The second argument in th article that Dr. Swamidass put forward,
Is found here:
“How to eat Pentachlorophenol.”
The argument claims tha the recently evolved process of metabolizing Pentachlorophenol would qualify as an IC system. However, this is false. What has happened is the evolution of a new enzyme that is then used as a step in a metabolic pathway. In Darwin’s Black Box Dr. Behe was careful to point out that metabolic pathways are not IC systems Why not? Because unlike protein machines, the enzymes do not interact directly with each other, but with the substrate that they metabolize. Thus, a metabolic pathway can be cumulatively evolved, as new enzymes evolve to further metabolize the end product.
So there is no challenge here to Behe’s concept of IC.