1. I was stunned that Darwin could attribute the eyelessness of cave-dwelling animals to disuse (p. 138), only to later hit on the correct explanation in the context of a discussion of why parasites lack organs that their free-living relatives need (p. 148). "Now the saving of a large and complex structure, when rendered superfluous...would be a decided advantage...by less nutriment being wasted in developing a structure now become useless." How could he not see that this argument about parasites applies equally well to eyeless cave-dwellers, and indeed to many cases of apparent "loss by disuse"?
2. That quibble aside, I found much of chapters V-VI to be very strongly written and argued. Darwin's best writing seems to go hand in hand with his best science--the writing flows well when Darwin knows what he's talking about. Hard to pick highlights, but I'll suggest a few and other folks can add their own favorites:
-p. 190, where Darwin points out that organs that perform multiple functions, and multiple organs performing the same function, provide fertile raw material for the evolution of new functions. This is exactly the same argument used today to counter Michael Behe's claims of the "irreducible complexity" of cellular biochemistry.
-p. 140, where Darwin writes, "We have reason to believe that species in a state of nature are limited in their ranges by the competition of other organic beings quite as much as, or more than, by adaptation to particular climates." Spot on. Unfortunately, many modern ecologists who work on describing species' ranges with respect to climate variables, and predicting future ranges under climate change, proceed as if this weren't true. They make the mistake of assuming that, because species' range boundaries often are coincident with some change in climate (e.g., "the northern range limit of species X coincides with the latitude at which minimum winter temperatures drop below zero), they are caused by that same change in climate ("therefore, this species must not be able to tolerate temperatures below zero"). Yes, the fallacy of "correlation implies causation" is alive and well in the science of range limits. Correlation is an especially poor guide to causation in this context because latitudinal and altitudinal range limits are almost necessarily coincident with some change in climate or other. If only everyone would read the Origin!
-p. 193-194, the discussion of convergent evolution, using the example of electrical organs in fish. Is there any better summary of convergence than Darwin's? "I am inclined to believe that in nearly the same way as two men have sometimes independently hit on the very same invention, so natural selection, working for the good of each being and taking advantage of analogous variations, has sometimes modified in very nearly the same manner two parts in two organic beings, which owe but little of their structure in common to inheritance from the same ancestor."
Convergent evolution is a huge thorn in the side of those (such as Gould) who want to argue against the importance of natural selection or for the importance of some other putative cause of adaptation. Gould liked to claim that, if you "rewound the tape of life" and played it again, it would come out completely differently--that the history of life is a unique sequence of historical contingencies. He used the bizarreness (to our eyes) of the Burgess Shale fossils of the Cambrian explosion to argue for this point of view. Many of the "body plans" that evolved in the Cambrian explosion were not passed down in the subsequent history of life, and we can't see any functional (i.e. selective) reason why some forms passed down and others did not, suggesting that the persistent forms were just lucky. Of course, one can interpret the Burgess Shale in other ways, as Simon Conway Morris does. And presumably, even if the particular adaptations observed over the history of life are contingent on ancient chance events, any possible history of life would presumably be filled with adaptations of some sort or other. So Gould's interpretation of the Burgess Shale fossils doesn't imply much of anything about the importance of natural selection in shaping the history of life. But leave all that aside. Instead of arguing about fossils that are so ancient we'll never be able to have much sure knowledge about them, why not look to other sources of evidence, sources that are readily accessible--such as living electric fishes? Convergent evolution is direct evidence against Gould's claim of radical contingency, and we don't lack for examples of it. Gould wrote a huge amount on evolution, but if you go through his writings you will find very few mentions of convergence. Gould deployed many rhetorical strategies, but raising objections to his own position in order to refute them was not one of them.
I'll put up a separate post on the Gould & Lewontin article. I'm glad we read it, I think it's a great article for students to grapple with. That doesn't mean I agree with a word of it.