Cornelius Hunter has, these last few days, been much better about updating his blog than I have been. To be sure, two of his recent articles have been little more than excuses to repeat his favorite complaint about "Darwinism" -- that it is supported primarily be metaphysical, even religious, arguments against intelligent design, and his favorite confusion, between "being an explanation" and "being logically possible". For example, in one essay, he deals with the claim that "If species had been independently created, no explanation would have been possible of this [consistent nested hierarchy]" as a claim that an Intelligent Designer would definitely not have created species whose traits were arranged in a consistent nested hierarchy.
But that is not the claim being made. The point is that descent with modification, at least as it typically works in eukaryotes, predicts that species will be arranged in a nested hierarchy; it explains why, e.g. we find species grouped in genera and families and orders, why animals that have one bone in the lower jaw and three in the inner ear also happen to have mammary glands and a left but not a right aortic arch. Yes, a Creator could have made separate species that way, but creationism doesn't predict such a pattern (indeed, ID proponents seem quite careful to make sure that intelligent design doesn't predict any pattern, except perhaps that we will never be able to conclusively prove that any feature is functionless) or explain why it should exist. Certainly designers in our own experience do not design in that way. This is less a metaphysical argument than an epistemological one, a preference for inferring known causes from their known results than in inferring unknown causes on the grounds that we can't say that the results couldn't be produced by them. Hunter complains that evolutionists, in citing evidence for evolution, "consistently turned to organic parts and geographic distributions that make the least sense." But that is not quite true; the parts that literally make the least sense are the parts that ID proponents crow that "Darwinists" cannot explain, such as the many problems involved in abiogenesis, that provide gaps ID proponents can stuff a Designer into. The parts cited by Darwin and later evolutionists are the parts that make perfect sense, given common descent from ancestors that had obvious reasons for such odd traits.
Hunter makes the point that Linnaeus certainly did not think that species falling into a nested hierarchy disproved special creation, and that Linnaeus was one of the greatest scientists of his day. On the other hand, attempts to impose Linnaean classifications to things that clearly aren't the results of branching descent with modification (e.g. orders and genera and species of clouds, or minerals) simply didn't work as well: one can arrange any suite of objects into a nested hierarchy, but getting a single, consistent hierarchy (rather than different ones depending on which traits one selected for comparison) proved impossible for such objects. There was something special about life, and it was something shared with suites of things (e.g. languages within the Indo-European family, breeds of domestic animals, etc.) that were derived through branching descent with modification.
Darwin's argument, and Phillip Kitcher's argument, and many other arguments for common descent, is not that a good Creator would not have made bad designs, or that an Intelligent Designer would not have made a world laced with "natural evil," it is that common descent with opportunistic modification can explain these features rather than simply accept them as the ineffable whims of a Designer/Creator. But to Cornelius Gordon, a preference for explaining data is a religious bias when it is even acknowledged; mostly, he treats all such arguments simply as strawman attacks on Intelligent Design. Intelligent Design is simply the position that "somewhere, sometime, Somebody did something;" insisting that the Somebody was competent, or benevolent, or supernatural, is just imposing extraneous fillips on the basic ID model (though somehow, when ID proponents are not complaining about such misrepresentations of their model, they manage to imply that ID will manage to save human dignity, fight racism, and give purpose to our lives and hope in the face of death: ID has facultative details).
Now, Hunter's latest argument is a bit different. It deals with a recent paper by Carl Woese et al. on the origin of the genetic code. The paper is an attempt to explain the origin of a (more or less universal -- with slight variations) genetic code in light of Woese's ideas that the original life didn't have species, that it was a community of replicating entities that freely exchanged genetic material among themselves in a truly promiscuous fashion (even more so than modern bacteria), and were especially subject to group rather than individual selection. Hunter's complaint, basically, is that Woese doesn't explain in detail how the ability to exchange genes arose (that is, he deals with the origins of the modern genetic code rather than with earlier stages of abiogenesis) or exactly how it works (this is in stark contrast, of course, to the detailed explanations that ID theorists provide for the origin and implementation of intelligent design). That gene exchange, at least in bacteria, is well-demonstrated and that there are at least well-evidenced theories of how it can happen even between eukaryotes (such as plants and animals) goes unmentioned.
I'm rather hesitant to comment on Woese's paper; I'm very far from an expert on biochemistry, genetics, or abiogenesis, and do not particularly trust my competence to exegete it. On the other hand, I can't quite help but notice that Hunter's take-away message from Woese's article seems to be that the genetic code is just a "frozen accident," something Woese is rather explicitly arguing against (and which is dismissed in Nick Lane's widely acclaimed Life Ascending, which offers a quick sketch of an attempt to explain the genetic code in terms of the chemical properties of different nucleotides, a subject alluded to in Woese's paper as well). I'm pretty sure that Woese doesn't solve the problem of abiogenesis. I doubt he even definitively solves the problem of the origin of a (more or less) singular, optimized genetic code. But he does make use of known processes to move a few steps closer to such an explanation.
Hunter gets a number of interesting comments in his blog. One of his commentators, replying to a creationist's objection (implicit in Hunter's original critique) that Woese was either oblivious or hypocritical to use an intelligently designed computer program (that simulated gene exchange in his hypothetical early community of living protocells) to argue against the intelligent design of the genetic code, noted that programs used to model and predict the weather are also intelligently designed, but this doesn't argue that thunderstorms are designed (much less designed in the same way). This is, I think, a splendid retort to a common creationist critique of genetic algorithms and biological simulations of many types.