Thomas was born in Kingsport, Tennessee. He studied law and was a lawyer early on in his career up until 1865, serving as county clerk of Jackson County, Illinois in the early 1850s. In 1865 he entered the ministry of the Evangelical Lutheran Church. Four years later in 1869 he joined the expedition of Ferdinand Vandeveer Hayden, who had organized a scientific corps for the exploration of the Rocky Mountains. He was the agricultural statistician and entomologist on the Hayden Geological Survey of 1871, whose work supported the creation of Yellowstone National Park in 1872.
In 1873 Thomas was appointed a professor of natural science at Southern Illinois University, which gave him a public forum for his ideas. He was later named to the United States Entomological Commission to serve alongside Charles Valentine Riley and Alpheus Spring Packard before accepting the position of chief entomologist in 1879 for the State of Illinois. 
Thomas was a leading early student of archaeology of Native Americans. In the 1890s he played a crucial role in debunking the previously common theory that the Mound Builders were a separate lost race, rather than ancestors of more recent American Indians. Though he debunked the theory of the "lost race", he also concluded that the mounds were built after Europeans made contact with the Native Americans. This theory has long-since been thoroughly disproved following the advent of scientific dating techniques which have established the rise of complex indigenous civilizations that built major earthworks more than a thousand years before European contact. He also made early studies of Mayan hieroglyphics.
Thomas also wrote on climatology, a new field in the 19th century. He was a leading proponent of the now-debunked theory known as "Rain follows the plow", which stated that increased population and cultivation of the Great Plains would render the land lush and fertile. This theory was used to promote expansion into the American West, in order to assuage would-be settlers that the "current" lack of precipitation would not hinder their ability to engage in agriculture.
- ^ Merrill, Marlene Deahl, ed (1999). Yellowstone and the Great West-Journals, Letters and Images from the 1871 Hayden Expedition. Lincoln, NE: University of Nebraska Press. pp. 31–32. ISBN 0803231482.
- ^ Entomological Society of Ontario By Entomological Society of Ontario, Ontario. Dept. of Agriculture (1877)
Historic events and personalities from Yellowstone National Park ExpeditionsCook–Folsom–Peterson Expedition • Washburn–Langford–Doane Expedition • Hayden Geological Survey of 1871 Explorers Photographers, artists and illustrators Park management Events
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