The Ciphers of the Initiated

Uncovering Secrets Not Intended for Our Eyes


The quest for lost secret knowledge can take many forms. The survivors of Atlantis, some believe, might have taken steps to guard their advanced knowledge against the dark ages, which they saw coming, preserving it for rediscovery by some future, similarly advanced, society. Their knowledge, it has been speculated, could have been preserved in well-hidden archives. Edgar Cayce, the renowned sleeping prophet of Virginia Beach, VA predicted we would find more than one ‘Hall of Records’, and to this day many continue to search for it. Whether or not such an archive is to be found, there may be another place to look for lost knowledge from the past. Some of the greatest thinkers and writers in history, it turns out, have embedded important secrets in their work, where only the initiated, who knew what to look for, could find them and where, as in a buried archive, they may still await discovery by those researchers equipped with, what the Bible called, ‘eyes to see and ears to hear’.


The Copiale Cipher

A strange, eighteenth century, German manuscript seems straight out of fiction—a handwritten message in abstract symbols and Roman letters meticulously covering 105 yellowing pages hidden in the depths of an academic archive. Now, more than three centuries after it was devised, the 75,000-character Copiale Cipher finally has been broken.

According to Suzanne Wu, in a 2011 press release from the University of Southern California, the mysterious cryptogram, bound in gold and green brocade paper, reveals the rituals and political leanings of an eighteenth century secret society in Germany. The rituals detailed in the document indicate the society apparently had a fascination with eye surgery and ophthalmology, though it seems members of the society were not eye doctors.

Of course, biblical parables directed to those who had ‘Eyes to see’ might also have been considered by the uninitiated to be optometrically related, but that would have missed the point.

The Copiale translation “opens up a window for people who study the history of ideas and the history of secret societies,” said computer scientist Kevin Knight of the USC Viterbi School of Engineering, part of the team that finally cracked the cipher. “Historians believe that secret societies have had a role in revolutions, but all that is yet to be worked out, and a big part of the reason is because so many documents are enciphered.”

To break the cipher, Knight and colleagues Beáta Megyesi and Christiane Schaefer of Uppsala University in Sweden tracked down the original manuscript, which had been discovered in the East Berlin Academy after the Cold War and is now in a private collection. The team transcribed a machine-readable version of the text, using a computer program created by Knight to help quantify the co-occurrences of certain symbols and other patterns.

“When you get a new code and look at it, the possibilities are nearly infinite,” Knight said. “Once you come up with a hypothesis based on your intuition as a human, you can turn over a lot of grunt work to the computer.”

With the Copiale cipher, the code-breaking team began without even knowing the language of the encrypted document. But because they had a hunch about the Roman and Greek characters distributed throughout the manuscript, they isolated these from the abstract symbols and attacked it as the true code.

“It took quite a long time and resulted in complete failure,” Knight said.

After trying 80 languages, the cryptography team ultimately realized the Roman characters were “nulls” intended to mislead the reader. It was the abstract symbols that held the message.

The team later tested the hypothesis that abstract symbols with similar shapes represented the same letter or groups of letters. Eventually, the first meaningful words of German emerged: “Ceremonies of Initiation,” followed by “Secret Section.”

Knight now is targeting other coded messages, including ciphers sent by the Zodiac Killer, a serial murderer who passed taunting messages to the press but has never been caught. Knight also is applying his computer-assisted code-breaking software to other famous unsolved codes, such as the last section of “Kryptos,” an encrypted message carved into four, large copper plates on the grounds of CIA headquarters at Langley, VA, and the Voynich Manuscript, a mysterious medieval document that has baffled professional cryptographers for decades. Some of the most curious and complex ciphers, though, have been passed down to us by the greatest geniuses in history.


The Francis Bacon Enigma

As millions of fans of Dan Brown’s book and movie The Da Vinci Code know, Leonardo is said, by some, to have buried deep secrets of Christian origins in his paintings and drawings. And he may not be the only renaissance artist to have resorted to such tactics. Recently two, art-loving Brazilian doctors claimed to have uncovered secret lessons in human anatomy left by Michelangelo in his paintings on the ceiling of the Sistine Chapel in the Vatican.

The unraveling of secret codes left by the giants of Western culture has become a passion for some researchers. Sleuths—both professional and amateur—still rummage through dusty archives and libraries in search of hidden knowledge. Of all the candidates for the title of ‘greatest literary mystery’, some scholars argue, there are none more intriguing than those in the Shakespearean plays. Many wise men, including Mark Twain and Friedrich Nietzsche, have believed that the secret author of the plays or, at least, the leader of the group of Grey’s Inn ‘wits’ who produced and loaded them with secret messages, was Francis Bacon.

