One of my best friends is currently spending his honeymoon on the Galápagos Islands, suffering a little, it has to be said, from a lack of broadband access, but otherwise content to be rubbing shoulders with giant turtles and komodo dragons, and still able to tweet about the experience.
This remote archipelago remain evolution's ground zero. 201 years after the publication of Darwin's account of what he learned there, I can only claim to have unearthed one credible argument against the actions of Natural Selection in nature. It's essentially a reasoned quibble, rather than one based on observation or experiment — and it goes like this...
Given the known tendency of certain genes to associate themselves in a relationship known as correlation, genes B and B* can be inherited together, even though only gene B is providing an advantage with respect to the environment. Gene B* is thus along for the ride and not being selected for in quite the same way as its partner, and yet nevertheless spreads through the population in a more or less identical fashion.
Now I'm sure you could murk up this neat little protest against Darwin should you choose to delve deeper into the biological complexities of the matter. (Darwin of course knew next to nothing himself about the mechanism of inheritance: genetics. )
But Jerry Fodor — the philosopher who posits this adjustment to our understanding of evolution — has, in doing so, knowingly re-opened one of the great fault-lines in western thinking: between those who favour external factors and those who favour internal ones. See for instance empricism vs rationalism, nature vs nurture, behaviourism vs well, common sense. Fodor looks at evolution as conceived by Darwin and smells a rat, because the process appears to be almost entirely driven, as he puts it, by an external factor: the environment.
Now, for a rational non-scientist (and historian to boot) such as myself, the notion that internal and external factors nearly always work in combination to produce change is close to sacrosanct. So I have to admit to some sympathy for Fodor's position, even while acknowledging that a simple intellectual prejudice may be at work here.
The LRB recently reviewed What Darwin Got Wrong — the book Fodor has co-authored with Massimo Piattelli-Palmerini — and concluded that they have had to create a caricature of contemporary Dawinian thinking in order to find several non-fatal faults within it. So when the pair state that the theory of Natural Selection "overestimates the contribution the environment makes in shaping the phenotype of a species and correspondingly underestimates the effects of endogenous variables," they themselves are underestimating the extent to which scientists include internal or endogenous variables within their modern conception of the 'environment'.
Still, for the reasons described above, I'd find it rare indeed if the most important process of change within the natural world was driven entirely by a combination of undirected variation and external environmental factors, and my suspicion is that biological science will indeed have to accommodate an increasing number of endogenous factors in the years to come.