We also know that they are not complete. Although they are well tested in some domains, in others uncertainties remain about their detailed application. Indeed, we expect that they will be modified or extended to explain new evidence. But they will not disappear; just as Newton's laws did not become invalid when we understood special relativity, but rather were seen to be a very accurate approximation under well-defined conditions. Theories such as those listed in the previous paragraph are strong enough that we can use them to say we know certain things - we know that protons and neutrons are composed of quarks and gluons, we know the relationship between mass and energy, we know that Earth's surface is not a single rigid structure. These are facts, but not just simple observational facts. They come from the amalgam of observation and theory development and testing that is the essence of scientific knowledge development. It diminishes the status of our understanding greatly to say that scientists "believe" these things. We know them!
When we seek to extend and revise our theoretical frameworks, we make hypotheses, build models, and construct untested, alternate, extended theories. These last must incorporate all the well-established elements of prior theories. Experiment not only tests the new hypotheses; any unexplained result both requires and constrains new speculative theory building - new hypotheses. Models, and in the modern world computer simulations too, play an important tole here. They allow us to investigate and formulate the predictions and tests of our theory in complex situations. Our hypotheses are informed guesses, incorporating much that we know. They may or may not pan out, but they are motivated by some aspects or puzzles in the existing data and theory. We actively look for contradictions.