Such expressions as that famous one of Linnæus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent,—the only known cause of the similarity of organic beings,—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications (Darwin, 1859, p. 413f).

Monday, 14 December 2009

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!

Monday, 7 December 2009

Paraphyly Watch 4: Monoclady and Paraclady

ResearchBlogging.orgJust 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.

Wednesday, 30 September 2009

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.

Saturday, 19 September 2009

(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!

Tuesday, 15 September 2009

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.

Thursday, 6 August 2009

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

Wednesday, 29 July 2009

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.

Thursday, 11 June 2009

Paraphyly Watch 3: Transitional Fossils, Microbes & Patrocladistics

ResearchBlogging.orgIt looks like there is some pretty stiff competition for the 2009 Pewter Leprechaun. This month alone we have: an article showing us the virtues of transitional fossils (Prothero, 2009); a plea that protists are microbes too (Caron et al. 2009) and a defense of patrocladistics (Stuessy & König, 2009).

The Wonders of Transitional Fossils

Evolutionary Transitions in the Fossil Record of Terrestrial Hoofed Mammals by Donald R. Prothero is a somewhat perplexing article. It attempts to identify "transitional fossils" as evidence for evolution and ancestors. Not exactly 'new' or 'exciting' by any standard, but it is why and for whom the article is written - Evolution: Education & Outreach. Not exactly the best way to promote evolution to an audience of science school teachers, especially when you have this to say:
    "Creationists often scoff at the notion that there are fossils that show how the giraffes evolved, but they could not be more mistaken […] However, Nikos Solounias (2007, personal communication) is currently publishing a description of a new fossil of the giraffid Bohlinia that preserves a neck that is intermediate in length between Giraffa and the okapi. Thus, we do know how the giraffe got its long neck, and we have the transitional fossils to show how and when it occurred! Once again, the fossil record has provided a specimen whose very existence the creationists have long denied" (Prothero, 2009:297-298).
And this:
    "Creationists attempt to discredit these examples by saying that our switch from an orthogenetic linear model of the 1920s to the modern bushy branching pattern somehow denies that this fossil evidence does show change through time, but this only reveals the creationists’ lack of training in anatomy and paleontology" (Prothero, 2009:301).
Oh, and this:
    "Arguments such as this reveal the dogmatism and complete intellectual and scientific bankruptcy of creationists" (Prothero, 2009:301).
We would like to start with this disclaimer - We are not, never have been and never intend to be creationists. We do not defend creationist dogma or any other idea disguised as creationism (i.e., Intelligent Design). We do, however, point out where evolutionary biologists make unwitting mistakes, which may fuel further creationist attacks. Creationists are getting cleverer and are starting to see through arguments supporting paraphyly (i.e., ancestors, transitional fossils, transformations etc.). We warn our fellow evolutionist colleagues not to fall into this trap. We also urge them never to intellectualize the arguments of creationists by entertaining them at any level (i.e., defending paraphyly). Doing so makes matters worse, as we shall show using the case of Prothero (2009).

Discovering "that preserves a neck that is intermediate in length between Giraffa and the okapi" is not evidence for a transition between a short and a long neck. Firstly, we have no evidence to suggest that either taxon is ancestral to the other, thus leaving the "short neck – medium sized neck – long neck" a hypothetical transformation that is as equally valid as "long neck – medium sized neck – short neck". Prothero (2009) is using a very old paleontological argument that was rejected in systematics many years ago during the cladistic revolution. No matter how well we understand our group, its taxonomy, paleontology and anatomy, we can never know if one taxon is ancestral to another. Identifying an ancestor is purely speculative and subjective and not empirical in any sense. So, sadly for Prothero (2009), the fossil is merely, well, a … fossil. Not "transitional fossils to show how and when [evolution] occurred!"

Another example is the discovery of a four legged sirenian:
    "Known as Pezosiren portelli ('Portell’s walking sirenian'), it has the characteristic skull and teeth of a sirenian and even the dense bones of the ribs so typical of the group. Yet this creature had four perfectly good legs complete with terrestrial hands and feet, not flippers as seen in the living sirenians [...]One could not ask for a better example of a transitional fossil! It closely parallels the intermediate pattern of locomotion seen in walking whales such as Ambulocetus (Thewissen, this volume). When creationists have addressed this discovery at all (on their websites; none of their books mention it yet), they show their complete ignorance of the basics of anatomy and paleontology. Their argument boils down to 'if it has four legs and feet, it can’t be a sirenian,' even though the details of the teeth, skull, and even the ribs share the specializations unique to the entire order Sirenia" (Prothero, 2009:301).
The creationists are of course wrong. The four-legged Pezosiren portelli is a sirenian. But the presence of legs instead of flippers doesn’t mean it's a transitional fossil. For instance, the number of possible evolutionary scenarios is endless - sirenians may have come back to land and then returned to water. The discovery of Pezosiren portelli does not constitute the discovery of a transitional fossil and ancestor.

The danger of inventing transitional fossils in this way degrades systematics and makes it far easier for creationists to prey on evolutionary biologists. We have all the evidence we would ever need to state that sirenians are an evolutionary group. Namely monophyly:
    "In the past decade, the monophyly of the Tethytheria was also confirmed by later molecular analysis" Prothero (2009:300).
The article by Prothero (2009) would benefit the readers of Evolution: Education & Outreach (e.g., science teachers) if it actually listed the evidence for evolution, not evolutionary scenarios that are immune to testing.

We nominate Prothero (2009) for the 2009 Pewter Leprechaun for the abuse of paraphyly by unnecessarily using transitional fossils to support arguments for evolution when other sufficient evidence exists (i.e., homology and monophyly).

A Plea: Protists are microbes too!

Not so much a Paraphyly Watch but more of a 'non-group quest', Caron et al. (2009) make the request that "Protists are microbes too". Now, one might wonder what a microbe is. Caron et al. (2009) provide some insight:
    "Strictly speaking, microorganisms [microbes] are defined by their size; that is, organisms that are smaller than can be resolved by the naked eye ..." (Caron et al., 2009:6).
And:
    "If we define microbes by cell size, then most protists qualify as microbes" (Caron et al., 2009:6).
They provide a figure that plots approximate size range of certain organisms against their membership of a particular supergroup, with a mark at about the size visible to the human eye. What they mean by this is that each organism plotted on the table is a representative of a supergroup that is suspected to be monophyletic. There is no correlation between size and supergroup. So clearly they recognize that (1) size does not mark out any natural group at all; (2) that supergroups (putatively monophyletic) groups are independent of any possible group called or assembled under the name of microbe. It’s a non-group, para- or more likely, polyphyletic.

Of course, they never get around to defining a protist – because they are undefinable as well – and paraphyletic (or even polyphyletic). Given this logic, we ask "Why stop there?" Let's add mites, fleas and tardigrades too!

