Divisions: Who watches the philosophers of science?

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:

1. Morphology and Molecules
2. Homology and analogy
3. Homology and homoplasy
4. Transformational and Taxic Homology
5. Synapomorphy and symplesiomorphy
6. Congruence and consensus
7. Cladistics and Phenetics
8. Simultaneous analysis and separate analysis
9. Ecological and Historical Biogeography
10. 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!

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::

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


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


3. It should instead be trying to make a classification


4. 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

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:

1. Fish have scales and no limbs.
2. Amphibians lay eggs on land and live in water.
3. Reptiles lay eggs, have scales and live on land.
4. Birds lay eggs and have feathers.
5. 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

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

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

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

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

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

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

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

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!

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Terminology and the "Sensible Way"

Terms in systematics and biogeography often have different even conflicting meanings. "Monophyly", "homology", "cladistics" and "evolution" are used in varying ways. The reason for this discrepancy is that terms, like people, change over time. A majority of concepts, like evolution, were in use before 1859 and have altered drastically since. The reason for this change is the ever increasing befuddlement between form and explanation, a symptom of 21st century systematics and biogeography.

A term such as "spoon" can be given many different definitions that attempt to represent meaning. The most fundamental definition being a "small concave dish that tapers into a stem posteriorly". The definition only describes its form and not its function. The reason why such a definition is "fundamental" is that it does not need a functional description in order to convey meaning. Someone who has never seen or heard of a spoon before may choose to use in an unconventional way. The spoon however used is still recognized as a spoon based on its fundamental definition. Whatever function the spoon has at one time (i.e., a tool for eating soup, a bowl scraper or medicine applicator) should not detract from its fundamental definition. The same is true for conceptual terms in systematics and biogeography.

Fundamentally, monophyly is defined as a "natural group or classification". What this means is that it is a "natural group or classification". That is all. We may choose to interpret monophyly in different ways. It could be "a group that includes a most recent common ancestor plus all and only all of its descendants" (Kitching et al. 1998: 210). It could be a group that may have a ".. general typical organization" (Agassiz, 2004: 182). In either case, the fundamental definition remains universal despite the explanation given.

The Sensible Way
The concept of a natural group stems back before Linnaeus and ultimately is a "pre-evolutionary" concept with a 20th century term, namely "monophyly". The explanations assigned to it, whether they are true or not, reflect the attitudes popular at the time, which we choose to term the "Sensible Way", referring to Felsenstein's recent commentary in a previous post.

The "Sensible Way" always refers to "Darwin and Wallace" in some elusive or nostalgic way as in "... since the time of Darwin and Wallace ..." (Waters, 2007: 871) or to a particular interpretation of a term (i.e., biogeography = population genetics etc.).

This usage often appears to indicate that no sensible ideas were espoused during the time between Aristotle and Darwin/Wallace. We call this the 1859-syndrome, which is synonymous with the phrase the "beginnings of Evolutionary Biology", another vague term. Everything prior to this is often thought of as "pre-evolutionary". It is only logical to conclude from this argument that the term "evolution" is pre-evolutionary.

Evolution means "change over time". This is a simple definition that can refer to any number of evolutionary mechanisms such as natural selection, Lamarckism and hologeneis. The term "evolution" does not exclusively relate to a particular explanation but to all. The "Sensible Way", however, dictates that evolution = natural selection. By associating a universal concept with a particular mechanism has been the cause of great debate in science and unfortunately has given fodder to anti-science (i.e. creationists).

