[Taxacom] Drosophila melanogaster name change?

Richard Zander Richard.Zander at mobot.org
Fri Apr 16 09:37:09 CDT 2010


Typical. Taxonomy is "different opinions." Funny how much taxonomy is generally agreed on, while those groups inflicted with "different opinions" are actually being dealt with scientifically.
 
_______________________
Richard H. Zander
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166 U.S.A.
richard.zander at mobot.org
 

________________________________

From: taxacom-bounces at mailman.nhm.ku.edu on behalf of Stephen Thorpe
Sent: Thu 4/15/2010 4:04 PM
To: David Remsen (GBIF); TAXACOM
Subject: Re: [Taxacom] Drosophila melanogaster name change?



actually, of course, there is no such thing as a "name change" - only different opinions on what the name ought to be, opinions that may be more or less accepted by particular people/groups, but rejected by others. The real issue is whether an average follower of, say, Drosophila melanogaster genetics, would still be able to follow it if the name Sophophora melanogaster started being used instead. Would this cause serious confusion? I doubt it, not in the internet era when a simple Google search would probably suffice to figure out what is going on...




________________________________
From: David Remsen (GBIF) <dremsen at gbif.org>
To: TAXACOM <taxacom at mailman.nhm.ku.edu>
Sent: Fri, 16 April, 2010 2:15:39 AM
Subject: Re: [Taxacom] Drosophila melanogaster name change?

Some of my concerns regarding the ease of addressing this are:

1. Most people who reference scientific names are not familiar with 
the reality or the reasoning of name changes so wouldn't think of 
looking up a name change
2. There is no one authoritative place to look up such information.   
There exists a patchwork of resources that return a very heterogenous 
set of information in various formats with varying degrees of 
structure.  This is a process that can, and to some degree is being 
consolidated into useful services.
3. Until such solutions are in place there is no practical way for 
someone to stay up to date and names change anytime and anywhere.
4. Names change for a variety of reasons some of which might be 
universally agreed and some of which remain in contention so that two 
different names may be in use concurrently.  A case in point is the 
squid, Loligo pealeii, now referred by some as Doryteuthis (Amerigo) 
pealeii.  Other cephalopod biologists don't buy the rationale for the 
move and continue to refer to the Loligo form.  What's the average 
neurobiologist who uses this species to study Alzheimer's supposed to 
do when they publish their next paper?
5. Simply substituting one name for another isn't a solution for many 
cases.
6.  Uptake seems to be a problem from both sides.    Google hits for 
the red-beard sponge name, Microciona prolifera, outnumber the correct 
(according to Van Soest) name Clathria (Clathria) prolifera,  yet the 
former (and quite incorrect) name didn't even appear in the world 
sponge database until I mentioned to them last year that biologists in 
Woods Hole happily publish articles every year referencing it.

David Remsen


On Apr 15, 2010, at 12:12 AM, Stephen Thorpe wrote:

