Phylocode debate


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"Phylocode debate -- Mike Lee (for); Gary Nelson (against)" held during the Joint Conference of the Australasian Evolution Society and the Society of Australian Systematic Biologists, 16-18 July 2001, University of Melbourne."

an unpublished talk reproduced with the permission of Gary Nelson


Phylocode claims to be a new and alternative system of nomenclature for botany and zoology.

It exists as a draft document on the Internet, perhaps to be further developed, perhaps one day adopted, or perhaps forgotten, by the future.

It claims to apply the idea of common ancestry to biological nomenclature, so as to complete the Darwinian Revolution -- the overthrow of alleged essentialism and typological thinking of Linnaean systematics and its nomenclature.

It claims that Linnaean nomenclature, whether botanical or zoological, is defective enough so as to be insufficient for modern needs.

It claims that Phylocode is fully sufficient for modern needs, achieved by abolishing ranks and binomial nomenclature, and by adopting a certain distinction between the ideas of definition and diagnosis.  The distinction leads to an original proposal about types and their function.

These claims stem from herpetological research done in California during the 1980s primarily by graduate students Kevin de Queiroz and Jacques Gauthier, at San Diego State and UC Berkeley.  Kevin is currently a curator at the US National Museum, and Jacques a Professor at Yale University.

These claims, or slogans, have been repeated enough in recent years to cause discussion and to provoke criticism.

I begin with criticism.

First from Norman Platnick during an NSF workshop on systematic monographs, for the benefit of students, held at the US National Museum about a year ago.

Let me read some of Norman's words:

"Now one thing I've learned from 30 years of watching biologists is that whenever you find one systematist calling another one an essentialist or a typologist, you can be 100% sure that the name-caller is purely, simply, and entirely, wrong, and is just creating a smokescreen to cover his or her tracks.  In this case, those tracks rank about as high on the SIP scale as any I've encountered; the SIP scale, incidentially, measures the levels of sanctimony, inflation, and pomposity.  Rest assured, these authors truly believe that their proposals have already created (and here again I quote), 'a new era in biological taxonomy' (de Queiroz & Gauthier, 1990:312).  That one brave new world I'd choose to slide from!"

Next a review paper published last year in Cladistics by the botanist Kevin Nixon and the entomologist James Carpenter.  They contested all the claims of Phylocode.

They are most unsettled by the:

"condescending tone toward the vast bulk of taxonomists."

And the implication that

"Taxonomists have been largely unaware of Aristotelian perspective on definitions."

Next a paper published last year in Biological Reviews by Michael Benton, a vertebrate paleontologist from the UK. 

I'll pass to the last sentence, which refers to Linnaean nomenclature:

"if it ain't broke, don't fix it."

Next, a botanical symposium, a few months ago at the US National Museum: 

Linnaean Taxonomy in the 21st Century.

And a contribution from Peter Forey, fish paleontologist from the British Museum.

The title tells it all: 

"Phylocode -- Pain No Gain"

From Platnick to Forey, spiders and fossil fishes;

Nixon & Carpenter, plants and wasps;

Benton, fossil tetrapods;

There is commonality of perspective and of criticism damaging to Phylocode -- enough perhaps to leave it dead on the vine.

Finally, some contributed comment [to the Bot. Symp.].

From Quentin Wheeler, the eloquent entomologist:

"Linnaean nomenclature is stable enough to say what we know, flexible enough to accommodate what we learn; independent of specific theory, yet reflective of known empirical data; compatible with phylogenetic theory, but not a slave to it; particular enough for precise communication, general enough to reflect refuted hypotheses.  LN is an effective international, inter-generational, and trans-theoretical system of classification that was forged and tested by those describing the earth's biota, not touting political slogans.  It has weathered more worthy adversaries than the Phylocode and will be in wide use long after the latter is a curious footnote to the history of taxonomy."

I turn now to the distinction, fundamental to Phylocode, between Definition and Diagnosis.

This appears in the Master's Degree of Kevin de Queiroz, San Diego State, Fall 1985 -- a thesis on bones of iguanas, Richard Etheridge supervisor:

"For each taxon I include: 1) the type on which the taxon is based, 2) the etymology of the name, 3) a phylogenetic definition (Gauthier et al 1986), 4) a diagnosis consisting of hypothesized synapomorphies, 5) the current distribution, 6) fossil records 7) various comments."