The "Sensible Way", namely a misinterpretation between a thing or concept with a particular explanatory mechanism, is the bane of systematics and biogeography. So is the 1859-syndrome, which shows an ignorance of history and the literature. The majority of concepts in systematics and biogeography are pre-1859 and their definitions fundamental and their explanations tend to be post-1859, deriving in the late 19th century and during the Modern Synthesis. The term "homology", which is fundamentally defined as "manifestations of the same form", is constantly given an explanation in order to suit the "Sensible Way". At first it was a functional role (i.e. Carl Gegenbauer, Adolf Remane etc.) and later with the onset of molecular data, just "similarity between characters". The homology concept underpins systematics and biogeography and has been a topic of discussion over a 200 year period. Noteworthy 18th and 19th century naturalists including Vic D'Ayzr, Johann Wolfgang Goethe, Geoffroy Saint Hilaire and Richard Owen debated the relevance of homology. By 1858, all we know about homology had been discovered. Post-1859 "sensible" interpretations (i.e. explanatory mechanisms) were postulated and confused with its actual definition "manifestations of the same form". No further meaning had been added, only an endless variety of ad hoc ("sensible") explanations.

Explanations do not add greater meaning to form or to such fundamental definitions. They only confuse and cause senseless debates over which explanation has the most rational argument based on what is known at the time. These "sensible" explanatory mechanisms have taken terms and definitions beyond their intended role. Richard Owen's special homology and its relationships to an archetype have been contorted into mechanisms of transformation. Sclater's biogeographic regions transformed into evolutionary centres of origin and Goethe's urpflanze into an ancestor. Definitions such as archetype, homology, evolution and natural classification that originally had no explanatory mechanism, helped to establish systematics and biogeography. Why do we need them now?

References
Agassiz, L. 2004. Essay on Classification, with an introduction by Edward Lurie. Dover Press, Mineola, N.Y.
Kitching, I.J., P.L. Forey, C.J. Humphries, and D. Williams. 1998. Cladistics, 2nd ed., The Theory and Practice of Parsimony Analysis. Oxford University Press, New York, NY.
Waters, J.M. 2007. A review of: Biogeography in a changing world. Systematic Biology 871-873.

The Great Phenetic Revival 2 Revisted: A Reply to Felsenstein

Recently on our blog we received a reply to our posting on The Great Phenetic Revival 2: Phenetics from Joseph Felsenstein (University of Washington). We thought it would be a pity to relegate our reply to the comments section and instead include it as separate post.

Felsenstein claims not to have been "trying to give the history of "phylogenetic methods" in his chapter 10. Nevertheless, this seems not to have prevented him from making sweeping (and damning) statements concerning classification - some published before the publication of his book: "The focus of systematics has shifted massively away from classification: it is the phylogenies that are central, and it is nearly irrelevant how they are then used in taxonomy" (Felsenstein 2001: 467), "Systematists get so worked up declaiming the centrality of classification in systematics that I have argued the opposite' (Felsenstein in Franz 2005, p. 495); others see things in much the same light: "Many phylogeneticists now see nomenclature and classification as largely irrelevant to phylogenetics..." (Hillis 2007: 331).

Still, Felsenstein sees himself as commenting only upon "algorithmic methods", when, of course, any method proposed can be made 'algorithmic' and many attempted to do so in constructing early versions of data matrices, way before Sneath or Sokal (see figure above as well as Tillyard 1919, Abel 1910 and Willman 2003).

Cladistics and phenetics might (erroneously) be seen as methods. Felsenstein wished to drop the terminology: "Making this distinction [between phenetics and cladistics] implies that something fundamental is missing from the 'phenetic' methods, that they are ignoring information that the 'cladistic' methods do not. In fact, both methods can be considered to be statistical methods, making their estimates in slightly different ways ... In this book we will give the terms 'cladistic' and 'phenetic' a rest and consider all approaches as methods of statistical inference of the phylogeny" (Felsenstein 2004: 145-146). Our comment on Felsenstein's wish to drop the terms 'cladistic' and 'phenetic', was "to grant equal time to all quantitative (numerical) methodologies", which now leaves us puzzled as to what, exactly, in this passage was "an outrageous misrepresentation of the content of my Chapter 10".

