Music "theory" as we find in books today contains none of the properties of a modern theory that we find satisfying ... We are sometimes told for example that the Major Scale comes from the Ancient Greeks. We are sometimes told it is arbitrary and it only sounds good because we have heard it since childhood.
There are some very interesting portions of that paper, but I really wish the author would focus on the science and omit the jabs at what he considers "music theory".
He's correct that music education doesn't typically start with Pythagoras, but should it? It would be almost impossible from this paper to aurally appreciate his points about intervals, tonal variety and intonation schemes without having a fairly broad knowledge of harmony already.
It's certainly interesting, but it does not provide a framework that can reliably reproduce the characteristics of music he describes, which is the bulk of theory and harmonic analysis.
EDIT: I don't think it needs to be portrayed as competing with existing theory -- it's something that has been extensively studied and dovetails well with the history of scales and harmony.
I've noticed that intervals whose beat frequency is a subharmonic of one of the notes in the interval, or a subharmonic of a small integer multiple of one of the notes, are particularly consonant. Is there any discussion of beat frequencies in that paper?
It might make you feel better to split the octave into two parts and eliminate the interval in the middle, i.e.
Do-re-mi-fa, pause, So-la-ti-do.
Each of those four note sections has the same intervals.
So arguably it's closer to being a "pi vs. 2pi" problem. (I am not really serious)
Isn't fa a half step down from being exactly between do and do'?
As far as the fencepost error, it helps to remember that musical intervals are multiplicative, rather than additive. An octave above do is f_Hz(do) • 2. Half an octave (fa#) would be f•sqrt(2). Generalized to a twelve tone scale, each half step is f_0•2^(1/12), dividing the octave into twelve equal multiplicative intervals.
I'm not saying fa is half way, I'm saying you can take the scale in two sections which are just transposed versions of the same intervals. This is not helpful, but it is true.
Pretty sure you can't get out of the fact that do appears twice by invoking multiplicative rather than additive logic:
two octaves played together contains 3 dos, 3 octaves contains 4, etc.
To be fair, it's not just the octave. The interval between a C and a C is a unison. The interval between a C and a D is a second. Two octaves are a fifteenth (not a sixteenth). The entire thing is one-indexed.
It's perhaps better to think of it as the number of notes you have to count before you reach the second note, starting with the first. If you start with C, you have to count one note before you get to that same C. You have to count 8 before you get to the second C, and 15 before you get to the third.
A related problem in music is how rhythm is counted, e.g. in recording software. Each new bar in 4/4 starts on beat 1, 5, 9, 13, rather than 0, 4, 8, 12, which makes it surprisingly difficult to figure out where you are.
http://arxiv.org/html/1202.4212v1/