[Taxacom] Does the species name have to change when it moves genus?

Dr.B.J.Tindall bti at dsmz.de
Wed Jun 20 06:37:23 CDT 2012


Rod,
A couple of quick points:

Quoting Roderic Page <r.page at bio.gla.ac.uk>:

> Dear Brian,
>
> The example is nice, and a great demonstration of what we could aspire to.
>
> A few minor quibbles. It's a pity the example isn't Open Access,  
> that it can't be downloaded in XML for data mining, and that the  
> Names4Life system is patented  
> (http://www.google.com/patents/US7925444 ) (but then again, uBio has  
> a patent as well http://www.google.com/patents/US7650327 ). George  
> Garrity was at the first TDWG GUID meeting (2006?) when Names4Life  
> was already up and running. He found proceedings rather amusing -  
> he'd already settled on DOIs as identifiers.

Open access - well someone has to pay for the cost of publishing  
(which is either the authors - open access - or the subscribers - pay  
per view/subscription) - but having said that all journal content is  
open access two years after publication. Patents - same issue, someone  
has to pay the bills. DOIs have a working infrastructure and are known  
to publishers.

>
> It's worth thinking about why this system is possible. The situation  
> for bacteria is rather different to, say, animals, for several  
> reasons.
>
> 1. There not many named bacteria compared to other taxa (I realise  
> that vastly more bacterial lineages exist than meet the criteria for  
> being named). The Catalogue of Life for 2008 had about 9,500  
> bacterial species listed. In 2010 there were a total of 859  
> nomenclatural changes (including new names as well as synonyms,  
> emendations, etc.  
> http://www.bacterio.cict.fr/twothousand/twothousandten.html ).  
> That's compared to 20,068 new zoological names (never mind new  
> combinations, etc.).

While true its nice to have a small model and I think if you get down  
to the details it is well accepted that the vast majority of not  
properly documented life is in the microbial sector, a significant  
proportion of which is prokaryotic. At the same time I can only think  
of one or two scientists left in the UK who have published in  
prokaryote taxonomy with that breed set to become extinct within the  
decade. However, the current state of the art also has a significant  
impact on the analysis of the raw data (as you outlined in an earlier  
e-mail) - where significant taxonomic revisions are badly needed, but  
there are far too few people to do it or who those who are active  
don't have the time - a ticking time bomb if you rely solely on the  
names (or even LSID/UUIDs for that matter).

>
> 2. All bacteria names and changes are published (or announced) in  
> one journal, and articles in that journal have DOIs. We have some  
> attempts to capture new names (ION and ZooBank), a diverse, often  
> obscure literature, and our major journal (Zootaxa) has yet to adopt  
> DOIs.

Yep, we were in first with registration - wonderful idea and we know  
the benefits and problems too......

>
> 3. There is commercial value in knowing about bacterial names, e.g.  
> http://intellogist.wordpress.com/2011/06/22/namesforlife-adds-value-to-your-searches/ .  The commercial value in zoological names is perhaps less clear, although providing services to publishers would be an obvious  
> application.
>

Strange the use of the word commercial also suggests that one could  
pay for what one has to offer which also pays the bills and keeps the  
system running, rather than relying on part time work and short term  
grants.

> There's no reason, in principle, why we couldn't have the same  
> system for animal names, although the scale of the task is rather  
> larger than for bacteria.

As I said getting to know how things react in a small data set helps  
to solve issues that might be more difficult to solve in a larger data  
set - over to Rich Pyle.........

