Jefferson is referring specifically to Native Americans in this quote. This statement is written, like Jefferson's description of the flora and fauna in Virginia, to refute the Comte de Buffon's contention that species degenerated in the New World. Jefferson is arguing that whatever "inferiorities" Europeans observed in Native Americans were a product of their environment, not inherent to them as people. Buffon, for example, had suggested that Native Americans were not as prolific as whites, an assumption rooted in Europeans' belief that North America was largely uninhabited wilderness before whites arrived. Jefferson claims that any lack of virility on the part of Native men (an flawed premise to begin with) was due to the difficulties of their lives, and would quickly become equal to whites if they practiced settled agriculture (which, of course, many of them did.) Jefferson goes on to extol their prowess in war, as well as in oratory:
Of their bravery and address in war we have multiplied proofs, because we have been the subjects on which they were exercised. Of their eminence in oratory we have fewer examples, because it is displayed chiefly in their own councils...I may challenge the whole orations of Demosthenes and Cicero, and of any more eminent orator, if Europe has furnished more eminent, to produce a single passage, superior to the speech of Logan, a Mingo chief, to Lord Dunmore, when governor of this state.
That these statements are made in the context of disproving Buffon's thesis is significant. They did not reflect any particular sympathy for the political plight of Indians. If Jefferson admired Native Americans, including some aspects of their culture, he also advocated their "extermination" in the sense that he wanted them to give up that culture, settle onto farms and to give up hunting lands so that white farmers might move west, creating the nation of smallholding farmers that he waxed poetic about elsewhere in Notes. These statements are also significant when juxtaposed with his views on African-Americans in the same work.