Scholars have variously depicted Thomas Jefferson as everything from a crypto-Unitarian with a deep love of Jesus to a priest-baiting infidel. My own view is that the latter comes closer to the truth, but, more important, he was helping to invent something new: American nationalism. His contributions to American nationalism are unique. In the two-party system, the two long-established political parties have both taken their names from Jefferson’s Democratic-Republicans. No one wrote more eloquently about freedom, nor did anyone do more to expand slavery and authorize racism. No American president was more closely associated with Europe, yet none did more to foster American exceptionalism. In the Declaration of Independence, he authored the Revolution’s most important contribution to world political literature. He knew both the state of scientific and religious learning of his time better than any subsequent president has known either one. Despite the fact that it has never been an accurate description of the relationship between American religious and civil authority, his phrase “wall of separation between church and state” continues to serve, for many in and outside the United States, as an ideal. In the story of religion and the development of early American nationalism, Jefferson was a kind of nationalist mystic. In terms of intellectual history, at a time when the Enlightenment was replacing angels with geniuses, Jefferson may be best understood as an angel of the Enlightenment. The contradiction of the phrase makes it more, not less, fitting.

The political content of Jefferson’s Declaration of Independence was not unique. In the War of Independence, which was also a civil war between Anglo-Protestants who had for generations lived together as British subjects, patriots from South Carolina to Massachusetts issued dozens of declarations of independence. American towns and counties in fact issued over 90 different declarations of independence, many of which preceded Jefferson’s. It was Jefferson’s eloquence, and the authorization of Congress, not the singularity of his political ideas, that made his effort “the” Declaration of Independence. The Declaration drafted by Jefferson, and revised by a congressional committee, contains a turn of phrase that captures a bit of the mysticism, and a trace of theology, that nationalism requires. “We hold these truths to be self-evident,” proclaims the Declaration. The peculiar act of declaring as “self-evident” matters that were anything but such had a history. Readers of Locke knew the tactic from Locke’s defense of Christianity, which relied upon the doctrine of self-evidence. Locke argued that Jesus was Christ because of his miracles, and that the truth of the Christian religion and its obligations and rights was therefore “self-evident.”

To proclaim truths “self-evident” (or “sacred and undeniable,” as Jefferson’s first draft read) is to announce that one is not willing to debate the matter. This “proof” was not intended to convince skeptics, much less opponents, but to strengthen the bonds among believers. Benedict Andersen has called nations “imagined communities,” but “communities of faith” may be as accurate a description of the material with which nationalists work. Because nations are impossible to experience in any direct, tangible way, they depend on faith, in the scriptural sense. Patriots must believe in the “evidence of things not seen, the substance of things hoped for,” as the scriptures define faith. The bonds of belief among nationalists are vital, especially early in nationalist movements. This mystical quality inherent within “We hold these truths to be self-evident” helps account for its status as a patriot proverb. It does not represent an argument, or even an idea, but a statement of belonging to what the French scholar Ernest Renan called the “spiritual family” of the nation.

Importantly, the problem of slavery brought forth perhaps the most notable appearance of religion in Jefferson’s writing. This instance, in Notes on the State of Virginia, differs from the playful pirating of theological concepts and mystical invocations of nationalist bonds of the Declaration. It comes in Query 18, on “Manners,” and it is also a bizarre moment (the historian Lewis P. Simpson called it “chilling”) in the only book Jefferson published: inconsistent, angst-ridden, and fantastic. Consideration of the manners, or character, of Virginians brings Jefferson to the influence of slavery. The subject propels him into imagining supernatural interference, a just God reaching down and turning slaves into masters and masters into slaves. One can see Jefferson losing, regaining, and again losing his Enlightenment bearings. In a deistic work, meant to foster the authority of natural science over that of religion, the specter of divine intervention in human affairs hits an odd note:

And can the liberties of a nation be thought secure when we have removed their only firm basis, a conviction in the minds of the people that these liberties are of the gift of God? That they are not to be violated but with his wrath? Indeed, I tremble for my country when I reflect that God is just: that his justice cannot sleep forever: that considering numbers, nature and natural means only, a revolution of the wheel of fortune, an exchange of situations, is among possible events: that it may become probable by supernatural interference! The Almighty has no attribute which can take side with us in such a contest.

