A recently published letter to the New York Times reminds us that relativity is "just a theory" and so is the Big Bang. Scientists and science educators need to set the record straight on this "just a theory" meme any time we get a chance to discuss science with kids and grown-up nonscientists. So here's my shot at it.
A good analogy is to think of facts as being like bricks: solid and dependable, but one or a few bricks are not very useful by themselves ("an electron passed through my detector at 11:58:32.01" or "the high temperature in Davis, CA on September 1, 2013 was 96 F"). Only when we assemble lots (lots) of bricks into a coherent structure do we get the benefits of having a building (the theory of relativity, or a climate model). Not only is an isolated brick rather useless, but the building can easily survive the removal of a few bricks here and there. A good theory integrates millions or billions of observations into a coherent whole. Calling relativity "just a theory" is like calling the Great Wall of China "just a fence," the Panama Canal "just a ditch," or the Golden Gate Bridge "just a road."
There's a reason that calling the Great Wall of China "just a fence" sounds more outrageous than calling relativity "just a theory"---I used the word fence which connotes something less important than a wall. There's a rich vocabulary to describe to describe barriers: from weak to strong we might use tape, rope, cordon, railing, fence, and wall. But most people don't use a similarly rich vocabulary to describe levels of sophistication of mental models. From weak to strong I might suggest educated guess, working hypothesis, model, and theory, but most people in practice indiscriminately use the word theory for any of these. So it's our duty as scientists to make clear that well-accepted scientific theories integrate an incredible range of observations into a structure which is so coherent that it is difficult to imagine all those pieces fitting into any other structure. Maybe a better analogy to calling relativity "just a theory" is calling an assembled jigsaw puzzle "just one way to fit the pieces together."
Gotcha, the just-a-theory crowd says, by making that analogy you are showing that you are rigid in your thinking and unwilling to accept alternative explanations. Nonsense. Scientists are constantly trying to prove accepted theories wrong. Anyone who succeeds in disproving relativity, the Big Bang, or evolution will win a Nobel Prize and eternal fame, so we'd be happy to do so. But we know from experience that the most likely explanation for an isolated fact that seems to contradict relativity, the Big Bang, or evolution is that the fact itself was taken out of context or is not being properly interpreted, rather than that an extremely well-tested theory is wrong.
This doesn't mean that we will twist any fact to make it fit into our well-accepted theories. It does mean that surprising facts may end up extending the theory rather than replacing it. For example, Newton's theory of gravity explains a ton of observations about the motions of the planets and stars, but in a few extreme circumstances (such as very close to the Sun) it doesn't predict exactly what is observed. Einstein developed a theory of gravity (general relativity) which does correctly predict these situations. Einstein's theory is more complicated than Newton's, but in most situations the complicated parts of Einstein's theory have very little quantitative effect so we can simplify it a great deal and in those cases it turns out to be identical to....Newton's theory! This almost had to be the case, because Newton's theory accounted so well for so many observations that it would be hard to imagine that it was wrong rather than incomplete.
This example shows that a small number of facts can be critically important and that scientists do pay attention to facts which don't fit the theory. But we don't modify or overturn theories willy-nilly. When the planet Uranus didn't move exactly as Newton's theory predicted, modifications of the theory were considered but so was the possibility that some mass other than the Sun and the known planets was pulling on Uranus, and that led to the discovery of Neptune. If we rejected well-established theories at the first hint of any discrepancy with new observations, we would be giving undue weight to the new observations and too little weight to the vast range of previous observations explained by the theory. If you want to overthrow a theory because some new observation seems to contradict it, then give us a better theory which explains the new observation while still fitting the previous observations just as well as the old theory. That latter part seems to be conveniently forgotten by people who want to reject well-established theories.
A closely parallel situation is that of criminal investigators and prosecutors who present their "theory of the crime" to a jury. ("Model of the crime" would better fit my vocabulary hierarchy, but this is the word actually used.) A lot of facts may be introduced into evidence ("a car with the suspect's license plate was recorded crossing the Tappan Zee Bridge at 2:20am on August 31"), but by themselves they don't mean anything important. A good theory of the crime provides a coherent explanation of so many different facts that the jury is forced to conclude that it is true beyond a reasonable doubt. If you want to call it "just a theory" then offer us a different theory which fits the facts just as well. The defense is given sufficient time and strong motivation to offer a good alternative theory, so failure to present one is damning.