In 1880, Ignatius L. Donnelly, U.S. Congressman, and author of Atlantis: the Antediluvian World, wrote in The Great Cryptogram, that Bacon had revealed his authorship of the Shakespearean works by concealing secret ciphers in the text. A few years later Orville Ward Owen took the idea a little further. A physician, Owen used a “cipher wheel” of his own devising to unlock many cryptograms found in Shakespeare’s works. With the aid of his machine, Owen could quickly collate printed pages from the works of Shakespeare, Bacon, and other authors, combining passages that appeared to have some connection with key words or phrases. In his 1893 book, Sir Francis Bacon’s Cipher Story (1893–5), Owen claimed to have discovered nothing less than a secret history of the Elizabethan era hidden in the Bacon/Shakespeare works. Bacon is also said to be the man who, behind the scenes, guided creation of the King James Bible. Owen and others have deduced that Bacon was the secret love child of queen Elizabeth I and Robert Dudley, the Earl of Leicester, and was forced by the highly sensitive nature of his personal saga to rely on ciphers to disseminate his knowledge.

Ciphers are a system for writing codes, so that those with special knowledge—some might call them ‘initiates’—can find hidden messages left in places where the uninitiated would find nothing of interest. Bacon is widely credited with creating the bilateral cipher based on steganography (the hiding of a message’s existence). Otherwise innocuous text could be made to carry a hidden message, which could be extracted using a prearranged key to identify the letters forming the secret message. Only the intended recipient would even know to look for a message. Bacon wrote that he created his bilateral cipher when he was a young man in Paris. He and the Rosicrucian fraternity, which he founded, used several kinds of cipher. Placed in various published works issued outwardly under different names or pseudonyms, the ciphers were intended to convey messages to those in the know. Many of Bacon’s coding techniques were later picked up by the clandestine services of various world powers and, ultimately, by modern computer programmers to create binary and machine codes.

Researcher William Henry is among those who believe that Bacon used a cryptic double-A (one light and one dark: ‘AA’) as a key to many of his ciphers. Facsimiles published during Shakespeare’s time of the Sonnets, Hamlet, Richard III, all bear the light A and dark A on their title pages. It also appears in the King James Bible of 1611.

Whether or not Bacon is actually Shakespeare, he is still universally respected as one of the greatest thinkers who ever lived, one gifted with extraordinary prophetic vision. “He seemed to be able to see through time,” wrote Henry, “describing inventions of great imagination such as a pillar of light at the center of the New Atlantis.” A true initiate, he hid his secrets in cryptograms buried in writing products, which his workshop turned out, many bearing the AA head piece, including books written by other authors but under his direction.

Five rival publishers independently produced the works of Shakespeare bearing the AA head piece, lending credence to the idea that this is the signature of a hidden author, Bacon.

Bacon had his own wood blocks of devices or emblems, some of which were his own design, and every book produced under his direction, whether written by him or not, was marked by the use of one or more of these logos. Authors include Edmund Spenser, Christopher Marlowe, Shakespeare, Walter Raleigh, and others.

Bacon’s mastery of ciphers and symbols, say scholars, enabled him to use these works to send messages or teachings. According to Henry, Bacon’s greatest code may be English itself. “The English language,” wrote Henry in Atlantis Rising, #45, (“Bacon and the Double A”) “as is widely acknowledged, is founded upon the English translation of the King James Bible (which, some believe, God enabled and Bacon guided) and upon the plays of Shakespeare. There are about 22,000 different English words in the plays, of which 7,000 are new words, introduced—as Murray’s Oxford Dictionary tells us—into the language for the first time.”


The Torah Prophecies

If English itself is a code hiding many ancient secrets, Hebrew may well be another. Some, like best-selling author Michael Drosnin, have argued that God himself foretold the events of all times, including our own, in a code buried in the letters of the Hebrew Torah. The Bible Code, Drosnin’s 1997 book, was based on the findings of Israeli mathematician Eliyahu Rips.

Widely respected for his research in geometric group theory, Rips became known to the general public following his co-authorship of a paper on what he argued were coded messaging in the Torah. In the late 1970s, Rips began using a computer to look for such codes. In 1994, with Doron Witztum and Yoav Rosenberg, he published an article in the journal Statistical Science, “Equidistant Letter Sequences in the Book of Genesis,” which claimed the discovery of encoded messages in the Hebrew text of Genesis. This became the inspiration for Drosnin’s book.

In 1994 Rips wrote a letter, based on his research, to Israeli prime minister Yitzhak Rabin, “The reason I’m telling you about this is that the only time your full name—Yitzhak Rabin—is encoded in the Bible, the words ‘assassin that will assassinate’ cross your name. That should not be ignored, because the assassinations of both John and Robert Kennedy and Anwar Sadat (the Egyptian leader) are also encoded in the Bible—in the case of Sadat with the first and last names of his killer, the date of the murder, the place, and how it was done. I think you are in real danger, but that the danger can be averted.”

