Part 2 (was: rankless nomenclature)

[Richard Pyle]

(CONTINUED FROM PART 1)

Doug Yanega wrote:

> You really think it's
> practical to get sequences and construct phylogenies for that many taxa?
> Me, I think we shouldn't waste time arguing about new codes until
> we've got names on all these critters.

...don't forget the weeds.... :-)

But seriously, no, it obviously is not practical to get sequences and
construct phylogenies for that many taxa **under the current paradigm**.
But I'll be dead in 50 or 60 years, and my kids will be dead 30 years later,
and their kids will be retiring as they watch the next generation of
taxonomists take over.  The optimist in me assumes that Homo sapiens will
continue to thrive, and that it will continue to be fascinated by the
diversity of life it shares the planet with, and (this requires additional
optimism) that there will still be substantial diversity left to be
fascinated by. It's easy to say that we should wait for then to develop a
more phylogenetic approach to taxon classification; however, why should we
wait? Development of such a system requires only that we have a good
understanding of the process (i.e., that most life diversity arises from
evolutionary mechanisms that produce phylogenetic pedigrees of form) -- we
need not have complete genomes of every species on the planet, nor even most
species (nor any species, really). All we need in order to develop and start
"beta-testing" the system is a few phylogenetic hypotheses (biology seems
replete with those), and also some phylogenetic systematists eager to be
freed from the "bondage" of the Linnaean classification system (I'm guessing
we've got a few of those as well).

> Again, if you want to adopt the PhyloCode for select taxa, I guess I
> wouldn't have a problem with that. I can live with the ICBN being
> different
> from the ICBN, I suppose I could just as easily adapt to the idea of fish
> and mammals and birds, etc. being under a different system from insects.

You may not have a problem with that, but I certainly would.  For example,
who would decide which groups are governed by each system?

> But you can't use two systems for the SAME taxa

This, I believe, represents the crux of our disagreement. Why can't we have
two different systems of nomenclature, when they serve different functions?

There seems a great deal of concern that two systems would be confusing.  As
I already asked in a previous message: confusing to whom?  I can't imagine
why the new system would be used by anyone who doesn't already understand
it.  What publications besides those dealing explicitly with phylogenetic
research would ever include names from a system such as PhyloCode?  I would
imagine that the rest of biology would go on using the Linnaean names as
they always have, and would be all the happier without the
cladistically-induced instability of late. The only ones who would actively
use the new system would be the ones who already understand it intimately,
and need it as a tool to express their phylogenetic ideas.  Of course, it
would certainly be a wise move for those who deal in Linnaean nomenclature
to at least understand how to read publications that make use of the
PhyloCode system.  Who knows -- perhaps some insight generated from
phylogenetic analyses would inspire even a conservative non-phylogenetic
taxonomist to consider altering the established Linnaean classification (but
only after cautious and reasoned interpretation of the stability and
reliability of the proposed phylogeny). The important thing is that we need
to view PhyloCode not as a competing system that would "litter the
nomenclatural landscape" (to paraphrase Ken Kinman's earlier post), but
rather as a separate system, designed for a different and independent
function.

There is one caveat to this:  we'd have to make sure that PhyloCode names
don't simultaneously qualify as Linnaean names under the ICZN/ICBN/etc.  We
wouldn't have to worry about species names (at least within Zoology - I
don't have copies of the other codes), not only because PhyloCode does not
plan to treat species initially, but also because, even if/when it does, it
likely won't treat them as binomials.  However, I'm not so sure about genus
and family names.  I would assume that because PhyloCode is explicitly
"rankless", there would be no risk that a PhyloCode name would also qualify
as a Linnaean genus- or family-group name.  A quick look through ICZN 4th
edition last night, however, left me without an explicit exclusion for
rankless names.  Does anybody know for certain whether or not rankless
monomial PhyloCode names would be excluded from consideration as available
Linnaean names?

Philip Cantino suggests:

> A name that is accepted under the PhyloCode but was
> published without any indication of its rank cannot be a correct name
> under the ICBN.

...but I couldn't find anything concrete after a quick look through Chapters
4, 7, 8, or 9 of ICZN. Such an exclusion should be well-founded before
PhyloCode goes into practice.

That caveat notwithstanding, I can't understand why any of us who practice
non-phylogenetic systematics (i.e., the old-school Linnaean taxonomists
among us) would object to a system that allowed us to take back Linnaean
nomenclature, away from the evil cladists who hijacked the system for their
own dubious deeds... (tongue planted firmly in cheek) Hell, we should be the
ones pushing *hardest* for it!

