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.