Complex Biological Mechanisms: Cyclic, Oscillatory, and Autonomous

Abstract

The focus of this chapter is the implications of complex systems modeling for mechanistic explanation in biology and our understanding of it. These implications are substantial. The nonlinear and non-equilibrium nature of the interacting operations within organisms often is downplayed in initial proposals of how the parts and operations are organized so as to comprise a mechanism, but they are critical to the orchestration of operations that is required for the mechanism to perform its task. Moreover, the operations performed by the parts, and even the very identity of these parts, are affected by their interactions with other parts. Consequently, the characterization generated in other, typically simpler, contexts may have to be revised as researchers come to understand the dynamical interactions occurring within organisms. Openness to such recharacterization of parts and operations fortunately lies within the mechanistic framework—as does recharacterization of their organization, if that framework is appropriately extended. Consider that mechanistic research often begins with an extremely simple conception of organization. The components are thought to operate largely independently, with each feeding the product of its internal operations to another component that has limited if any impact on the earlier component. Such systems are nearly decomposable. Numerous systems do not fit that description, but biological mechanisms properly conceived generally do not. Increased recognition of their complexity has prompted inquiry into previously neglected temporal dynamics and the implications for understanding of how operations are orchestrated in real time.