[SEEK-Taxon] LinneanCore Group Work - PART 1

Richard Pyle deepreef at bishopmuseum.org
Thu Nov 11 13:42:30 PST 2004


Hi Jessie,

Many thanks for the long email, and I hope your vacation in NZ was
enjoyable, and your return to the "real world" not too overwhelming!

I'm especially glad to hear that you find the nomenclatural discussions on
the LC Wiki helpful.

> It would be really valuable for me and I guess others if someone
> could provide for zoology what Sally has for Botany in terms of examples.

I will try to get some examples up as soon as I can.  I am going nuts at the
moment with other work, so it's hard to find free time.  I will make a point
of trying to get some thorny Zoologial name examples up before I disappear
to Fiji in a couple of weeks.  I hope others on this list will be able to
provide Zoological examples as well.

> Although I was under the impression that at the Taxon
> Concepts/Names subgroup on the Saturday at TDWG there was general
> understanding of the goals and rationale for the TCS and how it
> intended to deal with nomenclature issues in addition to concepts
> issues within the one framework, I can see from the discussion
> that either I (and those present at the meeting) was wrong or it
> no longer seems to be the case amongst those contributing to the
> Wiki.

I have to say that I don't understand what you mean by this exactly.  As far
as I can see, the goals are the same as they were in Christchurch, and have
not changed in any fundamental way since then.  Yes, we have had some
lengthy discussions on the Wiki about the line between TCS and LC, and
you've alluded to comments by Gregor on this -- but in my many off-Wiki
conversations with Gregor it is clear to me that he agrees that there should
be no actual "concept" information (i.e., "AccordingTo" information, or
concept mapping) supported the LC schema.  I problem, I think, is much more
one of communication barriers, than real differences in understanding (at
least from my interpretations of the various discussions).

> During TDWG Linnean core was being pushed by some as a simple way
> of providing access to lists of valid names with Darwin core

I have to interrupt you here and ask what you mean by "valid names".  This
has at least two VERY different meanings, and the word "valid" when
associatied with "names" has caused tremendous volumes of misunderstanding.
The two main meanings of "valid" in this context are:

1) Names that were "validly" created in accordance with a relevant code of
scientific nomenclature, and are available for use as such by those codes,
with absolutely *NO* indication of whether the names are/should be currently
treated subjectively as junior or senior synonyms of some other name. This
is a (mostly) "objective" meaning of "valid", citing only the rules of the
relevant Code of nomenclature, and having NOTHING to do with taxonomic
concepts/circumscriptions.

2) Names that are subjectively treated as "valid" according to some
authority, in the sense that other names may be subjectively considered to
be junior synonyms of that name. This is a (completely) "subjective" meaning
of "valid", citing the opinion of any given taxonomic authority, and having
EVERYTHING to do with taxonomic concepts/circumscriptions.

[Emphasis added only to highlight points of contrast].

The nomenclatural community (and LC) is unambiguously focused on the first
of these meanings of "valid" names.

> being used as an analogy i.e. it would be a simple list of
> fields. That was basically what the name components from ABCD
> which were incorporated into TCS were and what I was informed was
> being discussed and re-considered by the Linnean core group to
> ensure the requirements of the nomenclator community were being
> addressed (and I was and am grateful that this work is being done).

I'm not sure exactly what you mean by "simple list of fields".  If, by
reference to Darwin Core, you mean a completely flat structure, then I
disagree completely.  Nomenclatural information is not flat, and a
"most-useful" schema to deal with purely nomenclatural information would not
be flat.  That the ABCD structure is flat is one of the reasons why it fails
to meet the data exchange needs of nomenclators (many of us also feel that
the separation of Kingdoms [=Codes of nomenclature] is a suboptimal approach
to representing nomenclatural information).  However, it is unambiguous in
my mind, and I *think* in the minds of most/all other members of this CC
list, that the fundamental "unit" of a LC instance (all of the fields of
which can be distilled down to the "Label" element of LC 0.1.4 -- which I
believe should effectively map 1:1 with the TCS "NameSimple" element) is a
"name" object, and most definitely NOT a concept object.

> It is unfortunate that following years of work by the ABCD group
> that there doesn't appear to be an ABCD representative
> contributing to the discussion - are you sure that you aren't
> overturning well reasoned and argued decisions on why things were
> designed the way they were?

I don't know who is, or is not (would, or would not be) considered as an
"ABCD representative".  Certainly any/all input from anyone directly
involved with ABCD would be most welcome. However, as far as I can tell from
reviewing ABCD v1.49, taxonomic elements exist only in the context of
identifcations of specimens, not as "name objects" with all of the
associated information relevant to nomenclators (almost all of which is
non-concept information).

