Abstract
Part I presented a theological basis for naturalism in science. As an intentionally limited discourse, science is sustained in a subsidiary context of religious/philosophical beliefs, whose adequacy and scope affects its creative horizons. I argue that biological systems cannot be adequately understood in terms of the materialist, mechanist, and reductionist assumptions appropriate to physical science, but require broader naturalistic explanatory paradigms. An organizational logic concerned with certain types of function or achievement is manifest in biological organisms, which is distinct from the principles of physics. Examples are given showing how tacit use of this logic influences current biological research.