Natural Classification

One of the recurring creationist attacks on evolution is, “If we evolved from monkeys, why are there still monkeys?” I responded to this once before but it is time to revisit it. Why? Because Marty Robbins has attacked the British media, itself always a noble thing to do, for constantly conflating apes and monkeys. In the course of it he posts this image:

A monkey contrasted with an ape. Note the ape’s larger body and brain, shoulder mobility, and tendency to bellow “I’m Brian Blessed” at high volume.

Now John Hawks, who I usually defer to in these matters (he is, after all, an echt anthropologist, while I am a parasitical philosopher) has taken exception to this, and it is a complaint I have heard from a number of systematists. “Ape”, “monkey” and so on are not terms that have any biological meaning. Here is why: the following diagram indicates the technical names given to primates apart from “monkeys”:

Hominini.png

If you are referring to “humans” then you can either mean the species Homo sapiens, or the genus Homo without ambiguity. But any higher in the taxonomic tree and you have to include the two Pan species (the chimps), and so on. [Note: the ranks here are purely conventional and have no biological meaning in themselves. There could be an indefinite number of unknown branches between any two rank nodes, and probably are quite a few.] But “ape” in ordinary use means HominoideaHomininae (the African Great Apes) minus Homo. And “monkey” means all primates, Old and New World, minus Hominoidea. So, goes the argument, “ape” and “monkey” mean nothing useful. They are no more terms of biological relationship than “kind” is a rank in systematics like “species”, etc.

A similar debate is hotly exchanged amongst paleontologists who discuss the origins of birds. Fewer issues generate as much ad hominem and ire. The BAD crowd claim that Birds Are Dinosaurs, while the BANDits hold that Birds Are Not Dinosaurs. The debate here, though, is rarely about whether or not “bird” means a feathered beaked thing, but whether or not birds arose from within the clade known as theropod dinosaurs that include T rex and other carnosaurs. However, BANDits often assert that the vernacular word “bird” has a meaning that excludes dinosaurs as an adjunct argument.

I’m going to call this the Ordinary Use argument. The idea here is that language has a technical use and an ordinary use and never the two shall meet in science. Systematists use new words to name the results of their taxonomic activities. Just as whales were once thought to be fishes, but systematists like Linnaeus recognised them as mammals, modern systematists have named natural groups that ordinary terms like “fish” do not capture. In phylogenetic terms, a name must be monophyletic, which is a way of saying that the group must have evolved just once. But an ordinary term like “fish” or “monkey” can have either many independent origins or classes of organisms (“fish” used to include waterfowl, crocodiles and whales) or can be a monophyletic group excluding some arbitrary part, like “monkey” excludes apes and humans. In neither case, according to a systematist, are these groups real (or, in their term, “natural”).

The problem I have is not a point about monophyly. There are those who object to the cladistic (“phylogenetic”) definition; they are often called “evolutionary systematists”. That view is widely thought to have been abandoned by all but a few holdouts. I have problems with their view because what they count as significant is often subjective, but that’s for another day. My point is instead, why should we take common or ordinary use as in any way important?

Wittgenstein famously wrote: “the meaning of a word is its use in the language.” [Philosophical Investigations §43, see also §563], but he also said this was true of most, not all terms. In any case, where do language users get their uses as they learn their language? I learn what a crankshaft is from someone who knows how to fix and build engines. I do not learn it from a political pundit or my mother, if either of those two individuals do not know much about engines. Meanings do not sit on the landscape like trees, waiting for somebody to come along and pick their fruit. They are constructed by the community on the basis of the division of linguistic labour; we learn terms from experts. “Fish” was initially defined on the basis of the best natural philosophy of the day (in Latin, of course). Why can’t we redefine folk taxonomic terms now? Even Linnaeus initially named whales as fishes, and in a later edition of the Systema Naturae he revised that. And now we do not call whales fishes (although it took a long time for the message to filter through, as shown by the excellent book Trying Leviathan).

“Dinosaur” is a case in point. The term was coined by an anatomist, Richard Owen, in 1842. That it later entered the public imagination and became a term of folk art in no way means we must now restrict the term (say, lowercased) to apatosaurs and carnosaurs. Instead, we must correct ordinary use, by pointing out the inclusion of birdlike dinosaurs such as Compsognathus and the recent feathered dinosaur discoveries, and on this basis we should revised “dinosaur” to include “bird” just as we excluded “bat” from “bird” on the basis of expert classifications by Linnaeus and others.

