Spirit and conciousness are basically the same thing, spirit is in a sense applied conciousness. We invented the concept of conciousness to define thought or mental processes, but scientifically speaking they are just chemical reactions, complex chemical reactions, but still so nonetheless.
That being said, there aren't any fundamental phyiscal differences between a living thing, dead thing, and a thing that was never alive.
I still don't understand. Are you saying a spirit is just complex chemical reactions, going by the fact that you say spirit and conciousness are basically the same thing?
There's a fundamental physical difference between a living thing and a thing that was never alive, though. A living thing can manipulate things that were never alive, whereas it cannot happen the other way around.
Conciousness does not describe the chemical reactions, it describes the human perception, the concept of self, which is what spirt boils down to at the core. There is a gap between how that translates from the chemical reactions that we observe and for all intents and purposes they might not be distinguisable.
Your second premise is not true however. Viruses are the titular example of inert material, that hijacks "living" cells to make copies of itself. Viruses are complex chains of protiens but they are not defined as living.
Living systems typically do two basic things: preserve and replicating genetic information, and maintain an organized system that decreases entropy by consuming energy and increasing entropy externally. Simply put make babies, eat, and shit. But we can and have created mechanical systems that can do these things to a degree.