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Thomas Jefferson was as much of a connoisseur of secret codes as he was of fine wines. So in December 1801, his friend Robert Patterson, a mathematics professor at the University of Pennsylvania, sent him a coded message that he promised would be so difficult to decipher it would “defy the united ingenuity of the whole human race.” Indeed, for more than two centuries the message remained buried in Jefferson’s papers, untranslated, until Lawrence Smith line, a professional cryptographer from Princeton, N.J., recently cracked the code with the aid of nearly 100,000 calculations carried out by a computer.

Deciphering the jumble of letters turned out to be like opening a 200-year-old bottle of wine from the Monticello wine cellar—more exciting in the act than in the result. Patterson’s message to Jefferson was a reworded version of the preamble to the Declaration of Independence: “In Congress, July Fourth, one thousand seven hundred and seventy six. A declaration by the Representatives of the United States of America in Congress assembled. When in the course of human events….”

We can only guess how Jefferson might have reacted to the elaborate joke. Even to his contemporaries, he was a man enveloped in a largely impenetrable mystique. Describing the “person and manner” of Jefferson when he took the oath of office as president in 1801, Henry Adams wrote, “The liveliest description was worth less than a moment of personal contact.” What is easier for us than for many of Jefferson’s contemporaries—who knew in the flesh what Adams called this “loose, shackling person”—is to grasp the way his extraordinary mind habitually worked. We have, after all, nearly the whole of his papers to illuminate the grand contours of his personality—his powers of rational expression, the sense of natural rights that permeates the Declaration of Independence, his urbane, yet agrarian manner of life. But the belated cracking of his friend Robert Patterson’s code offers a tantalizing glimpse of more unfamiliar corners of his mind. To think of Jefferson hard at work, by daylight and candlelight, attempting to decode a cryptic message or carefully writing out the form and pattern of a new cipher is to witness Jefferson at work and at play simultaneously.

Jefferson’s words resonate with such power across the ages that it’s easy to forget he lived in a world where secret codes of all sorts proliferated and much of what he wrote was encrypted. For long-distance communications, he was able to rely on nothing more secure than a folded and sealed piece of paper. He was, as well, one of the leaders of a revolutionary movement that was planning rebellion in the midst of an occupying, enemy host. As the American minister to France, he served an incipient government that—like all governments then and now—routinely used codes and ciphers. As president, he equipped Meriwether Lewis not only with the authority to conduct his voyage of discovery but also with a complex cipher for secure communication. As an inventor, he devised a wheel cipher—a mechanical device for encoding and decoding messages.

Jefferson’s papers are filled with numerous examples of ciphers, including an encoded version of the Lord’s Prayer. Some are simple—based on substitution or using a dictionary as a key. Some are not simple at all—like Patterson’s, which yielded, finally, to a complex computer algorithm. Take, for instance, one of the documents included in the Jefferson collection at the Library of Congress. It is a sheet of paper in Jefferson’s handwriting dated 1784, just as he was beginning his ministerial career. The page is filled with vertical columns of numbers. Beside each number is a word or phrase—“reign” (792), for instance, or “special” (864) or “States General” (871)—1,046 of them in all, followed by a series of cryptic signs for punctuation marks and titles like “His Most Christian Majesty.”

Superficially, this list looks a lot like the published numerical codes that were compiled when telegraphy was king. But the purpose of Jefferson’s list wasn’t to speed up communication. It was to conceal it. Jefferson’s list of numbered words—a lexicon suited to diplomatic correspondence—was matched by an identical list in his recipient’s hands. As a result some of Jefferson’s letters—or critical parts of them—look like an exercise in numerology. That sheet of painstakingly numbered words is a reminder that Jefferson was nearly always his own cryptographer. And it’s a reminder of the tedium that task must have entailed sometimes.

Did Jefferson’s interest in cryptography reflect a heightened passion for secrecy on his part? If so, it was a passion he shared with James Madison and many other delegates to the Continental Congress. As Madison put it, in 1784, uncoded letters were written “in expectation of their being read by the postmasters.” But to work with codes, as Jefferson so often did, is to begin to wonder about their inherent properties. How do you balance the need for a code that’s simple enough to be usable with a code that’s complex enough to be unbreakable?

Contemplating such a nuanced problem would have been irresistible to Jefferson, both as a matter of practicality and elegance. A code’s essential purpose is to transpose the regularity of language—the familiar repetition of letters and clusters of letters— into an apparent randomness. But there is clearly more to Jefferson’s code sheets than cryptographic necessity. They convey the elaborate gratification of a man who understood the value of order and system, the look of an inventive mind sorting out the problem of how to hide the visual signs of the mind’s workings.

To the illiterate, written language already looks coded, and in a sense it is. Its key is called the alphabet. Jefferson was, of course, a master of written language. As a writer, he is, for his time, a paragon of clarity and directness, whether he’s giving business directions, writing diplomatic briefs or proclaiming the natural rights of man. The paradox of using a cipher is that in certain situations it allowed Jefferson to write more freely, “without restraint,” as Madison put it, by limiting his audience to precisely the persons he intended. It allowed him to say in the private space of code what he did not want to say in the public space of ordinary writing.

In an odd way, thinking about Jefferson’s interest in cryptography helps us frame his most famous piece of writing— the Declaration of Independence. To read Robert Patterson’s intricately coded version of the preamble to the Declaration is to realize how uncoded, how boldly public that document really is. In fact, the peculiarity of Patterson’s message—like Jefferson’s cipher version of the Lord’s Prayer—is that it encodes something that needed no encoding. It’s a game, a kind of mathematical amusement.

And that lets us see, from another angle, the radicalism of what Jefferson does in the Declaration of Independence. He uncodes the private and public feelings of rebellious Americans, gathers together the arguments and assumptions that justify an intent that had been nursed along in varying degrees of secrecy. The Declaration of Independence is not a message meant to find its way through diplomatic channels—coded at one end, decoded at the other and then uttered aloud with a sense of political balance and restraint. Instead, it uses the plainest possible language, as emphatically as possible. It is self-sufficient in its arguments, confident in the universality of its audience.

Verlyn Klinkenborg is a member of the New York Times Editorial Board and author of The Rural Life, Making Hay and Timothy.

Originally published in the December 2009 issue of American History.