I agree with previous posts that the reality of inferring evolutionary
relationships is often messy, but there is no excuse for being unclear
on the concepts and, in particular, for use of the % homology construct,
still far too common in supposedly good journals.
BTW, %identity is clear but not always unambiguous...
May AC. Percent sequence identity; the need to be explicit.
Structure. 2004 May;12(5):737-8. PMID: 15130466
Dan
On Sat, 2008-12-06 at 21:33 +0100, Anastassis Perrakis wrote:
> 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
--
Dr Daniel John Rigden Tel:(+44) 151 795 4467
School of Biological Sciences FAX:(+44) 151 795 4406
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