A two-sorted logic for structurally modeling systems

Structural modeling of complex biological systems relies on formalisms inherited from physics. These formalisms scale poorly when dealing with interactions with many variables and agents working in systems that cohere at multiple layers. We propose a two sorted logic that supplements existing formalisms to mitigate these problems. The purpose of this second logic is to track how multiple contexts relate to each other, as well as to the dependent structures they inform: a situating of situations. In this way, we aim to capture the multi-layered and multi-system dynamics that have been elusive in modeling emergent systems. An apoptosis example is explored in the context of mental concepts.