If I had to pick one, single theme that I feel is most prevalent in The Chrysalids, I would say that the theme of discrimination is most apparent. The discrimination that the novel contains though is very interesting. It is not racism, sexism, or even class discrimination. It's something completely different. The discrimination is "genoism." That word was actually coined by Andrew Niccol for his 1997 film GATTACA. There are a lot of parallels between that movie and the The Chyrsalids.
Genoism is present throughout the novel. David Strorm is taught from birth to discriminate against and hate any kind of genetic change that Waknuk society doesn't deem "normal." In fact, the Strorm household has framed sayings hanging up that remind David of that concept.
WATCH THOU FOR THE MUTANT! . . . THE DEVIL IS THE FATHER OF DEVIATION.
Despite the emphasis on hating genetic mutation, David doesn't behave that way. For example, he doesn't turn Sophie into the authorities even though she has six toes. Unfortunately, her secret is discovered and she is forced to flee to the Fringes. Had she not done that, Sophie likely would have been killed just for having a genetic difference. Once David and the other telepaths are discovered, they must escape to save their own lives as well. Even when the Sealand woman shows up, she also helps perpetuate the novel's theme of discrimination through genoism. She tells David that he is genetically superior to the Waknuks, and that they deserve to be eradicated.
"For ours is a superior variant, and we are only just begin-ning."
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