Fwd: Re: rankless nomenclature

[Richard Pyle]

Thomas Lammers wrote:

> At the same time, I will assert that not every new idea generated by the
> theoreticians is a good one.  In my opinion, I do not think the PhyloCode
> will be able to achieve its stated goals.  I think it will be a source of
> confusion, not only within the taxonomic community, but in our user
> audiences at large.  Do we seriously think that confusion will be reduced
> by having TWO co-extant systems of nomenclature?

As it is now, the Linnaean system is being contorted into something that it
was neither intended to do, nor is optimally designed to do (i.e., reflect
details of hypothesized phylogeny among organisms).  Following the current
path, as phylogenetic systematics expands (and with increasing molecular
technology, you can be sure it will), this contortion will increase and (I
fear) the intensity of the present controversy will only escalate.

We, as a community of biological taxonomists, face a decision among three
options:

1 - Abandon efforts to develop a new foundation of communication (e.g.,
PhyloCode) to be used as a tool among phylogenetic systematists, and
continue to try to "speak" phylogenetics using the "language" of Linnaean
nomenclature.

2 - Abandon the Linnaean system altogether, and make a wholesale switch to a
new system such as PhyloCode.

3 - Accept that each system serves different needs, and allow the
development of something like PhyloCode in parallel to maintaining the
Linnaean system.

Option 1 essentially means continuing down the path we currently find
ourselves on.  I fear that this already-rocky path will only become more
tumultuous while phylogenetic analysis expands as a distinct branch of
biological investigation. Does anyone really believe that phylogenetic
analysis will prove to be a passing fad? That it will disappear altogether
eventually? Of course not -- this would be akin to assuming that the study
of evolution will eventually vanish. Can the existing Linnaean system
continue to be contorted to fulfill the needs of phylogenetic systematists
indefinitely without massive instability?  I doubt it -- phylogenetic
systematics is still relatively young compared to taxonomy as a whole, and
look at the havoc already wreaked (in the form of this ongoing and
increasingly passionate controversy).  What we're hearing from the people
actually involved in phylogenetic research is that the Linnaean system
simply won't meet their needs, and when they try to use it in a way that
does meet their needs, feathers get seriously ruffled among the more
classical taxonomists. Consequently, the controversy grows.

I think even the most staunch supporters of a PhyloCode approach would agree
that Option 2 is overly idealistic.  Simply abandoning a 250-year legacy
that has served vast numbers of biologists of different disciplines would
be, well, foolhardy (to put it mildly).  Perhaps decades hence, when we're
at the point where technology has advanced to the stage of immediate
whole-genome comparisons at the press of a few buttons, we might look back
respectfully on Linnaean taxonomy as a remarkable tool that served the needs
of vast hoards of biologists and naturalists amazingly well; but as a tool
which, like so many other endeavors rendered unnecessary by
technology-induced paradigm shifts, has run its course. Having witnessed the
accelerative nature of technology, I am confident we will one-day reach that
state - maybe even within my lifetime.  But clearly we're nowhere near that
Utopia right now, so abandoning Linnaean nomenclature altogether would yield
unnecessary and excessive chaos.

That leaves us with the third option, about which Thomas Lammers raises very
justifiable concerns:

> Just think about what
> things were like a century ago when we had the American Code and the
> International Code as "alternatives".  We're STILL trying to clean up the
> mess THAT bad idea left behind!  What is USDA, F&WS, APHIS, TNC,
> etc. going
> to make of this?  "Well, under the PhyloCode, this family is
> called ABC but
> under the ICBN it's called XYZ."  Does this make ANY sense to anyone who
> doesn't have a vested interest in the thing?  I understand that you and
> others have put a lot of hard work into this, and would dearly love to see
> it fly, but it is still a bad idea for systematics.

I can state emphatically that I do NOT have a vested interest in PhyloCode.
My business is alpha taxonomy and new species discovery, not reconstruction
of phylogenetic histories (my PhD thesis notwithstanding).  Nevertheless, I
do see some sense in maintaining two parallel systems of nomenclature (or,
as I termed it earlier, one system of nomenclature, and one system of
numenclature). And, I also see how confusion can be minimized, if not
eliminated.  The alternate codes you reference represent a different
situation:  two tools attempting to solve the same problem.  I see the
current system as two tools addressing distinct problems.  One problem is
how we, as human beings, communicate with each other about critters & weeds
(I apologize for consistently excluding microbes, but I simply lack
sufficient understanding of microbe taxonomy, and the unique problems
therein, to confidently comment). This is the problem that the organizations
you cited are primarily concerned with (USDA, F&WS, APHIS, TNC, etc.).  This
is also the problem that concerns ecologists, ethologists, physiologists,
and a whole suite of other biologists, as well as amateur naturalists of all
sorts. That problem is solved admirably by the Linnaean system, so those
folks will continue to use Linnaean nomenclature as they always have.

A second problem is how a very small subset of human beings (phylogenetic
systematists) will effectively communicate with each other about ideas
concerning phylogenetic relationships among those critters & weeds.  When
cladistical approaches to taxonomy first started gaining widespread
implementation, I harbored a lot of resentment to the entire cladistic
community for, what was my impression, the "hijacking" of Linnaean
nomenclature for a very specific scope (i.e., strict reflection of
evolutionary lineages); stability be damned.  But a numenclatorial system
such as PhyloCode gives us an "out" to this mess -- it provides this subset
of human beings with a structured language that helps increase communication
efficiency, without pissing-off (pardon my American) the rest of the
biological community, who find great value in the Linnaean system as a
useful communication tool for their needs.

