Afarensis

It was supposed to be a great hulking beast, a mind boggling behemoth that strode the firmaments and rid the world of evolution much like Heracles cleaning the Augean Stables. Witness what Behe said about the book:

When future intellectual historians list the books that toppled Darwin's theory, The Design of Life will be at the top. I'm sure he read that in his horoscope. Witness, also, what Evolution News and Views had to say:

For the ID-guru, Design of Life covers many hot topics. This includes a lucid explanation of the integrated, unevolvable complexity in the neck of the giraffe, a potent critique of the alleged transition from reptiles to mammals, and a critical analysis of the evidence used to support the hypothesis that whales evolved from land-mammals.

So when I got my hands on a copy I was very interested to hear what it had to say about fossils. The chapter on human origins turned out to be a cut and paste job of Dembski's paper published in ISCID, or PCID or whatever that defunct magazine was called, basically William Sidis this and William Sidis that. The book does mention hominins:

And yet, there is no clear genealogical evidence demonstrating the evolution from Homo habilis into Homo erectus into Homo neanderthalensis into ourselves, Homo sapiens. To be sure, there are similarities. Homo neanderthalensis is, by any criterion (anatomical, physiological, cultural) closer to Homo sapiens than is Homo erectus, and similarly Homo erectus is closer to us than is H07720 habilis. At best, this shows that if humans evolved, then the common ancestor of Homo sapiens and Homo neanderthalensis is more recent than the common ancestor of Homo sapiens and Homo erectus. And this common ancestor, in turn, is more recent than the common ancestor of Homo sapiens and Homo habilis. But such an inference presupposes rather than establishes that humans evolved.

Okay, a little wobbly for a beginning, but hey, even Heracles stepped in some poo while cleaning the Augean Stables. Let skip this and go to the chapter on fossils. This starts with a section on how paleontology and evolutionary biology are historical science and rely on narratives to reconstruct the past and how this is no basis for a rigorous science (okay, Heracles is stepping in a lot of poo, but he is a demigod and he will recover and clean the stable of all that stinky evolution). Let's skip ahead to the discussion of transitional fossils:

What did paleontologists find? Many new fossils, to be sure. But what they didn't find were the numerous intermediates that, according to Darwin's theory, had once existed. Rather than plugging gaps in the fossil record, new fossils tended to create new gaps.

Oh, Snaps! Everytime we find one transitional fossil we create two gaps (okay, Heracles is a little gassy and is contributing to the poo, but he is the son of Zeus and he will recover and clean the stable). Let's skip ahead to the part about our coverage of the fossil record:

How imperfect is the fossil record? Looked at not in terms of the sheer numbers of organisms that failed to be preserved, but in terms of the different types of organisms in fact preserved, and how representative they are, the fossil record actually looks quite good, at least in drawing the broad contours for the history of life. How do we know this? It's a simple matter to check how many known living types of organisms are represented in the fossil record. The percentage of living types recovered as fossils then gives a good indication of the degree to which different types of organisms have been preserved in the fossil record generally. For instance, among 43 known living orders of terrestrial vertebrates (the level of classification just below classes and phyla), 42 have been found as fossils. Thus, 98 percent of extant terrestrial vertebrates at that level of classification were fossilized. It is therefore a good bet that if there were other orders of terrestrial vertebrates, they too would have been fossilized. As one moves from broader to more specific levels of classification, the percentage of organism-types preserved in the fossil record gets smaller but is still significant. For instance, among 329 known living families of terrestrial vertebrates (the level of classification just below orders), 261 have been found as fossils--that's a fossilization percentage of almost 80 percent. If one removes birds (which tend to be poorly fossilized), then among 178 known living families of terrestrial vertebrates that are not birds, 156 of them have been found as fossils--which raises the fossilization percentage to 88 percent. A fossilization percentage of 66 percent at the level of genera is not uncommon.

Humph, it is only about 6% for primates. Note what is being done here, by Dembski and Well's logic since we have found Purgatorius modern apes are represented in the fossil record (Heracles boss just told him to put a little Preparation H on it and get back to cleaning the stable). Seriously:

The evidence here is clear and points overwhelmingly to the fossil record as being a faithful preserver of organisms at higher levels of classification.

Okay, so Heracles is getting violently ill and projectile fluids are emanating from both ends. Lets jump ahead to the reptile/mammals and whales. Let us see this potent critique. In discussing the reptile/mammal transition we find this:

For instance, if mammals arose from just one of these lineages, then the others are not ancestral to them. But if several unrelated species have the same mammal-like features as the "actual ancestor," how compelling are these features as evidence of ancestry? If the same mammal-like features of therapsids keep emerging without being related by common ancestry, then why should mammals be regarded as related to the therapsids by common ancestry? Do shared features require a Darwinian interpretation? Do they merely suggest it? Are they simply consistent with it? Or are they carefully chosen to illustrate it?

Ouch! Did they just admit to being ignorant about the nature and subject matter of cladistics? Have they really not paid any attention to the discussion about the meaning of derived characters?

Let's examine the proposed evolution of the mammalian ear more closely. The skull and mandibles (lower jaws) of the therapsids are said to have bones similar (homologous) to those of the first mammals. The upper and lower jaws of reptiles articulate (fit together) with two bones (one each located at the back of the upper and lower jaws) not found in mammals. According to Darwinian theory, these two bones relocated in the middle ear of the mammals in the course of descent with modification (see figure 3.11). Darwinists describe the reptilian jaw bones as "migrating" to their new locations in the mammalian ear. Nevertheless, there is no fossil record of such an amazing process.

Great galloping Gish! Pity that we actually do have the fossils to demonstrate that amazing process. Speaking of Gish:

Consider that to make this change, one of these bones had to cross the hinge from the lower jaw into the middle ear region of the skull.Thereafter the neo-Darwinian mechanism would have had to reshape and refine these bones into a highly specialized, delicate instrument of sound transmission.

In between these two quotes is an argument from incredulity concerning the ability of natural selection to accomplish this change. This is going from bad to worse. So let's skip ahead to the whales. Surely, Heracles will have recovered and will, finally, clean the Augean Stables of the perfidious stench of evolution. Let's see what the promised critical analysis has to say. Turns out the critique is an inset box some seven paragraphs in length. The first five or so paragraphs recounts the discovery of Pakicetus and Ambulocetus and the box concludes with:

The "whippo" hypothesis sets at odds fossil and molecular evidence. Fossil similarities suggest that hippos are close evolutionary relatives of other even-toed hoofed mammals such as pigs and camels, but far removed from whales. On the other hand, molecular similarities suggest that hippos are close evolutionary relatives of whales, but far removed from pigs and camels. But if the original fossil similarities are not evidence for common ancestry, then by the same logic molecular similarities need not be, either. There's no compelling reason to trust either hypothesis.

That's it. No mention of the astragalus with the double pulley only found in artiodactyls (such as hippos, a finding which brings the morphological and genetic evidence in line with each other), no mention of any of the other whale fossils.

At this point Augeas fired Heracles, muttering under his breadth "That's the last time I'll trust supernatural dieties to do something I can do myself" as he turned to clean his now overflowing stables.

Update 1: One of the things I forgot to mention is that in discussing the evolution of the jaw from reptiles to mammals Dembski and Wells ignore the vast and abundant literature on bone growth and remodeling and the literature on biomechanics.