Assumptions in Science

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Over at Unqualified Offerings, Thoreau writes:
"In a continuing effort to highlight the way that even the most fundamental assumptions are subject to experimental testing in science..."

This, of course, logically cannot be the case. How, for instance, could the fundamental assumption that experimental testing is a good way to get at the truth be tested experimentally without logical circularity? Or the idea that their is some sort of quantitatively stable relationship between a sequence of measurements? (You have to simply assume this, or all of your measurements are merely random pokes in the dark that prove nothing.)

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