Intracellular Molecular Pathways and the Biosystems that Arise from Them: An Ontological Investigation

Abstract

The cell’s ability to metabolize foodstuffs, synthesize proteins and nucleic acids, and transduce extracellular signals, all rely on an intricate intracellular network of biological systems. These biosystems are the dynamic manifestations of the molecular pathways that define them and arise when these molecular pathways are activated. In this paper, I ask if the transformation from pathway to biosystem (abbr., bioSip, for intracellular pathway biosystem) is accompanied by a change in ontological status, and if so, what this new status is. After introducing key biochemical concepts, including the difference between pathway and biosystem, and the concept of enzyme coupling that transforms an ensemble of enzymes into a bioSip, I analyze the ontological status of bioSips, specifically asking if the empirical data support the view that bioSips exist in nature as ontological unities, as actualities. I conclude that certain highly structured bioSips, known as metabolons, are indeed actualities. Finally, I explore the metaphysical foundations for the ontological unity of metabolons, considering three metaphysical systems that emphasize the dynamic and relational nature of reality: process philosophy, Aristotelian-Scholastic substance philosophy, and Ivor Leclerc’s philosophy of nature.