The metabolic world of Escherichia coli is not small, by M Arita (2004) PNAS. This brief communication illustrates that analyses of biological network topologies must always be cognizant of how the networks are constructed. By extracting atomic fluxes between metabolites from a genome-scale model of metabolism in E. coli, Arita concludes that the average distance between any two metabolites is much greater than suggested by earlier topological analyses which did not consider atomic fates. Ultimately, though we may try to deduce meaning from these increasingly thorough topological studies on biological networks, Arita's paper introduces something of possibly greater utility: a mass-centric network reconstruction method with homogeneous node types and physically meaningful edges. A reader is forced to wonder whether this method will generate as much insight as the better known flux-centric networks used to predict physiological bounds on metabolic, signaling, and even regulatory networks.

* written by guest reviewer