The scholarly peer review process is a human process and thus, by definition, is far from perfect. "Type 1 and 2" errors abound, along with good-faith differences of opinion. Some truly outstanding papers emerge in less-prestigious journals and first class journals sometimes publish truly flawed papers. As Andrew Gelman's (Columbia--Statistics) post helpfully reminds us, however, the "peer review" process hardly ends with publication, especially for empirical work. Indeed, publication can often simply mark the beginning of another, enduring round of "peer reviews," for the better and worse, for journals and authors.
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