Over the past several years, the concept of natural genetic engineering > has been advanced to encompass biochemical functions that make up the cellular toolbox for changing genome sequence composition and organization. Natural genetic engineering activities range from the introduction of point mutations by mutator polymerases to large-scale chromosome rearrangements mediated by transposable elements and non-homologous end-joining to incorporation of viral and microbial DNA into the genomes of host organisms.

The recent literature on whole genome sequences provides abundant evidence for the action of natural genetic engineering in evolution. Discoveries about natural genetic engineering have coincided with rapid progress in our understanding of epigenetic control > and RNA-directed chromatin formation. Both natural genetic engineering and chromatin formatting exemplify the "read-write" potential of the genome as an information storage organelle. Special attention needs to be paid to the role of viruses and other so-called "parasitic" elements in the origin of genome formatting ("natural genome editing") and natural genetic engineering capabilities. A critical question concerns the role of non-random genetic change operators in the production of complex evolutionary inventions.