Behe explains, patiently and politely, exactly where Mark Shea - and many, many others - go wrong in their ID criticisms.
One of the reasons I maintain a tremendous amount of sympathy for ID arguments is because they are mangled and misrepresented by critics to an absurd degree - easily on par with any misrepresentation of the Five Ways or cosmological arguments in general.
What I find amazing, though, is that someone like Mark Shea will go absurdly public with damning criticisms of the Intelligent Design argument, without even bothering to check whether they're representing the argument in anything close to an accurate way. Now, I can understand if you were firing from the hip in a blog comments section. But an article with your name on it, that people can use to evaluate whether or not you're even reasonably reliable when it comes to representing an argument?
Either way, if you're at all curious about the fundamental claims and rationale behind ID reasoning, the above article is worth a read. It's clear, direct and pleasant. Behe is a good writer when it comes to these topics.