Within The Apothecary’s world of magical realism, mysticism and folklore exist alongside real-world places, circumstances, and concerns. The looming nuclear threat of the Cold War with Russia grows even as Benjamin and Janie learn about the existence of the Pharmacopoeia and the apothecary’s hidden world of magical, healing remedies. In the novel, much more is possible for the characters than people in the reader’s world generally consider, and science is responsible for most of those possibilities.

Janie accepts such possibilities more readily than Benjamin does, largely because she “allow[s] for [them]” (71), as the gardener instructs. Benjamin relies on what he has learned about the natural world in school rather than the information contained in the Pharmacopoeia. Of the recipe for the avian elixir, he says, “There are physical laws—the conservation of mass, for one thing. A human being can’t just become a tiny bird-sized thing. We’d have to become something the size of us. Like a baby ostrich” (107). However, given that individuals turn into birds with similar personalities and characteristics, their transformations follow a kind of logic. When they use the invisibility serum, Janie realizes that “no one expects to see a finger or a paper clip floating down the hall, so no one does” (168). This explains why people in the novel don’t balk at seeing the disembodied pieces of children and suggests that the reader’s world might be more magical than they realize: When one doesn’t expect magic to exist, one simply doesn’t see evidence of it.

Janie and Benjamin learn that what seems like “magic” is actually just science. When Danby tells Sakharov about Burrows’s work, he says, “He’s—a kind of alchemist. Or a magician,” to which Janie responds, “No, he’s a scientist […] just like you are” (315). Her correction highlights the link between science and the things that seem improbable, like creating a net composed of reactive polymers and the Quintessence to contain and absorb the radiation from a bomb detonation. Furthermore, Burrows describes the Quintessence as the fifth element and the “source of all life. A life force to combat a killing force” (212). This explanation builds on the scientifically known four elements: water, air, fire, and earth. In addition, following Newton’s third law—which proposes an equal and opposite reaction for every action—Count Vili explains, “Whenever we tamper with natural laws, there are consequences […] The larger the disruption, the larger the consequence” (286). In short, the principles of science still apply to the events or inventions that seem magical in nature.