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I remember in my high school chemistry or physics class or something, we WERE told that "by the way, atoms don't REALLY look like this; the truth is a lot more complicated, but we still use this, because it lets us work out what's going to happen with electron shells and stuff -- even if it doesn't REALLY look like this, this is a useful model, because the math works on it, so we can use it to get the right answer." They didn't make a big deal about it, but they did hand out a photocopied paper with little pictures of what electron clouds, even though it wasn't on the test or anything. Still, it was at least MENTIONED. They at least MENTIONED that we work with models that are useful, which are usually simplified from what's really going on. Maybe we only spent ten minutes on it in the whole year, but it was there.
Was that something that was brought up in your primary or secondary school science education?