Jerry Coyne, Grand Inquisitor

Through his popular web site, Why Evolution Is True, University of Chicago evolutionary biologist Jerry Coyne has become one of the most famous arbiters of Darwinian orthodoxy.

Why is it that, of all the sciences, evolutionary biology alone requires these counterparts to the Spanish Inquisition to keep the faithful in line? Where is the blog called Why Cosmology Is True? And who is the blogger who spends as much energy as Coyne does ferreting out heresy within the cosmology community and beyond?

Just asking.

Anyway, Coyne has been stoking the flames of late underneath the distinguished molecular biologist—and, as Coyne grudgingly admits, his University of Chicago colleague—James A. Shapiro.

In a recent post misleadingly entitled “A Colleague Wrongfully Disses Modern Evolutionary Theory,” Coyne employs snark, misrepresentation, and faulty logic in equal measure to try to cow Shapiro into recantation and repentance.

The title is misleading because Shapiro is one of the chief architects of the new evolutionary theory that is now being forged to accommodate the explosion of new information discovered by molecular biologists over the past two or three decades. Thus, it is Coyne who is really “dissing” modern evolutionary theory, not Shapiro—at least, if we take “modern” to mean what is happening right now.

But that is not how Coyne sees it. He is not pleased, and he makes his displeasure known in a variety of ways.

First, he condescendingly deigns to accept Shapiro as a colleague, in spite of the latter’s never having sought him out to kiss the Grand Inquisitor’s ring:

. . . I suppose he could be considered a colleague, though I’ve had almost no interaction with him.

Then, Coyne comes to his real objection:

I have, however, followed his activities in the literature—and with some dismay.  Shapiro, it seems, has devoted much of his writing to pointing out that the modern theory of evolution (“neo-Darwinism”) is deeply flawed and needs a new paradigm.

Pointing out the flaws in neo-Darwinism and calling for a new paradigm—clearly Shapiro is guilty of nothing short of apostacy!

What, precisely, is the nature of Shapiro’s thought crime?

For the past couple of decades or so, Shapiro has been publishing his views on what he calls “natural genetic engineering” in a series of landmark papers. He also has a new book out called Evolution: A View from the 21st Century (FT Press, 2011), in which he summarizes the evidence for his modified theory of evolution in a semi-popular form.

However, Coyne’s diatribe was leveled specifically against an essay Shapiro had published on the Huffington Post web site called “What Is the Key to a Realistic Theory of Evolution?,” so that is what I will draw upon here.

If the new theory is realistic, then by implication the old theory—that would be the Modern Synthesis–view, uniting Darwin’s original theory of natural of selection with modern genetics—is not realistic. One can see why Grand Inquisitor Coyne is concerned.

What is “natural genetic engineering”? Here is how Shapiro explains it:

. . . the last 60 years of molecular biology and genome sequencing have established that genome change is very much an active cellular biochemical process. I call this “natural genetic engineering.” In my book, I argue that DNA biochemistry has changed our 21st-century view of the genome. We now have to consider the genome a read-write (RW) memory system.

In other words, the genome is more like an iPod than a CD.

Moreover, cells can target genome changes controlled by cell regulation and sensory inputs. Cells and organisms with RW genomes can respond creatively to life-threatening challenges.

Shapiro accepts that these claims may sound extraordinary to those raised on the famous “central dogma” belief that there can be no feedback from the physiology of the organism onto its genetic material, and therefore that all genetic changes must take the form of strictly haphazard mutations.

We now know that this is simply not so, and Shapiro briefly outlines the knowledge gained over the past few decades that has rendered the standard neo-Darwinian picture passé:

Decades of molecular biology research show that organism traits result from action by protein-RNA-DNA networks, which also respond to multiple sensory inputs and signals.

