Though the most Deistic of the Founding Fathers, even Jefferson was not a full-fledged Deist if we accept that philosophy as having had two fundamental tenets: a rejection of biblical revelation and a conviction that God, having created the laws of the universe, had receded from day-to-day control and intervention. Jefferson clearly did agree with the first part of Deism. But he did not agree with the second.

Jefferson seemed to believe in a God who was still present in, and intervened in, the lives of men and nations. After having read Jefferson attack so many of the legs of religion, it might seem jarring to now read his regular invocations of God as a personal force in life”sometimes in terms so direct and literal, they surpass those of today’s politicians.

In his first inaugural address, he declared that we should be “acknowledging and adoring an overruling Providence, which by all its dispensations proves that it delights in the happiness of man here and his greater happiness hereafter.” In his first message to Congress, in 1801, he thanked the “beneficent Being” who instilled in thee warring politicians a (temporary) “spirit of conciliation and forgiveness.”

In his second message, he credited the “smiles of Providence” for economic prosperity, peace abroad, and even good relations with the Indians. He never stopped asserting the importance of separating church and state, but he did this in the context of repeated public pronouncements about the powerful role of an intervening God in the fate of America. These two somewhat contradictory themes came together most directly in his second inaugural address. In the first part of the speech, he defended his practice of not issuing days of fasting or thanksgiving proclamations. But toward the end, he said that to avoid making the mistakes to which he, as a human, was prone, “I shall need, too, the favor of that Being in whose hands we are, who led our fathers, as Israel of old, from their native land and planted them in a country flowing with all the necessaries and comforts of life.”

Some look at Jefferson’s public pronouncements and sense cynicism. Recall his comment about “cooking up” an effective prayer proclamation to rally lethargic Americans. Perhaps he was just being a pol, using the language he thought would most appeal to his audience. But the evidence is stronger that Jefferson genuinely believed in a personal God and a spirit life. For one thing, he went much further in his pronouncements than he needed to, attributing a wide range of events and policies to God’s “smiles.” More important, his private letters reflected a similar view about the nature of God. In a letter to Eliza Trist, he declared that “it is not easy to reconcile ourselves to the many useless miseries to which Providence seems to expose us. But his justice affords a prospect that we shall all be made even some day.” In 1763, he wrote John Page that if we hope to fortify ourselves from misfortunes, “The only method of doing this is to assume a perfect resignation to the Divine will, to consider whatever does happen, must happen.” In 1801, he commended “your endeavors to the Being, in whose hand we are.” When Napoleon was defeated, he wrote to a friend: “It proves that we have a god in heaven. That he is just, and not careless of what passes in the world.”

How could this ultra-rationalist”a believer in science and reason”so fully embrace a supernatural God watching over our lives? This is another case in which today’s activists and scholars, by applying the standards and definitions of our time, misunderstand the ideas of a Founding Father. Remember: In this era before Charles Darwin: most of the Enlightenment leaders were not arguing against the existence of God. On the contrary, they argued that the laws of science actually proved the existence of God, if one knew how to look at it the right way.

Jefferson believed that our spiritual journeys must be led by reason, not faith. In a letter to his nephew Peter Carr, he urged rigorous application of scientific principles to the Bible. For instance, he encouraged Carr to look at the story of Joshua making the sun stand still and then added, “You are astronomer enough to know how contrary it is to the law of nature that a body revolving on its axis, as the earth does, should have stopped” without then having “prostrated animals, trees, buildings.” Jefferson conceded that such an investigation might take the young man away from God. “Do not be frightened from this inquiry by any fear of its consequences. It if ends in a belief that there is no God, you will find incitements to virtue in the comfort and pleasantness you feel in its exercise, and the love of others which it will procure you.” If, on the other hand, “you find reason to believe there is a God,” you will find comfort and happiness in that, too. And you should not feel badly or anti-God should your mind take you away from the church, since “your own reason is the only oracle given you by heaven.”

It’s not absurd to read such passages and conclude that Jefferson was a relativist. It it’s up to everyone’s individual reasoning process to determine religious truth, then is there any genuine reality? This impression was reinforced by his statement in Notes on the State of Virginia that “it does me no injury for my neighbor to say there are twenty gods, or no god.” But Jefferson did believe in religious truth; he just had an overriding conviction that it was reason, acting in the marketplace of ideas, that would lead people to find it. “It is error alone which needs the support of government. Truth can stand by itself.”

Jefferson himself was not an agnostic on this point. He applied reason and critical scientific thought to the world and concluded that God does exist. Read this extraordinary letter from Jefferson to John Adams on April 11, 1823, and it’s possible to see how his anti-Christian, rationalist approach nonetheless led him to a deep love of God.

I hold (without appeal to revelation) that when we take a view of the Universe, in its parts general or particular, it is impossible for the human mind not to perceive and feel a conviction of design, consummate skill, and indefinite power in every atom of its composition. The movements of the heavenly bodies, so exactly held in their course by the balance of centrifugal and centripedal forces, the structure of our earth itself, with its distribution of lands, waters and atmosphere, animal and vegetable bodies, examined in all their minutest particles, insects mere atoms of life, yet as perfectly organised as man or mammoth, the mineral substances, their generation and uses, it is impossible, I say, for the human mind not to believe that there is, in all this, design, cause and effect, up to an ultimate cause, a fabricator of all things from matter and motion, their preserver and regulator while permitted to exist in their present forms, and their regenerator into new and other forms.

We see, too, evident proofs of the necessity of a superintending power to maintain the Universe in its course and order. Stars, well known, have disappeared, new ones have come into view, comets, in their incalculable courses, may run foul of suns and planets and require renovation under other laws; certain races of animals are become extinct; and, were there no restoring power, all existences might extinguish successively, one by one, until all should be reduced to a shapeless chaos. So irresistible are these evidences of an intelligent and powerful Agent that, of the infinite numbers of men who have exited thro’ all the time, they have believed, in the proportion of a million at least to Unit, in the hypothesis of an eternal pre-existence of a creator, rather than in that of a self-existent Universe.

Yes, Thomas Jefferson”hero of modern liberals”believed in intelligent design.

Jefferson’s important actions on behalf of religious liberty took place from 1776 to 1809; his anger at the priesthood, however, intensified as he aged, and his focus on Jesus sharpened, but the basics of Jefferson’s views were evident all his life. What emerges is a picture of Thomas Jefferson that belies stereotypes created by modern culture warriors. He was anti-Christian and pro-Jesus. He was against blind faith and in favor of reason-based belief. He turned to the power of science to explain the world, and to prove the existence of God. As he put it later, he was a “sect of one.”

How does this all relate to the history of religious freedom in America? What it shows is that the classical view of how Jefferson came to support the separation of church and state and fight for religious freedom”that his views grew out of his study of Locke and other thinkers”misses on part of the picture. The author of the Declaration of Independence was on a personal spiritual journey that took him outside the mainstream. He resented being considered a heretic, because he believed that his approach to God and Jesus was more faithful to both of them. He believed that oppression of “the mind” not only led to persecution but also constrained the process of rational exploration that would lead to religious truth. This was no mere abstraction for him. He knew that had he been forced to believe the official line, he would have been deprived of an unobstructed journey to God. Jefferson wanted religious freedom in part because he wanted to be, religiously, free.

Steven Waldman is founder, CEO, and editor in chief of Beliefnet.com . This essay is excerpted and adapted from Founding Faith: Providence, Politics, and Religious Freedom in America (Random House).

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