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Firstly, free will isn't what you think it is. A random choice might seem "free" but it's not "willed" in any meaningful sense. So let's leave aside the free will question because that term is pretty much undefined at this point.

What your post sort of hints is what's known as the hard problem of consciousness. I recommend reading the Wikipedia pages on it and qualia if you're interested.

Suffice it to say, given our current understanding of physics, we are no better than finite state automata (see the Bekenstein Bound). The only escape from this inevitability is if we collectively decide that the hard problem of consciousness is irreducible, and then something like panpsychism becomes preferable.

This is unlikely though, and we've been through this once before in the debate over how living matter differs from non-living matter. Must there be some "secret sauce" added to non-living matter to bring it to life? This was the proposal of vitalism, but eventually biology came to prominence and all of those who insisted living matter had to be different just died off and we were left once again with a reducible, mechanistic understanding of living matter. So it will be with consciousness (see [1] for an example of how this might work).

[1] http://journal.frontiersin.org/article/10.3389/fpsyg.2015.00...

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