> ALL agreed at the meeting that specimens or observations should
> be labelled with concepts_names (or concept GUIDs) not scientific
> names ( e.g. binomial plus original author) therefore I don't
> understand why is this even being given wiki space unless you're
> starting the modelling process from scratch again.

This touches on what I see as the *only* real *potential* point of
contention between the LC camp and the TCS camp.  I use the word "real" here
meaning not simply an artifact of miscommunication and/or misunderstanding;
and the word "potential" because I do not think that it necessarily must be
a point of contention.  That is, how to deal with the designation of type
specimens (particularly primary type specimens).  What makes this particular
topic unique is that it represents the only true intersection/overlap
between "name" information and "concept" information.  From one perspective,
Primary type specimens are an attribute of a name object in the form of a
Code-regulated typification event.  From the other perspective, a taxonomic
name is an attribute of a primary type specimen object (and therefore a
matter repating to concepts) in the form of an identification/determination
event.  This topic will undoubtedly need substantial further discussion.

> There seems to be confusion about what a transfer schema should
> do. To support the community at large it should not dictate how
> any application should be implemented, nor should it dictate what
> any database system must or must not contain, nor should it
> present a view of the world from only one of the community's
> perspective - if we want a community standard exchange format
> everyone must move from their own view/model of the
> problem/requirements but still be able to map their data to the
> schema to exchange their data. (Why I explained the different
> types of users/views of what concepts/names were in my presentation)

I'm not sure I understand why you think that anyone is in disagreement with
you on this (in the context of LC).  Like Sally, I think it would be helpful
if you could point to specific examples of where you think there is
confusion on this.

> Some of the discussion is about what a particular application
> i.e. a nomenclature tracking system or name resolution system
> should do and requires - I don't believe this should be encoded
> in the schema - it should be documented in the mapping from that
> database onto the schema or in the specification of the software
> design. This is still important and the work may still to be
> done....but not as part of a schema design.

Again, I guess I would need to know specifically what provoked this concern
of yours.  There has certainly been discussion about how the information
would be used and by whom -- which I think is absolutely fundamental to a
schema design discussion.  In many cases, it is possible to represent the
same information in different ways.  Both may be equally elegant solutions
to the information structure problem, but one may have advantages over the
other if you have a sense for how the information will most often/most
likely be used.

> Although the process of nomenclature is separate from the process
> of classification (and yes I'm co-author on a paper in Taxon
> arguing this), as soon as one considers the use of names - either
> by taxonomists or other biologists or even nomenclature
> specialists I haven't seen a convincing discussion or proposal
> that actually keeps names separate from concepts and I am even
> more convinced of this having talked to a wide range of potential
> users this past year. So let me re-iterate: people can't refer to
> concepts without names nor does a name exist without some kind of
> relationship to a concept.

I agree with you on the first part of your last sentence quoted above, but
not on the second part.  And I think this may well be the source of a lot of
the confusion and misunderstanding.  The only biological material that is
neccessary for a taxonomic name to exist is the implication that a primary
type specimen-individual (or syntype series-individuals) existed at one
time.  That is, the only "concept" that must exist in order for a name to
exist is a single individual organism.  To me, this is not a meaningful
"taxonomic concept" -- by anyone's definition. In other words, a
circumcription of one specimen is so unbelievely useless a concept, that it
really shouldn't be thought of as a concept at all.  "Aus bus Smith, 1949"
refers to a name object -- which means that Smith, in her 1949 publication,
complied with the relevant Code of nomenclature to make the name "Aus bus"
available according to the Code.  It is linked to the real world of biology
only through the primary type specimen(s). This is an altogether different
object from what is implied by "Aus bus Smith, 1949 sensu Smith 1949".  This
is a concept object, and it's definition has little to do with Codes of
nomenclature, and everything to do with the information that Smith 1949
included in her publication to identify the full scope of organisms (over &
above the primary type specimens) that exist/have existed/will exist in the
real world that are encompased by the *taxonomic concept* that Smith, 1949
had in mind.

These two different object units -- the name object, and the concept
object -- need to be handled separately.  LC needs to include the
publication details of the "Smith 1949" publication, because there are of
*nomenclatural* importance in identifying the nomenclatural act that
established the name "Aus bus".  TCS needs to *separately* include the
publication details of the "Smith 1949" publication, to place within the
"AccordingTo" structure, to show that we mean the name "Aus bus Smith 1949"
according to the usage of Smith 1949.

I know you know all of this, but my point is that what may *appear* to be
overlap between LC and TCS (e.g., both needing to point to the publication
details of SMith, 1949), are in fact quite different pieces of information,
and do not represent overlap at all.

Unfortunatley, I've run out of time to read/respond to the rest of your
email, so I'll send this out now for your consideration, and will address
the rest later tonight.

Aloha,
Rich





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