Taxonomists generally classify organisms on the basis of overall similarity. For example, the pygmy chimp and the common chimp are classified in the same genus because they look so similar overall. Taxonomists did this for many species, long before they knew what is a protein or how it can be used to classify organisms. Linnaeus, for example, classified a bunch of organisms without knowing what proteins are. Prior to the 20th century, most organisms are classified on the basis of morphology. However, good taxonomists have always taken good care to figure out whether the similarities shared by a group of organisms is due to convergent evolution or whether they are inherited from a common ancestor. They mostly do this by comparing the similarities in minute detail. Using this technique, we can tell, for example, that bat wings and pterosaur wings are only convergently similar, since bat wings are contructed with all 5 fingers of the hand, whereas the pterosaur wing was constructed from a single, grossly elongated finger.
