From the beginning it has been commonplace to present the theory of evolution by random mutation and natural selection as an alternative to intentional design as an explanation of the functional organization of living organisms. The evidence for the theory is supposed to be evidence for the absence of purpose in the causation of the development of life-forms on this planet. It is not just the theory that life evolved over billions of years, and that all species are descended from a common ancestor. Its defining element is the claim that all this happened as the result of the appearance of random and purposeless mutations in the genetic material followed by natural selection due to the resulting heritable variations in reproductive fitness. It displaces design by proposing an alternative.
First of all, Dr. Nagel is overlooking some 15 other mechanisms involved in evolution. It's one thing to say you doubt something happened by random mutation and natural selection, it's another thing to say you doubt something happened through random mutation, gene duplication, frame shift mutation, gene flow, recombination, cellular symbiosis, environmentally generated changes to DNA decoding, protein changes (prions, etc.), natural selection, sexual selection, random genetic drift, kin selection, speciation, punctuated equilibrium, extinction/competition/invasive species, mass extinction events, and parasitic/symbiotic relationships.
More importantly, evolution does not displace design. I'm not sure how much Dr. Nagel (or myself :), for that matter) understands of the history of biology from the 19th century, but the word "random", in this context, has always been understood by me to be a relative term, that mutations are random as opposed to being dictated by the needs of the organism in its environment, random as opposed to Lamarckian. The classic examples include things like the giraffes don't have long-necked children because they stretch their own necks looking for food, or even if a bear loses his tail fishing in the water, his cubs will still have tails. The power of the Lamarckian meme is significant, you find such stories in the folk tales of people on six continents. The only design notion that the "random" of evolutionary theory opposes is Lamarckian design.
With regard to ID, there are at least two different ways that modern evolutionary theory is compatible with a designed outcome: the notion of a front-loaded system, where the universe was initially arranged to produce life, and the notion of a God who makes small adjustments in evolutionary history, using means that could have had a natural cause as well as a supernatural one. Science offers no position on these notions of design.
The contention seems to be that, although science can demonstrate the falsehood of the design hypothesis, no evidence against that demonstration can be regarded as scientific support for the hypothesis. Only the falsehood, and not the truth, of ID can count as a scientific claim. Something about the nature of the conclusion, that it involves the purposes of a supernatural being, rules it out as science.
Neither is a scientific claim. Perhaps Dr. Nagle is listening too much to the Dawkins and similar philosophers in this regard. Science can rule out certain claims about the natural world that have a religious origin, such as an Earth less than ten thousand years old, when using the assumption that there has been no supernatural intervention in the processes described. However, ultimately it can't even rule out Last Thursdayism. It's a philosophical choice to say the universe acts now as it has always acted, not a scientific one.
I'll get another part or two up this weekend. Happy Thanksgiving.