Systematics and Biogeography

Publications for 2011

2012-01-09T14:49:00.000-08:00

Below is our list of publications for 2011. For those with no access to the links, will be happy to provide pdf copies on request.

Cecca, F., Morrone, J.J. and Ebach, M.C. (2011). Biogeographical convergence and time-slicing in cladistic biogeography: Concepts and methods. In P. Upchurch; A. McGowan & C. Slater (eds.), Palaeogeography and Palaeobiogeography: Biodiversity in Space and Time. Taylor & Francis (CRC Press), Boca Raton, Florida, pp. 1-12.

Ebach, M.C. (2011). Taxonomy and the DNA Barcoding Enterprise. Zootaxa, 2742: 67–68.

Ebach, M.C. (2011). Biogeógrafos del mundo... ¡uníos!: un camino hacia la unificación. Revista de Geografía Norte Grande, 48: 5-10.

Ebach, M.C., de Carvalho M.R. and Nihei, S.S. (2011). Saving Our Science from Ourselves: The Plight of Biological Classification. Revista Brasileira de Entomologia, 55: 149–153.

Ebach, M.C., de Carvalho, M.R. and Williams, D.M. (2011). Opening Pandora’s Molecular Box. Zootaxa, 2946: 60—64.

Ebach, M.C. and Williams, D.M. (2011). A Devil's Glossary for Biological Systematics. History and Philosophy of the Life Science,s 33: 251—258.

Ebach, M.C., Valdecasas, A.G. and Wheeler, Q.D. (2011). Impediments to Taxonomy and Users of Taxonomy: Accessibility and Impact Evaluation. Cladistics, 27: 550–557. Levkov, Z. and

Williams, D.M. (2011). Fifteen new diatom (Bacillariophyta) species from Lake Ohrid, Macedonia. Phytotaxa, 30: 1—41.

Mooi, R.D., Williams, D.M., and Gill, A.C. (2011). Numerical cladistics, an unintentional refuge for phenetics – a reply to Wiley et al. Zootaxa, 2946: 17—28.

Williams, D.M. (2011). Synedra, Ulnaria: definitions and descriptions – a partial resolution. Diatom Research, http://dx.doi.org/10.1080/0269249X.2011.587646

Williams, D.M. and Gill, A.C. (2011). ‘Adventures in the fish trade’ by Colin Patterson, edited and with an introduction by David M. Williams & Anthony C. Gill. Zootaxa, 2946: 118—136.

Williams, D.M. and Kociolek, J.P. (2011). An overview of diatom classification with some prospects for the future. The Diatom World (Sebach, J & Kociolek, JP, eds), pp. 47—91.

Agnosticism in Comparative Biology

2011-12-15T13:29:00.000-08:00

Gnostic adj. of or relating to knowledge (from gnōstos meaning 'known')

Agnostic adj. a person who believes that nothing is known on some topic, either at the present, or in principle

In the philosophy of religion and recent public debates over atheism, a distinction is made of the difference between believing in God (theism) and not believing in God (atheism), but a third option, agnosticism is often regarded as the equivocation or uncertainty about whether or not there is a God. In fact, agnosticism is the denial that the existence of a God can be known one way or the other, and that we should stick to the facts we do know. Agnostics reject gnosticism of either kind. In biology, there are similar matters to consider.
Comparative biology is a now relatively unpopular (and often thought to be outmoded, replaced by unqualified reliance upon molecular data) approach to the nature and relationships of living things. So, what is knowledge in comparative biology? We are able to observe and therefore know organisms and their parts from fossil and living specimens to some degree through direct acquaintance, under microscopes, or as gels and know something of their behaviour, genetics and ontogeny. We can even see fertilization, cell growth, life cycles and environmental conditions in modern organisms. Knowledge, in comparative biology, is inextricably linked to what we can observe. It is empiricism of the highest order, and relies upon actual observations as the basis for knowledge claims. However, it is what we can predict (rather than observe), which makes comparative biology 'interesting' to the majority of contemporary biologists.

Given the hypothesis-driven emphasis in of 21st century comparative biology, many systematists and biogeographers have made their careers on predictions and modelling. We believe we can, for instance, predict divergence times based on molecular clocks. We attempt to predict which taxa and areas are ancestral based on models of evolution and geography. However none of these predictions are knowledge to the comparative biologist, as proponents of these models can never prove their predictions beyond a hypothesis, best guess or hunch. At best, they have tested, and to that extent warranted, theories. Warranted theories are far less reliable and certain than observations, and they hitchhike on data.

Call this "experimental envy" if you wish, but comparative biology is simply that - comparative. Knowledge for the comparative biologist lies in the ability to recognise organisms and their parts (as described above). If, for instance, a prediction proves to be true at some point in time, it was the comparative biologists' observation and knowledge of the organism, rather than a knowledge of a particular evolutionary process, that grounded that prediction. Theories and hypothesis are dependent on evidence (e.g., observation).

But knowledge of an organism is not enough. In their quest to predict and model, the contemporary comparative biologist is insisting a certain 'knowledge' of processes that extend beyond known and observable material phenomena. They claim to know what they cannot: that their hypotheses are true. Using their prior hypotheses, they ground their later ones on probabilities and likelihoods that are no better founded than the strength of the priors. Hypotheses build on hypotheses. This is inference, but it is not knowledge.

It appears that some comparative biologists appear to exhibit a certain form of non-religious and secular gnosticism - analogous to the gnosticism of atheists and theists described by Huxley when he coined the term "agnostic". That is, they claim to know more than what the evidence (i.e., data) can possibly claim. One example is ancestors. Having found the oldest known specimen of trilobite does not mean one has found the ancestor of all trilobites. What is known is that it is the oldest at the time of discovery - an older one may still exist. A trilobite's relations are inferred and always defeasible by new data. Data are not defeasible, however.

This phylogenetic agnosticism does not deny the existence of ancestors or centres of origin, only of our ability to recognise them with much certainty based on what we know (as opposed to what we merely think).

We recognise that a form of gnosticism has arisen in comparative biology since the 19th century due to the blurring of what we know for sure and what we believe we know. What we know is limited and restricted to what we can observe. What we believe to be happening, however, is not knowledge, but a best guess or informed opinion. Confusing it with actual knowledge creates a gnosticism that is already quite widespread in biology.

We appeal for warranted agnosticism, one that recognises the distinct difference between what we do know and what we believe we know. For instance, we may say that "I know this is a mammal" based on the diagnosis of mammals. We may also confidentially state that "I believe this to be the centre of origin for all palms" based our conviction of the truth of a theory of dispersal and speciation. For example we may be convinced that method x is better than say method y. On this basis we can determine which method is better. However, knowing which method is better does not guarantee that method will extend our knowledge of other unobservable processes.

What agnosticism in comparative biology is not, is banning, denigrating or rejecting certain hypotheses because they are not based on knowledge. Every comparative biologist has the right to express their convictions and opinions. They do not, however, have the right to confuse knowledge with a hypothesis. Doing so illicitly validates a hypothesis (i.e., a conjecture or best guess) as a discovery or known fact. A good comparative biologist is agnostic to all hypotheses and theories, until they are demonstrated to be true.

The highest happiness of man is to have probed what is knowable and quietly to revere what is unknowable (Goethe).

John S. Wilkins contributed a portion of this post. Please cite as Ebach, M.C., Wilkins, J.S. and Williams, D.M. (2011). Knowledge and Agnosticism in Comparative Biology. Systematics and; Biogeography Blog, http://urhomology.blogspot.com/2011/12/agnosticism-in-comparative-biology.html

Tweeted Histories I #Homology

2011-11-09T12:58:00.000-08:00

@Goethe1824 I can relate a worm and a man via a third thing! I'll write a poem about it!
@sexy_Blumnbch What?
@henrich.B if you hang a human skeleton next to that of bird, you can compare their structures #Bronn1858

@Darwinathome's birdy

@sexy_Blumnbch Eww!
@MonsterMoa nah! what you want is a bauplan. #Owen1849
@Swiss_Pride What evidence have you got? You need space, time as well as form! #Agassiz1859
@Embryo.boy I think he means comparing embryos and how they develop #Gegenbaur1859
@Swiss_Pride no I don't!
@Darwinathome I found a birdy!
@MonsterMoa just compare the forearms of bats, humans and whales. See? Analogy!
@RayL Don’t just compare: find the origin of things. Homology? Bah! Homogeny!
@asagray I like @Darwinathome's birdy. Can u send photo?
@Stammbaum Origins, we need origins! My own Stammbaum gives origins; now all is homogeny
@Darwinathome can someone tell @Stammbaum to leave me alone?
@RayL Not all is homogeny, some comparisons are not true: homoplasy!
@Stammbaum Who cares. I have lots of stammbaume, one for every creature. All with homogeny, homoplasy and homology
@naefnotnaf @Stammbaum got it wrong. You can't mix phylogeny and systematics #Naef1919
@naefnotnaf homology is a systematic relationship separate from phylogeny
@angry_mayr Typologist!
@Zimmermann no it's not! homology is a transformational relationship.
@a.remane or a process #Remane1952
@willi Why not compromise? Use @naefnotnaf's systematics for taxa and @Zimmermann for their characters! #Hennig1950
@ggsimp what about ancestors? Homology is similarity between the bits of us and ancestors
@sokal_123 you mean overall similarity at a node? #SokalSneath63
@willi no, special similarity, that is synapomorphy #Hennig66
@angry_mayr Cladist!
@nelson_usa perhaps it's a non-transformational relationship? #NelsonPlat81
@beaty.boy Pattern Cladist!
@Colin82 non-transformational but based on similarity #Patterson82
@ron.brady forget similarity, homology is simply an affinity. See @Goethe1824
@normlovesspiders homology is a three-item relationship regardless what is based on
@hennig_superstar %$#%! Homology is synapomorphy?
@k.nixon homology = synapomorphy + symplesiomorphy #NixonCarp11

The Autonomous Algorithm: Malpractice in Theory

2011-11-06T15:48:00.000-08:00

In our last post we introduced the topic of the Autonomous Algorithm, a black box that acts as the foundation for a theory and method. In this post we explain what we mean by theory and method and why we believe that no tool can function as a logical foundation. Doing so is a form of malpractice.

For all the non-philosophers reading this post, we define theory as a set of mathematical principles on which an activity is based. The set of principles that underlie the study of geophysics is that radio waves and sound waves for instance have different levels of penetration. When a sound wave is reflected it can tell us the density and depth of an object, like a rock. These principles are based on physics, and not on the actual program that models the depth and density of rock. Doing that would be putting the cart before the horse. If we change the way we model the results of our acoustic test, we do not change the underlying principles of physics.

A method is a procedure to accomplish something. Methods are generally activities that can be done by pen and paper (although sometimes they are easier when automated) in which we determine the steps, for instance, to find out how to tell what is beneath a particular surface. The implementation is the tool that is used to do implement the method. This is usually as a computer algorithm. So, an algorithm is a tool that is based on a method that is underpinned by a theory. Seems simple enough, but this is often misinterpreted.
Take parsimony for example (and by parsimony we mean Wagner parsimony). It is a method that has several implementations. It is not a theory. The theory is phylogenetic systematics. In recent times, however, many have unwittingly chosen to treat the implementation as a tool for testing a method that in turn decides what the theory should be. Not only is this non-empirical and non-scientific, it is also a form of malpractice within systematics.

Algorithms are simply tools. The algorithm/s in parsimony programs, for example, are not capable of recognising reversals, parsimony, evolution, plesiomorphy, homology and synapomorphy. They are tools that manipulate binary digits to do certain things. When character-state 0 in character 1 of Taxon A is forced to be basal (because of a 0 present in the outgroup), its appearance further up the branching diagram is interpreted as a reversal by the operator (us), not by the algorithm. Parsimony programs have no concept of transformation. That concept lives with the operator (us).

So what are these programs doing? In one sense they are mimicking concepts that would remain incomprehensible to any machine (naturally). To use one of Douglas Adams' analogies, an algorithm doesn't know what transformation is as much as a "tea-leaf knows the history of the East India Company".

Transformations, reversals, plesiomorphies are all concepts interpreted by us. What is a reversal to one user is homoplasy to another. The current crop of algorithms act upon and manipulate 'similarities' not homologies. They are phenetic methods. While this is not a bad thing (providing we do not interpret our cladograms to be the real thing), phenetics does have its limitations: it cannot identify homology. This is left to us, the observer and user of a program.

Malpractice in phylogenetics is due to interpreting a quantitative result as qualitative reality. For example, representation is a relationship interpreted by similarity only. Algorithms represent real objects (e.g., think of two binary characters depicting the presence of wings). Representation however is often confused with replication, namely a copy of a real object. Algorithms cannot replicate evolution, reversal, transformation, homology and so on. Assuming that it does and presenting results in this way is a form of malpractice.

Where this type of thinking has lead us is to the incorrect notion that a homolog (the part of any organism) is actually a homology (that organism's relationships). But more of this in the next post.

The Autonomous Algorithm

2011-08-24T13:46:00.000-07:00

The S&B Blog will be running a series of posts dealing with the rise of the black box and the fall of the foundations of systematics.


The Timetree of Life: A product of the Autonomous Algorithm?

Presently, the majority of systematic analyses are constructed in the same way - a matrix is assembled and fed into a computer that then produces a branching diagram. Students of systematics are taught how to produce this branching diagram, using the algorithm, without context to the foundations of systematics. The result is a whole new generation of computer users ignorant of the basic fundamentals of systematics, such as theory (i.e., homology, monophyly), history (i.e., why we do what we do) and methodology (i.e., how to find homologs and construct a cladogram by hand). This also results in an increased dependency on algorithms, which in turn creates a new systematic history and theory that revolves around algorithms rather than concepts. The former black box, which implemented basic algorithms to find approximations of cladograms, is now totally autonomous to the theory, method and history that had gone into its creation. We call this the Autonomous Algorithm.

The Autonomous Algorithm is a self perpetuating phenomenon. Many users of phylogenetic software are unaware of the foundations of systematics and are totally reliant on algorithms to do their work. They are also dependent on the developers and programmers, who themselves are dimly aware of the foundations and their relevance to each new published algorithm. The Autonomous Algorithm has created a number of problems which we will attempt to address, namely:

Malpractice in Theory: Homologs as Homology
Misaligned Methodology: Cladistics as Phenetics
A Misconstrued History: Systematics as Phylogenetics

Before we begin, we wish to reemphasise our terminology to avoid any confusion.

Rationale of Terms

Theory herein are the basic fundamental principles underlying what we do. This means defining what we do and its associated logical procedures.

Methodology herein is the practice of what we do. Creating cladograms by hand, finding homologs, understanding the anatomy of an organism etc. are all part of what a systematist does.

Implementation herein refers to the numerical tools we use. These are generally black boxes (i.e., software that uses numerous algorithms that process our data). Most systematists are generally unaware of how these work exactly, but use them by proxy. An implementation is not equivalent to a methodology.

History herein is the history of an idea. This is sometimes referred to as an ‘internalist history’, since we are concerned with the theory and methodology of systematics over time. Whatever external history has occurred generally is irrelevant to how a systematic method works.

A natural classification herein is a hierarchical ordering of organisms based on systematic relationship.

A systematic relationship equivalent to kinship, that is, when two taxa are more closely related to each other than they are to any other taxon (herein systematic Monophyly or sMonophyly). Relationship here means a shared history. In hindsight this shared history is a result of some known or unknown evolutionary process/es. This relationship is only true if the relationship is based on two homologs that are more closely related to each other than they are to any other homolog (sHomology).

The Cladistic Parameter (herein CP) is a hierarchical representation all manifestations of a systematic relationship. Homology, for instance is a systematic relationship of homologs, or the parts of an organism, while monophyly is a relationship of taxa based on homologies. This can be expressed diagrammatically (as branching diagrams) to highlight the dependancy of one relationship within another, that is to say monophyly cannot exist without homology and homology cannot exist without a relationship between homologs, or:

The Cladistic Parameter = Relationship : sHomology : sMonophyly : sTaxon

sTaxa herein are deemed to be relationships between organisms (e.g., their parts, individuals, populations, etc.). We recognize that there are many artificial taxa that share closer relationships to other taxa than they do to themselves (e.g., reptiles, fish etc.). These taxa are not informative and add little to our knowledge of natural classifications. When we refer to sTaxa we refer to natural classifications.

In the next post we will tackle Malpractice in Theory, namely the widespread phenomenon of confusing homologs with homology.

Willi Hennig (1913 - 1976)

2011-04-20T02:30:00.000-07:00

The great entomologist Willi Hennig (1913—1976), founder of ‘Phylogenetic Systematics’, was born on this day. Had he lived, he’d be 98.

So Long, and Thanks for All the Fish

2011-02-04T01:08:00.000-08:00

It’s time to say goodbye to Paraphyly Watch, paraphyly, holophyly and all who sailed in them. It was fun while it lasted but all good things must come to an end and, alas, as you can see, we are moving on, redesigning, removing and rolling on. The year 2010 witnessed a spate of relevant papers to the Watch but time and inclination prevent us from devoting ourselves to their contents and absorbing their message. Save one last remark.

For us, organisms and taxa, taxa and areas call our attention, and our time might be more usefully spent elsewhere, doing these other things. It is these other things our blog will now be chiefly devoted, such that we might find subjects worthy of study, particularly classification and all its implications. Evolution is one such implication. Evolution, too, is a subject we find of interest. Hennig devoted many pages to the subject of classification – and evolution, as it happens. Our view contrasts with that of Cavalier-Smith:

“Real evolution often ignores Germanic cladistic logic; its messiness and lack of rules makes classification an art where compromise is necessary and rigid formalism harmful” (Cavalier-Smith 2010, p. 115).

German logic? ‘Real’ evolution? Classification as ‘art’? Cavalier-Smith continues:

“I agree with Mayr (1974), Halstead (1978) and others that the Hennigian perspective impedes realistic scientific discussion of phylogenetic history, because of its evolutionarily unrealistic formalism based on an intellectually impoverished view of the complexities of actual phylogenies, especially its failure to come to grips with evolutionary transformation, the reality of ancestors, and not least its dogmatism” (Cavalier-Smith 2010, p. 116).

“Realistic scientific discussion of phylogenetic history”? Cavalier-Smith embraces paraphyly; it looms large in his many works, they are sprinkled liberally among his various, ever-changing classifications, his artworks(Cavalier-Smith 2010, p. 115, fig. 1). An aversion to paraphyletic groups is, of course, anti-evolutionary:

“Cladistic aversion to paraphyletic groups, and lumping of paraphyly and polyphyly as ‘non-monophyly’, are logically flawed and anti-evolutionary” (Cavalier-Smith 2010, p. 117, legend to fig. 2).

János Podani (2010) echoes the sentiment:

“For pattern cladists, paraphyly is a less useful concept, because paraphyly together with polyphyly are “explanations for non-groupings, or more accurately, excuses for the absence of monophyly” (Williams, 2007). Paraphyletic and polyphyletic groups are therefore referred to “non-monophyletic groups” (Williams & Ebach, 2007; definition P4). For pattern cladists, non-monophyletic groups do not exist, being unnatural (“nongroups”). The approach is an evidently non-evolutionary one, paraphyly and polyphyly having very different evolutionary implications (Cavalier-Smith, 2010)” (Podani 2010, 1014).

Non-evolutionary? Anti-evolutionary?

Hörandl & Stuessy, when summarising the various concepts of paraphyly, understood it as a tool for classification – and evolution. For them “Cladistics put considerations of evolution, i.e., phylogeny, back into classification” – but left a bit out. They cite, with approval, Podani. With respect to monophyletic classification they suggest it “neglects important evolutionary processes” – which must be ‘Real’ evolution (Hörandl & Stuessy 2010, p. 1646)

The statements above, from Cavalier-Smith, Podani, Hörandl & Stuessy: Are any true, or even any part of them true?

It is time to say goodbye to Paraphyly Watch and paraphyly. It is time to devote our attention to classification, what we see is the saviour of comparative biology, maybe even all of biology.

Cavalier-Smith, T. 2010. Deep phylogeny, ancestral groups and the four ages of life. Phil. Trans. R. Soc. B 365: 111—132, doi: 10.1098/rstb.2009.0161

Hörandl, E. & Stuessy, T.F. 2010. Paraphyletic groups as natural units of biological classification. Taxon 59: 1641—1653.

Podani, J. 2010. Monophyly and paraphyly: A discourse without end? Taxon 59: 1011—1015.

A Makeover

2011-02-02T00:53:00.000-08:00

You like it? The Blogger Template Designer calls it "Simple". We like it and hope that it is easier on the eye.

Above you will see our new design, a 'Chtenopteryx ontogeny motif', and below that, an additional quote that will change from time-to-time (this month it's Darwin).

We hope to hear from you, dear Systematics & Biogeography reader, especially those can enlighten us on the ontogeny in the header above. You will be hearing from us.

Adventures with my DNA Barcoder

2011-01-23T13:35:00.000-08:00

"But humanity is bioilliterate. Yes, there is a high priest for the name and natural history of some species. That person, however, is almost never standing by your side. But with Google, can you get it? No, there is no hole in your computer or handheld into which to insert the biobit to link through Google. Who is going to give you that name in the dark, the rain, the backyard, or the rain forest? True bioliteracy is being able to link what humanity knows to the biodiversity in hand, eye, or mouth, and build on it. What is the cost to let all seven billion of us read wild biodiversity, now? The barcorder in the back pocket" (Janzen, 2010, Biotropica, 42:540-542).

Thursday, 25th
I am so excited! Today I bought my DNA Barcoder from the gift shop at my local natural history museum. It comes with a two page booklet that tells me I need 6 AAA batteries and something to barcode.

Friday, 26th
I went down to the university to show my new barcoder to my sister. She needs lots of fresh tissue to do her molecular work and always complains that her specimens are either too old or contaminated. "Not with this!" I told her. She looked at me and my barcoder and started laughing. Stuck-up cow.

Saturday, 27th
Today is my first barcoding day (it rained all week, so there was nothing to barcode). I barcoded my cat, which it turns out, is 'human'. Perhaps it's because humans and cats are closely related? Perhaps I need something more distantly related?

Sunday, 28th
I barcoded an ant that I found crawling behind the sofa. The barcoder tells me it's a fungus. I see no other ants. Later on I find a honey bee trapped in my kitchen window. It comes up as a 'geranium'. The barcoder really needs to be calibrated or something.

Wednesday, 1st
Finally, a hot and sunny day! I tried to entice a bird with bread crumbs. No luck.

Thursday, 2nd
Couldn't get close enough to the house sparrows in my park to barcode them. I barcoded various trees in the arboretum. Amazing! The barcoder gets it right every time. There was only one plant sign in the whole park that was wrong!

Sunday, 5th
What a day! Yesterday morning I found a whip snake sunning itself on my porch. I managed to barcode it before it bit me in self defense. Luckily the hospital knew which anti-venom to use because my trusty barcoder got it right again!

Tuesday, 7th
I’m going to be famous! I barcoded a cicada and found that it was 7 different species! I rushed down to the local natural history museum to tell them of the news. Perhaps they can name a news species after me? Apparently the museum barcodes species from all over world and no longer employs taxonomists (the ones who describe new species). A barcoding technician pointed out several local amateur entomological groups I could join. "That's where you find taxonomists now" he said. Perhaps I’ll try Google.

