I would advise that you check out this page that debunks Philip Johnson's pseudoscientific (for a lack of a more precise word) junk. Another good read can be found here
Have you read Johnson's book? If you've read Johnson's book and are impressed with this "refutation," then there's really no point in further discussion. The article fails to even mention the two pillars of Johnson's critique of evolutionary theory: the complete lack of fossil evidence for the development of various species through micromutations and the plain absurdity of punk eek.
Medved outlined the pretty much insurmountable problems in #303.