Realism and reference ontologies: Considerations, reflections and problems

In "Ontological realism: Methodology or misdirection?" I offered a detailed critique of the position referred to as "realism" taken by Barry Smith and Werner Ceusters. This position is claimed to serve as the basis for a "realist methodology" that they seek to impose on the development of scientific ontologies, particularly within the biomedical sciences. Here, in part responding to a reply to those criticisms by Smith and Ceusters, I return the focus to an examination of fundamental incoherencies in this realist approach and propose an alternative that is amenable to much of what Smith and Ceusters hope to accomplish. And I sketch what I believe is needed to advance ontology theory and practice in the sciences.