Publications for 2010

2011-01-09T14:42:00.000-08:00

Below is our list of publications for 2010. For those with no access to the links, will be happy to provide pdf copies on request.

Christenhusz, MJM., Baker, W., Chase, MW., Fay, MF., Lehtonen, S., Van Ee, B., Von Konrat, M., Lumbsch, T., Renzaglia, KS., Shaw, J., Williams, DM and Zhang, Z-Q. (2010). The first anniversary of Phytotaxa in the International Year of Biodiversity. Phytotaxa, 15: 1–8.

Ebach, M.C. (2010). Paleobiological Revolution: Essays on the Growth of Modern Paleontology. Systematic Biology, 59: 753-755.

Ebach, M.C. (2010). A new book on biogeography. Cladistics, 26: 560-562.

access free pdf here

Ebach, M.C. and Williams D.M. (2010). Aphyly: A Systematic Designation for a Taxonomic Problem. Evolutionary Biology, 37: 123-127.

Ebach, M.C. and Williams D.M. (2010). Systematics and Biogeography: Cladistics and Vicariance. Systematic Biology, 59: 612-614.

Parenti, L.R. and Ebach, M.C. (2010). Wallacea Deconstructed. In D.M. Williams & S. Knapp (eds.), Beyond Cladistics: The Branching of a Paradigm. University of California Press, Berkeley, pp. 303-318.

Reid, G. and Williams, D.M. (2010). Notes on the genus Semiorbis Patrick with a description of a new species. Diatom Research, 25: 355—365.

Toyoda, K, Nagumo, T. and Williams, DM. (2010). A new marine monoraphid species, Achnanthes pseudolongipes sp. nov. From Miyagi, Japan. Diatom Research, 25: 185—193.

Tuji, A, Williams, D.M, Sims, P.A, and Tanimura, Y. (2009) [2010] An Illustrated Catalogue of Type Specimens from the H.M.S. Challenger Voyage in Castracane’s Slide Collection in the Natural History Museum, London. In: Joint Haeckel and Ehrenberg project: Re-examination of the Haeckel and Ehrenberg Microfossil Collections as a Historical and Scientific Legacy Y. Tanimura and Y. Aita, eds). National Museum of Nature and Science Monographs, No. 40, pp. 7—11.

Williams, D.M. (2010). Historical biogeography, microbial endemism and the role of classification: everything is endemic. In Biogeography of microorganisms. Is everything small everywhere? (Fontaneto, D, ed.), Cambridge University Press, Cambridge, pp. 11—31.

Williams, D.M, Chudaev, D.A, Lomonosov, M.V and Gololobova, MA.. (2010). Punctastriata glubokoensis spec. nov., a new species of ‘Fragilarioid’ diatom from lake Glubokoe, Russia. Diatom Research, 24: 479—485.

Williams D.M. and Ebach, M.C. (2010). Molecular Systematics and the Blender of Optimization: Is There a Crisis in Systematics? Systematics and Biodiversity, 4:481-484.

Williams, D.M, Ebach, M.C. and Wheeler, Q.D (2010). Beyond belief: the steady resurrection of phenetics. In D.M. Williams & S. Knapp (eds.), Beyond Cladistics: The Branching of a Paradigm. University of California Press, Berkeley, pp. 169-197.

Williams, DM and Kociolek, JP. (2010). Classifications of Convenience: The Meaning of Names. Diatom Research 25: 213—216. Williams, DM and Morales, EM. (2010). Pseudostaurosira medliniae, a new name for Pseudostaurosira elliptica (Gasse) Jung et Medlin. Diatom Research 25: 225—226.

Yanling Li, Williams, D.M, Metzeltin, D., Kociolek, J.P. and Zhijun Gong (2010). Tibetiella pulchra gen. nov. et sp. nov., a new freshwater epilithic diatom (Bacillariophyta) from River Nujiang in Tibet, China. Journal of Phycology, 46: 325—330.

New Book: Beyond Cladistics

2010-07-17T16:22:00.000-07:00

Beyond Cladistics: The Branching of a Paradigm

Edited by David M. Williams and Sandra Knapp

Available worldwide

Third title in the Species and Systematics Book Series, published by the University of California Press

Pre-publication Sale! Save 20% if you order directly from UC Press!

Click here to see other titles in the Species & Systematics Book series.

Awareness in Classification 2

2010-04-06T21:55:00.000-07:00

In response to Michael from last 'Awareness in Classification' post

Several relationships are proposed, some conflict with others:

1. Bird - dinosaur

2. Humans - Apesor:

3. Bird - non-avian dinosaur

4. Human - non-human apeIn examples 1 and 2 above dinosaur implies some distinct group of animals, as does apes. In examples 3 and 4 above 'non-avian' stands for 'not-bird', and 'non-human' stand for 'not human'. Thus,

5. Bird - not bird

6. Human - not humanIt is tempting to explore the idea of what a 'not bird' might be (resisting exploring what a 'not-human' might be): a flower, a rabbit, a house...

Another relationship might be:

7. Vertebrate-invertebrateor

8. Vertebrate-not vertebrateIt is tempting to explore the idea of what a 'not vertebrate' might be: a flower, a rabbit, a house...

One might argue that context is all important. Of course, a 'not vertebrate' doesn't mean a flower. Well, once again, what does it mean? 'Not vertebrates' are paraphyletic. One might re-classify all 'not vertebrates' as vertebrates, thus making 'not vertebrates' monophyletic (One might re-classify birds as dinosaurs making them monophyletic). Does this mean, now, that birds are invertebrates? Prokaryotes are paraphyletic. One might re-classify all 'prokaryotes' as eukaryotes, thus making 'prokaryotes' monophyletic. Does this mean, now, that birds are prokaryotes?

Words do indeed have multiple meanings. A taxon name is best associated with a relationship. Then the meaning can be empirically explored.

Awareness in Classification 1

2010-03-28T18:19:00.000-07:00

Our recent post reveals a few things we believe are simply misunderstandings:

1) Paraphyletic groups and their reality

2) Taxa descending from other taxa

3) Phylocode adjustements to make taxa monophyletic.Let's change to a more general issue, that of invertebrates. Are invertebrates real? No. Wikipedia begins:

"An invertebrate is an animal without a backbone. The group includes 95% of all animal species - all animals except those in the Chordate subphylum Vertebrata..."Can invertebrates be defined? Yes. We could list all taxa that are included within and then list as absent all the characters vertebrates have: "An invertebrate is an animal without a backbone" -- but anything can be so defined. Are invertebrates monophyletic? No. They are paraphyletic, they exclude vertebrates. But if we include vertebrates within them, then do they become monophyletic? Yes, but then that is chordates. Are vertebrates descended from invertebrates? It's a nonsense question as invertebrates do not exist in any meaningful way - from nothing comes something?

Now, replace the terms 'invertebrate' for 'dinosaur' and 'vertebrate' for 'bird'.

To say dinosaurs are amniotes is like saying invertebrates are animals. Both true but neither telling us what dinosaurs actually are (lots of thing are amniotes). Are dinosaurs monophyletic? Are inverterbrates monophyletic?

The Mystery of the Siberian Pinkie: When Classification goes Wrong

2010-03-26T04:01:00.000-07:00

Biological classification is often misunderstood and misused in the scientific literature and especially in the media:

New York Times

The Australian

“Scientists have identified a previously unknown type of ancient human through analysis of DNA from a finger bone unearthed in a Siberian cave” (BBC News Online).These slogans, popular with the public, are completely misinformed and provide inaccurate information about biological classification. Let’s start with birds are dinosaurs.

The slogan assumes we know something about the classification of dinosaurs, namely that they include birds. This assumption derives from a cladogram that shows that some dinosaurs (feathered therapods) are more closely related to birds than they are to other dinosaurs (see Gauither et al., 1998).

Moreover, birds are diagnosed as any amniote that possesses feathers, meaning that therapods are birds. The slogan then should instead read “some dinosaurs are birds”. This then begs the question “what are dinosaurs?”

The phrase “Humans are apes” has been used quite often as a slogan, most notably by Richard Dawkins. Like the dinosaur bird example, it assumes that we know something about human classification. In fact, the term ‘ape’ refers to:

“... any of two families (Pongidae and Hylobatidae) of large tailless semi-erect primates (as the chimpanzee, gorilla, orangutan, or gibbon) ...” (Merriam-Webster Online Dictionary, 2010).Humans on the other hand belong to the Hominidae. In classification and in common usage, we are hominids and not apes. So why the confusion?

Many scientists misuse existing terms in classification to make assumptions about evolution. Since evolution and classification are two separate issues, there is a degree of confusion. The slogan “humans are apes” is supposed to infer that humans evolved from apes or both apes and humans evolved from something else. In classification, this slogan is meaningless, unless it is meant to say that humans are members of either pongidae and hylobatidae. The same misuse of classification can be seen in a recent report of a newly discovered hominid from Siberia. The report by Krause et al (2010) states:

“DNA sequence retrieved from a bone [the distal manual phalanx of the fifth digit, or the 'pinkie'] excavated in 2008 in Denisova Cave in the Altai Mountains in southern Siberia. It represents a hitherto unknown type of hominin mtDNA that shares a common ancestor with anatomically modern human and Neanderthal mtDNAs about 1.0 million years ago (Krause et al., 2010).mtDNA is not used in taxonomy to diagnose new species. Moreover the variability in mtDNA has been found to be high between individuals (see He et al., 2010). So what is this hullabaloo about? It appears it concerns itself over a newly discovered pinkie and there isn't much it can tell. You need more evidence than a pinkie to determine and describe a new species into an existing taxonomy. What Krause et al (2010) have found is a reconfirmation that hominid mtDNA is highly diverse. But yet, reading both Krause et al (2010) and the media, we are led to believe that a new species of hominid has been discovered. This is clearly not the case. Until further evidence is found (e.g., bones or bone fragments) and a diagnosis made can we be sure that “scientists have identified a previously unknown type of ancient human”.

References

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

He, Y., Wu, J., Dressman, D., Iacobuzio-Donahue, C., Markowitz, S., Velculescu, V., Diaz Jr, L., Kinzler, K., Vogelstein, B., & Papadopoulos, N. (2010). Heteroplasmic mitochondrial DNA mutations in normal and tumour cells Nature, 464 (7288), 610-614 DOI: 10.1038/nature08802

Krause, J., Fu, Q., Good, J., Viola, B., Shunkov, M., Derevianko, A., & Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia Nature DOI: 10.1038/nature08976

Publications for 2009

2010-03-22T03:44:00.000-07:00

Below is our list of publications for 2009. For those with no access to the links, will be happy to provide pdf copies on request.

de Carvalho M.R. & M.C. Ebach 2009. Dearth of the specialist, rise of the machinist. History and Philosophy of the Life Sciences 31:467-470.

Ebach, M.C. 2009. Goethe to Linneaus. In (eds. Wheeler, Q.D. & Knapp, S.) Letters to Linnaeus. Linnean Society, London, pp. 81-83.

Ebach, M.C. & Williams, D.M. 2009. How objective is a definition in the subspecies debate? Nature 457:785.

Ebach, M.C. 2009. Phylogeny. In: Brix J.H. (ed.) Encyclopedia of Time. Sage Publications Inc., Thousand Oaks, CA.

Ebach, M.C. & Wheeler, Q.D. 2009. Cybertaxonomy. In: Brix J.H. (ed.) Encyclopedia of Time. Sage Publications Inc., Thousand Oaks, CA, pp. 252-260.

Karthick B., Toyoda, K., Ramachandra, TV., & Williams, DM. 2009. A note on the identity of Ceratoneis iyengarii Gonzalves & Gandhi (Fragilariophyceae, Bacillariophyta). Diatom Research 24: 233-236.

Li, Y., Williams, DM., Metzeltin, D., Kociolek, J.P., & Gong, Z. 2010. Tibetiella pulchra gen. nov. et sp. nov., a new freshwater epilithic diatom (Bacillariophyta) from River Nujiang in Tibet, China. Journal of Phycology Published Online: Dec 11 2009; DOI: 10.1111/j.1529-8817.2009.00776.x

McNamara, K.J., Feist, R. & Ebach, M.C. 2009. Patterns of evolution and extinction in the last harpetid trilobites during the Late Devonian (Frasnian). Palaeontology, 52:11-33.

Parenti, L.R. & Ebach, M.C. 2009. Comparative Biogeography: Discovering and Classifying Biogeographical Patterns of a Dynamic Earth. University of California Press, Berkeley.

Parenti, L.R., Viloria, Á.L., Ebach, M.C. & Morrone, J.J. 2009. On the International Code of Area Nomenclature (ICAN): a Reply. Journal of Biogeography, 36:1619-1621.

Stachura-Suchoples. K& Williams, DM. 2009. Description of Conticribra tricircularis, a new genus and species of Thalassiosirales, with a discussion on its relationship to other continuous cribra species of Thalassiosira Cleve (Bacillariophyta) and its freshwater origin. European Journal of Phycology 44: 477-486.

Stachura-Suchoples, K., Williams, DM. & Jahn, R. 2009. On extinct, freshwater taxa in the genus Thalassiosira with observations on Thalassiosira species from Pliocene deposit in Oregon, U.S.A. Diatomededelingen 33: 111-113.

Toyoda, K., Tanaka, J. & Williams, DM. 2009. A new brackish water diatom, Achnanthes secretitaeniata sp. nov. from Japan. Journal of Japanese Botany 84: 19-26.

Tuji, A., Williams, DM., Sims, P.A. & Tanimura, Y. 2009. An Illustrated Catalogue of Type Specimens from the H.M.S. Challenger Voyage in Castracane's Slide Collection in the Natural History Museum, London. JOINT HAECKEL and EHRENBERG PROJECT: Reexamination of the Haeckel and Ehrenberg Microfossil Collectionsas a Historical and Scientific Legacy, edited by Y. Tanimura and Y. Aita, pp. 7-11. National Museum of Nature and Science Monographs, No. 40, Tokyo 2009.

Williams, D.M. 2009. 'Araphid' Diatom Classification and The 'Absolute Standard'. Acta Botanica Croatica 68: 455-463.

Williams, DM, Chudaev, DA, Lomonosov, MV, & Gololobova, MA. 2009. Punctastriata glubokoensis spec. nov., a new species of 'Fragilarioid' diatom from lake Glubokoe, Russia. Diatom Research 24: 479-485.

Williams D.M. & Ebach, M.C. 2009. What, exactly, is cladistics? Re-writing the history of systematics and biogeography. Acta Biotheoretica, 57:249–268.

Williams, DM. & Reid, G. 2009. New Species in the Genus Colliculoamphora. Williams & Reid with Commentary on Species Concepts in Diatom Taxonomy.Beihefte zur Nova Hedwigia (Eugene Stoermer Festschrift) 135: 185-200.

Australian Postgraduate Award in Biogeography Available at UNSW

2010-02-12T04:34:00.000-08:00

An Australian Postgraduate Award (APA) is available for a PhD in the Biogeography Lab of Dr Malte Ebach at the School of Biological, Earth and Environmental Sciences, University of New South Wales. The Biogeography Lab investigates the biotic evolution of Australasia and the geographical and geological processes responsible for biotic diversification over time. We seek a highly motivated student with a good honours or Masters degree in biology/ evolutionary biology or geology/palaeontology to choose from two projects:

1. Evolution and biogeography of water-bugs of Eastern Australasia

This project, in collaboration with Professor Gerry Cassis (UNSW), examines the morphological and molecular systematic relationships of selected endemic taxa of water-bugs (Gerromorpha and Nepomorpha) in Australasia and the relationships between the biotic areas they inhabit. The broader project investigates the biotic evolution of Australasia and the geographical and geological processes responsible for biotic diversification. Requirements: Interest in evolutionary biology, taxonomy, biogeography, field work and natural history. Experience in either systematics, biogeography and molecular techniques would be an advantage.

2. Palaeozoic biogeography and trilobite evolution

This project, in collaboration with Dr John Paterson (UNE), investigates the systematic biology of Carboniferous trilobites (Proetida) and their evolutionary relationships in order to infer palaeogeographic and tectonic reconstructions. The broader project investigates the biotic evolution of Australasia and the geographical and geological processes responsible for biotic diversification.

Requirements: Interest in palaeobiology, palaeobiogeography, field work and natural history. Experience in either sedimentology, biostratigraphy and taxonomy would be desirable.

Please note that applicants must be a citizen or permanent resident of Australia.

Please direct all enquiries and applications to Dr Malte Ebach (mcebach@gmail.com).

Darwin came from Essex (via Peru) says cat's DNA

2010-02-09T13:01:00.000-08:00

From the Wollongong Herald

The DNA recovered from Charles Darwin's cat has proven that the 19th century naturalist was descended from South American Indians.

The aspirant Find-an-Ancestor Project uses the DNA from celebrity pets to map human origins. Tiddles, Charles Darwin's first tabby, is one of 30 exhumed ex-pets. "We'd never thought we'd find Tiddles, or any of the 10 cats Darwin owned during his life" says Prof. Trevor Bruce of the University of Ulladulla".

Research funded by the Geelong Anti-ageing Centre tested Tiddle's preserved DNA and discovered that Darwin's ancestors came from a small village in present-day Peru. From there they travelled directly to Essex, possibly via a land bridge made of ice, or by small raft, from France. "The evidence is astounding" says Prof. Bruce, "it is amazing how much information one can extrapolate from DNA".

Tests have led scientists to propose the 'Out of Anywhere hypothesis'. Prof. Bruce explains: "Look, it doesn't matter whose DNA you have, people just seem to originate anywhere. We had the late Liberace's budgie examined and found out that 'The Glitter Man' was descended from Eskimos".

Further research hopes to discover the centre of origin for all humans. Dr. Karen Hall hopes that this will herald a new hypothesis. "Palaeoanthropologists say that humans and apes originated in Africa. Show me one celebrity with a pet gorilla!"

You can participate in the Find-an-Ancestor Project by sending $120.00 for a 'detection kit'. The kit includes a swab and a shovel for extracting pet DNA.

Related Post: Charles Darwin's genetic history unlocked by DNA project

Paraphyly Watch 2009: Pewter Leprechaun Awards Ceremony

2009-12-14T15:34:00.000-08:00

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

Nature

Dennis P. Gordon

Species 2000 & ITIS Catalogue of Life Annual Checklist

Donald R. Prothero

Evolution, Education and Outreach

Todd F. Stuessy and Christiane Konig

Taxon

János Podani

Taxon

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

2009-12-07T13:40:00.000-08:00

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

2009-09-30T04:50:00.000-07:00

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)

2009-09-19T12:54:00.000-07:00

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!

2009-09-15T03:46:00.000-07:00

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)

2009-08-06T03:02:00.000-07:00

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

2009-07-29T13:12:00.000-07:00

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.

Paraphyly Watch 3: Transitional Fossils, Microbes & Patrocladistics

2009-06-11T10:57:00.001-07:00

It 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:

Giraffa

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:

Pezosiren portelli

Ambulocetus

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

Long Distance Dispersal Thwarted

2009-06-05T15:43:00.000-07:00

"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".

Hidden Agendas: The Media & Science

2009-05-28T13:55:00.000-07:00

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:

Wilford, 2006: Online

Holmes, 2006: Online

BBC Online 19 May, 2009

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.

The Science of Systematics

2009-05-10T13:24:00.000-07:00

In 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:

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.

Notice to Readers: Comments now moderated

2009-05-05T09:09:00.000-07:00

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.

Paraphyly Watch 2: Paraphyly & the Catalogue of Life

2009-05-01T13:31:00.001-07:00

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

2009-05-01T09:13:00.000-07:00

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).

Biology & Teleology

2009-04-28T08:31:00.000-07:00

“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:

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.

Phylogeology – A New Revolution in Phylogenetics

2009-04-23T09:13:00.000-07:00

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

Myths that Evolutionary Taxonomists live by

2009-03-19T09:04:00.000-07:00

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

Dionysia, Dodecatheon, Soldanella, Omphalogramma

Cortusa

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.

Wordle: A Wonderful Thing

2009-02-17T13:39:00.000-08:00

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.

Media Watch: Sponges

2009-02-06T08:31:00.000-08:00

Surfing 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:

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

An Interview with Mr. Darwin

2009-01-23T09:46:00.000-08:00

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]

[Darwin paused for a moment and seemed to relax].

[Dave and Malte think this is a pun and giggle]

Origin

the

[David and Malte look at each other].

Classification and Non-Trees

2009-01-22T08:26:00.000-08:00

In spite its role as a ‘central metaphor’ and two decades of effort to promote ‘tree-thinking’, evolutionary relationships are now being portrayed in ways other than the simple bifurcating tree, recent examples being the ‘ring of life’ (Rivera & Lake 2004), the interlinking, anastomosing networks of major eukaryote groups (Doolittle 1999, 2000, Doolittle & Bapteste 2007, for commentary see Arnold 2007, Lane & Archibald 2008, McInerney et al. 2008, Dagan & Martin 2006), interconnecting networks relating various taxa (Hertel et al. 2006), and so on, the idea being summarised in a recent New Scientist article “Why Darwin was wrong about the tree of life”.

Most of this recent batch of non-trees have resulted from analysis of molecular data, although the general argument – if biological classification is hierarchical, then it prevents the representation of ‘real’ reticulate patterns – was explored in a cladistic context some three decades ago (Bremer & Wanntorp 1979).
Significance (or explanation) for many of these molecular diagrams is offered via the process of Lateral (or Horizontal) Gene Transfer (LGT, HGT), the horizontal transfer of a gene or genetic material from one organism to another, distantly related organism (Dagan & Martin 2006), first outlined some years ago to support the theory of serial endosymbiosis (Margulis 1998) to explain the origin of chloroplasts and mitochrondria (see Journal of Phycology 44 (1) and Lane & Archibald 2008). LGT is a mechanism to explain instances of xenology (“foreign genes”, Gray and Fitch 1983, p. 64), “a form of homology (inferred common ancestry) in which the sequence (gene) homology is incongruent with that of the organisms carrying the gene, and horizontal gene transfer or transfection is the assumed cause” (Patterson 1988, p. 612). Xenology finds its closest morphological equivalent in parallelism, a term which remains hard to define but can be simplified by associating it with incongruent homologies (similarities); xenology finds its biogeographical equivalent in dispersal, a term equally hard to define but simply suggests incongruent distributions (Williams & Embley 1996, pp. 581—582). Parallelism (Arendt & Reznick 2008) and dispersal (Queiroz 2005) are being discussed again, within the fresh gloss provided by molecular data, although interpretations of parallelism never really disappeared (Roth 1984:14; Sluys 1989; Wagner 1989:55, 66; Brooks 1996; DeSalle et al. 1996; Gould 2002), with suggestions being made such as “the significance of this similarity [parallelism] is thus dependent on the existence of a relevant underlying process” (Sanderson and Hufford 1996:328). Even earlier, Simpson wrote:

“In the most restricted sense virtually all evolution involves parallelism. Homologous genes tend to mutate in the same way (p. 9)… Homology is always valid evidence of affinity. Parallelism is less direct and reliable, but it is also valid evidence within somewhat broader limits. It may lead to overestimates of degree of affinity, but it is not likely to induce belief in wholly false affinity (p. 10)” (Simpson 1945, pp. 9—10).Simpson’s words turned out not to be so, for the parallelisms he noted simply mislead determination of exact relationships among mammals (McKenna & Bell 1997): those similarities identified as parallelisms (like xenology and dispersal) are simply incongruent characters.
All the same, it has been argued that reticulate networks allow incongruent ‘homologies’ to be accommodated on the same diagram relative to congruent homologies (Huson & Bryant 2006). The general idea seems similar to that explored by William Sharp Macleay and his circular systems: an attempt to represent what he called analogies and affinities (homologies) in one system (Macleay 1819, Fig. 6).

