Hierarchical Self-Organization in the Finitary Process Soup
  Current analyses of genomes from numerous species show that the diversity of organism's functional and behavioral characters is not proportional to the number of genes that encode the organism. We investigate the hypothesis that the diversity of organismal character is due to hierarchical organization. We do this with the recently introduced model of the finitary process soup, which allows for a detailed mathematical and quantitative analysis of the population dynamics of structural complexity. Here we show that global complexity in the finitary process soup is due to the emergence of successively higher levels of organization, that the hierarchical structure appears spontaneously, and that the process of structural innovation is facilitated by the discovery and maintenance of relatively noncomplex, but general individuals in a population. 
Olof Goernerup and James P. Crutchfield