APS fully accepts the reality and importance of biological mechanisms.
Mechanistic explanations identify entities, activities, interactions, causal organisation, and the processes through which biological phenomena occur. They are indispensable to biological science and may provide sufficient explanations for particular biological questions.
APS investigates mechanisms in relation to living organisation where that relation is relevant to the explanatory target. It asks how particular biological activities bear upon viability, regulation, and the maintenance or re-establishment of organised persistence.
This does not establish that mechanisms explain only how processes occur while organisation explains why they matter. Nor does it imply that mechanisms merely realise an organisational explanation or become biologically intelligible only when reconstructed through APS.
Mechanistic and organisational explanations may address different or overlapping questions. Where they address the same explanatory target, their relationship must be assessed rather than assumed: they may overlap, complement one another, remain independent, enter into tension, or provide different degrees of explanatory gain.
APS therefore rejects the identification of mechanistic explanation with mechanistic reductionism. Its emphasis on organisation does not subordinate mechanism, but provides a framework for investigating living organisation where that organisation is itself explanatorily relevant.