The alchemical motif
Though Isaac Newton is considered in modern opinions as a scientist, there is simply no getting around the fact that science was a different process in the 13th century, and so there are references to alchemy, most important when Isaac Newton dies and is resurrected by the Philosopher's Stone according to alchemical folklore. The effect is that Newton is regarded symbolically as a permanent, eternal, golden part of human life, because of his scientific contributions.
The tampering with Pyx
When Jack Shaftoe manages to steal a mint for money, he can begin printing fake currency which allows him to be very rich, a symbolic reminder that although one can struggle for wealth their whole lives and never find it, dishonest people find it very quickly. This represents Jack's willingness to get rich at the literal expense of his community.
Eliza and Caroline
There is a duo in the novel, the historical Princess Caroline and Eliza her servant who both wants to be her and who feels that she might be in danger. Together they form a kind of symbolic pair, where Caroline represents royal naïvete and privilege, and Eliza represents paranoia, scarcity, and fear.
The Whigs and Tories
These British political factions are like political parties except that in this novel, they arm themselves and fight it out in the streets. This explicit violence is a symbolic reminder of what is lurking underneath party lines: Anger, hostility, victim mentality, and aggression. Because the problems in their community were so radically divisive to them, they end up killing each other instead of solving problems.
The escape to wealth
When Jack and Eliza escape to the court of French monarch, Louis XIV, that represents an ironic twist of fate. Why should Newton and all of Europe suffer while the bad guys simply party in wealth and luxury? That is because they feel no loyalty to their community, which allows them to do whatever is most expedient. Their freedom and luxury suggest a kind of brokenness in the systems of society.
