There are students whose religious upbringing is going to make them feel uncomfortable in a class where certain kinds of secular ideas are presented. There are students whose ideas about history or sexuality are going to be similarly challenged to question, to affirm or to change those ideas. That doesn't mean they shouldn't be exposed to them; that's why they're at school. That's why they come to university: to be taught how to think well and critically about material that they're being presented with. But it's the teacher who is certified to teach them how to do that.
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