We have established (ok, stipulated more than formally proved, for the moment) that we can use a number line as a similarity metric. Now let's pin down what we are measuring--in other words, what we mean by similarity.
I've seen this diagram in tons of comparative anatomy books, so I'm not bothering to attribute it--I think it's pretty standard as common knowledge in the field, and it was intuitive enough to come up with from memory rather than looking it up.
It illustrates the three kinds of similarity that comparative anatomists have traditionally considered: homology, or similarity of evolutionary origin; homoplasy, or similarity of appearance; and analogy, or similarity of function.
(Actually, it's even more complicated than that--remember the pesky homonymy problem I referred to in my earlier post? Well, when it comes to "homology", there are differences even among biologists in what they mean by it. Molecular biologists talk about genetic homology in quantitative terms, and I really don't want to get into that right now. We use the term homology in the traditional way that morphologists have used it to indicate evolutionary relationships between gross structures, where they are either homologous or not, but in no case, for example, "80% homologous".)
Naturally, these similarities are not mutually exclusive, so any two structures being compared across species may have 0, 1, 2, or 3 of these similarities.
0: the mammalian nipple and the fish gill do not look alike, function alike, or have the same evolutionary origin.
1: the three tiny bones in our ear have a common origin with certain bones in the jaws of snakes, although they no longer either look like them or function like them.
2: the "torpedo" body shape shared (more or less) by the tuna, the dolphin, and the ichthyosaur look alike (roughly a cylinder tapered at each end), and function alike, aiding swimming by reducing hydrodynamic resistance, but each of them got their similar body shapes in a different way (convergent evolution, rather than shared evolutionary origin).
3: Human, dog, and mouse hearts: except for scale (remember, we are not being quantitative), one mammalian heart is pretty much like another in origin, function, and appearance.
Ongoing research is being done in description of anatomical appearance and function, but for now, we are concentrating on structural descriptions alone. For this reason, we examine similarity of homologous structures only, and describe their similarity or difference in terms of their distance on the number line. The next post will discuss how we do so.