So why not say “Birds are dinosaurs”? They exist as a natural group within another natural group and the usual way to express this is to say they are members of that group. Likewise, apes are monkeys, and there is no way to avoid it. In a similar way, if “fish” has any meaning at all as a term that describes the world, we are fishes, as Neil Shubin pointed out in that wonderful book Your Inner Fish. So Brian Blessed is a monkey. He is also an ape. And he is also a human, and the English and other languages had better catch up. So in the end we might actually have to allow that the British media might not be wrong (on this point), even if they are accidentally right. As a beautifully written piece in the Times Higher Education Supplement by Eric Michael Johnson quotes, the Roman poet Ennius once wrote Simia quam similis turpissima bestia nobis, which translates as “How like us is that very ugly beast, the ape”. That’s because, when all is said and done, we are, and Brian Blessed in particular is, an ape. And a monkey, and a mammal. And a vertebrate, and a boney fish…

A new paper has been published in the History and Philosophy of the Life Sciences, entitled “Pattern Cladism, Homology, and Theory-Neutrality” by Christopher Pearson. Either the journal has done something horrible to the text, or the author doesn’t know the difference between Willi Hennig and William Hennig, or between Gareth Nelson and Garrett Nelson.

But this is not the worst aspect of the paper. It states “save for a few notable exceptions in John Beatty (1982), David Hull (1988), and N.R. Scott-Ram (1990), pattern cladism has avoided philosophical scrutiny”. This leaves me aghast. Apart from anything else (the extensive debates of a philosophical nature during the 80s and 90s in journals like Cladistics and Systematic Biology and its predecessors), there is the work of the late lamented Ron Brady, who debated pattern cladism as a philosopher (1979, 1982, 1985). Pearson mentions Brady later in the paper, but not his defence of pattern cladism in general.

The three philosophers (well, two philosophers and one philosophically minded systematist) who Pearson mentions all opposed pattern cladism (PattC), which is the point I wish to draw out here. There has been a strong mythologising of the “debate” over pattern cladism over the years, begun by its opponents (especially Steve Farris, and Mark Ridley), accusing it of being “anti-evolutionary” or “anti-Darwinian” or even “creationist”. At some point in the late 80s, editors got sick of the topic, and it no longer was discussed. Now, if you submit a paper on the matter (and I have been part of a collective that has tried), you are told either that the issue was resolved in the 80s, or that it represents an outmoded metaphysics. But debates, especially philosophical debates, are not resolved because editors tire of them, nor are the issues any less (or for that matter, more) important because nobody talks about it any more. Perhaps Brady is no longer cited because he was pro-PattC.

Pearson has actually focused on an interesting issue: theory-neutrality. I’ll get back to that in a minute. First, let me make a few points. Pattern cladism is, in the mythology that Ridley others set in play, essentialistic and antievolutionary. This is rather odd, given that one of the leading lights of the movement, Colin Patterson, wrote a book on evolution which is (in its second edition) still one of the best introductions to the topic I know. But the mythology is strong, and few scientists think much past that propaganda. What pattern cladism actually was, although like any movement of ideas the originators are sometimes less than clear on the matter, was the claim that before one can work through the history of taxa, one first has to make a relationship scheme that can test that history. In short, classification and historical reconstruction are distinct activities.

The alternative form of phylogenetic systematics (the correct term for “cladistics”) in effect conceded this point by denying that we did classification at all. Phylogenetics was only, and always, historical reconstruction, a view espoused to philosophers by Elliot Sober’s Reconstructing the Past. I call this process cladism, a term also used by Marc Ereshefsky. I won’t argue this here as I have often done so before. Before I proceed, I should note that I am neither pro-PattC nor anti-PattC. However, I do think that PattC arguments have a philosophical bite that has never been successfully dealt with either by the process cladists nor by philosophers; that is, the indefinitely large number of reasonable histories that a single cladogram supports. If reconstructing history is based on our cladograms, then the one to very many mapping of cladograms to histories means that at best any history is only something that is likely on the basis of prior assumptions and models. Of course, that is fine, so long as that is what we understand that we are doing here. It rarely is.