Brian
>
> Food for thought...
>
> Regards
>
> Rod
>
>
> On 20 Jun 2012, at 10:25, Dr.B.J.Tindall wrote:
>
>> Rod,
>> While I appreciate that much of what has been discussed is slanted  
>> towards those organisms traditionally treated as zoological taxa  
>> and botanical taxa, the principles are the same for prokaryotes and  
>> viruses.
>>
>> Linking information from taxonomic publications back to a central  
>> database (that has information on synonyms etc.) that in turn links  
>> to other databases is already implemented for the test case of one  
>> journal for prokaryote names and their associated taxonomy. Try  
>> this link and click on the taxonomic names that are highlighted in  
>> green:
>>
>> http://ijs.sgmjournals.org/content/62/Pt_6/1342.abstract
>>
>> The system also uses GUIDs.
>>
>> The various issues of whether a genus name should change when a  
>> species is reclassified in another genus and the use of LSID/DOIs  
>> sometimes looks different once a system operates and one starts to  
>> ask questions that the system isn't set up to solve. Only then does  
>> one get a clear idea of what questions one should have asked in the  
>> first place.
>>
>> Brian
>>
>> Quoting Roderic Page <r.page at bio.gla.ac.uk>:
>>
>>> Dear Rich,
>>>
>>> Thanks for the insightful response. I agree that we are in a  
>>> transitional period (from analogue to digital), and things will be  
>>> messy for a while (as we can see by looking at what's happened as  
>>> the music, newspaper, and movie industries have struggled with  
>>> this transition). Of course, I want things to go much faster, in  
>>> part because I'm not convinced that the rest of biology will hang  
>>> around patiently waiting while taxonomy makes this transition.
>>>
>>> As William Gibson wrote "the future is already here -- it's just  
>>> not very evenly distributed"  
>>> http://en.wikiquote.org/wiki/William_Gibson ZooKeys is one vision  
>>> of the future, and it's a great journal, it's just a tiny fraction  
>>> of the current taxonomic output.  In 2010 ION recorded around  
>>> 18,000 new names, of which a little over 400 were published in  
>>> ZooKeys. The widely distributed nature of taxonomic publishing  
>>> means that even the dominant journal (Zootaxa) publishes only  
>>> 15-20% of all new names. That means there's a lot of publishers to  
>>> convince to move to new ways of publishing (e.g., XML markup). If  
>>> we're publishing ~20,000 animal names a year, and the rate of new  
>>> species description has been relatively constant over the last few  
>>> years, we still have 50 years to go to double the number of animal  
>>> names we already have.
>>>
>>> You ask
>>>
>>>> Why
>>>> not focus on the brave new world of electronic publication, where the
>>>> included information is not limited to what is seen by the human eyeballs,
>>>> and where all this stuff can be harvested seamlessly via unambiguous GUIDs
>>>> (rather than via crude OCR and fuzzy text matching of messy text-string
>>>> names)?  To me, that's where the answer lies going forward.
>>>
>>> Partly because the new stuff is relatively easy, in the sense that  
>>> marked up XML is straightforward to generate and work with  
>>> (where's the fun in that?), and partly because once the new stuff  
>>> is marked up, we still have the question "what does it link to?"  
>>> If I click on a name, I want to see everything about that name,  
>>> not just the most recent literature. If an article cites a paper  
>>> that is only available in a digital library like BHL, I want to  
>>> have a link to that. If the user clicks on that link, I want them  
>>> to be able to view the BHL content in much the same way as the  
>>> more recent literature (i.e., names and literature cited also  
>>> clickable). Our legacy literature will vastly outweigh the newly  
>>> generated, nicely marked up literature for a while yet.
>>>
>>>
>>>>> I'm not proposing a change in how we cite names,
>>>>
>>>> Yes, you are.  Since Linnaeus, we have cite species names in the form of a
>>>> species epithet preceded by a genus name, and the genus name is  
>>>> selected to
>>>> reflect the classification of the epithet.  You're proposing that we strip
>>>> the classification information from the binomial, and treat it as though
>>>> it's a single text string that happens to include a space within  
>>>> it.  That's
>>>> a change in how we cite names.  Maybe we're operating on different
>>>> definitions of the word "cite"?
>>>
>>>
>>> I suspect we are. To me, if I write "Homo sapiens" that's the  
>>> name. I gather you are saying that actually the name is "sapiens"  
