When Alexander was thirteen, Philip, to this point not much involved in his son's upbringing, decided to choose a tutor for him. The result would become one of the most famous mentors-student relationships in history. Philip's reasons for choosing Aristotle were not purely academic. First, there was Aristotle's family connection: his father had served as court physician to an earlier Macedonian king. Moreover, Aristotle had previously served in the court of Hermeias in Atarneus, and an alliance there would be useful for Philip's plans to invade Persia.

The position suited Aristotle as well. Not only did it offer a high honor and the chance to pursue his research under the most powerful of the Greek states, but it also gave him the opportunity to influence the development of that state's future leader. As the ultimate payment, Philip also restored Aristotle's native city of Stagira, which he had himself conquered years before.

Alexander's education took place in a setting removed from the capital city of Pella, in the more isolated village of Mieza, within the so-called Precinct of the Nymphs. In this rural seclusion, Alexander was joined by several of his most notable peers, some of them future kings themselves. At Alexander's departure, Philip urged his son to work hard and to learn to avoid repeating his father's mistakes. In response, Alexander rebuked his father for having had children by other women. In this regard, Alexander seems to have been troubled not so much by any moral compunction, but rather concerned for future conflicts over succession to his father's throne. Alexander's ambition was therefore evident even at this stage, if not earlier.

Alexander's education was for the most part formal, not the kind of life training that we might envision in a mentor relationship. Rather, the curriculum consisted mainly of standard subjects such as poetry, rhetoric, geometry, astronomy, and eristics–the practice of arguing a point from either side. Alexander developed a particular interest in medicine–and not merely a theoretical interest, for he actually prescribed treatments for sick friends throughout his life. When Alexander set off on his Asiatic invasion, he brought along with him a large group of zoologists and botanists, who returned with collected materials and information that would form the basis for several groundbreaking scientific works. Another of Alexander's favorite subjects was Greek poetry. He held an especially strong reverence for Homer, and he even saw the mythical Achilles as a model to follow in his own life.

Though perhaps best known for his scientific treatises, Aristotle also published his Ethics and Politics, and his influence in these areas also reached Alexander. Aristotle asserted this influence particularly with regard to the so-called barbarians–a term that was used to characterize essentially all non-Greeks. Alexander himself was already passionately anti-Persian; and Aristotle provided him with the intellectual justifications for his fated and inherited mission. Aristotle believed that slavery was a natural institution, and that barbarians were by nature meant to be slaves. He therefore encouraged Alexander to be a leader to Greeks and a despot to barbarians, treating the former as friends and the latter as beasts.

Aristotle saw barbarians as living only through and for their senses, incapable of rising above hedonism. Alexander, in his desire to follow a heroic paradigm, naturally placed great value on honor, and with it the virtues of self-control and self-denial. Therefore, in his own life he ate sparingly, gave generously while keeping little for himself, and had a cautious attitude toward sex. In these respects, Aristotle's influence was likely essential, for he pushed Alexander along a path that diverged greatly from the more precarious model set by his father.

Alexander spent three years studying with the great philosopher. In the meantime, his father was mobilizing troops to pay a visit to noncompliant allies in Perinthus and Byzantium. In 340 B.C., Philip he summoned the sixteen-year-old Alexander to return and serve as Regent of Macedonia and Master of the Royal Seal in Philip's absence. Thus Alexander would retire from the Academy and begin the lessons of real-life responsibilities.

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