Conceptual Challenges in the Theoretical Foundations of Systems Biology

In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, we claim that a relational ontology is a necessary tool to ground both the conceptual and explanatory aspects of Systems Biology. A relational ontology holds that relations are prior-both conceptually and explanatory-to entities, and that in the biological realm entities are defined primarily by the context they are embedded within-and hence by the web of relations they are part of.