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Harmonic Evolution is the missing link in Darwin’s Origin of the Species. Recent studies on the mesoscopic structures of water and carbon, together with the latest geometric DNA mapping theories, suggest that life emerges and grows according to predictable harmonic patterns found in organic chemistry, preserving and propagating specific atomic geometries into living organisms. Based on this and the latest neurophysiological research, a harmonic Gaussian interference model for cellular entrainment is presented to explain the origin of common organic geometries, including cardioid, ellipsoid and spiral primitives, as well as 3-fold exo- and 5-fold endo-skeleton structures. From this, a recursive harmonic Hilbert space is defined for use in evolutionary classification, physiological analysis and organic simulations. Examples are provided, including a step-wise analysis of the human body. Avenues for additional research are discussed, including application of harmonic Gaussian interference models to cosmology, cognition, medicine, social theory and philosophy.