No, they make up 'flaws' that aren't there.
This is from a column I wrote for the local paper.
Having determined to teach the ‘controversy’ about evolution — and lets specify right here that both the School Board and real scientists agree that evolution is the theory that all life descended from a common ancestor by the mechanism of mutation and natural selection — the School Board found themselves in the awkward position of having to identify some aspects of evolution that were scientifically controversial. So they came up with three ‘scientific’ arguments against common descent. The trouble is, not one of the three withstands scrutiny.
The first argument is that there are ‘discrepancies in the molecular evidence’ for evolution. In fact, this is a complete inversion of the truth. The fantastic advances in molecular genetics over the last six decades, which have revealed to us the entire genomes of hundreds of living organisms, is a comprehensive and completely independent corroboration of the truth of Darwin’s theory. If I take the genetic sequences of the smaller strand of RNA from the large subunit of the ribosome – the tiny apparatus that makes proteins in cells, and exists in almost every living creature – and I group together the sequences based on how similar they are, what I get is a ‘tree’ structure that mirrors in detail and nearly exactly the ‘tree of life’ inferred from old-fashioned, Darwinian evolutionary biology. The few minor differences between the trees are usually where some details of the older tree were conjectural anyway, and the molecular tree has resolved an existing controversy. The ‘discrepancies’ that IDers claim are either instances where lateral gene transfer happened between our single-celled ancestors – a known process which complicates the analysis for some proteins but can be identified and accounted for, or where the ID ‘scientists’ have simply goofed and tried to compare the wrong proteins. No legitimate, credentialed molecular biologist accepts these alleged discrepancies.
The second argument is the hoary old ‘Cambrian Explosion’: the assertion that most complex animal phyla appeared all of a sudden 450 million years ago. First of all, we now know they didn’t; still older Ediacaran rocks show an even more diverse fauna than the Cambrian, but because the creatures were soft-bodied the fossils are rarer and more poorly preserved. The major happening in the Cambrian may have in fact been the appearance of protective hard skeletons, in an evolutionary arms race between predators and prey, which as a side-effect left far more and better fossils.
But in any case, we know of many instances where rates of evolution have suddenly and dramatically accelerated. When finches arrived in new habitats on the Galapagos or Hawaiian islands, and found pristine, unpopulated environments to inhabit, we know they diverged rapidly to fill the empty ecological niches. Nebraska finches all look pretty much like finches. Explore the Hawaiian rainforest, and you can find finches that resemble sparrows, finches that resemble woodpeckers, and finches that resemble hummingbirds. But the molecular data says they’re all finches. Environmental stasis leads to evolutionary statis; environmental change causes evolutionary change. And, in any case, none of this is an argument against common descent.
The third argument – that embryos from different types of organisms develop differently – is truly obscure. Just because I and a honeybee might, a long long time ago, have shared a common ancestor, why should my children and the honeybee larva look the same? So, in order to manufacture a controversy to fuel their religiously-inspired attacks on evolution, the School Board has resorted to scientifically false counterarguments.