Yet if even orthologous (homologous) genes do not support ‘tree-thinking’ (Bapteste et al. 2005), incongruence among gene-trees presents problems for the effectiveness of these data, rather than provide alternative explanations for incongruence (LGT = parallelism=dispersal). Simply put: Cladograms deal with character distributions and their implications for taxon relationships (classifications), rather than vehicles for explaining incongruence.

References

Arnold, M. 2007. Evolution through Genetic Exchange, Oxford University Press, Oxford.
Arendt, J. & Resnick, D. 2008. Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation? Trends in Ecology & Evolution 23: 26—32.
Bapteste, E., Susko, E., Leigh, J., MacLeod, D., Charlebois, R.L. & Doolittle, W.F. 2005. Do orthologous gene phylogenies really support tree-thinking? BMC Evolutionary Biology, 5:33; doi:10.1186/1471-2148-5-33.
Bremer, K. & Wanntorp, H.-E. 1979. Hierarchy and reticulation in systematics. Systematic Zoology 28: 624—627.
Brooks, D. R. 1996. Explanation of homoplasy at different levels of biological organisation. In M.J. Sanderson and L. Hufford (eds) Homoplasy. The Recurrence of Similarity in Evolution, pp. 3—36. San Diego: Academic Press.
Dagan, T. & Martin, W. 2006. The tree of one percent. Genome Biology 7: 118.1—118.7.
DeSalle, R., Agosti, D., Whiting, M., Perez-Sweeney, B., Renson, J., Baker, R., Bonacum, J. & Bang, R. 1996. Cross-roads, milestones, and landmarks in insect development and evolution: Implications for systematics. Aliso 14:305—21.
Doolittle, W.F. 1999. Phylogenetic classification and the universal tree. Science 284: 2124—2128.
Doolittle, W.F. 2000. Uprooting the tree of life. Scientific American, Feb. 2000: 90—95.
Doolittle, W. F. & Bapteste, E. 2007. Pattern pluralism and the Tree of Life hypothesis. PNAS 104:2043—2049.
Gould, S.J. 2002. The Structure of Evolutionary Theory. Cambridge MA: Harvard Univ. Press.
Gray G.S. & Fitch, W.M. 1983. Evolution of antibiotic resistance genes: the DNA sequence of a kanamycin resistance gene from Staphylococcus aureus. Mol. Biol.Evol. 1: 57–66.
Hertel, J., Lindemeyer, M., Missal, K., Fried, C., Tanzer, A., Flamm, C., Hofacker, I.L., Stadler, P.F. and the Students of Bioinformatics Computer Labs 2004 and 2005. 2006. The expansion of the metazoan microRNA repertoire. BMC Genomics 2006, 7:25.
Huson D.H. & Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Molecular Biology & Evolution 23:254—67.
Lane, C.E. & Archibald, J.M. 2008. The eukaryotic tree of life: Endosymbiosis takes its TOL. Trends in Ecology and Evolution 23: 268—275.
Margulis, Lynn. 1998. Symbiotic Planet: A New Look at Evolution. New York: Basic Books.
McInerney, J.O., Cotton, J.A. & Pisani, D. 2008. The prokaryotic tree of life: Past, present...and future? Trends in Ecology and Evolution 23: 276—281.
McKenna, M.C. & Bell, S.K. 1997. [with contributions from G. G. Simpson et al.]. Classification of mammals above the species level. New York: Columbia University Press.
MacLeay, W.S. 1819—1821. Horae entomologicae: or Essays on the Annulose Animals, &c. Vol. 1, Pt. 1 & 2. S. Bagster, London.
Patterson, C. 1988. Homology in classical and molecular biology. Molecular Biology and Evolution 5: 603—625.
Rivera, M.C. & Lake, J.A. 2004. The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature (9th September 2004) 431: 152—155.
Roth, V. 1984. On homology. Biological Journal of the Linnean Society 22:13—29.
Sanderson, M.J. and Hufford, L. (eds) 1996. Homoplasy. The Recurrence of Similarity in Evolution, San Diego: Academic Press.
Simpson, G. G. 1945. The principles of classification and a classification of mammals. Bulletin of the American Museum of Natural History 85:1-350.
Sluys, R. 1989. Rampant parallelism: An appraisal of the use of nonuniversal derived character states in phylogenetic reconstruction. Systematic Zoology 38:350—70.
Wagner, G.P. 1989. The Biological Homology Concept. Annual Review of Ecology and Systematics 20: 51—69; doi:10.1146/annurev.es.20.110189.000411
Williams, DM. & Embley, TM. 1996. Microbial Diversity. Annual Review of Ecology and Systematics 27: 569-595.

Paraphyly Watch 1: Fossil Fish & Missing Links

2009-01-21T08:35:00.000-08:00

There are many ways to say "Oh #!@*! My group is paraphyletic! The following is perhaps the most eloquent:

Nature 2009, 457:234

Paraphyly sure is a 'common problem'. But what has lead to this devastating discovery?

Ptomacanthus

It certainly is! According to cladistic and phenetic (Bayesian) analysis Palaeozoic ‘acanthodians’ are paraphyletic. Why is this problematic?

"Current conceptions of gnathostome phylogeny depict a rather simplistic arrangement of nominally monophyletic and, apparently, morphologically disparate groups. The emerging picture of acanthodian (and perhaps placoderm) paraphyly does not overturn a general consensus about gnathostome interrelationships. Instead, it populates the long, naked internal branches, revealing a much richer picture of character evolution in early gnathostomes" (Brazeau 2009:307).What Brazeau had found is analogous to the platypus - an organism that has characteristics of two different groups, in this case, osteichthyans and chondrichthyans. Like the platypus, Brazeau (or at least the media) are tempted to state that a 'missing link' has been found, but to their surprise, this missing link (read 'ancestor') turns out to be nested within the chondrichthyans. Whoops! Not only is the missing link gone, but so too is the assumed monophyly of acanthodians. What to do?

What any systemtist should do - re-classify the osteichthyans and chondrichthyans in light of this new evidence. Brazeau is naive to suggest that this discovery will "...not overturn a general consensus about gnathostome interrelationships" If Ptomacanthus is more closely related to chondrichthyans then bang goes the acanthodians. They need to be reclassified along with the chondrichthyans. But rather than saying the obvious, Brazeau descends into evolutionary explanation "... populates the long, naked internal branches, revealing a much richer picture of character evolution in early gnathostomes". No it does not reveal anything other than that Ptomacanthus is a chondrichthyan and that acanthodians are paraphyletic! And this is exactly what the media has picked on:

BBC Online, 19 January 2009

This is false and misleading - the study shows quite the opposite.

I place Brazeau (2009) as the first Paraphyly Watch entry for 2009 (and the first in the race for the Pewter Leprechaun) for mis-using paraphyly. Rather than reclassifying the gnathasomes, Brazeau (2009) as alluded to a missing link (which admittedly could have been done without the cladistic and phenetic analyses).

References

Martin D. Brazeau (2009). The braincase and jaws of a Devonian ‘acanthodian’ and modern gnathostome origins Nature, 457 (7227), 305-308 DOI: 10.1038/nature07436

The Absence of Evolution (Homology)

2009-01-20T12:19:00.001-08:00

We almost labeled the paper entitled Bringing Homologies Into Focus by Anastasia Thanukos as 'Paraphyly Watch'. Here is why.

The paper is part of a new journal called Evolution: Education and Outreach - aimed at science school teachers rather than academia in general. The paper is a rather typical guide to homology - for instance:

"Homologies are traits present in two or more organisms that were inherited from the common ancestor of those organisms. The human five-fingered hand and the five-toed foot of a lizard, for example, were both inherited from our common ancestor that lived more than 300 Mya" (p. 498).Almost right. Homologies, as a concept, existed in the literature before 'ancestors' were accepted in an evolutionary context - so it would be technically incorrect to associate them with ancestors per se - in the same way Alexander von Humboldt wasn't a biogeographer (the concept may have existed but not as we understand it today; and the term was coined much later to refer to something else). Is this a case of whiggish history? Possibly. Homologies are the only evidence we have of a common history, that is evolution. We may be splitting hairs but explanations as to how things originate does rather detract from the meaning (as we will show later). A clearer definition is "Homologies are relationships and occur when the same structure exists in two organisms but as different manifestations (in this case forearm and wing)". What this implies (and how it got there) is another matter that detracts from the homologies themselves. And this is exactly what happens with the rest of the paper.

Why would a paper titled 'Bringing Homologies Into Focus' give more space to explaining analogies and homoplasies? Is the absence of homology really more interesting? If so, we would assume non-evolution is of greater interest. This is a typical trend in evolutionary biology - attempting to explain why evolution is not present by invoking other assumed 'evolutionary' mechanisms. This is contradictory and send out the wrong message. What is important is when evolution is present - namely homologies. When it is not present it should really be of little or no interest. Then why probe into the absence of evolution?

There is a misconception in science that everything needs to be explained. This is the underlying premise of paraphyly 'enthusiasts'. When a group turns out to be non-monophyletic, that is non-evolutionary, people insist that evolution has gone on anyway. Apart from flying in the face of empiricism, explaining the absence of evolution by using other explanatory 'evolution' mechanisms is meaningless. Convergent evolution is not evolutionary. It does not result in homologies, only in analogies, that is non-homologies. Why this is even taught as 'evolution' mystifies us. We wonder if this happens in other fields? When volcanic rocks are absent from an area, do geologists explain it through volcanism? They could, but it would be very silly indeed.

References
Anastasia Thanukos (2008). Bringing Homologies Into Focus. Evolution: Education and Outreach, 1 (4), 498-504 DOI: 10.1007/s12052-008-0080-5

Paraphyly Watch 2009

2009-01-07T05:37:00.000-08:00

Welcome to the New Year and the start of a new campaign: Paraphyly Watch 2009

The aim is to document, as comprehensively as possible, all the misuses and abuses of paraphyly in the scientific and popular literature for 2009.

paraphyly

misuse

abuse

If you wish to read up more about paraphyly and it's role in classification, see our previous post here.

In December we will award the Pewter Leprechaun to the most outrageous misuse and/or abuse of Paraphyly for 2009.

To start off our watch we have picked up two exemplary cases of paraphyly misuse and abuse in last 2008 issue of Taxon 57(4) by R.K. Brummitt and R.A. Zander.

Brummitt's Evolution in taxonomic perspective consists of several abuses of paraphyly:

evolution

This is what monophyly is all about. Once you discover monophyly you have discovered evolution within your group. Unfortunately, this is contrary to Brummitt (and his followers) who believe that their taxonomies alone (without any need for testing, it seems) are evolutionary. This runs counter to empiricism in science, which makes hypotheses of relationships (e.g., taxonomies) and uses cladistics to test them. It seems that Brummitt's taxonomy is the yardstick that cladistics has to abide. If it doesn't (i.e., the taxon is paraphyletic) cladistics is wrong, not Brummitt. Therefore paraphyly is evidence and empiricism politely excused.

"To overcome these objections to cladistic taxonomy, its proponents argue that we are dealing only with present day taxa and must ignore ancestors because we do not have them and so cannot name them. So at the same time as they define paraphyly in terms of ancestry, they insist on ignoring ancestors (Brummitt, 2008:1050)."Wrong again! Ancestors exist, we just have no empirical way of finding out who they were. Just because we cannot discover ancestors does not mean we only include 'present day taxa' and exclude fossil taxa in cladistics. This is another major flaw in Brummitt's thinking. Fossils can be used along side extant taxa in any cladistic analysis.

Possibly Brummitt's most incredulous slogan is

"One cannot avoid paraphyletic groups. Again, 'Evolution is paraphyly all the way'..."Paraphyly means evolution is not present in a group. Evolution is absent in paraphyletic groups, this is why they are paraphyletic. No matter how many times this is stated, Brummitt simply doesn't seem to get it - perhaps this is why he ignores the literature that has made these calls in the first place. Ignorance for some must really be bliss.

Zander's Evolutionary inferences from non-monophyly on molecular trees starts off promisingly:

"I here suggest that not only is paraphyly acceptable, but non-monophyly in general may be evolutionarily informative. Non-monophyly of taxa is satisfied by either a paraphyletic" (Zander, 2008:1182).Not surprisingly, Zander's argument falls apart in the next paragraph:

"Two different species of the same non-monophyletic genus imply an ancestor with phenotype resolvable only at the genus level" (Zander, 2008:1182).The sentence is in need of some explanation. Two different taxa with a non-monophyletic taxon may not belong there as they may be more closely related to something else. Relationship after all is what evolution is about. Whether this implies an ancestor is truly hearsay. Paraphyly is not a test for ancestors. It never has been. Such a test is non-empirical as it is based on something not being there - in this case a natural grouping. There is nothing to be resolved other than revising the taxonomy. Using a explanation that can not be tested is purely subjective. This leads on to:

"Classifications based on phylogeny should be changed to accommodate non-monophyly-based taxon trees" (Zander, 2008: 1183).Zander makes the same mistake as Brummitt. The cladistic analysis is the test, not the original taxonomy. If cladistics shows that the taxonomy (in this case a genus) is non-monophyletic, then it is the taxonomy that needs to be changed. Current taxonomies made by taxonomists are there to be tested by cladistic analysis, not the other way around! This mistake keeps coming up time and time again. Taxonomies are not evolutionary unless we are able to test them and discover monophyletic groups. If they are not monophyeltic, they are not evolutionary. Zander and Brummitt however see this the other way around.

The blight of paraphyly abuse and misuse is one commonly associated with other mistakes such as confusing taxa as species:

"The exemplars A1 and A2 are paraphyletic, and if A is a species, then the ancestor of A1, A2 and species B is species A" (Zander, 2008: 1184).and confusing supporters of the Phylocode as a cladistic movement and cladistics in general

"The cladistic movement of the late 20th century has now split into two. Some can see the impossibility of classification into ranked taxa without any being paraphyletic, and have moved on to the PhyloCode with all its practical disadvantages arising from the abandonment of ranks" (Brummitt, 2008:1050).We suggest that Zander and Brummitt actual read the cladistic literature in order to resolve their inherent misuses and abuses of paraphyly, cladistics and systematics.

* Hennig (1966: 146) defines paraphyletic groups as " ... distinguished from the monophyletic ones essentially by the fact that they have no independent history and thus possess neither reality nor individuality".

References

Brummitt, R.K. (2008). Evolution in taxonomic perspective Taxon 57:1049–1050.

Hennig, W. 1966. Phylogenetic systematics. The University of Illinois Press, Urbana.

Zander, R.H. (2008). Evolutionary inferences from non-monophyly on molecular trees Taxon 57:1182-1188.

More Whiggish Historians

2008-12-23T09:52:00.000-08:00

The recently published book, Real Essentialism by David S. Oderberg, is another example of Whiggish History and Philosophy of Science.

I refer to Oderberg's use of Elliott Sober's and Mark Ridley's work to make statements about cladistics:

"See also Sober 1993:Ch. 6 for a defense of cladism and criticism of competing methods" (Oderberg 2008: 214).

Ridley is a little less sanguine about the implications of cladistics ..." (Oderberg, 2008:222).

"Ridley notes briefly that [t]here is no orthodoxy among evolutionary biologists [I take him to mean mainly cladists] ..." (Oderberg, 2008:222).The problem of using the work of non- or even anti-cladists to defend cladistics is remarkable - especially when making outlandish claims:

"So it looks like the cladist has to believe in the existence of inorganic evolutionary descent at every stage in the past history of the universe" (Oderberg, 2008:220).

"Common sense - which is not, as I will argue, the same as cladistic sense ..." (Oderberg, 2008:215).Yet the only cladists Oderberg cites are:

Another bizarre consequence of cladism is the following (LaPorte 2004: 50-62; Okasha 2002: 205-7)" (Oderberg, 2008:220).

"Yet this absurd result of cladistics is accepted by LaPorte with equanimity, and taken by Okasha (2002: 205-7) at face value since he upbraids essentialists ..." (Oderberg, 2008:221).LaPorte and Okasha may 'upbraid essentialists', but they are not representative of cladistic theory nor do they represent the views of all cladists - in the same way that not all historians and philosophers of science are Whiggish in their views.

References
LaPorte, J. (2004). Natural Kinds and Conceptual Change. Cambridge University Press, Cambridge, UK.
Oderberg, D.S. (2007). Real essentialism. Routledge, London.
Okasha, S. (2002). Darwinian metaphysics: species and the question of essentialism. Synthese 131:191–213.
Sober, E. (1993). Philosophy of Biology. Westview Press, Boulder.

Publications for 2008

2008-12-23T07:21:00.000-08:00

Below is our list of publications for 2008. For those with no access to the links, will be happy to provide pdf copies on request.

pdf

Reid, G. & Williams, DM. The diatom slide collection and bibliography of the Reverend Richard Fraser Bastow (c. 1888-1 October 1960). Diatom Research 23: 117-128.

Reid, G. & Williams, DM. Some commentary on molecules and morphology, species and higher taxa in diatoms, with a note on the relationships of the genus Cistula Cleve. Proceedings of the 1st Central European Diatom Meeting 2007, Kusber, W.-H. & Jahn, R. (ed.), Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, pp. 135-138.

Toyoda, K, Williams, DM, Tanaka, J., & Nagumo, T. 2008. Nomenclatural problem[s] on [in] Conferva armillaris Müller (Bacillariophyta). Bulletin of the Nippon Dental University 37: 65-70.

Williams, DM. New names for three fossil species in the genus Tetracyclus Ralfs from Shangu County, Inner Mongolia, P.R. China. Diatom Research 23: 249-253

Williams, DM. Studies on species of the genus Tetracyclus (Bacillariophyta, Diatomaceae), with recognition of a 'cruciform' sub-group, and comments on their paleogeography. Micropaleontology 53: 1-9.

pdf

Flyer

QOR: Relationship / Intrinsic & Extrinsic thinking [Part 1]

2008-12-22T09:50:00.000-08:00

The serialization of our forthcoming book A Question of Relationship (QOR) investigates relationship as an active way of thinking and interacting with the world in contrast to providing epistemological, metaphysical, transcendental or structural explanations. By adopting this way of thinking we are able to identify problematic trends in systematics and biogeography without having to resort to comparing methods, theories or epistemologies. The way systematists and biogeographers do their science is based on the way they perceive and interact with the world, rather than on philosophical stand points. Understanding how we think about day to day concepts will help us identify problems and ways to resolve them without having to rely on philosophical arguments outside our own field.

We are not philosophers or historians of science and will not use current philosophical arguments to justify our arguments. Our experiences lie in practicing systematics and biogeography; therefore we prefer to present our case from this position as it will provide a clearer discussion without adding any confusion to a field that rarely uses philosophical jargon.

RELATIONSHIP / INTRINSIC & EXTRINSIC THINKING

In this chapter we will define the terms used in this book and how they are used in comparative biology. We aim to provide a simple example for each term and how each can be interpreted differently. Moreover, these definitions will be revisited in each of the following chapters in order to show how they are used in systematics and biogeography to represent different ways of thinking.

Defining Relationship, Intuition, Anschauung & Knowledge

Relationship
A relationship is an aspect or quality that binds or connects two or more things as being the same kind, that is, a fundamental quality or nature (Merriam – Webster, 2008). In other words, a relationship is a qualitative expression of different manifestations of a single form. In the strictest sense, form is the shape and structure as distinguished from its material nature (Merriam – Webster, 2008). Within comparative biology however, form is restricted to the shape and structure of what we study. For instance, a DNA molecule is no different from a shoulder blade considering they are all parts of an organism, which have shape and structure and, are studied by comparative biologists (see discussion below). The material nature of form therefore is purely at the atomic level, where shape and structure are subject to different laws (i.e., quantum mechanics).

The way we recognize form is by comparing its parts to other forms we have experienced. The act of recognition occurs in two fundamentally different ways, either by seeking similarities or by intuiting manifestations. The former can be done quantitatively and the latter through direct experience. For example, Sam is on a blind date in a cafe. The woman Sam is meeting is wearing a purple blouse. He found her by comparing the color of the clothes of other people in the café who look like women. The act of seeking similarities simulates recognition artificially because Sam has never seen the woman and therefore has gained no experience of her appearance. A list of quantitative characteristics acts as an artificial system for identification.

The process of intuiting manifestations occurs in a completely different way. Charlotte has five cats. On her visit to her sister she sees and instantly recognizes a cat ambling across the street. Charlotte does not need a list of characteristics or even a language to identify a cat. Her experiences are sufficient.

These two ways in which a person recognizes form are fundamentally different, as we will demonstrate later on. The first uses an artificial system of recognition, such as a list of characteristics, a key (e.g., as a card catalog) or a pictorial map. The latter uses our own intuition or active participation.

The difference between artificial and natural recognition is not one between a false reality and a true reality. Rather it denotes a mechanical operation from a natural occurrence. We encourage readers to challenge the notion of truth, namely the notion of a hidden mechanism, which can only be revealed by rational explanation. Intuition, as immediate cognition, presents an entirely different way of thinking.

Intuition
The concept of intuition is commonly associated with 'subjectivity', however it is rarely defined in this way. The Oxford English Dictionary for instance defines intuition as "direct or immediate insight", "Immediate apprehension by the intellect alone", "The action of mentally looking at; contemplation, consideration; perception, recognition; mental view" and "The action of looking upon or into; contemplation; inspection; a sight or view". These definitions, in our view, are expressed best as '“knowledge without recourse to inference” (Ornstein, 1996, p. 24). We will also use the term Anschauung (a.k.a. intuitive perception) to refer to the act of 'mentally looking' or 'knowing without recourse to inference'.

Anschauung
Anschauung is one way in which we can view the world and understand without referring to explanatory mechanisms or purpose. Inferences, such as explanatory mechanisms, are tools we use to make sense of phenomena. At times, they provide a reason or purpose for a phenomena coming into existence. For example, seeing a bird sing on the bough of a tree may be expressed into two different ways - either as a sexual/territorial behavioural mechanism, or as a bird and a flower

The explanatory mechanisms provide us with an explanation and/or purpose. The bird for instance may be attracting a mate or warding off potential suitors or competitors for food. The purpose could be genetic survival, Divine will, or mere joy. Since we are in this case referring to inference, the best rational argument will suffice. This would mean that the same bird behaviour has equal valid meanings in three different rational worlds. Within a modern western 21st century society, survival is the best rational explanation whereas in 11th century Gaul divine causation would be the best explanation. Inference is linked to what we know and what rational arguments are accepted within our society at any given time. The bird behaviour symbolizes an explanatory mechanism, rather than representing two observable forms.