In defense of Patrocladistics

Oh dear:
    "Rigid cladistic viewpoints in classification face a serious difficulty in that they disregard evolutionary data (Stuessy & König, 2009:347).
Welcome to evolutionary taxonomy – a field where genealogies are classifications and classifications are genealogies. In the evolutionary taxonomic cosmos cladograms are best guess estimates for phylogenies and nodes ancestors. A branching bifurcating tree represents cladogenesis and anagenesis is totally ignored. Here monophyly is paraphyly and parapyhyly is monophyly:
    "For us, paraphyly is a type of monophyly (groups with a single common ancestor […]), and this is acceptable in classification depending upon the degree of divergence of the derivative group from its progenitor" (Stuessy & König, 2009:347).
And:
    "Cladistics has provided us with significant quantitative avenues to reconstructing branching patterns of phylogeny, but quantitative evolutionary approaches offer classification with the highest information content and predictive value for society. Self-limiting only to branching patterns, however easy it may be, is not the solution for evolutionarily based biological classification" (Stuessy & König, 2009:348).
There is not much to say about patrocladistics other than mass delusion on part of evolutionary taxonomists. They don't seem to understand that evolution and classification are separate entities and that only the latter is the key to the former. To them cladistics rejects evolution entirely and taxonomy should use all available evolutionary evidence. Thus, the creation of a super-duper form of cladistics:
    "We propose here a method of incorporating patristic distances, or evolutionary divergence within lineages, into an explicit method of producing a branching diagram (called a patrocladistic tree or patrocladogram) […]morphological divergence). This should eliminate, or at least significantly reduce, the controversy over how to deal with paraphyletic groups. Discussion will rather shift to the characters and states involved with patristic distance and their relative weighting against synapomorphic character states. Such discussions on which" (Stuessy & König, 2008:595).
We don’t know whether to cry to bang our heads against the wall. We blame Ashlock (1971) (to whom most evolutionary taxonomists refer) as the Root of all Evil Blunders in systematics - but we'll leave that for another post.

Our money is on Stuessy & König (2009) as winners of the 2009 Pewter Leprechaun (at least by 2 lengths). We hereby nominate Stuessy & König (2009) for the coveted prize for the misuse of paraphyly by confusing it as monophyly or meaningful.

References

Ashlock, P.D. (1971). Monophyly and associated terms. Systematic Zoology 20:63-69.
Caron, D., Worden, A., Countway, P., Demir, E., & Heidelberg, K. (2008). Protists are microbes too: a perspective The ISME Journal, 3 (1), 4-12 DOI: 10.1038/ismej.2008.101
Prothero, D. (2009). Evolutionary Transitions in the Fossil Record of Terrestrial Hoofed Mammals Evolution: Education and Outreach, 2 (2), 289-302 DOI: 10.1007/s12052-009-0136-1
Stuessy, T.F. & König, C. (2009). Classification should not be constrained solely by branching topology in a cladistic context Taxon, 58, 347-348

Friday, 5 June 2009

Long Distance Dispersal Thwarted

"An Australian man has saved a kangaroo from drowning in shark-infested waters by using his surfboard to rescue the exhausted animal." From the Telegraph

From the Wollongong Herald

In what has been described as the biodiversity bombshell, Australian fauna are dispersing from Down-under. "We have up to 600 volunteers patrolling beaches for any fleeing kangaroos, parrots or wombats" says Eric Hedgers of Dispersal Watch. "Last month we had two successful escapees, a goanna [large lizard] and an echidna". Biologists closely monitoring the exodus believe there is an overwhelming preference for New Zealand. Mr. Hedgers seems amazed at all the media attention. "I mean it's so close, why wouldn't you disperse? It seems unusual that a small freshwater Alpine fish wouldn't cross 1000kms of deep sea and migrate up a mountain. We’re surprised this hasn't happen earlier".

However Prof. Bush from the Wellington University of Technology believes the Aussie invasion is only temporary. "They've got their minds set on South America, possibly Chile or the Amazon. A small lizard for instance could easily raft across the Pacific on the back of an otter for over six months - except Australia doesn’t have any otters". Could this mean the end for Australia's biodiversity?

Australian ornithologist, Dr. Betty Simmons has her doubts. "We'll just get all the African species". Navy officials have confirmed the sightings of three elephants and a hippo 300 kilometers off the South Australian Coast. "On the positive side this could potentially save our economy. Tourists can save time and money visiting Uluru and going on safari at the same time".

An outback filled with wildebeest, lions and giraffes have conservationists like Mr. Hedgers worried. "Can you imagine Australia without its iconic fauna?" There is however some hope. "The echidna came back after a week. I think it didn’t like the ants".

Thursday, 28 May 2009

Hidden Agendas: The Media & Science

Over a conversation about the decline of paleontology versus the rise of fossils in the media, my mate and colleague Tony Gill pointed out several interesting points. The hype and media attention surrounding Jurassic Park, Tiktaalik roseae the 'fish-to-tetrapod' transition and most recently, Ida the lemur-like fossil, all misrepresent paleontology. Furthermore, the medias handling of fossil ‘news’ is indicative of the decline of paleontology overall. This ‘hidden agenda’ namely, promoting a cheap technology or highly applied field at the expense of a scientific scholarship and endeavor, is endemic to current science reporting.

At first glance, Jurassic Park is an adventure movie about dinosaurs. A dinosaur expert gets to do what most paleontologists only dream of – walking with living fossils. Add a little romance and adventure into the script and "Hey Presto!" you have the kids hooked. Dinosaur figurine sales go up and you need to queue to get into your local museum. All a perfect recipe for promoting paleontology and getting the message that what paleontologist do is 'cool'. Think again: "What is Jurassic Park actually about?"

The answer, quite rightly is genetics, more accurately genetic engineering. Jurassic Park may show off some stunning (albeit incorrect) CGI reconstructions of dinosaurs, but mostly it is about how modern technology can progress science to unbelievable heights. What most people remember from the script is how dinosaur DNA can be extracted from fossil blood-sucking insects trapped in amber. Jurassic Park did more for genetics than it did for paleontology. For example, the "National Science Foundation and the National Institutes of Health, and by the Ben F. Love Endowment, the ARC Federation Fellowship and the NHMRC C.J. Martin and R. Douglas Wright Research Fellowships" (Choi, 2008) supported a project to resurrect the extinct Tasmanian Tiger from DNA retrieved from a preserved fetus. Paleontology got peanuts.

