I ask that you please read the comments before you make your own comments, just as you asked people to read the paper before commenting (I did!)
> Your assertion that it is all culturally relative ("nurture") and none from the structure of the most efficient algorithm for recognizing the harmonic series ("nature") has no basis in fact
I never said that. I said "Though it's built on harmonics and overtones which can be explained objectively, you cannot make a fully scientific theory of harmony since cultural expectations factor in just as much (and maybe even more) than the expectations around harmonics." To put it in your terms, "you cannot make a fully scientific theory since nurture factors in just as much (and maybe even more) than nature". The world is not black and white, just because I believe sociology to be critical to understanding the emotional effect of music on people, does not mean I'm claiming there is no objective, measurable component.
> If so, then an octave is too simple to fire the recognizer"
Ok so the happiest music is perfect fifths? Or is 3/2 ratio also too simple? So when does this recognizer get complicated enough to fire? 5/4? For someone claiming to have a scientific theory, you are making a lot of assumptions to make this theory work. Scientific theory is about testing hypothesis to reveal truth and not making hypothesis up to match what you already believe. You make an assumption that the brain wraps/aliases frequencies, create a theory of the recognizer, and then make that recognizer have a very convenient threshold that it makes a physical process suddenly the reasoning for "happy". To the "fully scientfic theory" above, I absolutely agree that ratios play a part, simple ratios are boring, and get more interesting as they get complex, then get too complex and it sounds dissonant. That part I think we, and most people, can agree is objectively true, and fits in the theory of expectation vs surprise at a microscale. I just don't agree this translates to "happy" or "sad". Please show me an experiment that indicates the kind of recognizer that you're talking about, or some kind of cross cultural link between ratios and emotional quality. I'd actually be very curious about that, as it's been a while since I've been reading papers about this.
> The music was played into the brain with the root removed; when coming out of the brain of the owl, brain had restored the root
Yes, I'm sure you know this, I'm just showing I know this too - this is called psychoacoustic bass, and happens as part of the feedback loop between the brain processing and the actual ear - the ear actually generates the root tone! This could also be a product of pattern matching though, as we're used to hearing related harmonics (say 200, 300hz) with a root (100hz), so if we just get the harmonics without a root (200, 300hz) the psychoacoustic part of your brain helps out by filling in the 100hz - this is an alternate theory to the aliasing/halving/doubling theory you put out, not saying either one is absolutely true, just that there are other explanations for the owl thing.
It also has nothing to do with the emotional effect of the music.
> So at Berklee they teach recognizer algorithms and artifacts thereof?
Again, I did not say that. I'm not talking about the speculative, non-experimentally backed parts of your theory, just the parts of your essay that are part of the common scientific consensus. I said "ratios and how chords derive from that was absolutely part of my education at Berklee". Nothing more.