Jefferson begins by reconsidering the secular achievement of the Revolution, an achievement he cherished, as a reckless gambit. He wonders about divine justice, veers suddenly back to rational criteria (“numbers, nature, and natural means only”), only to get carried away by fears of a vengeful God reaching down to turn the planters into slaves (“by supernatural interference!”). In this short section, interestingly, on “Manners”—as opposed to the more obvious homes for the subject in the sections on “Population” or “Manufactures”—slavery pushed him into manifold contradiction. In addition, just before this fearful fantasy of supernatural justice, Jefferson referred to Virginia’s slaves as “citizens.” With “what execration should the statesman be loaded,” he wrote, “who permitting one half the citizens thus to trample on the rights of the other,” thereby corrupts the moral fiber of the masters as he subjugates the slaves. Slaves in Virginia were not citizens, of course. With nationalist measures, Jefferson seemed in command of his mystical and theological maneuvers. When the subject of slavery arose, however, it pushed him into a different engagement with religion, that of the fantastic and supernatural.

The fact that Notes on the State of Virginia is essentially an extended essay on natural history makes Jefferson’s mention of divine intervention more notable. Modern readers sometimes find its chapters, organized as “Queries” (“Rivers,” “Sea-Ports,” “Mountains,” “Cascades,” and “Productions Mineral, Vegetable and Animal”) perplexing. They were Jefferson’s response to a prejudice, fashionable among European intellectuals, and popularized by the influential French naturalist and mathematician the Comte de Buffon, known as creolean degeneracy theory. “In America,” wrote Buffon in his Natural History: General and Particular, “animated Nature is weaker, less active, and more circumscribed in the variety of her productions.” Jefferson included tables, “A Comparative View of the Quadrupeds of Europe and North America,” for example, providing the respective weights of hedgehogs, shrew mice, otters, and other animals in North America and Europe. He also described, in detail, mineral deposits, river currents, soil composition, and arboreal life. Natural history writings were a favorite genre of Enlightenment intellectuals, one especially consonant with the practice of sophisticated plantation agriculture. The empirical, scientific approach of natural history transformed God’s creation, or the wilderness, into the natural world. The natural history perspective challenged core claims of Christianity to the organization of time. At times, such as in Jefferson’s explanation of the origin of the Blue Ridge Mountains and the Shenandoah Valley, the challenge to the Christian account of creation was almost explicit:

The first glance of this scene hurries our sense into the opinion, that this earth has been created in time, that the mountains were formed first, that the rivers began to flow afterwards, that in this place particularly they have been dammed up by the Blue ridge of the mountains, and have formed an ocean which filled the whole valley; that continuing to rise they have at length broken over at this spot, and have torn the mountain down from its summit to its base. The piles of rock on each hand, but particularly on the Shenandoah, the evident marks of their disruptive and avulsion from their beds by the most powerful agents of nature, corroborate this impression.

The words “this earth has been created in time” and “the most powerful agents of nature” were not subtle code phrases. Jefferson’s acutely Christian political opponents, mainly New England Federalists, responded to Notes on the State of Virginia with accusations of immorality and irreligion. “Howling atheist” and “confirmed infidel” were among the verdicts. Jefferson complained, “O! that mine enemy would write a book! has been a well known prayer against an enemy. I had written a book and it furnished matter of abuse for want of something better.” James Madison had tried to dissuade Jefferson from publishing Notes, warning, “Perhaps an indiscriminate gift might offend some narrow minded parents.” Jefferson however was undeterred and, one senses, incorrigible before the prospect of contributing a natural history of Virginia to the causes of American equality and science.

