Elizabeth started another thread (http://theskepticalzone.com/wp/?p=256) stating that methodological naturalism (MN) “underlies the methodology that we call science.” Later she spoke of “methodological naturalism, as in the working assumption that scientists make about the world in order to predict things.” Then she quoted Wikipedia, which states: “all scientific endeavors—all hypotheses and events—are to be explained and tested by reference to natural causes and events,” adding that this is “more or less the definition I have been assuming.” In other words, science studies ‘nature-only’ because it is naturalistic – it sees nothing other than nature that *could* be studied. Elizabeth sticks with this definition when she says “Science occupies the domain of natural explanations.”
Still later, Elizabeth admitted she is ‘not wild about’ MN (or what I suggested as more accurate of her statements: science applies ‘methodological probabilism’) and also that “‘methodological naturalism’ is a poor term.” Thus, her concession: “now that I realise that the term [MN] appears to denote different things to different people, I will avoid it.” So, the main argument in the OP was deserted.