Abstract

Understanding the operation and evolution of gene regulation networks is critical to understanding ontogeny and evolution. According to Stuart Kauffman's view, (1) each cell type cycles through its own repeated pattern of gene expression, (2) the order of ontogeny is dependent on these cycles being short, and (3) evolution is possible because these cycles mutate gradually. This view of gene regulation reflects Kauffman's view that ontogeny is fundamentally the process of cells repeating cycles of activity. I criticize Kauffman's view of gene regulation networks and offer the connectionist theory of gene regulation as an alternative. On this view, the generic order of gene regulation mechanisms is due to the qualitatively consistent way that one gene product influences the expression of another. This allows networks to be stable and evolve to regulate accurately, allowing cells to react appropriately to their microenvironments, due to design by natural selection. 1. Introduction2. Kauffman's Model of Gene Regulation3. Explaining the Order of Kauffman's K = 2 Networks4. The Importance and Relevance of Kauffman's Explanations of the Order of Gene Regulation5. Additional Orderly Facts of Transcription6. The Order of Network Accuracy7. The Accuracy of Connectionist Networks8. The Evolvability of Gene Regulation Networks9. Laws of Structure.