Seeing the bird as a form in time and space does not require any explanation or purpose. The bird is an explanation in itself, regardless of what purposes or rational explanations are acceptable or not. The bird and flower are forms that can be understood by intensive observation or anschauung. The rational explanations for their interaction may vary or not be correct at all. Explanations, no matter how absurd or rational, are considered to add to our wealth of 'knowledge', even if they ignore the phenomena themselves. Observing the world through anschauung, we come to appreciate that knowledge, based on inference, is no more than abstract observation and rationalization.

Knowledge
Defining knowledge is difficult. It is used in different ways to express what we know. The example Oxford English Dictionary has several contradictory definitions, including "intuition" and "perception gained through information or facts about it rather than by direct experience" . Herein we use these two definitions to distinguish between intuitive and abstract knowledge. Each is obtained via a different facility. Intuitive knowledge is gained via experience and abstract knowledge is gained via reasoning. The division highlights the difference between acquiring knowing naturally and artificially as described above. identifying an object through recognition is based on intuitive knowledge, whereas using a list or key to identify a phenomenon is artificial. The distinction between artificial and natural, intuitive and abstract become apparent when we investigate the type of thinking we do.

A Question of Relationship: The Role of Homology in Systematics and Biogeography is a forthcoming book by David M. Williams & Malte C. Ebach. The book will be published by Forrest Text.

References

"form" Merriam-Webster Online Dictionary. 2008.
"kind" Merriam-Webster Online Dictionary. 2008.
"relation" Merriam-Webster Online Dictionary. 2008.
Ornstein, R (1996). The mind field. Cambridge: Malor Books ISHK.

Whiggish Historians of Science

2008-12-19T08:57:00.001-08:00

Recently we came across Richard A. Richards chapter on 'Species and Taxonomy', in the edited volume The Oxford Handbook of Philosophy of Biology by Michael Ruse. Reading it, we discovered the following:

"Pattern cladists, like pheneticists, typically claim their method is superior because it is theory-free and relies only on pure observation (Sober 2000, 185-86). Pattern cladistics has remained on the fringe because of, first, its implausible assumption that there can be pure observation untainted by theory; and second, its rejection of the evolution assumption" (Richards, 2008 :171).

How could anyone be so wrong?

We guess it is because Richards has not actually read the pattern cladistic literature [also known as transformed cladism]. Instead he relies on Elliott Sober's work (see below) - one that contains many misinterpretations, especially when referring to cladistics. What fascinates us, however, is why historians and philosophers of science refer to his work when there is ample primary literature and, real live pattern cladists available for comment? Shouldn't philosophers and historians of science refer to or cite primary sources, especially when making claims such as Richards has above? Many don't, and doing so has created a whiggish history and philosophy of the science of cladistics promoted by several extremist views. Let's dissect Richards's argument in context of this whiggish history:

"Pattern cladists, like pheneticists, typically claim their method is superior because it is theory-free and relies only on pure observation".

Pattern cladists have never claimed 'superiority' or used the term in above context. Pattern cladists have long argued that their method finds homologies based on proximal relationship - i.e., 0(11) - rather than assumptions of character-state transformations - i.e., 0 => 1. The argument centers around transformation and its use at the character-state level rather than at any other level. Pattern cladists reject the notion of any hypothetical transformations (taxa, character-state or otherwise) in order to find the most parsimonious, compatible or most likely cladogram. Instead they believe that characters and their states be treated like taxa, in that they are related by proximity rather than by hypothetical transformation. This does not mean that the method is phenetic or theory-free (the differences between cladistics and phenetics has been argued on another post). Pattern cladistic theory assumes that character-states can be related prior to analysis (as hypotheses of homology) and tested (i.e., contra to phenetics). Incongruent hypothetical character-state relationships are rejected in favour of congruent relationships. The question is not about superiority or theory-free methods, but about treating characters and their states as taxa. Richards's point merely romanticizes the apparent 'anti-Darwinian' nature of pattern cladistics and it's conflict with mainstream cladistics.

Where does Richards's get these ideas? Most likely from Elliott Sober:

"The [pattern cladistic] idea is that evolutionary ideas are dispensable " (Sober, 2000, Box 6.3 on p. 186)

And quite possibly from the anti-pattern cladistic literature advocated by Hull (1988):

"Sara Fink (in Hull, 1988:257) in her report noted that the "tug of war between the pattern viewpoint and the phylogenetic viewpoint in cladistics is leading on the one hand to an attempt to divorce hierarchical pattern from evolution and create a nearly assumption-free methodology, and on the other to new approaches to the study of the transformation of form".

Richards, like Hull, has made the same error - to choose sides in a conflict rather than to report both equally and without prejudice. This creates a whiggish history one that, ironically, historians of science have warned us about (Hull, 2000). It is strange to see it endemic within the works of historians and philosophers of science. Richards's whiggish history continues:

"Pattern cladistics has remained on the fringe because of, first, its implausible assumption that there can be pure observation untainted by theory ..."

Richards's 'implausible assumption' is clearly another example of fiction. No pattern cladists has ever endorsed or even entertained the idea of 'pure observation untainted by theory'. Again this is the work of reading anti-pattern cladistic literature rather than primary sources:

"Because this work [Sober (1988)Reconstructing the Past, Parsimony, Evolution & Inference] is about phylogenetic inference, not classification, nothing will be said about the current controversy concerning so-called "pattern" cladism ... See Ridley [1986] for references to the primary literature" (Sober, 1988, footnote 7, p. 8).

Just as Richards refers to Sober to make his assumptions about pattern cladism, Sober refers to Ridley (1986). Finally we arrive at the source of Richards's misunderstandings:

"... transformed cladism has no justification, and is nakedly subjective" (Ridley, 1986:91)"

"If cladism transforms into phenetic classification it will make itself subjective too. It will lose its justification, and become quite arbitrary. And despite the arguments we are about to examine ... transformed cladism does admit that its position is arbitrary and unjustifiable"(Ridley, 1986:92)"

"In a similar style they [transformed cladists] assert that it is perfectly possible to classify species without any help from any theories ..." (Ridley, 1986:14).

"There, what matters is the rejection of evolution (Ridley, 1986:10)

Just how many cladists are extreme transformed cladists, in the sense of rejecting (or finding 'unnecessary') the theory of evolution from cladism, is not clear" (Ridley, 1986:88)

"... the rejection of evolution from classification is the most far-reaching ambition of transformed cladism ..." (Ridley, 1986:125)

"The transformed cladistic argument thus fails"(Ridley, 1986:156)Ridley, a zoologist, is clearly not a friend of pattern [transformed] cladism*. Why then refer to Ridley?

Sober has already made up his mind. Pattern cladistics does not fall into his world view and referring to primary sources serves no purpose. The purpose, it seems, is to write a history of classification and phylogenetics from an extreme 'process' viewpoint. Hull should heed his own advice:

"Science is important, scientists use a wide variety of strategies to get their views accepted, including the publication of Whiggish histories of science, but historians must be firm" (Hull, 2000: 70).

That same warning extends to Richards and Sober.

The final and most common critique of pattern cladism is:

"... its rejection of the evolution assumption."

This is perhaps one of the most incredulous assumptions made about pattern cladism. The most commonly cited reference is to Colin Patterson (2002), British paleoichthyologist and the author of the text Evolution. This is where some historians and philosophers of science share commonality with creationists - confusing Darwinism with evolution. Patterson was a critic of using evolutionary narratives to build classifications. A narrative is a hypothetical explanation or story that is immune to testing or pattern. We may say that A is the ancestor of B, which is the ancestor of C, or; A is the ancestor of C, which is the ancestor of B or; A is the ancestor of B and C. Either way, the relationship A(BC), namely B and C are more closely related to each than they are to A, is true in each case. The narratives add little to the relationship other than scenarios that are impossible to validate. Whether B or A are the ancestors of C will not affect the relationship in anyway. Rather than obsess with which narrative is the best one, Patterson, like many other pattern cladists is interested to see whether these taxonomic groups are related or not. Evolution, for Patterson, was simply whether a taxon is monophyletic or not - whereas superficial narratives can be discarded without affecting the result. The equation Evolution = Darwinism has caused this misinterpretation (i.e., the process of evolution being equated to a particular theoretical explanatory mechanism, in this case Natural Selection). Similar ridiculous associations include: Cladistics = Parsimony (e.g., cladistic analysis can be done using compatibility); "Similarity = Homology" and; Arabs = Terrorists.

Referring to the secondary literature and, in the case of Richards and Sober, tertiary literature has caused philosophers and historians to create a Whiggish history - one that consists of grave misinterpretations based on hearsay.

*In fact, Ridley (1986) thanks Richard Dawkins, Joseph Felsenstein and David Hull for commenting on previous manuscripts in the acknowledgments of his book. This again emphasizes the extreme subjectivity and bias of the work.

References

Hull, D.L. 1988. Science as Process: An Evolutionary Account of the Social and Conceptual Development of Science. Chicago: University of Chicago Press.
Hull, D.L. 2000. The Professionalization of Science Studies: Cutting Some Slack. Biology and Philosophy 15: 61–91.
Patterson, C. 2002. Evolutionism and creationism. The Linnean 18: 15-33.
Richards, R.A. 2008. Species & Taxonomy. In: M. Ruse (ed.) The Oxford Handbook of Philosophy of Biology. Oxford University Press, New York.
Ridley, M. 1986. Evolution and Classification: The Reformation of Cladism, Longman, London.
Sober, E. 1988. Reconstructing the Past: Parsimony, Evolution, and Inference, Bradford Books/MIT Press.
Sober, E. 2000. The Philosophy of Biology. Second Edition. Boulder: Westview.

Serializing our New Book: A Question of Relationship

2008-12-08T09:23:00.000-08:00

David Williams and I have signed our contract for a new book to be published by Forrest Text. The book A Question of Relationship: the role of homology in systematics and biogeography (our working title) will be serialized on this blog over next few months (or until we get it written).

We hope that our book addresses some of the more important issues in systematics and biogeography, as well as getting your feedback. The task will be an arduous one as we hope to cover the following topics recently discussed in the literature and on this blog:

Defining Relationship
Bortoft's Intrinsic & Extrinsic Thinking in systematics and biogeography
Complexity and Classification
Homology versus Similarity
Paraphyly and Monophyly
Phenetics versus Natural Classifications
Phylocode and Artificial Classifications
Molecules and Morphology
DNA Follies and the Thin Blue Line

We hope that this interactive experiment in science writing ends in a well rounded and balanced text. Let the writing commence!

Complexity, Pattern & Process

2008-10-23T11:29:00.000-07:00

Species are biologically complex. The Merriam-Webster Online Dictionary define Complex as "a whole made up of complicated or interrelated parts", that is 'interrelated parts' that are "consisting of parts intricately combined". Species on the other hand are harder to define.

I will not define a species here. There are enough species concepts to go around and adding another one will not aid the growing problem of understanding species. The difficulty that many have with species is that they do not classify well. This presents us with a problem: if classification makes sense of complexity, then why can't we classify species? Why, for instance, do some claim species are never monophyletic? If species are presented by genealogical and therefore reticulated lineages that include ancestors and descendants, it will be impossible for us to classify them - to divided up related individuals into separate groups. The same argument can be made of genera and families too, but we are able to classify them. Why do species present us with this problem. The answer lies in what we mean by pattern and process.

A pattern is a repeating relationship. The character-states 0(11) for instance represent a relationship or homolog that relate the taxa A, B and C. If A = 0, B= 1 and C = 1, the relationship can be expressed as A(BC). If this taxic relationship occurs many times in different characters, it forms a pattern or homology. Process however is harder to define.

Returning to the Merriam-Webster dictionary we find the process means "a natural phenomenon marked by gradual changes that lead toward a particular result". For example, ontogeny is a process. What of the processes we are unable to see or measure? These processes can be discovered through patterns. The homology A(BC) is a discovery of evolution. That is a common and shared history. A 'hidden' process, such as the sexual behavioral traits of hadrosaurs is completely unknown to us (if they had any at all). We are able to model these traits based on assumptions, wild guesses or on the behavior of related living taxa such as birds. What ever result is generated (artificially produced) will never represent a discovery. We will never see such behavioral traits, so our models are merely speculations. The same is true for genealogical relationships. We only know who we are related to simply by observation, written documentation or by word-of-mouth. Through our DNA we are able to discover how similar we are to other people, either dead or alive, but we will never know if they are our direct descendants. Genealogy, as an unobserved process, is therefore often hypothesized. In order to make that process consistent we assign a rational hypothesis or explanatory mechanism. Genealogical relationships that move beyond our understanding (i.e., observation, recorded history etc.) rely on this hypothesized explanatory mechanism.

Explanatory mechanisms (unobserved processes) do not discover patterns. They generate artificial and ad hoc hypotheses. Observed processes however do. They provide a more robust explanation, but offer little in the way of a direct or trivial narrative (e.g., who begot whom).

Let us return to species. We assume that they are interbreeding classificatory 'units' real or otherwise. Species that are defined on an unobserved 'process' are mechanical. For some this helps conceptualize a species, for others it has little to do with classification.

Biological classification is based on patterns and the observed processes that help to uncover them. We may infer explanatory mechanism from patterns, but we will never be able to discover patterns from explanatory mechanisms. Species, as defined by explanatory mechanisms, have no place in classification. As arbitrary taxa (like genera or families), however, they make perfect sense.

The Evolution Slogan

2008-10-11T08:52:00.000-07:00

The term "evolution" can be used recklessly in a variety of ways: "If evolution was outlawed, only outlaws will evolve", "Paraphyly is evolution all the way" (Brummitt, 2002:40) and most recently, "Because we understand how evolution happens, we can also guess where it will go next" (Jones, 2008; see also John Wilkins's post). The two main points of contention, highlighted in the latter statement by Steve Jones, are our "understanding" of evolution and our ability to "guess".

The late Colin Patterson, ichthyologist at the then British Museum, Natural History in London, gave a presentation that questioned the term. The talk, titled "Systematics and Creationism", was given at American Museum of Natural History (Patterson, 2002) in November 1981. There Patterson noted:

"...the theory is evolutionary theory, descent with modification" (Patterson, 2002:23; see also Martin Brazeau's post)

Combined with the above slogans we may suggest that 'evolution' is: a process of descent with modification that results in paraphyly problem arises. How do we see this process?

In order to know we need to be able to observe or measure. Paraphyly, for instance, cannot be observed. It exists only when an artificially delineated taxonomic group is discovered to be monophyletic (homologous) - like 'invertebrates' or 'aliens'. Descent with modification is also difficult to see in action. Although we can see genealogy and ontogeny, they do not constitute 'descent with modification', at least not in the way Jones uses the term.

What systematists and biogeographers know is that evidence for evolution is based on retrodictions - that is past 'predictions' or patterns. These patterns are homologies or relationships - evidence for evolution. Our task as systematists is to discover whether our groups are a result of evolution, rather than poor taxonomy. Evolution should not be taken for granted - just because we know it exists doesn't mean we should stop looking. Reptiles, for example, are not an evolutionary group. They are a poorly defined taxonomic group like 'insectivores' and 'creepy, crawling things'. Discovering that taxa within the reptilia share closer relationships with taxa in mammalian than with any other taxon does not validate reptiles as an evolutionary group. The task of herpetologists is find those evolutionary groups and, not to defend existing names that have no evolutionary significance. Patterns, homologies, relationship and monophyletic groups are all the same thing: evidence for evolution.

Now we return to Jones. He, like many other evolutionary biologists, has committed a classic error - assuming that life progresses from an incomplete to complete phase: also known as 'primitive to derived'. A typical example is the 'primitiveness' or 'plesiomomorphy' of Archaeopteryx lithographica. The half bird-half reptile is always considered to be transition - fossilized in the middle of evolving. Like all living things dead or alive, Archaeopteryx is perfect in its own right. It has no hidden agenda, no purpose other than to be Archaeopteryx. If we were to assume, unwittingly and in hindsight, that it was primitive, then we are advocating some purpose or teleology, namely that Archaeopteryx was aiming to become a bird. This sort of thinking gives evolution a bad reputation and opens it up to attack from protagonists of anti-science. The logic behind it does not work. Let us assume for the moment that we could go back in time, back when Archaeopteryx was alive. We would assume, that this is a highly evolved 'reptile', a derived form. See the problem? Archaeopteryx is both derived and primitive at the same time in form and space but not in geological time. The whole 'primitive – derived' argument is based stratigraphic sequence and not evolution (homology).

To counter Jones's argument - we are complete, so is Archaeopteryx and all other life that has ever existed and will ever exist on this planet. What does this completeness say about evolution? Absolutely nothing at all. Instead it tells us of a desire for explanation.

We may think 'nothing in biology makes sense except in the light of evolution' (Dobzhansky, 1973), but without a doubt, evolution only makes sense in the light of homology. Biological classification provides us with the tools to discover relationships and a way to understand the evolution of life. Without it we are just telling never-ending stories. I am sure that in 200 millions years time, an octopod biologist, will wonder how something as incomplete and primitive as Homo sapiens lived for as long as it did.

References

Brummitt, R. K. 2002. How to chop up a tree. Taxon 51: 1-41.
Dobzhansky, T. 1973. Nothing in Biology Makes Sense. Except in the Light of Evolution. The American Biology. Teacher, 35:125-129.
Jones, S. 2008. Evolution is complete: so where do we go from here? Daily Telegraph Online, http://www.telegraph.co.uk/earth/main.jhtml?xml=/earth/2008/10/07/scievolution107.xml
Patterson, C. 2002. Evolutionism and creationism. The Linnean 18: 15-33.

Naef and Cephalopod Awareness Day

2008-10-08T19:40:00.000-07:00

Cephlapodcast has announced the Second Annual Unofficial International Cephalopod Appreciation and Awareness Day. I wonder what Adolf Naef would have said?

Naef said a lot about cephalopods and their relationships. As a respected world authority on octopuses and their relatives, Naef has produced several texts that have until now only interested David and I in parts (mostly the systematic theory and methodology). Our only foray into the fascinating world of calamari occurred recently when were contacted by Jan Strugnell - a cephalopodist from the University of Cambridge and admirer of Naef's work. Jan had an interesting question - why did Naef's phylogeny and classification of Argonautoidea differ?

The Argonautoidea Lamarck, 1809 (paper nautiluses and their relatives) are divided into two subfamilies: Tremoctopodinae and Argonautinae. The former includes Alloposidae and Tremoctopodidae and, the latter Argonautidae and Ocythoidae. Naef produced the following diagram (Figure 1a) with the following accompanying text:

"The typical relationship between the 4 genera which form the family are shown in the following graph: i.e., the genera developed by secondary specialization from forms I-IV in a direct series.
The ideal or hypothetical form I corresponds to the type of the family; form II corresponds to the type of the 3 genera, form II to the type of the 2 highest genera. Form IV is the ancestral form of Argonauta. The forms derived from II and III are clearly natural groups which can be defined, despite the specialization of their recent representatives. The important morphological relationships, however, call for a division into 2 subfamiles by drawing a line between II and II, i.e. a distinction between lower (I) and a higher (II) stage of variation. This is, of course, arbitrary ... and is only intended to introduce order for practical purposes by stressing the essential and omit characters of less importance. This division stresses the distance between forms II and III and creates the two natural subfamiles: Tremoctopodinae and Argonautinae (Naef 1972: 732).

These two conflicting statements (one pictorial and one as text) pose an interesting problem. What does the diagram represent and what was Naef thinking?

Naef believed both subfamilies to be monophyletic (natural groups). What Naef did diagrammatically shows a transition from the Haeckelian tree-thinking to modern systematics.

In order to understand what Naef did we go to the introduction of his work on the Fauna and Flora of the Bay of Naples. Firstly the graph is a phylogenetic tree as we understand it today. Back in Naef's day (prior to molecular systematics) the graph was termed a 'genealogical' tree. Phylogenetic trees were considered to be true depictions of ancestor-descendant relationships, an idea rarely entertained today. In Naef's phylogenetic tree, we see that forms are placed at the nodes. Naef's forms are types, namely "an abstract but naturally possible form from which a multitude of actually existing forms may have developed ..." (Naef, 1972: 15). Forms are not ancestor-descendant relationships but rather abstract transitional series between basic and specialized forms based on the concept of metamorphosis. Incorporate theses points together and you have a tree depicting the transition of forms that relate directly to the relationships of the taxa on the branches.

Confused?

Naef is depicting a back-to-front cladogram. In Naef's diagram the forms are being shown to be transitional within a dichotomous framework (Figure 1b); very much like showing a character tree within a consensus tree at the same time. A modern representation of Naef's tree would place the forms at the nodes (Figure 1c). What at first appears to be a rooted phylogentic tree, turns out to be a poorly drawn cladogram that places too much emphasis on transitional forms than it does on taxic relationships.

Naef's tree represents a transitional period between Haeckel and Hennig. Naef attempted to save us from the Haeckel's 'oak' trees that later inspired the neoDarwinian Modern Synthesis by emphasizing the importance of natural (monophyletic) groups. Naef's methodological and theoretical work should also be celebrated on Cephalopod Awareness Day.

References

Naef, A. (1972). Cephalopoda (systematics). Fauna and Flora of the Bay of Naples (Fauna e Flora del Golfo di Napoli), Monograph 35, Part I, [Vol. I], Fascicle II. Washington, Smithsonian Institute Libraries.

Three tales of Systematics and Biogeography

2008-09-07T12:24:00.000-07:00

Would it be wrong to write fables of systematics and biogeography? A fable may be defined as conveying a moral concerned with accepted rules and standards of human behavior. Is this the stuff of science? Science purports to eliminate human 'bias' in its findings. However, there are many journals and institutions that suppress the publication of alternative or contradictory methods and theories in the name of scientific culture or 'morals'. One method may be favored not because of its logic or aims, but because it represents the scientist’s or editor’s own personal views. We evidently cannot write human bias out of the process of science. Nevertheless, we must endeavor to reveal where human judgment is impeding scientific rigor, if science is to progress.

Below we have done this in the form of tales that covey scientific concepts and catalog common mistaken processes. Most 'new' scientific methods are independent discoveries of old methods or theories that have already been proven as failures or successes, were recorded in scientific literature and promptly forgotten by the majority of active researchers. Many scientists see their methods as being wholly new, or as exceptions to existing scientific rules and laws. The same 'logic' is used by speeding drivers. They accept the endless warnings that 'speed kills', but most believe that they are an exception.

There are no exceptions in comparative biology. Unlike general biology, comparative biology has no laws or rules. In systematics and biogeography however many have taken it upon themselves since the Modern Synthesis to apply a synthesis (or a series of laws) in order to unify of field of science under a common goal. These so called 'laws' are:

1. There is a fundamental difference between the type of data one uses (i.e., morphological data = macroevolutionary/plylogenetic and, molecular = mircoevolutionary/genealogical).
2.Ancestor-descendant relationships can be either 'seen' or measured.
3.Centres of origin are known quantities that are supported by evidence.

The scientific literature of this field is full of these three 'rules'. We however dismiss these three 'rules' as irrelevant to systematics and biogeography. We have done so frequently, adding even more publications to the vast literature dedicated to warning biologists of the three troublesome 'rules'. For the first time, we will express the moral dilemma that one enters when adhering to these 'rules' in the form of three short allegorical tales that convey 'a moral concerned with accepted rules'.

