[Taxacom] A little more on Species Entities

Peter DeVries pete.devries at gmail.com
Fri Oct 2 02:51:32 CDT 2009


Hi Stephen,
I would not say that it is an enlightened attitude, just one I have run
into.

You might not be able to actually get all of the original literature for
free, but this provides a mechanism that would make it much easier to get
hard to find publications. A related issue is that you often have to be an
expert in a particular taxa to be able to interpret these papers. Part of
this are page and photo limits in printed journals.

Also the Biodiversity Heritage Library is helping improve the accessibility
to the older literature.

I have no problem's with names, I would just like to mitigate some of the
problems caused by the current system.

It should also be a lot easier to determine the meaning of a particular name
or term. There are differences in how groups interpret
the meaning of the same term.

Here is a problem with the current system:

The current system forces the placement in a genus when describing a new
species even if you are not sure what that should be.

The process for describing that species should be split into two parts.

1) Describe the new species
2) Propose a particular phylogenetic placement for that species.

You should be able to describe a new species and then later recommend a
particular phylogenetic placement.

And I agree with you that we should be spending more time describing new
species than perhaps less reorganizing
the current list. The first it time sensitive, the second is not and gets
cheaper every year.

> If existing names need to be changed, this is to make them more meaningful
and useful indicators of relationships.

Yes, but the name does not have to serve both as an identifier for the
species and as a phylogenetic hypothesis.

*Aedes triseriatus* and *Ochlerotatus triseriatus* are one species with two
different phylogenetic hypotheses.

This part of the system is what is complex.

It is much simpler to say here is a species. This week this species is
thought to be in this place in the phylogenetic tree.

Understanding how the current system works is the complicated, and easily
misunderstood part. It requires specialized knowledge
about rules which are not really not about biology at all, but are human
crafted and interpreted procedures. Different groups have
their own versions of these procedure, differences that have nothing to do
with biology itself.

> The problem is with managements of institutions whose main focus is on
"the bottom line".

This seems to be a contradiction, it is about money. A number of the
problems you describe will be solved with money.

You need to step back and put yourself into their heads and understand how
they think, because they are not going away.

> From what I have seen and heard, the initiatives underway are in danger of
suffocating themselves in their own complexity...

If there is a problem it is more about them having to address, but not fix
fundamental problems that are built in to the present system.
Also they have to placate every different groups way of thinking - ways of
thinking that often conflict with each other.

For instance, they have to deal with millions of name variants for ~1.8
million species.

Why? Because in many cases the species identifier has to change based on 1)
rules or 2) a new phylogenetic hypothesis.

Even when the species is exactly the same entity as it was before.

Respectfully,

- Pete




On Fri, Oct 2, 2009 at 1:39 AM, Stephen Thorpe <s.thorpe at auckland.ac.nz>wrote:

