Tweeted Histories I #Homology

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

@Darwinathome's birdy

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

The Autonomous Algorithm: Malpractice in Theory

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

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

A method is a procedure to accomplish something. Methods are generally activities that can be done by pen and paper (although sometimes they are easier when automated) in which we determine the steps, for instance, to find out how to tell what is beneath a particular surface. The implementation is the tool that is used to do implement the method. This is usually as a computer algorithm. So, an algorithm is a tool that is based on a method that is underpinned by a theory. Seems simple enough, but this is often misinterpreted.

Classification and Non-Trees

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

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

“In the most restricted sense virtually all evolution involves parallelism. Homologous genes tend to mutate in the same way (p. 9)… Homology is always valid evidence of affinity. Parallelism is less direct and reliable, but it is also valid evidence within somewhat broader limits. It may lead to overestimates of degree of affinity, but it is not likely to induce belief in wholly false affinity (p. 10)” (Simpson 1945, pp. 9—10).

Simpson’s words turned out not to be so, for the parallelisms he noted simply mislead determination of exact relationships among mammals (McKenna & Bell 1997): those similarities identified as parallelisms (like xenology and dispersal) are simply incongruent characters.
All the same, it has been argued that reticulate networks allow incongruent ‘homologies’ to be accommodated on the same diagram relative to congruent homologies (Huson & Bryant 2006). The general idea seems similar to that explored by William Sharp Macleay and his circular systems: an attempt to represent what he called analogies and affinities (homologies) in one system (Macleay 1819, Fig. 6).

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

References

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

The Absence of Evolution (Homology)

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

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

"Homologies are traits present in two or more organisms that were inherited from the common ancestor of those organisms. The human five-fingered hand and the five-toed foot of a lizard, for example, were both inherited from our common ancestor that lived more than 300 Mya" (p. 498).

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

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

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

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

The Evolution Slogan

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

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

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

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

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

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

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

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

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

References

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

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.

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.

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.

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.

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.

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.