byrnema comments on Belief in Belief - Less Wrong
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I am in occasional contact with religious people, and they don't behave as the "separate magisteria" hypothesis would predict.
For instance, I have heard things along the following lines: "I hope my son gets better." "Well, that's not in your hands, that's in God's hands." All this said quite matter-of-factly.
There is active denial here of something that belongs in the magisterium of physical cause and effect, and active presumption of interference from the supposedly separate magisterium of faith.
Of course most of those people back down from the most radical consequences of these beliefs, they still go see a doctor when the situation warrants - although I understand a significant number do see conflict (or at least interaction) between their faith and medical interventions such as organ transplants or blood transfusions.
This isn't just an epiphenomenal dragon, it's a dragon whose proscriptions and prescriptions impinge on people's material lives.
Interactions between the magisteria are contradictions for you, not necessarily to a dualist who believes it all works out, somehow. (For example, somehow we know about the second magesterium, and knowledge of it has significance on our interaction with the first.)
Also complicating matters is that each religious person has their own location on a scale of self-consistency. I find that most religious people fall well short of self-consistent, but not as short as claiming the dragon doesn't breath just so the CO2 detector won't be used.
My point in the comments above is that when religious people claim that there is no evidence or counter-evidence for God, it's not as often a desperate measure to protect their belief, but simply that their belief in God is not meant to be about an empirical fact like a dragon would be.
Contradictions are contradictions. If, in general, the magisteria don't interact, but in some specific case, they do interact, that's a contradiction. It's a model that doesn't meet the axioms. That is a matter of logic. You can say "The dualist asserts that no interaction is taking place", but you can't say, "for the dualist, that is not a contradiction".