"Science is based on observation not naturalism. Since we observe order and function in the universe, I think it is legitimate to infer a Designer, according to the laws of Cause and Effect."
Observation requires something to observe. Methodological naturalism is a requirement of science because no other stance allows one to test your claims. It does not follow logically that when one has found order that one has also found a Designer of that order. The existence of a deity/designer is not testable by science. That's the realm of theology and philosophy. Science can't say that a deity/designer does or doesn't exist; it's simply not a scientific question. Science has limits.