Fascinating! It is interesting you should mention protein folding and machine learning. Any thoughts on Alpha Fold 2 being touted as a big breakthrough?
I just realized that the reason why even a computer linear traverses a tree is due to the underlying abstraction of a turing machine right? which is a head operating on a linear tape. That fundamentally limits the power of a computer to simulate reality as reality is non-linear as you point out.
Conscious thought, as you say, is linear but much of the heavy lifting in cognition is not done at the conscious level for eg., sensory perception or skills like walking or driving.
Also in the context of using ideas like complements attract or similarity attracts it makes sense when you explain it, but I feel silly in trying to think in that fashion which I suspect is due to the heavy conditioning of contemporary education. Reminds of a comment(clearly a non sequitur) on this blog post – “revel in the delusional comfort of anthropocentric vanity about the way the world was imaged to be thousands of years ago”. My question regarding this is – For creating laws of how protein sequences (as meanings) form / interact, do you get the ideas from human / psychological interactions?