Just as Nestor begins with references to an unnamed "him" who turns out to be the ancient Greek general Pyrrhus, the first paragraph of Proteus finds Stephen thinking of an unnamed thinker: "Bald he was and a millionaire, maestro di color che sanno." The Italian phrase, which comes from Dante's Inferno, means "the master of those who know" and refers to Aristotle. The other details (baldness and riches) come from medieval biographical traditions about Aristotle, and the term "diaphane" is a transliteration of the ancient philosopher's Greek. Stephen seems to be preoccupied with Aristotle ("he," "he," "his," "he") throughout this first paragraph, but Aristotle's empiricism clashes in his thoughts with a mystical search for absolute truth inspired by Jakob Boehme and George Berkeley.
In canto 4 of the Inferno, Dante is in Limbo, the antechamber of Hell which houses those who lived without sin but are not saved, in many cases because they lived before the coming of Christ. In a particularly "honored" part of Limbo, lit by bright light that seems a pagan approximation of Heaven, Dante meets the great poets of antiquity (Homer, Virgil, Horace, Ovid, Lucan) and then enters a castle where he encounters many more virtuous pagans. One figure in particular stands out: "When I raised my eyes a little higher, / I saw the master of those who know, / sitting among his philosophic kindred. / Eyes trained on him, all show him honor. / In front of all the rest and nearest him / I saw Socrates and Plato." In writing of Aristotle so admiringly, Dante is following the lead of Thomas Aquinas, who referred to Aristotle simply as the Philosopher. In A Portrait of the Artist Stephen has revered Thomas Aquinas. In Ulysses he turns to Aquinas' inspiration and model, Aristotle. Nestor, Proteus, and Scylla and Charybdis all find him musing on Aristotelian ideas.
At the beginning of Proteus the subject is vision, sight, "thought through my eyes." Against the idealistic approaches of Boehme and Berkeley, who see the objects of sight as "coloured signs" conveying an immaterial meaning ("Signatures of all things I am here to read"), Aristotle discusses sight as an avenue to understanding the reality of physical bodies. In his treatise On the Soul, as Gifford observes, the philosopher identifies color as the distinctive object of sight. And in his supplementary treatise On Sense and the Sensible he identifies the property of diaphanousness (transparency) as something that inheres to different degrees in all physical bodies and allows color also to inhere in them. The idea seems to be that light passes through bodies to varying degrees and bumps up against color as a kind of limit to the transparency. From this analysis Stephen draws the not very earthshaking (but amusingly phrased) conclusion that Aristotle was a materialist: "Limits of the diaphane. But he adds: in bodies. Then he was aware of them bodies before of them coloured."
Soon, though, Stephen is reeling back into the mystical way of understanding experience. He takes his own advice to "Shut your eyes and see," but what he wants to see is the apocalyptic disappearance of the created universe: "Am I walking into eternity along Sandymount strand?" This thought experiment fails, however, and empiricism wins the day: "Open your eyes now. I will. One moment. Has all vanished since? If I open and am for ever in the black adiaphane. Basta! I will see if I can see. See now. There all the time without you: and ever shall be, world without end."
The phrase "world without end" is not only part of a Christian doxology but also a fair description of Aristotle's understanding of matter. In the Physics Aristotle argues that in some form the world must have existed forever, with no beginning in time, because all existent things (which he understands as formed matter) come into being from some preexisting matter, and to suppose that the matter itself came into existence from preexisting matter involves one in an infinite regress.
Six sentences later in Proteus Stephen will think of the Christian idea of "Creation from nothing," which contradicts Aristotle's conception of eternally existent matter. But there is good reason to suppose that Joyce is seriously advancing the Aristotelian conception when Stephen thinks "world without end." The Linati schema identifies the "sense" of the episode as "Prima materia (ΠΡΟΤΕΥΣ)". Prima materia (an alchemical term meaning first matter) is a concept whose origin is often attributed to Aristotle, and by identifying it with PROTEUS Joyce seems to be suggesting that eternally existing matter is the stuff from which all the protean shapeshifting of life emerges.