Bill mentioned Richard Owen, the first director of the Natural History
Museum (formerly, British Museum of Natural History) and the fact that
he coined the word "homologue".
His definition was that it was "the same organ under every variety of
form and function". This will extend to molecular sequences very nicely
- two amino acid positions are homologues if they are the 'same organ',
not an analagous organ. Two proteins are the 'same organ' if they are
derived from a common ancestor.
I don't believe the original definition would have allowed for the lower
jaw and the kidneys to be considered homologous, even though it can be
argued that they must have sometime derived from common stock. In the
same way only those protein sequences that really are the 'same organ'
could be considered homologous.