But let’s examine the question of theory-neutrality. This is an interesting problem. Clearly Hennig thought that some theory was essential to systematics. And those who in systematics played the theory-free or objectivity card most often were the numerical taxonomists (NumTax), the so-called pheneticists. So pattern cladism, which seeks to be both phylogenetic in some sense, and theory-free, appears to be in conflict with both styles of systematics; but this is only the case if you question-beggingly define phylogenetic systematics as process cladism, and theory-free classification as phenetics.

So, can systematics be theory-free? Another way to ask that question is to ask if systematics can be objective. Most now agree that the older style of systematics, as practised under the rubric of “Linnean systematics”, was often arbitrary and subjective, leading to splitting and lumping based on the predilections of the systematist. But that isn’t really the issue now. Instead, it has to do with arcane issues in the philosophy of science itself.

Pearson recounts the usual story against essentialism, in the “species-as-individuals” account that is now the consensus in philosophy of biology (almost). He notes that this is not a necessary conclusion, however. Still, the argument here is that if one is a pattern cladist, one is essentialist, and if evolution mandates the view that taxa are individuals, then pattern cladism is false.

Pearson says “Patterns in nature will be recognized as patterns only if the observer is armed with the relevant theory to recognize them as patterns.” This claim, which is crucial to the theory-ladenness hypothesis (I can’t call it a truism, nor can I think of it as a theory in its own right) is faintly absurd, ranging through to completely overblown. Did nobody observe before we had theories? Or do we all have theories, in which case why does theory-ladenness have any special purchase in science (it’s like saying that when we throw an object we calculate the differential equations needed to find the optimal trajectory)?

Theory-ladenness only means anything when the very act of observing is itself theoretically charged, such as identifying the meaning of particle tracks in cloud chambers (the classical example). However, if there is any act of observation we are able to make in the absence of any theory (apart from the adaptiveness of our evolved sensory capacities), it is in the observation of most macro-organisms. There are theories that explain how we do that, yes. They were worked out as we developed physiological and psychological accounts of the mechanisms of our senses. But before we learned or developed those theories, we did not need theory to observe. There is a logical or category error here akin to the use-mention distinction in philosophy of language: a “use-account” distinction. That there is a theory of how telescopes work (the theory of optics) does not mean that I need to know that theory to use the telescope. Indeed, as Hacking argued, I can iteratively refine my confidence in the fact that telescopes work by testing it initially with things I can inspect with the naked eye, so that I am sure of what it does even if I do not know why. Presumably there is an account of how it is that we identify taxa through observation (in the normal conditions that we evolved to do so). But until that account is formulated and tested, nobody knew it, and did not depend upon it to be able to identify taxa.

[Parenthetically: in my opinion, that account is a complex of the properties of neural nets as classifier systems, along with cultural and economic interests in getting the classifications right. Basically, if you are an animal and you hunt for food and evade predators and dangers, then you will tend to evolve sensory systems that correctly classify. Some call this evolvedness "theory"; I think that it beggars the meaning of the term "theory" to call biological adaptedness theoretical.]

Why did the PattC proponents and the numerical taxonomists think that we needed to be theory-free in order to classify objectively? This has a history that relates to the course of positivistic thinking in the first half of the twentieth century. Basically, when in the philosophy of science the post-positivists asserted the primacy of theory in science to the exclusion of observation sentences and sensory data “clips”, they insisted that to observe relied upon prior theory. PattC and NumTax arose at a time when this was the brave new idea in philosophy.

Now there was an ambiguity in that claim. It is one thing to assert that logically, if one is to justify an act of observation, one must have an account of observing because the act of observing is constituted by some prior capacities that need explaining. Nobody, I think, objects to this. Animal A observes its world, and we need to explain why; that account relies upon a theory T. But does the animal employ T in observing? Almost all animals do not, and yet they manage quite satisfactorily to evade predators, find food, and in some cases, learn quite sophisticated facts about their world.