Further, "... numerical phylogenetics is not 'based on simple similarity'. It just isn't. There is no way you can compute either a parsimony tree, or a likelihood tree, from a table of similarities between species". What, then, is it based upon? The matrices that grace our systematic accounts certainly look to us as if they are sets of similarities.

To many (us included), cladistics was about the reform of palaeontology rather than the elaboration, support and promotion of one kind of method or another. That reform began in the 1960s almost entirely independent of the numerical development of data manipulation, of which the latter manifests itself as the ever present pernicious influence of phenetics (regardless of that manifestation as 'parsimony', 'compatibility', 'likelihood', etc.). Felsenstein doesn't mention palaeontology in his history chapter but does later in "Phylogenies and Paleontology" (Felsenstein 2004: 547 et seq.). Here his imprecision seems a little troubling: "...If the fossil record of a group has been searched thoroughly enough, then we should not only be allowed to interpret fossils as ancestors, we should be encouraged to do so" (Felsenstein 2004, p. 547) - searched thoroughly enough; we should not only be allowed to...we should be encouraged to do so. How thorough is enough? And since when has the scientific endeavour required 'permission' to be 'allowed' and 'encouraged' to 'believe' something? It was with such 'beliefs' that the first cladistic revolution was necessary. It is from the ever present phenetics that the second cladistic revolution will (eventually) be born.

References
Abel, O. 1910. Kritische Untersuchungen über die palaogenen Rhinocerotiden Europas. Abhandlungen Kaiserlich-Koenigliche Geologische Reichsanstalt 20: 1-22.
Felsenstein, J., 2001. The troubled growth of statistical phylogenetics. Systematic Biology 50: 465-467.
Felsenstein, J., 2004. A digression on history and philosophy. In: Felsenstein, J. (Ed.), Inferring Phylogenies. Sinauer Associates, Sunderland, MA, pp. 123-146.
Franz, N. 2005. On the lack of good scientific reasons for the growing phylogeny/classification gap. Cladistics 21: 495-500.
Hillis, D. M. 2007. Constraints in naming parts of the Tree of Life. Molecular Phylogenetics and Evolution 42: 331-338.
Tillyard R. J., 1919. The panorpoid complex. Part 3: the wing venation. Proceedings of the Linnean Society of New South Wales 44: 533-717.
Willman, R. 2003. From Haeckel to Hennig: the early development of phylogenetics in German-speaking Europe. Cladistics 19: 449-479.

The Great Phenetic Revival 3: DNA Barcoding

DNA Barcoding is not often directly associated with phenetics or numerical taxonomy. Given that it is without any methodological or theoretical foundation, DNA Barcoding has very little to with anything associated with taxonomy or comparative biology. Then we happened upon Sokal & Rohlf (1970) The Intelligent Ignoramus, an Experiment in Numerical Taxonomy published in Taxon (19: 305-319).

What is striking about Sokal & Rohlf's "Intelligent Ignorumus" is that it totally undermines our in-built ability to classify, even groups we do not know. Any one from the southern hemisphere would know how to group "Song Birds" based on characters that have not been pointed out to them. It is what we do naturally. Consider the European Robin (Erithacus rubecula), the American Robin (Turdus migratorius) and the European blackbird (Turdus merula). Based on their common names we group them as Blackbird (E. Robin, A. Robin). But if we look at them, it becomes clear that the European Blackbird looks like an American Robin. See for yourself. You don't need a detailed list of pre-defined characters; it is what we do naturally. But Sokal & Rohlf don't think so.

The Intelligent Ignoramus is a simpleton. They are "unprogrammed" with little to no training in biology, meaning the are unable to identify the organisms before them as "bees" and therefore are presumed to lack the ability to classify bees in general. Sokal & Rohlf's test was to assess: "The feasibility of using technicians untrained in taxonomy to collect data for use in numerical taxonomic studies .. [and ] ... the analysis of their descriptions were compared with the data of Michener and Sokal (1957)" (Sokal & Rohlf 1970: 305). The results astounded the authors.

