The Pythagoreans linked musical intervals with integer ratios, cosmic order, and the human soul. The empirical approach of Aristoxenus, based on real musicians making real music, was neglected. Today, many music scholars and researchers still conceptualize intervals as ratios. We argue that this idea is fundamentally incorrect and present convergent evidence against it. There is no internally consistent “Just” scale: a 6th scale degree that is 5:3 above the 1st is not a perfect 5th (3:2) above the 2nd (9:8). Pythagorean tuning solves this problem, but creates another: ratios of psychologically implausible large numbers. Performers do not switch between two ratios of one interval (e.g., 5:4 and 81:64 for the major third), modern studies of performance intonation show no consistent preferences for specific ratios, and no known brain mechanism is sensitive to ratios in musical contexts. Moreover, physical frequency and perceived pitch are not the same. Rameau and Helmholtz derived musical intervals from the harmonic series, which is audible in everyday sounds including voiced speech; but those intervals, like musical intervals, are perceived categorically. Musical intervals and scales, although they depend in part on acoustic factors, are primarily psychocultural entities—not mathematical or physical. Intervals are historically and culturally variable distances that are learned from oral traditions. There is no perfect tuning for any interval; even octaves are stretched relative to 2:1. Twelve-tone equal temperament is not intrinsically better or worse than Just or Pythagorean. Ratio theory is an important chapter in the history Western musical thought, but it is inconsistent with a modern evidence-based understanding of musical structure, perception and cognition.