ok, let me try to get this argument clear. the claim that the universe is a natural system (which i am going to parse as "contains only material things'): is it an empirical or scientific claim? if it is, then so is the claim that the universe is not a natural system. evidence for one of these would be evidence against the other: either they are both empirical or neither is. in that case "intelligent design" is a perfectly acceptable scientific hypothesis. but of course the difficulty of deciding what might consitute a test of its truth leads you to suspect that it's not empirical. but if it's not, then neither is the claim that the universe is a natural system. if the latter is not empirical, then scioence rests (as it does in any case) on a worldview it is not in a position to establish, or even give any evidence for. its structure is in principle identical to religion by revelation: here are the indubitable foundations; here the incredibly elaborate structure produced on that basis. one might assay a pragmatic justification: it's true means it works. but i think the jury is out on the pragmatic value of science. and i think an argument could be made for the pragmatic justification for catholicism or buddhism. and i think that when you import such a standard of justification you are again making a sewries of foundational assertions that you are in no position to support; indeed, that they form the foundation of science is enough to show that they cannot be scientifically justified.