Paraphyly Watch 4: Monoclady and Paraclady

Just when you thought all possible abuses and misuses of paraphyly have been thoroughly exhausted, one totally mind-boggling and confused piece of writing appears in the Journal of Paraphyly Taxon. We refer to Taxonomy versus evolution by János Podani, a dainty ditty that transcends all boundaries of comprehension and ventures into the field of evolutionary science fiction.

The story so far...

On the planet Zog, the Mayrian Monks enforce rigid elections that decide the fate of the foundations of science. One day new heretical “discoveries” of what are called ‘natural groups’ questions the validity of Reptiles - rulers of the land. The heretics have called them a group of ‘unrelated animals’ - nothing more than systematic bastards! The Mayr-Monks are never wrong and, science never gets in their way. A snap election is called, the ballot counted and science-democracy enforced. The vote was unanimous: 130 in favour - zero against. “Good to see science done” says one Monk to another. That night they all sleep peacefully with a clear conscious, awaiting morning when their sun will rotate around their flat earth once again.

The Mayrian Monks will do anything to protect paraphyletic groups. Rather than revise a taxonomic group, evolutionary taxonomists will dabble in systematics in order to change the foundations of classification. This is akin to the alcohol fueled idea of trying the change the laws of gravity in order to balance this year’s Christmas tree in the front sitting room. It doesn’t work. Neither does monoclady and paraclady. Oh dear, where does one start?
Let’s kick off with Podani’s arguement, namely:

“... that there are four major aspects of taxonomic systems in which achievements of evolutionary biology are not recognized fully and properly, if evolution is considered at all” (Podani, 2009: 1049).

Podani does this by distinguishing diachronous and synchronous classifications (not to be confused with similar terms used in Ebach & Williams [2004] as Podani does). In Podani’s view a diachronous classification includes fossil organisms, which he equates with ‘ancestors’ and synchronous taxa that he describes as extant. Apparently, classifying fossils with extant taxa poses problems hence the need for both classifications. He goes on...

“If we use a synchronous classification for extant organisms, we are concerned with the result of evolution, history is only relevant as long as common ancestry is to be detected, and an inclusive hierarchy is suitable to summarize diversity of life” (Podani, 2009: 1050).

and...

“On the other hand, a diachronous classification cannot be Linnaean for two reasons: (1) units of classification and the groups change in time and, more importantly, (2) wide gaps necessary for separating supraspecific taxa are evolutionary absurdities in the spatio-temporal continuum of populations” (Podani, 2009: 1050).

Got it? Now, onto the next bit...

“The only tool for representing the diachronous pattern of life adequately is the Darwinian phylogenetic tree, showing ancestor–descendant relationships between extinct and extant populations” (Podani, 2009: 1050-1051; original emphasis).

...so [drum roll]...

“I suggest restricting the original definition of monophyly to phylogenetic trees, so that it is a diachronous phenomenon and can only be examined in a diachronous classification. For cladograms, I introduced the new term monoclady: a group is monocladistic if it includes all terminals of a given clade. This condition has to do with extant taxa and is particularly meaningful for a synchronous classification” (Podani, 2009: 1051; original emphasis).

...therefore...

“Reptiles are most certainly para- phyletic because extinct ones include the ancestors of birds and mammals as well. Extant reptiles are paracladistic, since crocodiles are sister to birds rather than to other reptiles” (Podani, 2009: 1051).

...and to sum it all up...

“If a collection of organisms is found to be monocladistic (in a molecular study, for example), then the taxon which includes this group in a diachronous classification is not necessarily monophyletic. Paraclady means that the group cannot be embedded into a monophyletic taxon, and it is therefore indication of paraphyly or even polyphyly in the corresponding diachronous classification. A Linnaean taxon, which is preferably synchronous as the above logic dictates, can only be monocladistic, paracladistic or polycladistic and the monophyly/paraphyly problem vanishes. Paraphyly, as understood earlier, may often be reflection of the disagreement of a diachronous classification with a synchronous analysis. Therefore, the central tenet of contemporary taxonomy is perhaps not about paraphyly and monophyly, but around the contrast between synchronous and diachronous classifications” (Podani, 2009: 1052).

