President Bush dumped a couple of gallons of gas onto the Intelligent Design bonfire. There's a lively discussion going on in the comments of Jeff Goldstein's response to the issue. Ever one to jump on a pretense, I'm going to offer another thought against ID.
One line of Intelligent Design is to deny the role of randomness in evolution. Namely that each any every evolutionary change was thought out in advance by the Creator. I limit this to one Creator because the whole project would still be on hold if it were a committee project.
The issue comes up when one notes that there is no qualitative distinction between a useful mutation and a birth defect. It is not until the organism has developed and attempts to function in the environment. If every mutation is the responsibility of the Creator, then it must be responsible for every failed mutation and the suffering that comes about because of it. The Creator then becomes a bumbling craftsman who sweeps his mistakes under the rug while proclaiming the beauty of his rare successess.
A second issue is when one considers the many organisms that work well in the environment, yet can in no way be said to add to the smooth functioning of creation. Things like ebola, AIDS, leprosy, etc. One would believe that all that is in creation has designed into it. Hard to believe that a Creator that cares for its top of the chain would do something like that.
Either way, those who idolize the Creator can not logically consider him to be both omnipotent and omnibenevolent. The thin pretense of Intelligent Design seems to be creating its own philosophical problems for the understanding of the Creator.
One last note: This is NOT a scientific argument, it is a philosophical argument. Because nothing in creation can be outside the purvue of the Creator, anything we see will be inherently biased.
Upadate: Some people like to make the argument that evolution is not scientific because one can not perform experiments that replicate the process. Putting aside the virtual experiments in the process, it is not precisely true that experiments can't be conducted. Given that evolution occurs over hundred of thousands of years for large animals, the difficulties are of a practical nature rather than a theoretical limitation. At this point, I don't know if there are any scientists quite willing to put in the time, their own and their professional progeny, to properly conduct such a line of research.