Before I continue with more examples, I want to quickly explain what I mean by paleontological research. The majority of paleontologists are taxonomists and systematists. Many expand their research to include stratigraphy, paleoecology, taphonomy and functional morphology. Taxonomy however is essential in paleontology. Without it we are describing bits of shell and pieces of bones. Taxonomy gives us a name a diagnosis and most importantly a classification. Systematics helps us to establish evolutionary relationships. Equally important are the circumstances in which the fossil was preserved (taphonomy), it age (stratigraphy), the depositional environment (paleoecology) and what sort of life the organism led (functional morphology). Together they form a well rounded paleontologist and a paleontological project. For the media, paleontology as a scholarly endeavor, sells few magazines and doesn't cover the cost for airtime. Many people share a passion for paleontology, but what sells tons of plastic stegosaurus in museums could never satisfy the public's hunger for sensationalism.

In the same way that Jurassic Park appeals to our belief in modern technology, the hype around Tiktaalik roseaeand Ida ( Darwinius masillae) is our human desire to find out who we are and where we come from. The desire to know our own family genealogies is transposed onto evolutionary biology as the search for ancestors and origins – different concepts all together.

Ancestors and centers of origins are only place-holders to make statements about ancestor-descendants and dispersal. In order to propose evolutionary scenarios about individual taxa, say hominids or just humans, we need the evolutionary equivalent of Adam and Eve and the Garden of Eden. As systematists, however, we don’t need either. Taxa are related in some way based on their 'derived' characters so too are biotic areas. Stating a new discovery, such as Harpetidae are more closely related to Harpididae than they are to Entomaspidae, require no ancestors, only homologies. Therefore, homologies are necessary evidence in discovering evolution, where ancestors may be used in explaining evolutionary scenarios – they are not essential. The aim of any field, be it paleontology or entomology, is to find homologies and natural classifications first before we can even entertain the idea of ancestors and their centers of origin. Hence systematics lies outside evolutionary biology or, in other words, evolutionary biology depends on systematics.

The media however are unaware of this process of discovery and explanation. We have no way of knowing whether Tiktaalik roseaeand Ida are our ancestors or not. All we can discover are their systematic relationships. Anything beyond that is simply speculation and lies outside the realm of empiricism. The media’s hidden agenda feeds off the latter.

If paleontology were to be promoted responsibly by the popular media, more is to be done about reporting about systematic relationships. The media’s hidden agenda however is to personify these discoveries in the context of human genealogy. For example:
    "Scientists have discovered fossils of a 375-million-year-old fish, a large scaly creature not seen before, that they say is a long-sought missing link in the evolution of some fishes from water to a life walking on four limbs on land" (Wilford, 2006: Online).
    "Meet your ancestor – the fish that crawled" (Holmes, 2006: Online).
    "In the PLoS paper itself, the scientists do not actually claim the specimen represents a direct ancestor to us. But Dr Hurum believes that is exactly what Ida is" (BBC Online 19 May, 2009).
    "Fossil Ida: extraordinary find is 'missing link' in human evolution" (Randerson 2009: Online).
The media are excited about a "missing link" (read "ancestor") rather than a new systematic discovery. For instance neither article tells us what has been discovered. Ida is a "47m-year-old primate" that is "not on the lemur line because she lacks two key characteristics shared by lemurs" (Randerson, 2009) or "She belongs to the group from which higher primates and human beings developed but my impression is she is not on the direct line" (BBC Online 19th May, 2009). Neither report states what Ida is or who she is related to. Rather we are told what she isn’t. The same is true for Tiktaalik roseae, a "375-million-year-old fish" that "… is significantly closer to the midpoint of the transition than Panderichthys," says Per Ahlberg, a palaeontologist at Uppsala University in Sweden. "Panderichthys is clearly a fish. With Tiktaalik, you're not entirely certain what to call the thing" (Holmes, 2006: Online).

What then, reading these media reports, do we know about either of these fossils from a systematic or classificatory stand-point? Not much, other than what they represent within an evolutionary scenario – a ‘missing link’, a transition from sea to land or a potential ancestor. In effect, the media has used the discoveries of fossils, and not classifications, to push evolutionary scenarios. The discoveries that were made are not reported or at best briefly covered. Tiktaalik roseae and is closely related to Acanthostega and Ichthyostega and belongs in the family Elpistostegidae. Ida, or Darwinius masillae belongs to the subfamily Cercamoniinae; however, their systematic relationship within that group is currently unknown. These two taxonomic and systematic discoveries represent scholarship within paleontology, a field that is slowly declining in importance and prominence. The evolutionary scenarios are merely speculations, guess-work based on little empirical evidence. The media, as well as the science community, need to decide which deserves greater recognition. The future of paleontology is at stake.

Sunday, 10 May 2009

The Science of Systematics

ResearchBlogging.orgIn a recent post, by John Wilkins (Evolving Thoughts), there is a quote by Borgmeier (1957):
    "As the science of order ("taxonomy"), Systematics is a pure science of relations, unconcerned with time, space, or cause. Unconcerned with time: systematics is non-historic and essentially static; it knows only a simple juxtaposition of different conditions of form. Unconcerned with space: geographical factors are not primary criteria in the definition of taxonomic units. Unconcerned with cause: systematics has no explanatory function as far as the origin of the system is concerned; it is merely comparing, determining, and classifying" (Borgmeier, 1957: 53).
On further reading we find this:
    "Systematics is independent of the theory of descent. This is admitted today [1957] even by convinced evolutionists. The reasons are as follows. (1) Systematic methods provide definite results without reference to the idea of evolution; phylogenetics has no special methods, it is essentially the interpretation of systematic facts. (2) Systematics is a science; phylogeny is a hypothesis of a historical process containing a fundamentally unverifiable element (Thompson) and can therefore never be the foundation of a science. (3) Systematics is [an] investigation of facts; phylogenetics is often 'a dangerous play with mere possibilities' (Hennig); Kant called it 'a daring adventure of the mind'

    Of course, any systematist is free to speculate on the probable phylogeny of certain species or genera, on the basis of systematic facts" (Borgmeier, 1957: 54-55; see also Williams & Ebach, 2009).
Notice the date – 1957. Cladism was gestating at the height of the Modern Synthesis. Mayr had already named his enemy – 'typology' – and created the essentialist myth. What was Borgmeier playing at? Was he an early cladist (Wilkins pers comm., 2009), or, was he someone, like Candolle (1813), who understood the importance of classification over inference?

The insistence that systematics and phylogeny should be treated separately would ally Borgmeier with Naef (1919) and Systematic morphology, rather than with the emerging numerical methods that would later predominate Hennigian cladistics. Borgmeier was not a cladist, but someone who understood the difference between phylogenetic inference and systematic classification, two fields that were as confused then as they are now. Borgmeier's message was aimed at readers of Systematic Zoology, namely evolutionary biologists and phylogenetists who insisted that their phylogenies (trees) were classification schemes (cladograms).

