Current belief about evolution is that it only acts to refine manifest 'phenotypic' features - it can't favour or improve hidden or silent genes.
This belief is wrong.
Evolution can and does act on genes that only indirectly affect the phenotype. This aspect of evolution is more than a mere scientific curiosity. It is central to understanding how evolution can act rapidly, or equivalently how evolution can evolve structures of 'extreme perfection'.
In fact a number of genetic mechanisms that affect DNA and that are understood at the molecular level can and should be reinterpreted in this light. It is no accident that genes exist that affect other genes. These indirectly acting genes have evolved because they have an evolutionary advantage. They make evolution more rapid than it otherwise would be. They have been selected along with the phenotypic features they have indirectly given rise to.
The selection on indirectly acting genes need not even be weaker than on directly acting genes - for an indirectly acting gene may have more far reaching effects on the phenotype, through influencing a number of genes, than any one single direct gene.
Evolution is a multi-level feedback system. It is 'recursive'.
The net effect is that evolution can act more rapidly than one might otherwise expect. This is 'Meta-evolution', the evolution of traits that makes evolution 'go faster'. To make the ideas concrete, I'll now give examples that show how meta-evolved traits work. These traits are subject to the evolutionary process because they affect other genes.
Two extended examples of meta-evolution are given in the next two pages: