----- "Anastassis Perrakis" <[EMAIL PROTECTED]> 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.
Even this is unclear without qualification. Identity is always determined by alignment, and you can get different %ID by using different matrices. > 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