Form

Once a tailor stood on a hill admiring an immense tree and an old philosopher perched beneath. The tree blossomed the most beautiful flowers that the tailor had ever seen. The blossoms grew off branches that twisted and joined a haggard trunk that has grown strong with the passing of time. The tailor noticed that the etched face of the philosopher also bore the traces of time.

“I have lived in the village below for many years and yet I had never before seen nor heard of the large magnificent tree.” Remarked the tailor.
The old philosopher maintained his silent mediation.
“Each branch” contemplated the tailor, “reminds me of the links I have with my fathers, fathers and mothers, mothers.’
The philosopher stirred.
“So you know of your fathers, fathers and your mothers, mothers?” Replied the philosopher.
“Yes, I do.”
The philosopher smiled and remembered a long forgotten thought. “I once knew a mason who claimed the same.”
“Did he have evidence?” Enquired the tailor.
“Oh yes, he showed me heirlooms, trinkets, precious and rare.”
The tailor reached for his large pocket. “I have no trinkets, but proof. Pictures. Each member of my clan, as far back as my grandmothers’ mother, her sisters and brothers.” The tailor displayed several cameos before the philosophers’ wizened eyes.
“Just heirlooms. No more, no less.” The philosopher replied.
“No, they are evidence of my mother and of my kin.”
“The mason claimed to have those.”
The tailor dismissively flicked his hand. “You say those are heirlooms and not real proof. The pictures show in detail their faces and features, not mere possessions like heirlooms, but actual parts passed down our bloodline”.
“Did you paint these pictures yourself?” Asked the philosopher.
“No. I have never met my relatives for I am adopted. This is why I seek my clan among the many that walk in this world. All I possess of my family are these pictures to help me find them in the many lands through which I will pass.”
“Then how do you know that these are true depictions? How do you know who is who and when they lived?”
“I have been told on good authority that the artists all painted the portraits from live sittings. The age does not matter, I know by their features who is who.” The tailor seemed proud to have achieved this understanding.
The old philosopher sighed. “Like you, the mason said the same. He knew his bloodline by the name of the owner inscribed on each heirloom that was passed to an ambitious orphan like you.”
The tailor winced as the philosopher continued.
“The features on these pictures may show parts of your clan. They are heirlooms, precious and rare but not real proof.”
“No!” cried the tailor. “They reveal my past, my bloodline and who begat whom.”
The philosopher shook his head. “You imagine you see your past and your bloodline, but all I see are members of your family, related somehow and in some fashion. Perhaps that man you see is not your father, but your uncle, and this woman a cousin, not an aunt.”
The tailor retorted. “I share their features. I see them pass from mother to mother. They tell the truth about me and about by mothers, mothers.”
A deep weariness flooded the philosopher. “Your pictures are the heirlooms of forgotten and lost relatives. They only speak of features of a thing. The mason orphaned in birth thought the same as you. Those heirlooms, these pictures, are artefacts of the past. You cannot tell who is your mother, any more than she could recognize you.”

Time

A collector of heirlooms trudged along a narrow, winding mountain path. The air was cold and the collectors’ mule stumbled over the uneven gravel surface, tiring of its heavy burden. Night fell and the collector decided to find a camp in a cleft that dominated the rocky terrain. Before him he saw a fire and a white robed philosopher crouched before it in deep mediation. The mule and its owner drew near.
“A fine beast you have there.” The philosopher was looking at the tired mule. “A fair creature, but laden with a great burden. Are you a merchant?” The philosopher asked.
“No. I am a collector of fine antiques.”
“Come sit beside me and relate your tale”. The philosopher beckoned to the collector.
“I have been sitting here by my fire admiring the great folds in the mountains yonder.”
The collector sat and gazed out into the great valley below.
“You say you collect antiques. For pleasure, or for business?”
“For the sake of my heritage” answered the collector.
“Heritage, that is a fine thing. The antiques you carry must be old and valuable?”
The collector’s eyes brightened. “These are exceptional antiques. They not only show the skills and the tools that were used in our long lost heritage, but they also identify the makers style and craftsmanship.”
“What do you gain from collecting these articles of old?” the philosopher enquired.
“I can tell the lives of their makers, their dates of their very first works and the dates of their very last. I admire the antiques, yet I wonder at the minds and hands that created them.”
“So, you too study the art of craftsmanship?”
“With these works I can recreate the clays, glasses and fires that were used. See here!” The collector sprang up and retrieved an object wrapped in silk from a leather pack strapped to the mules side. “Behold, this object from the second period!” The collector held a beautifully crafted trinket before the philosopher. “This work of art betrays its maker. See the fine textures in the glass and the way the iron is gently wrought?” The philosopher nodded. “Those are the trade marks of the great fire welder of the second period and this is his last piece,” said the collector.
“Oh dear, did the artist die once he had created it?” The philosopher looked saddened.
“Yes. All craftsmen tinker to their last day. It is these great works of mature masters and the first brave attempts by the artist as a naive youngster are what I seek. Like my father before me, I have scaled the many mountain paths that divide these vast lands and scoured every corner to retrieve every last piece that was created by these artisans!”
“How do you know that these are their last works? There have been many wars and restorations since the second period, not much survives, only memories and myths.”
“I am certain that I have found the last works of these great creators. Alas, now their secrets are gone. They all perished in the Great War at the end of the second period. Since then, no others have been able to create the artefacts in the form that you see before you.”
The philosopher returned his attention to the fire. “Perhaps they gave up their craft to join the war and perished much later.”
“No, never! These artists tinkered till their final breath. None would have left his toil for the fortunes of war!” The collector laughed.
“How do you know that these artists did not return to their craft after the wars and made more precious trinkets?”
The collector was amazed at the naivety of the question. “Because I, and my fathers before me, have never found such antiques after the second period. It is obvious that the disappearance of these works marks their demise.”
“Is it?” the philosopher mused. “But you can never know. These trinkets that you hold could be the oldest, but there could be many more made by the great fire welder lying shattered in the rubble of ruins or in the crypts of proud and jealous owners.”
“I and my forebears have considered these notions, but there may be a few that still lie hidden. However, there will be none that is any older than the one I hold. The great fire welder did not live beyond the second period and here is evidence of that.” The collector held the antique out in one hand.
The philosopher remarked; “What you hold in that hand is an antique made by someone that lived during the second period. What you hold in the other is all you know of the great fire welder’s demise.”
The collector stared at his second, empty hand. The philosopher continued. “You cannot assume that what you do not have is evidence of the demise of great artists, any more than I can conclude that those who rule these lands are dead because they do not sit by my side.”

Space

One fair morning an orphan lay in an open meadow enjoying the spring sunshine and contemplating his journey and the direction he should take.
The orphan lay thinking of a family that he never met and of the many parchments that he had collected in the town halls on his travels. The youth had wanted to find his roots. There had been no family to show him the way, no uncle or cousin to guide him, and he had been alone except for his meagre inheritance, a certificate of birth. No place, no date, just a name, his name.

It was now a long time ago since the boy had set off on his long journey. He thought hard and counted the seasons. He thought it must now be ten or maybe more. The long northern winters seemed to last forever, yet he still moved on.

When he was just old enough to read he thought that his long deceased relations would have the same parchment, with a similar name. Curiosity got the better of him, and after enquiring with the local town cryer of the whereabouts of such parchments he was guided to the local town hall. There he found that other town halls have such records and he reasoned perhaps that in those he would find the same seal of his fore fathers. The orphan enquired about the seal on his parchment. The officer was not certain of its origin and suggested that the boy head north. “Town seals such as that belong to the wealthier lands in the north”.

His journey had been marred by sickness, and only a few villages could offer a state official who all too often knew little of such documents. Success came one summers’ day when he found a parchment in the archives of a small town. There he had evidence at last. Someone did share his name. Finally the journey became worthwhile. The parchment had a little more information to offer him. A woman who had been born in the village of the seal had moved to this place with her kin. That woman came from his village, with his name. The seal in the bottom left corner resembled the one on his own parchment. The officer that tended the archive knew little of the seal and of the towns and great cities of the north. He too suggested that the seal may have originated there, and that the boy seek his luck even further north.

The boy lay still in the long grass. He rolled over and began to unroll his parchment and study the seal. Only one other person had found his journey interesting, a wizened, old philosopher that he had met last winter.

The boy had told the philosopher his story and his ambition to seek his fore fathers’ home. The philosopher asked why he wanted to go there?
“To seek my fore fathers, those whom I had not known. I want to be close to them and their home. My home.”
“But your home is your ambition, your wit and desire to seek” Replied the old philosopher. “Once you reach that goal you will be alone in a foreign land without further ambition and wit that kept you company on you long journey.”
The young boy was stirred by the philosopher’s remark.
“But reaching those lands of my kin is all that I desire.” The boy could not find any other answer.
“Surely by finding your ancestral home, you will not be content. Are there not other mysteries you seek?”
“I have one mystery,” said the boy. “Why do all the lands have different seals?”
“It is the lands that claim you. It is you that belongs to them. A wanderer like yourself can not claim to belong to all that he sees.”
The boy was confused. “But I know I was not born in the town in which I was brought up. The seal proves this. But others I know were born there and they have never seen a seal like the one my parchment bore.”
The philosopher explained. “Everyone is born in a town or a village. The officials of that town stamp your parchment and claim you as its citizen. The towns lie in the valleys that are separated by the high mountains in the east and the wide deep seas in the east. Every person whether they are born there or not can only live in one town at a time. Your seal states that you are different, but yet you are part of at least one town and one family.”
“But my family lives in one town. This seal proves my case.” The boys’ confidence was waning.
“Some of your relatives may have been born there but yet grew up elsewhere like yourself.” The boy remembered the woman’s parchment that bore his seal as the philosopher spoke. “People move and what remains of their home towns are no more than memories and parchments stamped with seals.”
“Then my time is wasted seeking the origin of this seal?” The boy sulked.
“Perhaps there is fairer game in seeking why each town has a seal and why some seals resemble others. Your ambition is your life. You aim to seek and to discover. Once you see the impossibility of finding the origin of that seal, you will be lost. You will have no aim, your ambition like your seal, will then become a mystery.”
The saddened eyes of the orphan brightened slightly.
The philosopher smiled. “There are many lands, more with seals of this kind. There are kingdoms and cities in the north that even I, in my old age, have never seen. Perhaps they may tell the story of the significance of your seal and the others that you have encountered.”

The crickets sang sweetly and the thick scent of spring flowers perfumed the air. He knew that he had set off on a journey that he would never complete. Now he realized, it was why his seal differed not how it came to be there, that sent him on his journey. The philosopher was right. If he did find the origin of the seal his life would change from ambition to old memories of where he had been. He did not want to live on memories, or to find the home of his fore bears. It is the seals that hold the key to the histories of the lands between the vast mountains of the east and the wide deep seas of the west. That was his ambition. He now realized he had never been alone. Now his journey could begin.

The Culture of Molecular Systematics

2008-08-01T11:16:00.000-07:00

The longer one reads papers on molecular systematics, and speaks to molecular systematists, the more one is convinced that there is a prevalent molecular systematic culture. What makes it so convincing is the consistency of language, attitude and ignorance that is standard worldwide. What then is this molecular systematic culture?

Consider this response to a recently rejected manuscript:

"This manuscript seems inappropriate for [journal name removed]. Its purpose is to question the foundation of molecular phylogenetics, a well-established field. Moreover, the definitions of phylogeny, genealogy, cladogram are non-standard, and poorly articulated. I doubt that the readership of [journal name removed] would find the arguments presented particularly compelling. It is well known that DNA is the material of inheritance, and that morphological homoplasy is common. Nucleotide sequence similarity due to homoplasy is detectable using standard cladistic methods. No new data are presented, and most of the arguments rehash discussions from 20 to 30 years ago".

The response is an exemplary in its language, attitude and ignorance of comparative biology, that is taxonomy, systematics and biogeography.

Let us start with the first point, namely, attitude:

"Its purpose is to question the foundation of molecular phylogenetics, a well-established field".

Molecular Systematics, like any other field in science, is open to questioning. It is not immune like faith or religion as some, I suspect, believe. Moreover, it is not "well established", that is based on a sound foundation. There is little discussion about the foundations of molecular systematics, which the next comment reveals, namely:

"the definitions of phylogeny, genealogy, cladogram are non-standard, and poorly articulated".

These "non-standard" definitions are presented below:

Homologies are the only evidence for relationship; A molecular tree based on the relationships of taxa at the terminal branches is not a genealogy, but a cladogram. A cladogram however can be tested and represents all possible relationships in a taxon

One might ask, "Where is homology in molecular systematics?" The question of homology has been raging in morphological systematics for almost 300 years. In molecular systematics it is simply ignored. I ask what are the foundations of molecular systematics? What makes it so well established? Why is it one of the few fields in science where its foundations are rarely discussed? These questions make sense in the light of molecular systematic culture.

Molecular systematics also uses a convincing language. Stating that "DNA is the material of inheritance" creates an air of reverence that defies questioning. In fact it is a diversion. We are the material of inheritance. DNA is just part of it. The above statement is reductive, that is to say, it says that only our smallest 'bits' are relevant. We may take that statement further and say that 'Morphology is simply an expression of DNA', or take it one step further and state 'DNA tells us everything about genealogy and phylogentics, morphology is irrelevant, after all morphological homoplasy is common'. Language can be used in a deceptive way as the above example demonstrates.

Ignorance is another part of the molecular systematic culture. Consider for instance this statement:

"Nucleotide sequence similarity due to homoplasy is detectable using standard cladistic methods".

This conflates a few important points. Firstly homoplasy, that is, the "correspondence between parts or organs acquired as the result of parallel evolution or convergence" (Merriam-Webster's Dictionary Online), is not exactly 'detectable' in cladistic analysis. It causes characters to conflict resulting in polytomies, that is the absence of pattern, and therefore, of information. Cladistic analysis is there to find patterns, not uncover homoplasy.

Ignorance of history is another vital part of the molecular systematic culture, for instance:

"No new data are presented, and most of the arguments rehash discussions from 20 to 30 years ago".

We have addressed this point in an earlier post. No matter how old an argument or discussion is, the points made may still be relevant today. In the case of the above comment, the discussions of yesteryear still have not concluded. The discussions were replaced by a thirst for technology. Molecular systematics is enslaved in a technological culture. The algorithms or black boxes determine which phylogeny is best. The question of whether it is really homologous is never discussed. The foundations of molecular systematics lies in its applications, literally the programs made to run molecular sequences. We ask, is this a science that is based on solid foundations - a "well established field"?

The Dispersal Myth

2008-07-25T10:33:00.001-07:00

Organisms disperse. We do it, birds do it, plants do it. Dispersal is a fact of life. As an unobserved mechanism that explains distribution and evolution, dispersal fails. The evidence that 'supports' hypotheses of dispersal is the same 'evidence' that discredits the same mechanism. Like any explanatory mechanism, evidence that apparently 'supports' it is the same that also supports a competing and conflicting hypothesis and so forth. Dispersal in its descriptive form (i.e., iguanas disperse within their area of distribution) can be shown empirically. Dispersal as an explanatory mechanism (i.e., iguanas dispersed to an oceanic island and subsequently evolved into a new species) is merely hearsay.

Despite its non-empirical and highly subjective nature, many still feel that dispersal is the best or unifying theory for organic distribution and subsequent evolution. However, the less evidence there is it seems, the greater validity the hypothesis gains. In the case of pan-Pacific distributions, for instance, there is little or no geological evidence to suggest what the Pacific Plate looked like 200 million years ago. Without such geological evidence, dispersalism gains greater validity as being the only possible mechanism to explain distribution. The option of not knowing how things got to where they are, or using phylogenetic patterns to retrodict former area relationships, are rarely considered. For the most part a trivial answer will suffice - How else do things get to where they are?

The introduction of the molecular clock has only increased our obsession with dispersal (see de Querioz, 2005). These 'clocks' are based on geological (i.e., palaeontological) data (i.e., the age of fossils) in order to measure divergence times. Since we will never know if we have the oldest fossil, the chance that a single fossil will tell us any more is highly unlikely. But yet proponents of the molecular clock believe it does. This reinforces what I herein term the Dispersal Myth, namely, the less data there is, the more likely things are to disperse (Figure 1).

But what if we lack data altogether, that is, we have no information regarding the organism and its distribution? Do we still speculate in a highly subjective and non-empirical manner, or do we give up this flight of fancy altogether?

This week in Astrophysics and Space Science: An International Journal of Astronomy, Astrophysics and Space Science Wickramasinghe & Wickramasinghe (2008) push the limits of the Dispersal Myth. In short they propose the hypothesis that life may have dispersed from Venus to Earth.

The thinking behind this incredulous theory (first proposed by Barber in 1963) links three ideas together:

1. The discovery of complex "molecular structures" in Martian meteorite ALH84001.
2. Possible "transfer pathways" between Venus and Earth via solar winds and;
3. The possibility that extremophilic "Venusian microbes" may form within the atmosphere of Venus.

So why resurrect something endemic to the psychedelic 60s? Namely "at the time a mechanism for aerosol transfer between the planets was not identified ...", that is, there was no satisfactory explanatory mechanism proposed at the time. In other words, the mechanism makes the theory appear real, even if evidence, in this case extremophilic "Venusian microbes, are completely missing or unknown. What is more, the theory gains acceptance because the explanatory power of the mechanism now makes the eventuality of life on Venus more likely or predictable.

The hypothesis proposed by Wickramasinghe & Wickramasinghe (2008) is extremely subjective. It puts the cart in front of the horse. It proposes a mechanism to explain data before the data even exists. Even if life was discovered on Venus, it does not make the explanatory mechanism more likely. In fact, the reverse is true. If we, for arguments sake, we investigated Venusian microbes, we would know more about their physiological limits to disperse via solar winds than if they did not exist. Therefore the possibility of microbial dispersal from one planet to another is far more likely if the evidence was non-existent.

The message in figure 1 rings loud and clear - the less data there is, more "relevant" or "likely" dispersal appears. Dispersal, as an explanatory mechanism, is highly subjective, non-empirical and is nothing more than a myth.

References
Barber, D. (1963) Perspective 5: 201–208.
de Queiroz A. (2005). The resurrection of oceanic dispersal in historical biogeography. TREE 20: 68-73.
Wickramasinghe, N.C. & Wickramasinghe, J.T. (2008) On the possibility of microbiota transfer from Venus to Earth. Astrophys Space Sci. DOI 10.1007/s10509-008-9851-2

Goethe's Philistines

2008-07-14T08:34:00.000-07:00

The Sturm und Drang movement of the 18th and 19th centuries not only produced Romantic literature and Naturphilosophie but also a nemesis - the philistine.

The typical materialistic bourgeois, content with all the pleasures without delving in or appreciating culture, art and nature, was labeled a philistine. They had no interest in nature, no compassion or pity. The philistine also favored a life dedicated to industry, profit and security, rather than a life devoted to following ones dreams. Where those of the Strum und Drang movement, for instance, would applaud a devoted artist, whose self sacrifice has led to a life of hardship in order to follow the pursuit of happiness, the philistine would dismiss it as thoughtless and naive. Imagine the reaction of Mr. Potter of a Wonderful Life, to the self sacrifice of van Gogh.

Goethe also made the philistine his nemesis. Those who considered Goethe the greatest living poet and dramatist did not appreciate him for his obsession and devotion to natural history. During his life time he was criticized for his work on the Theory of Colours. A living legend, one that presents all things German, was, it seems, forbidden to make any contribution outside his own area of 'expertise'. These were the philistines speaking.

Today they still exist, each with their own copy of Werther, gathering dust, prominently in their book cases. The German middle class, obsessed with success and measuring history, culture, art and nature as expendable commodities, dismiss Goethe's scientific contributions. Goethe is unsellable to future generations as a natural historian. Leave that to the English who had Newton, Darwin and Wallace. Germany had the poets, composers and philosophers. These are the philistines speaking.

The philistines have the power and industry to rewrite or edit history. Goethe's work on color was misguided and his ideas on morphology naive. Darwin discovered evolution and provided the means to do biogeography. French are all Gallic and the Germans are all Huns. Non-Greeks are barbarians and people in the middle ages thought the Earth was flat. These are the philistines speaking.

No wonder Goethe thought that:

It is laughable when Philistines praise themselves for possessing the greatest knowledge and enlightenment of their age and call those of the past barbarians. Reason is as old as the world! (Goethe to Riemer May 10, 1806).

The philistines have there point of reference in history, theory, culture, art and natural history. These are simply markers, to give unappreciated things meaning in the form of measurement, value and commodity. Before Darwin there was no evolutionary biology; before Aristotle, no science and before Adam, no people. These are the philistines speaking.

FSB Online

2008-06-25T13:50:00.000-07:00

The Foundations of Systematics and Biogeography can be viewed online at Google Books. Although it only offers a limited preview, it does list the table of contents and a few chapters.

International Code of Area Nomenclature (ICAN)

2008-06-17T16:18:00.000-07:00

The International Code of Area Nomenclature (ICAN) is available in a printed format from the Journal of Biogeography.

The project is a long term initiative of the Systematic & Evolutionary Biogeographical Association (SEBA), which seeks to introduce a naming standard in biogeography. The ICAN is also available online from the SEBA site (for those that do not have access to Blackwell Online). If you would like a reprint please send us an email.

The abstract of the printed version is given below:

"Biogeography needs a standard, coherent nomenclature. Currently, in biogeography, the same name is used for different areas of biological endemism, and one area of endemism is known by more than one name, which leads to conflict and confusion. The name ‘Mediterranean’, for example, may mean different things to different people – all or part of the sea, or the land in and around it. This results in ambiguity concerning the meaning of names and, more importantly, may lead to conflicts between inferences based on different aspects of a given name. We propose the International Code of Area Nomenclature (ICAN), a naming system that can be used to classify newly coined or existing names based on a standard. When fully implemented, the ICAN will improve communication among biogeographers, systematists, ecologists and conservation biologists" (Ebach et al. 2008).

References
Ebach, M.C., Morrone, J.J., Parenti, L.R. & Viloria, Á.L. (2008) International Code of Area Nomenclature Journal of Biogeography. 35 (7) , 1153–1157.

Investigative Science Journalism: Who Guards the Guards?

2008-05-22T08:50:00.000-07:00

Plato’s reaction was simple: they will guard themselves. Distaste for power and a desire for righteousness will prevent them from taking advantage of their position. This is Plato’s Noble Lie – a valiant failure at best.

The media, journalists, editors and reporters, are also the guardians or watchmen of science. Not only do they report news and events, but they also keep politicians or spheres of power in check by questioning their actions and reasoning. Such is the power of the media in Britain that is can (almost) topple politicians and governments.

The same media also cover scientific discoveries and events, but there is a catch. Unlike politicians and government officials, scientists are not subject to critical questioning by the media. Whereas politicians acquire their positions through elections, scientists are assumed get to where they are through expertise and merit.

Any form of expertise may separate one field or profession from another. Take chamber music for example. It takes a typical violinist many years to reach a level of expertise required to perform in a chamber ensemble or symphony orchestra. In addition to other than the extracurricular training they receive as children, their university degrees and auditions, musicians are always open to scrutiny and also in their performances by the media. Newspapers dedicate columns to either praise or rubbish performances. Medical doctors and dentists are also open to scrutiny. Malpractice is often exposed first in a newspaper before it is reported elsewhere. The media also seem to find space to criticize new alternative medicines, the forms of chemicals used in chemotherapy, which diet is best, which isn’t and so on. This aside, scientists appear to be all but immune from critical scrutiny any from of questioning by journalists.

