The traditions, tools and approaches of the molecular biologist may differ radically from those of the functional morphologist, but the fabric of living systems is seamless. There is nothing that makes design at the molecular level any more special than design or organization at any other level in biology. If anything, molecular design may be somewhat easier to account for, because the components of molecular machines are frequently the products of identifiable genes. But we know this is not the case. Many of the proteins in the eye lens, for example, begin their careers doing something completely different and unrelated to vision.
Evolution is a creative scavenger, taking what is available and putting it to new use.
The correct metaphor for the Darwinian process is not that of a First World engineer, but that of the Third World auto mechanic who will get your car running again, but only if parts already lying around can be used for the repair. Ironically, it is at the molecular level that this recycling of available parts is most apparent. This homeotic complex of genes is an exquisite piece of molecular machinery, precisely of the sort that the author finds so imponderable in a Darwinian world. Then we can see that just as the aging home-run hitter is drafted to be the designated hitter, the homeotic complex that helps guide the development of the vertebrate hindbrain predates the vertebrates by hundreds of millions of years. The homeotic complex did not evolve to regulate hindbrain development, it was recruited.