I discuss two questions: (1) would Duhem have accepted the thesis of the continuity of scientific methodology? and (2) to what extent is the Oxford tradition of classification/subalternation of sciences continuous with early modern science? I argue that Duhem would have been surprised by the claim that scientific methodology is continuous; he expected at best only a continuity of physical theories, which he was trying to isolate from the perpetual fluctuations of methods and metaphysics. I also argue that the evidence does not support the conclusion that early modern doctrines about mathematics and physics are continuous with the subalternation of sciences from Grosseteste, Bacon, and the theologians of fourteenth-century Oxford. The official and dominant context for early modern scientific methodology seems to have been progressive Thomism, and early modern thinkers seem to have pitted themselves against it.