The question: What are the limits of Darwinian explanations?
Natural selection can't possibly account for everything in evolution any more than human selection can account for everything in a chihuahua.
Selection only works where there is a given range of candidates. Selectionist theorists take this range for granted, treating the selectees as if they were indefinite, passive objects with no natural tendencies of their own. But (as helpful scientists have lately pointed out) at every stage, from the initial molecules to the most complex living organisms, these participants are themselves specific, active entities.
They are primed to move positively in a particular range of directions and are capable of determining its details. For instance, a particularly enterprising mouse which suddenly decides to move into a new valley can defeat the best-laid plans of its former evolutionary pressures. And we can see that an alien observer might well suppose that it would be quite easy to turn a person into a kangaroo or a chihuahua into a slug. But in fact no amount of selection will achieve these feats. The moral is that the tendencies of the materials present are every bit as important in evolution as the selective forces.
It is not surprising that Darwin overlooked this. No scientist can be expected to notice more than one enormous new aspect of things at a time. He did say, emphatically, that natural selection was not the only cause of evolutionary changes and he was very cross when people kept misrepresenting his views on this.
In fact, he made it clear that he had never meant to exalt selection – as Daniel Dennett claims – into a kind of "universal acid", a nostrum with unbridled powers. This was a kind of sweeping, magical thinking which never tempted him. He did indeed, think that it was the main cause of change, and this is not very surprising when you consider that no other possible ones had yet been suggested. But he made it clear that he was always unhappy about the apparent inadequacy of this cause to explain the whole range of actual effects. When he said that thinking about the problem of the peacock's tail made him feel positively sick he was clearly expressing this deep uneasiness – this sense that the change was too large to be explained in such a way. No doubt this is why he always remained interested in the idea of inheritance of acquired characteristics, which would have added an extra way of facilitating change. And it is surely clear that, if anyone had begun to suggest other new possible explanations, he would have been extremely interested.
The way in which this one-sided exclusiveness has been hardened into dogma is remarkable and does seem to need some explanation. I suspect that the supposed passivity of the candidates for selection flatters the control-freakery of those speculating about these things. Lyell did point out that this unbalanced approach can't be right, asking why Darwin only seemed to have noticed the third member of the Hindu trinity, Shiva, the destroyer? Why wasn't he interested in Brahma the creator and Vishnu the preserver?
The question still remains and is, of course, a solid scientific problem, never mind Lyell's mythical language. In fact, it is the mythical aspect of Darwin's Shiva that has received the most emphasis, with plenty of talk about nature red in tooth and claw, etc. The literal, empirical aspect of the other two questions is only now beginning to get some serious scientific attention. Let's hope that this balance can finally be restored.