Phillip Johnson doesn't tell us what his own detailed story of the origin and history of life is but simply charges that natural selection can't generate complex adaptations. He is quite right to point out that the best understood instances of natural selection involve rather small modifications. That's in the nature of the case. Processes that we can observe and analyze in fine detail--like the famous example of industrial melanism in moths--occur on a time scale that is far too short for most examples of speciation.
Yet biologists can advance more speculative hypotheses about more dramatic evolutionary changes, suggesting how natural selection has operated to increase leg length in the line ancestral to modern horses or in the emergence of feathers and flight in the first birds. The trouble with these conjectures is not that there's no explanation, but that we require more evidence to discriminate the possibilities. Perhaps as we learn more about the genetic details and about the development of the traits that we want to explain, we'll be able to be more authoritative about the history of selection that has led to large evolutionary modifications.
Johnson, however, like many other neo-creos, is captivated by the "boggle" argument. The cell is so complex, has so many constituent proteins--how could anything like that have arisen by natural selection? Without knowing more about the molecular biological details, accounts in terms of natural selection must inevitably be highly speculative. But there's no basis for thinking that natural selection couldn't have given rise to the molecular complexity.
Evolutionary biologists tend to think that's the end of the argument, that we should believe in some history of natural selection and patiently try to work out just what it was. Neo-creos, however, will take that attitude to be one of dogmatic faith. Are they right?
No. There are two fundamental points that ought to be widely appreciated. First, there are lots of hard, unsolved problems all over the map of science. How do proteins fold? Chemists don't know. How do you reconcile quantum theory and special relativity? Physicists struggle with this. Maybe all the sweat is unnecessary. Simply intone "intelligent design" and the troubles will vanish. But so will the opportunity for learning how the world works.
The second point is that it's highly unclear how "intelligent design" helps. If Johnson and his friends want to play science with us, then they ought to tell us just how their pet hypothesis solves the problem. There are three possibilities. No. 1: An intelligent creator made all the organisms just as they are in the beginning. Problem: This account won't fit the fossil record. No. 2: The intelligent creator created in successive waves, and the fossil record shows the pattern of extinctions and new creations. Problem: This account won't fit with the anatomical, physiological, biochemical, and genetic relationships that link later organisms to earlier organisms. No. 3: The intelligent creator started the evolutionary process and helps it out by supplementing the action of natural selection; transitions that natural selection can't manage are effected by the designer's power. This is better than the first two, in that it concedes the age of the earth, the succession of organisms, and the fact of evolution.
But how exactly does the intelligent designer operate to help out natural selection? Is the problem that lots of genetic changes are needed at once and the Creator waves the magical mutating finger to supply them? Or is it that some transitional organisms need protection from the rigors of the environment and the Good Lord tempers the wind to the shorn bacterium? Plainly I put words into the neo-creos' mouths. But they are so reticent, so coy, so tactically silent that there's no alternative. "Intelligent design" is a sham, an empty device that explains nothing.
Johnson has it exactly backward. Rather than being desperate to reject a plausible theistic explanation, contemporary biologists are heirs to a tradition that struggled to fit knowledge of the natural world to their belief in "intelligent design." No serious intelligent-design hypothesis will work. That's why the neo-creos are mute on the details.
So what are the children of Kansas to be told? That the earth is about 4 billion years old? (If not, why not?) That the earth has seen a succession of organisms? (If not, why not?) That all organisms are related? (If not, why not?) That natural selection is known to be capable of producing some kinds of evolutionary change and not known to be incapable of producing very large changes? (If not, why not?) I agree with Johnson that they should be given the evidence. Fairly. Explicitly. Honestly. Lying for God ought not to be an option.