P.H.A.G.E.S.: A Framework for Understanding Biological Systems

Understanding biological systems in order to facilitate scientific progress requires a framework that can reduce dimensional complexity. Herein, we summarize the P.H.A.G.E.S. framework, which can be used to understand, model, and manipulate living systems. P.H.A.G.E.S. comprises six major principles in biology: Predation, History, Assembly, Governors (energy, matter, space), Expansion, and Selection. All living things must navigate a landscape where energy is used to move matter in space. Together energy, matter and space are the Governors. Simultaneously, all living things must avoid Predation while they prey, and they must interact with other living things to form Assemblies, replicate themselves through Expansion, and generally do a better job at expanding than other living things, a process called Selection. Where each living system starts is History. Also proposed herein is the Goldilocks Line, a hypothetical line where the abundance of electron donors (e.g., organic carbon) is perfectly balanced with the abundance of electron acceptors (e.g., oxygen). No ecosystem exists on the Goldilocks line, but ecosystem deviation on either side of the line (excess electron donors or acceptors), determined by P.H.A.G.E.S., speaks to each ecosystem's health and function. Each aspect of P.H.A.G.E.S. affects, and is affected by, viruses, which are the most important members of the wholobiont, i.e., an ecosystem of organisms that make up each individual plant or animal. In this publon, we summarize the argument that a virocentric P.H.A.G.E.S. approach can be used to better study and understand ecosystem dynamics.