In a draft of the Declaration of Independence, Jefferson lambasted George the III for the abominable sin of slavery, which was against the same rights of liberty and equality the colonists were claiming were violated during the imperial crises of the 1760s and 1770s. Slavery, in republican ideology, was not racial but political - the colonists were enslaved to Parliamentary supremacy and monarchical corruption. Black slaves, the literal slaves in the colonies, were thus potential analogues to the patriots. Jefferson, to obviate any need for patriots to emancipate their slaves upon independence, cast blame on the British for the institution itself.

In terms of Jefferson's theory of race itself, I would recommend Bruce Dain's "A Hideous Monster of the Mind" (2002). Here, Dain suggests Jefferson was representative of most Euro-Americans who tried to proclaim liberty and rationalize self-interest by denying that liberty to all Americans. It was a fatalistic outlook. According to Jefferson's Enlightenment education, slavery would ultimately destroy the republic since slaves were incompatible within a white, rational, nationalist vision.

Even more, Jefferson understood that blacks represented the Old World infliction of baseness, inferiority, and alien-ness that threatened the balance of nature and society. Unlike Benjamin Franklin, who saw blacks as capable of whiteness (meaning inherent intellectual ability and rights, and for some, even skin color), Jefferson saw blacks as naturally inferior.

But most importantly, perhaps, Jefferson never really had a coherent racial theory to justify slavery. As Dain says, he was "less race theorist than racial obscurantist." For Jefferson, race was undefined, while blackness was a "god-given natural entity," evil and sinful. Thus, Jefferson's conviction that slavery was an intractable problem, a "fire-bell in the night" doomed to destroy the republic - hopefully, he thought, after he was long dead.