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If you mean "Irrational" as in "He exhibited irrational behavior, officer!" then no, they are not irrational - rationality in that sense is only a property of Agents (And things that you can conveniently shorthand as Agents, e.g. Societies, Ant Colonies etc.)
@MoziburUllah Right, but "Perfect Copy" in that sense does not mean the same as what we're talking about, e.g. the electrons are allowed to be in different orbitals.
A point re the novel: Even if, as Mozibur Ullah states, one "hasn't understood the nature of the novel" when one knows all the physical facts of it, you HAVE reached the point where you can recreate it perfectly - even if you don't know what it is about.
But as soon as you remove the label "God," it becomes trivial - instead of "God" "Upholds Reality," you get "[Label for what principle is necessary, which may or may not exist]" "[Upholds reality to the degree that it is necessary, which may or may not be no degree at all.]" but that is a useless maximum-entropy answer.
This isn't a question of philosophy, it's a question of demographic statistics - but I don't think anybody has ever researched which of his five proofs have convinced more atheists.
Additionally, there are plenty of things God has decided that I am NOT free to do: Fly by flapping my wings, change color at will, bend my limps against my joints etc., so he has specifically decided that "free will" means I am free to be evil, instead of free to fly. Thanks, God.
@MoziburUllah: I think you misunderstood Rex Kerr: He's not saying "Let's replace religion with the matrix," he's saying that if you proposed The Matrix as an explanation for things, that would be considered a claim which you'd need evidence for and the fact that God slips by untested is a sign of bias; he is refuting Neil's first claim "question of God's existence is not a scientific question."
Non-overlapping Magisteria is a political dodge - the scientifically inclined get to say "We're not talking about God and we're not letting him into Science Class because NOM," the religious get to say "I don't have to scientifically prove a DAMN THING and can take it all on faith!" As such, it is useful to both theists who don't want public disproof of their claims and scientists who don't want to be part of that controversy. So it stays. In politics. For useful epistemology, I suggest disregarding it entirely.