On a similar line of thought, Doug Yanega raised the following issue:

> Let's assume for a moment that both codes are up and running, side by
side.
> A PhyloCode taxonomist publishes a paper in which new names are created.
IS
> IT POSSIBLE that these new names can, on occasion, be valid under the
> PhyloCode and NOT valid under the ICZN? If there is any way this can
> happen, what then is to prevent someone else from taking those same names
> and taxon groupings and publishing them again in a manner compliant with
> ICZN rules, thereby establishing them as if he/she were the original
> author?

First of all, as I mentioned above, I would think not only that it be
"possible" that PhyloCode names not be valid under one of the other codes,
but indeed prevention of such cross-validity should be *mandatory* (as
outlined above). If I understand Doug's concern, it comes down to an issue
of scientific ethics.  That we still have taxonomists with marginal ethics
is clear (case in point:  the 2nd Coelacanth species). But I think that is a
perpetual risk regardless of the code or set of codes we choose to recognize
(see case in point above).  Granted, publication of PhyloCode names might
inspire unethical sorts to claim those same names under one of the Linnaean
codes, more so than if the PhyloCode names had never been published; but I
have to believe that professional "karma" would limit the frequency of such
cases to a trivial level.

Doug notes further:

> Along with this, if Linnaean taxonomists adapt an original
> PhyloCode name and alter its meaning in a way the PhyloCode would not
> permit, can't this lead to confusion in the future, or do PhyloCoders
> ignore actions taken by ICZNers that aren't consistent with their rules?

Except for names initially erected under Linnaean codes that are
subsequently converted to registered PhyloCode names, I would think that the
PhyloCode system would ignore reverse conversions to the same extent that
the Linnaean codes would ignore new PhyloCode names. One of the interesting
things that sets the PhyloCode names apart from Linnaean names is the
concept of "registration".

It would seem to me that the main objection to PhyloCode would come from
cladistic systematists who don't want to have to learn a new system, or who
feel that a single system can (and should) accommodate the needs of all.
Their preferred approach is to continue modifying the Linnaean system so
that it suits the needs of the cladist, while still preserving functionality
for the "eclecticists" (e.g., Wiley's 1979 system, Kinman's system, etc.).
Ken Kinman has provided compelling rationalization for this approach as a
favorable alternative, as have others on this list and elsewhere. The idea
is certainly appealing in that it maintains a single unified system shared
by all of biology.  I also like the idea of distinguishing the
"phylogenetic" codes from the "Linnaean" names by their form, so that the
distinction is self-evident (inclusion of numerals also avoids the caveat
concern mentioned above), and "trimming the fat" off the proliferation of
ranks beyond the "basic" ones would probably make life a lot easier for
future taxonomists (the current taxonomists would probably have some
reservations, though).

But my concern about this approach is that we may not resolve the
controversy, but rather merely shift its focus.  While I certainly like the
idea of a "best of all worlds" approach, my experience tells me that such
efforts generally foster a situation in which almost nobody is satisfied,
rather than everyone being satisfied. We also still have the problems
associated with phylogenetic schemes that cross the "basic rank" Linnaean
landmarks. Maybe now I'm the one playing too much the role of pessimist, but
looking at how long some of these basic ideas have been around without
achieving widespread implementation, I have to wonder if this direction is
really the best one to move in (keeping in mind Pierre Deleporte's
counterpoint to this, which is that the time for such a shift in thinking
may finally have arrived).

Richard Jensen wrote:

> A key here is to
> provide access to information in a stable and predictive way. A rankless
> classification has the same goal, except that it is designed specifically
> to reflect phylogenetic relationships.  So, I suggest that Richard Pyle
> consider history.

I assume that by "history", you mean the previous suggestions by others
along the same lines as what I am suggesting (as outlined in your ensuing
paragraph)? I hope I didn't seem to imply that my suggestions are in any way
original. It certainly wasn't my intent to imply as much.  I only stepped
into this conversation because it appeared to me that there was some
miscommunication going on, and I hoped to try to add my own perspective
(lengthy though it may be) as a way to perhaps add some clarity. I fear
however, I may have only muddied the waters.....which leads me to my final
point:

In my earlier postings, I used the term "numenclature" (contrasted with
"nomenclature") to represent a system like PhyloCode, which seeks to
represent true phylogenies.  My cutsie term was intended to underscore how
phylogenetic systematics derives classification schemes from the
mathematical process of parsimony analysis, whereas the traditional Linnaean
system was based more on informed qualitative interpretation of biological
patterns.  Philip Cantino rightly pointed out to me the concern that such a
term could perpetuate the misconception that PhyloCode uses numbers, rather
than Latin words, to represent taxonomic names (which, of course, it does
not). I hereby retract my use of that fabricated term.

Aloha,
Rich

Richard L. Pyle
Ichthyology, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org
"The views expressed are the author's, and not necessarily those of Bishop
Museum."