Cells and Their Organelles as a Testing Ground for Process- and Substance-Based Ontologies in Biology

Recently, a shift from substance-based to process-based ontologies of living beings and biological entities has been widely advocated, largely on the grounds that traditional substance thinking, by encouraging biological reductionism, fails to adequately capture the nature of biological wholes. Process-based approaches are instead taken to provide a more appropriate metaphysical framework for the constitutive dynamicity of living systems. These arguments, however, have been criticized for relying on overly reductive characterizations of substances, which both classical and contemporary accounts describe as inherently involving change and activity. In this essay, I address the substance-versus-process debate from the perspective of contemporary cell biology. I argue that conceiving the cell as a substance is not only compatible with the centrality of processes, but that the cell continues to function as the fundamental reference point in biology precisely because it entails processuality as intrinsic to its dynamic mode of being. Within this framework, subcellular entities are identified by their functional subservience to the cellular whole. On this basis, I propose an empirically grounded criterion for distinguishing between purely processual and substance-like subcellular entities. Processual entities, such as the Golgi complex and the nucleolus, lack dedicated repair systems and tend to disassemble upon inhibition of specific metabolic activities. By contrast, substance-like entities, including cell-derived organelles such as the mitochondrion and the nucleus, depend for their persistence on specific repair systems, and their eventual dismantling under non-permissive conditions cannot be straightforwardly understood as the mere interruption of a process, but instead appears as the outcome of an active, regulated response.