As a composition of natural history, Jefferson’s Notes on the State of Virginia is part of an inherently anti-supernatural genre. It replaces the supernatural creation story with an account of natural generation. Jefferson could, however, enlist Adam and Eve in the service of democratic nationalism, such as, when he wrote a friend that he would like to see the world cleared for Adam and Eve to seed the cause of republican freedom. “I would have seen half the world desolated,” he wrote, in 1793, “were there but an Adam and Eve left in every country and left free, it would be better than it is now.” It is characteristic of Jefferson’s complex role in the historical development of American nationalism that he brought religion to nationalism while subjecting religion to rationalism. He learned Greek to write The Life and Morals of Jesus of Nazareth, though he never published the book. The book’s title, and its last lines, tells much of the story: it pointedly does not confer the Christ appellation. Instead, Jefferson depicted Jesus as a man, one of a certain time and place—Nazareth—whose life has passed but remains instructive because of his moral example. In Jefferson’s book, Jesus was a moral man and a great teacher, but not divine, not the son of God. Because miracles were an impossible transgression of natural law, The Life and Morals of Jesus of Nazareth offers none. Nor did “Jefferson’s Bible” offer any resurrection. “There laid they Jesus,” concludes the work, “and rolled a great stone to the door of the sepulchre, and departed.” Historians should leave it to Christians to decide who is and who is not a Christian. At the same time, if words are to have any meaning, it is difficult to see how someone who did not think that Jesus was Christ should be called a Christian.

For the inscription on his tombstone, Jefferson chose three accomplishments: the Declaration of Independence, the founding of the University of Virginia, and Virginia’s 1786 Statute for Religious Freedom. Each of these achievements is related to the problem of religion and nationalism. In the Statute for Religious Freedom, Jefferson characteristically brought high rationalism to the subject of religion and poetry to the scientific spirit. His testimony to the power of truth and free inquiry, closing the first section of the statute, is the very essence of the Enlightenment: “Truth is great and will prevail if left to herself,” wrote Jefferson: “She is the proper and sufficient antagonist to error and has nothing to fear from the conflict unless, by human interpolation, disarmed of her natural weapons, free argument and debate—errors ceasing to be dangerous when it is permitted freely to contradict them.” Madison’s deft stewardship through the Virginia House of Delegates made the bill into law, and he wrote to Jefferson exulting that we “have in this country extinguished forever the ambitious hope of making laws for the human mind.” Jefferson concurred, replying that “kings, priests, & nobles” had for centuries conspired to keep man in ignorant subordination. It was Virginia’s great honor “to have produced the first legislature who had the courage to declare that the reason of man may be trusted with the formation of his opinions.” In the context of early modern political philosophy, to state that the reason of man may be trusted with the formation of his opinions was another way of stating the radical content of “all men are created equal.” The famous phrase did not mean that men possessed equal physical or intellectual capacities. It meant that all men could reason and were capable of acting as responsible, and accountable, moral agents. It was, and remains, a radical idea.

Disestablishment and freedom of religion amounted to historic secular achievements, but Jefferson and Madison had intended them as simply creating the conditions of possibility, as the first steps, toward a secular society. Positive measures must follow. The most important were founding schools and libraries, educating qualified teachers, and providing the people with rudimentary scientific and literary education, especially in philosophy. Scientific and philosophical education was necessary to replace the moral influence, social programs, and historical teachings of the churches. So Jefferson proposed alternatives to Christian institutions. In the 1785–1786 session of the Virginia Assembly, his “Bill for Establishing Religious Freedom,” was bill number 82 of 126 proposed bills. Bills 79, 80, and 81 were also Jefferson’s. These bills proposed to create a nonreligious school system, organized by county and providing free education through the elementary grades; to sever the College of William and Mary’s church ties and make it a republican college; and to establish a public library system built around science, philosophy, and civics. An ally of Jefferson’s aptly described the ambition of the measures. They “propose a simple and beautiful scheme, whereby science . . . would have been ‘carried to every man’s door,’” he wrote. Emphasizing the need to reach and, through education, change the public, he wrote: “Genius, instead of having to break its way through the thick opposing clouds of native obscurity, indigence, and ignorance, was to be sought for through every family in the commonwealth.” Churches would have been the big losers of this “systematical plan,” but their opposition was not the only reason it failed to materialize. The nature of Southern plantation society did not permit potential alternatives, such as state-run school systems, to planter authority. Slavery was simply more important to American nation-building than secularism. The planters, however, cannot be held uniquely responsible. With notable exceptions, for example the French state education system, secularists generally failed to build institutions that offered alternatives to Christian social, political, and personal morality.

