Part 1 (was: rankless nomenclature)

[Richard Pyle]

Folks,

I initially had no intention of becoming drawn into this discussion as much
as I have.  I also sense that maybe at most a couple dozen subscribers to
this list are really passionately interested in this topic (count me among
them), and the rest of the 1,300 or so subscribers are probably becoming
increasingly bored and perhaps frustrated with their cluttered email
inboxes.

I do feel the need to clarify a couple of points, however; and to avoid
further misunderstanding, I'd like to post some further elaborations on my
own perspective.  For those couple of dozen of you, please read on.  For
everyone else, please don't hesitate to press 'Delete'. It's a long one. In
fact, it was so long that I had to break it into 2 parts (in addition to the
4-message-per-day limit, there is also a 250-line-per-message limit).

Doug Yanega wrote:

> I get the impression that Richard was suggesting that we split the taxa
> among the codes - i.e., butterflies go under the PhyloCode *exclusively*,
> and other insects (including moths) go under the Linnaean system
> *exclusively*.

Well, actually no.  First of all, my use of Lepidoptera was only to provide
an example of a taxonomic group outside of the vertebrates, that is
relatively well known, and is conducive to fruitful phylogenetic
investigation.  Secondly, I most definitely do NOT advocate dividing up the
diversity of critters & weeds into "thems that are named by Linnaean names",
and "thems that are named by PhyloCode names".  I don't even like this sort
of division at major groups (e.g., critters vs. weeds vs. microbes), let
alone among orders of insects.

We have an existing Linnaean system that encompasses all manner of life.
Those names are used by a wide variety of people, for a wide variety of
purposes.  For most of those purposes, the 250-year old system works
marvelously, and many feel that we shouldn't do anything drastic to disrupt
it. Within biology, however, there is a discrete (and relatively recent)
subset of researchers whose interests lie in elucidating phylogenies. The
assumption has always been that these researchers should use the language of
Linnaean classification to communicate with one another about their
hypotheses of phylogenetic relationships. This assumption is an intuitive
one, if you start with the premise that the hierarchy of Linnaean
nomenclature should represent a strict reflection of the phylogenetic
hierarchy resulting from historical evolution. However, as close as the
Linnaean system comes as a useful tool for mapping phylogenies (again I
point to Gould's essay), modern systematists have become painfully aware
that the traditional Linnaean system does not provide adequate resolution or
flexibility for optimally communicating phylogenetic hypotheses.  Moreover,
in trying to force-fit discussions of phylogenetic hypotheses within the
Linnaean system, there has been a tendency towards instability as names have
been changed and re-changed to reflect the phylogenetic hypothesis du jour.
What we're left with is phylogenetic systematists frustrated with trying to
use an old language to communicate new concepts (the foundations of which
post-date the inception of the old language); and we also have a vast array
of other biologists and amateur naturalists who are, to a greater or lesser
extent, quite aggravated by the trend towards instability of names caused by
revolving cladistic interpretations. The current controversy exists because
we have two groups of researchers, with somewhat different goals, playing
"tug-of-war" with the Linnaean classification system.

In short:  Nobody is happy.

What to do?

It seems to me that what we need is a separate language tool; one that can
be used primarily by phylogenetic systematists to communicate ideas about
discrete nodes in their hypothesized relationships, without disrupting the
stability of existing biological language tool of Linnaean classification.
Cladistic systematists would have the freedom to express their ideas about
phylogenies using a tool designed explicitly to fulfill their needs.  The
rest of the world's biologists can go on using Linnaean classification they
way they always have, to fulfill the needs this system has always fulfilled,
without suffering the trauma of cladistically-induced nomenclatural
instability.

In short:  everybody gets happy (except those who thrive on perpetuating
controversy).

PhyloCode seems to me to be a pretty darn good candidate to be this new
tool. I have to confess that, until last night, my comprehension of it was
limited to what I have gleaned from this list, and from brief discussions
with colleagues.  However, yesterday I downloaded the draft PhyloCode and
read over most of it while I awaited David Letterman. It seemed like an
extremely well-thought out concept, and is fairly easy to comprehend for
anyone with a basic understanding of cladistic approaches to systematics
(especially for those familiar with ICZN/ICBN).  I would strongly recommend
that anyone truly interested in this issue take the first step and read it.

> >Maybe 25
> >years from now obtaining a complete genome of an organism will
> be as simple
> >as dropping a tissue sample in a portable "Mr. Genome" machine
> and pressing
> >a big blue button.
>
> Even if we could do that starting *today*, that would leave somewhere from
> 10-50 million species we would have to find DNA-containing specimens of,
> identify, and drop into the Mr. Genome machine. Let's be really generous
> and say we can get our hands on an average of 10 species each day. That's
> still a minimum of 2,739 years of work ASSUMING we *have* a Mr. Genome
> machine handy.

First of all, how can you describe "10 species each day" as "really
generous"?  If "Mr. Genome" was mass-produced and could attach to any
desktop or laptop computer throughout the world, why couldn't we do 10-100
species per researcher per day, multiplied by 1,000 researchers?  Also, why
do we have to assume that the entire complement of biodiversity must be done
in order for phylogenetic interpretations to be stable and convincing? I
don't mean to come off as some wide-eyed idealistic chap with his head in a
fantasy cloud here -- anyone who knows me well, knows I am about as
pragmatic as they come.  But at the same time, we have to keep in mind that
technology accelerates, and what seems impossible today, might seem trivial
a few years hence.  If we lock ourselves within the box of today's paradigm,
then we're left stumbling when that paradigm shifts. If we want to lay a
solid foundation for the future, we need to keep thinking outside of that
box.

> Worse still, when
> you start doing sequencing, you discover that there are all sorts of
> cryptic molecular "species" that mean instead of 10-50 million unnamed
> taxa, you've got to contend with 100-500 million.

Indeed, with whole-genome comparisons we'd likely discover that essentially
no two sexually-reproducing organisms share precisely identical genomes, so
perhaps we should name 'em all?  Now we're talking trillions (quadrillions?)
of names.... My point here is that we will obviously encounter genetic
diversity within assemblages of organisms that fall under a single species
"umbrella".  Why does recognizing and acknowledging this diversity compel us
to name it? I'm not convinced that we will ever discover a "true",
objective, natural definition of "species". Sure, some of the lines we draw
will follow clear natural contours, but inevitably some delineations will
require arbitrary (and artificial) threshold criteria. That's why Pyle's
fundamental definition is: "A species is what a taxonomist says it is." (It
was with a mixture of pride and humility that I discovered Darwin had beaten
me to the punch: "Hence, in determining whether a form should be ranked as a
species or a variety, the opinion of naturalists having sound judgment and
wide experience seems the only guide to follow.") Of course, Pyle's
elaborated definition is: "A species is what a community of taxonomists
agree it should be." (Alas, Darwin scooped me again: "We must, however, in
many cases, decide by a majority of naturalists, for few well-marked and
well-known varieties can be named which have not been ranked as species by
at least some competent judges.")  My point is, we will only increase the
number of species by 10-fold if we decide such fine-scale division serves
our needs as taxonomists best.

But, I digress...

(TO BE CONTINUED IN PART 2)


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."