2015/06/03 by Cameron Smith, Ximo Pechuan, Ximo Pechuan-Jorge +5 · 4 citations
Biochemistry, Genetics and Molecular Biology · Mathematics · #Artificial intelligence #Bioinformatics #Bioinformatics and Genomic Networks #Biological network #Biology #Computational biology #Computer science #Constraint (computer-aided design) #Context (archaeology) #Distributed computing #Evolution and Genetic Dynamics #Function (biology) #Gene Regulatory Network Analysis #Isolation (microbiology) #Mathematics #Modular design #Network architecture #Network topology #Process (computing) #Selection (genetic algorithm) #Theoretical computer science #Topology (electrical circuits) #q-bio.MN #q-bio.PE #q-bio.QM
paper · pdf · doi:10.1098/rsif.2015.0179
published in Journal of The Royal Society Interface 12(108), 20150179 (Royal Society) · 40 pages, 11 figures, 1 table
openalex publication_date 2015/06/03 · arxiv created 2015/06/09 · arxiv updated 2015/06/10 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
Constraints placed upon the phenotypes of organisms result from their interactions with the environment. Over evolutionary time scales, these constraints feed back onto smaller molecular subnetworks comprising the organism. The evolution of biological networks is studied by considering a network of a few nodes embedded in a larger context. Taking into account this fact that any network under study is actually embedded in a larger context, we define network architecture, not on the basis of physical interactions alone, but rather as a specification of the manner in which constraints are placed upon the states of its nodes. We show that such network architectures possessing cycles in their topology, in contrast to those that do not, may be subjected to unsatisfiable constraints. This may be a significant factor leading to selection biased against those network architectures where such inconsistent constraints are more likely to arise. We proceed to quantify the likelihood of inconsistency arising as a function of network architecture finding that, in the absence of sampling bias over the space of possible constraints and for a given network size, networks with a larger number of cycles are more likely to have unsatisfiable constraints placed upon them. Our results identify a constraint that, at least in isolation, would contribute to a bias in the evolutionary process towards more hierarchical -modular versus completely connected network architectures. Together, these results highlight the context dependence of the functionality of biological networks.