Scientists are theoretical animals par excellence, but one may reasonably doubt that they employ theory in every act they make as a scientist. But for the theory-dependence claim to work, this is exactly what must be true. Not just that there is a theory of how observation is being done, but that the scientist must necessarily employ a theory (whether or not it is the right one) in observing. Taxonomy, more than most disciplines, rests on the observation of traits of things, but seeing a spider’s pedipalp (the mobile sensory appendages on its head) is untheoretical, even if identifying these appendages as pedipalps, or at least naming them thus, is not. Pearson uses a similar point: the abdominal spinneret on spiders, which David Hull famously (among systematists) used as a reductio of theory-free observation in the context of PattC. But there is a theory-free way to identify a spinneret: look to where the silk comes out on the lower abdomen. A five year old could do it, unless you think identifying an abdomen or silk needs prior theory.


Pedipalps in a Striped lynx spider, from Wikipedia. Do you really need a theory to see them? Could you identify these in another spider without theory?

Returning to Pearson’s argument, let us ask why systematists insisted upon theory-free observation; it is the solution to a long standing goal in systematics: to have a natural classification that is logically prior to theory, and which is also not subjective. For a long time, systematics was driven not so much by theory as by authority. My colleague Malte Ebach and I call this, somewhat unfairly to German-speaking science, the German Authority Syndrome. Sociologically, for a long time it was the case that if an Authority had worked on a group, nobody else could work on that group while the Authority was alive. This was especially true in German traditions, where authority is widely respected, but it exists even now in most systematics across cultures. This meant that the personal preferences of individuals who held senior positions could become established for wildly contingent reasons, such as the psychological dispositions or the individual to lump or split, or because of professional exigencies like unifying or splitting departments or funding.

Everybody thought this was a mistake, but nobody knew how to avoid it. As theory took hold as the arbiter of cognition in mid-twentieth century philosophy of science (particularly Kuhn’s view of paradigms constraining normal science), it became fashionable among philosophically inclined scientists to assert that theory drove observation, and this was therefore a way to avoid German Authority Syndrome. And the obvious theory that could unify all observation and determine what was and what wasn’t good taxonomy in biology was obviously evolution, and particularly theories of phylogeny (biological diversity and its development over time).

Pattern cladism objected to this. Again it depends on ambiguities in terms. By “the theory of evolution” do we mean the theory that all things have evolved by branching descent, or instead the hypothesis of the evolution of this group of organisms? This was not always kept clear and distinct in the debates of the 70s and 80s. PattCists held that we cannot, logically, presume a given mode of evolution or a given history in order to classify if we then expect that we can use phylogenetic classifications to test our hypotheses of relatedness. So, they asserted that some theory-free observation, particularly of homologs, was possible, to kick-start the process. Have observation sentences from the positivists been revived?

I suspect they never died, really, but the reality is much more complex than simple nomological deductive accounts of explanation and inference in science indicate. There is what I call a domain-relativity in play. That is, sure, theory is sometimes used in observation, but in a classificatory activity like systematics, the theory you use had better not be question-beggingly the theory you are trying to test or support with your classification. That is, you can use theories from outside the domain under investigation. If you were a Bayesian, this would set up some of the priors you use in testing the present hypothesis. An example might be using the ways a subgroup of spiders spin webs to set up their relations, in the context of wider views about how spiders in general spin webs. You do not come to the issue or domain ignorant of spiders, or, if you do, you might not be doing systematics. Nobody addresses any issue knowing nothing to begin with. But a lot of our knowledge is not theory-driven in any reasonable sense. I do not avoid large rapidly moving objects because I have a theory of cars, for example. I don’t even have a theory of large moving objects. I have learned that large moving things hurt me when they hit me, from experience (one broken leg and a crushed foot later…).

Observations can be theory-free for the domain investigated, even if they are theory-driven (that is, the theory is employed by the observer) by extra-domain theories. Moreover, the domain and its theory are in temporal relations. What one knows at one time tests what one previously knew, and what one knows now will test theories in that domain in the future that may, if successful, end up revising observations (“you were mistaken to think this was a spinneret; we know now it is a different structure not homologous to spinnerets”). Science is an iterative refining of observations and inference. Hennig, borrowing a term from stemmatics (the science of manuscripts) called “reciprocal illumination”, made the same point.

I have used Pearson’s paper as a jumping off point, and not given it the treatment it deserves, but I wish to end this post on a comment he makes almost en passant. He writes:

Indeed, as Scott-Ram (1990) argues at length, the very idea of a natural hierarchy by which pattern cladists seek to categorize the living world is problematic in the absence of evolutionary theory. For Scott-Ram, either the pattern cladists must recognize the role of evolutionary theory for a cladistic taxonomy or accept a Platonic view of the natural world. A Platonic view is, of course, unsupportable for the biologist, thus evolutionary theory should be recognized.