Borgmeier's points above may appear slightly heretical to modern day evolutionary biologists. After all 2009 is Darwin Year and a time to celebrate the achievements of evolutionary biology, rather than to dissect them. But if we do wield our scalpel at the underbelly of evolutionary biology, what do Borgmeier's three points mean for present day phylogenetics?

Decoding Borgmeier's Points for the 21 Century Phylogenetist

Point 1 "Systematic methods provide definite results without reference to the idea of evolution; phylogenetics has no special methods, it is essentially the interpretation of systematic facts." This quote consists of three parts. Take the relationship A(BC) for example. The result is definite in the sense that it states a relationship (i.e., homology, monophyly). This relationship is part of a classification, not a genealogical or phylogenetic lineage. That is, A does not necessarily have to be an ancestor of of either B or C. In fact A could be an extant mammal where as B and C could be trilobites (now extinct). This means there is no notion of time or transformation in cladograms (e.g., trilobites did not evolve from mammals). Cladograms are classifications, which depict systematic relationships that may include numerous hypothesized genealogical or phylogenetic lineages. If we skip to the third part of Borgmeier's point, namely '... it is essentially the interpretation of systematic facts', we see that phylogenetic inference comes from systematic relationships, not the other way around. In a modern context, we can hypothesize genealogical or phylogentic lineages once we discover cladograms and not the other way around (i.e., evolutionary taxonomists hypothesize lineages prior to finding classifications, hence the creation and acceptance of paraphyletic groups).

The second part to Borgmeier's point, '... phylogenetics has no special methods' is more relevant today than it was in 1957. Phylogenetic 'methods' are based only on inference. This means phylogenetic 'methods' are confused with phylogenetic models. Since models are immune to testing hypotheses, from a historical context, they fail. That is, models themselves are hypothetical and not based on actual observations. Phylogenies therefore remain hypothetical whether they fit the model or not. We will never know if A is actually ancestral to B or C through scientific methodology (i.e., testing). We can however only hypothesize which model is most 'likely', 'parsimonious' or 'similar'.

Point 2 "Systematics is a science; phylogeny is a hypothesis of a historical process containing a fundamentally unverifiable element (Thompson) and can therefore never be the foundation of a science." Point 2 proposes an interesting problem - Systematics as a science and phylogenetics as a hypothesis. Given this, the term Phylogenetic systematics appears to be an oxymoron. At one level taxa are treated in a systematic way (i.e., no concept of time or transformation), whereas on the other, characters and their states are treated as phylogenies (i.e., transformation, reversals, dating nodes etc.). Borgmeister may have seen the flaw in Hennig's system, however he didn't refer to it directly. Separating systematics as 'a science' from phylogenetics as 'a historical process' muddies the waters of cladistics. Hennigian cladistics happily confuses the two, whereas pattern cladists (sensu Brady, 1982) treats them separately (see Ebach et al. 2008). Moreover, Borgmeier's statement today would read differently; phylogenetics is now considered as a science and systematics its method. The confusion still continues.

Point 3 "Systematics is [an] investigation of facts; phylogenetics is often 'a dangerous play with mere possibilities' (Hennig)" I will not go into what 'facts' are, but for the purpose of this argument we may refer to systematics as an investigation of relationships. Point 3 is a more concise rephrasing of Point 1. Any systematic relationship may contain multiple hypothetical phylogenetic or genealogical lineages. The 'play with possibilities' becomes 'dangerous' once we use systematics to choose between them. Considering that systematics is silent about time, transformation and descent, it is impossible to use cladograms to choose one possible phylogeny over another. Other evidence is needed. After all, it is not the goal of systematics to find or propose lineages or find ancestors.

Borgmeier's three points are still relevant today. Whether phylogenetists will understand the dangers of confusing systematics with phylogenetics is another matter. The literature on this topic is readily available, but many do not realize that there is a problem. Understanding the nature of systematics and phylogenetics, their role in our research and their limitations, has more to offer than just another computer algorithm.

Malte C. Ebach & David M. Williams

References

Candolle de, A. P. (1813). Théorie élémentaire de la botanique ou exposition des principes de classification naturelle et de l'art de décrire les végétaux. Paris.
Borgmeier, T. (1957). Basic Questions of Systematics Systematic Zoology, 6, 53-69
Brady, R.H. (1982) Theoretical issues and 'pattern cladistics'. Systematic Zoology 31: 286–291.
Ebach, M.C., Morrone, J.J. & Williams, D.M (2008). A new cladistics of cladists. Biology & Philosophy 23: 153-156.
Naef, A. (1919). Idealistische Morphologie und Phylogenetik (zur Methodik der systematischen). Verlag von Gustav Fischer, Jena.
Williams, D.M & Ebach, M.C. (2009). What, Exactly, is Cladistics? Re-writing the History of Systematics and Biogeography. Acta Biotheoretica DOI:10.1007/s10441-008-9058-5.

Tuesday, 5 May 2009

Notice to Readers: Comments now moderated

The Systematics and Biogeography Blog does not tolerate hostile, intimidating or threatening comments and emails from its readers*. One such Troll, Matts Envall of Manrax AB Consulting, has been banned from this blog for hostile and threatening behavior. Other blogs and websites have also banned Envall, including Evolving Thoughts, Archetype and Wikipedia. Please note that all comments are now moderated.

* We refer to the Draft Blogger's Code of Conduct.

Friday, 1 May 2009

Paraphyly Watch 2: Paraphyly & the Catalogue of Life

A recent draft discussion document, Towards a management hierarchy (classification) for the Catalogue of Life (Gordon, 2009), contains a discussion on paraphyly:
    "It is not the purpose here to summarise the various viewpoints but a need to consider what we want from a classification is inescapable. Cavalier-Smith (1998) has given a useful discussion. One bone of contention in recent decades has been whether or not to allow the use of paraphyletic taxa in classification. A paraphyletic taxon is a monophyletic group that does not contain all the descendents (derivatives) of that group. One of the best-known examples is that of Reptilia, nominally a class of Chordata. Since it is agreed that birds (nominally class Aves) have a reptilian ancestor, and Reptilia by convention does not include Aves, then Reptilia is a paraphyletic group. But paraphyletic groups potentially abound at all levels of the taxonomic hierarchy. Indeed, there are many thousands of taxa where it is not yet known if they are paraphyletic (including some of the descendants) or holophyletic (including all of the descendants). Cavalier-Smith's classical understanding of monophyly is pragmatic, including both paraphyletic and holophyletic groups. On this understanding, Reptilia + Aves [+ Mammalia] is holophyletic whereas Reptilia alone is merely paraphyletic; either way, both are monophyletic" (Gordon, 2009, Online).
Note the definition of paraphyly: "A paraphyletic taxon is a monophyletic group that does not contain all the descendents (derivatives) of that group". This is of course an incorrect definition of paraphyly. Moreover, it uses monophyly to validate paraphyly as a 'natural' group. Paraphyly is an artificial assemblage of unrelated taxa. Dubious definitions of paraphyly fall under the category of misuse, thus making Gordon (2009) a contender for the coveted Pewter Leprechaun. But Gordon (2009) goes further: "Since it is agreed that birds (nominally class Aves) have a reptilian ancestor …" Is it? If reptiles are a group of unrelated taxa, that is some 'reptiles' are more closely related to mammals than they are to other reptiles, then it would mean birds would have multiple ancestors and therefore multiple origins. Gordon (2009) does not stop there: "Cavalier-Smith’s classical understanding of monophyly is pragmatic, including both paraphyletic and holophyletic groups. On this understanding, Reptilia + Aves [+ Mammalia] is holophyletic whereas Reptilia alone is merely paraphyletic; either way, both are monophyletic." This is a case of abuse. Reptila cannot be automatically assumed to be monophyletic just because grouping them with mammals and birds results in a monophyletic group.

