Darwin never understood the mechanism underlying the process of evolution. There was chance variation and natural selection, but how was this information passed on from generation to generation? Gregor Mendel knew the answer. Ironically, this unassuming monk had published the basic principles of genetics in an obscure journal, which was found uncut and therefore unread in Darwin's library. His article was discovered many years later and integrated into a revised theory of evolution. James Watson and Francis Crick provided an even deeper understanding of the process of evolution when they uncovered the genetic code in which we are written [WATSON JA]. It is a language of four letters arranged in a double helix.^₄

The next step was the Human Genome Project in which the sequence of letters in the human genome were laid out. This was accomplished in a surprisingly short time - partly because of vast improvements in the technology and partly because there was a race between private and public institutions. Private won but, rather than attempt to copyright and make a fortune, as many people feared, the leader of the private team made it available free to everyone on the internet [SHREEVE].

There were further surprises in the human genome itself. It turned out to be short (there are varieties of rice with more genes), and there are master genes which control other genes (those we shared with very simple, primitive organisms). This lent some support to Steven Jay Gould, Richard Lewontin, and other evolutionary psychologists who argued that there could be sudden, dramatic shifts in the evolutionary process. Such changes could be attributed to changes in those master genes which cascaded throughout the entire system under their control.

A major problem with the theory of evolution, as Darwin presented it, is that gradual change through very occasional mutations (errors) in the transmission of the genetic code could not explain the emergence of complex systems like, for example, the eye. The search for missing links, like simple versions of the eye, have been futile. This provides further evidence for sudden shifts in evolution (evolution by jerks) as opposed to gradual evolution (evolution by creeps).

In modern evolutionary theory, the problem of the emergence of complex systems shifts from the eye (structure) to language (function). There are no simple languages - that is, missing links, which would lend support to the theory of evolution as first formulated by Darwin. Fritjof Capra argues that, whereas master genes may help explain sudden shifts, the answer lies outside the genetic system [CAPRA]. What is passed on from generation to generation is not just the genetic code, but the entire organization of metabolic networks. The so-called secret of life is written not just in the genes but in the entire cellular network of enzymes, membranes and other cellular structures. The process is not just genetic but epigenetic. Mutations are not random but are "actively generated and regulated by the cell's epigenetic network, and (thus) evolution is an integral part of the self-organization of living organisms." [CAPRA, Page 167].