I was reading John Baez’s paper on operads and phylogenetics trees where he formalizes a Jukes–Cantor model of phylogenetics. Because biological questions receive different answers depending on the model used, I was wondering if the operad that represents that model could be compared to an operad representing a different model. i.e., with some distance metric or structural similarity, or perhaps by choosing an appropriate topology on them? So, for example, we might instead adopt a model with more parameters like the Kimura one to better treat the patterns in our data. And it would be interesting to quantify, conceiving of the first model as a predecessor and the second as a recently discovered successor, what was retained in the successor model.

I've been hoping to measure structural continuity across theory change (e.g., the preservation of Newtonian mechanics in a limit of GR, and the same for classical mechanics to quantum which can be measured by deformation theory). But I'm having trouble doing this with biological models, specifically phylogenetic ones formalized in a category theoretic way.

I've talked to Baez about this a little on twitter, so let me know if attaching that would help answer this.