[Taxacom] Drosophila melanogaster name change?

Paul Kirk p.kirk at cabi.org
Tue Apr 13 09:20:07 CDT 2010

Thanks for your input David ... by a strange quirk in the Code only
typified names which have been used in a sense excluding the type are
subject to mandatory conservation proposals - e.g. by changing the type
to protect current usage - before a change in name, such proposals to be
either accepted or rejected after debate, whereas untypified names, even
with a clear 'circumscription', can be summarily 'replaced' without
regard to '... the provision of a stable method of naming taxa ...'.
With actions like this who can defend taxonomy as serving it's
customers. As I remarked at the time - what does the rat (or other
mammal) care if the name of the organism infecting it has to change? I
intentionally avoid the use of the word species in this instance.


-----Original Message-----
From: David Remsen (GBIF) [mailto:dremsen at gbif.org] 
Sent: 13 April 2010 15:08
To: Paul Kirk
Cc: David Remsen (GBIF); TAXACOM
Subject: Re: [Taxacom] Drosophila melanogaster name change?

Pneumocystic jiroveci appear to have been split from Pneumocystic

http://www.ncbi.nlm.nih.gov/pubmed/828240 is the earliest reference in
1976 but it doesn't appear that people noticed until this article

http://www.ncbi.nlm.nih.gov/pubmed/12194762  was published in 2002 .    
The title indicates that the human form of this fungus (P.  jiroveci) is
distinct from the species that infects rats and other mammals.

The problem is that it's very difficult to retrieve all articles linked
to this new taxon because the uptake of the new name is not

Since the 2002 article over 680 publications in PubMed reference P.   
jiroveci however also in that time 985 articles were published that
reference  Pneumocystic carinii.  Since the species still exists  
perhaps they all refer to this narrower version of carinii.    PubMed,  
however, allows me to narrow this search result only to articles  
relating to humans.    This leaves me with 742 articles.

This means that to retrieve articles on this taxon via PubMed you need
to search for "Pneumocystic jiroveci"  AND ("Pneumocystic carinii"  
with a limit to HUMAN published since 2002),  since P. carinii still
exists and infects other mammals and existed sensu lato prior to 2002.

Unique taxon identifiers would eliminate this problem.  In the meantime
it's a good thing they have a decent informatics framework at the
National Library of Medicine.

David R

On Apr 9, 2010, at 10:21 AM, Paul Kirk wrote:

> as this organism is a fungus it's nomenclature is governed by the ICBN

> where, in the preamble, is stated ... 'This Code aims at the provision

> of a stable method of naming taxonomic groups, avoiding and rejecting 
> the use of names which may cause error or ambiguity or throw science 
> into confusion'. Conservation and Rejection are the ultimate 
> mechanisms in the Code which permit this aim to work in the real world

> - in the Pneumocystis case these mechanisms were not explored and were

> not used, so the customers of taxonomy [NOT other taxonomists] are 
> just going to have to change the name, right?
> Paul
> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu
> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Geoff Read
> Sent: 09 April 2010 09:07
> To: taxacom at mailman.nhm.ku.edu
> Subject: Re: [Taxacom] Drosophila melanogaster name change?
> Talking of total red herrings. What about the renaming of Mao Zedong 
> (Mao Tse-Tung)?  Who do we blame for that one?  And those big 
> corporations which call themselves and their products by words that 
> most of us always thought had other common meanings. They shouldn't be

> allowed to do it.
> In Pneumocystis is it that one species was split into two in the same 
> genus? With evidence based reasons for so doing or not? And if with 
> reason the problem with that is what? The claimed new knowledge must 
> not have an effect on namings? Ain't possible.
>>>> On 9/04/2010 at 6:29 p.m., "Paul Kirk" <p.kirk at cabi.org> wrote:
>> the problem IS the taxonomist ... they are capability driven rather 
>> than customer led ... with obvious consequences.
>> same thing has happened with the name of the organism which is one of

>> the largest causes of death in ummunocompromised people ...
>> pneumocystis carinii ‑ became pneumocystis jirovecii ... but 
>> it's more complicated than the Drosophila case.
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