Hi Gregory, I like your essay very much. I like that you considered the question before taking a particular approach to answering it. I had not thought of explanatory structure as fundamental. You are absolutely correct that it is explanatory structures that are fundamental to our understanding. I think your arguments are very well set out and the essay very readable.
You thew down a gaunlet - I'm not sure what to make of the challenge. It seems to me that studying emergent phneomena and using reductionist approaches are both valid ways of investigating how the universe is and is functioning. That there is emergence is fact. While the shell of a bird's egg can be explained by reductionism as a arragement of calcium carbonate atoms, the how its shape was formed requires the functioning repoductive anatomy of the bird. It seems that for a more complete understanding of nature both are needed. Yet also for happening in space, such as the laying of eggs, and for agency of the bird, rather than just existence (in spacetime), a struture of the universe with open future and seqenetial passage of time is needed too (in my opinion).
Whether the minutiae, or the organisation or complexity, or the way the universe functions is more fundamental depends upon that question of what we mean by fundamental. Fundamental to our human understanding or fundamental to the function of the universe. You have focused on the former and I have focused on the latter.
The chemical clock is interesting . I have taken a look at Belousov-Zhabotinsky reaction. I think from a quick search that name order is conventional. Its a problem I will enjoy thinking about. I like that you have set out those characteristics an overarching explanatory structure should have. I also agree very much with your point about interdisciplinary science. There is such a lot that I like I can't list it all.
Ended on an optimistic note was nice. The explanatory framework once established is settled, until it is found wanting and superseded. Whereas the study of nature is not, there is so much to explore and re-explore. Emergence offers opportunity. Another undervalued but important opportunity is evaluation of science. There is a vast amount of dead wood ( or possibly prune-worthy), that has accumulated over the decades of investigation.
Kind regards Georgina