Paraphyly Watch 1: Fossil Fish & Missing Links

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

"These recent fossils [Palaeozoic ‘acanthodians’] started to make us question: are these a natural group or are we looking at a bunch of organisms closely related to the common ancestor of all jawed vertebrates?" says Brazeau. "It's tempting to put them all into one group; however, they might come from different groups but all look very similar." This, Brazeau adds, is a common problem" (Nature 2009, 457:234).

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

"Ptomacanthus is placed as a basal stem chondrichthyan, but this result should be viewed with caution. A large part of the acanthodians, including Acanthodes, form a cohesive monophyletic group on the osteichthyan stem. However, the position of Ptomacanthus is problematical" (Brazeau 2009:307).

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:

"The study also suggests that some acanthodians are ancestors to all modern jawed vertebrates" (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)

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

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.

By paraphyly we mean non-monophyletic groups or taxa (e.g., grades).

By misuse, we mean accepting paraphyletic groups* as informative (e.g., using them in analysis).

By abuse we mean treating paraphyly as being evolutionary or evidence for evolution (e.g., accepting non-monophyletic groups in taxonomy and evolutionary biology).

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:

"... emphasis has been increasingly placed on the need for a classification which recognises evolution" (Brummitt, 2008:1050).

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

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

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.

Ebach, M.C., Williams, D.M., & Gill, A.C. (2008). O Cladistics, Where Art Thou? Cladistics, 24: 851–852. [pdf]

Ebach, M.C., Gill, A.C. & Williams, D.M. (2008). Ebach et al. reply: A Future for Astrobiogeography. Astrophysics and Space Science, 317: 147. [pdf]

Ebach, M.C., Gill, A.C. & Williams, D.M. (2008). The Pitfalls of Astrobiogeography. Astrophysics and Space Science, 317: 143-144. [pdf]

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

Ebach, M.C., Morrone, J.J. & Williams, D.M. (2008). A new cladistics of cladists. Biology and Philosophy, 23: 153-156. [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.

Williams D.M. & Ebach, M.C. (2008). Evolutionary theory: don't skimp on teaching its history. Nature 453: 719. [pdf]

Williams, D.M. & Ebach, M.C. (2008). Foundations of Systematics and Biogeography. Springer, New York. [Flyer]

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

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.

Serializing our New Book: A Question of Relationship

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!