  Complex systems with tightly coadapted parts frequently appear in living
systems and are difficult to account for through Darwinian evolution, that is
random variation and natural selection, if the constituent parts are
independently coded in the genetic code. If the parts are independently coded,
multiple simultaneous mutations appear necessary to create or modify these
systems. It is generally believed that most proteins are independently coded.
The textbook rule is one gene for one enzyme. Thus, biochemical systems with
tightly coadapted parts such as the blood clotting cascade pose a difficulty
for Darwinian evolution. This problem can be overcome if the current
understanding of the genetic code is incomplete and a system-level genetic code
in which seemingly independent proteins are encoded in an interdependent,
highly correlated manner exists. The methods by which human beings design and
fabricate complex systems of tightly coadapted parts are explored for insights
into the requirements for a system-level genetic code. Detailed examples of
system-level codes for networks of matching parts are presented. The
implications of identifying and deciphering the system-level genetic code if it
exists for the prevention, treatment, and cure of heart disease, cancer, immune
disorders, and for rational drug design are discussed.
