Design Characteristics of Biomolecular Systems

Michael Samoilov
Lawrence Berkeley National Laboratory

To control their development and respond to environmental cues,
organisms rely on a complex network of reacting and interacting
molecules to execute the program stored in their genome. Analogous to
electrical ones, these chemical circuits have “devices” which – after
an often complex signal processing sequence – finally execute a
behavioral or developmental change. The lowest level devices are
regions of genomes and molecules making up the network itself: genes,
promoters, proteins, small ions, metabolites, etc. The signals are the
activities of each of the molecules or complexes at any given time and
at their sites of action. Higher level devices may be identified in
networked collections of chemical reactions that form “regulatory-
motifs” and/or “modules”. However, the rules for such biomolecular
network assembly appear to be quite different from the ones we have
come to expect in dealing with the silicon-based systems. From the
mechanisms of signal processing to the choices between robustness and
performance, even the most basic of organisms appear to be driven by a
particular set of design principles, which – when applied to their
intracellular processes – manifest themselves through such system
properties as fault-tolerance, redundancy, efficiency etc. Identifying
key factors in the emergence of such properties can lead to better
understanding of the organization principles of the underlying complex
biological systems.

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