Throughout the Xenogenesis series themes of sexuality, gender, race, and species are explored. The Oankali believe that humans have an inevitable self-destructive conflict between their high intelligence and their hierarchical natures. According to the Oankali this is what caused the war that almost ended the human race and this is why they cannot leave the humans alone. Lilith and the Oankali-human hybrids are constantly battling with this inner conflict. According to TOR.com's Erika Nelson the trilogy parallels the story of African slaves in America and the conflict that latter generations of African Americans feel regarding their integration into American society. The human-oankali hybrids feel that they have somehow betrayed their human side by integrating into Oankali society, but at the same time, because of the vast power imbalance, they never really had another viable option. This theme is again acknowledged by Timothy Laurie of the University of Melbourne, who contrasts the common nurturing image of womanhood with Lilith's drive to survive at any cost, even if it mean sacrificing some of what she believes it means to be human. The series also draws upon elements of the myth of Lilith, the first wife of Adam.
In addition to the social themes, the possible results of developing genetic science and biologically based technology are shown by the Oankali's genetic mastery. Joan Slonczewski, a biologist, published a review of the series in which she discusses the biological implications of the ooloi and how they can, through genetic engineering, achieve positive effects from "bad" genes such as a predisposition for cancer.
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