Doubt

These are the areas I have a hard time believing 'official doctrine' whether it's science or religion:
If our universe is bottom up, materialistic, determined by laws of physics, our human/social relations defined by genetics and maybe the action of memes on the software running in our brain, then how can we behave as if we embraced certain values? Or free will, for that matter, and hence responsibility for our actions? How can we even claim something to be true, as that very belief itself may be the inevitable outcome of the deterministically firing neurons in our few pounds of wetware that we call brain?
Right and wrong? Meaningless words. Same as beautiful, ugly, good and bad, you can see where this is going. But then, if all our thoughts are merely products of natural laws, such as the laws of electrochemistry, or even cybernetics, then there is nothing to restrain our actions in any way. We would do well to emulate Stalin, or any great materialist dictator, and exploit our fellow humans as much as we want for our own gain, and with the clear knowledge that they are in no way less than us, or deserving of any such abuse. But neither do they have the right to be spared, to be treated with dignity, nor any other right for that matter.
This to me is the great pitfall of all 'scientific' explanations of the world, that in order for their often claimed humanism to be plausible, they have to stop thinking the thread through all the way to the end.
If the universe is top down, however, then what is its purpose? Why make it so hard to see God and his will, why hide him from us, why construct a world that functions so smoothly by deducible and seemingly ultimate laws? Also, if man is fallen, has sinned, why not clearly mark the way to salvation? What about those born retarded and unable to tell right from wrong, or who are psychopathic, autistic or whatever? If theistic religion is true and condones some behaviors while forbidding others, don't these people start with a significant handicap? Or are they exempt from the rules? And why would God make humans who have no or a sharply reduced choice in their actions?

There are others:         If man is the centerpiece of God's creation, then why is the universe so large? So old?
                        If science claims to explain everything, why are its laws becoming so muddled at the smaller levels?
                        Can we trust our senses and our reasoning, if our brains' actions are materialistically determined?