You’re implicitly suggesting that the brain “operates like a piece of machinery” and that we just need to adjust the form of “simulation”. The problem with this is that you’re also implying that the brain (and human mind) is a
deterministic system.
The implication of determinism is that everything is predictable. Given a set of inputs, in a deterministic system whose rules we fully know, the output is entirely predictable. We could extend this determinism to the whole universe, and reduce the universe into a pure function 'f' with a some specific initial state 'x'. Starting with f(x), for every unit quantization of time, f is applied on its previous result --- f(f(f....f(x)....))). And that's reality. (If you believe in a Big Crunch / Big Bang cycle, the output of 'f' at some point cycles back to the original 'x'.) The initial state 'x', and the definition of the universe function 'f' _is_ existence -- the totality of all that is.
I don't have any proof that we are not living in a deterministic universe, but all I can say is that, philosophically, I find the idea of determinism to be extremely upsetting. It empties life of any meaning. Why even continue living if everything you do was pre-programmed at the beginning of the universe? Determinism implies that the values of 'f' and 'x' could be blamed for the Holocaust. Moral responsibility becomes meaningless, because everything is pre-programmed. I think a lot of people, if they deep-down believed in this sort of mechanical determinism, they would sink into a very deep deep depression. I struggled with this myself, as a teenager—and I’ve emphatically rejected human mind determinism.
Believing in free will on the other hand, is very empowering. Believing in the concept of free will can in and of itself imbue one's life with a certain degree of meaning, purpose and drive. It means what you choose to do, matters. Life is meaningful; we’re not just empty automatons executing our pre-programmed futures under illusion of choice / free will. We are sentient beings with free being.
From the point of view of physics, I think free will in biological organisms will eventually be proven to some degree. The fact that in the last century, practically every physicist has come to accept that there's a lot of unpredictable behavior in matter, that cannot be deterministically predicted, and can only be described with probability distributions, has been very reassuring. My theory is that free will emanates from somewhere in these probability distributions, and is amplified in living organisms.