Message 2004-06-0009: Anti-Phylogenetic Comments in The Botanical Review (part 2)

Thu, 10 Jun 2004 22:04:50 -0700 (PDT)

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Date: Thu, 10 Jun 2004 22:04:50 -0700 (PDT)
From: "Jaime A. Headden" <>
To: List PhyloCode <>
Subject: Anti-Phylogenetic Comments in The Botanical Review (part 2)

Carpenter, J.M. 2003. Critique of pure folly. _The Botanical Review_
69(1): 79-92.

“A critique of the draft PhyloCode is presented. Its stated goals cannot
be met by the proposals in the current draft, which also fails to uphold
its stated principles. Its internal contradictions include a cumbersome
reinvention of the very aspect of the current Linnaean system that
advocates of the PhyloCode most often decry.”

This paper offers a rundown of his problems with the Phylocode rule by
rule. Well, selective rules. But first, issues of stability and (again)

  “A name is used in two different senses if it does not refer to the same
set of taxa in two applications; that is instability, in taxonomy and in
language. By contrast, if a name is used in one case, say, for a family,
and another for a subfamily, but in each case circumscribes exactly the
same included taxa, that is trivial for communicating the meaning -- the
content -- of the name. Any experienced taxonomist understands this, but
advocates of the PhyloCode completely fail to grasp this point.”

“[A]dvocates of the PhyloCode have ignored the actual measure of taxonomic
stability in terms of content,” by which is meant, that undergoing a
conversion from traditional to phylogenetic system and name alterations
(rather than coining), it was “demonstrated” (also by Kojima) that more
changes occur in converting a relationship (A ((B, C)(D (E, F)))) into
phylogenetic terms than into traditional terms, whereas it is ignored the
opposite would occur for a “comb-like arrangement” where (A (B (C (D (E,
F))))) [this example requiring 5 names for each “family,” and the
necessary 1-3 superfamilies to group them all as required under the ICBN
and ICZN, not to mention suborders, orders, etc. So, while Carpenter
criticized phylogenetic nomenclators for one thing, he ignores the system
that de Quieroz used to prove his point, and vice versa. Mutual values of
change between systems; neither has a foothold on the other. Yet THIS is
what it thought by the authors in this volume as “stability.”

  “Any hierarchy is inherently ranked, whether a cladogram or formal
Linnaean classification. The named categories in a Linnaean classification
convey information on exclusivity: Taxa at the same rank are not included
within one another; taxa at higher ranks are not contained within taxa of
lower ranks. This information is immediately communicated in a given case
simply by stating the ranks or, even more efficiently, by the use of
standardized suffixes for family-group categories in the classification
and binominal nomenclature for species. The suffixes are relatively few in
number, and readily learned, as is the convention of binomina, even by
nonspecialists or the general public. In contrast, in so-called
phylogenetic rankless classifications no indication of relationships of
taxa is communicated by the names at all. Reference to a cladogram is
required to communicate any information on group membership, thus a
so-called phylogenetic classification would be understood and used only by

I can easily call comment on how I would need to be stupid and silly for
the ranked system to make sense to me. I am, afterall, a specialist in
another group altogether different than botany. But then, who will be
reading my papers? Geochemists interested on the arguments of cranial
kinesis in a group of theropods whose number totals less than 100
specimens world-wide? Indeed, a cladogram is usually neccesary for most
specialists IN the group to understand character transformation and
evolutionary relationships. The conveyance of Suborder Theropoda to me is
virtually meaningless, because it connotes NO special data on the NUMBER
of species. Indeed, the Class Aves is included within this Suborder, but
not ONE systematist has offered a change in ranks that has ever made it to
print. At this point, the rank system, and the accompanying easily-learned
chart and mnemonic (which I ignore because I know the order anyway), are
virtually useless to me when I am studying the relationships of organisms,
not how to address them to the “stupid, silly” public. -- Now, that’s a
good boy, eat your bread; you couldn’t comprehend the nature of the bread
anyway, but you can eat it, can’t you? -- It seems a proxy to stay with
something familiar.


  “ ‘1. Reference. The primary purpose of taxon names is to provide a
means of referring to taxa, as opposed to indicating their characters,
relationships, or membership.’
As if taxa can be referred to without some indication of attributes or
membership, let alone the fact that for clades to be specified there has
to be some indication of relationships.”

