Deep in the Vatican Library, a mysterious 408-page manuscript had sat unread for over four centuries. Its pages were scrawled with strange symbols—34 different cipher characters mixed with Arabic script—that concealed secret remedies "for affections of the human body." Healing practices hidden this way because they could attract accusations of witchcraft. But now, AI has cracked it open.

The Borg Cipher Breakthrough

The manuscript, known as the Borg cipher, was decoded using machine learning by researchers including Beáta Megyesi, a professor in computational linguistics at Stockholm University. The decrypted text revealed thousands of bizarre treatments: drinking several glasses of high-quality red wine for what ails you, fermenting nutmeg in dough to combat dysentery. "It is like detective work where every symbol, pattern, and partial solution may bring us closer to someone's secrets," Megyesi says.

From Royal Love Letters to Diplomatic Panic

This isn't just about medieval home remedies. Coded documents historians have uncovered include diplomatic intelligence, secret society rituals, love affairs, and political plots that reshape what we know about famous figures. A collection of coded letters written by Mary Queen of Scots during her imprisonment in England revealed her involvement in conspiracies to regain her throne and her tense relationship with her son James VI. Another letter from Charles V—the Holy Roman Emperor and King of Spain—written using 120 different cipher symbols, exposed how one of the most powerful men of his era was paralyzed by fear of assassination plots.

The Transcription Bottleneck

Before any code-breaking can begin, researchers must first transform handwritten ciphers into digital documents. Bad handwriting, fading ink, and invented symbols make this painstaking work. Cecile Pierrot, a cryptologist at France's INRIA research institute, estimates it takes about a day to transcribe a two-page letter with unfamiliar symbols. AI tools like Transkribus are starting to accelerate transcription by detecting text blocks, analyzing individual lines character-by-character, and handling 17th-century German script—though manual corrections remain necessary.

The Descrypt Project: Building Universal Cipher-Cracking AI

Megyesi is now leading the multinational Descrypt project to develop adaptable AI models that can handle rare scripts, obscure alphabets, and symbolic repertoires. "We are developing more adaptable models trained and tested across a broad range of scripts," she explains. The team recently showed how AI could skip transcription entirely and directly analyze page photos to decipher simple substitution ciphers.

An AI Chatbot for Dead Languages

The researchers built an AI chatbot that combines decryption algorithms with large language models trained on historical texts from different periods, plus image recognition for handwriting analysis. When tested on the Borg cipher, it decoded a 500-symbol extract in just over 29 minutes and provided an English translation—while documenting why its solution was plausible to prevent hallucinations.

What Remains Uncracked

Some of history's most tantalizing puzzles could fall to these tools: the 4,000-year-old Phaistos Disc from Minoan Crete and Linear B, the early Greek script that sat undeciphered for decades before Michael Ventris cracked it in the 1950s. "What excites me is not only the possibility of solving one specific historical puzzle, but the prospect of creating methods that can assist researchers across many different cases," Megyesi says.

Key Takeaways

  • Around 1% of all material in world archives and libraries is fully or partially encrypted, representing centuries of hidden history
  • Modern ciphers used multiple symbols for single letters (up to eight variants for 'E') plus decoy characters specifically designed to thwart snooping
  • AI transcription tools like Transkribus are reducing what took cryptologists days down to hours, with full decryption pipelines now emerging
  • Researchers have collected 400 mysterious cipher postcards from the late 1800s—early decoded scraps reveal love letters written in German

The Bottom Line

This isn't just academic curiosity. We're watching AI prove it can reconstruct history that powerful people went to extreme lengths to hide. Four hundred years of suppressed medical knowledge, royal conspiracies, and secret society rituals are about to get a thorough audit—and I wouldn't be surprised if a few established historical narratives need serious revision.