The reference to Gauthier et al. is to a paper subsequently published in a memorial volume to Charles Camp, on the subject of phylogenetic relationships among lizard families.

Kevin begins with the subfamily Iguaninae, with the definition: 

"The most recent common ancestor of Brachylophus, Dipsosaurus, and [the tribe] Iguanini, and all of its descendants."

There are some 30 species in the subfamily.  The relationships of these New World lizards are shown here, a figure from the Camp volume.

Remember the definition:

"The most recent common ancestor of Brachylophus, Dipsosaurus, and [the tribe] Iguanini, and all its descendants."

I recall William K Gregory, of the American Museum two generations before me.  He received a PhD from Columbia University in 1907.  He said that, traditionally, there are two ways to define, diagnose, describe, or differentiate a taxon -- as if the difference between the two ways were between tweedle-dum and tweedle-dee: 

1:   To make a list of its characters. 

2:  To make a list of its members -- its subtaxa:

Brachylophus, Dipsosaurus, and [the tribe] Iguanini.

Anyway, in the Gauthier et al. paper in the Camp volume one reads:

"The above criterion also has the virtue of clearly distinguishing between the definition of a taxon and its diagnosis.

Taxa that are defined by characters possessed by their members are typological concepts.

By defining taxa in terms of ancestry, as we have done, such taxa will be truly phylogenetic concepts (de Queiroz, 1988).

Characters, which enable us to recognize taxa, are used to diagnose taxa in phylogenetic taxonomies, but they cannot define them."

Does the reference to "the most recent common ancestor" add anything to Gregory's simple list of subtaxa? -- Brachylophus, Dipsosaurus, and [the tribe] Iguanini? 

The question can be argued, but I don't argue it here.

Instead, let me tell you about my friend Charlie.

We went fishing in the ocean the other day, caught lots of big ones, and as they were hauled aboard a few remoras dropped off onto the boat deck.

Up to a meter long, rémoras, or remóras if you like,

lack a spinous dorsal fin.  In its place is a sucking disk on top of the head, permitting the fish to attach to, and ride along with, larger animals -- billfishes, sharks, whales, turtles, even boats and ships -- as they move through the water.

Charlie sorted through the remoras on the deck and exclaimed:

"There are eight different species here -- all that are known in the world.  There's Remora brachyptera, Echeneis naucrates, Phtheirichtys lineatus…."

"That's nice, Charlie," I said.  "This must be the first time in history that they were all collected together."

"I've been thinking," he said, "how fish families should each have a phylogenetic definition, like in the Phylocode.  I'm gonna give one for the remora family."

"That's nice Charlie," I asked, "how do you do that?"

"Oh, it's easy.  Anybody can do it.  You don't have to know a thing."

"That's nice Charlie, but how can that be true?"

"I'll show you," he said. 

He selected one specimen of each of the eight species, put them into an array like this one, took a picture with his digital camera, and, in a loud voice and pointing to the eight specimens on the deck, said:

"The most recent common ancestor of these eight fishes, and all its descendants."

"Charlie, what are you on about?"

"Oh," he said, "with a phylogenetic definition the family becomes really meaningful.  Before, it was only an empty abstraction in the mind."

"And now, Charlie?"

"Now?  Well, the old family had just one type, the genus Echeneis.  That's typology and essentialism. 

The new family, well it won't be called a family, will have eight types, well they won't be called types.  Now, that's evolution and population thinking.  It'll have a new name, too, I never liked Echeneis.  It sounds like an echinoderm."

"Tell me, Charlie, do you often do this sort of thing?"

"Oh yes, I have done it for many of the 500 fish families of the world.  I have them in a database in my computer -- with pictures, too, representing all the new type taxa -- at least two per family, but often more.  The more types, the more precision and meaning.  I can hardly wait to add the remoras.  It's all on my website.  When I've done the families I'm gonna do the genera and species -- really pin down those 60,000 names.  Or change 'em, when I want.  Easy-peasy, now that we have a complete catalog of fish genera and species in the old system."

"And each family, Charlie, once it has a common ancestor in its definition, does it really become more meaningful?"

"Oh yes, each and every one, but I don't call them families.  That's too old-fashioned.  None of my friends knows what the family means any more.  And they don't like typology.  Even the word type sends them up the wall."

