"Anything that has effects can be studied by its effects."
But do things have to have effect to exist?
And the point I was getting at was that "methodology" is an aspect of a philosophy. Science is thus a philosophy, and as such, is an attempt by Man to answer the questions he sees before himself. "Why" is just as valid as "How", yet science only addresses "How."
To get a complete answer, one must answer both. This makes scientific reasoning incomplete reasoning, thought essential to finding out what the Truth is.
"Why" is just as valid as "How", yet science only addresses "How." Answer enough How questions and you get to a lot of Why questions.
Disease, birth defects, storms, drought, earthquakes, floods, meteorites, etc. All of these have at one time been Why questions, and are now How questions.