Alex and William,

I agree with Mario B. that a foundation
for ontology based on systems is far and away superior to a foundation
based on physical things -- primarily because systems presuppose
non-physical mathematics and the supra-physical laws that govern the
physical things/stuff.

Without mathematics, science,
engineering, finance, business, etc., are impossible.  Without the laws of
science, there can be no explanation for any regularities in the world --
not even systems.  Without the habits of behavior of living things, there
can be no regularities in life.
That brings us to the supra-level
for all acceptable ontologies: (1) Mathematics as the foundation for all
logically possible patterns of anything that can exist in any possible
world.  (2) Actualities as the totality of everything that is observable
in our universe by any method that is possible.  (3) Necessities as the
laws, habits, conventions, and agreements that govern all events and
processes in actuality.

And -- surprise, surprise -- that
foundation happens to be the  top level of C. S. Peirce's ontology -- or
as he called it, the the three universes of discourse for any version of
logic.
As for reality, Peirce defined reality as whatever exists
independently of anything we may think about it.  That includes
mathematics, physical stuff (matter/energy or whatever), and the behavior
of all that stuff, including the habitual patterns of all living things,
including other people.

And by the way, this is the primary
reason why I have a low opinion about BFO -- because it does not recognize
the primacy of the three-way split.  Mario B's adoption of systems as the
basis for ontology is an important step beyond BFO because it implies
Peirce's three-way split.

John
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