A major theme in the Novum Organum is the flawed foundations of epistemology in Bacon’s time. He presents existing approaches to science and philosophy as riddled with problems due to their historical roots and argues that they therefore require enormous change. Book 1 is the main vehicle for this, but the theme also features in Book 2, in which it is a counterpoint to his own suggestions.

Bacon argues that there are “three sources of error and three species of false philosophy; the sophistic, empiric, and superstitious” (18). He associates sophism, as a school of teaching, with a dogmatic attitude and an approach revolving around “disputatious” verbal argument that “entraps the understanding” (19), all of which is inimical to true scientific enquiry. His primary example of sophism is the “impure and corrupted” approach of Aristotelian logic (36). Central to this is the syllogism, in which axioms, or statements asserted to be true, are used to create further axioms. Bacon traces this form of reasoning through medieval Scholasticism to his contemporaries, identifying it as a central factor in damaging the pursuit of knowledge.