One reason maybe that much scientific expertise differs from other forms in that it does not seem to directly affect our day-to-day lives. While many people have a favorite recording of Beethoven’s 9th symphony, their own opinions on dieting and whether smoking or drinking too much is harmful. However, the average person’s opinion on evolutionary biology for example, is often no more than received wisdom, given little personal reflection. In fact the science press, that is the popular media who report on science, struggle to correctly interpret the scientists message and to attract the attention of the average reader. The recent debate in Framing Science (Nesbit & Mooney, 2007) addresses how scientists and the media can work together to express a scientific idea or discovery in such a way that it informs the public in a clear and engaging manner. The article draws much needed attention to the still burning question: who watches the watchmen?

Recently the popular press reported the discovery of a new fossil 'amphibian' nicknamed the 'frogamander' (Gerobatrachus hottoni). The article went on to state:

"The discovery of a "frogamander," a 290 million-year-old fossil that links modern frogs and salamanders, may resolve a longstanding debate about amphibian ancestry … Modern amphibians -- frogs, salamanders and earthworm-like caecilians -- have been a bit slippery about divulging their evolutionary ancestry. Gaps in the fossil record showing the transformation of one form into another have led to a lot of scientific debate." (Reuters)

The press, keen to promote science, clearly do not question what they are being told. In this case the "showing the transformation of one form into another" is impossible without the aid of a time machine. The media did not concoct the story, they simply translated what the scientists said:

"It's a missing link that falls right between where the fossil record of the extinct form and the fossil record for the modern form begins,' said Jason Anderson of the University of Calgary, who led the study" (Reuters).

This is not a problem of framing, but that of the media blindly accepting a "story".

The science media rarely question the scientist. The level of expertise that separates the scientist and the reporter is the same between that of the violin soloist, general practitioner, attorney general, civil service account and engineer. If a politician clearly fabricates a story in order to win favor with voters prior to an election or, a police commissioner justifying the arrest of a member of a suspects family under dubious terrorism charges, the media wouldn't think twice of questioning their reasoning. If a geneticist however states that the platypus is "...the semi-aquatic animal is a genetic potpourri - part bird, part reptile and part lactating mammal" (ABC News), no one questions their poor reasoning or understanding. Clearly the platypus is a mammal (along with the fish-like dolphin and bird-like bat). This distinction was made in the 19th century and every school child would be able to pick this out at once (except perhaps science journalists).

The problem is not one of not understanding the technical nature of science or the way scientist "frame" their arguments. Scientists can be just as uninformed as the rest of us. The media do question the expertise of professionals from other fields excepting that of science. What is needed is investigative science journalism, not glossy parroting. By investigative science journalism, I do not mean exposing practices outside of mainstream science such as anti-science (e.g., creationism), pseudo-science (e.g., homeopathy) or malpractice (e.g., evangelical healing). Neither do I mean exposing scientific fraud (e.g., cloning) or moral issues (e.g., stem cell research) (see Knight Fellowships). Investigative scientific journal would be far more effective in keeping science in check if it uncovers its inner workings, including the politics behind certain ideas and the funding supporting one method or theory over another as well as simple misinterpretations or downright untruths that scientists make which enter the mainstream media as "facts". Through exposing the malpractice of scientists, investigative science journalism can inform the public where their money goes and how it is at times misused. So far there is no such caliber of journalism in science has not been equal to the challenge. Presently, many biologists, geologists, geneticists and astronomers have no representation in the media and no voice. To let them suffer in silence seems unjust when experts in most other fields enjoy the guardianship of investigative journalism and the attention of the public.

Reference

Nesbit, M.C. & Mooney, C. 2007. Framing Science. Science 316: 56.

Defining Phenetics ... one last time

2008-05-21T14:04:00.000-07:00

The term phenetic is defined in the Oxford English Dictionary (OED) (online version) as:

"Designating or relating to the classification of organisms on the basis of their observed similarities and differences (often assessed in numerical terms), without reference to functional significance or evolutionary relationships".

The term was first used by Cain and Harrison (1960) "[f]ollowing a suggestion made by Mr. H. K. Pusey, we shall refer to the arrangement by overall similarity, based on all available characters without any weighting as phenetic, since it employs all observable characters (including of course genetic data when available)" (Cain and Harrison, 1960: 3).

The OED defines the term phenetics as "phenetic taxonomy or the systematics of phenotypes". It was first used by Ehrlich & Holm (1963) to refer to "[t]he study of relationships of individuals [which] may permit the creation of a 'population phenetics' which will add new dimensions to the study of microevolution" (Ehrlich & Holm, 1963: 240-2).

If the first definition of phenetic is true, then phenetics by definition cannot find evolutionary or phylogenetic relationships, only similarities.

References
Cain A.J. & Harrison G.A. (1960) Phyletic Weighting. Proceedings of the Zoological Society of London 135: 1–31.
Ehrlich P. & Holm R.W. (1963) Letter to the Editor. Science 139: 240 – 242.

The Enduring Legacy of Misinterpreting Darwin

2008-05-01T09:36:00.000-07:00

Kevin Padian's (2008) claim that Charles Darwin founded the main principles of biogeography and ecology is clearly incorrect. Biogeography was alive and well long before Darwin's birth, in fact Augustin Pyramus de Candolle and Alexander von Humboldt produced the founding works of biogeography four years before Darwin was born, while the younger Alphonse Candolle and Ernst Haeckel erected the foundations for chorology and ecology in 1855 and 1861 respectively.

Prior to the publication of Origin of Species in 1859, Darwin would have had access to an extensive array of literature, including biogeographical concepts espoused by Charles Lyell, Louis Agassiz, Joseph Dalton Hooker and Phillip Lutely Sclater. Furthermore, Padain's claim that in "Darwin's day, dispersal through migration was the only mechanism thought possible for species to move among continents" (p. 633) is also erroneous as concepts such as vicariance were already in existence. Darwin's contribution to biogeography and ecology was to provide a synthesis or unifying mechanism that explains why organisms are distributed the way they are today, namely natural selection.

References
Padian, K. 2008. Darwin's enduring legacy. Nature 451: 632-634.
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The Problem of Similarity

2008-04-03T10:22:00.001-07:00

Systematics and Biogeography has a problem: similarity. Ever since Goethe, naturalists and biologists have been rejecting similarity. It is the foundation of artificial classifications, non-evolutionary groupings and the basis for many arguments against evolution (i.e., homology).

Similarity implies that organisms are similar and not the same, that is it remains silent about sameness. The difference between being similar and the same is astronomical. Any two things in the universe can be similar. It is not a discovery. It demands no explanation. It is a means unto itself. However, when two things are discovered to be the same, they require explanation. This is when the study of evolution begins. By denying sameness -- or ignoring it -- we remain in the realm of artificial classification.

So why, then, is similarity so popular? All methods in molecular systematics use "similarity methods", herein phenetics, in order to measure nothing more than similarity. No evolution is (or can be) discovered, nor even touched upon. Molecular trees are simply meaningless in the context of evolution. They tell us nothing about sameness and therefore demand no explanation whatsoever. Regardless of this fact, all molecular systematists seem to explain similarity as if it means sameness. A molecular tree is generated and not discovered. They are means unto themselves. The gargantuan task of sequencing, aligning and building trees to find similarity ends with nothing at all. We are by no means poo-pooing similarity methods (phenetics).

Similarity methods are vital for understanding in non-evolutionary fields, such as geology. The chemical composition of rock is important for classification and identification. The same is true for biological keys and other artificial classifications. They helps us identify organisms based on their characteristics. The key will still work if the characters are homologous, not homologous or a mixture of both. Similarity will never be able to show which is which. Phenetics is useful outside of systematics and biogeography and evolutionary biology as its popularity shows. But popularity alone will not validate phenetics, or any similarity, in evolutionary biology.

What do we do with all the data, the matrices and the trees, produced by phenetics? We hope that their owners have fluked it - actually found a meaningful evolutionary, that is a monophyletic group. The sad news is that they'll never know.

Of course, molecular data have meaning and we should not be understood as attempting to trash molecular systematics. We simply feel they have been sold short. Maximum likelihood, parsimony optimization, and so on, are all kinds of phenetics: they are similarity methods. They are useless in the pursuit of evolutionary patterns, namely homology and monophyly. Molecular systematists need to stand up and shake loose the shackles of similarity, realize that their data and their methods are two separate issues and question those that wrongly promote similarity methods as "evolutionary".

Didn't we discuss this before?

2008-03-31T13:44:00.000-07:00

I once walked into my colleague's room and pointed out that his sink was leaking and getting some boxes full of reprints wet. I suggested he should get it fixed or move the boxes. We discussed it a little and after a short while it was forgotten. A year later I noticed that the problem had not been fixed. The reprints were all moldy and the leak had spread staining his carpet. I pointed it out to him again. He simply dismissed it with the line "Didn't we discuss this before?"

That same line is used throughout systematics and biogeography to dismiss lengthy heated debates that never were resolved. Who, for instance, were the victors in the following debates?

Cladistics versus Phenetics

Pattern Cladistics versus Numerical cladistics

Modern Synthesis versus Cladistic Revolution

Dispersal versus vicariance

It is said that history is written by the victors. Looking at the above examples we assume that cladistics triumphed over phenetics (overall similarity); Pattern cladistics simply lost a pointless debate; The Modern Synthesis was expelled from numerical revolution and that the dispersalist have finally won in their campaign against the dusty old vicariance biogeographers. In every case above, a heated debate occurred, the problems were addressed and everyone went home feeling like something was resolved. If this is the case why is vicariance still the most prominent theory in systematic biogeography? Why does everyone use phenetic methods? Where have all the cladists gone?

None of the above debates were resolved. Phenetists kept doing phenetics. The idea of overall similarity (a non-cladistic idea) swept over all of numerical phylogenetics. The pattern cladistics never left, the Modern Synthesis never died and vicariance was never abandoned. If we are to complain that this was all discussed before, then isn't it because the debate never really ended?

In a recent paper all opposition to DNA Barcoding was dismissed has “... having been controversial” (Lahaye et al. 2008). The paper suggests that by doing DNA Barcoding regardless of its flaws, immunizes it from any criticism. I am sure if another paper is published criticizing barcoding it would be dismissed with that one line "Didn't we discuss this before?" This is the same tactic used by phenetists (overall similarity), Modern Synthesists and Dispersal Biogeographers. It seems that history is not written by the victors, but by those with leaky sinks, a stained carpet and no ambition to do anything about it. But surely "we have discussed this before?"

References

Lahaye, R., van der Bank, M. Bogarin, D., Warner, J, Pupulin, F., Gigot, G., Maurin, O.,Duthoit, S., Barraclough, T.G., Savolainen, V. 2008. DNA barcoding the floras of
biodiversity hotspots. PNAS.10.1073/pnas.070993610395.

Biogeography & Systematics: Call for Papers

2008-03-27T10:50:00.000-07:00

Biogeography is a complex discipline, in the sense that it deals with complex processes — of evolution of life in space through time — not directly observable, occurred in the geological past. Biogeographical reconstructions demand precise and complex data — systematic and distributional information — and intricate methods. It should be no surprise to learn that evolutionary biogeography is a relatively recent area of research within the history of comparative biology.

The late 1970s and early 1980s faced an especially rich period of development of biogeographical theory and methodology, with the inclusion of the concept of vicariance in the mainstream of biological literature. The journal Systematic Zoology played a major role in the publication of papers in this area during that period. The intricacies of the subject, however, along with decisions concerning the policies of the primary main journals of the subject — Systematic Biology, Cladistics and Journal of Biogeography — resulted in problems publishing large papers with analytical studies of historical biogeography. Typically large papers with biogeographical studies also contain analyzes of the relationships of a group of organisms, often requiring new taxa to be named, to properly identify the nodes on a cladogram.

To fill this publishing void, the Systematic and Evolutionary Biogeography Association (SEBA) has decided to launch a new, open-access online journal, Biogeography and Systematics, to occupy such niche in the primary literature.

Biogeography & Systematics will publish original papers on historical biogeography and phylogenetic systematics. The journal will have the following sections:

Invited Papers — for topics of major interest in biogeography and systematics under invitation from the editor-in-chief;
Original articles – on analytical, historical, epistemological, and methodological aspects of biogeography and systematics, without page limit;
Forum – opinion pieces on any topic of biogeography or systematics (maximum, 3000 words).
Book Reviews – usually under invitation, but submitted reviews (including classical works) may be considered (max. limit 1000 words).

The editorial policy of Biogeography & Systematics is to ensure that articles published are of the highest quality and relevant to the interests of our readers. The journal is peer-reviewed. The journal is not biased towards any biogeographic region, in terms of taxa studied or author affiliation, nor any method of analysis. All papers shall be written in English (US spelling).

The first number of the journal is scheduled for August, 2008.

Please click here to see the Guide for Authors.

Editorial Policy
Biogeography & Systematics has an editorial policy in order to ensure that the articles we receive are of high quality and relevant to the interests of our readers.

Biogeography & Systematics publishes in English (US spelling) only.

Biogeography & Systematics publishes original research papers in biogeography and systematics.

Biogeography & Systematics is a peer-reviewed journal.

Biogeography & Systematics publishes monographic taxonomic, systematic and biogeographical treatments.

Articles may cover any aspect of biogeography, systematics or taxonomy.

Types of Articles
Biogeography & Systematics publishes the following types of articles:

Biogeographical anaylses, revision of methods or epistomological reviews.

Systematic revisions that may include biogeographical analyzes.

Taxonomic treatments that include systematic analyzes.

Historical revisions in biogeography, systematics and taxonomy, including biographies.

If you have been invited to contribute an article please submit your manuscript as an .odt, .rtf or .doc. We ask authors to only use Primary (bold) headings.

Citations
All citations are to be made without using commas between author and year (Wallace 1855) and commas between multiple authors (e.g. Nelson and Platnick 1981, Brandon-Jones 1998). Quotes should be cited as (Willis 1922, p. 100). Please refer to this issue for further usage of figures (see figure 1 or Fig. 1), tables and numerals.

References
Please include the full titles of journals and books. Do not use abbreviations! Please keep your references in the styles listed below.

Brandon-Jones D. 1998. Pre-glacial Bornean primate impoverishment and Wallace’s line. In Hall R, Holloway JD eds. Biogeography and geological evolution of SE Asia. Leiden: Backhuys Publishers, pp. 393-404.

Heads M. 2006. Panbiogeography of Nothofagus (Nothofagaceae): Analysis of the main species massings. Journal of Biogeography 33: 1066-1075. Merriam CH. 1898. Life zones and crop zones of the United States. U.S. Department of Agriculture Division Biological Survey Bulletin 10: 1-79.

Nelson G, Platnick NI. 1981. Systematics and biogeography: Cladistics and vicariance. New York: Columbia University Press.

Wallace AR. 1855. On the law which has regulated the introduction of new species. Annals and Magazine of Natural History 16 (2nd series): 184-196. [http://www.victorianweb.org/science/science_texts/wallace_law.html; http://www.wku.edu/~smithch/wallace/S020.htm; http://www.zoo.uib.no/classics/new_species.txt].

Proofs
Authors will be given a chance to proof their paper prior to publication. The final proof will be published on the SEBA website simultaneously as the journal is printed.

Copyright Form
Authors will be asked to complete a copyright form upon acceptance of their manuscript.

Submissions
Please submit your articles in electronic format to the Editor-in-Chief, Dalton de Sousa Amorim

Biogeography & Systematics is printed by the Instituto Venezolano de Investigaciones Científicas, Venezuela.

Defining Phenetics, Intentions and Mimics

2008-03-16T09:19:00.000-07:00

Many reading this blog are probably wondering why we seem to call everything phenetics. Phenetics is a term used, incorrectly, to only describe a certain type of methodology, namely clustering based on similarity (i.e., neighbor-joining etc.). In fact phenetics is nothing more than Numerical Taxonomy (Sneath & Sokal, 1973), a topic that we have discussed in a previous blog (Phenetic "Natural" Classifications).

Phenetics attempts to classify organisms based on over-all similarity. An excellent definition of phenetics, which can be found at Wikipedia, goes one step further:

"In biology, phenetics, also known as numerical taxonomy, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation".

Where phenetics becomes problematic is when these classifications are considered to be natural, that is monophyletic. A monophyletic taxon is based on relationship, namely homology. Homology is not a measurement of similarity but an expression of relationship. Phenetically grouped organisms may not necessarily be more closely related to each other than they are to another group. In other words, phenetics cannot distinguish paraphyly from monophyly. An analogous problem exists in biogeography.

Parsimony Anaylsis of Endemicity (PAE) is a method developed in order find similarities between areas (see Rosen 1988). The method simply requires a data matrix of presence and absences of taxic distributions. In contrast, cladistic biogeography demands that taxa used in analysis are monophyletic, however many fossil groups have no relations that coexisted in the same period. This means that some paleontologists are forced to deal with higher taxon biogeography (i.e. at family or ordinal level) or abandon cladistic biogeography altogether. The idea behind PAE is to use any group within a phenetic context. Monophyly is not a requirement of PAE therefore absences can be used to cluster organisms into areas since no notion of homology or relationship is assumed. As with phenetic findings in systematics, some users have made the mistake of assuming that PAE can find phylogenetic signals based on non-evolutionary data, that is, non-homologous information, in the data matrix.

On closer examination we find that many systematists and biogeographers intent on discovering homology, monophyly and endemism are nevertheless using phenetic methods. Perhaps this is due to a lack of readily available methods in the literature. After all, cladistics and cladistic biogeography started off as "pen and paper" methods whereas phenetics was always a numerical method (hence numerical taxonomy). The issue at stake is whether using phenetic methods jeopardizes our intent, namely to search for homologies, monophyly and endemic areas. We argue that it does.

The problems lie in transposing data into a data matrix using neighbor-joining, clustering, parsimony or compatibility as are all phenetic - that is, methods that use overall similarity in order to find classifications. These methods can not distinguish natural (monophyletic) from artificial (non-monophyletic) classifications.

Our favorite programs are rightly pointed out as black-boxes yet we shrug this off and cite Farris (1983) or recite some algorithm. In some extreme cases we justify our intentions by making sure that our data is compatible to our methods (sensu Patterson 1982). But we cannot continue skirting this issue. Similarity is an anathema that our forebears, Goethe, Vic D'Azyr, Saint Hilaire, Owen, the founders of homology had quickly disposed. Similarity is the foundation of phenetics, not cladistics. Our intent to find homology, monophlyly and endemicity (rather than the superficial cousin, similarity) must be held when selecting methods and programs that we use, ne c'est pas?

Assumptions held so dearly by some cladists, such as Patterson's test for homology and similarity as a requisite for monophyly, are all phony. Cladists should not use phenetic methods in order to make sense of classification, instead they should use homology and relationships. The only way (if any) which we are able to use phenetics meaningfully is to treat it as a mimic of the real thing (cladistic pen and paper methods). After all that is what phenetics is about, mimicking reality.

A mimic in cladistics is any phenetic method that attempts to implement a genuine theory or intention. Any phenetic implementation needs to be considered carefully since they were originally not intended for cladistic for biogeographical analysis. Many of the methods and implementations we use today have existed in statistical and mathematical classifications (i.e., data matrix, parsimony, compatibility, clustering, subtrees etc.). Rather than accepting these methods wholeheartedly as being "cladistic", cladists should fool the mimics. This has been successfully done by a program called TAX (Nelson & Ladiges, 1991). TAX fools the program into treating areas of no relationships as questions marks, without treating absences as evidence.

If cladistics is to survive as an evolutionary field intent on finding homologies and monophyly, it needs to re-examine the phenetic methods that it uses. A field that is becoming dependent on phenetic methdology can easily become phenetic.

The image above was made by David Maddison in 1981 when "... Cladistics versus Phenetics debates were still fresh in people's minds". We hope that the same image may re-spark some of that debate. The image may be found on his website.

References

Farris, J. S. 1983. The logical basis of phylogenetic analysis. pp. 1-47 in Advances in Cladistics, Volume 2, Proceedings of the Second Meeting of the Willi Hennig Society. ed. Norman I. Platnick and V. A. Funk. Columbia University Press, New York.
Nelson, G., & Ladgies, P.Y. 1992. TAS and TAX: MSDOS programs for cladistics, version 3.0. Pub- lished by the authors, New York and Melbourne.
Patterson, C. 1982. Morphology characters and homology. In: K. A. Joysey and A. E. Friday (eds.), Problems of Phylogenetic Reconstruction. Systematics Association Special Volume, 21: 21-74.
Rosen, B.R. (1988) From fossils to Earth history: applied historical biogeography. Analytical biogeography: an integrated approach to the study of animal and plant distributions (ed. by A.A. Myers and P.S. Giller), pp. 437–481. Chapman & Hall,
London
Sneath, P.H.A. & Sokal, R.R. 1973. Numerical taxonomy — The principles and practice of numerical classification. W. H. Freeman, San Francisco.

Evidence and Motive: Anna's Hummingbird and Loretta's knife

2008-02-05T00:20:00.000-08:00

As comparative biologists we are limited in our knowledge of the natural world. We know for instance that some groups are natural and that they share closer relationships with each other than they do to other groups. We also know that some taxa belong to certain groups while others do not. Take the case of Anna's hummingbird (Calypte anna). It is a taxa that belongs to a monophyletic group called birds. We discover that Anna's hummingbird shares closer relationships with other birds than it does to say mammals. As a systematist relationships are all we know of the phylogeny of Anna's hummingbird.

Knowing a relationship doesn't seem to grab the attention of the general public, students or granting bodies as much as evolutionary mechanisms do. What if we proposed that Anna's hummingbird originated in Madagascar and generated a plausible rational argument to support that hypothesis? Suddenly we stir some interest within the biogeographic and marco-ecology communities. When we propose that hummingbirds and birds as a whole are not only related to therapods, but are also their descendants, do we really get everyone excited. But what happens when we reverse the situation - swap our knowledge of hummingbird relationships as explanatory hypotheses and explanatory hypotheses as knowledge? Ebach & Williams (2004) proposed a thinking exercise that is analogous to the suggested proposition above.

Loretta the Murderess

A hypothetical group of detectives kick down a locked door. Behind it stands a woman who answers to the name of Loretta. Next to her on the floor lies a man with a knife in his back. All three objects are covered in blood, which upon further investigation turns out to belong to the deceased. For added effect, the knife has the word "Loretta" inscribed on it in black ink. How do we interpret the scene?

As the title suggests we may call it a "murder", and "a horrible accident", or even "an act of self defense". Whatever the motive is, what is unmistakable is that the locked room contains a woman (Loretta), a man (deceased) and a knife (inscribed with the name "Loretta"). Since no one outside the room witness any action or event, all motives are suspended. All we know are the existence of these three objects.

Let us say that, for some unexplainable reason, the scene is no longer investigated and, for the sake of this argument, all information relating to the Man, the knife and Loretta vanishes. We are left are a series of conflicting motives (i.e., vengeance vs. victimization) and morals (i.e., justice vs. injustice) that all are supported by that same evidence. Now for the analogy - what would happen if we were to swap the evidence for motive and the motive for evidence?

