[Annelida] Traditional taxonomy discussion

Christos Arvanitidis via annelida%40net.bio.net (by arvanitidis from her.hcmr.gr)
Tue Feb 9 06:03:57 EST 2010


Dear all,

I have followed the discussion which has started as a response to 
Nando's article and I would like to make a few comments here:

1. Hypothesis-driven science expects scientists to gain knowledge 
through the testing of hypotheses and their subsequent acceptance or 
rejection, depending on the results of the methods applied.  In this 
context I cannot see more chances for molecular taxonomy to be real 
science than for conventional taxonomy. I prefer the term conventional 
simply because the term descriptive refers to the presentation of the 
various parts of a structure and taxonomy and systematics are much more 
than that. Therefore, either we use molecular or phenetic (or any other 
kind of) information to construct phylogenies, the methodological 
approach and the rationale behind is the same: we need to offer the most 
plausible way through which species have been formed and evolved over 
the evolutionary time. To this end, even if we have the whole genome of 
the species available, we are not able to bring any kind of information 
on what has really happened in course of the geologic eras simply 
because nobody was there to tell us about. Of course, we make use of the 
scarce information that comes from fossils and other sources but this is 
not enough, either. Additionally we have almost no chances to perform 
experiments over evolutionary time frames in order to bring information 
on what has really happened. Therefore, what we can do -and we do it in 
a rather good and fashionable way- is to bring the "best possible" 
scenarios, based on the rationale of the methods we apply. Consequently, 
both conventional and molecular taxonomy when offering phylogenies are 
at the same "inferential side" of science. The latter is not necessarily 
bad since the "best approximation" is much better than the unjustifiable 
hunting of the "absolute resolution" of the problem. "Best 
approximation" also brings some degree of order in our anarchy of 
knowledge and thus it IS science. I think that this part agrees with 
Kirk's comments.

2. I have supported Nando's views on the declining of the conventional 
taxonomy in many European meetings and Fora for 15 years now. I strongly 
believe that his view reflects reality in taxonomy, these days. Indeed, 
we run the risk of producing genomes of millions of species for which we 
will not be able to know their names and how they look like. Yet, we run 
the risk of building "skyscraper quality and dimension" information 
systems but the real information deposited in there would be of very low 
quality and thus useless - Nando loves to call it "garbage". Over the 
last 10 years, whenever we mentioned the term taxonomy to the EU 
officers, we got back the cliché answer: "taxonomy is not a priority for 
EU". This is a very dangerous attitude which could lead to the 
elimination of the very rich and diverse information produced over the 
last 250 years: literature resources, descriptions, figures and photos, 
keys, phylogenies, and type material deposited in a large number of 
Museums, Botanical Gardens, Zoological and Botanical University 
Departments and Research Centers and so on. Definitely, some initiatives 
such as the BHL will save a lot of this legacy but if we loose our human 
potential we will also loose the ability to think, state and test the 
main hypotheses in the discipline. Changes in the ICZN will inevitably 
follow, I am not concerned about this. The important question is, then: 
how we react? This would be the start of the white paper that Kristian 
proposes in his message. A few ideas are also cited in the comment below.

3. According to the CBD official text, "biological diversity means the 
variability among living organisms from all sources including, inter 
alia, terrestrial marine and other aquatic ecosystems and the ecological 
complexes of which they are part: this includes diversity within 
species, between species and of ecosystems". This definition, therefore, 
refers to all levels of the biological organization from the molecular 
to ecosystem and land(sea)scape and to all scales of observation. 
Consequently, it is a multi-disciplinary approach. However,  people 
often use the term biodiversity although they work in no more that a 
single level of biological diversity or on a single scale simply because 
it is fashionable. This attitude has brought a degree of confusion and I 
believe it is very negative for the conventional taxonomy, as well. The 
framework, however, offered by the term biodiversity offers a unique 
opportunity for many disciplines to work together and the most fertile 
zones for the production of new theory, concepts, ideas and hypotheses 
to test are found in the interfaces between these disciplines. I believe 
that these interfaces or "trading zones" offer a unique opportunity for 
conventional taxonomy to evolve and to play a major role in the years to 
come. This could be one of the issues during our discussions in the 
Conference.