We need to challenge this major premise, that a natural hierarchy is inexplicable in non-evolutionary terms. Historically, nothing could be further from the truth. The natural hierarchy preceded evolutionary theory, and was, indeed, the main motivation for Darwin to develop it. If history has any weight in this, then a natural hierarchy is exactly as the pattern cladists think: it is prior to, and tests hypotheses of, common descent. I do not know what a “Platonic view of the world” might be – many claims have been made that evaporate on closer inspection – but when people have been scientific Platonists they tend to think things that have little to do with the progress over time of physical objects, rather than trying to make an account of the physical world in terms of ideas or forms. It is a phantasm rarely encountered. And to assert that pattern cladism is this mythological chimera is poisoning the well in a major way.

I think that systematists should be local pattern cladists, even when they are global evolutionary theorists. Just like Patterson was.

Over the past few years there have been increasing numbers of calls for governments to properly fund systematics and taxonomy (and a number of largely molecular-focused biologists insisting they can do the requisite tasks with magic molecule detectors, so don’t fund old-school, fund new-fangled-tech). But I think that there is considerable confusion about what systematics and taxonomy are.

Now the usual way a philosopher resolves such questions, apart from interrogating their intuitions relying upon what they learned in grade school, is to go find a textbook or some other authoritative source and quote that. If it is someone they already know, all the better, like Mayr or Dawkins. This is problematic, so I thought I’d do a slightly better job at reviewing what people think. And then I will of course give my own view.

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Elliot Sober has published a claim (Sober 1999, Sober 2008: §4.1, 265ff) that Darwin used, and we should too, a particular syllogism: similarity, ergo common ancestry.

This cannot be right, for several reasons: logical, historical and inferential. First the logical, as this is rather vapid, and can be guarded against (although Sober does not so guard) relatively simply: it cannot be that similarity in itself is evidence of common ancestry, or every dice would have a common ancestor, and every rock that resembles Abraham Lincoln’s profile would too. Now the way to guard this might be to assert that yes, they do have common ancestors, in the general sense they have common etiologies. All dice resemble each other because there is a chain of cultural descent that links back to some “dice taxon” in the past somewhere in Asia. The rocks have a shared etiology in the physiognomy of Abraham Lincoln. But that is not quite the claim Sober is proposing. For this would involve the cognitive and cultural dispositions of ourselves as classifiers, and common ancestry in no way relies upon us, although our recognition of it of course does. Can we infer from similarity that the two objects that are similar (to us) have a shared causal history? The Lincoln case suggests not. One rock might be formed by a lava flow, while another might be half a world away and formed from the erosion of sandstone. Without limitations on the kind of similarity, it implies nothing at all about the objects (and perhaps quite a lot about the observers engaging in pareidola).

The historical objection is that Sober, and most other modern commentators, read Darwin wrongly. Darwin used not similarity, but affinity, as evidence for common ancestry, and technically, he inferred common ancestry from “group subordinate to group” taxonomy; that is to say, he explained this taxonomic arrangement with common ancestry, rather than defended the claim of common ancestry that way. Had he wanted to use similarity, there was a perfectly good term, before Owen’s invention of the notion of homology: analogy, as can be found in the discussions in the Quinarian literature. Darwin wrote, in chapter XIII of the first edition of the Origin:

… all organic beings are found to resemble each other in descending degrees, so that they can be classed in groups under groups. This classification is evidently not arbitrary like the grouping of the stars in constellations. [411]

Thus, the grand fact in natural history of the subordination of group under group, which, from its familiarity, does not always sufficiently strike us, is in my judgment fully explained. [413]

And he goes on to note

Naturalists try to arrange the species, genera, and families in each class, on what is called the Natural System. But what is meant by this system? Some authors look at it merely as a scheme for arranging together those living objects which are most alike, and for separating those which are most unlike; or as an artificial means for enunciating, as briefly as possible, general propositions,—that is, by one sentence to give the characters common, for instance, to all mammals, by another those common to all carnivora, by another those common to the dog-genus, and then by adding a single sentence, a full description is given of each kind of dog. The ingenuity and utility of this system are indisputable. But many naturalists think that something more is meant by the Natural System; they believe that it reveals the plan of the Creator; but unless it be specified whether order in time or space, or what else is meant by the plan of the Creator, it seems to me that nothing is thus added to our knowledge. Such expressions as that famous one of Linnæus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent,—the only known cause of the similarity of organic beings,—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications. [413f, emphasis added]

