Just recently, I looked at an abstract of a phonetics paper and saw this:

Many theories of speech production see phonetic implementation of underlying phonological structures as an automatic process governed by universal and sometimes language-specific constraints. Such assumption for example underlies the phonological account of…

I used to  grudgingly sign my name to such sentences back when I was a linguist.  But now I make my money in other ways and I have no reason to pay attention to the Linguistic community.   So, let’s take a look at the text and see what’s right and what’s nonsense.

“Many theories of speech production … phonetic implementation of … phonological…”   The trouble is that “many” is the wrong word because there are no Linguistic theories of speech production.  Linguists, when being careful, tend to call their things “paradigms” or similar terms, in recognition of the fact that they don’t normally predict what is going to happen.  [Often, they are intended as a way of looking at the data or organizing it.]

• In this context, a theory is something that predicts your phonetic implementation (i.e. how you say something, in terms of sounds or tongue positions) from some sort of phonology.   When one says the word “theory” in science, one means some sort of prediction that is clear enough that one could prove it to be false.    [This is standard Karl Popper stuff.  You make up a theory and then you test it by comparing it’s prediction to reality.  If it disagrees with a good experiment, the theory is wrong, and you change it or throw it away.  If it agrees with the experiment, it lives to be tested another day.   If it passes many tests, wow, maybe it’s actually correct!]  Now, the problem is that there are no linguistic theories in this area, because no one has written anything that makes clear predictions that one can test.  If you don’t believe me, take a look at the Google Scholar search for “phonetic implementation phonological theory predict” and try to find a paper that makes a detailed prediction of which speech sounds are produced when, or any kind of detail about where the tongue goes.  You won’t.
• You may find a few weak predictions along the lines of “the tongue will be raised…” but those don’t count for much because they have a 50% chance of being right by blind chance.  Another reason they are weak is because the “prediction” is usually derived just by trying to say something and feeling where the tongue goes; in science, that’s normally called “reporting the result of an experiment” rather than “predicting from a theory”.
• To an extent, such theories exist in the form of speech synthesis and/or speech recognition systems.  While linguists don’t treat those systems as theories, nevertheless they make detailed predictions of how a given text should sound, even if it is a text that no one has ever said before.  However, while these systems are much more predictive than a typical linguistic paper, they are still not entirely satisfactory because they are all based on recorded speech.   That means, they are not predicting as much as one might hope: their output is just a reproduction of what some human said, but sliced up and glued back together.  Their strongest claims to theory-hood are the places where they cut, and the details of what speech segments they glue back together.   They say that “if we cut speech here and here, then we can glue those bits and we’ll get a whole new word.”

“…underlying phonological structure…”    The word “underlying” is beautiful, because it subtly claims that phonology is the reality, and the tongue motions and sounds we hear are mere secondary phenomena.  But, that word has no right to be used: phonology could just as well be a convenient way of dividing up the sounds that we make, rather than something deeper and more important.   It might be just an artificial way of chopping the world up into convenient boxes.

• Is phonology underlying?  I.e. is it something that is more real and more stable than speech sounds?  That’s what “underlies” means in this context: for example electrons underlie the phenomena of electricity.  That means that electrons (and a few equations) are able to explain anything you might want to know about electricity.
• If phonology were really “underlying” in that sense, the evidence for it [hopefully experiments!] would be triumphantly taught in undergraduate courses.  These would be basic experiments that would support the entire field of Linguistics.  But, the evidence that phonology underlies behaviour isn’t taught, because (to the extent it exists at all) it is ambiguous.
• If phonology were really proven to be “underlying”, people who wrote the phrase in their academic papers would reference it.  [Unless it were so well and broadly known (like Newtonian Mechanics) that it was taught in undergraduate courses.]    Let’s search for it.   As of today, I get the following hits:
  * I. Y. Liberman, doi: 10.1177/074193258500600604 .  No reference.
  * I. Y. Liberman, book.  No reference
  * Bert Vaux, doi:10.1162/002438998553833.  No reference.
  * A. Lahiri, http://dx.doi.org/10.1016/0010-0277(91)90008-R.  No reference.
  * et cetera, through 50 references at least.
  Everyone writes as if their reader knows what “underlying phonological structure” is, but no one points to evidence.  Of course, they’ve all read each other’s papers, and they’ve gotten used to reading that phrase.
• In the real world, phonology is always derived by observing speech.  One cannot know what words someone is saying unless one listens to the speech and then deduces what the phonology ought to have been.    This procedure is a better match to “phonology is a convenient way of categorizing speech” than to “phonology underlies and explains speech”.
• Given the lack of proof that phonology underlies anything, it might be inappropriate to use this phrase.

Then after that rough start, the abstract improves.    The author is careful to say “theories see” instead of “theories show” and then later “Such assumption…”   The author does indeed know that this stuff is just assumed, rather than known.  Because so many of the basic assumptions of linguistics are not solidly established, it’s very hard to write carefully and still make an abstract sound impressively linguistic.