@pnelson , thanks for the response. I honestly feel like the five year old here, and as such am curious about some of the concepts being discussed. I understand that you are interested in seeking truth, as am I. I am not a scientist, so I am often running off to research terms to catch up…that being said, I understand Methodological Naturalism to be a portion of the philosophy of Naturalism that allows for theistic views where Naturalism does not, and therefore would be opposite of what you are stating. I agree that Naturalism presumes a godless world, but methodological naturalism simply requires that the explanation of natural science be made in terms that disregard super-natural explanation.
As a Christian, this makes sense to me. I can still believe what I believe, but to prove something scientifically requires me to use only naturally observable data that produce naturally observable results. I cannot hang my hat on “that’s what the bible says” or “that’s what the Spirit told me” as a way of proving creation or evolution scientifically. It must be done by scientific methods while observing the natural universe. I do not see, by this definition, how MN presumes anything other than setting a guideline of how to practice science regardless of religious belief. Carroll’s full quote (from @Tim above) seems to be mistaking the term methodological naturalism to be the same as naturalism. Then in the final (bolded) paragraph supports MN as important to the scientific process. Naturalism and MN seem to me to be clearly different concepts. Naturalism is a philosophy (that negates ID) MN is a scientific method (that does not negate ID).
My purpose for pointing this out is to fully understand the conversation, and to not get caught up in any unnecessary disagreement. Please correct any misunderstanding I might have.
From Wikipedia (so it must be true, right?)…
Methodological naturalism[edit]
Further information: Alternatives to natural selection
Methodological naturalism concerns itself with methods of learning what nature is. These methods are useful in the evaluation of claims about existence and knowledge and in identifying causal mechanisms responsible for the emergence of physical phenomena. It attempts to explain and test scientific endeavors, hypotheses, and events with reference to natural causes and events. This second sense of the term “naturalism” seeks to provide a framework within which to conduct the scientific study of the laws of nature. Methodological naturalism is a way of acquiring knowledge. It is a distinct system of thought concerned with a cognitive approach to reality, and is thus a philosophy of knowledge. Studies by sociologist Elaine Ecklund suggest that religious scientists in practice apply methodological naturalism. They report that their religious beliefs affect the way they think about the implications – often moral – of their work, but not the way they practice science.[29]
Steven Schafersman states that methodological naturalism is “the adoption or assumption of philosophical naturalism within the scientific method with or without fully accepting or believing it … science is not metaphysical and does not depend on the ultimate truth of any metaphysics for its success, but methodological naturalism must be adopted as a strategy or working hypothesis for science to succeed. We may therefore be agnostic about the ultimate truth of naturalism, but must nevertheless adopt it and investigate nature as if nature is all that there is.”[9]
In a series of articles and books from 1996 onward, Robert T. Pennock wrote using the term “methodological naturalism” to clarify that the scientific method confines itself to natural explanations without assuming the existence or non-existence of the supernatural, and is not based on dogmatic metaphysical naturalism. Pennock’s testimony as an expert witness[30] at the Kitzmiller v. Dover Area School District trial was cited by the Judge in his Memorandum Opinion concluding that “Methodological naturalism is a ‘ground rule’ of science today”:[31]
Expert testimony reveals that since the scientific revolution of the 16th and 17th centuries, science has been limited to the search for natural causes to explain natural phenomena… While supernatural explanations may be important and have merit, they are not part of science." Methodological naturalism is thus “a paradigm of science.” It is a “ground rule” that "requires scientists to seek explanations in the world around us based upon what we can observe, test, replicate, and verify.[32]
Schafersman writes that “while science as a process only requires methodological naturalism, I think that the assumption of methodological naturalism by scientists and others logically and morally entails ontological naturalism”,[9] and “I maintain that the practice or adoption of methodological naturalism entails a logical and moral belief in ontological naturalism, so they are not logically decoupled.”[9]