A definition. A name is a reference to a clade; the clade is determined by
it’s definition; it’s membership by its application to the cladogram; the
characters by the common features of the membership, or of the basal
members of the group named.

“ ‘2. Clarity. Taxon names should be unambiguous in their designation of
particular taxa. Nomenclatural clarity is achieved through explicit
It is scarcely unambiguous if a name does not change but its meaning
(content, or ‘designation of particular taxa’) does.”

They would only be ambiguous if one felt the name was equal to its content
at time of naming; if this is not so, there is no ambiguity. The
definition makes the clade VERY clear from that point on, even though
membership is only hinted at by one or two species as specifiers.

“ ‘3. Uniqueness. To promote clarity, each taxon should have only one
accepted name, and each accepted name should refer to only one taxon.’
Names can scarcely be unique if they can apply to taxa differing greatly
in content.”

This being a big difference between the two systems. The content defines
the use of the name … yet in the traditional system, you can move a name
around, change it -- what-have-you -- as you see fit, depending on what
you think it should apply at. There are no criteria for the determination
of which name goes to which clade, as there shouldn’t be, because a name
only labels a point in the tree one wishes to bring attention to. The
name, itself, is unique, and never changes, even if content does. This

“ ‘4. Stability. The names of taxa should not change over time. As a
corollary, it must be possible to name newly discovered taxa without
changing the names of previously discovered taxa.’
It is scarcely stable if names do not ‘change’ while at the same time
changing greatly in content.”

This is similar to point 3. Content is married to the affixes and rank, so
the name is unstable in traditional taxonomy. YET, content is never
specified. No one has, to my knowledge, been able to get many different
workers to agree that the family rank refers to a certain number of
genera, especially since it is mandatory for there to be a family
including a genus, no matter what.

“‘5. Phylogenetic context. The PhyloCode is concerned with the naming of
taxa and the application of taxon names within a phylogenetic context.’
But the first principle stated that taxa are to be referred to without
indication of relationships.”

Yeah … the problems of grasping the separation of these qualities to
people who feel they are bound at the hip.

“ ‘6. The PhyloCode permits freedom of taxonomic opinion with regard to
hypotheses about relationships; it only concerns how names are to be
applied within the context of a given phylogenetic hypothesis.’
True, but it is precisely how those names are applied that is the source
of the instability of the PhyloCode names relative to the Linnaean system
(see above, and Nixon & Carpenter, 2000).”

And some would argue it’s the lack of rules on application of names and
ranks that makes the traditional system more unstable. This, my friends
and colleagues, is the reason why there are so many systematic arguments:
too many assumptions.

We move on to the rules break-down:

Article 6 did not receive much comment apart for a vitriolic comment on
some of the recommendations of treating names in either phylogenetic or
traditional systems, as in adding P or L for these systems to the names,
respectively, or applying “Clade” or name of the rank to your nomen to
show how you are using the name under the system. Carpenter was not fond
of either idea, but preferred the latter to the former as it seems to
appeal to his sense of former versus informal recognition of names and

Carpenter says that the application and the nature of Article 9
contradicts the first principle (above), but as hopefully clarified by my
comments, this is not the case. His biggest problem seems to be with the
_recommendation_ that a clade name be accompanied by reference to include
a “description or diagnosis, a list of synapomorphies, and/or a list of
included taxa[,]” and “should be done with a thorough knowledge of the
group concerned, including its taxonomic and nomenclatural history and
previously used diagnostic features” (Recommendations 9c and 9e). I,
personally, agree that these should be mandatory, but they are already
accepted this way for most works that accept new names.

Article 11 is considered the most “revealing” so far. This is governing
specifiers, and if you thought that the authors in this volume had a
problem with type vs specifier before, hold on. Carpenter feels that,
while the PhyloCode can work with other codes, it is apparently
_dependant_ on them for some reasons, including references to species, and
I felt I should make a point that NO code has come even close to making
secure statements on the security and identification of a species. It is
not just left to defining the rank and type and describing it as a species
to be one, since the quality of evolution in phylogenetics (including
current use of the ICZN and ICBN) versus phyletics and typology treat
species succinctly differently. Carpenter cites Articles 11.5, 11.8, and
11.9, and I don’t understand then why he feels (as noted earlier) that the
code will cause chaos? Or as other’s feel, ignore the entirety of the
historical record.

