gene names

[Laurie Mets]

I heartily endorse Susan's recommendation that we standardize mutant gene 
nomenclature.  However, the upper case/lower case distinction that was 
established many years ago for yeast has, in my view, is too much of a 
simplification to make it informative for modern genetics.  The theory is 
that it distinguishes between "domant" and "recessive" alleles and that this 
distinction is evident in the name.  Therein lies the problem.  
Dominance is always judged in a vis-a-vis manner and then only by 
considering a limited aspect of the phenotype.  One pair of alleles may 
appear to have one dominance relationship for one aspect of their phenotype 
and another for a different - the classical example of cicle cell anemia 
comes to mind.  As we look more and more into the molecular phenotypes of 
mutant genes, this aspect of the problem becomes more acute.  In addition, 
multiple alleles may be arranged in dominance cascades or in one arrangement 
in one genetic background and in another in a different one.  This latter 
property of genotype-dependent shifts in dominance (read "inter-genic 
suppression" or "syntheitc lethal" or whatever your favorite paradigm for 
studying gene-gene interactions) is a vital aspect of modern genetic 
analysis.  For all of these reasons, incorporating a notion of dominance 
into the name of a specific allele suggests a fixity of properties that is 
rarely present.

It also seems to me to be unhelpful to use upper case names for "wild type" 
alleles.  Unless we standardize on a single wild type strain, the wild types 
that we use will be found to vary from one another.  What, then, do we do 
about naming the different alleles from the various strains?  Hopefully the 
strains will not often vary dramatically in their characteristics, but when 
they do, the arbitrary identification of wild type alleles as upper case 
will not work.

To correctly interpret the meaning of the suggested upper case vs. lower 
case distinction, a reader would have do know as much about the various 
alleles as if that distinction in naming were not present.

I recommend that we use all lower case letters in the names of all alleles.

I also recommend that we adhere to the present naming conventions for 
nuclear genes that code for components of the chloroplast.
Laurie Mets
mets at cells.uchicago.edu
(312)702-8917