The socially awkward genius
For someone who understands things so well and so academically, it's ironic that Stewart has not turned his intelligence to the hard task of making friends. He has accidentally neglected those skills that would make him a good friend to others, and Ashley serves as an indication of that failure, because she's not interested in him, even though Stewart is a person of great depth.
The absent-minded socialite
Just the same way, Ashley has been neglecting herself. She has failed to curate her own interests and curiosities, and the effect is that she's maybe a little bit dumb. That's not because she doesn't have what it takes to be successful; it's because she forgot to take care of herself in private, whereas Stewart forgot to provide for himself in public.
The parents in love
Step siblings know how ironic it is to see parents begin to date again after a divorce or death. To see the formation of a marital union is a weird thing for the children to experience, seeing as they are also beginning to wonder about romance themselves, and since most children don't see their parents in that stage.
The irony of the molecule
The main metaphor of the novel is that our bodies seem holistic, but actually, they're composites of many billions of molecules, all of which are in flux, and all of which continue to exist, even when we die. Therefore, when Ashley views Stewart as another being, in a way she's correct, but Stewart's case seems to be that, actually, in a much greater sense, they're the same.
The gay father figure
Ashley has a hard time forgiving her father for his leaving the family. It seems to be his sexual orientation that she has the hardest time coming to understand. As a recently outed gay man, Ashley's father is probably experiencing rejection of the same kind from many people in his life, so Ashley's relationship to her father is probably tragic and confusing. Now she has to deal with Stewart and his father, and although she wants to hate Stewart, she can't help but notice his similar emotions around the death of his mother.
