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When Jefferson spoke in terms of the "civilization" of Native American people, he was borrowing from Enlightenment philosophy. The "Enlightenment" is the term used by both historians and contemporaries to describe the sweeping intellectual changes of the late seventeenth and eighteenth centuries. The great scientific revolution of the seventeenth century led to the belief that the same principles of scientific inquiry could be used to understand human behavior, both in the individual and in entire populations.

A theory that grew from this was that of "environmentalism," which held that a human's environment - climate and geography, especially - shaped human appearance, culture, and political organization. European naturalists used the theory of "environmentalism" to argue that plants, animals, and the Native peoples of America were inferior to that of Europe due to climate and geography. Jefferson refuted these notions in his only book, Notes on the State of Virginia, and defended Native American culture. He appended to the Notes the speech of the Mingo chief Logan, who mourned the loss of his family in an attack by a white settler. Jefferson held up "Logan's Lament" as an example of great and powerful oratory, the equal of any European orator, classical or modern. "I beleive [sic] the Indian then to be in body and mind equal to the whiteman," Jefferson wrote to the Marquis de Chastellux. Jefferson believed that only their environment needed to be changed to make them fully American.

Even though many Native American people lived in villages and almost all engaged in some form of agriculture, hunting remained a common practice that many Native peoples held sacred. Hunting, a semi-nomadic life, a refusal to adopt Western European monoculture, and a denial of an individual right to exploit land and labor led Jefferson and others to consider Indigenous people inferior to Western Europeans and referred to them offensively as "savages." Jefferson believed that if American Indians were made to adopt European-style agriculture and live in European-style towns and villages, then they would quickly "progress" from "savagery" to "civilization" and eventually be equal, in his mind, to white men. As President, Jefferson would try to make these changes a reality. Of course, most Native American people had no interest in abandoning their cultures to satisfy any European or Euro-American concept of “progress.”