I don't have the will to read a 40 page pdf at the moment, but my initial reaction to that argument is that evolution is not perfect and does not produce the same results in all species. Some animals hibernate for months, while some sleep much less time than we do. Not to mention that it seems like a cop out that avoids any possibility of progress through technology.
Why should we expect an easy cure to syphilis in a drug if evolution has not found one? I don't know, but penicillin still works pretty darn well.
In fact, you shouldn't have expected an easy cure to syphilis. It's a dramatic exception. The vast, vast majority of problems the body has are not easily solved by a simple chemical. This is born out by the tremendous difficulty of finding effective drugs which don't carry unacceptable side effects.
Why should we expect an easy cure to syphilis in a drug if evolution has not found one? I don't know, but penicillin still works pretty darn well.