Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach

Abstract

Systems biology is a rapidly expanding field that integrates diverse areas of science such as physics, engineering, computer science, mathematics, and biology toward the goal of elucidating the underlying principles of hierarchical metabolic and regulatory systems in the cell, and ultimately leading to predictive understanding of cellular response to perturbations. Because post-genomics research is taking place throughout the tree of life, comparative approaches offer a way for combining data from many organisms to shed light on the evolution and function of biological networks from the gene to the organismal level. Therefore, systems biology can build on decades of theoretical work in evolutionary biology, and at the same time evolutionary biology can use the systems biology approach to go in new uncharted directions. In this study, we present a review of how the post-genomics era is adopting comparative approaches and dynamic system methods to understand the underlying design principles of network evolution and to shape the nascent field of evolutionary systems biology. Finally, the application of evolutionary systems biology to robust biological network designs is also discussed from the synthetic biology perspective.

On the Interplay between Entropy and Robustness of Gene Regulatory Networks

“…Suppose the gene regulatory network in (1) suffers the following random intrinsic parameter fluctuation and extrinsic disturbance in vivo [32,35,40,41,42,49,52]:…”

“…The investigation of robustness of gene networks in evolution is still in its infancy and needs to be discovered. In fact, robustness allows changes in the structure and components of gene networks owing to intrinsic random noise and extrinsic random disturbances, but specific functions are still maintained [52,53].…”

“…Therefore, the robust stability condition of a gene network at the equilibrium point x e (trait) is the same as (20) except the parameter fluctuations S l mainly due to the random gene mutations of sex-chromosome in evolutionary process, i.e., there should exist a positive solution 0 ) (  X V for HJI in (20) in the disturbance-free case [52]. If the gene network can tolerate the intrinsic random fluctuation and can attenuate the environmental disturbance to a level ρ simultaneously in the evolutionary process, then there should exist a positive solution 0 ) (  X V in (21) [52]. Similarly, by the global linearization technique, the robust stability of gene network to tolerate intrinsic genetic mutations in the evolutionary process is guaranteed for a trait if there exists a positive solution P>0 for LMIs in (31).…”

“…In the evolutionary process, the random transmission and random mutation of genes provide the diversities for natural selection. Gene networks need to robustly evolve under these random gene transmission and gene mutation to meet the natural selection [36,[50][51][52]. Therefore, the robust stability in network evolutionary process is a natural selection force.…”

“…This intrinsic robustness of a genetic network can enable co-option, so that new traits (or corresponding new genetic networks) can be generated in the evolutionary process [36]. The underlying principles of natural selection in network evolution can be discussed from the systems biology perspective [52,53]. A stochastic dynamic process is given to discuss robust genetic regulatory networks in the evolutionary process from the viewpoint of nonlinear stochastic regulation theory [50,[54][55][56][57][58][59][60].…”