Consciousness and Free Will: these two mysteries are, I suspect, intertwined. I feel fairly certain that both are largely unsolvable, in that the methods of science cannot fully explain them in the sense of understanding their origin and their mechanism. The reason for this is that consciousness is by its very subjective nature not amenable to direct, objective observation. This is of course disturbing, as we do not like to confess that a prominent feature of the real world is forever beyond our grasp. But it is also scary for a practical reason: the human race will surely soon create artificial life forms, i.e., highly sophisticated robotic beings that will by all outward appearance be conscious. Will we give them the “benefit of the doubt” and assume they are? Will we extend the same rights to them as are extended to humans (and to some extent, to other animals)? Will we hold them blamable for crimes? These questions are not urgent today, but perhaps in the next few decades will begin to be.
Now, I have little doubt that evolution has produced consciousness by purely natural means, and that it has its function and origin entirely within the neuro-chemistry of the brain. My point is only that we can not observe it, and hence study it in the way we do other phenomena of nature. And hence we cannot be sure when it is present in a “system”, and so the philosophical problems alluded to above. It is true that we do not, for example, directly observe quarks, but we do observe them indirectly through their predicted associated particles. But it is different there, because of course no conscious beings existence is threatened if we are wrong about the existence of quarks.
The concept of God: I do not see how the Judeo-Christian “concept” of God can be rendered coherent. We have no way to model, in out brains, the existence of a solitary, infinite, outside-of-time Being. This is one of the main reasons I consider myself an “agnostic”. But I resist the term “atheist”, in spite of the excellent defense of that term given by the likes of Daniel Dennett and Richard Dawkins, because I think physics has taught us to be wary of expecting reality to be describable in terms that seem coherent to our common sense. The prime example would be quantum mechanics, the theory that applies to the micro world, i.e., atoms and smaller. Even Einstein balked at this theory because it did not conform to his idea of what the world must be like. But it does now appear that his dislike of quantum theory was unfounded, since quantum mechanics seems to work, and the common sense ideas of classical mechanics have seemingly been shown to be invalid through Bell’s Theorem.
Well, I for one do not know if there is a God or not, or if the idea even makes any sense. But I suspect that “there is something going on”. While I very much doubt whether anything like the God of the major religions exists, the universe and conscious life is probably not an accident (whatever an accident means when we are talking about universes). As many of Albert Einstein's writings suggest, it does seem that there is some kind of "mind" involved in creating the awesome and intricate complexity of physical existence. We are either not expected to know what it is that is behind it all, or our brains are simply not suitable for the task of understanding it all.