The draft manuscript is a typical protest for paraphyletic groups commonly made by evolutionary taxonomists in places like Taxon or Taxacom. The usual comments are made such as plea for 'traditional Darwinian classification' and confusing cladistics with phylogenetic classification. I do hope that the problem of paraphyly is not over-looked in the final manuscript. Who am I kidding? Of course it will!

Malte C. Ebach

References
Gordon DP (2009). Towards a management hierarchy (classification) for the Catalogue of Life: Draft Discussion Document. In Species 2000 & ITIS Catalogue of Life: 2009 Annual Checklist (Bisby FA, Roskov YR, Orrell TM, Nicolson D, Paglinawan LE, Bailly N, Kirk PM, Bourgoin T, Baillargeon G., eds). CD-ROM; Species 2000: Reading, UK.

Thinking Exercise 1: Origins

Consider the following:

1
Centre of origin -----------------------------> Present Distribution


Ancestor -------------------------------------> Descendant


Plesiomorphy --------------------------------> Apomorphy

2
Each of these statements refers to a particular subject, namely an area, a taxon and a character-state. The arrow in each example indicates a transformation of some kind. For instance, taxa disperse away from a centre of origin; descendant taxa originate from ancestors and; plesiomorphic character-states transform into derived states.

3
The transformations are supported by dispersal ability, transitional fossils and plesiomorphic or apomorphic states respectively.

4
Finally, all three statements are assumed apriori to any data undergoing analysis and together form a synthesis, namely a taxon has an ancestor that dispersed from a single center of origin.

Problem 1 Dispersal ability

Just because an organism can disperse does not mean it has or will do so in the future. The seeds of alpine plants most likely are able to survive extended periods in salt water. Having this physiological tolerance to salt water does not mean for example that they have (or will) be transported from the Australian Alps, across the Tasman Sea and up into the New Zealand Alps. The same is true for rafting animals. A set number of animals are most likely able to survive extended periods rafting across seaways. Again, this does not mean that this is likely to occur.

Problem 2 Ancestors and Transitional Forms

Ancestors or transitional fossils are designated rather than real. Archaeopteryx was at one time a descendant. Since its demise in the Jurassic, it has become an ancestor and a transitional fossil without actually changing form. Transitional fossils, like ancestors, are simply terms assigned to designated forms.

Problem 3 Plesiomorphic and Apomorphic

Character-states, like transitional fossils and ancestors, are designated to be either plesiomorphic or apomorphic. The states themselves are fixed in time and space. An ancestor has plesiomorphic traits whereas a descendant has apomorphic states. The states may have a transitional form.

Qualifiers

Centers of origin, ancestors, transitional forms, apomorphic and plesimorphic character-states are all artificial designations. We have no objective or empirical way of knowing where an area is a center of origin, whether a fossil is an ancestor or whether a trait is apomorphic. These designations, however, are essential as they qualify the statements made above (1). Moreover, these qualifiers are assumed before examining data.

Data

Data are not neutral and are essentially theory / hypothesis laden. More important, data are not necessarily informative. Whether our data are informative is another matter entirely. If we use uninformative data in the above statements we are left with the same uninformative data. For instance, if a paraphyletic group is placed into each the above statements we will end up with multiple centers of origin for a single group and multiple ancestors of a single group. This would contradict our hypothesis of a single ancestor originating from a single area.

Teleology

In order for a taxon to be a descendant it requires an ancestor. If we had the means to go back in time and find this ancestor, we will find a descendant with apomorphic character-states, which has an ancestor and a center of origin. We can repeat this process again and again, but yet we will never find an ancestor, a plesiomorphic character-state or a center of origin. The reason is that these are all subjective hypothetical qualifiers that are needed to justify a theory. They are a means to an end. These metaphysical or teleological hypotheses are immune to empirical analysis.

Solution

The notion of transformation is hierarchical, particularly when it is assumed that one is a modification of the other (e.g., plesiomorphy -> apomorphy). To think otherwise is to have plesiomorphy and apomorphy as phenetic constructs requiring a method to unite (transform) them. Therefore:

Centre of origin --------------------------------> Centre of origin
-------------------------------------------------> Present Distribution

That is, for areas the occupation will be inclusive (descendant distributions = sum of all ancestral areas)

Ancestor --------------------------------------> Ancestor
-----------------------------------------------> Descendant

For ancestors the descendant will be inclusive (descendant characters = sum of all ancestral characters)

Plesiomorphy --------------------------> Plesiomorphy
---------------------------------------> Apomorphy

For apomorphy, plesiomorphic characters are included (with the apomorphy).

Tuesday, 28 April 2009

Biology & Teleology

ResearchBlogging.org

“Met the ghost of Stephen Foster at the Hotel Paradise
This is what I told him as I gazed into his eyes:
Rooms were made for carpets,
Towers made for spires,
Ships were made for cannonades to fire off from inside them ..."
(Squirrel Nut Zippers, 2002)


Findings of a recent study published in Cognition state that:
    "... college-educated adults display scientifically unwarranted teleological explanations with ease. Such findings highlight the challenges faced by educators in both the life and physical sciences. The source of popular resistance to scientific ideas appears to run deep" (Kelemen & Rosset, 2009: 143).
They certainly 'run deep' in biological systematics and in the philosophy of biology as a newly published article in the Journal of Biogeography by Heads (2009) clearly demonstrates.

According to Heads, Darwin's move away from teleological argumentation was rejected by neodarwinists who preferred purpose over structure:
    "... as his knowledge of biology and laws of growth deepened, Darwin learned to avoid teleology. Through this process he left his background behind and evolved into a modern (Renaissance) scientist. Nevertheless, Darwin's later work has been ignored whereas his earlier arguments have been co-opted as support for teleology, panselectionism and centre of originism." (Heads, 2009: Online)
Teleology and biology have been inseparable since Aristotle despite the attempts by Roger Bacon, Rene Descarte, Baruch Spinoza and Wolfgang von Goethe to undermine it completely. German idealists didn't help, neither did 19th century English naturalists, who like Kant sought to replace a theological or 'higher purpose' with Natural 'intention'.

