Francis, though primarily used in interrogations, was to use his learned cipher skills in what has been called the Lopez affair – an assassination plot. A Jewish-Portuguese doctor, Rodrigo Lopez, had become the Queen’s physician. He was accused by the Earl of Essex in this plot.
Lopez was said to have sent “obscurely worded” letters to Spanish agents. Though Phelippes was the primary decipherer for spy chief Sir Walsingham, in Hostage to Fortune [p. 158] we learn that “Francis Bacon was among those brought in to use the skills he had acquired in diplomatic service with Sir Amias Paulet to crack the codes.”
“Some historians and literary critics consider Lopez and his trial to have been an influence on William Shakespeare's The Merchant of Venice. " “Many Shakespearean scholars believe Dr. Lopez was the prototype for Shylock,"
Besides the close connection to Thomas Phelippes, Francis’ older brother Anthony was another cipher expert who “was an experienced intelligencer with links to the networks of both Walsingham and Lord Burghley….He remained in constant correspondence with his brother Francis….Anthony kept up a correspondence with spies in various places on the continent after his return to England in 1592.”
Sovereignty and intelligence: spying and court culture in the English Renaissance by John Michael Archer, 1993, [p. 124].
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From the same book [p. 121] above we find that “With the help of his brother Anthony, Bacon (Francis) became Essex’s principal strategist and decoder in the earl’s competition with Robert Cecil for the queen’s attention and gratitude.”
The point of the above is to again show Francis Bacon’s familiarity with ciphers and codes from both a theoretical and practical standpoint. And that it would have been well within his capability to make them fairly well-hidden in a sophisticated manner while still leaving them detectible to alert and diligent readers.
Returning to the Friedmans, they describe the most basic Baconian cipher using the Elizabethan 24-letter alphabet as:
A B C D E F G H I-J K L M N O P Q R S T U-V W X Y Z
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
In this system we are interested in the cipher numbers for ‘Francis’ which is 67, “Bacon” which is 33, and “Francis Bacon” which is 100.