>  Nice propaganda! :)
>
> >exists only in an obscure journal that no one can get to
> this is a problem, but DarwinCore isn't going to solve it. Instead, we need
> a centralised electronic library of digitised literature, made as
> comprehensive as possible, and freely available
> Can't see many publishing houses supporting this, though - unless we can
> pay them to release copyrights
>
> If there is a perception of taxonomists as "name changers", then that needs
> to be changed by way of education and "more appropriate propaganda". More
> emphasis needs to be put on the multitudes of unnamed species, requiring a
> name in the first place (for example, this new family of mite
> http://species.wikimedia.org/wiki/File:Enarthronota_new_family.jpg, which
> luckily is being described, based in large part on specimens I have
> supplied). If existing names need to be changed, this is to make them more
> meaningful and useful indicators of relationships.
>
> >I believe that it will also create a whole new funding stream to produce
> well documented species descriptions that are open and accessible
> I don't see a lack of funding per se as a problem - it costs
> relatively little to do taxonomy for many groups. The problem is with
> managements of institutions whose main focus is on "the bottom line".
> Taxonomy was never going to be a profitable enterprise, and so it struggles
> to survive in today's environment. If new databases and associated standards
> are going to change this at all, then they are going to have to be as simple
> and widely understandable as possible. From what I have seen and heard, the
> initiatives underway are in danger of suffocating themselves in their own
> complexity...
>
> Stephen
>
>  ------------------------------
> *From:* Peter DeVries [pete.devries at gmail.com]
> *Sent:* Thursday, 1 October 2009 9:06 p.m.
> *To:* Stephen Thorpe
> *Cc:* taxacom at mailman.nhm.ku.edu
> *Subject:* Re: [Taxacom] A little more on Species Entities
>
>  The new DarwinCore has a field that allows this *taxonConceptID.*
>  I think this will help working taxonomists since it provides an open,
> accessible repository for all that information that is currently to hard to
> find.
>
>  I believe that it will also create a whole new funding stream to produce
> well documented species descriptions that are open and accessible.
>
>  I think that funding agencies have been reluctant to fund another
> non-machine interpretable narrowly specialized description that exists only
> in an obscure journal that no one can get to. (*their perception not mine*
> )
>
>  Now those decision makers will think, *Hey they are acting like all the
> other biologists and producing something that could be widely usable ... I
> could see funding projects that follow this model**. **I guess taxonomist
> are cool, not just name changers that frustrate all the other biologists.*
> *
> *
> *I am on your side, and I think something like this will help the
> community. We can argue all we want amongst ourselves about the perception
> problem and whether it*
> *is accurate or fair, but in the end we need to do something to address
> the issue because it effects funding levels.*
>
>  *It is my opinion that something like this will improve:*
>
>  *1) productivity*
> *2) widely held perceptions*
> *3) funding*
>
>  *- Pete
> *
> On Thu, Oct 1, 2009 at 2:21 AM, Stephen Thorpe <s.thorpe at auckland.ac.nz>wrote:
>
>> >Demonstrating the difference between a change in how these two species
>> were seen vs. a simple mislabeling or misidentification
>>  In practice, a misidentification is a misidentification is a
>> misidentification, whether or not it reflected current thinking at the time,
>> or else was just the product of a rushed and sloppy identifier. From our
>> point of view today, we don't need to know which. Perhaps you could start up
>> a new discipline which studies old and defunct taxonomic concepts, but
>> trying to add that into a database will just massively increase the
>> complexity of the task for little or nothing of any use. Forgive the bad
>> timing of this analogy, but think of taxonomy as like being on the crest of
>> a wave - what we want to know is: are specimens correctly identified
>> according to our CURRENT concepts? Seems to me that somehow the bioinfo
>> people have lost sight of what the taxonomists actually do: when taxonomists
>> see a published identification, they don't ask: what taxon concept is this
>> talking about? Instead, and if they need to, they try to revisit the actual
>> voucher specimens and see if they are correctly identified according to
>> their present concept. In practice, this is the only way ...
>> ________________________________________
>> From: taxacom-bounces at mailman.nhm.ku.edu [
>> taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Peter DeVries [
>> pete.devries at gmail.com]
>> Sent: Thursday, 1 October 2009 7:59 p.m.
>> To: taxacom at mailman.nhm.ku.edu
>> Subject: [Taxacom] A little more on Species Entities
>>
>> The species entities can have many scientific names. These names are not
>> concepts just the literal string.
>>
>> Don't assume that a given name can't be linked to several different
>> species
>> entities.
>>
>> The names list just says, *what are the various legitimate names that this
>> species entity has had overtime.*
>>
>> It makes no assumptions that other species entities have not legitimately
>> used that same name string.
>>
>> Here is a very hypothetical (incorrect) example:
>>
>> http://lod.taxonconcept.org/ses/v6n7p now called *Puma concolor
>> (Linnaeus,
>> 1771))*
>>         => http://lod.taxonconcept.org/scinames/v6n7p_1001 => gni:505310
>>         => http://lod.taxonconcept.org/scinames/v6n7p_1002 =>
>> gni:12104361
>>
>> http://lod.taxonconcept.org/ses/kKOIv now called *Panthera leo*
>> (Linnaeus,
>> 1758)
>>         => http://lod.taxonconcept.org/scinames/kKOIv_1001 =>
>> gni:20753654
>>         => http://lod.taxonconcept.org/scinames/kKOIv_1002 =>
>> gni:12104361
>>
>> This would be the case where at one time it was thought that all large
>> cats
>> were one species called Felis concolor
>>
>> What this hypothetical example shows is that at one time these two
>> different
>> species were known by the
>> same literal name *Felis concolor* Linnaeus, 1771 (gni:12104361)
>>
>> Demonstrating the difference between a change in how these two species
>> were
>> seen vs. a simple mislabeling or misidentification.
>>
>> An old specimen might be labeled Felis concolor, but someone "Joe" may
>> choose to tag it in their own database as
>>
>> Label name "Felis concolor" interpreted by JoeSchmoe to be an instance
>> of *Panthera
>> leo* se:kKOIv
>>
>> What if someone decides that the Lion really should be in its own genus
>> (Leothera), but believes that all the specimens of Panthera leo are still
>> one species?
>>
>> Then *Panthera leo* se:kKOIv  => *Leothera leo* se:kKOIv
>>
>> Now the idea "this is a species"  is cleanly separated from the idea that
>> "this is a species in a particular genus".
>>
>> In my opinion, this is how it should have been done in the first place.
>>
>> 1) This is a species
>> 2) This species has this particular position in the tree of life
>>
>> Clearly two separate issues.
>>
>> Also:
>>
>> Need to know what the characters, definitive specimens, DNA barcodes etc,
>> are for a given species entity?
>>
>>  Puma concolor se:v6n7p <http://lod.taxonconcept.org/ses/v6n7p.xhtml>
>> *
>> *
>> Then click on namespaced version of the species entity URI in the line
>> above.
>>
>> - Pete
>>  _______________________________________________
>>
>> Taxacom Mailing List
>> Taxacom at mailman.nhm.ku.edu
>> http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>
>> The Taxacom archive going back to 1992 may be searched with either of
>> these methods:
>>
>> (1) http://taxacom.markmail.org
>>
>> Or (2) a Google search specified as:  site:
>> mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>
>
>
>
> --
> ----------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> GeoSpecies Knowledge Base
> About the GeoSpecies Knowledge Base
> ------------------------------------------------------------
>



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Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
GeoSpecies Knowledge Base
About the GeoSpecies Knowledge Base
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