Right away, the book demands an alchemical treatment, and because of the historical specificity of the prose, it is very likely that the reader here is being exposed to carefully plotted and planned alchemical ideas and patterns that will probably go unnoticed, except that they are intended to resonate artistically with the shape of the human consciousness, which is the basic premise of alchemy. This commentary is invited in the final act of the book, because that is the very theory that Newton is struggling to write when we meet him as a character in the book.
Newton does eventually publish a theory of everything, and he and Leibniz are co-credited with their spontaneous discovery of calculus. That is the silent climax of "The Junctio." The very name "junctio" is itself a reference to alchemy, where junctio refers to the combination of various chemicals and agents for the creation of something new that is often more than the sum of its parts. So where is the alchemy throughout the rest of the novel?
Well, remember that an alchemist predicts Eliza is not who Jack thinks she is, and they name the ship Minerva instead, an important reference to one of the most famous witches in all of alchemy. The highlight of Jack's criminal career is not the gold the Cabal seized in the Atlantic! It is the treasure he obtains "from the East," namely quicksilver, or mercury. Mercury is alchemically associated with the divine syzygy and the union of opposites, and his discovery of Mercury is a comment on his stage of enlightenment. It signifies that he has attained insight through balancing his character.
