Thank God John has revived Evolving Thoughts! 
As usual, his latest post contains lots of food for thought [God and evolution 2: The problem of creation]. I want to pick out one morsel because it's back in the news recently.
It's the problem of "methodological naturalism" and whether it restricts science. Kairosfocus recently posted an article on methodological naturalism at Uncommon Descent [Optimus, replying to KN on ID as ideology, summarises the case for design in the natural world]. He pointed out, quite correctly, that by restricting science to methodological naturalism it means that Intelligent Design Creationism becomes non-scientific by definition.
I've argued frequently in the recent past that science is not bound by methodological naturalism [Is Science Restricted to Methodologial Naturalism?] [Accommodationism in Dover] [Methodological Naturalism]. My stance has evolved over the past few years. Back in 2007 I was a staunch defender of limiting science to methodological naturalism [Methodological Naturalism].
Jerry Coyne agrees with my current position on methodolocical naturalism. We are both upset by the way it's used to support accommodationism at NCSE [The NCSE Position on Science vs Religion] and at AAAS [AAAS Supports Accommodationism, Illogically]. If you're new to the subject, read Jerry's latest post at: Must we assume naturalism to do science?. That will bring you up to date.
John Wilkins and I have debated this controversy several time [e.g. John Wilkins Defends Methodological Naturalism]. The important point, as far as I'm concerned, is that there are respectable philosophers who disagree with the idea that science can't investigate the supernatural because it is constrained by methodological naturalism.
Here's what John said yesterday (in my time zone).
The term “naturalism”, however, is ambiguous. On the one hand it can mean giving a natural explanation through the use of scientific methods such as the use of human reasoning and observation. Or, it can mean the claim that only “natural” things exist. The first is sometimes called “methodological naturalism”, and it is the underpinning of all science, and indeed all learning about the world. The second is sometimes called “metaphysical naturalism”, although I think it is instead a claim about what exists (which is called “ontology” amongst the philosophical community). God might be natural in that sense. There is no real sharp dividing line between the natural and the supernatural that would satisfy most believers. For example, human nature for some is held to include a soul, which is divine. So let us call the second kind ontological naturalism.Obviously I don't think that methodological naturalism is the "underpinning of all science." I think science is free to investigate claims of the paranormal (i.e. not naturalism) and can, in principle, discover things that don't meet the definition of naturalism.
What makes me nervous is that this is John's field. Is he saying that among philosophers of science the overwhelming consensus believes that that in science you can only give natural explanations? Or is he simply offering his personal opinion disguised to look authoritative?
Is there a slam-dunk philosophical refutation of the position held by the likes of Yonatan Fishman and Maarten Boudry that Jerry Coyne and I (and many others) are unaware of?
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