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I found the Scientific American article to be problematic in its focus on religious beliefs rather than just intuitive beliefs. Basically the whole study (as presented in the SA article) boils down to a correlation between analytical thinking and a rejection of intuitive beliefs that can be falsified by analytical thinking.

Religion does not really apply here, except for the fact that many Religious beliefs are intuitive and relatively easily falsified by analytical thinking. The thing is that only applies to a subset of religious beliefs, and it is entirely possible to hold religious beliefs that are not intuitive and are not really prone to being disproven by analysis. To usefully understand this study, I would want to know which specific beliefs were most likely to be disbelieved in the "thinker" sample while being believed in the control.

My guess, without having that data, is not that religion was being undermined, but that the study pushed religious people into a more theological frame of mind, which is not the same thing as making them disbelieve religion. I may have to look up the actual study, since I am now curious.

Also, the article seems to place the core of religion on belief in its headline's assumption that undermining belief is the same as losing religion. This requires a definition of religion that really only applies to Protestant Christianity. Given the core audience of Scientific American, this may be a valid assumption, but it's worth being aware what religion means in any given context as it is such a varied term.