The reason I think confusion can be mitigated is that, for the short-term at
least (next decade or two), the PhyloCode approach will likely remain
primarily a tool for phylogenetic systematists to advance their field.  Most
people who use the Linnaean system don't really care that much about the
detailed phylogenetic relationships, and therefore will have no need of
learning the system.  I don't ever envision anyone having to explain to
someone else outside of the field of taxonomy, "Well, under the PhyloCode,
this family is called ABC but under the ICBN it's called XYZ."  The
confusion will be mostly avoided, because the language will only be spoken
among those who understand it fluently.  I also think the system will be
extremely useful to those of us who consider ourselves more "classical"
taxonomists, even if we never plan to play the phylogenetic game. As I said
in a previous message, most of us who do classical taxonomy *do* want our
nomenclatorial schemes to reflect the evolutionary histories of the
organisms we study.  Many of us, however, don't want to be completely and
strictly bound to   rules of monophyly in establishing our named
hierarchies.  If one species in the middle of a genus-level clade of
otherwise mostly homogenous species exhibits amazingly unique and divergent
apomorphies (e.g., as by invading a novel environment), we want to recognize
its uniqueness among the clade by affording it its own genus name (heresy, I
know...). In addition, many of us are skeptical that phylogenetic approaches
are reliable enough, that we should trust them all at face-value.  I'm not
suggesting that more classical approaches to taxonomy are any more
"reliable", but the record shows that they have tended to result in much
more stable nomenclature.  I think that the stability issue is the one that
ultimately underlies the resistance to a phylogenetic system, and I don't
think these concerns are unwarranted.  But despite all of this skepticism,
we'd be fools not to pay close attention to phylogenetic studies of
organisms within our respective fields of interest.  Phylogenetic studies
can reveal a lot (especially if done well) that offers great insight to
those of us more concerned with Linnaean nomenclature. It would behoove us
to learn the new language.

In summary, I think confusion can be largely avoided if the stewards of
Linnaean nomenclature are careful enough to respect stability of names when
publishing their nomenclatorial assertions.  Establishing something like
PhyloCode frees those systematic researchers interested in investigating
postulated phylogenetic relationships from the burden of nomenclatorial
stewardship, allowing nomenclature to remain stable while pursuing their
interests using the language of numenclature.

If I'm not mistaken, this was Philip Cantino's point when he said:

> >   The PhyloCode will not
> >replace the other codes; it will complement them, making the work of
> >phylogenetic systematists a lot easier.  People who do not find it
> >useful are welcome to continue using the rank-based system.
>
> Yeah, I've heard THAT before.  Suppose I'm wrong; suppose the PhyloCode
> does survive and flourish, instead of joining Camp & Gilly's biosystematic
> nomenclature and the American Code in the dustbin of history?  Will we see
> a time not too far off when reviewers reject a manuscript for publication
> because the author refuses to utilize the PhyloCode?  Will we be told
> "You're not doing science" if we swear fealty to the ICBN?  Will grant
> proposals be declined because the work will not be published with a
> PhyloCode-based classification?

These, I think, are legitimate concerns, but they deal with issues that are,
for the most part, dictated by the taxonomic community as a whole.  My hunch
is that these fears will not be borne out - especially if the taxonomic
community as a whole recognizes the distinct value of the two systems as
serving distinct and separate purposes.

> I stand by my case: Our ability to accurately infer phylogenies is
> problematic.  We are not able to confidently recover the true phylogeny of
> a group.  We can only construct good hypotheses subject to additional
> tests.  Until such time as our confidence in the phylogenies we create
> exceeds 90%, a PhyloCode is premature.

Maybe this is true for life on Earth as a whole, at the present time ... but
certainly there are some well-documented groups for which a system such as
PhyloCode is NOT premature (birds, mammals, and a vast diversity of
lower-rank groups).  It makes sense to me that investigators interested in
sorting out those phylogenies with high confidence should be encouraged to
do so.  Providing them with a communication tool like PhyloCode allows them
to continue their endeavors without overly disrupting Linnaean nomenclature
in the process (as when phylogenetic hypotheses are modified based on new
information and new taxa), to the aggravation of folks like you and me.
Eventually, when the poorly-known groups do get "filled-in" (and I have to
believe they ultimately will), then we'll all be thankful for the efforts of
the phylogenetic pioneers who laid the groundwork for what will likely prove
to be the classification scheme of the future.

My basic point in all of this is that our ability to confidently elucidate
phylogenies will only continue to increase.  Eventually, we'll probably want
the primary classification scheme to be one that precisely reflects those
elucidated phylogenies.  The problems with immediate implementation of such
a scheme are mostly practical in nature (e.g., we don't yet have all the
species, the state-of-the-art in phylogenetic analysis is not yet effective
enough to be highly stable, there aren't enough taxonomists to spend time
working out the phylogenies, because the current techniques are laboriously
tedious and time-consuming, etc.).  None of these limitations are
fundamental laws of nature - they can all be overcome with adequate time and
funding.  I think the transition is inevitable in the long run, and I think
the key is to make the transition gradually, rather than abruptly. This
means that the new system needs to be developed, practiced, and
ground-truthed over time, without dissolving or disrupting the old system
(i.e., concurrent systems).  Now seems as good a time as any to commence
this long-term transition.

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 authors, and not necessarily those of Bishop
Museum