My Chicago colleague James Shapiro appears to have been badly stung by my repeated criticisms of his attempts to forge a new evolutionary view based on the “self-engineering” of organisms and their DNA (see here, here, here, and here, for instance).
This will be the last time I comment on Shapiro’s PuffHo pieces, as I don’t want to give him the attention that, as someone who wants to be seen as the founder of a new evolutionary pardigm, he so desperately wants.
Let me just point out Shapiro’s Big Error (also committed by those who approve of his PuffHo piffle) one more time. It is not rocket science, and even non-scientists should be able to grasp it. I’ve put it in bold so Shapiro and his followers will take note:
Regardless of the source of genetic variation, if new variants are to become “fixed” (i.e. ubiquitous) in natural populations after they arise, and to become part of complex adaptations, there is no credible alternative to natural selection for the process causing that fixation.
Like some molecular biologists, Shapiro repeatedly mistakes the source of genetic variation creating new “mutations” with how that variation comes to predominate in a population. He thinks that the former explains the latter, ergo that natural selection plays a very small role in evolution. And yes, we now know of a world of “mutations” undreamt of by earlier geneticists, including horizontal gene transfer (especially important in bacteria), gene duplication, mobile genetic elements, and the like. But what happens to variation generated by these processes depends on whether they give a reproductive advantage to the organism. If they don’t (i.e., natural selection doesn’t favor the variant), they get eliminated from populations. If they do, they get fixed.
It’s still natural selection, Jim. Why do you fail to understand that?
(Let me add right away that I accept other mechanisms of evolution such as genetic drift, which is certainly of importance in much molecular evolution. What I’m talking about here are complex adaptations, not only of morphology [e.g., the heart], but also complex molecular mechanisms like DNA repair or the immune system.)
Sadly, in his latest PuffHo piece (really, does the science section even look at what’s appearing on their site?),”Inconvenient truths: why are some self-styled defenders of evolution so resistant to lessons from molecular genetics?“, Shapiro is reduced to criticizing two readers who have left comments on my latest critique of Shapiro’s Big Idea. You’ll recognize their names if you’re a regular: Ben Goren and Torbjörn Larsson.
And Shapiro’s criticisms of both men’s comments are of the same ilk: the modern theory of evolution (“neo-Darwinism,” though I am going to stop using that label) is wrong because it doesn’t deal with “mutations” that aren’t simple changes in single nucleotides in the DNA. For a rebuttal of Shapiro’s thesis, just reread what’s in bold above. Horizontally transferred elements, transposable genetic elements, and the like, must be acted on by natural selection if they’re to become part of an adaptation.
I’m not a willy-nilly defender of my commenters, but in this case Goren and Larsson are right and Shapiro is wrong. Take, for instance, what Shapiro says about Torbjörn:
A second commentator, Torbjörn Larsson, argued that horizontal DNA transfer posed no challenge to the neo-Darwinian theory: “In other words the generic gradualism of Darwin mentioned in the article isn’t rejected by the observed degree of horizontal gene transfer.”
But Torbjörn’s claim does not make sense scientifically. Horizontal transfer is not the gradual Darwinian accumulation of changes. Horizontal transfer episodes rapidly incorporate complex evolved DNA structures into new genomes by coordinated molecular events.
There is no way we can reasonably apply the term “random mutation” to a DNA transfer process that utilizes dedicated surface structures for bringing two cells together, assembles a multi-protein DNA transport pore connecting the cells, and initiates DNA transfer replication at a specific site on plasmid DNA. [JAC: yes we can; for the transfer is a genomic change that occurs randomly!]
The well-established molecular details of horizontal transfer in the evolution of bacterial antibiotic resistance are difficult to reconcile with neo-Darwinism.
No they aren’t—not at all.
What Shapiro can’t see here is that it doesn’t matter how new changes in a genome come about: via classical base-pair “mutations” or by the more recently discovered processes of horizontal gene transfer (e.g. the movement of units of DNA from one species of bacteria to another via a virus vector). If those chunks cause antibiotic resistance in the recipient species, and there are antibiotics around, natural selection will go to work on the new “variant.” Indeed, this is how a lot of antibiotic resistance evolves in bacteria. But it doesn’t matter how a variant arises: they are all equivalent to classical mutations and their dynamics can be described by the classical equations of population genetics. After all, antibiotic resistance in bacteria is seen as a classic and easily-understood example of natural selection!
So no, there isn’t an insuperable problem here for “neo-Darwinsim.” We just have to expand our idea of “mutation.”
Shapiro can’t—or won’t—get this, and I give up on him. Time will tell if his “non-Darwinian” ideas gain any traction, but the fact that he propounds them at PuffHo rather than in peer-reviewed scientific journals (how about sending a piece to Evolution, Jim?) is not propitious. As one of my friends, who is both an evolutionist and molecular geneticist, emailed me after reading Shapiro’s piece:
Part of his problem has always been the one that some molecular biologists have: they confuse molecular causation with evolutionary causation. All of the mechanisms mediating horizontal transfer and so forth that he cites are indifferent to their effects on fitness: adaptation still arises as a consequence of the sorting agency of natural selection.
I sometimes wonder if there is a polymorphism in the human population for ability/inability to see the distinction. Jim would then be an example of someone who got a really bad version of the mutant gene for inability.
I’ll let Ben and Torbjörn defend themselves, but for me Shapiro sleeps with the fishes. He will go on crying in the wilderness that is the PuffHo science section until he leaves this earthly vale and his ideas fade into well-deserved obscurity. I’ve made my point, and I’m done with him. I may seem “strident and militant” about this, but one reaches a point when fulminating ignorance, pointed out but not corrected—much less admitted—must be shown for what it is.