The universe may be intelligently designed and yet not be a simulation. The theory of intelligent design does not rise or fall with the simulation hypothesis.
The idea of the book is not merely to dunk on the critics. Michael Behe, to be frank, doesn’t find of any their criticisms very meaningful.
The brain assists the organization and recall of thoughts by segmenting them and associating them with stimuli. But who is doing the thinking?
Believe it or not, many officially smart people think that (1) we are just computers made of meat, (2) computers will soon become conscious, or (3) both.
We know they are just molecular machines, but some proteins appear to have uncanny abilities to sense a situation and make decisions.