Just because something exists in the "natural" world (universe) does NOT mean it arose (came into being) via purely natural processes. By limiting science to look for only natural explanations does not help increase our knowledge base.
I don't know what to make of this discussion, since I don't know what "natural" means in this context. Science can study processes that generate objective observations and that have some kind of regularity, because those are the only processes it has the tools to handle. Do the non-natural processes you're talking about meet these requirements or not?
Steve