Not necessarily. In some cases it's a more efficient use of time to place the burden of proof on the person challenging a widely held assumption. Especially if you're a physicist who regularly receives letters from cranks with no background experience claiming to have overthrown physics. If you analyzed all of them in detail you'd never have time to do any real work.
Should people challenge assumptions? Sure. Are you required to challenge every assumption at every conceivable opportunity? No, that's OCD behaviour.
Does my attitude stifle progress? I don't think so - if someone has a way around the second law they should be able to build a machine utilizing it, and empirical data beats thought experiments every time.
Incidentally, the second law as commonly phrased "entropy always increases" is only an approximation. Entropy can decrease at times with small probabilities as outlined by the Fluctuation Theorem.
Sorry that I was unclear. The parent post seemed to be implying that anyone that comes up with a perpetual motion thought experiment should just have the phrase "can't exist it would violate thermodynamics" tossed at it. I'm not advocating working out every thought experiment that anyone could come up with, but to workout none of them is just putting blind faith in the law of thermodynamics. And so far as I understand it, blind-faith is not supposed to be part of the scientific process.
> thought experiments can't disprove reality
Reality is what it is. If thermodynamics is wrong, it doesn't change reality. It just changes our understanding of reality. Don't be so melodramatic. Once a law/theory is dis-proven there isn't some deja-vu-the-matrix-is-changing-something moment.
At the very least, figuring out where the energy loss is in the system will teach others something, and possibly yourself as well. Thought experiments are where theories come from. Unless you think that theories spring into existence without thought.
{edit} Please don't say, "but I already know about thermodynamics, so there is nothing more for me to learn!" because you would be entirely missing the point.
-- Sir Arthur Stanley Eddington
I suspect most physicists would sooner question their own sanity than question the Second Law, and with good reason.
likewise if we discover a physical phenomenon that violates our current understanding of thermodynamics we don't throw that understanding out. anything that succeeds it needs to explain all the data that it explained + the new stuff.
The point is that saying "Can't work because of X" is a cop-out to actually going through and proving where the loss of energy is. Thermodynamics just predicts that somewhere energy is lost from this system. Blindly saying "thermodynamics" and not critically thinking about how/where/why it applies is intellectually deficient. If people don't challenge assumptions, then progress is never made. Some day someone might be able to disprove thermodynamics in some really funky edge-case, but that knowledge will never be discovered if no one ever questions.