change, vaccinations, etc. Rarely does one find foaming-at-mouth denunciations of semiconductor physics, organic synthesis, or surface science by morons who have never written a scientific paper in their lives.

    • HaggisForBrains
      Posted April 8, 2012 at 10:26 am | Permalink

      +1

  10. MadScientist
    Posted April 8, 2012 at 2:59 pm | Permalink

    Is it just me or is Shapiro channeling Margulis?

    • BillyJoe
      Posted April 8, 2012 at 11:26 pm | Permalink

      They were like the magnetic and electric components of an electromagnetic wave, each propagationg the other to infinity and beyond.
      Of course, now Margulis is beyond.

  11. BillyJoe
    Posted April 8, 2012 at 11:27 pm | Permalink

    …so Shapiro can’t be far behind!

  12. stevehayes13
    Posted April 9, 2012 at 2:03 am | Permalink

    ‘Why are comments like this invariably accompanied by bad spelling, grammar and punctuation? More important, they’re never accompanied by evidence.’

    Dunning-Kruger effect?

  13. Posted April 9, 2012 at 12:43 pm | Permalink

    Gould statement (1980) is, “… if Mayr’s characterization of the synthetic theory is accurate, then that theory, as a general proposition, is effectively dead, despite its persistence as textbook orthodoxy.”

    The correctness of his statement depends on how Ernst Mayr describes the Modern Synthesis (synthetic theory). Here’s what Mayr said in 1963. (Remember that Mayr is one of the authors of the Modern Synthesis.)

    The proponents of the synthetic theory maintain that all evolution is due to the accumulation of small genetic changes, guided by natural selection, and that transspecific evolution is nothing but an extrapolation and magnification of the events that take place within populations and species.

    There’s no doubt in my mind that this was an accurate representation of the Modern Synthesis in the 1960s and it’s still how most people see it today. This definition of evolution is what we call “Darwinism” or “neo-Darwinism.”

    Gould says that it is effectively dead because modern evolutionary theory needs to include random genetic drift—something that had been purged from the Modern Synthesis and something that could never be classified as Darwinian—and higher levels of evolution that distinguish macroevolution from microevolution.

    I agree with Gould.

    The frustrating thing about Shapiro and many other opponents of the Modern Synthesis is that they seem to know nothing at all about the real challenges to the old Modern Synthesis. Most of them have never heard of random genetic drift and most of them have no idea why punctuated equilibria are important.

    Jerry Coyne asks,

    Why, exactly, is neo-Darwinism dead? What is wrong with the idea that randomly produced genetic variation, fuelling the processes of natural selection and genetic drift, is responsible for both the diversity of life and (in the case of natural selection) the remarkable “design” of creatures that used to be imputed to God?

    The problem here is that as soon as you emphasize random genetic drift you are no longer talking about the Modern Synthesis as described in the 1960s. It’s already been overthrown!

    The other problem is that it doesn’t help when you refer to this newer version as “neo-Darwinism” since that term is invariably associated with an adaptationist position on the mechanism of evolution.

    Why don’t we just call Jerry’s version “Modern Evolutionary Theory” and admit that it’s different than the old Modern (overthrown) Synthesis? Now we can judge all the newest attempts to overthrow evolutionary theory by checking to see if they even understand the difference between the old Modern Synthesis from the 1960s and the latest version that’s in today’s textbooks. If they don’t know what’s in the textbooks—as they invariably don’t—then we don’t have to pay any attention to what they are saying.

    • Posted April 9, 2012 at 1:00 pm | Permalink

      Or the Postmodern Synthesis? ;-)

      As an outsider, my understanding is that neo-Darwinism is the current synthesis. Hence my, “Neo-Darwinism is dead! Long live neo-Darwinism!” earlier.

      /@

    • John Harshman
      Posted April 9, 2012 at 1:38 pm | Permalink

      I can’t see this. There was always a “selectionist vs. neutralist” argument *within* the modern synthesis, ever since the genetic variability of natural populations was first seen. Nor did Gould emphasize genetic drift as a challenge to the synthesis as far as I can recall. His challenge was always in of macroevolutionary processes (e.g. species selection). He seldom referred to stochasticity at the genetic level (though he does mention the “molecular assault” in his Paleobiology manifesto), and his view of non-adaptive evolution was tied to morphology and grounded in pleiotropy.

      If we’re judging the synthesis entirely on the exact wording of one statement of Ernst Mayr’s, you may have a point. But is that a good idea?

      • Posted April 9, 2012 at 6:40 pm | Permalink

        Is that a good idea? No, it isn’t.

        Perhaps some readers could offer a concise view of how they define the Modern Synthesis in 2012 if they still think it’s the latest word in evolutionary theory?

        Here’s a good place to start: Modern evolutionary synthesis. I think the Wikipedia article is basically correct.

        Does anyone disagree?

        BTW, Gould was well aware of random genetic drift. It featured prominently in the attack on adaptationism in the Spandrel’s paper.

        He also discusses the hardening of the synthesis (exclusion of random genetic drift) in The Structure of Evolutionary Theory.

  14. Arlin Stoltzfus
    Posted April 10, 2012 at 1:19 pm | Permalink

    What is the substance of Dean’s defense of “Darwinism”? It is largely implicit. He notes that Huxley rejected Darwin’s gradualism and says that modern biologists accept Huxley’s view. That is true. Just read anything recently by Allen Orr, and you’ll see that the “micromutationist” dogma of the 20th century, which ultimately came from Darwin’s own insistence on “infinitesimal” changes as the basis of evolution, is dead as a doorknob.

    The problem with this argument is the part that Dean leaves out, which is how this connects with “Darwinism”. Historian Peter Bowler wrote a book called “The Non-Darwinian Revolution”, the point of which was that in Darwin’s lifetime, just about anyone could be a “Darwinian” if they stood with Darwin against the creationists, no matter what they thought about evolution. Huxley was a saltationist, but he stood with Darwin against the creationists, therefore he was a “Darwinist” by 19th-century standards. Dean is implying that, because Huxley is a Darwinist, we are all Darwinists today, even though we are saltationists.

    But the meaning of “Darwinian” changed when the discovery of genetics led to a crisis, and a re-examination of what Darwin actually believed about evolution. Geneticists like Morgan and Bateson who clearly believed in evolution and selection were now called “anti-Darwinian” because they were saltationists. Like Huxley. Like Shapiro.

    The point is that Dean’s argument only appears to succeed by using an implicit and variable definition of “Darwinism”. Apparently, by contemporary standards, anyone who is a Mendelian is automatically a “Darwinian”– an outrageous historical absurdity, given that Darwin’s followers initially rejected Mendelism and instead defended a view in which environmental fluctuations are the raw material for selection.

    Arlin


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