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Donald M. Baer was born on October 25, 1931, in St. Louis, Missouri. He was the second child of Russian immigrants who had not completed high school and who believed that in the United States, education was essential for success. Baer learned in early childhood that school was the most important thing in his life, that he should learn everything that was taught, and that he would go on to college. His mother supervised his homework, but Baer noticed that she and his teachers often disagreed about the correct answers to questions and solutions to problems. His curiosity about how these two sources of great authority could disagree on matters of fact caused him to wonder how people knew what was true and sparked his early interest in scientific proof.

By the age of 15, Baer was bored with high school and longed for the intellectual excitement of a university environment. His greatest dream was to go immediately to the University of Chicago, whose undergraduate college sometimes accepted students who had not finished high school. Baer's father, who earned a modest income as a union organizer, refused. He expected Baer to complete high school and go to the local state university, where the tuition was affordable. Baer's strong-willed mother immediately applied for and was offered three sales jobs in local department stores and announced that the money was needed to send Baer to Chicago. Baer's father could not permit his wife to work, as this violated the middle-class norms of the time (as his mother well knew). On the condition that she decline these offers, he agreed to pay the expenses, and Baer went to Chicago at the age of 16. He deeply loved the University of Chicago and never forgot his parents' sacrifices in sending him there. Within a week, he knew that he wanted to spend the rest of his life in universities. Decades later, he also enjoyed telling people that he did not have a high school diploma.

Baer spent 9 years at the University of Chicago, earning a bachelor's degree and a doctorate. Although he did not study psychology until graduate school, his undergraduate curriculum taught him the differences between experimental and other methods of study, and he soon realized that he was an experimentalist. Leon Nedelski, a physics professor and outstanding undergraduate teacher, was a powerful influence on Baer's later work in psychology, because he taught him experimental logic, operationism, and logical positivism.

As a graduate student, Baer initially studied mathematics but found it dull. One day, a friend who was studying psychology showed Baer the formula for the Weber-Fechner law in his textbook and asked Baer to explain the mathematics. Baer was intrigued and borrowed the book. Until then, he had thought that psychology was primarily Freudian and unscientific. He was surprised to see a mathematical formula in a psychology text and stayed up all night reading this book, amazed to discover the world of experimental psychology, where propositions about how behavior works required strong evidence from controlled experiments. As the sun rose the next morning, Baer finished the book and decided to study experimental psychology.

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