[Taxacom] A little more on Species Entities

Fri Oct 2 03:22:01 CDT 2009

Hi Pete,
Thanks for that - it makes clearer where you are coming from. I urge you to rethink your tendency to want to divorce species names from phylogenetic hypotheses, however! In retrospect it may have been more sensible to make species names phylogenetically neutral, but we have a 250 year history of the binomial system behind us, and there just ain't no going back! Too late, we are stuck with it! Nomenclature has to be governed by rules (the Code) or things would be even worse! Sure, the Code has nothing to do with biology per se, but it is a "necessary evil", like taxes!
Also, I agree that money is necessary to solve the problems, but it is certainly NOT sufficient! We can't just "throw money at the problem". We can't solve everything in one swoop. Ideally, we all need to work together to organise information one small group at a time. Instead of just saying "we want to know everything" about a taxon, we need to prioritise what we really want to know, and realise that not all information is equally important. We need to be able to cope with imperfect/incomplete/fuzzy knowledge, and, for example, just accept that Aedes triseriatus and Ochlerotatus triseriatus are two names currently in use for the same biological entity, depending who you talk to. Most importantly, when aggregating information, we must realise that if we can't verify it, then we can't rely on it. There is an awful lot of published misinformation out there. It isn't entirely irrelevant here to mention what I consider to be the single biggest mistake of the Wiki system. The idea behind it was that since there are lots of different opinions out there, if you let everybody have their say, then it will somehow all cancel out to the truth! The truth is that it will all just add to the chaos! Similarly, a database that uncritically tries to collate all available information on a taxon is likely to suffer from the same chaos. We need to pick and choose according to our specific requirements, but the notion of an overarching database to satisfy all possible requirements is about as sensible as the idea behind a Wiki! Having said that, I am working hard to keep Wikispecies as tight and solid and yet as simple as possible, and the big advantage of it is that what is there is there and working already, while we wait for the "ultimate database" to materialise - it could be a long wait ...
Cheers,
Stephen
________________________________
From: Peter DeVries [pete.devries at gmail.com]
Sent: Friday, 2 October 2009 8:51 p.m.
To: Stephen Thorpe
Cc: taxacom at mailman.nhm.ku.edu
Subject: Re: [Taxacom] A little more on Species Entities

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<mailto: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<mailto:pete.devries at gmail.com>]
Sent: Thursday, 1 October 2009 9:06 p.m.
To: Stephen Thorpe
Cc: taxacom at mailman.nhm.ku.edu<mailto: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<mailto: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<mailto:taxacom-bounces at mailman.nhm.ku.edu> [taxacom-bounces at mailman.nhm.ku.edu<mailto:taxacom-bounces at mailman.nhm.ku.edu>] On Behalf Of Peter DeVries [pete.devries at gmail.com<mailto:pete.devries at gmail.com>]
Sent: Thursday, 1 October 2009 7:59 p.m.
To: taxacom at mailman.nhm.ku.edu<mailto: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
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Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
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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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