“Ordinal names are not regulated in the International Code of Zoological
Nomenclature, but in ranked Linnaean classification Pinnipedia is an
order. As such, it is not contained within the order Carnivora, and vice
versa. If in fact the support for a sister-group relationship between part
of Pinnipedia and part of Carnivora is deemed sufficiently strong [oops --
sorry, that doesn’t matter], so that reclassification is required to
reflect changed ideas on phylogeny [oops, sorry again -- I forgot that
Linnaean classification can’t reflect phylogeny], then the sense in which
each ordinal name is used would have to change.”

Here we see another reflection of the problem of abandoning ranks. All
recent phylogenies show that the entirety of Pinnipedia is within
Carnivora, requiring that the use of orders as ranks being abandoned,
changed to fit the actual phylogeny, rather than forcing the phylogeny to
fit the ranks, and that the understanding that this segregation or
equivalency of groups by “equal” rank is precisely what is meant when
“Linnaean classification can’t reflect phylogeny.”

Carpenter tries to show through examples in attempting to define nested
nodes or node-stem triplets and how a different phylogeny will “mess up”
the definitions, and how it “really illustrates nothing more than the
inability of so-called phylogenetic nomenclature to retain the intended
meaning of a name as ideas on phylogeny change[,]” among other things, and
that ranking of these taxa performs this mutually exclusive effect …
except that names at ranks are supposed to be flexible, mutable, can move
about, even if their rank is fixed (which, as one can easily show, it is
not -- without encountering that “they are both orders, one can’t contain
the other!” argument). 

So, it would be easy to indicate that, for example, Dinosauria be defined
classically so that it excludes bird, which can be done with ranks by
using Mayr’s preferred example of “keeping Aves as a class:” “How exactly
the name Dinosauria would be specified so that it does not contain birds
is not detailed[.]” Rather, such a definition is easy, by providing a
stem-modified node, one can detail a clade’s composition, and include an
exclusive specifier of Aves, Avialae, etc. That is, of course, if you
enjoy the paraphyly of clades. Carpenter is laughing at this point because
he doesn’t see the irony of his bringing this up right after his
Pinnipedia refutal.

Carpenter seems to be laughing outright when it comes to bringing up
article 15, concerning conservation and rejection, when “names do not
change” under the PhyloCode. This is the final comments short of his
repeating conclusion and references to the foundation of the SPN upon the
founders of the PhyloCode itself being “funny.” Oh well, it amuses some


Keller, R.A.; Boyd, R.N.; and Wheeler, Q.D. 2003. The illogical basis of
phylogenetic nomenclature. _The Botanical Review_ 69(1): 93-110.

  “The current advocacy for the so-called PhyloCode has a history rooted
in twentieth-century arguments among biologists and philosophers regarding
a putative distinction between classes and individuals. From this
seemingly simple and innocuous discussion have come supposed distinctions
between definitions and diagnosis, classification and systematization, and
now Linnaean and ‘phylogenetic’ nomenclature. Nevertheless, the
metaphysical dichotomy of class versus individual, insofar as its standard
applications to the issue of biological taxonomy are concerned, is an
outdated remnant of early logical positivist thinking. Current views on
natural kinds and their definitions under a scientific realist perspective
provide grounds for rejecting the class versus individual dichotomy
altogether insofar as biological entities are concerned. We review the
role of natural kinds in scientific practice and the nature of definitions
and scientific classifications. Although inherent instabilities of the
PhyloCode are clearly sufficient to argue against the general application
of this nominally phylogenetic system, our goal here is to address serious
and fundamental flaws in its very foundation by exposing the
unsubstantiated philosophical assumptions preceding and subtending it.”

Keller et al. is, by itself, a singular drive to point out a particular
heavy-handed approach to calling “phylogenetic” taxonomy a hypocrisy. No
counting to the fact that their sources are at odds with one another: they
imply that work in the early 90’s by de Quieroz and Gauthier contradicts
work in the mid-90’s by Ghiselin, among other things, and that while
traditional taxonomy would point at individuals (and their special
meanings), the PhyloCode rejects individuals because it defines taxa by
relation to an ancestor, rather than defined by the characters, and thus
endorses “classes.” The bandied about “Aristotelian” system becomes the
scapegoat for why the PhyloCode is “bad.” Let’s ignore that arguments for
“individual” vs “class” are not apparent in the works cited, because this
is Keller et al.’s apparent observation of the matter; however, let’s jump
straight to the conclusions:

“The PhyloCode is intended to rest on the philosophy of individualism -- a
dubious philosophy about the nature of species and higher taxa.
Individualism purposed to ‘solve’ the species problem by endorsing a
problematic and outdated theory of meaning and definition. Arguments about
species-as-individuals and their supposed compatibility with evolutionary
theory are commonly deployed to persuade biologists to accept phylogenetic
nomenclature (e.g., Brochu & Sumrall, 2001; Bryant & Cantino, 2002);
however, their own methodological tools, ‘phylogenetic definitions,’ are
logically incompatible with those views. The Linnaean system, rather than
having been an obstacle to biological progress within an evolutionary
worldview, is a paradigmatic example of a natural language: a language
that has been able to incorporate the immense acquisition of knowledge
about the diversity of the organic world during more than 200 years and
that is consistent with the phylogenetic explanations behind our
classifications. Perhaps it may require revision or abandonment
(Ereshefsky, 1999, 2001), but this cannot be established by simple
philosophical arguments. It is ironic to see that de Queiroz’s claim that
‘taxonomists have been largely unaware of the philosophical positions
implied by their views’ (1994: 499) holds even more truly among the
fervent followers of the PhyloCode than among taxonomists in general.”

This is all at once erroneous. Keller et al. spend the entirety of the
paper describing how “phylogenetic” nomenclators are contradicting
themselves because someone, at one point, argued that definitions should
follow character assignments, rather than relationship to ancestors. This
is ignoring the nature of the term “diagnosis.” Their big support for the
“Linnaean” or traditional system? As noted in another paper in the same
volume: because it’s been around for over 200 years. No attempt was made
to compare the two systems or how they treat individuals, lineages, and
ancestors (they do so in VERY different ways), as well as the dichotomy of
separation of taxa (traditional system) vs joining them (phylogenetic
system). As for the philosophical arguments, the authors chose ONE version
of recognition of recognizing relation of taxa as the “fundamental” means
by which they reject the PhyloCode, rather than, as in their introduction,
by synthesizing all of their philosophical arguments into one cohesive
counter-argument. By this, Keller et al. fail in their task of rejecting
the PhyloCode, as they clearly have yet to read the document and how it
treats taxa. You CAN still use ranks, if you want to.


Nixon, K.C.; Carpenter, J.M.; and Stevenson, D.W. 2003. The PhyloCode is
fatally flawed, and the “Linnaean” system easily can be fixed. _the
Botanical Review_ 69(1): 111-120.

  “Promoters of the PhyloCode have mounted an intensive and deceptive
publicity campaign. At the centerpiece of this campaign have been slogans
such as that the Linnaean System will ‘goof you up,’ that the PhyloCode is
the ‘greatest thing since sliced bread,’ and that systematists are
‘afraid’ to propose new names because of ‘downstream consequences.’ Aside
from such subscientific spin and sloganeering, proponents of the PhyloCode
have offered nothing real to back up claims of greater stability for their
new system. They have also misled many into believing that the PhyloCode
is the only truly phylogenetic system. The confusion that has been
fostered involves several discrete arguments, concerning: a new ‘method’
of ‘designating’ names, rank-free taxonomy, uninomial nomenclature, and
issues of priority. Claims that the PhyloCode produces a more stable
nomenclature are false, as shown with the example of ‘paleoherbs.’ A
rank-free system of naming requires an annotated reference tree for even
the simplest exchanges of information. This would be confusing at best and
would cripple our ability to teach, learn, and use taxonomic names in the
field or in publications. We would be confronted by a mass of polynomial
names, tied together only by a tree graphic, with no agreed name (except a
uninomial, conveying no hierarchy) to use for any particular species. The
separate issue of stability in reference to rules of priority and rank can
be easily addressed within the current codes, by implementation of some
simple changes, as we will propose in this article. Thus there is no need
to ‘scrap’ the current Linnaean codes for a poorly reasoned, logically
inconsistent, and fatally flawed new code that will only bring chaos.”

  I have actually not read this one yet... sorry.

Jaime A. Headden

  Little steps are often the hardest to take.  We are too used to making leaps in the face of adversity, that a simple skip is so hard to do.  We should all learn to walk soft, walk small, see the world around us rather than zoom by it.

"Innocent, unbiased observation is a myth." --- P.B. Medawar (1969)

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