I agree with Gerard regarding "homology", but then it becomes significantly more problematic when you deal with "remote homology".
Nadir Mrabet -- Pr. Nadir T. Mrabet Cellular & Molecular Biochemistry INSERM U-724 UHP - Nancy 1, School of Medicine 54505 Vandoeuvre-les-Nancy Cedex France Tel : +33 (0)3.83.68.32.73 Fax : +33 (0)3.83.68.32.79 E-mail : [EMAIL PROTECTED] Selon Gerard DVD Kleywegt <[EMAIL PROTECTED]>: > 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. (*) > > A useful paper about homology and percentage sequence identity (and > structural > similarity) is Rost, 1999: http://www.ncbi.nlm.nih.gov/pubmed/10195279 > > --dvd ftw ;-) > > (*) For instance, when applied to fictional characters, Luke and Leia are > homologous since they share a common ancestor in Mr Vader. See: Vader, D. > (1980). "No, *I* am your father." Star Wars 5, and: Vader, D. (1983). > "Especially for... sister." Star Wars 6. > > > > > On Fri, 5 Dec 2008, Dima Klenchin wrote: > > >>> to models built on low-homology structures. > >> > >> since i'm currently preparing my bioinformatics lectures for next week's > >> teaching, i might as well be a Besserwisser and point out that homology, > >> much like pregnancy and death, is a binary concept. i'm sure artem knows > >> this and simply mistyped "low sequence identity" > > > > Well, although it is off-topic: > > > > Random House Unabridged Dictionary > > Homologous > > 1. Corresponding or similar in position, value, structure, or function. > > > > So if you insist that homologous is a binary concept then you should be > able > > to come up with the exact boundary between what's homologous and what's > not. > > What is it? 10% sequence identity? Less? More? Because if such a boundary > > cannot be defined then everything can be homologous to everything - it's > all > > in the eye of the beholder. And if so, then the binary concept of homology > is > > either meaningless or incorrect. > > > > Ergo: arguing about definitions of terms used to describe continua is not > > very productive in science (cf. "species", "sea/ocean", "hill/mountain"). > > > > Dima > > ****************************************************************** > Gerard J. Kleywegt > [Research Fellow of the Royal Swedish Academy of Sciences] > Dept. of Cell & Molecular Biology University of Uppsala > Biomedical Centre Box 596 > SE-751 24 Uppsala SWEDEN > > http://xray.bmc.uu.se/gerard/ mailto:[EMAIL PROTECTED] > ****************************************************************** > The opinions in this message are fictional. Any similarity > to actual opinions, living or dead, is purely coincidental. > ****************************************************************** >
