While I agree Newton may have reached the wall on explaining why/how, have we considered that he was simply trying to be politically correct? Just by saying what he did about how the universe works had , I am sure, already caused panic/concern among the masses who were most likely 99% fundy loons.
Maybe he was trying to cool the reaction (maybe also to avoid being burned at the stake)by throwing the creator thingy in there? We are not sure exactly how he really felt about the true existence of God. How do we know his intentions?
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