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From: ronald@uhunix1.uhcc.Hawaii.Edu (Ronald A. Amundson)
Newsgroups: bionet.molbio.evolution
Subject: Re: Homology/similarity/identity: proper usage.
Message-ID: <11223@uhccux.uhcc.Hawaii.Edu>
Date: 31 Jan 91 19:16:35 GMT
References: <3824@gazette.bcm.tmc.edu>
Sender: news@uhccux.uhcc.Hawaii.Edu
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In article <3824@gazette.bcm.tmc.edu> steffen@mbir.bcm.tmc.edu (David Steffen) writes:
>
>  I am again struggling with the proper use of the words "homology",
>"similarity", and "identity" in comparing sequences.  ...

I agree with some some of the followup already given, and I'm not a
great expert on molecular genetics.  But there is an interesting
problem here.  The term "homology" clearly is being used differently
in molecular genetics from its usage in traditional evolutionary
biology.  Steve Gould comments on the issue in his Natural History
column for Feb. 1988, BTW, wishing that the molecular biologists would
talk more like macro-biologists.  

The problem with calling identical molecular sequences "homologies" is
not _just_ that it implies a common source for the two sequences.  One
of the commentators is correct that _any_ evolutionary use of
"homology" infers a common source on less-than-certain evidence.  The
problem is that the criteria by which the common source is identified
is different in the molecular and "macroscopic" inferences of
homology.  I can think of two differences -- forgive my ignorance if
I've got facts wrong.

1)  Good macroscopic evolutionary inferences of homology are based on
"shared derived" characteristics.  The nests of other sets of traits
disallow certain similarities to count as homologies.  Mere similarity
alone can never be used to judge two traits as homologous.  (Unless
I'm wrong) the "mere similarity" (i.e. molecular identity or
similarity, in the absence of evidence provided by other hierarchies
of traits) of molecular sequences is used as a sufficient criterion
for the term "homology" in molecular genetics.

2) It seems to me (insert disclaimer again) that when molecular
biologists call sequences homologous, they mean that the two were
copied from a similar ancestral _molecular sequence_.  But the
processes of copying molecular sequences are not identical to the
processes of reproducing organisms.  As I understand it, sequences can
be copied within a genome, and with manipulation (and maybe some kinds
of viral infection and other exotic stuff) between genomes.  So the
geneological tree connecting up similar sequences with their molecular
ancestors will not be isomorphic with the geneological tree connecting
organisms with their ancestors.  

So it looks as if the molecular use of "homology" is a _different_ use
from the normal evolutionary use of the same term.  Whether that is a
tragedy or not depends on how confused we get by it.  But I think it
is worth noting that different concepts are being used.  There are
_lots_ of cases in the history of biology where different uses of the
same word led to long futile disputes (e.g. the term "mutation" at the
beginning of the century).

Ron Amundson
Dept. of Philosophy
University of Hawaii at Hilo
Hilo, HI  96720-4091
ronald@uhunix.bitnet