Ser or Bd[S]?

Dr. Alan Christensen christen at calvin.jci.tju.edu
Mon Jan 3 14:46:16 EST 1994


Re: New names for old mutants

Recently Yoshiaka Fuyama posted the following question:

>    The New Red Book says that Serrate (Ser) is a synonym of Bd[S]. But I
>  can't find any entry of Bd[S] in major stock lists though there are
>  numerous Ser. In a similar case, there are numerous bw[V1] but no Pm.
>    Is there sound reason for such inconsistency?

To which Bill Gelbart replied, in part:

>  You will undoubtedly find many such examples of inconsistencies between
>  the New Red Book and stock lists.  These inconsistencies are generally
>  historical or sociological, and evolve from the fact that different groups
>  have been maintaining these different data files.  Common names in use for
>  a long time (such as Ser) will only slowly be replaced in such independent
>  stock lists by their newer proper synonyms (Bd[S]).

Here's my two cents worth:
Although I realize that Bd is the older name, and therefore takes precedence,
I wonder if occasional exceptions shouldn't be made.
In this particular case, I found the following occurrences in the stock lists
on Flybase:
                                 Number of stocks listed
                                 _______________________
Stock Center                     Bd      Bd[S]       Ser
____________                     __      _____       ___
Bloomington                       1         0         30
Bowling Green                     1         0        177
Umea                              0         0        119
Ashburner                         0         0         29

Although most of the occurrences of Ser are on TM3, which is kind of
cheating, the point is that no one actually refers to Ser as Bd[S], and
that very few alleles of Bd other than Ser even seem to exist any more.
The addition of more lab stock lists would undoubtedly skew the distribution
more heavily _towards_ Ser.

There are inconsistencies in the Red Book that don't seem to cause problems,
most notably the peaceful coexistence of fa, Ax, Co, l(1)N, nd, spl, and N
under the umbrella of Notch.  These have not been renamed N[fa], N[Ax], etc.
This may not be the proper way to do it, but it seems to work.  In the case of
Bd[S], Serrate works.  Wouldn't it be better to just call it Serrate, and list
Beaded as an allele of Serrate?  (See also Stephen Jay Gould's "Bully for
Brontosaurus" for similar arguments in the Brontosaurus/Apatosaurus name
debate).

As a further argument for leaving Serrate alone are the fact that there are
4 publications since 1990 whose titles refer to the Serrate locus, but none
since 1949 that refer to Beaded (from the Flybase References section).
Furthermore, both sequence entries in GenBank (DMSER and DROTMLPA) refer to the
"serrate gene" and "serrate protein", and do not even list Beaded as a synonym.
This means that anyone doing literature or sequence database searches must use
the "incorrect" name to find anything. I revere the Red Book as much as anyone,
and I agree that a consistent and predictable nomenclature is important,
but I think Serrate is a good example of an exception that should be made.
Such cases will probably be rare, but may be justified by the preponderance
of usage, and by the fact that switching would cause more confusion than
leaving well enough alone.

--------------------------------------------------------------------
Alan C. Christensen, Ph.D.                              215-955-5190
Dept. of Biochemistry & Molecular Biology           FAX 215-955-5393
Thomas Jefferson University              christen at calvin.jci.tju.edu
233 S. 10th Street
Philadelphia, PA 19107-5541                "Curiouser and curiouser"
--------------------------------------------------------------------
P.S. I'm not going to tackle Pm vs. bw[V1].





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