The idea of organized matter performing specific functions, like the idea of intelligent design, is not by necessity theological. But it is logical, reasonable, and well within the confines of scientific endeavor. Your statement above is a clear example of favoring philosophy over science. Your interest is not in the accuracy of knowledge to be obtained by science, but in supporting the unscientific notion that all things are natural.
I am saying that science can only study those things that follow regular processes. Regular phenomena, by definition, are natural.
What is the confines of scientific endeavor?