On November 4, 1995, about a year after Rips’ letter was delivered to Rabin by his close friend, the poet Chaim Guri, Rabin was shot in the back and murdered by a man who believed he was on a mission from God. The murder, said Rips, had been encoded in the Bible 3,000 years before.

In the years since Drosnin’s book, the theory that the Bible contains such a hidden code has been dismissed by most experts, who say similar patterns can be found in just about any sufficiently large group of letters. The possibility of such divine coding, however, has fascinated many, not the least of which was Sir Isaac Newton. In the book Temple at the Center of Time: Newton’s Bible Codex Deciphered and the Year 2012 researcher David Flynn, claimed to have unraveled Newton’s “unified field theory of biblical prophecy” and suggested that the temple of Solomon is more than a mere place of worship, indeed that it intersects time and dimension making it a prophetic and supernatural structure, virtually “God’s Time Bomb.”

Flynn catalogued a number of anomalies surrounding the temple, including the prisca sapentia framework of Newton, which suggests that the distance between the temple of Jerusalem and the capital city of any nation historically affecting the chronicles of Jerusalem would be supernaturally connected.

“The description of Jerusalem as a terrestrial center point is found in Philo’s Legatio and Gaium,” Flynn notes. “The world is like a human eyeball. The white of the eye is the ocean surrounding the world, the iris is this continent, the pupil is Jerusalem, and the image in the pupil is the Holy Temple.”


The Plato Code

Many other potential ancient sources of secret meaning continue to come to light. Even the writings of the Greek philosopher Plato are now regarded by some scholars as veiling esoteric intentions. In fact, a science historian at The University of Manchester in the United Kingdom claims to have cracked what he calls, “The Plato Code”—the long disputed secret messages hidden in the great philosopher’s writings.

Widely regarded as the greatest mind of Greece’s Golden Age, the philosopher Plato laid the very foundation of Western culture and science. A 2010 paper by The University of Manchester’s, Dr. J. B. Kennedy in the U.S. journal Apeiron, reveals that Plato used a regular pattern of symbols, inherited from the teachings of Pythagoras, a century earlier, to give his books a musical structure. Pythagoras had declared that the planets and stars made an inaudible music, a ‘harmony of the spheres’. Plato imitated this hidden music in his books.

The hidden codes, says Kennedy, show that “Plato anticipated the Scientific Revolution 2,000 years before Isaac Newton, discovering its most important idea—the book of nature is written in the language of mathematics. The decoded messages also open up a surprising way to unite science and religion. The awe and beauty we feel in nature, Plato believed, showed that it is divine; discovering the scientific order of nature is getting closer to God.” This, says Kennedy, could transform today’s culture wars between science and religion.

Dr. Kennedy spent five years studying Plato’s writing and found that in his best-known work the Republic he placed clusters of words related to music after each twelfth of the text—at one-twelfth, two-twelfths, etc. This regular pattern represented the twelve notes of a Greek musical scale. Some notes were harmonic, others dissonant. At the locations of the harmonic notes he described sounds associated with love or laughter, while the locations of dissonant notes were marked with screeching sounds or war or death. This musical code was key to cracking Plato’s entire symbolic system.

A researcher in the University of Manchester’s Center for History of Science, Technology and Medicine, Dr. Kennedy says: “As we read his (Plato’s) books, our emotions follow the ups and downs of a musical scale. Plato plays his readers like musical instruments.”

Plato did not, however, design his secret patterns strictly for his own amusement—like Bacon, he did it for his own survival. Indeed, his ideas were a major threat to the official Greek religion of the time. Mathematical laws and not the gods controlled the universe, he said. Socrates, Plato’s own teacher, had been executed for heresy. Secrecy was common in ancient civilizations, especially for esoteric and religious knowledge, but for Plato it was a matter of life and death. Encoding his ideas in secret patterns was the only way to be safe, Kennedy believes.

The popular interest in secret codes of many kinds continues to grow. There is reason to hope that recent research may direct new light into some long hidden corners. Technology developed by NASA, for instance, for use with satellite imagery now holds promise as another tool for examining ancient manuscripts. The hope is that the faded ink of such texts may ultimately yield the secrets of lost worlds. Now, many scholars are eagerly waiting to see what the technique can tell them about such documents as the Dead Sea Scrolls, the Nag Hammadi texts, the Voynich manuscript, or maybe some, yet to be discovered, message from a lost civilization.

By Martin Ruggles