In the article, he (Ayala, the prizewinner) argues for the different magisteria approach to science and religion. This has been so thoroughly debunked by others (including Dawkins) that I can't summon the enthusiasm to talk about it here. However, we are fortunate that stupidity is the gift that keeps on giving and he says plenty of other things we can ridicule. From the article:
Man’s “flawed” design made evolutionary theory more compatible with the idea of a benevolent creator than intelligent design. “Because of the flawed design of our reproductive systems more than 20 per cent of all pregnancies end in spontaneous abortion,” said Professor Ayala. “Do you want to blame God for that? No, science has provided an answer. It is the clumsy ways of nature and the evolutionary process.”
Read that again. Go on, I'll wait for you.
This is one of the most tortuously contorted examples of begging the question I've ever seen. Begging the question is a logical fallacy that occurs when you assume the conclusion as part of your argument.
What Ayala is saying is this: Man's (why not woman's or any other organism's) design is evidently flawed. If we believe that god designed us that way, it's hard to conclude that he's benevolent. However, evolution is a blind process, so if we believe in evolution, we get to believe that god is benevolent. Yay us! I mean, yay god!
This is a painfully idiotic argument for obvious reasons. It assumes as a premise that god both exists and is benevolent in order to demonstrate god's existence and benevolence. I hardly need to spell out why this is entirely devoid of substance.
And it doesn't even work. If god is all-powerful, he could have devised a scheme of evolution that resulted in organisms that weren't flawed. Or he could have fucked evolution off entirely and simply designed everything perfectly out of the trap in the first plac... oh. Seriously, Professor Ayala: this is an argument?
I have one other point, which might be over-analysis. One of the many things I'm a geek about is the way people choose to phrase things within the context of what they are saying. You've probably seen A Beautiful Mind and if you haven't, you should. It's about John Nash, who is schizophrenic. In that movie, when Nash looks at a page or blackboard full of words or numbers, some seem to light up and seem more important than the ones around them. When I look at that quote from Ayala, I see it like this:
“Do you want to blame God for that? No, science has provided an answer. It is the clumsy ways of nature and the evolutionary process.”
I cannot imagine how an evolutionary biologist of all people could use the word 'clumsy' to describe evolution. It is breathtakingly elegant. It is the epitome of parsimony. If anything, he should be arguing that only god could create such a magnificent way of making things. But that wouldn't fit with his 'benevolent god' idea because evolution is cruel and wasteful. He needs to throw in the word 'clumsy' to muddy the waters.
Professor Ayala: nature isn't clumsy, but organisms are indeed cobbled together. Do what you like to reconcile this with your prior belief but I'm going to take the parsimonious high ground, if it's all the same to you. The Templeton Prize is ill-gotten-gains and you know it. Bask in the admiration of small-minded desperate idiots if that's what gives you a hardon, but you should give the money away. You don't deserve it. And you know you don't deserve it.