If there is no God, then ultimately there is no objective standard for good or evil. Gould's no-designer argument only are valid if a designer must always produce what human engineers consider perfect designs. Then he moved to his reasons for not believing in evolution. If Dawkins could demonstrate that small variations accumulate into big ones, by a purely natural process of gene selection, then there would be no debate. Johnson's point is that there is no real mechanism in PE that could explain the build-up of complex adaptations.
Embryonic recapitulation is dead.
Homologous organs do not have homologous genes. There is no simple gene-character correspondence. The molecular evidence does not reveal a sequential pattern. This peer pressure keeps it going. I think this is over-simplifying PJ's argument.