Painting by numbers

Last Friday Ed Feser gave us a longish piece (8 paragraphs, 1200 words plus) devoted to elaborating the metaphor that the picture that physics gives us of the world is colourless.  The colour that physics leaves out is, of course,  causation, as Ed makes clear in his second paragraph:
Now as I’ve emphasized in a couple of recent posts (here and here) the description of the world physics gives us is no less abstract.  Physics simply does not give us material systems in all their concrete reality; it focuses only on those aspects of a system that are susceptible of prediction and control, and thus on those aspects which can be modeled mathematically.  Hence there is no reason whatsoever to think that if the description physics gives us of some particular system does not include a reference to some cause, it follows that there is no cause -- especially since (as Bertrand Russell emphasized) it is arguable that causality of any sort is, strictly speaking, left out of the description of the world that physics gives us. 
Surely this begs the question against any metaphysic that eschews causes?  It amounts to saying that we simply know that the world is shot through with cause.  The physics account lacks cause.  Ergo, it is inadequate.  And anyway, physics leaves out plenty of other stuff such as natural objects and all their secondary properties, so why not cause too?

The question touches on what I see as the central problem for philosophy:  how to reconcile our common sense ideas about the world and ourselves with the picture revealed by science.  In Sellars's phrases, the manifest image versus the scientific image.  As we know from many of his posts, Ed's view is that the 'mechanistic philosophy' of Descartes and his successors, beginning in the seventeenth century and leading to the naturalism of today, is a huge mistake, only to be corrected by a return to the perennial philosophy of Aristotle and Aquinas.  I am not sure how a modern scientific understanding of the world is to be accommodated within this view.  It would seem to have to be placed to one side, as it were, as almost an irrelevancy, or perhaps seen in purely instrumentalist terms.   Does this give rise to an interesting philosophical research program?  Well, there has been a resurgence of Aristotelianism in recent years, with works such as Oderberg's Real Essentialism, but these seem a reinvigorated defence of the traditional metaphysics.  Perhaps this is the best that can be achieved.  But what one is looking for is an explanation why, given that the world is as Aristotelians say it is, the scientific image is so compelling.  On the other hand, the scientific image does appear to have some resources for explaining how we come to have the common sense notions that we do.  So, despite the obvious mountains to be climbed, there does appear to be an ongoing research program in the opposite direction.

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