You are wrong. God knows our choices which are determined by us, He doesn't chose for us.

https://www.youtube.com/watch?v=TMp30Q8OGOE

http://rationalcatholic.blogspot.com/2014/02/do-quantum-entities-have-free-will-and.html

If God chooses to momentarily suspend the laws of nature as in, say, miracles, then they are the opposite of random. Furthermore, matter created out of nothing does not necessarily contradict the laws of nature and is consistent with our current scientific hypotheses.

For a theist perhaps; for a deist definitely, but for the Jew or Christian there is no problem presented by the universe being indeterminate. God's omniscience is not based on knowledge of how everything works nor is His knowledge related to time. The Christian understanding of God's transcendence and being eternal makes His knowledge not a differing degree from our, but wholly other than ours. This is what people like Stephen Hawking seem to not appreciate when they say we'll know the mind of God when we discover the unifying theory/law of all things and are able to explain the great mysteries such as the big bang and black holes. I do not at all think it is unreasonable to think it possible for us to attain such knowledge (though I find it highly unlikely). However, all we will have done is be able to explain the processes of the universe in it's entirety and make more accurate predictions. There would still be other questions beyond our reach.

I vote for (2) as well, but I don't think it leads to deism. In the example of a London made of legos, the Designer could walk away after making and programming the first block. However, in the lego scenario there is no chance involved. That is the point of the article: classical physics doesn't allow for chance and quantum mechanics is all about chance. In other words, with quantum mechanics no thing has to be the way that it is. Considering the great number of factors involved for the development of intelligent life it screams for something more than a deist conception of God to me.

Unless you believe in God, in which case things like, gravity, the laws of motion, and so on are more like house rules you give to children that can be suspended and re-written on a whim and all matter can be created out of nothing through sheer will. Except for that, all laws of the universe are constant.

I'm not sure that the author has explained away this problem. I think he just says, god can know everything and there be free will because he's god. He's beyond all that.

Yes, but you need that as an additional premise to arrive at determinism.

I am not sure what difference it makes—at least to those of us who lean strongly toward materialism—if the brain can be completely explained by classical mechanics or if quantum mechanics must be brought into it. Now and then I have seen speculation that the brain may be subject to quantum effects, and that that (somehow) can be used as an explanation of how determinism is false and "free will" can exist. But I can only imagine that "freeing up" the brain in this manner—exempting it from determinism—couldn't account for "free will." It would just add an element of true randomness to the working of the brain, not some kind of special power to make "free" choices.

It is a statement about science that science is nowhere close to proving.

Science doesn't prove statements about science. And of course science has not "proven" that quantum effects don't enter into the baking cupcakes. It seems to me that good neuroscientists will make the working assumption that the brain can be explained by classical mechanics until they bump up against something that classical mechanics can't explain, which may be never.

It seems to me that it may very well be the case that believers in things spiritual (like souls) may be clinging to the mind/brain as yet another "gap" which only theology, not science, can explain and will have to keep retreating a bit every time neuroscience advances.

It is true that no one knows for sure. But, as far as I know, neuroscientists have not yet needed to concern themselves with quantum physics. Maybe this will change. Until then, it seems reasonable to treat the brain as a purely classical system.

Yes, but you need that as an additional premise to arrive at determinism. It is a statement about science that science is nowhere close to proving. That is that classical mechanics can explain ALL brain activity. We are a long was from fully explaining everything the brain does.