The polygraph is based on the assumption that you can detect if people lie or not based on their physical reactions: Sweating, heartbeat, etc. We know that lying isn't the only reason why people would feel this way, especially during a polygraph test.
Which, of course, completely blows the claim out of the water.
That is a very, very serious misunderstanding of how science works, at the most basic level.
The fact that the same effect can occur for reasons other than the one we're interested in would 'blow the claim out of the water' only if the claim was for a perfect technology that worked with 100% accuracy every time. (Of course, that could not be a scientific claim.)
Have you any idea how commonly we use tests that are known to be far from perfect, in many everyday areas – medicine, for example? In all scientific fields (though, no doubt, to a lesser extent in particle physics than in medicine) we expect that, no matter how sound the underlying theory, the accuracy of our tests will be degraded by confounding factors.
Actually, in the case of polygraphy, the original rationale
requires that deceptive and fearful responses give essentially the same results (and therefore can be distinguished only imperfectly, and only by expert questioners). This is mistaken - although it is not my area, I am somewhat persuaded by the NA report and digithead's posts on the issue of GKT vs CQT that polygraphy is likely to work better with questioning strategies that target cognition rather than emotion.
I wonder whether you realise how harmful your bulldog, non-scientific 'skeptic' approach is to the causes you're trying to promote? A casual reader of this thread might notice how much better informed the scientist posters are than you on this subject, and that we are concentrating on the point that polygraphy is a valid concept with some support from laboratory studies (because you've forced us to do so if we don't want your multitude of incorrect statements to go unchallenged). And might well conclude that real-world use of the polygraph is therefore justified.
As I have said, I agree with you that there is no case for
any use of routine polygraphy. In real-world applications it cannot be shown to be either safe or effective, because the test's discrimination (though well above chance levels) is far too low to allow confidence for practical purposes. It has become established because of uncritical acceptance of outrageous claims of efficacy. But we have to counter this with evidence and scientific analysis, not with political-style campaigns to label it 'pseudoscience'.