1) Quantum phenomenon -- ie, the universe and any given subsets of it you care to name -- are not Turing-equivalent. The universe has no problem factoring quantum configurations which may or may not represent prime numbers in linear time into amplitude distributions that overlap whenever they aren't prime. 2) There is nothing mysterious about the universe, correct. It is lawful. There are things mysterious about our crudely hand-drawn maps of the territory. 3) Arbitrarily small cause: The big bang. Large-scale effect: The universe.