"Do the people who are praising "just intonation" really know what it is? It isn't used in any folk tradition I can think of. "

I wasn't 'praising' it! The problem with people flinging around terms willy nilly, is what those who HAVE passed formalised study regimes tell me, is that if you get the terms confused, you won't pass the exams, but you can still keep running around rabbiting on in a misleading way, sounding like you KNOW what you are talking about - I point to Iraq for a current non-musical example!!!

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"isn't used in any"

Well, it WAS in history, depending on the historical period! That is IMPOSSIBLE nowadays in the modern world if you have instruments (such as the once extremely widespread piano accordion!) which are specifically tuned to BE NOT "JUST", and are manufactured with the intent to be 'played in tune' with all the others designed to be played in 'even 1/12 intonation'! - which I thought I had well and truly 'Shambled to Death!' (sorry!). I thought I had made it quite clear that 'Humpty-Dumpty-ing' Terms out of history to mean anything the user currently wants is not clarifying at all, merely obfuscation!.

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Words DO change meanings over time, and their fields of use are dying out, or being newly created: viz, Engine, Engineer... but those other than the uneducated ignorant layman know quite clearly which field they work in, and exactly what the words mean for their purposes. No educated Inter-disciplinarian thoughtlessly drags the meaning from one field into another!

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"Experiments have shown that when people with flexible-pitch instruments like fiddles are left to their own instincts, they tend to use Pythagorean intonation (pure fourths and fifths), which is quite different."

I do not have the expertise and related precise experience to argue with this! I must be confused, but I had gathered in my considerable educational travels (including formalised study programs) that "Pythagorean intonation (pure fourths and fifths)" WAS the original Western Music temperament, WAS the one used in 'Church Modes', and WAS the one called 'Just'!!!

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"Not all alternatives to equal temperament are the same"

Well, what most modern instruments (intended to be tuned with electronic tuners, anyway!) are BUILT to, and designed to be played with most other instruments built today, IS the temperament that involves equally dispersing the 'comma' of a few Hz equally among the octave - or precisely, defining all the semitones as 100 cents each. To say 'Not all alternatives to equal temperament are the same', is of course just an unhelpful tautology!

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To say "Dorian or mixolydian/major/lydian pentatonic is recognizable whichever of these intonation systems" seems to me be be starting to border on a matter of 'Faith', almost a Religion! It really would be more fair and reasonable to say that 'gapped scales with these defined patterns of Tone/Semitone(@@@) distribution sound similar in all intonation systems to untrained ears': saying anything else allegedly precise is 'fighting a semantic propaganda war'!

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Of course these words are defined differently in terms of the 'frequency range gaps' in each system, so you are just comparing apples and oranges anyway! And because of the differing temperings, BY DEFINITION, the actual pitches of 'notes with the same name' differ in frequency! And to CONFUSE things even more, practical instruments TUNED WITH EQUAL TEMPERAMENT, do not have all the note pitches tuned to these precise figures anyway - they are 'spread' for very good reasons, i.e. on many keyboard instruments the 'bass end' is flattened, and the 'treble end' raised to avoid nasty sounds!

I do not consider that I have sufficient knowledge to tune my own piano accordions. Tuning real instruments in the real world is ALL COMPROMISE! If you let some uneducated lout with an 'electronic tuner' loose on a valuable instrument, they will often stuff it up big time! I had some 'alleged international Hurdy Gurdy expert' hack into my Symphonia (without my knowledge or consent, I point out!) with a razor blade to 'fix' a subtle flattening (of about 2 mm) in one small spot on the wheel! His 'efforts' required that the original maker turn up a whole new wheel on the lathe! (And this clown was MOST offended when I told him to initiate a sexually self-oriented method of locomotion!)
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"There is some study of psychoacoustics, and how some frequencies do interact differently with the human nervous system than others"

And there is similar work on 'colours' - we have had some such threads here too - and the outcome seems to be that each individual reacts personally, not to and simple universal 'Rules'.