To be honest, I don't know how life arose. I have a general understanding of the standard model, and that's enough for me at the moment. Obviously the theories are changing as we learn more, especially since the whole purpose of the scientific method is to attempt to poke holes in theories. You keep the ones you can't prove are wrong, and change them if you discover they are.
In science, you start with observed facts, make up a hypothesis to explain them, then make predictions based on that hypothesis. Then you do experiments to test it. If it passes the experiments it moves on to a theory. So in order for something to be considered a theory, it has to have been used to make valid predictions.
Unfortunately, most people who use the phrase "only a theory" seem to think that a theory is an untested hypothesis, which isn't the case.