2009 is being celebrated as the 150th anniversary of Charles Darwin's famous book On the Origin of Species . . . . whose full title continued by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. Actually, 2008 was a more legitimate anniversary to celebrate, because it was a year earlier that Darwin's and Alfred Wallace's papers suggesting that species arose by the action of natural selection were read before the Linnaean Society in London.
We rightly celebrate Darwin's contribution to science, which clearly was among the most incisive, sweeping, and transformative scientific revolution that has ever occurred. The theory of evolution by natural selection has become the clear core of most of the life sciences, and its ideas have been borrowed by social and physical sciences--even by cosmology and astronomy (yes! where universes are seen as competing ecologies of galaxies, coming and going via black holes, based on their basic properties, etc.).
But was the Darwinian theory correct?
Natural selection is certainly a phenomenon of life, and it can lead to changes in traits whose basis is heritable (generally, this means is 'genetic', or encoded in DNA). Darwin equated that with the same process that leads to speciation. Over time, organisms become differentiated by virtue of the adaptive differences that arise by natural selection in different environments, and these adaptive differences make for new species. Clearly this can in principle lead to mating incompatibility, the criterion usually accepted as a definition of species, and once mating no longer occurs the populations, that started out as one, can diverge more and more. Hence, over very long time periods, we have sea creatures diverging into fish, reptiles, and mammals. Indeed, we have plants and animals diverged from single ancestral species.
But the relevant questions these days does not have to do with divergence from common ancestry nor how traits might evolve, nor even the definition of species, but the process of speciation itself. That is still not well answered, and facile Darwinian explanations don't work nearly as well as they are said to. In fact, in many ways they are as vague and assumption-bound -- and perhaps as wrong! -- as they were in Darwin's day, and for the same reason.
When populations are separated for long time periods, genetic differences arise among them. Mutations occur locally in each population, but they are relatively rare and basically unique at the DNA level. That's because the very same mutation, say an A to a G at some specific spot in DNA, only occurs once in every ten to hundred million parent-offspring transmissions, roughly speaking. Populations in each region occupied by a species will accumulate such differences across their entire genomes. These changes will have a range of effects -- some none at all, others affecting the organism's traits. Selection may or may not prefer one version over the other.
The upshot is that regional differences arise. Darwin thought these were mainly due to selection's screening of the variants, leading to different local adaptations in populations of what had been a single species, and hence to mating barriers.
This is true only if the changes affect mating compatibility, because sperm fails to fertilize eggs, or the individuals don't choose to mate, etc. But just having, say, different shaped beaks doesn't mean you can't or won't mate (if you're a bird). In fact, humans occupy the proverbial ends of the earth, and those in Tierra del Fuego have been isolated from those in southern Africa for fifty to a hundred thousand years (or more), they look very different, their genomes are so different that one would never mistake a Fuegian for a San. Yet they are sexually compatible. The same is true of baboon species that have been separated for millions of years. In both these primate examples, the regional genetic differences are genome-wide, not just in a gene here and there. And these are just a couple of many examples.
Yet the opposite can also be true. Ring species are those occupying a long linear region, in which individuals from adjacent parts of the range are mating-compatible, but individuals from the ends of the range are not. Yet, these are considered the same species. Ring species show the subtle nature of speciation (and, by they way, humans have not become a ring species despite long separation).
At the same time, single mutations can make mating incompatible in what are otherwise clearly the same species. Known mutations of this type are called 'hybrid sterility' mutations and several examples have been studied. Single mutations or chromosomal changes can lead to mating incompatibility, and hence effectively set up different species, with no other 'adaptive' changes in the Darwinian sense. Likewise, a substantial fraction of human matings, even within a single population (e.g., infertile marriages) shows that the usual kinds of physical and behavioral traits need not arise by Darwinian processes, in order for new species to form. Unless, of course, one wants to 'save' classical Darwinism as a dogma by defining the responsible mutations as being 'adaptively' different. Nothing we've said here invalidates the ideas of common ancestry and the potential of natural selection to mold traits, and mating-incompatibility mutations may literally be viewed as 'adaptations', but that distorts the meaning of adaptation and natural selection.
These are profound facts. They show that there are still many important problems, central problems, to work on in biology. Despite Darwin's brilliant insights, some of his basic reasoning and objectives were not as correct as they have been viewed for 150 years.