The Justifiability of War
This novel takes place in February of 2003, when protests were occurring against the upcoming British invasion of Iraq. The large-scale demonstration happening on this particular Saturday is the focus of much of Henry's thoughts and dialogue. Henry himself is a rational debater, intending to reach truth rather than win an argument, but his pro-invasion stance (self-described as an "anti-Saddam" stance) is a source of harsh contention with his daughter, Daisy, who is adamantly opposed to the war. Debates about the ethical justifiability of this war permeate the plot - the protest is the indirect cause of Henry's unpleasant encounter with Baxter.
Family
Henry's family is far from perfect, and strife arises between them rather quickly in many circumstances, especially when John Grammaticus ("Grandfather") is involved. Henry and Daisy have differing political views, Daisy and Grammaticus reach hostile standoffs concerning poetry, and Henry and Grammaticus just don't get along. Despite all these differences, however, the family comes together at the end in the face of calamity (Baxter's threats). When disaster strikes, the surface-level disputes of the family are shattered to reveal the strong bonds underneath, indicating the importance of family in the life of the individual.
Science and Literature
Perowne is a scientist, and most of his adult life was spent in the study of scientific texts. Accordingly, he is not too well-versed in literature. Daisy, his daughter, is a poet and an avid reader, and she is trying to educate her father in literature by giving him reading assignments. Henry admits that he doesn't really understand the appeal of poetry when solid science is an available field of study, but he attempts to understand all the same. Daisy, realizing her father's predisposition towards science, assigns him a biography of Charles Darwin. This conflict between science and literature is resolved at the end of the novel, when Daisy's poetry recital makes Perowne realize and appreciate the power of literature.