Darwin goes on to discuss how external resemblances are not evidence for propinquity (nearness, or kinship). He discusses how similarity is mere “adaptive or analogical characters” and that it is “a general rule, that the less any part of the organisation is concerned with special habits, the more important it becomes for classification”. Darwin knew well about convergence. “We must not, therefore, in classifying, trust to resemblances in parts of the organisation”, he concludes. That we need an ensemble of characters, and that they are not necessarily about similarity, is clear from this passage:

The importance, for classification, of trifling characters, mainly depends on their being correlated with several other characters of more or less importance. The value indeed of an aggregate of characters is very evident in natural history. Hence, as has often been remarked, a species may depart from its allies in several characters, both of high physiological importance and of almost universal prevalence, and yet leave us in no doubt where it should be ranked. Hence, also, it has been found, that a classification founded on any single character, however important that may be, has always failed; for no part of the organisation is universally constant. The importance of an aggregate of characters, even when none are important, alone explains, I think, that saying of Linnæus, that the characters do not give the genus, but the genus gives the characters; for this saying seems founded on an appreciation of many trifling points of resemblance, too slight to be defined. [417]

And he then discusses affinities by saying “Our classifications are often plainly influenced by chains of affinities” [419]. Affinities, not analogies (and as we argued, “affinity” means roughly shared sets of homologies). He summarizes by noting that

All the foregoing rules and aids and difficulties in classification are explained, if I do not greatly deceive myself, on the view that the natural system is founded on descent with modification; that the characters which naturalists consider as showing true affinity between any two or more species, are those which have been inherited from a common parent, and, in so far, all true classification is genealogical; that community of descent is the hidden bond which naturalists have been unconsciously seeking, and not some unknown plan of creation, or the enunciation of general propositions, and the mere putting together and separating objects more or less alike. [420, emphasis added]

It is plain that Darwin held that what was evidence for common ancestry was shared sets of homological relations independently of adaptive characters, which can converge. Affinities are evidence, not analogies, and Darwin knew this well.

This brings us to the inferential objection. Sober fails to deal with convergent evolution as a cause of similarity, and yet this is so well known to systematists as to be hardly worth discussing. Because he adopts what is basically a statistical notion of classification, Sober thinks, we suppose, that homoplasy, that is to say, convergence, is eliminated somehow by technique or methodological algorithms. However, every systematist strives to eliminate homoplasy before analyzing data, just as Darwin said. There is no magic method for doing this: what looks homological may turn out, upon comparison of many taxa, to be homoplasious or indeterminate, and vice versa. But despite our limitations here, we can do this successfully in most cases – if we could not, then we could not do natural classification at all.

In neither place where Sober advances modus Darwin, does he defend against this obvious objection. In conflating similarity with affinity, we are confused about what counts as evidence for a given scenario of common ancestry. Although we have suggested that there is no fixed or privileged direction of inference in a field, it does appear that if you begin with uncertainty, then recognition of naive classification based on homological relations is going to constrain and set up the explanandum for the hypothetical account to explain. The hypothesis, a historical narrative, is not evidence for itself.

Darwin is often used as a mythological figure upon whom the preferred philosophies of the writer may be painted. In that respect he is like the Bible, except that he is a lot clearer as to his intent. The actual inferential process Darwin used – the real modus darvinii[i] – is more like this: affinity, explained by common ancestry. Since affinities are groups of homological relations we might use a term of Hennig’s and say that synapomorphies give the pattern that the historical process explains. The two are not identical.

Note

i. I am indebted to Reed Cartwright for helping me with the Latin here.

References

Sober, Elliott. 1999. Modus Darwin. Biology and Philosophy 14 (2):253-278.

Sober, Elliott. 2008. Evidence and evolution: the logic behind the science. Cambridge, UK; New York: Cambridge University Press.

