This idea has been on my mind for a while (not latrines themselves, just this analogy), so I guess it's high time I got around to actually posting it. It's based on a story from WWII, which is most likely apocryphal. However, since the metaphor doesn't rely on the veracity of the story, I'll post it anyway.

The story goes that during preparations for the invasion of Tarawa, Allied commanders were having difficulty assessing the number of Japanese troops stationed on the island. The Japanese were expert at concealing their true numbers, but they had one fatal flaw: they were too meticulous about providing adequate bathroom facilities for their troops. Allied commanders learned that the Japanese would install one latrine for every X number of troops. While the troops could easily evade recon patrols, the latrines couldn't. All the Allies needed to do was count the number of latrines on the island, multiply by X and voila! They had an accurate troop estimate.

Ok, so what does that have to do with science and scientists? Well, like the Allied commanders, we often want to quantify something that we can't directly observe. We want to know what elements make up an alloy. We want to know the concentration of lead in our drinking water. Or (and this seems to happen to me a lot) we know that we haven't synthesized what we were trying to, and we need to figure out what exactly is sitting in our flask looking suspiciously like coal tar. Unfortunately (despite what your freshman chemistry textbook may have led you to believe), we can't directly observe atoms. Let me repeat that, just to make sure you got it. NOBODY HAS EVER SEEN AN ATOM.

This begs a few questions. The first, biggest question is "How do we know that atoms are there if we can't see them?" This is a fairly involved question, with an even more involved answer, and I'm going to leave that for a later guest post (or 3). So let's just assume that we know that atoms are there, it brings us to the next question: if we can't see atoms, how do we get awesome pictures like this:

This is a stereo image of the crystal structure of the protein I work with in my lab. If you cross your eyes and align the two images, you'll get a 3D view of it.

If we can't see atoms, or molecules (even most proteins, which are HUGE by chemistry standards, are invisible even under a microscope), how can we generate such pretty pictures? The answer is indirect observation. This crystal structure was generated using X-ray crystallography. Basically, we know that X-rays diffract through matter in predictable ways (i.e. we know how many soldiers per latrine). By precipitating the protein out of solution into a crystal, and the bombarding it with X-rays and observing the resulting diffraction pattern (i.e. counting the latrines), the positions of atomic nuclei can be established (i.e. we know how many soldiers there are on the island).

Ultimately, this what any physicist, chemist, and most biologists mean when the say, "It was observed that . . . " What they really mean is that they observed a phenomenon which has been related, by theory, to whatever it is that they're studying.

There is a point, however, at which this analogy breaks down; ultimately, the Allies invaded Tarawa, and saw firsthand how many soldiers were defending the island. In science, we're never so lucky. Ultimately atoms, electrons, photons, etc. are metaphorical constructions (models), and by definition we can never directly observe them. All we get are the indirect observations which indicate the nature, number, and behavior of these invisible soldiers.