Biology repeatedly asks what is “really” fundamental: genes, organisms, ecosystems, information, or selection. APS argues that these disputes can confuse explanatory priority with ontological priority.

What becomes central in an explanation depends on the question being asked, the available methods, and the explanatory framework being used. Genes may become explanatorily central in population genetics, organisms in physiology, and ecological relations in explanations of distributed biological interaction.

But explanatory usefulness does not establish metaphysical primacy.

APS therefore does not infer a privileged ontological level from explanatory success. Genes, cells, organisms, populations, ecosystems, processes, and relations may become explanatorily important for different biological questions without one thereby becoming the universal foundation of biological explanation.

Scientific emphasis also changes as measurement technologies improve, mathematical tools develop, and new conceptual problems arise. What is treated as fundamental within an explanatory programme may therefore reflect the explanandum, available evidence, methods, and theoretical architecture rather than an independently established hierarchy in biological reality.

The framework therefore distinguishes:

  • explanatory priority — what becomes central for a particular explanatory question or task;
  • ontological priority — a claim that something is more fundamental in what exists or in the constitution of biological reality.

The first does not establish the second.

APS itself proposes that life is viability-oriented, constraint-closed organisation and makes living organisation an explicit explanatory target. This substantive commitment does not mean that APS’s explanatory architecture establishes the ontological priority of its concepts, nor that other biological explanations must be reconstructed through APS.

Where APS and another framework address the same explanatory target, differences in explanatory priority, terminology, scope, or architecture do not by themselves establish comparative explanatory superiority.