Heads provides several excellent examples of natural teleology in systematic biology:
    "... many features of organisms are teleological, a bird's wings are for flying; eyes are for seeing ..." (Ayala, 2004:65).
    "A rock may not have a purpose but an eye does. Eyes and hands do not just happen for no reason" (Ruse, 2003:33).
Teleology, according to Heads, seems to be embraced by some philosophers of biology:
    "... a vitally important tool for looking into the organic world" (Ruse, 2002: 47).
The problem of teleology is rampant in systematics and biogeography, with few opposing it and others, like Ernst Mayr, using weak arguments:
    "[Mayr] recognized that the teleology in biology was a serious problem. His solution was to suggest that the modern synthesis is not really teleological, and that it uses teleological language but not teleological thinking" (Heads, 2009: Online).
I believe that Heads, like Kelemen & Rosset (2009), has pin-pointed the problem behind teleology, namely we start out as teleologists. Once we accept this fact, we have a lot of unlearning to do. I whole-heartily recommend Heads (2009) for students of systematics and biogeography.

Malte C. Ebach

References
Ayala, F.J. (2004) Design without designer: Darwin's greatest discovery. Debating design: from Darwin to DNA (ed. by W.A. Dembski and M. Ruse), pp. 55–80. Cambridge University Press, New York.
Heads, M. (2009). Darwin’s changing views on evolution: from centres of origin and teleology to vicariance and incomplete lineage sorting Journal of Biogeography DOI: 10.1111/j.1365-2699.2009.02127.x
Kelemen, D., & Rosset, E. (2009). The Human Function Compunction: Teleological explanation in adults Cognition, 111 (1), 138-143 DOI: 10.1016/j.cognition.2009.01.001
Ruse, M. (2002) Evolutionary biology and teleological thinking. Functions: new essays in the philosophy of psychology and biology (ed. by A. Ariew, R. Cummins and M. Perlman), pp. 33–62. Oxford University Press, New York.

Thursday, 23 April 2009

Phylogeology – A New Revolution in Phylogenetics

From the Wollongong Herald

Evolutionary biologists were stunned this week by the news of Geological Phylogenetics. "Genetics is dead" says geologist Prof. Trevor Bruce of the University of Ulladulla, Australia. For 20 years molecular DNA has changed the way biologists do phylogenetics. Geological Phylogenetics, or Phylogeology, proposes to dispense with biological data all together. Prof. Bruce explains, "Molecular systematics has removed any notion of morphology, anatomy and taxonomy. We intend to get rid of molecules, making phylogenetics essentially free of any biological data". The benefits of phylogeology are that only atoms will be analyzed. "All you need is a very large industrial-strength food processor and a mass spectrometer". Prof Bruce's team has successfully pureed an array of organisms including two pot plants, a goldfish and Dr. Hall's cat. "She wasn't too happy about it, so we made her first author" says Prof. Bruce. "So far we have analyzed percentages of 30 common elements including carbon, calcium iron and copper". And success! Already Prof. Bruce's team has the data for most common household pets and their relationships. "It's simple" explains Dr. Hall, "a dog and a cat will have a similar atomic make-up, just like two similar rocks. As genetics has brought its methods and theory into phylogenetics, we bring geological techniques. Pureeing and 'mass-specing' critters are one of them".

But phylogeology has its critics. Molecular systematists have dismissed Dr Hall's contribution. "DNA and molecular data is the basic unit of heredity. Nothing can replace it" say Drs Goodray and Frat. "Rubbish!" retorts Prof. Bruce, "molecular data is fraught with paralogy, xenology and dodgy alignment. They may be dealing with a 'basic unit of heredity', but we are dealing with the basic unit of all matter". Already new applications have been proposed. "Forget DNA Barcoding, now we have 'Tricording' – a way to measure all matter within an organism" says Dr. Hall. The proposal has lead large funding bodies to drop proposals for DNA research. The NSF, NERC and other national grants are excited by phylogeology. "Finally we can get rid of that expensive out-of-date DNA mumbo-jumbo. Now we can categorize phylogenetics as organic chemistry" says Dr. Komby of the Research Funding Board. "Imagine how much money we'll save, not sequencing data, getting rid of the Tree of Life (AToL) and all other biological systematic projects. This heralds a new age in evolution".

'Darwin Year', marked by the 200th anniversary of the father of evolution, represents a new era of development - from the biological toward the physical sciences. "Biology is simply stamp-collecting" remarks Prof. Bruce, "we're better off working out how the origin of the cosmos has shaped life on Earth". Even creationists have responded to Prof. Bruce's call. "This is the end of evolution" states Mark McCall, Director of the DIY Creationist Center, Kansas, "This new development disproves life altogether". Phylogeology has already made an impact on financiers who understand its cost-effective nature. Investors, like Arnold Grady, are beaming, "Considering that the technology behind food processors is rapidly evolving, we could puree, say a dog, in five seconds and have it mass-speced in ten. I'd buy into that".

Biology may be on its last legs, but what of the bird-watcher or fish-fancier? We ask amateur fish breeder Allan Cement, "They are fish, not atoms! Can't scientists just study them?"

Malte C. Ebach

Thursday, 19 March 2009

Myths that Evolutionary Taxonomists live by

Confused evolutionary taxonomists have once again made a stand in the pages of Taxon. The editorial by Brickell et al. (2008) represents a vote of no confidence in favour of paraphyletic groups - as if democracy in science has (or ever had) any valid scientific or empirical merit. This time the confusion stems from
    "Recent developments in taxonomic theory have resulted in the production of classifications of the Flowering Plants that are causing concern to all involved in horticulture — gardeners (both amateur and professional), nurserymen, landscape architects, foresters, designers, conservationists, and journalists, as well as to botanists engaged in many different, non-taxonomic disciplines and to other users of plant names generally" (Brickell et al., 2008:1047).
One wonders what those nasty molecular phylocodists and monophyly-peddling robbers of horticultural dignity are up to? Perhaps plotting horrid phenetic-cladogram-trees?

