The brain is a layered fossil record of its own evolution
Sagan builds much of his argument around the triune brain model, which describes the human brain as three distinct evolutionary layers stacked on top of one another rather than a single unified organ. The deepest layer, inherited largely from reptilian ancestors, governs basic survival instincts like territoriality, ritual, and aggression. Wrapped around it, the limbic system, shared with other mammals, adds emotion and social bonding. The outermost neocortex, most developed in humans, handles abstract reasoning, language, and planning.
Sagan uses this model to explain why humans can be simultaneously capable of extraordinary rational achievement and startlingly primitive, ritualistic, or aggressive behavior — both capacities are literally built into different, older and newer parts of the same skull, and neither has been erased by the arrival of the other.
While later neuroscience has complicated the triune model's simplicity, Sagan's core insight — that evolutionary history leaves physical structure behind rather than replacing it — remains a durable way to think about the coexistence of instinct and reason in human behavior.
Takeaway: your impulsive reactions may be running on older hardware than your careful thoughts.