System-Level Genetic Codes: An Explanation for Biological Complexity
  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. 
John F. McGowan, Ph.D