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Zkuq said:
Scientifically, we know a lot with a reasonably small degree of uncertainty. With absolute certainty... Well, that's more of a philosophical question than a scientific one, and I don't really care much about philosophy because in the end, I don't find it really gives very useful answers.

Very good point made. I remember a quote from a philosopher Auguste Comte in a book for my Spectroscopy course: "We will never know how to study by means the chemical composition of stars, or their mineralogical structure."

That is one sad conclusion to reach. I'd much rather actually base my work on empirical analysis than sit there twiddling my thumbs assuming we will never know anything. Also scientifically we can not get rid of uncertainty just because of how nature seems to be at a quantum mechanical level. If this is what you meant, then I agree with you OP that we will never know anything with 100% certainty, but we don't necessarily need to. Also, theories can be proven wrong given new measurements/observations, but that is a prospect scientists welcome rather than detest, because it opens up new areas to explore. The best we can do is to keep testing our established theories against newer observations and see if they hold. If not, try and find a new ones that do. This prospect by no means is bad as I mentioned before, in fact this is what makes science exciting: always having the possibility of finding something new. But for the time being, we just have to go with what we have.

I think most scientists use very a high degree of caution when stating "facts" and "theories", or so is the case that I've found inside the scientific circle (from professors/lecturers, etc). A lot of times it tends to be the media who put things in a way that which it was not intended, and I think that is what the problem of the OP is. As for things like "We've never stuck a thermometer inside the sun to know its temperature", the thermometer would melt if you tried. The way to measure the core temperature of the star is to measure the photon flux/radiance it is emitting and use that in conjunction with the blackbody function or something of the kind. I'd suggest you study how exactly the core temperature of the sun is measured or the composition of the earth is known. I think that may clear up some of your questions. You don't necessarily have to see something directly to know about it; you can also know about it from observing its effects.

And I will say once again: There is nothing wrong with not knowing something, as long as we keep trying to know.