Although their offices are located only one block apart on East 57th Street, within the University of Chicago campus, the biological perspectives of Jerry Coyne and Jim Shapiro might as well be located in different galaxies. Recently Coyne vented his ongoing frustration with Shapiro — in particular, with the latter’s disregard for the putative creativity of natural selection, which Coyne emphasized was “the only game in town.”
Coyne ended his post by complaining that Shapiro’s dissent from textbook neo-Darwinism “was an embarrassment to me, for Shapiro works at my university and, in my view, his writings impugn our reputation for excellence in evolutionary biology.”
Gosh, Jerry — you blush so easily. Any reader curious for a different (international) reaction to Shapiro’s iconoclasm should watch the Q&A following Shapiro’s May 9, 2012 lecture at the Instituto Veneto’s symposium on Evolution in the Time of Genomics. Among those commenting were University of Basel evo-devo guru Walter Gehring, Harvard geneticist Daniel Hartl, and National Academy of Sciences foreign member (and author of the nearly neutral theory of evolution) Tomoko Ohta. Rather a distinguished group of evolutionary biologists: precisely the community whose respect Coyne is so worried Shapiro will endanger with his naughty thoughts. Later in the day, Eugene Koonin of the NCBI/NIH offered an enthusiastic reaction to Shapiro’s presentation.
Well, watch the Q&A, which starts at 1:03:45. No one scolds Shapiro for embarrassing evolutionary biology. That would have been silly, and pointless, in light of the open questions Shapiro and the others were trying to answer during the three-day workshop, mainly having to do with the origins of evolutionary novelty. In that context, to assert — as Coyne advised in his blog post — that natural selection “is the only game in town” would have foreclosed discussion, debate, the presentation of new evidence, and the weighing of alternatives: in short, would have shut down biological science as it ought to be practiced. One can bang the podium with a shoe, of course, and claim all territory in the name of natural selection, but it’s likely the other participants would simply ignore the claim.
Nor does Shapiro kowtow to ID theorists or “creationists,” a calumny Coyne lards into his blog post. At 1:02:34, Shapiro explains that his ideas provide “an answer to the intelligent design advocates’ challenge that there’s no way evolutionary theory can explain complex adaptations.” Those in the ID community who have interacted with Shapiro over the past 15 years know well that he steadfastly rejects design-based solutions to evolutionary questions, if anything with a philosophical vigor rivaling Coyne’s own.
No Kneeling at the Darwin Shrine, However
But Shapiro has no patience for Darwin worship. This is clear when he responds (by name) to Jerry Coyne’s criticisms, pointing out that Coyne argues everything can be explained by “garden-variety natural selection.” Shapiro’s response is worth quoting at length:

I think the responsiveness, the triggering, the specificity, the capacities that cells have for restructuring their genomes, are things which traditionally have been treated as epiphenomena in evolutionary discussions. I think now that we know about them, and now that the genome data shows us how important they have been…they have to come to the center of the discussion — and I would pose the question: is natural genetic engineering more important for new features appearing in evolution than natural selection?

For his part, Coyne argues that Shapiro misrepresents the state of biological opinion about natural selection. He would ignore Shapiro, Coyne says, except that “na�ve readers might get the impression that biologists are beginning to doubt that natural selection is important.”
But doubts about selection are widespread within biology, and have been for a long time (although the doubts may be expressed with greater outspokenness recently). In an open-access review of Shapiro’s book, Evolution: A View from the 21st Century, biologist Adam Wilkins, former editor of the journal BioEssays, explains the increasing prevalence of skepticism about natural selection as a growing split within biology:

[Jim Shapiro’s] contention that natural selection’s importance for evolution has been hugely overstated represents a point of view that has a growing set of adherents. (A few months ago, I was amazed to hear it expressed, in the strongest terms, from another highly eminent microbiologist.) My impression is that evolutionary biology is increasingly separating into two camps, divided over just this question. On the one hand are the population geneticists and evolutionary biologists who continue to believe that selection has a “creative” and crucial role in evolution and, on the other, there is a growing body of scientists (largely those who have come into evolution from molecular biology, developmental biology or developmental genetics, and microbiology) who reject it.

Pace Jerry Coyne, doubts about the efficacy of natural selection aren’t hard to find. Just open any good evolutionary biology journal. Why?
The Unsolved Problem of the Origins of Evolutionary Novelty
A deeply fascinating insight into one of the most important reasons for dissent about selection can be gleaned from Dan Hartl’s response to Shapiro. Hartl recounts a conversation he had (concerning the origins of evolutionary novelty) with the famous neo-Darwinian theoretician Sewall Wright:

I want to tell a story. When I was a graduate student, I once asked Sewall Wright, who was a pre-eminent population geneticist, ‘What limited novelty in evolution?’ And he said, ‘Novelties came about from ecological opportunity.’… But then he said, ‘Unfortunately, you can’t make a theory out of that, because these events tend to be irregular and unpredictable.’ And what you need to make a theory is a reproducible series of events, so that you could test it. So population genetics was never designed to encompass all the things that you talked about — it was designed for the conventional, reproducible parts of evolutionary biology.

Think about Sewell Wright’s argument for a moment, because its implications are very telling:

1. Organismal novelties arise from unpredictable, irregular events.
2. Evolutionary theory, by contrast, is based on reproducible regularities (as captured in population genetics).
Therefore,
3. Evolutionary theory does not explain the origin of novelties, because — well, see Premise 1.

The search for the evolutionary mechanism of novelty-production, pursued since Darwin, will be frustrated by claims that “natural selection is the only game in town.” Selection is powerless without the right variations. Therefore, finding out how major variations arise — namely, those causing genuine novelties — must take precedence over everything else in evolutionary explanation.
Coyne knows this, of course, so why he beats up on Jim Shapiro is a total mystery.
Others, such as Eugene Koonin, are “tempted” (i.e., intellectually inspired) by Shapiro’s thinking, to consider changing the focus of their talks at the last minute. Now that’s the excitement, the thrill, the heart of natural science.