Doubting Thomas (Jefferson) and the Founders’ Great Mistake

The Enlightenment marked a fundamental shift from faith and focus on an afterlife to the material world and the pursuit of happiness in this life.

Editor’s Note: The beliefs of Thomas Jefferson continue to create controversy even though the Founding Father and third President of the U.S. died nearly two centuries ago. Just this past week, for example, World magazine reported that the large Evangelical publishing house, Thomas Nelson, decided to cease publication and distribution of David Barton’s controversial book, The Jefferson Lies: Exposing the Myths You’ve Always Believed about Thomas Jefferson, saying it has “lost confidence in the book’s details.” Barton is the president of the WallBuilders organization and a frequent guest on the Glenn Beck radio program; his book has been criticized for portraying Jefferson as sympathetic to Christianity while downplaying, or even ignoring, Jefferson’s criticisms of orthodox Christianity. The following essay, written by Dr. Edmund Mazza of Azusa Pacific University, situates Jefferson within the broader context of the Enlightenment, which was generally antagonistic to what Jefferson dismissed as the “monkish ignorance and priestly superstition” of the Catholic Church.

Most Americans know Thomas Jefferson as the principal author of the Declaration of Independence and the nation’s third president. But Jefferson is also the famed founder of one of America’s oldest institutions of higher education, the University of Virginia. In this connection he is reported to have quipped that he hoped it would never retain a faculty of theology,[1] nor ever become a den of “monkish ignorance and priestly superstition.” I have always found Jefferson’s pontificating to be quite ironic since it was precisely these prelates of the Church who invented the university system in the first place—some six centuries before he did!

Jefferson, however, was a man of his age, a period in history known as the Enlightenment. An ironic appellation to be sure, for it ushered in unprecedented shadows of doubt, obscuring centuries of illumination by the medieval masters of higher education. John Locke, another “luminary” of the Enlightenment took a similarly “dim” view of medieval or “scholastic” thinking when he wrote:

the Schoolmen… aiming at glory and esteem, for their great and universal knowledge, easier a great deal to be pretended to than really acquired, found this a good expedient to cover their ignorance with a curious and inexplicable web of perplexed words, and procure to themselves the admiration of others, by unintelligible terms, the apter to produce wonder because they could not be understood: whilst it appears in all history, that these profound doctors were no wiser nor more useful than their neighbours, and brought but small advantage to human life or the societies wherein they lived…[2]

The key phrase in Locke’s statement is that the scholastics were not “useful” to their neighbors and brought almost “no advantage” to their practical lives as individuals or society writ large. Whether or not Locke’s statement is an accurate one, it betrays a fundamental shift: from faith and focus on an afterlife to the material world and the pursuit of happiness merely in terms of this life, instead of the pursuit of the God Who bestows happiness in the next.

This Enlightenment utilitarianism was first expressed a century earlier by fellow Englishman Francis Bacon in the New Atlantis, in which he spoke of the promise of science, which would give us: “things of use and practice for man’s life.”[3] This was the age of the Scientific Revolution. Galileo’s claim to have proven that the earth was not the center of the universe but that it revolved around the sun seemed to challenge the accuracy of the teaching authority of both the Catholic Church and the Bible, as well as the science of the ancient Greek philosophers, notably Aristotle.

Sixteenth-century empirical observations through crude telescopes and microscopes revolutionized man’s view of his place in the universe and made many intellectuals question their common patrimony: the authority of received “tradition,” which had been the basis of medieval education. Or as Jefferson put it: “It is surely time for men to think for themselves, and to throw off the authority of names so artificially magnified.”[4] Chancellor Bacon was another such skeptic of “established authorities” and famously advocated the inductive “Scientific Method” instead:

But even though Aristotle were the man he is thought to be I should still warn you against receiving as oracles the thoughts and opinions of one man. What justification can there be for this self-imposed servitude [that]…you are content to repeat Aristotle’s after two thousand [years]…But if you will be guided by me you will deny, not only to this man but to any mortal now living or who shall live hereafter, the right to dictate your opinions…you will never be sorry for trusting your own strength…[5] (Emphasis mine)

Aristotle and the scholastics are to be rejected because the new science has proven many of their assertions erroneous. Common patrimony gone, the individual must only accept as certain what he can first rationally demonstrate to himself, Descartes’ “I think, therefore, I am.” This is the beginning of the end of medieval metaphysics, which asserted that a person’s existence must certainly precede any act of cogitation. With the loss of metaphysics, the entire celestial hierarchy, along with concomitant notions of sin and salvation, death, judgment, heaven and hell, fall by the wayside. We have only the empirical knowledge of the here and now concludes Bacon: “Man, being the servant and interpreter of Nature, can do and understand so much only as he has observed in fact or in thought of the course of nature: beyond this he neither knows anything nor can do anything.”[6] As John Donne lamented in less prosaic verse:

New Philosophy calls all in doubt,
The Element of fire is quite put out;
The Sun is lost, and th’earth, and no man’s wit
Can well direct him where to look for it.