In order to keep this argument short we will not discuss Podani’s bogus adventure into nomenclature, but start with his first and last points, namely, “... the central tenet of contemporary taxonomy is perhaps not about paraphyly and monophyly, but around the contrast between synchronous and diachronous classifications”. Is it? Taxonomy has always remained considerably neutral about how one groups extant and extinct taxa together, why then should there be two classifications? Because extinct taxa are more likely to be ‘ancestors’ and, genealogical relationships (as Podani correctly points out) make poor classification systems. So where does this leave taxonomy? Well, where it has always been - as a neutral way to classify taxa without needing to know who is ancestor to whom. The same is true for cladograms - extinct and extant taxa are placed at the terminals because there are related in some way. It appears that Podani has missed something here, such as the whole cladistic revolution from the 1960s to the 1980s. Cladograms remove the need for phylogenetic trees as all relationship can be shown equally. So both the diachronous and synchronous classification systems are utterly pointless as taxonomy remains neutral about ancestors and fossil taxa (they classify along with extant groups) and equally useless in systematics, as all taxa are treated equally. Podani’s rasion d'être for two classification systems is a vain attempt to preserve paraphyletic groups (number 2 for this year after Stuessy and Koenig [2009]).

Here is how it works. First debunk monophyly as irrelevant to classification by assigning them as problems found in phylogenetic trees. Since phylogenetic trees are diachronous and diachronous classifications “cannot be Linnaean” and, are therefore invalid. Clever. Now he introduces a new term monoclady and monocladistic, which means, “If a collection of organisms is found to be monocladistic (in a molecular study, for example), then the taxon which includes this group in a diachronous classification is not necessarily monophyletic” (Podani, 2009: 1052). There we have it. Monocladistic groups can be paraphyletic seen from a phylogenetic perspective. Get it?

Let’s put it another way. Take an existing term like monophyly and replace it with a similar term like monoclady (“includes all terminals of a given clade”), which of course does not change its overall meaning. Now dismiss monophyly as irrelevant to classification, but relevant to 19th century Haeckelian phylogenetics, hence radically changing not only its meaning but also its usage. Here comes the best bit - do the same to paraphyly. Replace its overall meaning with another term, like paraclady, and then dismiss paraphyly as irrelevant to classification. No problems here (as it is not relevant to classification). The coupe de grace is defining some forms of monoclady (formerly monophyly) as paraphyly! Wow, the sheer audacity!

Yes folks, I think we have a clear forerunner in the 2009 Pewter Leprechaun for the misuse and abuse of paraphyly.

As you read, judges are conferring in what is to be some pretty stiff competition. The results for the Winner of the 2009 Pewter Leprechaun will be announced very soon. Stay tuned!

References
Ebach, M.C. & Williams, D.M. (2004). Classification. Taxon 53: 791–794.
Podani, J. (2009). Taxonomy versus evolution Taxon (58), 1049-1053.
Stuessy, T.F. & König, C. (2009). Classification should not be constrained solely by branching topology in a cladistic context Taxon, 58, 347-348.

Myths that Evolutionary Taxonomists live by

Confused evolutionary taxonomists have once again made a stand in the pages of Taxon. The editorial by Brickell et al. (2008) represents a vote of no confidence in favour of paraphyletic groups - as if democracy in science has (or ever had) any valid scientific or empirical merit. This time the confusion stems from

"Recent developments in taxonomic theory have resulted in the production of classifications of the Flowering Plants that are causing concern to all involved in horticulture — gardeners (both amateur and professional), nurserymen, landscape architects, foresters, designers, conservationists, and journalists, as well as to botanists engaged in many different, non-taxonomic disciplines and to other users of plant names generally" (Brickell et al., 2008:1047).

One wonders what those nasty molecular phylocodists and monophyly-peddling robbers of horticultural dignity are up to? Perhaps plotting horrid phenetic-cladogram-trees?

They certainly are a confused mob as the above mockery demonstrates. One way out of this wet paper bag is to see the world from a evolutionary point-of-view. Artificial classifications, which are useful in identifying plants, for example, are not necessarily evolutionary (in the sense of monophyletic). Some may turn out to be, but only empiricism will provide us with the necessary evidence. That is we need cladistic methods to test taxonomic claims of relatedness (i.e., monophyly). Evidence and empiricism, however, appear to be of no use to Brickell et al.(2008).

"Cases such as these (and there are more that could be quoted) have arisen from a fundamentalist approach to cladistic methodology, which requires that a classification should not include paraphyletic taxa"(Brickell et al., 2008:1047).

