Within what might loosely be called the sceptical community there is a faction holding that scepticism should be confined to matters of "woo-woo" – in general such things as alternative medicine, astrology, lay-lines, dowsing, claims of psychic ability, spiritual mediumship, alien abduction and so forth, and should not be concerned with religion. Daniel Loxton, editor of Junior Skeptic, in his 2007 essay "Where Do We Go From Here?" – an impassioned rallying cry to sceptical endeavour – suggested that the atheism/theism debate was diverting scepticism from its true concerns, and urged a return to those concerns. (Incidentally you can hear him deliver the essay in episode 63 of the Skepticality podcast. Note also that there is now a follow-up publication, "What Do I Do Next?")
To me, this partitioning of religious scrutiny has a flavour of Stephen Jay Gould's non-overlapping magisteria (NOMA), an idea suggesting that science and religion are separate disciplines addressing different things: science being concerned with the material, physical realities of the universe, and religion with the spiritual, moral aspects of human life. I find this to be a false distinction, and it can be seen as such by looking at religious claims (and their tacit assumptions). For example the Catholic Church recently complained that Reiki, a form of "energy healing", isn't backed up by scientific evidence. It's hard to believe that those Catholics behind this statement don't see the huge irony of what they are saying.
From the scientific point of view NOMA would be just fine – science isn't concerned with the spiritual or moral aspects of life. At least, not until religion attempts its own overlapping on to the scientific side – which it does all the time (see the Catholics' objections to embryonic stem-cell research, or the Pope's claim that condom use increases the incidence of HIV in Africa, for example). NOMA is all very well, but "you leave us alone, we'll leave you alone" only works if both sides play by the rules. They don't, and the biggest offender is the religious side.
Science, I admit, does encroach on to the "spiritual" side occasionally, but usually only as a result of specific challenges. Scientists have little incentive to keep to their own side when religion is so blatant about not doing so itself.
Another problem with confining scepticism, as a movement, to "woo-woo" is the tricky matter of delineation. Does excluding religion also exclude spiritual mediumship? I think it does. But the existence of communicating spirits, or of ghosts in general (or faeries, or aliens for that matter) are clearly matters warranting scientific investigation. As is, therefore, the existence of a god.
Jerry Coyne fueled the debate recently with a blog-post entitled "Truckling to the Faithful: A Spoonful of Jesus Helps Darwin Go Down" in which he took issue with the US National Academy of Science and the National Center for Science Education's "accommodationist" stance regarding the compatibility of science and religion.
Coyne's post may be incendiary, but when we're dealing with what's true and what's false, clouding the issues with equivocation will be ultimately counterproductive.
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