Mechanistic explanation is central to biology, describing how processes are realised through structured interactions among components. APS retains this role but clarifies its scope: mechanisms do not explain biological phenomena in isolation but only within the organised systems they help sustain.
A mechanism specifies how a process is carried out—how molecular, cellular, or physiological interactions produce a particular effect. However, what counts as a biological effect, and why it matters, depends on the viability-oriented organisation of the system. Mechanisms therefore operate within, and derive their biological significance from, constraint-closed organisation.
APS does not replace mechanistic explanation but situates it within a broader explanatory framework. Mechanisms realise biological processes, while organisation defines the conditions under which those processes contribute to persistence. Mechanistic accounts are thus necessary but not sufficient for biological explanation.
Mechanism in APS is organisation-dependent: it explains how processes occur, but only within systems whose organisation makes those processes biologically meaningful.