>>> which I'm citing in the context of the genus "Homo" to indicate  
>>> its classification. That may well be, but I'd argue it's not how  
>>> most biologists treat names in practice (i.e., as simple text  
>>> strings to refer to a taxon).
>>>
>>>>
>>>> So in that context
>>>> (if you really believe that's where it's heading), why try to  
>>>> change one of
>>>> the core principles of binomial nomenclature right at the twilight of its
>>>> tenure in science?
>>>
>>> That's a very good question.
>>>
>>> Regards
>>>
>>> Rod
>>>
>>> On 19 Jun 2012, at 21:02, Richard Pyle wrote:
>>>
>>>>> I'm not actually suggesting we change the code, merely
>>>>> the convention to automatically  change the genus name
>>>>> if a species moves.
>>>>
>>>> I never said anything about changing the Code.  I was talking about 250
>>>> years of conventional practice.
>>>>
>>>>> Trivial in the sense that if we had all the information on names
>>>>> (synonyms included) linked to types we could resolve synonyms
>>>>> computationally, but we don't, certainly not at the scale of the
>>>>> 10x5 - 10x6 names that databases such as NCBI taxonomy and
>>>>> GBIF deal with. Yes, in principle, it is tractable, but why do
>>>>> we contribute to creating the situation in the first place?
>>>>
>>>> The "situation" is only as such because of the advent of computer systems.
>>>> Prior to computers, people had no issue with it.  Now that we have
>>>> technology that lets us mine vast volumes of historical literature, the
>>>> situation appears problematic because we are now doing at a much larger
>>>> scale something that hasn't really been done before, other than  
>>>> by Sherborn,
>>>> Neave, Linneaus, and a few others.
>>>>
>>>> I've always maintained that this period in history -- starting in the mid-
>>>> to late 1990s and ending probably around 2020-2025 -- is a  
>>>> somewhat awkward
>>>> one because it represents the transition between a centuries-long era when
>>>> paper was the primary mode of information dissemination and documentation
>>>> among humans, and the era when information is mostly documented and
>>>> disseminated via electronic signals.  It's awkward in general because not
>>>> all systems are moving in parallel and at the same pace, so  
>>>> various systems
>>>> get out of phase (e.g., the desire by modern taxonomists to publishe new
>>>> scientific names in electronic journals, vs. -- until recently -- the
>>>> requirements of the various Codes).  Specific to this topic, the  
>>>> awkwardness
>>>> relates to the fact that we have computer systems that index large numbers
>>>> of taxonomic name-strings (messy things, that don't always make it clear
>>>> which binomials are homotypic), but don't yet have computer systems that
>>>> index large numbers of taxonomic name "objects" (where homotypic binomials
>>>> are easily identified -- plus much, much more).  By about 2050 or so, this
>>>> period of awkwardness will warrant only a footnote.
>>>>
>>>>> Personally I suspect the taxon concept issue isn't going to be worth
>>>>> the effort expended, unless tackled with some clever tools for inferring
>>>>> context from citation, etc. it's simply unscalable.
>>>>
>>>> I'm not so sure about that.  Consider that we're rapidly shifting from
>>>> paper-based publication to electronic publication.  To make a major change
>>>> in practice in how we render text strings to human eyeballs (i.e., your
>>>> proposal to stop changing binomial combinations so we can maintain more
>>>> stable text-string labels) seems like using a Ferrari to drive down the
>>>> block to the local grocery store a little faster than the Toyota  
>>>> used to get
>>>> us there.  I imagine a world (not hard to imagine, really --  
>>>> given journals
>>>> like ZooKeys) where the text string name is something just to  
>>>> render on the
>>>> computer monitor for the benefit of human eyeballs.  Behind that  
>>>> text-string
>>>> name would be the necessary electronic link (or links) to the taxonomic
>>>> object, complete with all the metadata any taxonomist would ever  
>>>> want (type
>>>> specimens, concept definitions, literature citations, historical trends in
>>>> usages, etc., etc., etc.).
>>>>
>>>> You're talking about changing how we do things going forward, right?  Why
>>>> not focus on the brave new world of electronic publication, where the
>>>> included information is not limited to what is seen by the human eyeballs,
>>>> and where all this stuff can be harvested seamlessly via unambiguous GUIDs
>>>> (rather than via crude OCR and fuzzy text matching of messy text-string