The two technicians managed to find a similar classification of bees. Anyone looking at bees for the 170 hours (as mentioned in the results) would obtain a general knowledge of bee morphology. Obviously this time would be remarkably reduced if a trained taxonomist had pointed out the relevant morphology and the characters that relate various bee groups. Instead of seeing the obvious, Sokal & Rohlf make an enormous blunder. What if the technicians had measured all the specimens, that is quantifying the qualities that helped them group the bees? Quantities can be standardized and therefore automated. In fact, one "... could hire teams of technicians to study the specimens, make the necessary measurements, and record the data and perhaps even select the characters themselves. One step beyond this would be to automate the entire process completely" (Sokal & Rohlf 1970: 318).

The future of taxonomy envisioned by Sokal & Rohlf - groups of "Intelligent Ignoramuses" coding taxa to be processed by numerical methods - is typical of phenetics and their attempts to remove taxonomists from doing what they do best. Now, all of this is starting to sound familiar. "Intelligent Ignoramuses" that can identify and classify taxa without the burden of taxonomic training have reappeared in the guise of DNA Barcoding (identification) and the Phylocode (classification).

Can we re-label DNA Barcoding as Phenetic? Usually phenetic methods or techniques are considered, but rarely do we ever identify phenetic ideas or intentions. The Great Phenetic Revival is the revival not only of phenetic methods but the ideas endorsed by early phenetists like Sokal & Rolf. Read phenetics as Numerical Taxonomy and one quickly realizes that it's about numerical data - quantities, not qualities - and about obtaining such data mechanically and processing it quickly. The taxonomist is not a machine. He or she does not seek to provide measurements. The aim is to discover homologies. The same is true for classifications. They are based on monophyly, not on some general rule of classification. Unfortunately, the Great Phenetic Revival is about the rise of Intelligent Ignoramuses, those that wish to supplant taxonomy and systematics with phenetics under the guise of helping taxonomy. What a frightening thought.

The Great Phenetic Revival 2: Phenetics

To all intents and purposes, by the late 1970s phenetics was dead. Why, then, some 30 years after its death, does Felsenstein (2004) in chapter 10 (Digression on history and philosophy) of his book Inferring Phylogenies begin by acknowledging Sokal and Sneath (1963), the first bible of phenetics, as the beginning, if not the foundation of phylogenetic methods (Felsenstein, 2004:124)?

Felsenstein notes (2004:145):

"Many systematists believe that it is important to label certain methods (primarily parsimony methods) as 'cladistic' and others (distance matrix methods, for example) as 'phenetic'."

Why does Felsenstein reduce the theory of cladistics and phenetics to different types of method? Part of the reason is that Felsenstein wishes to grant equal time to all quantitative (numerical) methodologies. Unwittingly (perhaps), he makes phylogenetics a 'realist' agenda for numerical systematics - rather than 'phenetic', a term carefully avoided.

Methods to one side, Felsenstein sees no purpose in discussions of classification, noting 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)

Felsenstein's dismissal of classification should not be surprising. Homology and monophyletic groups, crucial to the enterprise of classification, are not necessary under phenetics (in fact, Felsenstein mentions neither homology nor monophyly in his book) (see Williams & Ebach 2005).

So, what, exactly is phenetics? Or what has it become?

Phenetics is more than just a method of grouping by overall similarity; it's more than just a method. It's way to not do (to avoid) classification, namely to group taxa without any notion of homology beyond mere similarity, to form arbitrary groups without any notion of relationship (paraphyly) and work comfortably with branching diagrams depicting similarity without any specified hierarchy (unrooted trees). Phenetics is a synthesis that unites various numerical procedures to find non-groups that stem from ancestral 'vices' in a world in which the taxonomist and systematist has no prior knowledge or conviction of classification.

