Spontaneous emergence of modularity in a model of evolving individuals and in real networks

Abstract

We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of modularity correlates with the rapidity and severity of environmental change. The modularity arises as a synergistic response to the noise in the environment in the presence of horizontal gene transfer. We suggest that the hierarchical structure observed in the natural world may be a broken symmetry state, which generically results from evolution in a changing environment. To support our results, we analyze experimental protein interaction data and show that protein interaction networks became increasingly modular as evolution proceeded over the last four billion years. We also discuss a method to determine the divergence time of a protein.

Ancient hot and cold genes and chemotherapy resistance emergence

“…Also, ancient genes have been shown to evolve more slowly, and hence are cold, and express more "core" functional proteins compared with young genes (24,25). As shown in Fig.…”

A nature-inspired approach to reactor and catalysis engineering

“…Some are more important, sensitive or robust than others. Collective behavior acts as an evolving, complex network [96][97][98][99][100], frequently with universal features, like scaling, clustering, and modularity [101 ].It would seem that insights in biological systems, reaction pathways and social networks, gained from topology, graph theory and information theory, could be useful not only in synthetic biology and process control, but also in generating more robust and adaptive bioinspired catalytic systems. …”

A physics-explicit model of bacterial conjugation shows the stabilizing role of the conjugative junction

“…HGT is a powerful force in biological evolution and is believed to drive processes such as the acquisition of antibiotic resistance genes [2,3] and virulence [4]. Since HGT involves direct interactions between mating cells, its dynamics is very rich and has been extensively studied by physicists [5][6][7][8][9][10][11].…”

“…HGT is a powerful force in biological evolution and is believed to drive processes such as the acquisition of antibiotic resistance genes [2,3] and virulence [4]. Since HGT involves direct interactions between mating cells, its dynamics is very rich and has been extensively studied by physicists [5][6][7][8][9][10][11].One of the mechanisms of HGT is bacterial conjugation [12,13] in which a plasmid -a small DNA molecule independent from the main bacterial chromosome -is copied from a donor cell to a recipient cell. Conjugation involves an initiation step upon contact between the donor and the recipient, the formation of a junction between the cells, and the transfer of a copy of the plasmid to the recipient cell.…”

“…This is the case of naturally occurring cellular agglomerates such as biofilms [17] and laboratory-cultured bacterial colonies [18]. Previous models of conjugation often assume well-mixed, unstructured populations [5][6][7][8][19][20][21][22] which is appropriate for bacteria cultured in shaken flasks or chemostats, but not for bacterial colonies growing on surfaces. Existing spatial models of conjugation [9][10][11] do not include mechanical interactions between cells, and conjugation is represented as an idealized, one-step stochastic process.…”