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Trevor_Blake comments on How to tell apart science from pseudo-science in a field you don't know ? - Less Wrong
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To answer your general method query, this essay by Karl Popper deals with the issue of distinguishing science v pseudoscience. However, from my reading of, you need to know a bit about the topic, or at least observe it in action, to make a judgement.
What gives you this impression? I'm not saying you're wrong - just that it's something I haven't picked up on myself.
Regarding Freud, I get the impression that his therapies have some merit (placebos work; all talk therapies seem to have some benefit iirc) but his theories are utter horseshit. I know a lot of people that work in special needs education, particularly dealing with autism, and there seems to be no real professional consensus as to what the best approach is. I will ask some questions for you though. I'd hazard a guess that it's important to reinforce whatever methods the kid's parents or educators are using, as long as those methods aren't counter-productive.
Up-vote for Popper!
Ask your friend: "How would you know if that treatment was not working?" And by 'not working' I mean (a) no change (b) a change for the worse (c) a change for the better, but not related to that treatment (d) a change for the better, but at a greater cost than benefit. The more clear the idea of how to know if that treatment was not working, the more likely it's science.
I don't know you, your friend or your son's friend. I don't know what any of you need, although I'm sure just being compassionate instead of always being right is a part of it. My Popper-inspired suggestion above is good for distinguishing science from non-science. It may not be helpful to what any of you need.