Cheers,

Christos.

    




Fauchald, Kristian wrote:
> I have been following the discussion via WoRMS etc., I am a bit concerned with setting us up as recommending a single way of handling taxonomy vs evolutionary biology and morphologh vs molecules etc.  I am increasingly getting to the point that the discussion ends up being pretty much like the famous description of the elephant by a series of blind people:  It depends on which end of it you happened to find!   Being (more or less) responsible for one of the largest polychaete collections, I very much appreciate having everything organized in a fashion which makes the specimens retrievable, and also as much as possible vouchers for the time and location they were collected, but also vouchers for example for various "variants" be they documented by genetic composition or by a study of their physiology (or whatever).  If we can make people understand that a single approach is probably futile at this point we can gain a lot.  We need to be able to voucher by morphology, by genet!
>  ics, by larval development, by feeding, by geographic distribution and so forth, so that we are able to document with as hard data as possible, everything that concerns a particular group of taxa.  Whether these are species or whatever they are, becomes more an issue of how our knowledge base develops.
> Now, having said that, let us see if we, lead by Nando, can get something together that makes a bit of sense.  It would be useful for us to have something in front of us once we start talking so that we don't wander around in terminology soups for hours, so some sort of introduction, a white paper, if you will, would be good.
> Kristian
>
> ________________________________________
> From: annelida-bounces from oat.bio.indiana.edu [annelida-bounces from oat.bio.indiana.edu] On Behalf Of Maria Cristina Gambi [gambimc from szn.it]
> Sent: Monday, February 08, 2010 11:19 AM
> To: paavo from wormguy.com; annelida from magpie.bio.indiana.edu
> Subject: Re: [Annelida] Traditional taxonomy discussion
>
> Dears all, we followed the discussion about the paper of Boero on
> Biodiversity, and the role and evaluation of taxonomy/systematics works ...
> we agree in general terms with the scenario depicted by Boero and we think
> that there is not a single or a best approach and solution... and possibly
> we need to integrate more in the future and the "classical" morphological
> approaches..., although a general re-evaluation someìhow of the taxonomic
> literature is urgently needed...
> We would like to inform that the first day- introductory lecture, related
> to taxonomy, at the next Polychaete Conference in Lecce (20-26 June 2010)
> have been planned by Nando Boero and we asked him to focus on this topic...
> so we invite all of you to consider that in the occasion of the 10th IPC we
> could come out with a common document, a "manifesto"  about the possible
> future ways to face the taxonomic crisis in the Era of Bioiversity....This
> could be discussed during the Conference and the IPA Committe and assembly,
> and the possible document could be disseminated in different venues.
> Please for those of you which have planned to come, we suggest to be
> prepared in advance and eventually with a draft for a common proposal.
> Thanks for the attention,
> Maria Cristina and Adriana
>
>
> At 23.36 07/02/2010, Brian Paavo wrote:
>   
>> Aloha,
>>
>> It was a bit heavy-handed Kirk and presenting haughty absolutes is rarely
>> productive.  Geoff, I agree that, given the complexity of developmental
>> and environmental interactions with phenotypes, that a genetics-heavy
>> approach to taxonomy is not a bad thing.  I also support your constructive
>> suggestion that our political efforts (feeble as they are) focus on
>> standardisation and improvements to descriptive procedures (e.g. allowing
>> digital descriptions, keeping a register, broadening the acceptable forms
>> - not substance - of names, etc.) .  I still believe that we need to train
>> more taxonomists and anatomists and diversity funding is currently an
>> important part of that.  Not only are such skills required to effectively
>> build upon the monumental work of the past, but observational skills lead
>> to mechanical and ecological insights which would often be missed by
