"So the real question is whether the 12th fret
harmonic is part of the intonation process."

Whoah, wait a minute. If anyone actually questions
this, they need to learn about very basic setup
and intonation. Assuming the frets are as
accurately laid out as possible, and the neck is
not warped, the strings are not worn out or
otherwise distorted, and, in short, the instrument
is of a quality and in a condition that it
can be intonated, matching the 12th fret to
the 12th fret harmonic is the only way to
do it. Make no mistake, there is no other
way.

I know people were getting into the esoteric "what
if" realm here, but I do not want anyone to think
that if they take their instrument to a local
luthier, and discover that to intonate it he is
"merely" going to set the 12th fret to the 12th
fret harmonic, there is anything wrong or even
questionable about this. This is the way it is
done, period.

And, whatever you do, don't take your instrument
home, check each note up and down the fretboard
with a tuner, and then go back and complain that
they are not all in tune. They won't be. They
can't be. It's just the nature of the instrument.

Kelly

Thanks for chiming in Kelly. All I've been saying throughout this thread is that there are a number of conditions that would make the 12th fret harmonic sharp or flat even though the string is otherwise properly intonated.

A mass defect in the string is probably the most common condition but, as you mentioned, a defective nut or bridge saddle could also cause this, among other things.

Assuming there are no defects affecting the harmonic then you can absolutely intonate by setting the 12th fret to the 12th fret harmonic.

I respecfully suggest, though, that after setting the intonation that way you should then check the open string because if there is some defect in the string, or elsewhere, the open string will not be in tune.

At that point the prudent bassist will look for an underlying cause.

Most of the disagreement here is, I think, due to the difficulties of communicating via a written forum. It's sometimes unclear what we are really saying.

i say you should wait until a drummer tells you your out of tune or your intonation is off....by then i am SURE somethign is out of whack on your bass