Category Archives: Epistemology

Pattern cladism and the myth of theory dependence of observation

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.

The heuristics of antiscience

I’m crowdsourcing here, to ensure that I don’t say anything more stupid than usual.

I’m writing a piece for a forthcoming book on antiscience, edited by Massimo Pigliucci. I want to consider the heuristics of antiscientific thinking, but, not being a psychologist or cognitive researcher, may be missing some obvious sources. Can people indicate what I should be aware of before I hang myself in public? I want to look good on the gallows.

It seems to me that little work has been done specifically on how people make decisions about science that leads to antiscientific conclusions. I suspect there is a general tendency of thought style – a difference between practical, problem-based thinking and theoretical, comprehensive thinking – that leads in extreme cases and the right circumstances to antiscience. That is to say, that this otherwise ordinary aspect of human cognition and heuristics can result in opposing knowledge for entirely rational reasons. I have already argued this for creationists in my Synthese paper [manuscript version here].

I would love to hear of any work on this, especially in book format that doesn’t show up on the usual searches.

Darwin Day: Enough already

I love studying about Darwin and his life and times. I have read enormous amounts, and taught Darwinian history. I’m teaching it again this semester. But enough already. Can we talk about modern biology now?

I get a strong impression ( and that’s all this is, as I can’t find empirical studies that support me, or that count against me here) that talking about Darwin reaches a plateau of interest fairly early on for the average sod, and that continuing to talk about him leads people to, possibly correctly, think that this is a cult of personality rather than something about the history and nature of science.

Compare this with the incredibly effective work of David Attenborough, who drops Darwin in where Darwin is needed to make sense of the material, but for whom the material – the living things he is fascinated by and imparts fascination of – is always paramount. We’ve had over fifty years of this apotheosising of Darwin, since the centenary. It has become tiresome.

At the time Darwin did his work we had the development of geography, ecology, systematics, comparative anatomy, early biochemistry, germ theory, epidemiology, modern medicine, physiology, pathology, cytology, geology and paleontology. All this happened more or less without reference to Darwin, and when he was employed in these fields later, often enough he was not all that useful. Now, I do not wish to imply that evolution is not a core concept in biology, as it clearly is, but it isn’t all that matters in biology, and if we wish to have an engaged and informed populace, it might be time to start talking about someone else.

Why Darwin is important is precisely not because he is a litmus test of rationality or modernity. It is because of the research program that he began. Note: not that he finished, but began. And he is wrong or incomplete about a great many things (I am not referring to heredity or genetics, either). We want folk to know modern science and act on it, not to stand on the Side of the Reasonable where that is defined as accepting Darwin as your epistemic saviour. We want informed decision making. But when scientists and pro-science promoters make it all about one guy and his ideas, however important, we have lost the plot a bit.

There. That should upset a few people.

Later: Richard Carter has more to add.

The nature of philosophy and its role in modern society

Those who spend their days obsessively noting every little change in blog designs will note that I have added a big red “P” at the bottom left. This links to the Philosophy Campaign – an attempt to make philosophy more relevant to modern society. So I got to thinking… what is the relevance of philosophy today?

It certainly isn’t its ability to contribute to the commodification and managerialism of modern tertiary education. Philosophy programs are being downgraded or even closed around the world. In Queensland, where I taught, only one major philosophy department was left after the entirety of Humanities was closed at other universities. Proper philosophy programs are becoming much rarer. Even moreso if you happen to threaten an authoritarian government or lobby (the latter case a pro-Israeli lobbyist politician). Why is this?

Philosophy is generally, whether it will or no, true to its main mission statement: to corrupt the minds of the youth. Well, that’s what Socrates was convicted of. He would have said it was to make young minds think critically, and for most authoritarian governments, that amounts to the same thing. Critical reasoning skills are dangerous! Students might doubt God, or the status quo or worse, the prevailing political platform. I think one of my major mistakes was to use advertising and media as examples of bad reasoning, because that is an economic challenge to the status quo, and nobody survives that.

Philosophy is relevant in ways that do not serve the interests of those in power, on either side of politics (as if there were only two sides, another comfortable truism that serves those in power). Mostly it is a threat for the third of the three questions of philosophy. These questions are:

What is there? [Metaphysics]

How do we know? [Epistemology]

What is its value? [Aesthetics, ethics and political philosophy]

All philosophy deals with one of these three questions or more. Me, being a moral vacuum and an aesthetic sink, I tend to focus on the first two. And even this can threaten elites. Suppose we took philosophy into schools, and allowed kids to ask a metaphysical question: do states exist? If they found themselves adopting something like methodological individualism, they might infer that states have no interests or rights, and therefore governments must be constrained in their infringement of actual right-bearers’ rights in pursuing faux wars on abstract evils. Imagine that. Fortunately for the elites this will never happen, of course.

Or suppose they adopted a corporatist view of nations and held that the only true reality was the entire population. They might begin to challenge the view that oligarchies can do with state instruments whatever they wish. And so on. The thing about philosophy is that it does not block ahead of time any view so long as it is coherent. And coherent views can lead to results that people who have vested interests may not want a populace to find.

So, on with corrupting the youth! While you are at it, corrupt some elders too.

What is systematics and what is taxonomy?

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.

Continue reading

Modus Darwin and the *real* modus darvinii

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.


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


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.