Instead, it would be the frontier revivalists, in particular the Methodists, who would pioneer, on the western periphery of the early republic, carrying their message from door to door. By the 1820s, the sons of the Northeastern elite, following the Methodists and working for an array of Protestant missionary and moral improvement associations, would follow, bringing a different message of bourgeois nationalism “to every man’s door.” Their system of Protestant auxiliary societies, ladies’ societies, libraries, and schools—not the republican and scientific system that would have been provided for by Jefferson’s Bills 79, 80, and 81 from the 1785–1786 session of the Virginia Assembly—would flourish across the frontier. Jefferson would be left with the University of Virginia, to which, after his retirement from the presidency, he devoted extraordinary energies. He refused to hire a professor of divinity, urging the College of Columbia, in Columbia, South Carolina, to follow his example and instead hire professors of geology and mineralogy. In defiance of long-standing architectural practice, in which the church stood at the center of a college campus, Jefferson made the library the central feature of the University of Virginia. The University of Virginia did not even have a chapel until 1889, when the university built Newcomb Chapel. UVA’s neo-Gothic Newcomb Chapel fit the idealizations of medieval Europe that late nineteenth-century Americans loved, particularly for their college campuses, but it could hardly be more at odds with Jefferson’s neo-Palladian campus, which honors the Italian Renaissance.

Amid the proliferation of upstart Protestants in the early republic, Jefferson’s countermeasures amounted to symbolic resistance. He found the birth of popular Protestantism a foreboding development, writing to a friend in 1822, “The atmosphere of our country is unquestioningly charged with a threatening cloud of fanaticism, lighter in some parts, denser in others, but too heavy in all.” Jefferson had expected that disestablishment would weaken religion, especially revealed religion. He believed, as Immanuel Kant put it, “if only freedom is granted, enlightenment is sure to follow.” Into the 1820s, John C. Calhoun and Thomas Jefferson were still predicting that America was well on its way to becoming a Unitarian country. “There is not a young man now living in the United States,” Jefferson wrote in 1822, “who will not die an Unitarian.” It was an absurd prediction. For Jefferson, Madison, and other genteel rationalists, democracy in religion had proven less sanguine than democracy in politics. If some supernatural act, comparable to the one Jefferson had imagined switching American masters and slaves, offered to replace the frontier of Millerites, Baptists, and Methodists with a periphery of Anglicans, the proposition might have given them pause. Decoupled from Federalism, which had by then imploded for its own reasons, and in contrast to the hothouse of sectarians, visionaries, and millenarians that were flourishing across the frontier, the Anglicans, whose church Madison and Jefferson had battled so hard to disestablish in the 1780s, would have had been more welcoming to their Enlightenment dreams.

In conclusion, the Virginia model, which the historian Lewis P. Simpson called “the secularization of spirituality” in America, is an ambiguous affair, but some pertinent conclusions emerge. First, secularism and religious freedom in Virginia were political battles, realized by an alliance between a small but politically skilled faction of elite freethinkers and a large group of evangelicals. These two groups came to share a position in support of disestablishment and religious liberty, but with contrary purposes. The deists saw disestablishment and religious freedom as steps to human freedom. Some conservative planters joined the fight, hoping to strengthen state control over churches, while an energetic group of evangelicals gave support for sectarian reasons. For the freethinkers, the Virginia model of secularism and religious freedom, which became the American one, was a distinctly partial victory. Seen in light of the aspirations of leading deists, who led the fight for disestablishment and religious freedom through the thickets of Virginia politics, it brought confounding, even contrary, results.

Some leading secularists, Jefferson and Madison among them, had also hoped for a state-run education program, consisting of libraries and schools teaching science, philosophy, letters, and the arts. They understood that religion brought a world of ideas, and sometimes a whole social life, as well as political opportunity, to Virginians rich and poor. Most people would not turn their backs on this world of religion simply out of political principle. The secularists would have to offer real alternatives: schools, libraries, ideas, stories, forms of community, an active and ongoing presence in the lives of Virginians. Jefferson knew this, and in Notes on the State of Virginia, he proposed a system of public schools that would replace sacred history with profane history. The schools were to be free, for everyone, for three years. Examinations would find the best students among “those whose parents are too poor to give them further education.” These students could receive more schooling, paid for by the state, through William and Mary College. “By this means,” Jefferson wrote, “the best geniuses will be raked from the rubbish.” The object, wrote Jefferson, was “provide an education adapted to the years” for citizens, rich and poor alike, “directed to their freedom and happiness” and suited to everyone’s natural ability. “Instead of putting the Bible and Testament into the hands of the children, at an age when their judgments are not sufficiently matured,” he noted, children should instead receive educations in “Grecian, Roman, European, and American history,” Latin, Greek, mathematics, and the sciences. No law, he wrote, was “more important, none more legitimate,” than one to provide secular arts and sciences education for the people at large. It would, he wrote, make them effective “guardians of their own liberty.”