Depending on which way you argue the "evidence" (read "motive") Loretta's innocence is based on the best argument based on the "motive" (read "evidence"). We may propose two explanations to defend or accuse Loretta, namely the "extremely vengeful person" hypothesis and the "victimized person" theory. Each of these totally conflicting theories however based on the same "motive" (read "evidence") - a knife, a dead man and Loretta covered in blood all located in a single locked room. Given that this is all that there is in terms of real evidence, any hypothesis can be made to fit based on nothing more than rhetoric.

Thankfully we no longer live in a society where motives are considered to be evidence (e.g., witch-hunts and other heresies). We do however live in a society that does treat its subjective mechanisms as evidence and its evidence as explanation.

There would be many people who would support the following argument below:

"Birds have evolved from Dinosaurs"

or

"The center of origin for hominids is Africa"

Let us take the first argument. The motive or explanation has been replaced as "evidence". Birds have not evolved from Dinosaurs because "Dinosuars" do not exist as an evolutionary group, that is a monophyletic or natural group. The Dinosauria as a non-monophyletic group is real evidence. The argument that Dinosaurs evolved into birds is by far a more exciting prospect. In doing so however we disregard the evidence to hand - namely that Dinosaurs are a non-evolutionary grouping. The second argument is similar.

We as outside observers have never seen Loretta place the knife into the man, we assume she did because it is her knife and the room was locked. Guilt by association is a terrible tragedy when it occurs in our legal system, but the practice is encouraged in systematics and biogeography. The oldest hominid remains are found in Africa, therefore it is assumed that this is where the group originated from. Guilt by association is not empirical or scientific in anyway as it is based mere speculation, namely what may or may not be there. Additionally no one has seen hominids originate in Africa, so the whole argument is superfluous and speculative, every much like the motive (if any) in the Loretta example. If an older hominid bone is found elsewhere, say Antarctica, the hypothesis will change, but be based on motive rather than on evidence. Systematics and biogeography may appear to become more interesting the more non-empirical hypotheses we spout, but by no means do we become more knowledgeable.

References
Ebach, M.C. & Williams, D.M. (2004). Classification. Taxon 53: 791-794.

Explanations and Bad Science

2008-01-04T04:19:00.000-08:00

Explanations are wonderful things. They provide the world around us with meaning, a way of reasoning with others and a path to understanding scientific processes. Explanations may also sow the seeds of bad science.

Bad Science can be interpreted in a number of ways. The media and “science” journalists interpret “bad” science to mean anti-science or “science” conducted by non-scientists, based on results that are corrupted, forged or spurious. We believe however that bad science is nothing more than “made-up-ology”, which is created by scientists in order to make highly speculative claims to explain natural phenomena. Strangely the media never pick up on our version of bad science, possibly because “science” journalists are there to report positively about science rather than to criticize scientific explanations.

Anyone with enough qualification to report on scientific endeavor has the ability to see through spurious claims, reconstructions or theories. Dinosaur reconstructions based on a single jaw fragments for instance, rate highly in our list of bad science. There are limits to reconstructions, many of which never see the light of day in scientific journals but feature on the cover of “scientific” magazines. The aim of such reconstructions apparently are to to communicate a predicted past event, such a meteorite impact, to a popular audience. The idea is analogous to comparing a period-dress Hollywood blockbuster to an actual historical event. The event most likely occurred, but since it was not recorded in detail nor witness by anyone living, still remains unknown. Discovering a dinosaur jaw or even complete skull does not mean we can determine its size or colour; reconstructions and films based on “true events”, the actual machinations, are fictitious. Reconstructions however are powerful ways to explain important events.

The Power of Explanation

Explanations are mechanical devices with which to predict or retrodict future or past events and processes that are unobservable. Most important is that explanations rely on discoveries.

In experimental science, such as chemistry, phenomena are observable and repeatable. We may discover for instance that two chemicals added together produce another. The event can be repeated, described and observed, therefore resulting in an explanation of the processes involved. Non-experimental sciences such as palaeontology however rely on retrodictions based on evidence to hand. The discovery of a fossil jaw bone for example, is limited to description and observation of its form. The processes that the jaw bone underwent when it was part of a living creature are unobservable and not repeatable. The resulting explanations are quite different from those in chemistry as they are based on assumptions, theories, hypotheses and comparisons. In palaeontology we choose the best explanation based on the most convincing and rational argument. That argument is tied to accepted theories and hypotheses at the time meaning that explanations are forever changing and ephemeral. This does not mean that non-experimental sciences like palaeontology are bad or non-scientific. Many scientific fields that involve the study of past events are far more reliant on patterns than the experimental sciences (i.e., ecology, systematics, biogeography, geology, geography). Explanation, it seems, provides greater meaning.

The non-experimental sciences are primarily descriptive and comparative, relying on form and its relationship rather than on explanations. Given that normal processes are taken for granted in the experimental sciences (i.e. photosynthesis, digestion, ontogeny etc.), they are not evident in the non-experimental fields. Without the luxury of observing processes, scientists are reduced to making up hypothetical explanations in order to provide some kind of meaning. This is understandable in a world where explanations are seen to be more meaningful that form. For us form, its description and comparison, is meaningful. The discovery of patterns and relationships between form is possibly the most powerful scientific endevour. Without it we live in the present with no knowledge of the past. Many scientists within palaeontology, geology, systematics and biogeography feel that the discovery of relationship is not enough. The rise of hypothetical mechanical explanations as “meaningful” is where we believe bad science to begin.

Divisions: Who watches the philosophers of science?

2007-12-06T05:40:00.000-08:00

There are a few things for the poor old philosophers of science to get over.

If Peter Lipton is right, namely that,

"Astronomers study the stars; philosophers of science study the astronomers. That is, philosophers of science—along with historians and sociologists of science—are in the business of trying to account for how science works and what it achieves" (Lipton, 2005: 1259).

then philosophers of science have to able to see beyond current trends and political avarice. After all who watches the philosophers of science?

The trend of embracing apparent dichotomies within systematics and biogeography rather than question them, is one of things that philosophers of science need to get over. Philosophers of science need to question, examine and assess such divisions and not blindly accept them as many seem to do.

Below we list the top 10 dichotomies in systematics and biogeography that philosophers of science need to get over:

Morphology and Molecules
Homology and analogy
Homology and homoplasy
Transformational and Taxic Homology
Synapomorphy and symplesiomorphy
Congruence and consensus
Cladistics and Phenetics
Simultaneous analysis and separate analysis
Ecological and Historical Biogeography
Dispersal and Vicariance

Just because scientists use these divisions does not mean they actually exist. Dichotomies often groups "us" from "them". Science is not immune from subjectivity or distortion of "the facts" through clever manipulation. Scientific decisions too are sometimes decided upon politics, personality and fashion.

Philosophers of science are there to make sure that fish caught last Sunday afternoon was indeed "that big". In believing, rather than questioning, the divisions between certain ideas that are made by scientists, philosophers of science are unable to for "account for how science works". For some philosophers of science, the one that got away was "ooh .. so big, bigger than anything you have ever seen".

Lipton concludes

"Indeed, one might go so far as to worry that if philosophy did have any impact on scientists, it would be pernicious, depriving them of the kinds of commitment and confidence upon which their practice depends" (Lipton, 2005: 1269).

Philosophers of science have already influenced science, based on some of the highly questionable divisions listed above, to the extent that that it has been fashionable to attribute the cladistics/phenetics "war" in systematics to real events rather than to a poor account of how science functions (i.e., Hull, 1988).

References
Hull, D.L. 1988. Science as Process: An Evolutionary Account of the Social and Conceptual Development of Science. Chicago: University of Chicago Press.
Lipton, P. 2005. The Medawar Lecture 2004: The truth about science. Philosophical Transactions of the Royal Society of London B, 360, 1259–1269.

Buddah: Look at the moon, not my finger!

2007-12-03T05:37:00.000-08:00

Joe Felsenstein has suggested an analytical example, one he felt we might like to examine. The example is simple:

"If we take a sequence alignment, perhaps an easy case such as an alignment of exon sequences of a gene, and then we run (say) a parsimony algorithm, and consider ourselves to be making an estimate of the unrooted evolutionary tree (perhaps later rooting it by outgroup), what do Ebach and Williams say of this?"(Felsenstein in Comments)

Felsenstein kindly offers a few suggestions ("guesses") as to what we might think. These are as follows::

It is not inferring the phylogeny because this process is "phenetic"

It is not making a classification so it is fine but not of interest to us

It should instead be trying to make a classification

It is making a classification but a "phenetic" one so not a good one.

Felsenstein offers a view as to which of the suggestions ("guesses") is correct, opting for number 4: 'It is making a classification but a "phenetic" one so not a good one'.

Of course, we welcome helpful suggestions ("guesses"), as our desire has been (and hopefully will remain) the examination of the process of systematics, a complex field that develops and grows, as does all science. Thus, we crave his indulgence at our dissection of his suggestions in the interest of scientific endeavour.

First, we find it a little troublesome to deal with efforts that are thought ‘good’ or "bad" and do not really know what those words might mean in the context above. To us, phenetics is neither good nor bad. Consider the following. Linnaeus created the Sexual System of classification for plants, a system he acknowledged as artificial. That system still has its uses, when one is faced with a particular plant and needs to know its name, then (usually) that can achieved by working through the Sexual System. It is an Artificial Classification – it is neither bad nor good (Linnaeus knew that). It is inappropriate when wishing to investigate the natural system; it is appropriate when wishing to find a name.

Second, whether one is "inferring the phylogeny" or just exploring the distribution of homologies, any branching diagram that results can be made into a classification. Thus, points 1—4 above are without meaning.

In our (several) posts we noted that Natural Classification is investigated using homologies – and similarities, in and of themselves, are not homologies. Consider a matrix of characters, with either 1's and 0's or A's and T's ("…take a sequence alignment…"). What are they? Similarities. The matrix is, one might say, phenetic. The application of UPGMA, or Neighbor-joining, or parsimony, or…well, whatever, cannot change that fact. And, it would appear, that UPGMA, or Neighbor-joining, or parsimony, and so on, are all forms of weighting, regardless of whether one might believe that the 'model' is an accurate representation of the evolutionary process. Now as we noted, "Phenetics uses a method in order to generate a classification that mimics a natural group. The method for doing so can be useful in order to work out similarities between taxa, but the method is only a mimic." Thus, we might offer the following: much of the last 40 years of exploration of methods has, inadvertently, focused on ways one might modify or adjust a matrix of similarities.

We do not have, nor do we promote, any "favorite approach…". This is not a competition. Systematics (classification, phylogeny) is about homologies and their distribution.

The cladistic revolution of the 1960s was necessary because of palaeontology, its promises, its claims, and what it delivered. Palaeontology is reformed as a consequence, yet its effect on systematics, mostly detrimental, lasted 100 years.

Perhaps it's time for another revolution.

Wag the Dog: Mimics, False Prophets and Phenetics

2007-11-30T03:09:00.000-08:00

Near enough is not good enough should be the motto of cladistics. For many however, near enough is not only better, but something worth pursuing. Phenetics is that "something". It is a mimic and some of its proponents are false prophets who prefer a "near enough" result to a real understanding. Systematics and biogeography can not rest on its numerical laurels too long. Already in molecular systematics the numerical method is defining the field. When the mimic starts to dictate what the science should be, we have a severe case of the dog’s tail wagging the dog.

Mimics

Artificial classifications are a key or classification based on a particular organ. This forms a System, one that can predict or mimic a natural classification.

Taxonomists, systematists and biogeographers often use artificial classifications or Classification Systems in order to identify and classify taxa. People around the world use classification systems everyday. This is one that many learn at school:

Fish have scales and no limbs.
Amphibians lay eggs on land and live in water.
Reptiles lay eggs, have scales and live on land.
Birds lay eggs and have feathers.
Mammals have skin and hair, mothers feed their young milk.

Classification systems are helpful in identifying taxa but they only mimic real relationships. In the case above only mammals and birds are natural (monophyletic) groups, but the classification system for birds may also apply to taxa that are categorized as reptiles. In other words, the system above only mimics the natural group (i.e., birds), but it does use the homologies that define that group.

Linnaeus was the first person to define a classification system that attempts to mimic natural groups. The system can still be used today in order to identify plants. What Linnaeus’s, or any classification, does not do is purport to be a natural method.

A method is a key or classification based on all of the organs of a taxon; methods are sub-divided into artificial and natural depending on their purpose.

Classification methods not only mimic, they also may predict. In either case they attempt to generate classifications that are near the mark. Phenetics uses a method in order to generate a classification that mimics a natural group. The method for doing so can be useful in order to work out similarities between taxa, but the method is only a mimic. Phenetics becomes problematic when it starts getting closer to the mark. In some cases a phenetic analysis can replicate a true relationship – a homology – without the need for homologies. Although these methods are praiseworthy, they do not actually find homologies. A mimic only replicates something, it does not actually discover. A phenetic analysis may for instance replicate a monophyletic group perfectly, using an assortment of homologues, but since the method uses similarity (i.e., non-relationships) it cannot, by definition, discover homologies, even though it replicates them perfectly.

An analogy would be to state that anything that lives in water and lays eggs on land is an amphibian. Although this behavioural trait is more likely to be common amongst toads, frogs, salamanders and newts, it is not a homology as it is something not unique to that group. Birds may lay eggs and bear feathers, but so do a number of therapod groups. Similarity is not a relationship, only a measurement of likeness based on one or more hypotheses.

False Prophets

Phenetics becomes problematic when it confuses the mimic for the real thing. Certainly phenetics can create a classification system using a method of similarity, but it does not discover natural groups. Therefore the term Natural System is a contradiction. A system cannot be natural as it is based on a single characteristic or assumption and not relationship. Natural groups, as pointed out in the post Phenetic "Natural" Classifications, are not based on a priori assumption:

"... system of classification is the more natural the more propositions there are that can be made regarding its constituent classes" (Sokal & Sneath 1963: 19).

Sokal and Sneath (1963) have turned the mimic into natural group.

Phenetics as purveyor of natural groups is erroneous and prophetic. Stating that natural groups can be reached through a system of quantification and similarity is appealing to those that rely on statistical programs. Most systematists and biogeographers rely on such programs and have swallowed the “phenetic prophesy” hook, line and sinker. Natural groups, it seems, is just a matter of quantity.

Wag the Dog

The phenetic prophesy states that similarity* is relationship, and can discover natural groups. This is wagging the dog.

Taxonomists, systematists and biogeographers can only discover patterns, homologies that give us insight into relationship. Before we do this we may impose a system of beliefs, hypotheses and theories about our own groups and their relationships. Some times we test these assumptions by discovering homologies and find that we were right. That is the nature of a robust scientific discipline. Once we turn that around and impose our own “natural” law, then we can only formulate more hypotheses in differing ways, never discovering only generating. Molecular systematics is now in a unique position to learn from 300 years of systematic theory that has discovered time and time again that homology is not similarity. Unfortunately many in the field ignore the past systematic literature and read that of the phenetic prophesy.

One day someone bent over a PCR machine may come to realise that they are part of a 300 year cycle of wagging.

*There are two forms of similarity. One is that of simile “That kangaroo looks like a rat”. The other is quantifiable and is born from statistics (i.e., divergence and possibility) “The ape is 22% banana”. We refer to the latter form throughout this post.

References

Sokal R.R. & Sneath P.H.A. 1963. Principles of Numerical Taxonomy. W. H. Freeman, San Francisco.

Natural and Artificial Classification: A reply to Wilkins

2007-11-29T06:37:00.000-08:00

The following post is a reply to John Wilkin’s The philosophy of classification on his blog Evolving Thoughts.

An Uninformed Consensus

John Wilkins in his recent post believe that our view is "radical" because

"… they have presented some views on classification that do, indeed, differ from the received consensus."

We beg to differ.

In late 20th and early 21st century literature there are very few discussions on the nature of classification. Most revolves around explaining existing classifications (i.e. Reptilia) or in the defence of poorly defined taxonomic groups that fail to form groups (i.e., paraphly). It is these debates (i.e., paraphly versus monophyly) that would benefit from the discussions of early 20th and late 19th century morphologists, would did hold a consensus view of natural and artificial classifications. That consensus was this,

We then follow a Natural Method, which cannot be called a system, because it is destitute of any unity of principle. (Candolle & Sprengel, 1821)

It is our belief that the pursuit for explanations to existing classifications that ended this debate and therefore any consensus. Furthermore, it is the addition of homology = similarity that radically altered how we view classifications, leading to the almost Fukuyamaist statement that,

"I would say that the effort put into this controversy is further evidence that systematists do not have their priorities straight. In their day-to-day work they really do not make much use of classifications, but they show a strange obsession with fighting about them for reasons that seem to me to be an historical curiosity" (Felsenstein 2005)

Currently there is no consensus over natural or artificial classifications. The topic is a moot point and very few concern themselves with its relevance to 21st systematics and biogeography. As systematists we are more or less tied to the consensus of the past, namely to the literature of the 19th century and early 20th century. In that sense we are not “radicals", but rather “old fashioned”.

Similarity and Homology

Similarity, as expressed in the usual kinds of data matrices, is 11, or, the molecular version, AA is not a relation. The 11 and the AA are, if anything, homologues, the parts, the 'namesakes' as Owen called them. We see homology as a relation: 0(11), or the molecular version, G(AA). We stated earlier:

"...all molecular systematic studies are phenetic as they ignore relationship, that is, homology". One might expand that and say, "...all numerical systematic studies are phenetic as they ignore relationship, that is, homology."

This would be more accurate.

In response to John’s comment,

"I'm not sure I follow this. According to current usage, molecular systematics does rely on homologies: they have a number of special terms devoted to identifying them: paralogy, xenology and orthology. Of course, they often don't use homology properly. And to identify a homology in molecular biology you need to do some prior work; homology is an inference from sequence similarity (including eyeball alignment). In short, if I understand the argument, molecular systematics derives homology from similarity".

In fact we would suggest that it would be more accurate to say:

"... molecular systematics does rely on HOMOLOGUES: they have a number of RELATIONS DERIVED FROM them: paralogy, xenology and orthology....And to identify a HOMOLOGUE in molecular biology you need to do some prior work; HOMOLOGUES ARE inferenceS from sequence similarity (including eyeball alignment). In short, if I understand the argument, molecular systematics derives HOMOLOGUES from similarity ..."

This certainly is not radical. What we are suggesting is that de Candolle (1813) presented a very clear account of classification, an account still of significance today.

Haeckel and Classification

In our understanding, Ernst Haeckel did more than most to promote the genealogical view of species relationships. It might be fair to say that all our genealogical endeavours stem from Haeckel. Adolf Naef (1917, 1919)was the first to critique that viewpoint His interest was in natural classification. Hennig (1950), quite deliberately, focused on Naef. Thus, it might be fair to say that Hennig's efforts were directed towards rehabilitating Haeckel. Further, one might see Systematics and Biogeography (Nelson & Platnick, 1981) as a further detailed critique of Haeckel - if the most detailed critique available - and a restatement of de Candolle's viewpoints on classification. In this sense cladistics sensu Nelson & Platnick is of greater significance than cladistics sensu computer programs.

We would venture the suggestion that Sober (1988) mistook cladistics sensu Farris (parsimony sensu Farris) as if it was the generally accepted view (in the mid-1980s that might have been possible). In fact Sober deliberately excludes the more general view, as if the argument really was about parsimony versus likelihood, one algorithm versus another,

"Because this work is about phylogenetic inference, not classification, nothing will be said about the current controversy concerning so-called 'pattern' cladism." (Sober, 1988:8, footnote 7).

Thus, in our view, the more general study of classification exclude Sober's work as a relevant commentary on the matter.

References
Candolle, A.P., de, & Sprengel, K. 1978. Elements of the philosophy of plants. Reprint of the 1821 ed.. New York, NY.
Hennig, W. 1950. Grundzüge einer Theorie der phylogenetischen Systematik, Deutsche Zentralverlag, Berlin.
Naef, A. 1917. Die individuelle Entwicklung organischer Formen als Urkunde ihrer Stammesgeschichte: (Kritische Betrachtungen über das sogenannte "biogenetische Grundgesetz"), Verlag von Gustav Fischer, Jena.
Naef, A. 1919. Idealistische Morphologie und Phylogenetik (zur Methodik der systematischen), Verlag von Gustav Fischer, Jena).
Nelson, G. & Platnick, N.I. 1981. Systematics and biogeography. Cladistics and vicariance. Columbia University Press, New York.
Sober, E. 1988. Reconstructing the Past: Parsimony, Evolution, and Inference. MIT Press, Cambridge, Massachusetts.

Artificial and Natural Classifications: A Clarification

2007-11-29T01:23:00.000-08:00

It was not by accident that we referred to de Candolle (1813): "Naef's concern was with the discovery of natural, as opposed to artificial classification, a problem examined in detail by A. P. de Candolle (1813)".

This is what de Candolle had to say about artificial classifications:

"Others have as their essential goal to give to persons who know nothing of the names of plants an easy way to discover the names in the books by inspection of the plant itself. These classifications have been given the name of Artificial Methods."

And,

"...there are those persons who want to study plants, either in themselves, or in their real relations among themselves, and to class them so that those plants most closely related in the order of nature are also those most closely related in our books. These classifications have received the name of Natural Methods."

De Candolle considers Systems and Methods.

A system is a key or classification based on a particular organ - leaf, flower, etc.

A method is a key or classification based on all of the organs of a plant; methods are sub-divided into artificial and natural depending on their purpose.

De Candolle again:

"classes that are truly natural, established on the basis of one of the major functions, are necessarily the same as those established on the basis of the other."

That is, congruence.

Bar-coding, based on "a particular organ", interpreted as a piece of DNA, is, in this sense, a system. It might be seen as an artificial classification as its purpose is to find the name of any given plant or animal.

Now, is molecular systematics a system or a method? It too is based upon "a particular organ", so it too might be considered a system. Now if considered a method, we see that there is no notion of congruence at all as no other datasets are given consideration. Molecular systematics as a form of measuring similarity constitutes a system, not a method.

Ancestors and other mechanical explanations are not of any concern in the debate between artificial and natural classifications. One does not decide on homology in advance. It is either there or it is not. Homology, as we understand, is a relation. A similarity such as 11, or AA, is not a relation. Thus, all molecular systematic studies are phenetic as they ignore relationship, that is, homology.

Adolf Naef - A Potted Biography

2007-11-28T01:54:00.000-08:00

Who was he?
Adolf Naef was a Swiss systematist, malacologist and a proponent of systematic morphology. He was born in Niederhelfenschwil on 1st May 1883 and passed away on May 11th 1949.

What did he do?
Naef studied at the University of Zurich, under the guidance of Arnold Lang (1855—1914), a former Professor of Jena University and close friend of Ernst Haeckel. Naef visited and worked in Anton Dorn’s Zoological Station in Naples, Italy in 1908, studying the squid Loligo vulgaris, the subject of his dissertation (Naef, 1909a, b). Naef returned to the Naples Zoological Station in the mid 1920s to study cephalopods, publishing a two-part monograph in the Station’s Fauna und Flora des Golfes von Neapel und der Angrenzenden Meers-Abschitte (Fauna e Flora del Golfo di Napoli) series (Naef 1921d, 1923c, 1928, later translated into English, Naef, 1972a, 1972b, 2000), which formed the basis for his two short but significant monographs on systematic theory (Naef, 1917, 1919). In 1922 he became Professor at the University of Zagreb, and in 1927 was Professor of Zoology at the University of Cairo.