"Charlie, what about this common ancestor that seems so important to the definition?"

"Oh, that's just an imaginary fish."

"Charlie, these imaginary fishes, one for each family, how do you tell which one belongs to the remoras?"

"Oh, that's easy," he said, "it's the imaginary fish with a disk on top of its head."

"Charlie, do you have a picture of that, too?"

"Not yet, but I'm working on a program to generate ancestral images.  It'll soon be ready.  I'm gonna copyright 'em.  I'll make a bundle."

So much for Charlie.

A Phylocode slogan:

"The use of phylogenetic definitions liberates biological taxonomy from a 2,000-year-old tradition of basing the definitions of taxon names on characters" (de Queiroz & Gauthier 1990, Syst. Zool. 39:310).

We are left with the distinction between definition and diagnosis. 

Is the distinction anything more than verbal?

The distinction between organism and character. 

Between the remora and its disk.

Between the whole organism and one of its parts, which one might, in this case, carve off with a knife.

I won't argue that question either.

The reference to de Queiroz (1988) is to a paper submitted in 1986, about the time he entered UC Berkeley as a PhD student.  Here some themes of Phylocode can be found.

Here one reads about

"the delay of the Darwinian Revolution in biological taxonomy"


"a general framework for a truly phylogenetic systematics."

Acknowledged is a "tremendous intellectual debt" to various persons philosophically inclined: Graham Griffiths, Michael Ghiselin, David Hull.

In the conclusion one reads:

"Perhaps this approach will ultimately lead to the replacement of the Linnaean taxonomic system (Griffiths 1976).  In short, embracing a truly evolutionary systematics will result in drastic taxonomic changes; this is why we talk about a Darwinian Revolution."

Pardon me, but I can't help remembering one of the old boys of the past, another fish paleontologist from the British Museum, in a presidential address to the Linnean Society, not so long ago:

"We shall certainly not advance matters by jumping up and down shrilling, 'Darwin is god and I, so-and-so, am his prophet." -- Errol White, Proceedings of the Linnean Society of London 177:8 (1966).

Do these words apply?

Are they proved wrong?

Jacques Gauthier, PhD in Paleontology, UC Berkely, 1984, friend and colleague for 25 years.  It is said that Berkeley was the only American University with a separate Department of Paleontology -- not any more, now, in this age of amalgamation.

This diagram, from Jacques' thesis, shows birds -- Aves -- and some of their fossil relatives according to him, beginning with Archaeopteryx, and from right to left continuing with a series of fossil groups from the Mesozoic:








Jacques  named some of the nodes basal to birds -- Aves, using existing terms, from vertebrate paleontology, such as



Saurischia and

Dinosauria --

extinct groups found by him to be paraphyletic -- similar to






In Jacques' usage, the terms apply to living birds, which in addition to being birds, become



Saurischians, and finally


In Jacques' usage all of these become names of taxa that are said to be not extinct because they include living birds.

Yes, with wordplay of the kind, birds become dinosaurs. 

The hocus-pocus seemed to lend Phylocode significance as a rationale for naming nodes of the kind, when perhaps the nodes are best left unnamed in such a way, so that Archaeopteryx and other such feathered creatures, recently discovered as Mesozoic fossils, can be considered birds in the technical sense of systematics as well as in their biology.

I won't argue this matter.  Rather, let me just give the alternative view, from yet another fish paleontologist of the British Museum.

"In the 150 years since Richard Owen names Dinosauria for a few bones of Iguanodon, Megalosaurus and Hylaeosaurus, the result of the efforts of palaeontologists has been to discover what dinosaurs are, not what birds are.  Perhaps surprisingly, dinosaurs turn out to be kinds of bird, a theory of relationships that is most clearly and economically expressed by including them within Aves.  Colin Patterson, Department of Palaeontology, The Natural History Museum."

"Are Birds Really Dinosaurs?"

Yes, says the average paleontologist, according to DinoBuzz from UC Berkeley.

There are several other questions that have the same general import, for example:

Are Fishes Really -- Invertebrates?

Are Humans really -- Apes?

Are Animals Really -- Plants?

Are Angiosperms really -- Gymnosperms?

Are Greeks really -- Barbarians?

And so on.  The list is endless.

When the paraphyletic group is extinct, the question is portrayed as meaningful, at least by the average paleontologist.  Shame on him!