Sometimes, as a philosopher, one forgets that not everyone has been forced to undergo a logic class. This is a problem, both because logic is taught as the second most boring subject after calculus, and because, like calculus, it is enormously relevant to everything we do. Most especially it is something that is relevant to scientists. Now, I do not want to imply that all scientists do not understand logic, or misuse it, but it is worthwhile occasionally revisiting the basics. Especially for the nature of classification and inference in science.

Last time I wrote about natural classification, I discussed the use of clades as a straight rule for induction. An induction, for those who do not recall their introductory philosophy of science, is an inference from a limited number of particular observations to a general conclusion: all the swans I have seen are white, so swans are white. Inductions can be wrong. Deductions move from the generalisation (“All swans are white”) to the particular case (“this is a swan, so it is white”). Deductions cannot be wrong if the premises (the generalisation itself, and the claim this is a swan) are true. Now, the most widely known philosophy of science, that of Karl Popper, is based upon a logical deduction – if the general claim (the “law”) says that all As are Bs, and this B is not an A, then the law is false. He called this “falsification”. It is based on what we call the modus tollens, and is bandied about all the time by philosophers and scientists alike. It seems to me that not everybody understands what is at issue here. So, a simple introduction follows below the fold.

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Biological topics are used widely in philosophy to illustrate arcane and recondite philosophical topics,and one of the most widely used, and most abused, are species as examples of natural kinds. Kangaroos, swans, tigers, lions, cats, and of course humans are all brought in to assist our intuitions. As Umberto Eco wrote once,

The history of research into the philosophy of language is full of men (who are rational and mortal animals), bachelors (who are unmarried adult males), and tigers (though it is not clear whether we should define them as feline animals or big cats with a yellow coat and black stripes). [1999: 9]

Why this is, is obvious. We need to understand abstract concepts of science and philosophy in terms that we are easily disposed to appreciate. Humans are classifiers of their world and the things they most easily classify are other (large, moving) living things. It’s our Umwelt. But this leads to all kinds of problems. There is a thing known as folk taxonomy, in which the default cultural assumptions of a society are imposed upon the living world. One of the basic tasks of a science is to overcome the folk taxonomy and find out, or classify the world, so that the local biases and simple misunderstandings of the tribe are eliminated and the classifications denote actual things.

Still, philosophers use species as natural kind terms, when every biologist knows this fails in most if not all cases. It might not even be malign: if what you are doing is discussing the meaning of words, then English (or German, etc.) words that denote kinds of animals and plants can stand in for natural kind terms, so long as nobody is thereby misled into thinking that because there is a word, there is out there in the world a kind that answers directly to it. I wish I could say this was a truism all philosophers understood.

Actual species are messy items in the world. Philosophers of biology (that subset of philosophers who attend closely to the uses and ideas of biological sciences rather than resting content with “what everybody knows” about biology) argue at length about essentialism, in which species and other kind terms in biology are supposed to share properties that are uniquely theirs, versus individualism, a somewhat complex suite of ideas that rest upon the assumption that species and other groups in biology are historical objects that have their properties contingently. Philosophers of language try to resurrect essentialism, or treat species as the very exemplar of a natural kind, but generally this fails. The lessons are, slowly, being learned.

But there is a higher level error that can be made, and it has just been made by Christy Mag Uidhir and P.D. Magnus in a paper forthcoming in Metaphilosophy. The paper is titled “Art Concept Pluralism”, and is an argument that the very concept of art is pluralistic. An analogy is drawn, not with a species, but with the concept of species itself, a subject about which I have a few ideas of my own. Now Magnus himself drew attention to a mistake he made by a cursory reading of the literature. He “used” a “concept” of species that he called “the phenetic concept”, and says:

The PHENETIC SPECIES concept (also called morphological or typological) divides species based on organisms’ exhibited characteristics.

This is wrong. It is, indeed, as wrong as a wrong thing can be wrong. I won’t go into the details, but it is not all, or even most, of Mag Uidhir and Magnus’ doing. Types and morphology are distinct, and phenetic means something else, although not quite what Magnus says in the blog entry. He writes

… biologists and philosophers of biology use the word [phenetic] more narrowly to distinguish a specific movement: people who self-identified as employing a phenetic approach and who distinguished species just by doing statistical analyses of observable features

Umm, no. “Phenetic” means the use of multivariate character components in an analysis using clustering algorithms. Not just any statistical analysis will do, and a few characters would not make an analysis phenetic. More widely, a phenetic approach treats not species, but “Operational Taxonomic Units” which are rank-free objects right up to and including entire phyla, or down to single individuals. There is no “phenetic species concept”; that’s the entire point. And phenetic is not something one defines in relation to other approaches such as “pattern cladist” or “biological … ecological … and evolutionary approaches”, either. It is a well defined and coherent approach. If none of those other approaches existed, it would remain well defined.