What’s the big idea?
Naef’s studies were framed within Systematische Morphologie (Systematic morphology) (Naef, 1917, 1919), the details he sketched out as early as 1913:

“Phylogenetic and natural systematics deal with the same factual material, and although each has different basic concepts, both disciplines can be united in a single concept because their objects are so similar. I have therefore proposed the name ‘systematic morphology’ for this concept (Naef, 1913: 344)…It is intended to show that there is an inner relationship between natural systematics and (comparative) morphology” (Naef, 1921-23: 7, from the English translation, Naef, 1972a: 12).

Naef’s concern was with the discovery of natural, as opposed to artificial classification, a problem examined in detail by A. P. de Candolle (1813). Naef expressed it as so:

“For decades, phylogenetics lacked a valid methodological basis and developed on the decayed trunk of a withering tradition rooted in the idealistic morphology and the systematics of pre-Darwinian times. There was talk of systematic ‘tact’ and morphological ‘instinct’, terms which were felt rather than understood and consequently insufficient to form the frame of a science which required sound definitions and clearly formulated principles” (Naef, 1921-23, pp. 6-7, from the English translation, Naef, 1972, p. 12).

And thus was born ‘Systematische Morphologie’, perhaps the beginnings of cladistics, in its most general form (of which more in a further post). Towards the end of his career, Naef published several detailed accounts of ‘Systematische Morphologie’ (Naef, 1931a, b, 1933a), including a succinct summary in the widely read 2nd edition of the Handwörterbuch der Naturwissenschaften (Naef, 1933b).

Naef might be considered a man out of time – as might many morphologists today, relative to the explosion of molecular data. In Naef’s day palaeontology and the post World War II hegemony of the modern synthesis was attracting the young minds. Today it is molecular systematics and DNA barcoding – versions of artificial classifications.

References

Candolle, A.-P. de (1813). Théorie élémentaire de la botanique ou exposition des principes de la classification naturelle et de l'art de décrire et d'étudier les végétaux. Deterville, Paris.
Naef, A. (1909a). Die Organogenese des Cölomsystems und der zentralen Blutgefässe von Loligo. Jenaische Zeitschrift für Naturwissenschaft, 45, N.F. 38:221—266.
Naef, A. (1909b). Die Organogenese des Cölomsystems und der zentralen Blutgefässe von Loligo. Inaugural-Dissertation, Univers. Zurich, 46pp.
Naef, A. (1913). Studien zur generellen Morphologie der Mollusken. 2. Teil. Das Cölomsystem in seinen topographischen Berziehungen. Ergebnisse und Fortschritte der Zoologie 3: 329—462.
Naef, A. (1917). Die individuelle Entwicklung organischer Formen als Urkunde ihrer Stammesgeschichte: (Kritische Betrachtungen über das sogenannte “biogenetische Grundgesetz”). Verlag von Gustav Fischer, Jena.
Naef, A. (1919). Idealistische Morphologie und Phylogenetik (zur Methodik der systematischen). Verlag von Gustav Fischer, Jena.
Naef, A. (1921—23). Die Cephalopoden (Systematik). In: Fauna e Flora del Golfo di Napoli, Monograph 35 (I-1), Pubblicazioni della Stazione Zoologica di Napoli. R. Friedländer and Sohn, Berlin, pp. 1—863.
Naef, A. 1931a. Allgemeine Morphologie. I. Die Gestalt als Begriff und Idee, pp. 77—118 in Bolk, L, Göppert, E., Kallius, E. & Lubosch, W., (editors) Handbuch der vergleichenden Anatomie der Wirbeltiere 1. Berlin: Urban & Schwarzenberg.
Naef, A. 1931b. Phylogenie der Tiere, pp. 1—200 in Baur, E., & Hartmann, M., (editors) Handbuch der Vererbungswissenschaft, Gebrüder Borntraeger, Berlin 13 (3i).
Naef, A. 1933a. Die Vorstufen der Menschwerdung. Eine anschauliche Darstellung der menschlichen Stammesgeschichte und eine kritische Betrachtung ihrer allgemeinen Voraussetzungen. Jena: Verlag von Gustav Fischer.
Naef, A. 1933b. Cephalopoda, pp. 293—310 in Dittler, R., Joos, G., Korschelt, E. Linck, G., Oltmanns, F. and Schaum, K. (editors) Handwörterbuch der Naturwissenschaften, 2nd edition, volume 2. Jena: Verlag von Gustav Fischer.
Naef, A. 1933c. Morphologie der Tierre (Allegmeines und Grundsätzliches), pp. 3—17 in Dittler, R., Joos, G., Korschelt, E. Linck, G., Oltmanns, F. and Schaum, K. (editors) Handwörterbuch der Naturwissenschaften, 2nd edition, volume 7. Jena: Verlag von Gustav Fischer.
Naef, A. 1972a. Cephalopoda. Fauna and Flora of the Bay of Naples (Fauna und Flora des Golfes von Neapel und der Angrenzenden Meers-Abschitte), Monograph 35, Part I, [Vol. I], Fascicle I. Smithsonian Institute Libraries, Washington.
Naef, A. 1972b. Cephalopoda (systematics). Fauna and Flora of the Bay of Naples (Fauna e Flora del Golfo di Napoli), Monograph 35, Part I, [Vol. I], Fascicle II. Washington, Smithsonian Institute Libraries.
Naef, A. 2000. Cephalopoda. Embryology. Fauna and Flora of the Bay of Naples [Fauna und Flora des Golfes von Naepel]. Monograph 35. Part I, Vol. II [Final part of the Monograph No. 35], pp. 3-461. Washington, Smithsonian.

The Curse of Complexity

2007-11-26T03:55:00.000-08:00

The world is biologically complex. Scientists have always known this and it is not a new discovery. Rather than accepting complexity as an everyday wonder, scientists are surprised that the world is indeed complex and some are annoyed with those who describe complexity in simple statements or methods. Here are a couple of examples:

"Historical biogeography has recently experienced a significant advancement in three integrated areas. The first is the adoption of an ontology of complexity, replacing the traditional ontology of simplicity, or a priori parsimony; simple and elegant models of the biosphere are not sufficient for explaining the geographical context of the origin of species and their post-speciation movements, producing evolutionary radiations and complex multi-species biotas" (Brooks, 2005: 79).

"The problem can be reduced to deciding when a collection of trees—a 'forest'—is a better explanation for evolutionary relationships among a set of sequences than is a single tree" (Ane and Sanderson 2005: 146).

We see no problem with simplifying a complex world in order to communicate in the form of classifications. We know for instance that a cat is a highly complex creature. So complex in fact, that the term cat or Felis silvestris and the classification of the Felidae are satisfactory in communicating that we are in fact referring to a tabby and everything associated with its complexity. These terms and classification are not however sufficient in explaining the highly complex nature of cat behaviour, sexual reproduction or neural activity. Classification is not about explaining complexity - this is job of General Biology.

Classification, an integral part of comparative biology, attempts to convey what information we have (i.e., about cats) without having to divulge and detail all its complexity (i.e., sexual behaviour). The aim of classification is to summarize (not reduce*) a relationship based on known homologues without recourse to inference. That means, comparative biology is about "simplicity" not causality or interconnectivity (sensu reductionism). We can for instance classify all mammals based on their hair and vertebrates based on the presence of forearms. The more complexity we introduce, the less unique traits there are to compare (i.e., eye colour). Since comparative biology is about comparing and classifying, explicit unobserved explanatory mechanisms have little to do classifications. They are statements about a type of complexity reserved for general biology (i.e., physiology, behaviour, sexual reproduction etc.). Although such explanations are unique events (or a series of events) based on careful considerations of general biological laws and processes, they can however be represented by a single classification.

Let us say for instance that the trilobite Eoharpes guichenensis evolved from E. cristatus which then evolved into E. primus. This can be represented as an anagenetic event and drawn accordingly. Another person may object to this explanation and suggest that E. guichenensis evolved into E. cristatus and E. primus through cladogenesis. Another may see that both explanations have avoided the explanation that E. guichenensis evolved in E. primus and E. primus into E. cristatus.

Regardless of how these species of Eoharpes have evolved, the phylogenetic trees and be summarized or simplified as relationships in the cladogram: E. guichenensis (E. cristatus, E. primus). What is more, is that the nodes on the cladogram are not events, ancestors or morphotypes, but simply junctions supported by homologues. Rather than accepting the cladogram as means of communicating three or more different evolutionary scenarios, it is rejected as being too simplistic or as an explicit scenario (i.e. "cladification" of Mayr and Bock, 2002).

As systematists and biogeographers, that is comparative biologists, we study the shadows of the past. We are at best able to find gross relationships between taxa or areas. The ability to extract any pattern at all from the bits and pieces of information at hand is an extraordinary achievement, but for some this is not enough. A complex world it seems must be shown to be complex, as though this something that is not already appreciated. The ability to communicate and understand such complexity is impossible without "simplification", that is, classifications. Simplifying the complexity that surrounds us is not a crime but a way to understand the world and to communicate that information to others. Without classification, complexity becomes a curse, which leaves us dumbfounded in a sea of information.

*It is important to note that reduction is not simplification. Mechanical explanations for instance are reductions. The philosophy of reductionism revolves around causality and not natural classification.

References

Ané, C. & Sanderson, M.J. 2005. Missing the Forest for the Trees: Phylogenetic Compression and Its Implications for Inferring Complex Evolutionary Histories. Systematic Biology 54: 146 – 157.
Brooks D.R. 2005. Historical biogeography in the age of complexity: expansion and integration. Revista Mexicana de Biodiversidad vol. 76: 79- 94
Mayr, E. & Bock, W.J. 2002. Classifications and other ordering systems. Journal of Zoological Systematics and Evolutionary Research, 40, 169-194.

Urhomology and Perfection

2007-11-21T01:29:00.000-08:00

Many of you may wonder why we have named the URL of our blog urhomology.blogspot.com.

The idea of a urhomology appeared to us when reading through Goethe’s scientific works on comparative biology. Goethe did not exactly discover homology, as the concept already existed. Vic D’Azyr and Geoffroy Saint Hilaire had already discovered serial and general homology respectively. Goethe was aware of the concept and closely followed the debate between Cuvier and Saint Hilaire.

Goethe did however have his own homology concept which he never coined nor referred to by name. We have therefore though it necessary to not only coin urhomology but also investigate its place in the history of homology.

Urhomology is undoubtedly influenced by the serial and general homology concepts. We chose to use the prefix ur in order to refer to an overall concept (i.e. urphenomenon) rather than to a functional homology concept (i.e. Remane's homology criteria).

Urhomology is a concept that states that two taxa are related by a third taxon by their characters. This does not appear to be remarkable at first glance until we discover what Goethe meant by characters.

In cladistics we refer to primitive and derived characters. The basal nodes of a cladogram contain the "primitive" or plesiomorphic characters and the terminal branches nested contain the apomorphic characters. The same terms are used for taxa. Plesiomorphic taxa represent "primitive" characteristics and so on. Goethe shunned the idea that a taxon or any organism can be primitive or derived. We may say that Archaeopteryx is a primitive bird. But from the point of view of the taxon it is perfect in its own right. Birds did not evolve to become "primitive" or "derived". Finches (part of the "derived" passerine clade) may appear to be derived today, but in a few 100 million years they too will be labeled “primitive” by future cladists. For Goethe primitive and derived were arbitrary terms, they meant nothing in classification.

Taxa however do possess general and specialized characteristics. A worm for instance has very similar looking organs where as a lemur has highly specialized organs. Goethe never used the terms “general” or “specialized” - possibly because they too are arbitrary and related to function rather than to structure – instead he used a "sliding scale" of "ideal" traits. A lemur is far more "ideal" in terms of structure than say a tardigrade. We however prefer to use the terms general and specialized.

Goethe's problem was how to compare different organisms that were not from the same group. How would one compare an echidna to a human when neither organism shares the same obvious structure? The answer is to use a third taxon. Goethe referred to this as an intermediary taxon, which should not be confused with a transitional form. As far as our reading of Goethe goes, he did not considered transformation between taxa. Instead Goethe saw that the same structure appears in different taxa. This was the key to relating taxa, by their same structures or homologues. In this sense echidnas can be related to humans based on the same structure, say a forearm, but it needs a third taxon in order to validate the relationship, such as a lemur. In short, Goethe's urhomology can be used to discover relationships between taxa no matter how general or specialized they appear, as long as they share the same structure.

Goethe did not go on to explore the concept of an urhomology further, but it stands a major contribution to science nonetheless - one that predates Owen and may have influenced the English anatomist's Special Homology. One concept that Owen did not correctly interpret from Goethe was that of the archetype or urphenomenon. But more of that in a later post.

The Giraffe's Long Neck

2007-11-13T02:47:00.000-08:00

Craig Holdrege at the Nature Institute has published a great book titled The Giraffe's Long Neck: from evolutionary fable to whole organism. Here an excerpt from my review in The Systematist

"The book consists of four chapters that cover existing theories of giraffe form, notably its long neck, physiology, development, ecology and evolution. The text is interspersed with elegant black and white line drawings and the text is written in an easy conversational style. The first chapter “Evolutionary stories falling short” is a critique of present evolutionary theories in relation to the giraffe's neck. Like most, I recall being taught sometime in school that the giraffe's long neck is an example of an adaptation, an explanation that championed neo-Darwinian theory over “inferior” Lamarckianism. In our texts there was a picture of an upright giraffe apparently feeding, with the story that by having a long neck the giraffe could reach the rare green foliage and therefore survive. Since no one in class experiences the giraffe directly, we accept the story and go no further. This is the starting point for Holdrege's argument. In considering the giraffe feeding it appears to have a long neck. With legs splayed cumbersomely to reach down while drinking, giraffes appear to have awkwardly short necks. What do we as taxonomists gain from this insight? Holdrege has exposed advantageous adaptation as an evolutionary fable, showing that in focusing on a single part of the giraffe we have lost sight of the whole organism" (The Systematist 2007 28:13-14)

The Giraffe's Long Neck: from evolutionary fable to whole organism is available from the Nature Institute website.

References

Holdrege, C. 2005. The Giraffe's Long Neck: from evolutionary fable to whole organism. Nature Institute Perspectives 4. The Nature Institute, Ghent, New York, pp.104. USD14.00.

Abstracting and Seeing – Homology and Similarity

2007-11-06T03:07:00.000-08:00

Abstracting and Seeing

Natural Classifications are often discussed as separate issues to our own experiences and observations. Debate rarely touches on the issue of what a natural classification means to a taxonomist or systematist. If natural classifications, like homologies, are supposedly "abstract things" that taxonomists make up in order to make sense of the world, why do we see them? Can we see abstractions or are we doing something else?

Abstractions are hypotheses conjured up in order to formulate a system or artificial "classification" - that is, categorizing things based on a set of subjective rules or characteristics. We may state for instance that anything with six legs is an insect, and so forth. We may view the world through our chosen abstraction and thereby simplify what we are observing. We call this abstracting. It is not observing but simply glancing, looking for particular characteristics rather than observing the whole organism. Artificial classifications are abstractions. An invertebrate, an organism without vertebrae or a spinal column, are unobservable. Reptiles and unicorns are also unobservable but we know what they are and what characteristics define them. Abstracting is not seeing or observing, but simply employing a hypothesis to do the job of "seeing" for you.

Not being able to "see" something does not mean it does not exist. At times artificial classifications contain real (evolutionary) characteristics. Microscopic organisms or electrons too are unobservable to the naked eye, but can be discovered through tools such as microscopes or experimentation. Invertebrates, like reptiles are not only unobservable, they are also undiscoverable.

Seeing is what taxonomists do in order to know an organism. When we see, we do not go through a predefined list of characteristics. Seeing a dog does not make us recite a list of mammalian characteristics. We just see and recognize it. This is what taxonomists do.

Taxa define themselves rather than the other way around. A white blackbird for instance is still a blackbird even if an artificial classification lacks some characteristics or contains a few conflicting ones. An artificial classification for instance may place the American Robin into the Muscicapidae (Old World flycatchers) because they are similar to the European Robin. We can, however, see that the American Robin is the same as a Blackbird, even though they are similar to European Robins. That sameness is a relationship or homology. Natural classifications are defined by homologies rather than the similarities between arbitrary sets of characteristics as in artificial classifications or systems.

The difference between seeing and abstracting is one that divides the biological community. That division runs deep, especially in the case of total similarly versus relationship.

Homology (Relationship) and Phenetics (Similarity)

Homology is about relationship

When the same characteristic manifests itself in other taxa (e.g., a forearm appearing in the wing of a bat), we have found a homologue (sameness). Homology is about the relationships between two homologues when compared to a third (the Cladistic parameter). Homologies are discoverable and tell us that taxa are related.

Phenetics is about similarity.

When a similar characteristic manifests itself in other taxa (e.g., a leaf ratio of 2:3), we have found a similarity. Phenetics is about the overall similarity between two homologues only. Similarities are generated, that is proposed, and predict that taxa may be related based on a measure of confidence.

Homology, then, is evolutionary, as it discovers homology. Phenetics is non-evolutionary as it only predicts degrees of similarity. The differences are evident and should be construed as a negative criticism on our behalf.

Phenetics is simply an artificial classification system. Even though it endeavours to use homologies, it can never discover homologies only propose them. The tools used in phenetics are borrowed from mathematics (statistics) in order to replace what we do naturally, that is observe. In this sense a number of techniques are phenetic. These range from DNA barcoding to Bayesian analysis to cladistic analysis (optimisation etc.). They are based on the fundamental rule of similarity and hierarchy mixed with ad hoc proposition of evolutionary mechanisms, many of which as at best hypothetical.

Homology (monophyly) is a natural classification system. It is a discovery based on sameness and similarity. The tools we use in homology are unsophisticated and at times phenetic (i.e., relying on similarity). Since homology is discoverable and can be observed, taxonomists have been relying on their own intuition to find out what these natural groups are by studying homologies. The same taxonomic method is used today, but is not as thorough as one would hope. Phenetics, however, has helped develop a number of tools that imitate what we do naturally, in order to test whether our groups are truly groups (monophyly). Where our objections lie is how these tools are used. Rather than use phenetic tools to test our hypotheses, many are replacing the practise of testing with observing, without recourse to our own experience. In other words we are allowing algorithms (no matter how good) to do the seeing for us.

All numerical or phenetic methods are secondary to our own knowledge. This should not be interpreted as a Jacobian outburst, but rather as a cautionary statement. Already many systematists are not looking at their organisms and proposing hypotheses of their groups. Instead they are accepting these tests as hypotheses. In our view phenetics, as a system for testing potentially monophyletic taxa, are becoming primary in taxonomy and systematics. This has resulted in non-taxonomic practises to govern taxonomy (i.e., DNA Barcoding, molecular systematics etc.). Our grudge is not against phenetics, a field worthy in its own right, but at those who feel that it is all there is to taxonomy and systematics.

Given the non-evolutionary nature of phenetics, namely its inability to find or even recognize monophyletic groups, why do we need it in systematics and biogeography? Its simplistic aim of proposing similarity is convoluted by numerous algorithms, neither of which advance our field or our knowledge of the natural world. The Great Phenetic Revival returns us to an age old argument fought at the end of the 18th century, namely artificial classifications versus natural classifications. Nothing in our field today has advanced our understanding of classification (i.e., homology and monophyly) since 1858, a point that we will return to later.

Haeckel, Hennig and History: Evolving Thoughts and Words

2007-11-05T01:08:00.000-08:00

John Wilkins, in his eminently readable and ever provocative blog Evolving Thoughts, presents an account of some historical matters relevant to Natural and Artificial Classifications, matters that might illuminate the differences of opinion between Joe Felsenstein and ourselves. To be sure, we differ on certain fundamental matters. But the issue of natural classifications is a subject that might repay closer attention and discussion. John's history is a cast of worthy individuals (Adanson, Linnaeus, Agassiz, Macleay, etc.), many who made worthy contributions to discovering the means with which to discover natural classification. They all, to one degree or another, had some sort of interpretation of that classification. They all, to one degree or another, had some sort of axe to grind. Never mind.

John moves on to note that "...it is with Haeckel and the early German paleontologists of the 20th century that phylogenetic relations become the core of classification, and we all know, of course, that Hennig defined a natural group as a monophyletic group." Haeckel is a something of a departure and one we see of significance. Here's Agassiz on Haeckel:

"It is not that I hold Darwin himself responsible for these troublesome consequences. In the different works of his pen, he never made allusion to the importance that his ideas could have for the point of view of classification. It is his henchmen who took hold of his theories in order to transform zoological taxonomy" (Agassiz, 1869: 375, our translation) (see also http://www.athro.com/general/atrans.html.

Those henchmen included Haeckel. Most of Haeckel's genealogical trees ('phylogenies') were linear schemes of hypothesized relationships, with some taxa 'giving rise' to others, that is, paraphyletic groups not so much created by him (many were, of course) but retained and explained in terms of ancestry and descent, in terms of evolutionary relationships, relative to a particular model of change. It was to Hennig's credit that Haeckel's paraphyletic groups were exposed for what they were: empty conventions. And thus, a circle was closed and certain groups understood as not part of the discovery process of classification - or so it seemed. Haeckel's problem was taking a viewpoint (ancestry and descent) and interpreting classification from that perspective.

Now that's not a whole million miles away from the current viewpoint:
find a model of evolution and interpret the data from that point of view. Still, again, never mind. What comes shining through most of the earlier contributions to the debate is that, one way or another, Adanson, Linnaeus, Agassiz and Macleay, among others, did have a notion of the centrality of classification: homology. So when John suggests that "...It does not seem to me that cladistic classification is in possession of a notion of taxon that grounds its classifications" he omits consideration of homology. But he is not alone. The entire crop of books recently published dealing with the 'mathemetisation' of phylogeny do not deal with that subject at all. Thus, or so it seems to us, the 'mathemetisation' of classification (phylogeny) has lead to a profusion of artificial methods.

We finished a recent (as yet unpublished) paper with the following words, the first few are from Gareth Nelson:

'"What, then, of cladistics in relation to the history of systematics? If cladistics is merely a restatement of the principles of natural classification, why has cladistics been the subject of argument? I suspect that the argument is largely misplaced, and that the misplacement stems, as de Candolle suggests, from the confounding goals of artificial and natural systems" (Nelson, 1979, p. 20). Cladistics is concerned with homology, monophyly, evolutionary patterns, taxa (species), and natural classifications. That is, natural classification is concerned with relationships.'

PS. One of us [DMW] is a Londoner. We are aware (sometimes painfully) of the relationship between Australia and the UK capital city, the latter a onetime plentiful source of persons to inhabit the former. The 'relationship' between Australian's and Londoner's is such that when travelling in the United States a London accent is often mistaken for an Australian accent. We mention these facts, partly because the other half of this pair [MCE] is an Australian. And partly because the word 'Barny' is also said to originate from Cockney Rythming slang, as in Barny Rubble = trouble, and thus (if true) a mingling of Australian slang, London slang and American cartoon characters - words really do have a life of their own!