The meaning lies solely in publicity generated for the media.  Birds might be related to some dinosaurs more closely than to others.  This does not mean that birds are dinosaurs or that birds evolved from dinosaurs.


"The concept of common ancestry is fundamental to the meaning of the names."

Fundamental to Phylocode is common ancestry.  How is this conceived?

So far as I can tell it is an imaginary species, organism, zygote, or spore -- take your pick as the occasion demands.

Its vagueness notwithstanding, the concept is seen as crucial.

Descent from a common ancestral organism -- an Eve or Adam or both?  For taxa generally -- a natural order, genus, or species -- Linnaeus had the same view.  For him, each natural order, genus, and species comprises the offspring of a single organism, or if the sexes are separate, from an original pair.

Phylocodists dismiss Linnaeus as an essentialist, typologist, Aristotelian.  Think about it.  Theirs is an essentialist approach to history -- as if the historical Linnaeus has an essence or type, The Aristotelian, which is to be vanquished so that The King Be Dead, Long Live the King.

Much of the Phylocode appears in a paper of 1992 in the Annual Review of Ecology and Sstematics.

Here we have more comment on the history of systematics:

"The principle of descent did not become a central tenet from which taxonomic principles and methods were derived (111, 115)."

I don't have to tell you who are the authors of the publications cited.

In the conclusions we read that:

"biological taxonomy must eventually outgrow the Linnaean system, for that system derives from an inappropriate theoretical context.  Modern comparative biology requires a taxonomic system based on evolutionary principle."

What is one to conclude? -- except that Phylocode is ideologically driven -- by postmodern hokum.

In the acknowledgements, we learn that herpetologist Richard Etheridge, supervisor of Kevin's Master's Thesis and now Emeritus at San Diego State, is at the root of this sorry history.

So there is another lesson, perhaps, to be learned:

To be careful with idle remarks to impressionable youth, lest he, or she, be inspired to "reform biological nomenclature,' so as to become, as it were, a second Linnaeus in the memory of the future.

This is the Phylocode document now available on the Internet:

PhyloCode: A Phylogenetic Code of Biological Nomenclature

Philip D. Cantino and Kevin de Queiroz
(equal contributors; names listed alphabetically)

Advisory Group: William S. Alverson, David A. Baum, Harold N. Bryant, David C. Cannatella, Peter R. Crane, Michael J. Donoghue, Torsten Eriksson*, Jacques Gauthier, Kenneth Halanych, David S. Hibbett, David M. Hillis, Kathleen A. Kron, Michael S. Y. Lee, Alessandro Minelli, Richard G. Olmstead, Fredrik Pleijel*, J. Mark Porter, Heidi E. Robeck, Greg W. Rouse, Timothy Rowe*, Christoffer Schander, Per Sundberg, Mikael Thollesson, and Andre R. Wyss.

Among this list of notables, there is no ichthyologist nor entomologist, even though these persons in North America are not in sort supply.  I am sure that they are not deliberately excluded.   Their absence is noteworthy.

Phylocode is not yet operational.  It remains to be adopted, imposed, or left to wither on the vine.

The phylocode is to progress through Registration:

"In order for a name to be established under the PhyloCode, the name and other required information must be submitted to the PhyloCode registration database."

'Tis a bit o' madness to expect delivery of such for 60,000 fish taxa, as if doing so would serve a real purpose.

But, then, Charlie has a lot of energy and, apparently these days, nothing else to do.

It was recently written:

"Espousing 'laws,' Linnaeus wanted to transform botany from an ungovernable living language with a multitude of provincial dialects, into a legislated code administered from a single centre."

                   Lisbet Koerner, 1999

                   Linnaeus: Nature and Nation

This is from Lisbet Koerner's 1999 biography of Linnaeus, published by Harvard -- another PhD thesis.

One may doubt that Linnaeus -- or anyone until very recently -- ever had such ambition.  Regardless, it was never achieved during Linnaeus' lifetime or at any time since.  Biological nomenclature, nevertheless, evolved into the state described above, accurately I think, by the Eloquent Entomologist, Quentin Wheeler.

Phylocode aspires to achieve a legislated code administered from a single centre.  Is this the legacy of Linnaeus?

As reinforcing background to Phylocode there is a body of philosophical literature.  A recent example is Ereshefsky's book on Poverty.

