Samuel Aughey, the first professor of the natural sciences and director of the Nebraska state "museum", was born on February 8, 1831 in Pennsylvania. He was raised as a farmer, but entered Pennsylvania College and studied the natural sciences. Afterwards, he entered the Lutheran Theological Seminary of Gettysburg. From the beginning, Aughey was a man of contradictions, with his grounding in science and his education in theology. This training in two very different areas was fairly common during the period, but calls to issue the assumption of impartiality in science.

His training in the natural sciences led him on an expedition to Idaho and Washington territories on a government-funded project to survey the geological area as a young man. He would continue such expeditions throughout his life. Aughey would continue his studies of the natural sciences as well as theology, and often was a very public figure on controversial issues, such as abolition. His public abolitionist stance led to his resignation of his post as a Lutheran pastor, although he kept in close contact with many leading abolitionists of the day.  During the U.S. Civil War, he worked in the Christian commission as a pastor. In 1864 he moved to Dakota City, Nebraska and began working as a Lutheran pastor for the settlers there; at the same time, he also contributed to scientific work for the Smithsonian institute in the territories of the Dakotas, Nebraska, and Wyoming, although he was scarely mentioned in their publications, a slight that Aughey felt acutely.

While in Nebraska, Aughey agreed to become the first professor of natural sciences for the newly-formed University of Nebraska. He was also given the title of Nebraska state geologist. In addition to these duties, Aughey performed chemical analyses of medicines for local physicians, liquors for the Lincoln Temperance Society, soils and sediments for the state, and autopsies for state law enforcement.

As a matter of convenience, he was also titled the director of the Nebraska state museum, which at the time was little more than a few cabinets filled with stuffed specimens that served as teaching aids for his courses. The Board of Regents minutes, June 24, 1874, list Aughey's appointment to "Curator of the Cabinet and Herbarium." Aughey helped to expand the collection by adding taxidermied Nebraska fauna (primarily bird specimens), as well as securing a large collection of marine shells and invertebrate fossils. Unfortunately, as noted by later director of the museum E.H. Barbour, Aughey had terrible record keeping. In fact, he stated, "All records prior to 1891...are of little use."  Aughey used the small collections of the museum in his courses of zoology, geology, biology, botany, and chemistry.