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Some points:
1) I think we have to keep in mind what the FCI (and similar tests)
is good for. We are trying to determine the best way(s) to present
the material in class so that students gain the maximum
understanding. The FCI is an attempt to compare one teaching method
against another. I think it can be used for that. If I try something
new next year (with a statistically valid sample of students) and the
scores go up then maybe I'm on to something.
2) If you are evaluating teaching methods you want to know how much
the student got out of YOUR class and YOUR methods. So It seems
important to me to both pre and post test. Most standardized tests
(such as the AP exam) are designed to be given once to assess
knowledge base. They do not tell you where this knowledge came from
(reading outside of class, mom is a mathematician etc.)