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When Shakespeare wrote (46), “What's in a name? that which we call a rose / By any other name would smell as sweet,” he implied that phenotypes (scent in this case) take precedence over nomenclature. In popular usage, they usually do. Cartoonists classify politicians by their ears or noses. Scientists use physical characteristics to delimit everything from species (e.g., cranium size in the genus Homo) to kingdoms. Throughout much of taxonomic history, macroscopic characters have been preferred for obvious reasons.
W. J. Broughton (Fri,) studied this question.