"The Poverty of the Linnaean Hierarchy:   A Philosophical Study of Biological Taxonomy.  Marc Ereshefsky.  Cambridge University Press. 2001."

The literature, generated by just a few persons forms a connected whole.

An early contribution is David Hull's paper on essentialism:

"The Effect of Essentialism on Taxonomy -- Two Thousand Years of Stasis."

David quotes Karl Popper:

"every discipline as long as it used the Aristotelian method of definition has remained arrested in a state of empty verbiage and barren scholasticism."

I've known David Hull for a long time.

He hates Karl Popper and always has.  He never believed a word that Popper ever published.

David also cites an earlier piece by Arthur Cain, one of a series by this early English pheneticist, now deceased.

Arthur Cain's thoughts on Linnaeus were apparently inspired by Ernst Mayr, himself apparently inspired by Karl Popper.

This is a complex matter, as is most philosophy.  Let me say only that, with respect to Linnaeus and Linnaean classification, it forms a miserable history of depreciatory comment without a particle of truth.

In sum, Phylocode is hungry for attention.  It is stuffed with slogans.  It is otherwise without meaning.


Anon. 2001. Are birds really dinosaurs? DinoBuzz: Current topics concerning dinosaurs. Website: http://www.ucmp.berkeley.edu/diapsids/avians.html

Benton, M.J. 2000. Stems, nodes, crown clades, and rank-free lists: Is Linnaeus dead? Biol. Rev. 75:633-648.

Cain, A.J. 1958. Logic and memory in Linnaeus's system of taxonomy. Proc. Linn. Soc. London 169:144-163.

Cain, A.J. 1959. The post-Linnaean development of taxonomy. Proc. Linn. Soc. London 170:234-244.

De Queiroz, K. 1985. Phylogenetic systematics of iguanine lizards: A comparative osteological study. MS Thesis, San Diego State University.

De Queiroz, K. 1988. Systematics and the Darwinian revolution. Phil. Sci. 55:238-259.

De Queiroz, K., and J. Gauthier. 1990. Phylogeny as a central principle in taxonomy: Phylogenetic definitions of taxon names. Syst. Zool. 39:307-322.

De Queiroz, K., and J. Gauthier. 1992. Phylogenetic taxonomy. Ann. Rev. Ecol. Syst. 23:449-480.

Ereshefsky, M. 2000. The poverty of the Linnaean hierarchy: A philosophical study of biological taxonomy. Cambridge University Press, Cambridge.

Forey, P. 2001. Phylocode: Pain no Gain. Smithsonian Botanical Symposium 2001 (30-31 March): Linnaean taxonomy in the 21st Century (from Internet Webpage).

Gauthier, J.A. 1984. A cladistic analysis of the higher systematic categories of the Diapsida. PhD Thesis, University of California, Berkeley.

Gauthier, J., R. Estes, and K. de Queiroz. 1988. A phylogenetic analysis of Lepidosauromorpha. In R. Estes and G. Pregill (eds), Phylogenetic relationships of the lizard families, pp. 15-98. Stanford University Press, Stanford.

Hull, D.L. 1965, The effect of essentialism on taxonomy -- Two thousand years of stasis. Brit. Jour. Phil. Sci. 15:314-326, 16:1-19.

Nixon, K.C., and J.M. Carpenter. 2000. On the other "phylogenetic systematics." Cladistics 16:298-318.

Koerner, L. 1999. Linnaeus: Nature and nation. Harvard University Press.

Patterson, C. 1993. Naming names. Nature:366:518.

Platnick, N.I. 2001. From cladograms to classifications. Smithsonian Botanical Symposium 2001 (30-31 March): Linnaean taxonomy in the 21st Century (from Internet Webpage).

Wheeler, Q.D. 2001. Clever Caroli: Lessons from Linnaeus. Smithsonian Botanical Symposium 2001 (30=31 March): Linnaean taxonomy in the 21st Century (from Internet Webpage).

White, E. 1966. Presidential address: A little on lung-fishes. Proc. Linn. Soc. London 177:1-10.


Gareth Nelson School of Botany University of Melbourne Parkville, Vic. 3052 Australia


On Wednesday 5 December, Dr. Norman Platnick gave the Annual Address to the Systematics Association AGM. The address was given in the lecture room of the Linnean Society of London.
From Cladograms to Classifications: The Road to DePhylocode

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