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According to scholars, the novel's main themes are nature versus nurture, rebirth, and the differing experiences of what society constructs as polar opposites—such as those found between men and women.

Instead of trying to create a separate person, I tried to pretend that I had this [physical feature] and that I had lived through this as much as I could".

He intended Middlesex to be "the story [he] wasn't getting from the memoir".

Eugenides spent the first few years trying to establish the narrative voice for his novel.

After discovering in his library research 5-alpha-reductase deficiency, an autosomal recessive condition manifested primarily in inbred, isolated population groups, his perception of the novel significantly changed.

Rather than a "slim fictional autobiography" of an intersex individual, the novel would be epic in scope, tracing the lives of three generations of Greek Americans.