The genome sequence record shows that these networks and their DNA recognition sites have evolved by well-documented natural genetic engineering processes. The examples include:

• How cells generate new proteins by combining parts of existing ones
• How families of proteins expand by copying segments of DNA & RNA
• How innovations spread from part of the genome to another
• How DNA “cassettes” move through the genome (with eerie similarity to familiar human technologies)

Now, all of this is well-established and utterly beyond cavil. Had Shapiro stopped here, our modern Torquemada (left) might have grumbled, but he could not have handed down an indictment of outright heresy.

The theory of natural selection is so vague and contentless that the Darwin brand has a near-infinite potential for expansion to cover any and all new discoveries in biology, no matter how inconsistent they may be with the original intent of the theory. So long as scientists are willing to accept the label and do proper obeisance to authority, all is well.

The reason why Shapiro has incurred the Grand Inquisitor’s wrath is because he dared to draw the logical conclusion from his own research and call a spade a spade:

Given these well-documented examples of molecular innovation by natural genetic engineering, the new century may be an appropriate time to revisit our basic assumptions about the sources of biological diversity. Perhaps natural genetic engineering plays a more important role than natural selection.

That “natural genetic engineering” should be the real driver of evolution, rather than just another of the diverse phenomena thrown up by natural selection—that is the doctrine that cannot be tolerated by the guardians of Darwinian orthodoxy, for it is tantamount to a declaration of schism.

What does Coyne have to say in reply?

Nothing substantive. In addition to expressions of indignation and discussion of irrelevancies (such as the tempo and mode issue), his only attempt at a relevant rebuttal is following:

While Shapiro rightfully points out that there are more sources of genetic variation than were dreamt of in your genetics, Watson and Crick, he is misguided in thinking that these new sources of variation completely destroy the Darwinian idea of gradualism and natural selection.  We see many examples of gradual evolutionary change in the fossil record, and natural selection is still the only game in town when in comes to explaining adaptations.  If Shapiro knows any other way that adaptation can occur, let him tell us.

Well, Shapiro did tell us—that was precisely what the discussion of “natural genetic engineering” was all about—but apparently Coyne wasn’t listening.

Or, rather, in the immortal words of Paul Simon: “A man hears what he wants to hear, and disregards the rest.”

In a follow-up reply to a response by Shapiro, Coyne elaborates:

First, he hasn’t produced evidence in either his rebuttal here or his original HuffPo piece that his mechanism is a viable alternative to natural selection. All variants have to be fixed somehow, and that is perforce through the increase in frequency of those variants. When Shapiro produces a theory that supplants natural selection in explaining mimicry, the beaks of finches, industrial melanism, and all the adaptations of plants and animals to their environment, then I’ll start thinking about whether natural selection is misguided.

Finally, we are approaching the heart of the matter.

Yes, it is true that genetic fixation of a novel trait occurs through the increase in frequency of that trait. That is one the undeniably great things about Darwinian thinking—its analytical truths stand up wonderfully well under the closest scrutiny.

But the crucial question is: Where do novel traits come from?

The whole point of Darwinism is to get rid of the “spooky” purposiveness, striving, and apparent intelligence in living systems. If novel traits are no longer attributable to random mutation or other mechanical processes, but are the result of clearly purposive “natural genetic engineering,” then we are indeed looking at a radically different account of life and evolution.

A theory of natural selection that abandons the condition of pure randomness on novel-trait generation is no longer a theory that bears any significant relation to neo-Darwinism.

At this point, one might be tempted to elevate Lamarck (right) as the new patron saint of evolutionary biology. However, Shapiro’s theory is not remotely connected to the ideas of the historical Lamarck, either.

Granted, if one had to choose between the two, then “natural genetic engineering” would have to be accounted closer in spirit, if not in letter, to Lamarck’s theory than to Darwin’s.

But why must we choose? Do we demand that physicists choose between Einstein and Newton?

Is it too much to hope that some day evolutionary biology will advance to the point where it will no longer require patron saints at all—or Grand Inquisitors?