Paraphyly Watch 2009: Pewter Leprechaun Awards Ceremony

Albert Hall, London.

Thousands of people gather outside in the snow, lining up and waiting to get in to what is tipped to be a star-studded awards ceremony. Inside, we see seats slowly being filled, hear the humdrum of excited voices and the clink of champagne glasses. The air is electric with excitement.

[Announcer] Welcome to the most awaited event of the year! Thousands of people are lining up outside to see the winner of the 2009 Pewter Leprechaun. The Hall is sold out and rumors have it that hawkers are selling tickets for over £1000. The air is tense and the crowds excited by the news that this year nominations are a close tie. Walking up to the booth I saw several of the judges looking tired and worn from the week-long debate as to who will be this year’s winner. We also have several famous scientists in the crowd. There I see ... I think ... is it Aristotle? Possibly. Since the introduction of the Simpson-Darlington Time Machine many international and temporal guests are able for the first time to visit on a whim. I guess it could be Plato ... err ... not to sure. Yes, there is the guest of honor Aristotle, carrying the ceremonial Great Chain of Being ladder - the Scala Naturae itself. He will of course be chairing the session from the right of the stage.

This year’s nominees are:

Martin D. Brazeau on ‘The braincase and jaws of a Devonian ‘acanthodian’ and modern gnathostome origins’ published in Nature (2009, 457:305-308)

Dennis P. Gordon on ‘Towards a management hierarchy (classification) for the Catalogue of Life’ a Draft Discussion Document published in Species 2000 & ITIS Catalogue of Life Annual Checklist (2009, on CD-ROM)

Donald R. Prothero on the ‘Evolutionary Transitions in the Fossil Record of Terrestrial Hoofed Mammals’ published in Evolution, Education and Outreach (2009, 2:289-302)

Todd F. Stuessy and Christiane Konig on the ‘Classification should not be constrained solely by branching topology in a cladistic context’ published in Taxon (2009, 58:347-348)

János Podani on the ‘Taxonomy versus evolution’ by also published in Taxon (2009, 58:1049-1053)

The audience is seated and the lights dim

[Announcer] I see that the lights are dimming and...

Applause

[Announcer] ... rapturous applause for the man himself - the father of paraphyly and host for tonight - Ernst Haeckel! He is walking onto stage, completely out-fitted in tweeds and ... is that a duck hanging from his belt....?

Applause ends

[Ernst Haeckel] Danke Schoen! Meine Damen und Herren! Tonight ve vill avard zi Pewter Leprechaun for 2009 to zi most admirable abuse and misuse of paraphyly. It iz my pleasu ...

Applause. Haeckel gets annoyed

[Ernst Haeckel] Aufhalten! Ve applaud at zi end! AT ZI END!

Applause ends abruptly

[Ernst Haeckel] Zat ist better. Ver vos I. Ach ja ... my pleasure to announce the vinner. Bevor I do, may vi present and bless die Pewter Leprechaun?

Haeckel looks around slightly confused. The main doors open and a procession starts at the back of the Hall

[Announcer] And we see the procession of the Pewter Leprechaun held aloft by George Gaylord Simpson. Following behind him is the Holy Order of the Lineage, Ernst Mayr, P.J. Darlington, Peter Ashlock all holding candles ... and ... there is some commotion at the back ... some shouting ... oh dear ... is that Adolf Naef? My word! Naef is attacking Simpson - he must just have read Principles of animal taxonomy during his brief visit here. He is not happy ... some more shouting ... OH! Simpson has punched Naef! The American has swiped the Swiss in a spectacular left-hook! Naef has recovered and is grabbing the Pewter Leprechaun.. has he got it? He HAS GOT IT! Mayr tackles Naef, Naef passes it on to ... Zangerl! My God, see that man run! Dodges Remane and Zimmermann ... who are discussing functional homology and ... knocks over Hennig, who was admiring Remane ... a crash-tackle by Ashlock and Zangerl looses the Leprechaun! They have lost the Leprechaun! .. It’s ... Ashlock ... picks up the leprechaun and passes it onto .... Darlington .... pushes over Hennig who just got up again ... passes it onto Mayr, back to Darlington who ... misses the catch! He has missed the catch! There is a scramble for the Leprechaun and Haeckel, yes Haeckel, joins in and ... punches out Hennig who just got up again ... and runs and leaps onto stage. What a performance from the German!