I tire of saying this: Paraphyletic taxa are not of any use. They do not represent natural classifications. They are not a result of a common shared history. Paraphyletic groups are not anything other than names, just as 'leprechauns', 'unicorns' and 'griffins' are only names. Why then do horticulturalists and evolutionary taxonomists want them in their classifications?

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

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

One common misconception is that of historical 'significance' or 'pragmatism' in science. For example, 'Reptiles' is a wonderful term and describes all manner of organisms such as fire-breathing dragons, sea serpents and the Sea Devils from Dr. Who. (Remember them?) This does not mean that the Reptilia are immune to scrutiny or empiricism - in fact they're not. The same is true for taxa within the angiosperms

"We, as horticulturists and horticultural taxonomists, wish to express our strong support for these pragmatic views, which will encourage the retention of familiar and widely used taxa [e.g., Dionysia, Dodecatheon, Soldanella, Omphalogramma, and Cortusa] which are distinctive and historically important" (Brickell et al., 2008:1047).

I empathize. Good names that are linked to poorly defined groups (which, incidentally is what makes them paraphyletic) sucks. But that's life ... sorry, that's systematics.

Myth 2: Taxonomy needs to be 'stable'

There is no such thing as a completely stable classification of living things. This is not because everything is fluid and 'moving' and 'unclassifiable'. As new evidence comes to light (e.g., molecular data), so do new discoveries. But Brickell et al. (2008) beg to differ

"We are not against taxonomic change, which will continue to be a standard outcome of taxonomic research, but insist that horticulture needs a stable (though not static) classification and nomenclature that can be understood and applied effectively by horticulturists (and others) who exhibit a very wide range of levels of taxonomic sophistication.

Clearly they are against taxonomic change as that is what paraphyletic groups inevitably lead to - taxonomic change.

Myth 3: The needs of end-users are important

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

Myth 4: Molecular systematists and cladists are all phylocodists

This is a myth that has been exacerbated by Brummitt (2006, 2008). Not all molecular systematists and cladists agree with the phylocode. In fact some of the most ardent critics of the Phylocode are cladists who use molecular data (e.g., see Nixon et al. 2003). Moreover, supporting monophyletic taxa does not automatically make you a Phylocodist or anti-Linnean. Here is an example from (Brickell et al., 2008:1047)

"(cf. Brummitt in a note to a colleague: ‘By any logical consideration either one has a monophyletic system with an infinite number of nodes but no ranks, for which the PhyloCode is designed, or you have the Linnaean system with ranks at very few levels, and paraphyletic taxa’".

Classifications are not divided into 'the Phylocode' versus 'Linnaean taxonomy'. This dichotomy is false. The Linnaean system of taxonomy remains silent about paraphyly or monophyly. Biological classification consist of artificial and natural systems, the modern Linnaean System belonging to the later. As taxonomists, we aim to find natural groups (a.k.a 'monophyletic groups') in our Linnaean System. But paraphyletic groups, like Linnaeus sexual system, are artificial. They may be useful in identifying organisms, but they do not reflect natural evolutionary groups and should be exempt from our classifications. Brickell et al. (2008) are misguided and confused if they are to believe that paraphyletic groups are 'natural' or even evolutionary in anyway.

Myth 5: What does the Molecular data mean?

There are many ways to tell someone to p*ss off and this is a beaut:

"In saying this we do not wish to imply that phylogenetic studies are unimportant or uninteresting; only that the purpose for which they are produced is not applicable to horticultural needs and practices. (Brickell et al., 2008:1047-1048)"

I agree. Molecular trees (which is what Brickell et al., 2008 are referring to above) do not have any characters listed at their nodes. If horticulturalists are to follow our lead and adopt new groups based on molecular data, then show us the characters that support it as a monophyletic group. If the group is paraphyletic then do the revisionary taxonomy. There is however a catch. Molecular systematists do not necessarily do all the work. Saying that something is paraphyletic and in need of revision without any morphological evidence is hard for any taxonomist or horticulturalist to swallow. I think that Brickell et al.(2008) are on to something here and it is well worth pursuing. Consider this myth busted.

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

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

Naef and Cephalopod Awareness Day

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

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

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

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

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

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

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

Confused?

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

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

References

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

Defining Phenetics, Intentions and Mimics

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

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

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

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

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

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

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

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

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

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

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

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

References

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

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

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

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

Loretta the Murderess

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

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

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

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

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

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

"Birds have evolved from Dinosaurs"

or

"The center of origin for hominids is Africa"

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

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

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