In 1911, Heisenberg enrolled in the Maximilians-Gymnasium, a school was headed by his maternal grandfather, Nikolaus Wecklein. Under Wecklein's leadership, the school had acquired a reputation as academically and socially elite. Its distinguished alumni included Max Planck, one of Heisenberg's major forerunners in quantum mechanics. Despite trends in Germany toward the teaching of more practical skills, the Max-Gymnasium's educational approach remained staunchly classical. Heisenberg therefore spent the majority of his hours on Greek and Latin, with slightly less attention paid to mathematics, and very little attention paid to physics, which was the least significant subject aside from drawing. Only the outbreak of war in 1914 was able to reverse the trend, as science and technology found favor in both students and the Interior Ministry.

In 1913 Heisenberg experienced one of the highlights of his youth. Ludwig, the Prince Regent of Bavaria, came to Max-Gymnasium for the dedication of a new building, and Heisenberg's mother had written a poem for the occasion. The 11- year-old Werner was allowed to recite the poem to the prince during the ceremony. Ludwig rewarded the young boy with a pair of cufflinks engraved with the letter "L"–a token that Heisenberg would cherish with pride.

When World War I began in August of 1914, many of its participants were enthusiastic. Few of fighting age had experienced the reality of warfare, and many of the participant countries were filled with romanticized images of victory, nationalist vehemence, and feelings of social unity. August Heisenberg, still an officer of the Prussian reserves, was called to active duty. August's political views were strong, and he was not content with mere garrison duty. By October of 1914, he was promoted to captain, and by January of the next year he was leading a company on the front in France. The esteem that Werner held for his father must have increased greatly during the early period of the war, for August showed courage both in word and action. By April of 1915, however, August had had enough of the war, as he soon suffered disillusionment out in the brutality of the trenches. He requested a transfer back to Munich, and it was readily granted on account of his age. Exactly how Werner perceived his father's move is not certain, but it likely contributed to a sense of disillusionment with the war and with his father.

The Max-Gymnasium was forced to make many adaptations, as Bavarian troops used the school's new building to quarter soldiers. Shortages of coal and other resources also forced many cutbacks, including the shutdown of a new physics laboratory. The school finally regained control of the building in 1920, only four months before Werner graduated. Nevertheless, he had mastered his studies, and because of all the interruptions, he had more time for independent study that brought him far beyond the assigned curricula. He taught himself calculus at the age of sixteen in order to tutor a family friend preparing for the mathematics section of a doctoral examination in chemistry. Werner also found number theory fascinating, but he did not show a strong inclination toward physics until he discovered a single comprehensive textbook that served as his only source of information.

For two years, Werner also took part in early training for younger pupils. THe war, however, ended a month before his seventeenth birthday. Meanwhile, food shortages would take their toll on the growing boy, and for the summer of 1918 he and his family decided that he would go to work on the farms. With almost 4,000 other students, Werner worked from 6:00 in the morning to as late as 10:00 at night. Though the work was monotonous and often grueling, he would later look back on the summer as significant for his development. The work experience showed him for the first time what labor really meant, and also exposed him to people from different classes. Exhaustion prevented any significant mental work, so Werner spent his free time playing chess–winning all his games–and playing the piano. He occasionally studied some mathematical texts he had brought along, as well as one of Kant's Critiques.

Upon Heisenberg's graduation, he was entered into a Bavaria-wide competition for the sponsorship of a foundation established in 1849 by King Maximilian I. The evaluating committee was enthusiastic about Werner's demonstrated ability in math and physics, but expressed reservation about his German essay. He took the eleventh and last available position. He also declined the offer of free room and board, preferring to live with his parents and to allow the support to go to needier students.

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