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

Thursday, 28 May 2009

Hidden Agendas: The Media & Science

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

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

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

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

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

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

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

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

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

Sunday, 10 May 2009

The Science of Systematics

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

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

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

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

Decoding Borgmeier's Points for the 21 Century Phylogenetist

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

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

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

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

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

Malte C. Ebach & David M. Williams


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

Tuesday, 5 May 2009

Notice to Readers: Comments now moderated

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

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

Friday, 1 May 2009

Paraphyly Watch 2: Paraphyly & the Catalogue of Life

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

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

Malte C. Ebach

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

Thinking Exercise 1: Origins

Consider the following:

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

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

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

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

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

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

Problem 1 Dispersal ability

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

Problem 2 Ancestors and Transitional Forms

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

Problem 3 Plesiomorphic and Apomorphic

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


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


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


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


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

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

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

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

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

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

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