Hi John,
Thank you for your interst in the essay!
First, I should mention that I believe in the priority of (object or data) representation in science over any logical considerations: the latter should follow the "logic" of the chosen representation, i.e.logic should emerge during our "manipulation" of data.
Regrettably, the concept of representation emerged basically outside natural sciences (and was driven by CS applications), mainly because mathematics has not yet addressed it (and that is why it has been developed properly).
It took me some time to gradually realize that when replacing "point" representation by a structural representation, you get a much richer "geometry", because of the much richer variety of various path between two entities (just look at the variety of paths between two strings over a finite alphabet under deletion, insertion, and substitution operations).
I am familiar with category theory, but I felt that the concept of category is useful under the conventional mathematical (point) representation. What would be necessary in the "structural" mathematics is not yet clear to me: in the conventional math one has to seek (and build) various math. structure "outside" the (point) representation itself, since such numeric representations are too "simple". So the "structural" math. in view of very rich natural data structure, there is much less pressure to seek it in a manner similar to the conventional math.
I will comment on your essay shortly, in your essay's page.