They certainly are a confused mob as the above mockery demonstrates. One way out of this wet paper bag is to see the world from a evolutionary point-of-view. Artificial classifications, which are useful in identifying plants, for example, are not necessarily evolutionary (in the sense of monophyletic). Some may turn out to be, but only empiricism will provide us with the necessary evidence. That is we need cladistic methods to test taxonomic claims of relatedness (i.e., monophyly). Evidence and empiricism, however, appear to be of no use to Brickell et al.(2008).
    "Cases such as these (and there are more that could be quoted) have arisen from a fundamentalist approach to cladistic methodology, which requires that a classification should not include paraphyletic taxa"(Brickell et al., 2008:1047).
I tire of saying this: Paraphyletic taxa are not of any use. They do not represent natural classifications. They are not a result of a common shared history. Paraphyletic groups are not anything other than names, just as 'leprechauns', 'unicorns' and 'griffins' are only names. Why then do horticulturalists and evolutionary taxonomists want them in their classifications?

This is because paraphyly is not a phylogenetic problem (phylogenies are essentially monophyletic - don't get confused with genealogies, which have nothing to do with classification). Paraphyly is taxonomic problem that evolutionary taxonomists refuse to face. If a group is paraphyletic, it means it has failed an empirical test for natural grouping. It needs to be revised. Revising groups is what taxonomists do best. Instead of embracing cladistics as a valuable tool, evolutionary taxonomists like Brickell et al. (2008) dismiss it because their favorite taxonomic groups under threat from revision. Acknowledging that one's group is paraphyletic and therefore requiring revision does not make you a bad taxonomist. Keeping non-existent groups however is. I don't want to say that Brickell et al. (2008) are 'bad taxonomists'. They a bunch of misguided evolutionary taxonomists who are confusing different things, namely artificial and natural classifications - an on-going problem since the 18th century. This confusion has led to several 'myths that evolutionary taxonomists live by'. I use Brickell et al. (2008) as an example.

Myth 1: If it ain't broke, don't fix it

One common misconception is that of historical 'significance' or 'pragmatism' in science. For example, 'Reptiles' is a wonderful term and describes all manner of organisms such as fire-breathing dragons, sea serpents and the Sea Devils from Dr. Who. (Remember them?) This does not mean that the Reptilia are immune to scrutiny or empiricism - in fact they're not. The same is true for taxa within the angiosperms
    "We, as horticulturists and horticultural taxonomists, wish to express our strong support for these pragmatic views, which will encourage the retention of familiar and widely used taxa [e.g., Dionysia, Dodecatheon, Soldanella, Omphalogramma, and Cortusa] which are distinctive and historically important" (Brickell et al., 2008:1047).
I empathize. Good names that are linked to poorly defined groups (which, incidentally is what makes them paraphyletic) sucks. But that's life ... sorry, that's systematics.

Myth 2: Taxonomy needs to be 'stable'

There is no such thing as a completely stable classification of living things. This is not because everything is fluid and 'moving' and 'unclassifiable'. As new evidence comes to light (e.g., molecular data), so do new discoveries. But Brickell et al. (2008) beg to differ
    "We are not against taxonomic change, which will continue to be a standard outcome of taxonomic research, but insist that horticulture needs a stable (though not static) classification and nomenclature that can be understood and applied effectively by horticulturists (and others) who exhibit a very wide range of levels of taxonomic sophistication.
Clearly they are against taxonomic change as that is what paraphyletic groups inevitably lead to - taxonomic change.

Myth 3: The needs of end-users are important

Let's face it, the end users of taxonomy are mostly other taxonomists. Regardless of the descriptions and keys out there, trilobite collectors and purveyors of fossils for instance, still insist on calling any large brimmed harpetid from the Devonian rocks of Morocco Scotoharpes. (The aforementioned genus does not occur in Morocco or in the Devonian). The concerns of end users is quite topical at the moment and will not be discussed in depth here (see Wheeler et al. 2004). The fact of the matter is that end users have to share the burden of changing taxonomies. This may make horticulture and conservation for example harder to do, but many are attempting to reduce this burden through employing new electronic media, which has created new emerging fields such as biodiversity informatics and cybertaxonomy.

Myth 4: Molecular systematists and cladists are all phylocodists

This is a myth that has been exacerbated by Brummitt (2006, 2008). Not all molecular systematists and cladists agree with the phylocode. In fact some of the most ardent critics of the Phylocode are cladists who use molecular data (e.g., see Nixon et al. 2003). Moreover, supporting monophyletic taxa does not automatically make you a Phylocodist or anti-Linnean. Here is an example from (Brickell et al., 2008:1047)
    "(cf. Brummitt in a note to a colleague: ‘By any logical consideration either one has a monophyletic system with an infinite number of nodes but no ranks, for which the PhyloCode is designed, or you have the Linnaean system with ranks at very few levels, and paraphyletic taxa’".
Classifications are not divided into 'the Phylocode' versus 'Linnaean taxonomy'. This dichotomy is false. The Linnaean system of taxonomy remains silent about paraphyly or monophyly. Biological classification consist of artificial and natural systems, the modern Linnaean System belonging to the later. As taxonomists, we aim to find natural groups (a.k.a 'monophyletic groups') in our Linnaean System. But paraphyletic groups, like Linnaeus sexual system, are artificial. They may be useful in identifying organisms, but they do not reflect natural evolutionary groups and should be exempt from our classifications. Brickell et al. (2008) are misguided and confused if they are to believe that paraphyletic groups are 'natural' or even evolutionary in anyway.

Myth 5: What does the Molecular data mean?

There are many ways to tell someone to p*ss off and this is a beaut:
    "In saying this we do not wish to imply that phylogenetic studies are unimportant or uninteresting; only that the purpose for which they are produced is not applicable to horticultural needs and practices. (Brickell et al., 2008:1047-1048)"
I agree. Molecular trees (which is what Brickell et al., 2008 are referring to above) do not have any characters listed at their nodes. If horticulturalists are to follow our lead and adopt new groups based on molecular data, then show us the characters that support it as a monophyletic group. If the group is paraphyletic then do the revisionary taxonomy. There is however a catch. Molecular systematists do not necessarily do all the work. Saying that something is paraphyletic and in need of revision without any morphological evidence is hard for any taxonomist or horticulturalist to swallow. I think that Brickell et al.(2008) are on to something here and it is well worth pursuing. Consider this myth busted.

Unfortunately Brickell et al. (2008) do not qualify for this year's Pewter Leprechaun although their attempts at misusing paraphyly have reached a particular zenith.

References
Brickell, C.D., Crawley, M., Cullen, J., Frodin, D.G., Gardner, M., Grey-Wilson, C., Hillier, J., Knees, S., Lancaster, R., Mathew, B.F., Matthews, V.A., Miller, T., Noltie, H.F., Norton, S., Oakeley, H.J., Richards, J., Woodhead, J. (2008). Do the views of users of taxonomic output count for anything? Taxon 57:1047–1048. Nixon, K. C., J. M. Carpenter, and D. W. Stevenson. 2003. The PhyloCode is fatally flawed, and the "Linnaean" system can easily be fixed. Bot. Rev. 69: 111–120. Wheeler, Q. D., Raven, P. H., Wilson, E. O. 2004. Taxonomy: Impediment or expedient? Science 305: 285.

