Leibniz as a sign of mysticism
As a real person, Leibniz is primarily important for his unimaginable contributions to mathematics, helping catch the essence of calculus before any other person—though Newton discovered it at the same time. Leibniz's presence in the novel is a sign of the times, because of his station in history between the scientific era and the era before it, but it also signifies a double entendre. Leibniz is also a continental philosopher with very perplexing, nearly sublime ideas about the mystic religious nature of reality. His dual contribution is a sign of both science and religion in one mystic perspective.
The alchemy motif
The title is a reference to alchemy, specifically referring to Quicksilver, or Mercury as it is now called. The invocation of Mercurial themes in the novel serves to show the duality of the novel's themes. Just as the element Mercury is both solid and liquid in one strange, perplexing state, so also the entirety of life is both obvious and hidden.
The end of an epoch
This novel is apocalyptic in tone because it signifies the drastic changes that mark the beginning of the scientific era. The season of European life before in all its regalia and opulence has given way to the real challenges of urbanization, and en masse, the government is a difficult Leviathan to reel in, to use a metaphor from Job. The motif is clear in the novel's consistent observations about breakthroughs in mathematics, science, separation of church and state, and in government.
The motif of submission and domination
Among the dualities of the novel, there is a clear play on this duality, the balance between domination and submission. The idea of controlling people is an important theme in the novel, and when Daniel finds himself in an archetypal role reversal (he is like the archetypal maiden in distress, because trapped in a tower), though in other seasons of the novel, Eliza is clearly the symbol for submission, because she is a slave. The point of the motif might be that in relationship to time, all life is submissive, because no one can control fate or human progress.
Revolution as a symbol
The Glorious Revolution ends the novel, and meanwhile Daniel passes painful bladder stones. The Revolution is a symbol for radical change at human hands. It is proof that in the epic journey of human progress, social order is gradually changed by a series of epic public conflicts. For this, France serves as a perfect backdrop, because the elements of Revolution are poignant as ever.