Methodological vs metaphysical naturalism

Science is an empirical and limited enterprise that is theistically agnostic, concerned only with the how mechanisms of nature as pointed out in chapter two. It is methodologically naturalistic; however, it is not metaphysically naturalistic. And the difference between methodological naturalism and metaphysical naturalism is immense. Science is metaphysically neutral.

Science, Creation and the Bible, Carlson and Longman, page 132