This has been a most remarkable entry for the Holy Order of the Lineage! The audience is wild with excitement. Aristotle stands up to bless the Leprechaun .. and ... it’s blessed! The Leprechaun has been blessed by the Great chain of being ladder! Haeckel struts back to the podium and puts his hand in his top pocket ... yes ... it’s a golden envelope!

[Ernst Haeckel] Meine Damen und Herren! Zi vinner of zi 2009 Pewter Leprechaun is ...

Haeckel slowly opens the envelope and pulls out a card

[Ernst Haeckel] Mein Gott!

Haeckel appears startled and looks to Aristotle holding out the card. Aristotle strains to see what is written on it. The audience titters

[Ernst Haeckel to Aristotle] Iz dis ein f*cking joke?

Aristotle shrugs. Haeckel composes himself

[Ernst Haeckel] Well ... zi judges ... have decided that the award should go to zi most prolific publisher of zi use and abuse of paraphyly. The vinner iz ... Taxon, zi journal of the International Association for Plant Taxonomy!

Audience applauds insanely

[Announcer] This is a surprise! The Pewter Leprechaun has never been awarded to a journal, in fact, it has never been awarded to anyone. I hope the nominees aren’t too disappointed. But aren’t the audience just loving it! Ernest Haeckel bows and leaves the stage. Aristotle leads the procession of the Holy Order out the Hall as the audience slowly rises in respect. Simpson and Darlington looking a bit bruised but enjoying the moment. Do I see a smile from Mayr? Err ... no, but I am sure he is loving every minute of it!

So ends the Pewter Leprechaun Awards Ceremony for 2009. We hope that 2010 brings forth a startling array of nominations. All entries can be submitted to the Systematics & Biogeography Blog via next year’s 2010 Paraphyly Watch post.

Have a Merry Christmas and a Happy New Year!

Paraphyly Watch 4: Monoclady and Paraclady

Just when you thought all possible abuses and misuses of paraphyly have been thoroughly exhausted, one totally mind-boggling and confused piece of writing appears in the Journal of Paraphyly Taxon. We refer to Taxonomy versus evolution by János Podani, a dainty ditty that transcends all boundaries of comprehension and ventures into the field of evolutionary science fiction.

The story so far...

On the planet Zog, the Mayrian Monks enforce rigid elections that decide the fate of the foundations of science. One day new heretical “discoveries” of what are called ‘natural groups’ questions the validity of Reptiles - rulers of the land. The heretics have called them a group of ‘unrelated animals’ - nothing more than systematic bastards! The Mayr-Monks are never wrong and, science never gets in their way. A snap election is called, the ballot counted and science-democracy enforced. The vote was unanimous: 130 in favour - zero against. “Good to see science done” says one Monk to another. That night they all sleep peacefully with a clear conscious, awaiting morning when their sun will rotate around their flat earth once again.

The Mayrian Monks will do anything to protect paraphyletic groups. Rather than revise a taxonomic group, evolutionary taxonomists will dabble in systematics in order to change the foundations of classification. This is akin to the alcohol fueled idea of trying the change the laws of gravity in order to balance this year’s Christmas tree in the front sitting room. It doesn’t work. Neither does monoclady and paraclady. Oh dear, where does one start?
Let’s kick off with Podani’s arguement, namely:

“... that there are four major aspects of taxonomic systems in which achievements of evolutionary biology are not recognized fully and properly, if evolution is considered at all” (Podani, 2009: 1049).

Podani does this by distinguishing diachronous and synchronous classifications (not to be confused with similar terms used in Ebach & Williams [2004] as Podani does). In Podani’s view a diachronous classification includes fossil organisms, which he equates with ‘ancestors’ and synchronous taxa that he describes as extant. Apparently, classifying fossils with extant taxa poses problems hence the need for both classifications. He goes on...

“If we use a synchronous classification for extant organisms, we are concerned with the result of evolution, history is only relevant as long as common ancestry is to be detected, and an inclusive hierarchy is suitable to summarize diversity of life” (Podani, 2009: 1050).

and...

