In Scientific Essentialism (2001), I attempted to develop an ontology of the kind envisaged in my 1987 essay. First, I argued that the ontology required for a scientific worldview should be a highly structured one. For one of the most striking facts about the world is the apparent dominance of natural kinds. There appears to be an immense hierarchy of substantive natural kinds, that is, natural kinds whose instances are what Aristotle would have called “substances”. For every different chemical substance (and there are hundreds of thousands of them) would appear to be a member of a natural kind. Each kind of chemical substance would seem (a) to be categorically distinct from all of the others, and (b) to have its own essential properties and structures. Moreover, the chemical kinds would all seem to belong in a natural hierarchy, the more general ones having essences that are included in those of the more specific. Given that this hierarchy of natural kinds exists, this is plausibly a significant fact about the world that should be reflected in any satisfactory ontology of scientific realism. The world is evidently not just a physical world, as I had assumed in the 1970s, but a highly structured one.

Secondly, there appears to be a vast hierarchy of dynamic natural kinds, that is, natural kinds whose instances are events or processes. Indeed, everything that happens in the world seems to consist of events or processes that are instances of such kinds.