Tuesday, 17 February 2009

Wordle: A Wonderful Thing


Ivonne Garzon has introduced me to Wordle - a world cloud generator. In the example above I simply entered the Systematics & Biogeography URL and it created several word clouds with names and terms that appear on the blog. This is great way to simply skim over a blog (or any URL that has a RSS feed) to find terms or names of interest. You can also cut and paste in text of your own as I did below - from the abstract of the forthcoming paper by Polly Winsor. Looks interesting!

References
Winsor, M.P. (In press). Taxonomy was the foundation of Darwin's evolution. Taxon.

Friday, 6 February 2009

Media Watch: Sponges

ResearchBlogging.orgSurfing the web I came across several news articles reporting on a recent comment in Nature by Brocks & Butterfield (2009). I wondered if I could get an idea of their research (or discovery) just through reading what the average punter would read in the newspapers or online. Would the news coverage be fair or sensationalist? Here is what I found.

This, from the free daily UK paper called the Metro:
    "If you felt a bit soggy while walking through the snow this week, it's because your relatives were sponges. Well, your ancestors who lived 635 million years ago were.
    Mankind is thought to have evolved from primitive sea sponges, according to a study of fossils found in rocks in Oman.
    They are thought to date to the last ice age, according to the US research in Nature journal."
The Daily Mail decided to run with:
    Meet the ancestors: Earliest evidence of life suggests humans descended from sponges 635 million years ago
The Scotsman leads with this perplexing title: In the beginning God created the sponge. The article continues:
    "Now scientists say they have discovered the missing link in the chain of evolution. They have found evidence of the oldest animal life yet discovered on Earth – ancient sponges that lived 635 million years ago".
The Telegraph seems to have passed on the 'Sponge Ancestor', sticking with their earlier (March 5, 2008) story Comb jellies were our first ancestor instead.

Anyone reading this on the 8.20 tube from Cockfosters would understand that the research is about discovering ancestors (i.e., missing links, a poriferan Adam & Eve). I had to see what Brocks & Butterfield (2009) wrote about 'ancestors':
    "So, what exactly were the organisms that produced these biomarkers? The most obvious answer, and the one that the authors plump for, is that demosponges had evolved and become ecologically prominent by at least the late Cryogenian. But this conclusion overlooks the evolutionary nature of biological taxa and the incremental assembly of defining characteristics along (now-extinct) 'stem lineages'. It is only with a full complement of such characteristics — in the last common ancestor of the extant 'crown group' — that modern taxonomic boundaries apply (...) Combined with new biomarker data and molecular phylo genomics, the identification of such signals promises to pinpoint the first appearance of our earliest animal ancestors." (Brocks and Butterfield, 2009: 673).
The press, again, have missed the point. Mankind did not evolve from primitive sea sponges - something the study by Brocks & Butterfield (2009) did not state. Moreover, the Metro makes the mistake of stating that "...your relatives were sponges". In fact all life is related (and in the presence tense - our relatives were and still are sponges. Same is true for trilobites and nudibranchs). Surprizingly however, the BBC News online managed not to bungle it and grab a relevant sound bite: "We're not saying we captured the first animal; we're saying they're an early animal phylum and we're capturing them when their biomass was significant" - a departure from their normal misquotes and stories invariably taken out of context.

The Daily Mail Online however, do go on to publish a Reuters report by Michael Kahn that best summaries the research: "Chemical traces left in 635 million-year-old rocks in Oman provide the earliest evidence so far of animal life, researchers said Wednesday". Why the Mail didn't go with Reuter's original title Scientists find earliest evidence of animal life has more to do with sensationalism than with science journalism.

References
Jochen J. Brocks, Nicholas J. Butterfield (2009). Biogeochemistry: Early animals out in the cold Nature, 457 (7230), 672-673 DOI: 10.1038/457672a

Friday, 23 January 2009

An Interview with Mr. Darwin

On Friday afternoon Dave and Malte step into the Hoop and Toy for their regular ‘end-of-the-week’ pint (or three).

At the bar they are approached by a dark and mysterious man with a cockney accent and an unlit cigarette hanging precariously from his lips. “’Ere, interest’d in a time machine?” David chokes on his beer. “‘Ow much den?” (David is also a cockney, so it’s going to be a bit complicated). Anyway, they buy it for a fiver (5 British Pounds Sterling).

It takes six pints and a Japanese translator (an unwitting tourist) to work out how the thing turns on. Within two hours and a spectacular light display, too complex to describe here, Malte and Dave make it to 19th century England. Due to the Earth’s orbit, and other dreary time-space continuum explanations privy only to Doctor Who fans, they end up in the village of Downe in Kent, 1862.

“Sh*t, where are we?”
“Dunno. Fancy a pint?”

After several hours in the
George and Dragon Inn – David and Malte discover that they are only 20 minutes away by horse-and-cart from Down House, home of Charles Darwin.

“Hang on. What if we interviewed Chuck for our blog, eh?” The pints were taking their toll.
“That’ll show them who's wrong!”


An Interview with Mr. Darwin

[Loud banging on door - followed by intermittent singing and shushing. A distinguished, but slight nervous looking, gentleman opens the door a crack. A brass chain can be seen securing it to the rest of Down House]
    “Chucky!”
    “I do not wish to purchase excessive merriment from two louts! Please be off with you!
    “Hey, Chuck … sorry Mr. Darwin. We are schistema … cystmena … nat … naturists …?”
    “I am ill. Please go away!”
    “… Naturalists!”
    “I am very sick. Please let leave me in peace!”
    “… from the futu… er … Australia …”
    “I’m not talking to you. I am too ill. Please remove your foot from my door!”
    “Look, in the future people are all fighting over your ideas and your work. Evolution has become an explanation for almost everything and you seem to be considered the originator of all modern ideas in biological classification, as well as, plant and animal geography!”
[Darwin paused for a moment and seemed to relax].
    “But why? Ideas are developed through time. Evolution is an idea to which I had been introduced. Most of it made no sense. Some of it was simply nonsensical. I make no excuse for my ideas, but surely a good rational explanation makes for a better understanding of the processes at work?”
    “… er… What?”
    “Where do you think I got my ideas from? I didn’t just invent them there and then! They evolved from other ideas.”
[Dave and Malte think this is a pun and giggle]
    But people in the future think 1859 and your Origin was a turning point for biology!”
    “Please make no such assumption! I, Monsieur Lamarck and probably others, have provided ways with which to explain the biological world. It is not the answer but simply an explanation that I am convinced is good and rational …”
    “But ..”
    “I am ill. Goodbye to you sir!”
[David and Malte look at each other].
    “He called me sir!”
    “Want to interview Agassiz?”