“On the other hand, a diachronous classification cannot be Linnaean for two reasons: (1) units of classification and the groups change in time and, more importantly, (2) wide gaps necessary for separating supraspecific taxa are evolutionary absurdities in the spatio-temporal continuum of populations” (Podani, 2009: 1050).

Got it? Now, onto the next bit...

“The only tool for representing the diachronous pattern of life adequately is the Darwinian phylogenetic tree, showing ancestor–descendant relationships between extinct and extant populations” (Podani, 2009: 1050-1051; original emphasis).

...so [drum roll]...

“I suggest restricting the original definition of monophyly to phylogenetic trees, so that it is a diachronous phenomenon and can only be examined in a diachronous classification. For cladograms, I introduced the new term monoclady: a group is monocladistic if it includes all terminals of a given clade. This condition has to do with extant taxa and is particularly meaningful for a synchronous classification” (Podani, 2009: 1051; original emphasis).

...therefore...

“Reptiles are most certainly para- phyletic because extinct ones include the ancestors of birds and mammals as well. Extant reptiles are paracladistic, since crocodiles are sister to birds rather than to other reptiles” (Podani, 2009: 1051).

...and to sum it all up...

“If a collection of organisms is found to be monocladistic (in a molecular study, for example), then the taxon which includes this group in a diachronous classification is not necessarily monophyletic. Paraclady means that the group cannot be embedded into a monophyletic taxon, and it is therefore indication of paraphyly or even polyphyly in the corresponding diachronous classification. A Linnaean taxon, which is preferably synchronous as the above logic dictates, can only be monocladistic, paracladistic or polycladistic and the monophyly/paraphyly problem vanishes. Paraphyly, as understood earlier, may often be reflection of the disagreement of a diachronous classification with a synchronous analysis. Therefore, the central tenet of contemporary taxonomy is perhaps not about paraphyly and monophyly, but around the contrast between synchronous and diachronous classifications” (Podani, 2009: 1052).

In order to keep this argument short we will not discuss Podani’s bogus adventure into nomenclature, but start with his first and last points, namely, “... the central tenet of contemporary taxonomy is perhaps not about paraphyly and monophyly, but around the contrast between synchronous and diachronous classifications”. Is it? Taxonomy has always remained considerably neutral about how one groups extant and extinct taxa together, why then should there be two classifications? Because extinct taxa are more likely to be ‘ancestors’ and, genealogical relationships (as Podani correctly points out) make poor classification systems. So where does this leave taxonomy? Well, where it has always been - as a neutral way to classify taxa without needing to know who is ancestor to whom. The same is true for cladograms - extinct and extant taxa are placed at the terminals because there are related in some way. It appears that Podani has missed something here, such as the whole cladistic revolution from the 1960s to the 1980s. Cladograms remove the need for phylogenetic trees as all relationship can be shown equally. So both the diachronous and synchronous classification systems are utterly pointless as taxonomy remains neutral about ancestors and fossil taxa (they classify along with extant groups) and equally useless in systematics, as all taxa are treated equally. Podani’s rasion d'être for two classification systems is a vain attempt to preserve paraphyletic groups (number 2 for this year after Stuessy and Koenig [2009]).

Here is how it works. First debunk monophyly as irrelevant to classification by assigning them as problems found in phylogenetic trees. Since phylogenetic trees are diachronous and diachronous classifications “cannot be Linnaean” and, are therefore invalid. Clever. Now he introduces a new term monoclady and monocladistic, which means, “If a collection of organisms is found to be monocladistic (in a molecular study, for example), then the taxon which includes this group in a diachronous classification is not necessarily monophyletic” (Podani, 2009: 1052). There we have it. Monocladistic groups can be paraphyletic seen from a phylogenetic perspective. Get it?

Let’s put it another way. Take an existing term like monophyly and replace it with a similar term like monoclady (“includes all terminals of a given clade”), which of course does not change its overall meaning. Now dismiss monophyly as irrelevant to classification, but relevant to 19th century Haeckelian phylogenetics, hence radically changing not only its meaning but also its usage. Here comes the best bit - do the same to paraphyly. Replace its overall meaning with another term, like paraclady, and then dismiss paraphyly as irrelevant to classification. No problems here (as it is not relevant to classification). The coupe de grace is defining some forms of monoclady (formerly monophyly) as paraphyly! Wow, the sheer audacity!

