The crumbling cliffs of Lyme Bay (Symbol)
As Charles walks the Lyme coast, searching for fossils and ruminating about the nature of science and evolution, he looks at the cliffs and they strike him as symbolizing something. The narrator writes that Charles "might perhaps have seen a very contemporary social symbolism in the way these gray-blue ledges were crumbling" (45). The narrator explicitly imbues the cliffs with symbolism here, but the character doesn't see this symbolism - Charles is not astute enough or self-aware enough to really think that his social position is in danger. It is for the reader's benefit that the narrator points out the possible and poignant connection between the crumbling class structure and the crumbling cliffs.
What the cliffs symbolize to Charles is the stately and monumental nature of time, in which nature builds on top of what exists to create huge edifices. He also sees the cliffs as symbolizing "the survival of the fittest and best," a subset of humans to which he feels he belongs (45).
Evolution and the changing class system (Allegory)
Darwinism is a central theme of the novel, and one of the ways in which it is used is as an allegory or explanation of the changing class system in Victorian England. Charles and his like-minded peers believe in the survival of the fittest - that the class system is the way it is because those at the top of the pyramid are most fit to rule. However, there are several indications in the novel that because of changing conditions, gentlemen like Charles will not be able to solidify their hold on the top echelon of society, and that other classes - primarily the bourgeoisie, represented by Ernestina's father - will rise to take their place. This process is described in Darwinian language; the gentlemen are "living fossil[s]," being replaced by "fitter forms of life" (230).
Ware Commons (Symbol)
Much of Charles and Sarah's initial interactions take place on the wild Ware Commons, which is used as a symbol of a world outside of the Victorian sphere of harsh morality and prudery. Typically conservative characters like Mrs. Poulteney are aware of Ware Commons' significance: for Mrs. Poulteney, Ware Commons is the "objective correlative of all that went on in her own subconscious" - that is, Ware Commons symbolizes all the things that she would prefer not to think about, like sex and crime and immorality (78). There is no supervision of Ware Commons, and so it is one of the only places in the novel that is free from society's rules - it is likened to "Sodom and Gomorrah" at one point, which underscores the seedy sexual connotations the place has for Lyme residents (76).
The novelist as God (Allegory)
The author of the novel compares himself to "a god" in Chapter 13: he and God have both created a world, over which they can exert some (or even full) control. Fowles writes in Chapter 13 that "[t]here is only one good definition of God: the freedom that allows other freedoms to exist" (82). He therefore allows, or pretends to allow, his characters some autonomy; while he has created them and provides the large story arcs of their lives, he is sometimes surprised by their actions, and they control him to some degree. He cannot always know what they are saying, thinking, or even doing - he writes at one point that Sarah is "too far away for [him] to tell" if she is crying or not (364). Fowles may compare himself to God, but the allegory can only be taken so far - he is a limited deity.
Charles as an ammonite (Motif)
As mentioned before, evolution and the changing class system are huge concerns of this novel, and one of the recurring ways that the author depicts this theme is through the motif of comparing Charles to an ammonite. Charles' lack of free will is represented by this analogy: the author writes in Chapter 29 that Charles felt he had "no more free will than an ammonite" (189). The ammonite motif is picked up repeatedly throughout the novel, and it is especially powerful because of its irony: Charles is compared to the ammonites he so loves to collect, and which he feels superior to - he is a thinking person, of course, and he is still alive, so he must be fitter than the extinct species he collects. But he is actually no freer to shape his destiny than they are, and he too will be caught up and frozen in time.
