I think we are getting a bit too philosophical on a matter which is
mainly terminology .....
1. To quantify how similar two proteins are, one should best refer to
'percent identity'. Thats clear, correct and unambiguous.
2. One can also refer to "similarity". In that case it should be
clarified what is considered to be similar, mainly which comparison
matrix was used to quantify the similarity.
3. Homology means common evolutionary origin. One understanding is
that homology refers to the genome of 'LUCA', the hypothetical last
universal common ancestor. I am not an evolutionary biologist, but I
would clearly disagree that homology is a leftover pre-Darwinian term.
The very notion of homology is only meaningful in the context of
evolution.
Thus, to me:
1. "These proteins are 56% identical" is clear.
2. "These proteins are 62% similar" is unclear.
3. "These proteins are 62% similar using the Dayhoff-50 matrix" is Ok.
4. "These proteins are homologous" is clear, but can be subjective as
to what homology is.
5. "These proteins are 32% homologous" is simply wrong.
Sorry for the non-crystallographic late evening blabber.
A.
On 6 Dec 2008, at 21:09, Dima Klenchin wrote:
>> Having a generic dictionary definition is nice and dandy. However,
>> in the present context, the term 'homology' has a much more
>> specific meaning: it pertains to the having (or not) of a common
>> ancestor. Thus, it is a binary concept. (*)
>
> But how do we establish phylogeny? - Based on simple similarity!
> (Structural/morphological in early days and largely on sequence
> identity today). It's clearly a circular logic: "Lets not use
> generic definition; instead, lets use a specialized definition; and
> lets not notice that the specialized definition wholly depends on a
> system that is built using the generic definition to begin with".
>
> Plus, presumably all living things trace their ancestry to the
> primordial soup - so the presence or a lack of ancestry is just a
> matter of how deeply one is willing to look. In other words, it's
> nice and dandy to have theoretical binary concept but in practice it
> is just as fuzzy as anything else.
>
> IMHO, the phylogenetic concept of homology in biology does not buy
> you much of anything useful. It seems to be just a leftover from pre-
> Darwinian days - redefined since but still lacking solid foundation.
>
> Dima
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