I argue that the concept of scientific explanation constitutes one of McCarthy’s central concerns in the Border Trilogy and that classical thought can be utilized to show that his position is remarkably similar to the Pre-Socratic philosopher, Heraclitus. I show that both McCarthy and Heraclitus share a desire to reject the ontological reductionism of naturalism, yet at the same time avoid the ontological dualism of thinkers such as Plato, Aristotle, and Descartes. The case for McCarthy’s Heracliteanism is made by analyzing his 2017 piece on the origin of language, “The Kekule Problem: Where Did Language Come From?” I conclude that the position put forth in the first non-fiction piece of McCarthy’s career offers a framework for interpreting the central concerns of the Border Trilogy that is decidedly Heraclitean.