[timinman]

Fair enough. He was specifically speaking to 'naturalness' as technical designation in physics. I am getting a little more general.

The scientific method seeks to be entirely empirical - which makes sense for understanding what we can observe.

But what happens when what you are trying to understand is not observable? You fool yourself if you think you are being empirical when you are not. (His comment about moving the yardsticks applies here).

Any endeavor to understand the universe, especially origins, ends up involving philosophical presuppositions. Science aspires to avoid that, but can it?