Over at A Monk's Musical Musings, Hucbald has been showing the physical generation of various chords in tonal progressions. I found myself writing a very long comment in one of his posts, and decided to subject all of my readers to a comprehensive look at this question. Theorists through the centuries have attempted to prove that tonality is the ultimate language of music because tonality is based upon natural principles of physics and psychology. The psychology side is rather messy, so I will wait to address that one.
The physical side comes from claims that tonality is based upon the harmonic series. Since the first sixteen harmonics can make the major scale (we'll ignore harmonics 7 and 14 right now) from the tonic/fundamental, this must mean that the major scale has special significance, something that resonates right from the very nature of the notes played by acoustical instruments.
Notice that this means of generation says nothing about the minor scale (any of the three). For Helmholtz, this means that minor keys are inferior to major keys, as they are distortions from the pure generation. Rameau tried to generate the minor scale from two different fundamentals, called the "co-generation" theory. This still makes the minor scale a second class citizen to the major scale, since it requires help from a second note to generate all of its notes. Riemann believed in "undertones", patterns of frequencies that follow the same pattern as the harmonic series except going down from the fundamental instead of up. (Hucbald mentions one of his teachers, so I'm pulling out Harrison, one of my History-of-Theory teachers.) With this new series, the minor scale can be generated. However, undertones have no physical basis, despite Riemann's claims of having heard them.
The problem is that in practice, minor keys are not treated as inferior to major keys by tonal composers, and indeed are not preferenced in perception/cognition studies either. All attempts to physically generate the scale are unsatisfactory at best, and plain wacko at worst. So, when practice conflicts with theory, the theory must be questioned. (Right, PZ?) I say that we should embrace the fact that such a complex and vigorous language is the result of artifice rather than from the happenstances of physics. Long live art!