Ayala leads off by drawing a distinction between designed artifacts and non-designed objects. He notes that organisms were left out of the original scientific revolution (which posited that the rules of nature are universal) because of the kind of thinking put forth by Paley and other intelligent design theorists. Ayala claims that Darwin’s great advance was to show how purposeful complexity may arise naturally, thus bringing life finally within the penumbra of a scientific revolution which had begun much earlier. He goes on to adduce several common evidences of evolution by natural selection operating over geological time. Ayala believes (as I do) that the most convincing evidence for common descent is that we find from a branch of sciences unavailable to Darwin’s contemporaries, that is, the evidence of molecular biology.
Craig leads off by defining intelligent design as a set of theories for inferring design from evidence. He briefly alludes to Bill Dembski’s argument from highly improbable complex patterns, and argues that the inference to design is justified on those grounds alone. Craig does not contest common descent (for which Ayala had argued) focuses his efforts entirely on the mechanisms of random mutation and natural selection. He makes an interesting argument that studies of the HIV genotype over a couple decades can give us any idea of what mutation is capable of producing over a time span very many orders of magnitude longer. He also argues that evolutionists must show definitively that mutation plus natural selection is powerful enough to get everything done in only a few billion years.
Ayala, on rebuttal, seems at first to ignore Craig’s opening statement, but he is actually trying to give an example of the power of mutation and selection in practice. He refers to a test tube experiment in which low-probability mutations can be made to take over an entire tube merely by changing the environment in which the bacteria breed. He then goes on to reiterate some of the evidence for common descent.
Craig picks apart Ayala’s opening statement and rebuttal, quote-mining from various fringe scientists to show that mutation plus selection doesn’t drive the creation of new biological mechanisms in under a hundred years or two. Funnily enough, Craig accuses his opponent of undue extrapolation, even as he stretches timelines from 10^2 to 10^9 in attempt to show that Darwinian mechanisms just cannot get the job done in the time available. Craig seems to conclude that while the universe is impressively fine-tuned for intelligent life, it is not fine-tuned enough to expect intelligent life to arise more than once.
This debate demonstrates amply that expertise in public debating and debate prep can overcome expertise in the topic under debate. Ayala clearly knows more about the subject matter, but he seems overwhelmed by Craig's relentless focus on the problem of how often mutations arise within a given population. I'd be interested in hearing a debate focused on that paritcular issue, but to my knowledge that's never been done.