>> gene-jocks.  We all need to guide the future of our work.  I personally
>> look forward to the deeper ecological insights to be gained using the
>> computational perspective of information (genes) influences on networks of
>> moving carbon constrained by the abiotic environment and I still want to
>> move our basic methodologies forward, but the 'old-fashioned' naturalist
>> skills of observing individuals, morphologies, behaviours, and populations
>> are what provide the context and value to our insights.  It is worthwhile
>> to collectively discuss what kind of future we'd like to see.  We've
>> heaped a lot of responsibility and faith upon the shoulders of the EOL folks.
>> What do we want and how can we and our respective institutions support
>> it?  I'm confident that 99% of us help broaden awareness locally.  Is it
>> useful to consider how we can unify our impact and entice more workers
>> through further-reaching media?
>> -Brian
>>
>> Geoff Read wrote:
>>     
>>> Hi Kirk,
>>>
>>> Thanks for the short fussilade. Forgive me if in my feeble attempt to
>>> introduce this article for discussion, be that subsequently fervent or
>>> otherwise, I have appeared to intrude into the world of science
>>> philosophy, where you are much more comfortable than I am. But you have
>>> presumed too much in the proximity of two sentences. I don't have an
>>> opinion on how scientific future or current molecular taxomomists might be.
>>>
>>> Best,
>>>
>>> Geoff
>>>
>>>
>>>       
>>>>>> On 8/02/2010 at 10:19 a.m., "Kirk Fitzhugh" <kfitzhug from nhm.org> wrote:
>>>>>>
>>>>>>             
>>>> "Personally I tend to agree with the outsiders that traditional
>>>> descriptive taxonomy has a weak claim to be real science. Soon only
>>>> molecular taxonomists will exist. This is not a bad thing as long as
>>>> they can also handle and include organism phenotype descriptions."
>>>>
>>>> How is 'traditional descriptive taxonomy' any less scientific than 'only
>>>> molecular taxonomists' [sic!]? I'd be fascinated to know of the
>>>> definitive text book on doing science that substantiates your claim that
>>>> presenting hypotheses isn't a fundamental part of doing science. None of
>>>> us should condone a world of 'only molecular taxonomists.' To do so
>>>> would be a bastardization of the very principles of science.
>>>>
>>>> Kirk
>>>>
>>>> ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~
>>>> J. Kirk Fitzhugh, Ph.D.
>>>> Curator of Polychaetes
>>>> Invertebrate Zoology Section
>>>> Research & Collections Branch
>>>> Natural History Museum of Los Angeles County
>>>> 900 Exposition Blvd Los Angeles CA 90007
>>>>
>>>> Phone: 213-763-3233
>>>> FAX:    213-746-2999
>>>> e-mail: kfitzhug from nhm.org
>>>> http://www.nhm.org/site/research-collections/polychaetous-annelids
>>>> ~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~
>>>>
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: annelida-bounces from oat.bio.indiana.edu on behalf of Geoff Read
>>>> Sent: Sun 2/7/2010 12:49 PM
>>>> To: Annelida from magpie.bio.indiana.edu Subject: [Annelida] Traditional
>>>> taxonomy discussion
>>>>
>>>> Hello,
>>>>
>>>> This commentary is being discussed. Personally I tend to agree with the
>>>> outsiders that traditional descriptive taxonomy has a weak claim to be
>>>> real science. Soon only molecular taxonomists will exist. This is not a
>>>> bad thing as long as they can also handle and include organism phenotype
>>>> descriptions. Many can't at the moment. I worry more about the problems
>>>> with the Zoological Code, and lack of consensus on the way forward, and
>>>> the energy wasted on futility of  archaisms such as gender agreement,
>>>> minutiae of revisionism in publication dates, obscure priorities, and
>>>> especially keeping to print-only validity of names, and not registering
>>>> all new names, than the issues raised here. Politics is everywhere.
>>>>
>>>> Boero F 2010. The Study of Species in the Era of Biodiversity: A Tale of
>>>> Stupidity. Diversity 2: 115-126.
>>>>
>>>> [Open access]
>>>> http://dx.doi.org/10.3390/d2010115 http://www.mdpi.com/1424-2818/2/1/115
>>>> Geoff
>>>>
>>>>
>>>>
>>>>         
>>> NIWA is the trading name of the National Institute of Water & Atmospheric
>>> Research Ltd.
>>>
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