Perhaps there is a broader question: What are the fundamental differences between the Modern Synthesis, numerical phylogenetics, numerical taxonomy and phenetics? We know of none; all are based on simple similarity.

References
Felsenstein, J. 2004. Inferring Phylogenies. Sinauer Associates Inc., Massachusetts.
Sokal, R.R., Sneath, P.H.A. 1963. Principles of Numerical Taxonomy. W.H. Freeman, San Francisco.
Williams, D.M., Ebach, M.C. 2005. Drowning by Numbers: Re-reading Nelson's Nullius in Verba. Botanical Review 72, 355-387.

Planet Bob

The guys at the International Institute for Species Exploration Arizona State University, in cooperation with Media Alchem of Seattle, have just released the trailer and movie to Planet Bob.

Planet Bob is a fantastic way to advertise the importance of taxonomy to a general audience. Making people aware of taxonomy through a large media campaign is a novel idea and one that I hope will attract the attention of policy makers and funding bodies. We wish Quentin Wheeler and the IISE the best of luck.

Please visit the Planet Bob website http://www.planetbob.asu.edu/

The Great Phenetic Revival 1: Stratophenetics

Phenetics haunts us again in what appears to be a great revival in molecular systematics and paleontology - two fields that are linked not by their data but by a common world view.

The molecular clock and all that is associated with it, mainly a belief in a new empirical attempt to date nodes on trees, is an old idea that stems back to stratophenetics, a term coined by P.D. Gingerich in 1979. The practice of stratophenetics is simple. Taxa that share similarities that can be clustered either as phenograms (or on graphs) and together with their respective fossil dates can be compared directly to existing hypotheses of classification (i.e. phylogenies). The practice of assigning dates to taxa as well as to nodes (i.e. ancestors or events) is the underlying principle. In short, the ingredients for the stratophenetic recipe are:

• Any taxic hierarchy (i.e. phenograms, cladograms, area cladograms etc.).


• The oldest known fossil date for each taxon.


• Interpreting nodes as either ancestors or events and cladograms and phenograms as explicit ancestor-descendant relationships.

This then can be turned into molecular clocks, stratocladistics or any other recent attempt at dating nodes (Wagner 1995, Hunn & Upchurch 2001, Donoghue & Moore 2003, Makovicky in press). Given the number of times that stratophenetics pops up in systematics and biogeography, many would be under the impression that it is a good idea. We beg to differ.

Stratophenetics like stratocladistics tests existing phylogenetic hypotheses based existing classifications (see Wagner, 1995). The test adds in the extra stratigraphical data (i.e. age of fossil taxa) to any given ancestor-descendant lineage. The better the stratigraphy the better rates of speciation can be retrodicted - something like a fossil clock. Unlike molecular clocks however stratophenetics and stratocladistics goes further. They use the fossil clock to test if the lineage is correct. If for instance the clock tells us that taxa A is the oldest followed by B, C and D sequentially, it would contradict a hypothesis that related A closer to D than to either B or C (if the lineage follows chronological order, namely A=>B=>C=>D). If we were to interpret phenograms and cladograms as real phylogenetic trees (rather than overall classifications) we could interpret the tree (AD)(BC) as the node that unites B and C (herein node X) to be older and therefore more ancestral than A. Many would go one step further and identify node X as an ancestor that is older than A but not necessarily older than the node that unites A and D. Molecular clocks do not go that far, only adopting the oldest known age as the "minimal" age for any given node.

Where both molecular systematics and paleontology share a common world view is that the oldest node of a group (e.g. Node X) is a real taxon or event - most likely an ancestor or radiation. Gingerich (1979) thought the same and would after some careful consideration also be the father of not only stratopehentics, but molecular clocks as well.

