Short answers, pulled from the story.
Ernst Krenek published a classification system in his book Studies in Counterpoint that ranked chords from 1 to 6 based on their internal consonance. A C major triad received the lowest rank of 1 because it contained three consonant intervals while a chord containing C, D, and B received a higher rank of 6 due to its inclusion of sharp dissonances like the minor second between C and D.
Dissonance sensation arises from the brain's response to unusual or rare sound perceptions entering the ears. An EEG pattern known as P300/P3b emerges when listening to such oddball events causing slight stress in the listener which explains why certain intervals feel more consonant while others feel dissonant regardless of cultural training.
Ancient Greek theorists used the term symphonos to describe intervals like the fourth, fifth, octave and their doublings. Aristoxenus applied this terminology to Pythagorean tuning where ratios of 4:3, 3:2 and 2:1 were directly tunable.
Johann Sebastian Bach inserted an unexpected B natural over the final chord of his St Matthew Passion before melting into a C minor cadence. Ludwig van Beethoven opened Symphony No. 9 finale with a startling discord inserting B flat into D minor chords.
Dan Haerle released The Jazz Language in 1980 extending harmonic consonance ideas to alter Paul Hindemith's Series 2 gradation table. He placed the minor ninth as most dissonant interval more dissonant than previously considered octave equivalent minor seconds while promoting tritone from most dissonant position to one slightly less consonant than perfect fourths and fifths.