Second, in the realm of political theory, Thomas Jefferson and James Madison struggled to leave religion behind. Unable to disentangle religion from techniques of governing and nation-state building, they turned to mystical and theological techniques for help in inventing modern nationalism. The depth of their drive to implement political separation itself suggests the potential affinity between religion and nationalism, which have been the two large cultural systems legitimating political authority in the West over the past few centuries. This is not to suggest that religion and nationalism are somehow the same. The British historian Lewis Namier was wrong when he wrote, “religion is a 16th-century word for nationalism.” Jefferson and Madison borrowed from religion in hopes of leaving it behind, a fact that makes the possibility of a more sincere alliance between the two easy to imagine.

Though in Virginia disestablishment and religious freedom were hard-won and important political accomplishments, they initiated rather than solved the problem of religion in the early republic. Most Americans presumed that an enlightened nation was by definition a Protestant nation, but Protestantism offered no clear model for enlightening the peoples of a large and expanding republic. The Puritans, who had never been democrats, much less secularists, were not nation-builders. Eighteenth-century Anglican missions had reaped at best modest results. Rational religion had always been an upper realm, a preserve for the educated elite. Did democracy require the proliferation of rational religion? Could ordinary people be inoculated against religious fanaticism? No clear answers presented themselves. Even Immanuel Kant, in his 1784 essay “What Is Enlightenment?” maintained that freedom of speech and freedom of religion required a wise and benevolent monarch. “A republic could not dare” enact the ideal of freedom of conscience, wrote Kant.

Pro-American partisans shared Kant’s misgivings. Confidence that the precarious republican experiment could withstand what Crèvecoeur called “the rage, the malice of an ignorant, prejudiced public” was shaky. In Letters from an American Farmer, Crèvecoeur warned that it would be “these country saints” from the “obscure parts” who, raised by the Revolution, “have assumed the iron sceptre and from religious hypocrites are to become political tyrants.” Indeed, the colonization of the continent was undertaken with a degree of desperation, amid considerable disorder, and stewarded by a government described by the historian John Murrin as a midget institution in a giant land. To many, the situation threatened to bring Crèvecoeur’s prediction of tyranny or chaos to pass.

Some notable New Englanders had strong views on these matters. They saw American nationality and empire not as a political possibility, but as a providential opportunity, one in which they claimed a proprietary stake. They were convinced that all depended on the spread of Reformed Protestantism and strong state institutions, the New England way.

Finally, disestablishment and religious freedom were Virginia accomplishments, not valued by many acutely Protestant Northerners, especially among New England’s Reformed Protestant elite. However partial, these real secular victories were achieved by a deist-evangelical alliance that grew out of a very different society from that which New England’s Christian Federalists represented. The New England Christians and the Virginians were simply at odds over the nature of American society and nationality, not just the role of religion. Given the depth and breadth of these differences, it is not difficult to understand why New England would threaten secession, or turn, in their search for a regenerate political community, from politics to missions. The depth of these differences turns attention back to the remarkable nature of the nationalism that had brought New England and Chesapeake plantation society together in the first place.

The picture that emerges is at once foreign and familiar, of provincialism and worldly ambition, of real radicalism and a state conservatism that never became part of the national political tradition.

Sam Haselby is senior editor at Aeon and a visiting scholar at the Institute for Religion, Culture, and Public Life at Columbia University.

Excerpt adapted from The Origins of American Religious Nationalism by Sam Haselby, with permission from Oxford University Press USA. © 2015 Oxford University Press