Subject: Fwd: gene nomenclature
From: Paul Sternberg
Date: Fri, 24 Oct 2003 16:33:36 -0700
CC: Paul Sternberg

Begin forwarded message:

Dear Ron et al.,

One thing occurred to me on the nomenclature front last night as I was walking home from work. Why, aside from running out of names, does it matter whether we mostly use elegans phenotypic classes or not?  Isn't it better to have more accurate names?

The answer, I think, is this:  most briggsae genes will have elegans orthologues.  As we start to clone our mutants, if most start off with briggsae-specific classes we would then have to systematically change the name of every gene for which that turns out to be the case.  This would plant the seeds of future confusion in the literature, and that's why I don't like it.  The name-changing issue still exists with my suggestion, the "Cb-unc-A" thing, but at least the prefix stays the same, and we could make it explicit to all who care that letters  are provisional until the gene is cloned.  If it's novel, the letter sticks; if it's an orthologue it gets switched to the appropriate elegans number.

This still leaves room for new phenotypic classes where appropriate, and in some cases genes in these classes will still end up having named elegans orthologues anyway, but it minimizes confusion.  In the end this differs from Ron's proposal more quantitatively than qualitatively, I think, but philosophy is important.

Thoughts?  Hopefully we're close...



                                          Eric S. Haag, Ph.D.        ~
  Assistant Professor                                   ~
  Department of Biology                               ~ ~
  University of Maryland
  College Park, MD  20742               ~                       ~   ~
  phone:  (301) 405-8534    fax:  (301) 314-9358      ~         ~
                                    "I'd rather be here now."