Jon -- Interesting article and theme -- "Conceptual barriers to integrative universities" -- and "the two cultures".
Both of these ideas have been highly motivating for me, and do tend to drive my interest in "the structure of knowledge"
https://en.wikipedia.org/wiki/The_Two_Cultures
"The Two Cultures" is the first part of an influential 1959 Rede Lecture by British scientist and novelist C. P. Snow which were published in book form as The Two Cultures and the Scientific Revolution the same year. Its thesis was that science and the humanities which represented "the intellectual life of the whole of western society" had become split into "two cultures" and that this division was a major handicap to both in solving the world's problems.
Perhaps over-simplistically, I tend to view the relationship between the two cultures ("deep intuition versus empiricism " -- or perhaps "humanities versus science") as essentially involving levels of abstraction (and generalization) – and I called that idea “the bridge across consciousness”
And I saw a basic beak in the definition chain as happening or emerging somewhere along a common spectrum that should be connecting these levels – but for various reasons, including those you cite, is not actually working in practice, except maybe in rarified or experimental cutting-edge integral or new-age kinds of environments.
My sense is – this is the biggest epistemological/ontological/philosophical challenge of our moment in history. We need to figure this out and build a bridge that works.
PS – I like this too:
> The way I see it, then, logic is more an application of mathematics than a subfield of it.
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