The title of the novel can be found on page 157 when Stewart tries to educate his would-be sister on the technicalities of molecular chemistry. He explains that while our human bodies seem to be self contained, they are in flux, and molecules are constantly shifting from being part of us, and then part of the external world again. He explains that actually, although on the surface, things look different, everyone is made of the same thing: molecules. That's a pretty good theme statement.
Since this novel is young adult fiction, it's not the mind-bending plot twists that make the story good, nor is it flowery academic prose—rather the meaning comes from the sweet, unlikely pair of new siblings. Stewart's social paranoia and grief from his mother's death makes Ashley a difficult friend. Ashley's safety and comfort in her social life make her new relationship to Stewart something of an embarrassment for her.
In the end, it requires both parties moving toward each other to really be friends. Ashley must begin to think for herself and to find her curiosity in life. Stewart must realize that he needs other people in his life. That's a pretty good reason to learn the skills it takes to become less awkward. In the end, they realize a wonderful timeless truth: they don't have to like each other at first to eventually be friends. Time brings them together without their permission, and they begin to love each other as siblings.
