title: The regulatory genome and the computer.
abstract: The definitive feature of the many thousand cis-regulatory control modules in an animal genome is their information processing capability. These modules are "wired" together in large networks that control major processes such as development; they constitute "genomic computers." Each control module receives multiple inputs in the form of the incident transcription factors which bind to them. The functions they execute upon these inputs can be reduced to basic AND, OR and NOT logic functions, which are also the unit logic functions of electronic computers. Here we consider the operating principles of the genomic computer, the product of evolution, in comparison to those of electronic computers. For example, in the genomic computer intra-machine communication occurs by means of diffusion (of transcription factors), while in electronic computers it occurs by electron transit along pre-organized wires. There follow fundamental differences in design principle in respect to the meaning of time, speed, multiplicity of processors, memory, robustness of computation and hardware and software. The genomic computer controls spatial gene expression in the development of the body plan, and its appearance in remote evolutionary time must be considered to have been a founding requirement for animal grade life.
authors.affiliation: Center for Computational Molecular Biology and Department of Computer Science, Brown University, Providence, RI 02912, USA.
authors.forename: Sorin
authors.initials: S
authors.lastname: Istrail
authors.forename: Smadar Ben-Tabou
authors.initials: SB
authors.lastname: De-Leon
authors.forename: Eric H
authors.initials: EH
authors.lastname: Davidson
mesh_terms: D003201:Computers; D005809:Genes, Regulator; D016678:Genome; D008957:Models, Genetic; D012984:Software