References
Donoghue, M. J. and B. R. Moore. 2003. Toward an integrative historical biogeography. Integrative and Comparative Biology 43: 261-270.
Gingerich, P. D. 1979. The stratophenetic approach to phylogeny reconstruction in vertebrate paleontology. In J. Cracraft and N. Eldredge (eds.), Phylogenetic Analysis and Paleontology, Columbia University Press, New York, pp. 41-77.
Hunn, C. A. & Upchurch, P. 2001 The importance of. time/space in diagnosing the causality of phylogenetic events: Towards a "Chronobiogeographical" paradigm? Systematic Biology 50:391-407.
Makovicky, P.J. In press. Telling time from fossils: a phylogeny-based approach to chronological ordering of paleobiotas. Cladistics.
Wagner, P.J. 1995. Stratigraphic tests of cladistic hypotheses. Paleobiology 21:153-178.

Phenetic "Natural" Classifications

Why would any one talk about Phenetic "Natural" Classifications? Strangely the concept turned up in a recent review of Johann-Wolfgang Wägele's book Foundations of Phylogenetics by Norman Platnick in The Quarterly Review of Biology (Vol. 81: 56 - 57).

What caught our eye was the following:

"Phenetics is the theory that clustering by raw similarity (i.e., by counting as significant both the presence and absence of characters, the 0s as well as the 1s in data matrices) will retrieve natural groups" (Platnick 2007: 56).

Phenetics and Natural Groups? We had to investigate.

The concept of a Natural Groups or a Natural Classification in phenetics was championed by P.H.A Sneath and R.R Sokal. Their claim followed Gilmour's dictum, namely a "... system of classification is the more natural the more propositions there are that can be made regarding its constituent classes" (Sokal & Sneath 1963: 19).

If we look at Gilmour (1951) wee see that his definition states: "In the general theory of classification, classifications which serve a large number of purposes are called natural, while those serving a more limited number of purposes are
termed artificial" (Gilmour 1951: 401).

It is clear that the meaning of the term "Natural" has been misinterpreted, both by Gilmour and Sokal & Sneath. No one who wished for a Natural Classification would have bought into the idea that Natural = more data whereas Artificial = less data. Moreover, Sneath and Sokal (1973) went as far as to defend their version of natural classification by using A. P. Candolle's distinction that Artificial Classifications, namely Systems (i.e. Linnaeus' system) should rejected in favour of Natural Classifications, namely a Method (Candolle, 1813) - a concept that was also supported by Goethe.

Gilmour's Natural Classification is a System of Classification and not a Natural Classification or Method. The former imposes a way to order nature (i.e. overall similarity) whereas the other discovers the way nature is ordered (homology and monophyly). The mistake is monumental and is one that often gets made (i.e. Phylocode).


References

Candolle A.-P. de 1813. Theorie elementaire de la botanique. Deterville, Paris.
Gilmour J.S.L. 1951. The development of taxonomic theory since 1851. Nature 168:400- 402.
Sneath P.H.A.& Sokal R.R. 1973. Numerical Taxonomy. Freeman, San Francisco.
Sokal R.R. & Sneath P.H.A. 1963. Principles of Numerical Taxonomy. W. H. Freeman, San Francisco.

The Authors

The authors after two days of correcting proofs (at Gabana's in Berlin).

The new Blue Book?

It certainly is blue but Foundations of Systematics & Biogeography focuses on the history of comparative biology from Goethe to 21st century systematics and biogeography. The book is the history of our field from Ernst Haeckel to Adolf Naef, a rather neglected story that is unfairly dismissed as "typology" and forgotten. Perhaps this is Mayr's great undoing of what seems to be the foundations of 21st century systematics and biogeography.

The book is a combination of our collaborative efforts since 2001. During that time David and I have tried to unravel what is for us key-stones in our understanding of comparative biology. We are still mulling over a few, such as the role of homology in molecular data and why paraphyly is still the biggest problem in systematics. We hope that the book and this blog will help people try the unravel that same history.

The book is available from Springer in December. Watch this space for more news!