I would think 'to upset' here means 'to disturb or distract from the normal routine' in the sense that art is meant to send a disruptive message to the viewer, the listener, the reader etc... that will waken him to new emotions and sensations. Whereas science is intended to demonstrate that the humans do have some grasp or control on the world that surrounds them ; or at least some understanding of it ; which somehow reassures them and makes them feel more comfortable with this world.
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