Bavaria found itself in turmoil again as prewar tensions between liberals and socialists returned and escalated. The liberal Heisenbergs had to choose sides, especially when the Bolsheviks became involved. Paranoia soon set in, and more than a thousand suspected communists died in the frenzy. Werner himself had to dodge a blockade to retrieve black-market provisions. Though he chose to focus on his studies rather than join the service, he did serve several brief stints in the military. On one occasion he was assigned to guard a "red" prisoner who was to be tried and executed the next day. The young Heisenberg asked the man his life story, which was probably similar to the standard history of other soldiers, who were more in need of high army wages than truly committed to any political ideology. By the next morning the man had convinced Heisenberg of his innocence, and the latter managed to secure the man's release.

The confusion of postwar Germany left many young members of the bourgeoisie searching for answers, and Heisenberg found them in the youth movement he joined. He was approached by a group of boys several years younger who sought the guidance of an elder but who refused to accept an adult leader. The group became known as Gruppe Heisenberg, officially under the auspices of the Regensburg reform movement and the Young Bavaria League. At one point, Heisenberg's group joined a larger meeting of about 250 Pathfinders, which came together at an isolated medieval castle. There, surrounded only by nature, the boys debated the questions that had plagued them all, focusing on their new political situation and how they were to respond to it.

For the most part, the youth movement was about solidarity and bonding rather than activism in any real sense. Heisenberg led his group on hiking tours and served as a father figure, while he himself made loyal friends upon whom he could fully depend. In addition to debating politics, the group also read poetry and enjoyed music together: rather than attempting to change the world, much of their time was spent reveling in an isolated realm. Heisenberg also led the group on more dangerous outings–perhaps as part of his competitive side, he enjoyed taking them to mountains and peaks that no other group had dared to climb. On one two-week hiking tour, he contracted typhoid fever and nearly died. Heisenberg's uncle, Dr. Mutert, was able to save him only by procuring the milk- and-eggs remedy from a patient in the country, as they were nearly impossible to find in the years immediately following the war.

The group also made time for more abstract discussion. Their general feeling of disillusionment made politics an unworthy subject during those idyllic retreats, so Heisenberg and his friends instead spent much time on topics of philosophy and theology. Heisenberg always maintained the reputation of a pragmatist, and later as a scientist he was seen as utilitarian. His fellow youth leaders tried to change this, engaging him in metaphysical discussions and forcing him to consider the philosophical consequences of his science. One man in particular had a strong influence on Heisenberg: Robert Honsell, who was only slightly younger than he. Later, Heisenberg would recall Honsell as the second most influential person in his intellectual development, after only Niels Bohr. Honsell, a very well-read man, introduced Heisenberg to much of the Western philosophical tradition; he later became a district judge. Honsell's impact was clear: though Heisenberg was not prone to philosophical reflection any more than most scientists, the interests he did have could often be traced back to Honsell.

The effects of the youth movement on Heisenberg's career are numerous. The youth movement pushed him to question traditional values, including scientific tenets that he would later challenge. In many ways, the possibilities opened up by the youth movement made him see that his path lay in science. Although his friends in the movement pushed him to pursue classical music, he saw that he had a great deal of potential in physics. He therefore chose utility over beauty, to the disappointment of many of his idealist companions. In a similar choice, Heisenberg would always regard science as above politics, foreshadowing his reaction to the arrival of the Third Reich, whose coming the youth movement had hoped for, though not envisioning it under the leadership of someone like Hitler.

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