> if the problem is that much of the literature uses the generic term 
> Drosophila as a substitute for D. melanogaster, then that is a 
> lesson to be learned by the non-taxonomists who publish genetics, 
> etc. Other than that, I still don't see a problem with a name change 
> that anybody can easily find out about from readily available 
> internet resources like Wikispecies ...
>
> Stephen
>
> From: David Remsen (GBIF) <dremsen at gbif.org>
> To: Stephen Thorpe <stephen_thorpe at yahoo.co.nz>
> Cc: David Remsen (GBIF) <dremsen at gbif.org>; Kim van der Linde <kim at kimvdlinde.com
> >; TAXACOM <taxacom at mailman.nhm.ku.edu>
> Sent: Wed, 14 April, 2010 7:22:57 PM
> Subject: Re: [Taxacom] Drosophila melanogaster name change?
>
> One of the comments in the Nature piece by David States provides a 
> perspective on this:
>
> "Y2K came and went with a whimper. This change unfortunately will 
> not be so imperceptible. "Drosophila melanogaster", "Drosophila" and 
> "DM" are so embedded in so many pieces of software that the 
> consequences of this name change will be annoying scientists for 
> years to come. This includes many applications that are "frozen 
> alive"; databases and pieces of code written by a grad student or 
> postdoc who has since moved on to other interests. The code is still 
> actively used, but there is no one actively maintaining it, and no 
> one to dig into the source code to find all the places were the term 
> "Drosophila" is embedded.
> The change will also reverberate through other standards. For 
> example, the US National Library of Medicine MeSH system has five 
> different headings and thousands of substance names incorporating 
> the word "Drosophila" (Drosophila, Drosophila proteins, etc.) and a 
> formal process for proposing, vetting and promulgating changes to 
> the MeSH. Change is not going to happen quickly.
>
> If new scientific evidence (e.g. complete genome sequence) suggests 
> that existing genus assignments need to be reassigned, the naming 
> should reflect usage in broader world. There are more publications 
> on melanogaster than there are on all of the other Drosophila 
> species combined. melanogaster is de facto the type species for the 
> Drosophila genus. If a new genus name is to be created, melanogaster 
> should stay Drosophila melanogaster and other species renamed. This 
> strategy may induce more changes within the taxonomic nomenclature, 
> but in the broader world it will be MUCH less disruptive."
>
> The case of being redirected to information on Pneumocystis jiroveci 
> when one types Pneumocystis carinii wouldn't appear as 
> straightforward as suggested either since P.  carinii remains as a 
> distinct taxon.    Nomenclatural synonymy is more amenable to this 
> but only partially addresses the problem and there aren't easily 
> accessible lists of nomenclatural synonyms, particularly for the 
> animals.  Good coping strategies do help but we aren't quite there 
> yet.  But, yes, some are working on this.
>
>
>
> On Apr 13, 2010, at 11:45 PM, Stephen Thorpe wrote:
>
>
>> Surely, all this fuss about a name change is unwarranted, 
>> particularly in today's internet world. Maybe it would have been 
>> more of a problem for D. melanogaster to have changed its name in 
>> the pre-internet era? Surely, one of the main things that 
>> bioinformatics people work on is how to cope with name changes? 
>> Even the relatively unsophisticated (by bioinformatics standards) 
>> Wikispecies can easily cope. If D. melanogaster changes name to 
>> Sophophora melanogaster (or whatever) then somebody who types 
>> Drosophila melanogaster into the search box will be redirected to 
>> Sophophora melanogaster, and thus can easily find out the new name. 
>> Name changes are a reality - the trick is to develop good coping 
>> strategies ...
>>
>>
>>
>>
>> ________________________________
>> From: Kim van der Linde <kim at kimvdlinde.com>
>> To: taxacom at mailman.nhm.ku.edu
>> Sent: Wed, 14 April, 2010 7:32:19 AM
>> Subject: Re: [Taxacom] Drosophila melanogaster name change?
>>
>> Richard,
>>
>> On 4/13/2010 12:17 PM, Richard Zander wrote:
>>> I read way too much agreement (about paraphyly, survival of 
>>> ancestors
>>> after speciation, robust taxa, phylogenetics not being the end-
>>> all) in
>>> what you say.
>>
>> I am sorry if I made you uncomfortable, I will see if I can find some
>> disagreement with you.....
>>
>>> Are you a member of the Post-Phylogenetic Systematics
>>> Society? Have you been taught the secret hand-shake? Have you paid 
>>> your
>>> (nominal) dues?
>>
>> LOL, maybe we have to start one. No, I had a decent taxonomic 
>> training
>> when I did my masters (just imagine how hard I had to laugh when 
>> someone
>> tried to kick my legs from under me by telling me that I should 
>> take a
>> decent course in taxonomics), but it is my nature not to adhere to 
>> the
>> mainstream ideas (if I had done that, I would not have proposed to 
>> split
>> the genus in the first place) but think for myself.
>>
>> During my Masters, we had a semester long colloquium just on species
>> concepts and how you could determine when something was a species. 
>> That
>> was when cladistics was still done with a software package called 
>> Hennig
>> ##. Together, it taught me is that each of the various species 
>> concepts
>> have their value, each in their proper context. I think the 
>> phylogenetic
>> species concept is much more valuable for phylocode than for rank 
>> based
>> taxonomy.
>>
>> The same problem that you have with phylogenetics, I have with
>> traditional morphology based cladistics. It is very easy to rake up a
>> lot of traits, run an analysis and find a single trait that is 
>> dividing
>> the species in two nice groups. Whether or not that trait is
>> evolutionary relevant, that is often ignored. And that is in part the
>> problem with Drosophila.
>>
>> The good thing in Drosophila is that the phylogenetic work actually 
>> has
>> a reasonable similarity with the evolutionary work that has been 
>> carried
>> out over the past decades.
>>
>> What we have now with Drosophila is the remnant of 18 decades of 
>> fussing
>> around with the genus. We can easily spend another decade or 5 to 
>> figure
>> out all the details for each and every species in the genus and the
>> included genera before taking any action. I am convinced that the
>> outcome is not going to be substantially different, other than that 
>> we
>> can fill in many more details about obscure and rarely investigated
>> species. The upcoming proposal to split the genus is in many ways a 
>> very
>> modest proposal (4 main (250+ species), some smaller (1-10 species)
>> clades). I think a much more comprehensive revision, with some more 
>> risk
>> of making the wrong decisions would split the genus in 7 major clades
>> (50+ species) and a lot of smaller clades (1-50 species). The main 
>> thing
>> this revision will do is to eliminate the Sophophora melanogaster
>> problem, which I think is a good thing.
>>
>>> I largely disagree that different genetics make different taxa. I 
>>> think
>>> that different evolutionary directions are, yes, mediated by 
>>> genetics,
>>> but different genetics do not necessarily, or even usually, imply
>>> speciation processes. We need more information about evolution 
>>> than the
>>> genetic element.
>>
>> Agreed, although I am personally okay with deciding that two clades 
>> are
>> different species if the genetic difference is large enough not in
>> absolute terms, but comparatively with regard to the variation within
>> the two clades.
>>
>> Regards,
>>
>> Kim
>>
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>
>
>

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