IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP


Mon May 30 22:03:38 EST 1994

  There's something I'm missing in this discussion. Aside from
the minor clarifications, what is the motivation for changing the
current conventions? Changing the conventions is not entirely
trivial -- we should have some reason for it. 

I can see two general reasons for any changes:

1) The current system is clumsy, or confusing or complicated. I'm
not convinced that this is the case (actually no one has really
tried to make the case). A quick look at a few other systems
(actually it's hard to get a feel for a system just looking at a
few papers, but anyway...) suggests that ours is pretty similar
to S. pombe (another organism with no vegetative diploid phase in
its usual life cycle), and that there's a lot of variations out

2) People just don't like the current system.  If a majority of
people want to use something else, then I guess we should do so.
We should bear in mind that changing the system will create some
confusion. (Of course, a look at the literature shows we already
have that.) I suspect many people use The Chlamydomonas
Sourcebook as a reference -- do we want that usage (e.g. pp. 448-9) 
to be incorrect? 

   A quick look at Chlamy literature will show that lots of
people are not using the current conventions, as I understand
them anyway. Lots of people are using upper case -- whether it
means wild type or dominance, only the author knows for sure.
Will changing the convention improve the consistency of the
literature? (Or is that even a goal of the change? Do other
organisms have this problem?) 
   We need to ask why people don't follow the current
conventions. If it's due to carelessness, indifference or
ignorance of the standard, then changing them may not improve the
situation. A little education (maybe we need a style sheet, with
examples) and prodding by reviewers and editors may be in order.
Alternatively, if people are not complying because they don't
like the conventions, we had better pick a system that most
people will agree (if grudgingly) to follow, or we will just end
up with continuing inconsistency in the literature -- it will
just be a different group of people flouting the rules. 

  A few comments on specific issues:

  Some people commented on using + and -. If we stick with lower
case, we can't really escape these (can we?). Either wild type is
NIC-7 or nic-7+. In papers the + is superscripted, but it
wouldn't have to be on the computer. In practice, I believe
people say nic-7 gene or nic-7 locus, i.e. the + is only used to
specifically talk about the w.t. allele.
  The fact the mt- is not a mutant of mt+ doesn't strike me as a
problem. It is a unique exception we are all aware of (note also
the lack of locus or allele numbers). The use of arg-7+ to
mean arg-7 mt+, rather than wild type arg-7 (I've seen it,
infrequently, in recent papers, although the + is not
superscripted when used this way) should, IMO, be discouraged. 

  I like the idea of flagging dominant mutant alleles with a d
(D? superscript? subscript? italic? Do what you feel?). This
gives an author a way to draw attention to this property of a
particular mutant allele, without imposing a system on the entire
nomenclature. Chlamy is haploid, after all. 

  If we really want upper case, there seems to be a convention in
some organisms of using only an initial cap -- i.e. do we want
NIC-7 or Nic-7? (I have not seen anyone using the latter in
Chlamy papers, however.)

  Perhaps if we allow that NIC-7 or nic-7+ are both acceptable
ways to indicate wild-type, we might get nearly full compliance?
This appears, after all, to be the reality in the literature at
the moment. If there is a clear majority for one usage, I suppose
we could indicate that as the "preferred" usage, in an attempt to
push people towards a uniform usage. 

Patrick Ferris
Washington University, St. Louis
ferris at wustlb.wustl.edu

More information about the Chlamy mailing list

Send comments to us at biosci-help [At] net.bio.net