>>>> names)?  To me, that's where the answer lies going forward.  Not putting a
>>>> band-aid on a centuries-old practice that is still trying to use  
>>>> text-string
>>>> names as unique identifiers.
>>>>
>>>>> Why not focus on what is tractable and will add immediate value?
>>>>
>>>> It would appear that you and I have different ideas about what is  
>>>> tractable
>>>> (or maybe we define the word differently?)
>>>>
>>>>> I'm not proposing a change in how we cite names,
>>>>
>>>> Yes, you are.  Since Linnaeus, we have cite species names in the form of a
>>>> species epithet preceded by a genus name, and the genus name is  
>>>> selected to
>>>> reflect the classification of the epithet.  You're proposing that we strip
>>>> the classification information from the binomial, and treat it as though
>>>> it's a single text string that happens to include a space within  
>>>> it.  That's
>>>> a change in how we cite names.  Maybe we're operating on different
>>>> definitions of the word "cite"?
>>>>
>>>>> and suggestions that embed more semantics in names (such as author, date,
>>>> first name)
>>>>> are just asking for trouble http://bit.ly/KQ6o46
>>>>
>>>> Perhaps.  But why not instead leverage the move towards electronically
>>>> published works by embedding GUIDs (which are themselves hidden from human
>>>> eyeballs), rather than continue to overload the feeble text  
>>>> string with more
>>>> information than it's capable of representing?
>>>>
>>>>> Citing a reference for "what I mean by" is useful, but I'd be
>>>>> happier if that was linked to actual data.
>>>>
>>>> We're in agreement on this one -- the key word being "linked".
>>>>
>>>>> Ironically, if you read the tea leaves the way I do, we are
>>>>> moving to a biodiversity science without names, where
>>>>> specimens will be the unit of choice, and taxa will be
>>>>> computational inferences, not vague assertions supported
>>>>> by a citation at best. But that's another story...
>>>>
>>>> ...and I wouldn't necessarily disagree with that story.  So in  
>>>> that context
>>>> (if you really believe that's where it's heading), why try to  
>>>> change one of
>>>> the core principles of binomial nomenclature right at the twilight of its
>>>> tenure in science?
>>>>
>>>> Aloha,
>>>> Rich
>>>>
>>>>
>>>> Richard L. Pyle, PhD
>>>> Database Coordinator for Natural Sciences
>>>> Associate Zoologist in Ichthyology
>>>> Dive Safety Officer
>>>> Department of Natural Sciences, Bishop Museum
>>>> 1525 Bernice St., Honolulu, HI 96817
>>>> Ph: (808)848-4115, Fax: (808)847-8252
>>>> email: deepreef at bishopmuseum.org
>>>> http://hbs.bishopmuseum.org/staff/pylerichard.html
>>>>
>>>> Note: This disclaimer formally apologizes for the disclaimer below, over
>>>> which I have no control.
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>
>>> ---------------------------------------------------------
>>> Roderic Page
>>> Professor of Taxonomy
>>> Institute of Biodiversity, Animal Health and Comparative Medicine
>>> College of Medical, Veterinary and Life Sciences
>>> Graham Kerr Building
>>> University of Glasgow
>>> Glasgow G12 8QQ, UK
>>>
>>> Email: r.page at bio.gla.ac.uk
>>> Tel: +44 141 330 4778
>>> Fax: +44 141 330 2792
>>> Skype: rdmpage
>>> AIM: rodpage1962 at aim.com
>>> Facebook: http://www.facebook.com/profile.php?id=1112517192
>>> Twitter: http://twitter.com/rdmpage
>>> Blog: http://iphylo.blogspot.com
>>> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>>>
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>>
>>
>>
>> Dr.B.J.Tindall
>> Leibniz-Institut DSMZ-Deutsche Sammlung von
>> Mikroorganismen und Zellkulturen GmbH
>> Inhoffenstra├če 7B
>> 38124 Braunschweig
>> Germany
>> Tel. ++49 531-2616-224
>> Fax  ++49 531-2616-418
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>>
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>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
>
> Email: r.page at bio.gla.ac.uk
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
> Skype: rdmpage
> AIM: rodpage1962 at aim.com
> Facebook: http://www.facebook.com/profile.php?id=1112517192
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>
>



Dr.B.J.Tindall
Leibniz-Institut DSMZ-Deutsche Sammlung von
Mikroorganismen und Zellkulturen GmbH
Inhoffenstra├če 7B
38124 Braunschweig
Germany
Tel. ++49 531-2616-224
Fax  ++49 531-2616-418
http://www.dsmz.de
Director: Prof. Dr. J. Overmann
Local court: Braunschweig HRB 2570
Chairman of the management board: MR Dr. Axel Kollatschny

DSMZ - A member of the Leibniz Association (WGL)

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