Yes folks, I think we have a clear forerunner in the 2009 Pewter Leprechaun for the misuse and abuse of paraphyly.

As you read, judges are conferring in what is to be some pretty stiff competition. The results for the Winner of the 2009 Pewter Leprechaun will be announced very soon. Stay tuned!

References
Ebach, M.C. & Williams, D.M. (2004). Classification. Taxon 53: 791–794.
Podani, J. (2009). Taxonomy versus evolution Taxon (58), 1049-1053.
Stuessy, T.F. & König, C. (2009). Classification should not be constrained solely by branching topology in a cladistic context Taxon, 58, 347-348.

The Aquatic Ape

More fossil news:

Fossil hunters arrive in Darwin country, but will they find a pub?

The story ends with this snippet:

In the corridors and coffee areas, some students were angling for jobs – the recession hits fossil hunting too – while others were hijacking experts to help them with their work. Such as Bristol student, Brian Machin, whose thesis is on the theory that a type of monkey found in South America got there by floating from Africa on a raft. "It's nonsense of course," he said, "But it's hard to prove it's nonsense."

Who is Brian Machin? We need to know.

(Not) Lars (Brundin)

Nestling, possibly unread by many, in the first comment on the announcement of the downloadable copy of Systematics and Biogeography, is an offering from Professor Lars (of whom about we know absolutely nothing). At first we thought it a jape, one of our friends or colleagues trying to tease us. But no! (“Blimey!!”, that was Williams [he’s British]; “Cricky”, that was Ebach [he’s Australian]). We read the text closely and could see that the well thought out and reasoned commentary was, indeed, real – a series of penetrating observations on the state of systematics today – and, of course, the follies of the past. We were humbled in its presence – but unwilling to let it pass and, because we are both very humble people, have decided to bring it to wider attention. Read on and enjoy, and consider what might be the follies of present day systematics and systematists.

Lars said...
I can't see why cladists (remember this term was first used by Ernst Mayr to distinguish them from other schools) consider themselves "revolutionaries". Cladistics is only efficient when one is dealing with morphology, and this kind of information is so terribly biased by subjectivity, that it should never be used as phylogenetic inferential data.

Molecular data, on the other hand, is much less biased (bias comes from sequencing errors, lateral gene transfers and poorly chosen alignment parameters) and should reflect the correct evolutionary relationships if correctly analyzed. With the advance of genetic barcoding, the Cladistic methods has become obsolete.

Morphology can be interpreted in many ways by different authors, and given the infinity of manners the same information can be scored, it becomes not much more than an exercise of subjectivity.

Cladistics is traditionally viewed by serious molecular biologists as a sectarian (almost a religious cult / secret society!) branch of evolutionary research that claims to possess the most efficient and and best logic to propose hypotheses on organismal relationships.

Unfortunately, this is not true. Cladists are often narrow-minded and do not accept their "parsimony" method is much more prone to LBA artifact than those usually referred to as "Phenetics", such as Neighbor-Joining and Maximum-Likelihood. This last is the pinnacle of evolutionary inference, since it uses both raw nucleotide data AND genetic distance in its calculations, thus using all data explanatory power.

Hence, considering the high subjectivity implied in morphologic matrices, the risk of LBA bias, and the suboptimal use of data explanatory power, Cladistics should be avoided.

This makes Phenetics, and not Cladistics, the actual revolution!

Systematics and Biogeography: Cladistics and Vicariance Online!

Every now and then a scientific discipline undergoes a revolution, an episode that changes the way a subject is perceived, the way it is understood and undertaken – a new vision emerges that prevents a return to the subject matter as it was before, a paradigm change, some genuine progress. In the last century, there was a revolution in phylogenetics and systematics that began with the work of entomologist Willi Hennig (1950, 1966) and its interpretation by Lars Brundin (1966), a chironomid specialist. The need for revolution was succinctly put by palaeontologist Colin Patterson, some years later

“By about 1960 palaeontology had achieved such a hold on phylogeny reconstruction that there was a commonplace belief that if a group had no fossil record its phylogeny was totally unknown and unknowable” (Patterson 1987:8).

