It’s true that when you confront biologists with a particular complex structure like the flagellum they sometimes have a hard time saying which part appeared before which other parts. But then it can be hard, with any complex historical process, to reconstruct the exact order in which events occurred, especially when, as in evolution, the addition of new parts encourages the modification of old ones. When you’re looking at a bustling urban street, for example, you probably can’t tell which shop went into business first. This is partly because many businesses now depend on each other and partly because new shops trigger changes in old ones (the new sushi place draws twenty-somethings who demand wireless Internet at the café next door). But it would be a little rash to conclude that all the shops must have begun business on the same day or that some Unseen Urban Planner had carefully determined just which business went where.

[...]

Although proponents of I.D. routinely inflate the significance of minor squabbles among evolutionary biologists (did the peppered moth evolve dark color as a defense against birds or for other reasons?), they seldom acknowledge their own, often major differences of opinion. In the end, it’s hard to view intelligent design as a coherent movement in any but a political sense.

It’s also hard to view it as a real research program. Though people often picture science as a collection of clever theories, scientists are generally staunch pragmatists: to scientists, a good theory is one that inspires new experiments and provides unexpected insights into familiar phenomena. By this standard, Darwinism is one of the best theories in the history of science: it has produced countless important experiments (let’s re-create a natural species in the lab—yes, that’s been done) and sudden insight into once puzzling patterns (that’s why there are no native land mammals on oceanic islands). In the nearly ten years since the publication of [I.D. proponent Michael] Behe’s book, by contrast, I.D. has inspired no nontrivial experiments and has provided no surprising insights into biology. As the years pass, intelligent design looks less and less like the science it claimed to be and more and more like an extended exercise in polemics. [Emphasis added - Ed]

The rest of the article is well worthwhile.