Not proteins, but cell to cell (this is still an interesting mechanism to contemplate and develop ...
Either way, the idea of machines or systems as "living" and able to communicate intent and process, even if only within their own "umwelt", is really interesting. Even a taste of that would make modern systems easier to debug and understand, if not more robust (which would be a better starting point for many systems anyway I suppose).
Neural networks definitely are black boxes, at least at an individual level. Sure the concept remains the same generally, but the internals are different and hidden from case to case