Not really. I think Darwin’s theory is one of the great human achievements and shows us the deep and beautiful patterns and processes at work in life. I don’t think it’s finished, though. Darwin didn’t know about the mechanism of heredity, and I don’t think we fully understand it, either.
Why does a zebra have one large hoof at the end of each leg? Evolutionary biologists sometimes answer questions like this by assuming that there must be an evolutionary advantage, that in the case of the zebra’s foot a single large hoof is the best sort of foot it can have for its environment, and that natural selection has worked on the variation produced by random mutation to find the ideal form.
I think the zebra has one large hoof on each leg because it’s a horse, and that’s what all horses have.
Horses, zebras and donkeys are odd-toed ungulates, perissodactyls, as are rhinoceroses and tapirs. Most ungulates are even-toed, the artiodactyls: deer, sheep, antelope, giraffes, pigs, bison and buffalo. It was not always so. Perissodactyls are much more common in the post-dinosaur fossil record and artiodactyls were rarer, generally smaller and seemed to live in more marginal environments. The change in fortune might be due to the spread of grasses as the dominant vegetation in many habitats. Artiodactyls are ruminants with multi-chambered stomachs and are better at extracting nourishment from grass, a pretty poor food stuff, so when, about 20 million years ago, grass conquered the world, the artiodactyls could out-compete the horse family. This difference in digestion is why horse manure is much better for your garden than cow manure.
It could be that cloven hoofs are as good as single ones. Bison, gnu and wildebeest are good large animals that find them so. The zebra, though, is probably incapable of changing its inheritance. The family line has committed to a single toe and it can’t easily change.
This is one of the things that I don’t think evolution as usually presented fully explains. Most animals and plants display clear signs of their heritage. That is, their form is not solely shaped by selection, it is partly determined by the characteristics of their ancestors. This is recognised in that branch of biology known as cladistics. This analyses the relationships between organisms according to their lineages: which branch (literally, a clade) they are on. Organisms are, to an extent, variations on themes. I’ve never read a book about cladistics though, and I don’t know how it is responding to the ability we now have to analyse genomes and therefore evolutionary relationships more accurately. Certainly there is a fair amount of reclassification going on. The point, though, is that by no means all characteristics of an organism can be expected to have an evolutionary advantage. Some of them are simply the hand the creature was dealt.
There are two related things. One is the persistence of ancient lineages. Tuataras in New Zealand, Coelacanths in the Indian Ocean and Indonesia, and Ginkgos or maidenhair trees in a few valleys in China are well-known examples, perhaps rather extreme ones. They don’t appear to have completely stopped evolving, but their basic form is very similar to extremely ancient examples known from scores or hundreds of millions of years ago. Environments change all the time, putting shifting pressures on organisms. After all, the environment includes the predators, prey, parasites and disease organisms for any animal or plant, and they are all evolving. These creatures, though, seem to have hung on in remote environments, just a single species or two, developing very little, and not giving rise to new branches. Are they evolved out, in some way?
And in contrast, there are examples of very similar species, swarms or clusters of species, that show great diversity. I’m thinking of, for example, perching birds, gulls, ducks, some types of fish, antelope, cats, and the grasses that I mentioned before. If you look up mackerel, for example, you’ll find that it isn’t one type of fish, but a cluster of similar species. It looks as if an evolutionary branch has been extraordinarily fertile, like a branch on a tree giving rise to an immense thicket of twigs. Is that because there are huge numbers of environmental niches that suit that rough body form? Or is it that the genetic machinery of that branch is unusually good at creating useful adaptations?
I suspect the explanation for both the dwindling persistence of some ancient lines and the exuberant speciation of others owes as much to details of the genome of these creatures as to their interaction with the environment. And that isn’t pure Darwinism, and is a conclusion that some biologists would, I think, strongly, if not dogmatically, reject.