Dear Sara,
Congratulations on such a fine essay. Your essay is information dense and deserves a second reading. I kept picking up on ideas that I had previously missed or hadn't fully connected.
Tegmark suggests the Universe is a mathematical structure. I, on the other hand, believe the Universe is purely physical, and it is our job to discern the laws, which we do by constructing ontologies that are both mathematical and conceptual. In my area of interest, particle physics, the scale makes the force laws simpler to handle. At the scale of humans complexity reaches its limits as we currently know. At lesser scales emergent phenomena occur in a myriad of ways, which we generally quantify successfully with mathematics. But logic and math have their limitations, which our purely physical Universe ignores. Whilst our scientific method shines as a beacon for discovery, our experiments and their interpretations are generally flawed, but are slowly improving. At the scale of sub-atomic particles the going gets tough as our current best tools are quantum field theories that do not allow us to see clearly through the fog of accelerator data. The particle ontology needs a shake-up. Wolfram is trying a new way, by using 3D cellular automata, to visualise structure at these scales. His efforts can be short tracked by using rules that correctly manage the true symmetries of charge and spin.
Your essay touches on many of these ideas. I discuss the idea of relative presentism, which covers how 'abstractions exist and interact with the material world'. You say "we do not know in of itself what matter is beyond our mathematical descriptions of its interactions.". I would argue that to describe matter (say a fundamental particle) we need to describe both its properties (volume, charge, spin) and its force laws (attraction, repulsion, strength of action), which is a point that you also cover later in your essay. I enjoyed reading about constructor theory which you detailed very well.
We both have common ground in the notion of causality, which is where my idea of presentism shines.
I hope you can also comment on my essay.
Best wishes,
Lockie Cresswell