Tis all in pieces, all coherence gone;
All just supply, and all Relation:
Prince, Subject, Father, Son, are things forgot,
For every man alone thinks he hath got
To be a Phoenix, and that then can be,
None of that kinde, of which he is, but he.[7]

(Emphasis mine)

Since ancient and medieval authorities had proven incorrect about the natural world, early modern intellectuals threw the baby out with the bath water, and rejected nearly all of what those commonly accepted authorities had said about the human world: God, man, and public society. Aristotle’s dictum, “man is by nature a social animal” was no longer acceptable. Human nature is not inherently relational. The human race is merely a gaggle of completely separate and unrelated individuals. Each of us is not a specimen of a class, but a class unto ourselves! Each man is an island…a phoenix. As Jefferson wrote, “I am of a sect by myself, as far as I know.”[8] This was also Locke’s thinking:

Men being, as has been said, by nature all free, equal, and independent, no one can be put out of this condition and subjected to the political power of another without his own consent. The only way whereby any one divests himself of his natural liberty, and puts on the bonds of civil society, is by agreeing with other men to join and unite into a community for their comfortable, safe, and peaceable living one among another…he [is] absolute lord of his own person and possessions, equal to the greatest, and subject to nobody, why will he part with his freedom, why will he give up his independence and subject himself to the rule and control of any other power?

Rejection of received authority and the enshrinement of the individual were believed to be effective bulwarks against tyranny, and the promotion of liberty, but had the unfortunate effect of forcing all but the most basic religious beliefs to the private sphere. As Elshtain writes,

There was a worm in the apple from the very beginning of the move for toleration. If one traces that beginning from John Locke’s classic Letter on Toleration one discovers that in order for religion to be tolerated it must be privatized. There is a realm of private soulcraft and, a realm of public statecraft, and never the twain shall meet…This privatization, even subjectifying, of religion feeds into the bad odor surrounding any hint of proselytization. Proselytizing seemed at best bad manners; at worst a way to try and force something on me that I do not want, am not interested in, but may be gulled or intimidated into accepting. The general animus against proselytizing flows from a conviction that those driven in that direction will, almost invariably, be persons of strong religious conviction: those, therefore, who, should they become dominant, would move to end the very toleration that has made their open proselytizing possible. So, in the name of preserving a regime of toleration, we must not tolerate unrestrained proselytism.[9]

Voltaire, a contemporary French philosophe-atheist had affirmed as much when he said that one religion was tyranny, two religions civil war, but the toleration of multiple factions, a just republic. In other words, Enlightenment toleration is based on the supposition that there can be no certainty with regard to religious claims to truth.[10] “I never will, by any word, or act, bow to the shrine of intolerance, or admit of a right of inquiry into the religious opinions of others,” said Jefferson.[11] Men may follow their private beliefs to their own peril, but should not endanger the general welfare on account of their peculiar denominational folly.

This is the genesis of the notion of Separation of Church and State and neatly summarizes the prevailing politically correct consensus in Washington, various levels of the judiciary, the “mainstream” media, and academia today. As my colleague Mark Eaton recently observed:

Some would prefer to exclude believers from public discourse altogether. Stanley Fish never tires of reminding us that religion stands as the litmus test of pluralism. Because there are always “some believers who hold to their faith in a way that is absolute and exclusionary,” he argues that religion is ultimately incompatible with pluralism and tolerance, those twin pillars of secular modernity. The philosopher Jurgen Habermas insists that believers must simply come to terms with the “inevitability of religious tolerance,” while so-called new atheists like Christopher Hitchens exclaim more shrilly that the “inevitable biases” of believers “should be enough” to exclude them from rational debate. For these and other champions of secularism, religion is safe only when it is confined to the private sphere, since any form of “deprivatized religion,” as religious studies scholar Talal Asad puts it, is deemed “intolerable to secularists.”[12]

Just ask Amherst College President Anthony Marx about the “bad old days,” before religion was privatized:

In the medieval epochs of Europe, leading right up to the edge of the modern, authority was established by deity or absolutism. Monarchs and priests directed humanity’s understanding of nature, of sickness and health, of earth’s horizon, of the motion of the stars. It is hard for you now to imagine that way of life, in which such authority was not questioned. But the power of individual insight, yearning and industry were just beginning to coalesce, producing revolutions that replaced despotism with democracy, feudalism with capitalism and fundamentalism with religious choice…

Amherst prizes individual reason over unearned authority…We believe in “progress”: that new knowledge advances us. Just as we believe in science, we also respect and take strength from faith, not as a closed system but as an inspiration [i.e. private not overarching], as another kind of journey, for each to examine and decide for herself or himself. Although we know we cannot reach perfection [i.e. certitude], we believe in striving for the improvement for all.[13] (Emphasis mine)

Religion may serve as personal “inspiration,” but may not condition philosophy, science, or societal structure. According to this view, Joseph Cardinal Ratzinger explained, faith is definitively divorced from reason:

We could suggest that Descartes, Spinoza, and Kant are points along the way in this process of separation. The attempt at a new comprehensive synthesis by Hegel did not give faith back its proper place in philosophy but tried to transform it completely into reason and to do away with it as faith. To this giving absolute status to the spirit, Marx opposed a system of solely material values; philosophy was now to be based upon exact science. Only scientific knowledge was knowledge at all…A comprehensive theory of evolution, intended to explain the whole of reality, has become a kind of “first philosophy”, which represents, as it were, the true foundation for an enlightened understanding of the world. Any attempt to involve basic elements other than those worked out within the terms of such a “positive” theory, any attempt at “metaphysics”, necessarily appears as a relapse from the standards of enlightenment, as abandoning the universal claims of science. Thus the Christian idea of God is necessarily regarded as unscientific.[14]

But what if the men of the Scientific Revolution and the Enlightenment got it wrong? What if God is not merely a fact of religion—but a fact? What if sense-knowledge is not the only path to truth? And what if individuals as a consequence have an obligation to obey not only material truths, but transcendent truths, if (paradoxically) they truly aspire to freedom?

While it is hardly to be doubted they made few miscalculations with regard to planetary motion or representative government, early-modern thinkers were surely not endowed with infallibility in their presumption that human knowledge (and therefore pursuit of happiness) was limited to this world. The statement “that all propositions are meaningless unless they can be empirically verified,” is itself empirically unverifiable![15] And to insist: “There is no such thing as absolute truth,” is actually to proclaim one.


[1] Thomas Jefferson, Letter to Thomas Cooper, October 7, 1814, as cited in hist/quotes

[2] John Locke, Essay on Human Understanding, Book 3, Chap 10, ed. Jack Lynch; www.

[3] Francis Bacon, The New Atlantis, as cited in Thomas F. X. Noble, Barry Strauss, Duane J. Osheim, Kristen B. Neuschel, Elinor A. Accampo, eds. Western Civilization, (Houghton Mifflin, 2008), 531.

[4] Letter to William Short, August 4, 1820.

[5] Francis Bacon, The Refutation of Philosophies

[6] Bacon, The New Organon

[7] John Donne, “An Anatomy of the World”

[8] Jefferson, Letter to Ezra Stiles Ely, June 25, 1819.

[9] Jean Bethke Elshtain, “Proselytizing for Tolerance,” First Things, 2002

[10] “The notion that all religions are ultimately equivalent appears as a commandment of tolerance and respect for others…The Christian has to resist this ideology of equality.” His Holiness Pope Benedict XVI (Joseph Ratzinger), Truth and Tolerance, Christian Belief and World Religions, (San Francisco: Ignatius Press, 2004), 105.

[11] Letter to Edward Dowse, April 19, 1803.

[12] Mark Eaton, “Holding Fast to Our Beliefs: Religion and Pluralism Since 9/11,” in APU Life, Azusa Pacific University Magazine, 23:1 (2010): 17.

[13] Anthony W. Marx, Convocation Address, September 3, 2007, Amherst College.

[14] Ratzinger, Truth and Tolerance, 177-78.

[15] Charles Rice, Fifty Questions on the Natural Law, (Ignatius Press, 1997), 132.

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About Dr. Edmund J. Mazza 6 Articles
Dr. Edmund J. Mazza is host of the “Discover Christ Channel” on YouTube. His podcasts can also be heard on “The Bar of History,” at