I’m being picky, I know. The distinction between “character-based” and “process-based” that he makes has some purchase, although I would suggest that it is the distinction between empirical and theoretical classifications. But despite his honesty and self-correction, there is an interesting, and crucial, point in their paper that he has not corrected.

First, let me note that he is using a folk taxonomy of scientific concepts. Scientists do use concepts and words in ways that are relatively reflexive, but that doesn’t mean we should take them at their word. Like any subject of investigation, they are as likely to employ culturally biased and sociologically determined meanings as anyone else. They are a tribe. As philosophers we have to look at them closely and determine if they are clear on their ideas or not. The essentialist story I have so often railed against is just such a social construction. But that is not Magnus’ problem, that is mine.

However, he invents a concept and then crucially uses it in the argument. Here is the way he does so with Mag Uidhir. ART (concepts are capitalised) is like SPECIES, and what is true of SPECIES may be, mutatis mutandis, true of ART. We know species concepts are pluralistic, and so too may concepts of art be. Multiple concepts of SPECIES are used by biologists profitably, so we can presume this for ART. While one might dispute untrammelled pluralism works in biology, either to delimn the natural world or to aid communication, thus far an argument has been made. Then this:

Some of the concepts involve an arbitrary fineness of grain. Using the PHENETIC SPECIES concept, biologists may make species larger or smaller depending on the refinement of their observations and their need to distinguish populations from subpopulations. The PHYLOGENETIC SPECIES concept is similarly plastic. For a monist who thinks that there is a single correct partition of species, this open parameter in a SPECIES concept is a terrible embarrassment. Provided specific biological projects sufficiently constrain the scope of a SPECIES concept, the pluralist may simply accept this result.

What he seems to be saying is that we can enlarge or reduce the scope of a species kind term arbitrarily. But the arbitrariness in phenetics is the threshold at which we include or not organisms in the OTU. It depends, rather centrally, on what we know about the organisms. For bacterial species, we may use a 70%, or a 95% or even a 99% threshold of clustering and similarity. We cannot just arbitrarily say that we will pick one of these in order to redescribe or reclassify bacteria. You do that based on what works at identifying relevant strains or ecotypes and so forth. In fact bacteriologists use a “polyphasic” approach, utilising multiple lines of evidence (genetic, molecular, phenotypic, ecological, cf. Colwell 1970 and Vandamme, et al. 1996). What is arbitrary is what the natural world makes work, not the choices of the taxonomists. Iterative refinement of the thresholds depends on what nature does.

But is there an “open parameter” here anyway? Well not if you think that we can identify species in the absence of prior theoretical commitments, as I do. In other words, we may have no rank for species, as Ereshefsky (1999, 2000) argued, but that hardly licenses the view that species is entirely arbitrary, to be identified as it suits the taxonomist. We named species in the 16th century, before any definitions or theory existed, that we still think are species. That needs explanation. My answer is that we observe species, often. Species are phenomena.

The same point can be made for the so-called “phylogenetic species concept” cluster of ideas. If there are unique traits that all and only members of a species have, which we have identified, then perhaps the PSC will enable us to identify species. But most species have structure well below the species level, such as haplotype groups. We do not identify them as species (although taxonomic inflation is a serious problem in conservation, mostly to do with the over-reliance upon molecular genetic criteria). But pretty well any specialist in, say, fishes or beetles or even eucalypts will be able to say where the species are, nearly all the time.

How does this affect the argument given? ART is a human concept, based upon what humans do and think. SPECIES is not. If there are many kinds of SPECIES, it may be because the world is complex. I have previously argued that the modality of a species is an evolved property, like a trait. Such properties are historically contingent. One cannot be an unrestrained pluralist. Can one be unrestrained about ART? I cannot say. It seems to me that what counts as art has more to do with social structures, economics and functional roles than it does any shared meaning, but that is perhaps my cynicism in play. In any case, the parallel with SPECIES is fraught with problems.

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