The UK university I work for gives foreign students a US book which teaches the FANBOYS rule, which states you should have a comma before for, and, but, etc (all conjuctions) which separate clauses. (My mother taught the polar opposite).
That's a rotten rule for the UK, I'm sure, but does it have any real validity in the US? A quick google survey of "I like coffee but I don't like tea" type sentences suggests to me that it isn't.
I've seen something which suggests that the rule is valid but doesn't apply if one clause is not a complete thought with subject and verb. Also, some think that it doesn't apply for short sentences.
fanboys
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I'm also fairly partial to the comma-as-pause school of thought, but yes, academia doesn't seem much in favour (Mr.Pullum attacked the idea very recently on LL, I seem to recall). I think that clearly very many native writers use commas that way, because they don't know clause from gauze for one thing, and usage is after all supposed to be king these days.
Of course, the trouble is my students may not be pausing in the right place, since they are not native speakers.
Of course, the trouble is my students may not be pausing in the right place, since they are not native speakers.