That ‘commonplace belief’ was eventually rejected in favour of determining relationship from evidence (characters, homologies) provided by organisms (living or extinct), a shift from the preoccupation of discovering ancestry directly from the fossil record to determining common ancestry. As Brundin later noted, “little by little some palaeontologists have perceived that Hennig’s principles of phylogenetic systematics meant a revolution to their science.” Hennig called his approach Phylogenetic Systematics, the title of his 1966 book (Hennig 1966), an approach that eventually became known as cladistics, hence the cladistic revolution: the cladistic revolution overturned the central position of palaeontology in determining phylogenetic relationships: turning Ernst Haeckel’s Systematische Phylogenie into Hennig’s Phylogenetic Systematics.

By the early 1980s three books were published, all dealing with cladistics. Each approached its topic from a different perspective: Phylogenetic Analysis and Paleontology by Joel Cracraft & Niles Eldredge (Columbia University Press, New York, 1981), Phylogenetics: The Theory and Practice of Phylogenetic Systematics by Ed Wiley (New York: Wiley Interscience, 1981) and Systematics and Biogeography: Cladistics and Vicariance by Gary Nelson and Norman Platnick (Columbia University Press, New York, 1981).

While all three books have their merits, it is the last, Systematics and Biogeography: Cladistics and Vicariance that broke into new ground; and it is the last that, some 28 years after its first appearance and almost impossible to get a copy, is being made available by the University of California Press at http://www.ucpress.edu/books/series/spsy.php

Cladistics, as outlined in Systematics and Biogeography: Cladistics and Vicariance, might be understood as a reaction to phylogeny reconstruction, or more specifically, Haeckel’s paleontological version of it, developed by Matthews and Simpson. Systematics and Biogeography is a detailed critique of Haeckel’s legacy and an outline of what can be understood as natural classification, as first sketched by Candolle in his Théorie élémentaire de la Botanique – the question addressed being: How do ancestor—descendant relationships relate to natural classification?

Since Systematics and Biogeography there have been discourses on ‘tree-thinking’, ‘group-thinking’ and ‘population-thinking’, none seemingly appropriate for classification: Classification (and phylogeny, and systematics) are all best referred to as relationship-thinking, of which Systematics and Biogeography is a meditation on.

Download this book now from the University of California Press website – and see if you can start another revolution.

Chris Humphries – Natural History Museum, London (1947—2009)

Chris Humphries, botanist and biogeographer, died on Friday 31st July. Chris was a leading figure in the cladistic revolution in systematics and biogeography. He worked in the Botany Department of the Natural History Museum from 1972 until his retirement in 2007.
Chris was one of the first to explore, develop and promote cladistics in botany, examining classification and biogeography from its novel perspective. Chris produced a classic in biogeography, Cladistic Biogeography (1986) (with Lynne Parenti, of the Smithsonian; a revised 2nd edition appeared in 1999) and produced a widely read and used manual for cladistic systematics, Cladistics: A practical course in systematics (1992) (with staff of the Natural History Museum; a revised 2nd edition appeared in 1998 as Cladistics: the theory and practice of parsimony analysis).
Chris’s research extended from organizing and annotating the first complete full-colour edition of Banks’ Florilegium to addressing conservation issues with WorldMap (with Dick Vane-Wright and Paul Williams, both of the Entomology Department, NHM).
Chris received the Linnean Society’s Bicentenary Medal in 1980 and their Gold Medal in 2001. He was President of the Systematics Association (2001—2003) as well as its Treasurer (1996—1999), and President of the Willi Hennig Society (1989—1991), being elected a Fellow honoris causa in 1998. Chris was also Vice-President and Botanical Secretary of the Linnean Society (1994—1998).

David M. Williams & Charlie Jarvis
Botany Department
The Natural History Museum
Cromwell Road
London SW7 5BD
UK

FSB: Reviews

Finally, reviews of Foundations of Systematics and Biogeography are out!

Norman Platnick has a review in Systematic Biology and Andy Brower has published one in Systematics & Biodiversity.

Unfortunately the links are only limited to subscribers or those with institutional access.

References
Brower, A.V.Z. (2009) Science as a Pattern David M. Williams and Malte C. Ebach. Foundations of Systematics and Biogeography Springer Science+Business Media, New York, 2008, xvii + 309 pp, ISBN 9780387727288. Systematics and Biodiversity, 7: 345-346.
Platnick, N.I. (2009). Foundations of Systematics and Biogeography. Systematic Biology, 58: 279-281.