Coyne disapproves of Margulis's book Acquiring Genomes, to make an understaement, but what seems to have earned his disapproval is simply that Margulis' saw any need for any explanation. In order for her to see any explanatory gap (Altenburg 16, anyone?), she had to be completely ignorant of all the advances in evolutionary speculation over the last 30 years.
You don't need to look any further, of course, than the title of the article: By "dissing" neo-Darwinism, Margulis has dissed evolution. Typical anticreationist fare.
Once again, macroevolution is a simple consequence of population genetics, not so simple that one has to be knowledgeable about a great many articles (the very many exciting scholarship to which Coyne alludes) in order to appreciate just how macroevolution has been explained to the satisfaction of neo-Darwinists.
Coyne seems to have missed (or "dissed") that Margulis' endosymbiotic theory ideas have caught on and become much more mainstream in evolutionary science. If, as recent and sketchy jurisprudence has it, science is what scientists do, Margulis' "crazy" ideas, as he puts it, have wormed their way into science without his approval. The explanatory gap is illusory, in Coyne's opinion.
Personally, I think there are some serious problems with Margulis' ideas with regard to the specific explanandum of generating novelty, but I believe she's very right about the explanatory gap:
This is the issue I have with neo-Darwinists: They teach that what is generating novelty is the accumulation of random mutations in DNA, in a direction set by natural selection. If you want bigger eggs, you keep selecting the hens that are laying the biggest eggs, and you get bigger and bigger eggs. But you also get hens with defective feathers and wobbly legs. Natural selection eliminates and maybe maintains, but it doesn’t create.After quoting the above, Coyne completely dances around Margulis' insight that selection is severely constrained and that natural selection is not omnipotent.
Coyne also defends his old friend Richard Lewontin. I think it may well be possible that Margulis remembers Lewontin's words in a more unflattering light than he said them (and I don't see a complete retraction there from Lewontin) but I think Lewontin more than likely said something akin to what Richard Feynman recounts in his Cargo Cult Science speech:
For example, I was a little surprised when I was talking to a friend who was going to go on the radio. He does work on cosmology and astronomy, and he wondered how he would explain what the applications of his work were. "Well," I said, "there aren't any." He said, "Yes, but then we won't get support for more research of this kind." I think that's kind of dishonest. If you're representing yourself as a scientist, then you should explain to the layman what you're doing-- and if they don't support you under those circumstances, then that's their decision.Unlike Feynman's friend, Margulis did not claim that Lewontin mischaracterized his work but was honest about it. Lewontin has since clarified that Margulis' recollection made it sound like Lewontin's work with disappointing formulas was so he could get grant money for himself where as it was to get money to “run an institution”: to “fund a group of creative people to do what they want.” Once again the selfish gene has led to altruism. I think maybe Coyne's overstated umbrage over Lewontin's alleged hucksterism disguises that he is reacting to Margulis getting dangerously close to the fact that there is big money in overflated claims of what has actually been explained, and neo-Darwinism has been a TROUGH.
Are all the papers on evolutionary biology written by hobbyists? It takes money for people to spend their working life speculating on historical contingencies of how one organism changed into another during such and such an epoch and speculating on what natural selection may explain. Whence cometh the money? How might the money flow be affected by perceptions that evolutionary biology might be making popular evolutionary views more elaborate and more consistent with what it known about how organisms work, but not necessarily deepening our understanding of how organisms work? Once you stop defining the deepening of knowledge in terms of refining "biology's unifying principle," it may be that our understanding is actually being stunted by so much number-crunching in the service of idle speculation.
I'll add here that Jerry Coyne also has a beef with secular creationist Mary Midgely, and anyone who undermines the popular credibility of the Modern Synthesis. So if you want to know how the Modern Synthesis is falling apart, find out what Bilbo Baggins, er... I mean, Jerry Coyne hates. Look up all the people he tries to discredit, and you will have an idea what's going on. In tune with Thomas Nagel's "dangerous sympathy" for Darwin skeptics, Coyne thinks that Margulis may be "worse for science than creationists [Coyne probably has ID proponents in mind here], since her scientific credibility remains high." Actually, an anticreationist usually doesn't mind people doubting Darwinism as long as (a) they are in the minority (among tax-payers and grant-funders) and (b) they can all be denied "scientific credibility."