I think you didn't read my post. Either that or you didn't grasp the point. I wasn't defining natural/supernatural in terms of material/immaterial, that's your baggage not mine. My take on it was more to do with comprehensible/incomprehensible. That we have been able to build abstracted models of reality and test them is because we find that things invariably obey natural insentient laws; if there were some other category of phenomena that appear to not derive from underlying law they would be incomprehensible to us, just meaningless random noise in our rule-structured world. So I agree with you, an assumption of naturalism makes sense, everything is natural, and whatever we don't currently understand we can investigate, and we do so by taking a stab at an explanation, often no more than a hunch in the first place, building a theoretical framework round the hunch, see what predictions the theory would make and devise tests to gather evidence to either verify or falsify the theoretical model. If you can improve on that model for investigating things then by all means shout out.
Take the case of NDE's. How does the issue of comprehension change anything? Currently, people assume that all the NDE experience is merely brain related and that the person is not actually dead....and so there is no need to go for the after-life idea.
Why is this conclusion arrived at? Simply because the assumption is what leads to the conclusion. No one has investigated the possibility of after-life at all. They have only investigated the brain related theory.....and concluded that it is only a brain related experience. As circular as that.
Now suppose scientists assume that an NDE is actually an after-life experience, would they be checking out the brain MRI's? No. They would be racking their brains about how to possibly investigate the after-life. They would eventually have to realize that instead of treating the phenomenon as a 'supernatural' experience....they could think of it as a very natural experience except that it is at a different end of the natural spectrum.
This is how new ideas will be born, news ways of looking at the world....and new methodologies and new methods will evolve. Its not about me or someone handing out methodologies on a platter.
This is what I mean by science evolving and developing new methodologies and systems to investigate subtler and more intricate areas.
Its no use saying...we have checked all the NDE stuff with our tried and trusted methods and they don't show any results ...therefore sorry...these phenomena are just peoples imagination, they cannot be real!! That is rubbish way of trying to gain knowledge of the world.
Same goes for medical 'miracles', ESP's and many other phenomena.
The assumptions and premises that we start of with make all the difference in the direction the research takes.