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Tag: Natural Classification

Is Brian Blessed a monkey or an ape?

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…

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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.

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Logic, evolution, and classification

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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The false analogy between species and art

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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Phylogeny, induction, and the straight rule of homology

Continuing my “natural classification” series, which I am writing with Dr Malte Ebach of UNSW.

After having experienced the circulation of the blood in human creatures, we make no doubt that it takes place in Titius and Maevius. But from its circulation in frogs and fishes, it is only a presumption, though a strong one, from analogy, that it takes place in men and other animals. The analogical reasoning is much weaker, when we infer the circulation of the sap in vegetables from our experience that the blood circulates in animals; and those, who hastily followed that imperfect analogy, are found, by more accurate experiments, to have been mistaken. [Philo, in David Hume’s Dialogues in Natural Religion, Part II]

Phylogenetic classification is a form of induction. It enables us to infer the properties of an as-yet unobserved member of a clade with a very high degree of likelihood, as was pointed out by Gary Nelson in the 1970s. [1] For inductive inferences to be successful, we have to guard against the grue problem outlined by Nelson Goodman. [2]

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While this is very familiar to philosophers, it is less well known to biologists, so a short summary is in order. The grue problem is based on a kind of “broken” predicate or property: ordinarily we might infer from the fact that all prior emeralds have been observed to be green and the future emeralds would also be green – this would be a case of inductive inference. But in the absence of prior certainty about what the rules are, without a “straight rule”, [3] we cannot rule out the existence of another property, which Goodman calls “grue”, in which emeralds are green if observed before some time t and blue thereafter. Hence, every observation of a green emerald strengthens the inference that after t emeralds will be seen to be blue. It must be noted that this is not a claim that emeralds will change color. It is about what we can infer of unseen members of a class. A gruelike predicate is unprojectible, which is to say that it cannot be projected to unobserved entities. What inductive inference promises is projectibility, so that we can say things that are very likely to be true about unobserved members of the class.

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This is more than a mere thought experiment. The infamous “black swan” example so beloved of logicians is a simple case. Swans were all observed to be white, until black swans were discovered in West Australia in the late 17th century. Had swans been defined by a white plumage (which was common at the time), then swan plumage would have been a grue property. More generally, consider such classes as Mammalia. Mammals are defined as tetrapodal (four limbed) animals which give live birth, lactate, and have hair. But whales have secondarily lost their hindlegs and hair, not everything that lactates is a mammal*, and monotremes lay eggs. More recently it has become clear that lineages of species are not straight but gruesome. What defines a group of organisms may change in a daughter species. Consider sexuality as a trait of a group of lizards. When one species becomes parthenogenic (secondarily asexual) we encounter a grue property for real. This applies to any single property of a group, potentially. Evolution leads to grue problems.

And yet, biology is not deeply troubled by grue problems, even though it is precisely the science that should be. While the colour of the swan’s plumage turned out not to be projectible, the new black swan was not placed in a new order or class. It was recognised to be a swan nevertheless, and placed into the existing genus, hitherto a monotypic genus. Although philosophers, who anyway tended then as now to rely upon folk taxonomic categories for their examples, were shocked in the manner of Captain Renault, biologists simply shrugged, reported the new species, and added it to the existing taxonomy. The reason is quite obvious by now: the swan was not defined, but classified upon the overall affinities it exhibited, and the fact that one homolog differed in character state from the rest was not crucial, any more than if it had a different shaped beak from the rest of the genus.

The issue here is with what Peter Godfrey-Smith calls the “dependence relations”:

We should not make a projection from a sample if there seem to be the wrong kind of dependence relations between properties of the sampled objects. [4]

It is our claim here that homological affinity does act to provide the “right” kind of dependence relations between properties of taxa. A single failure of a homolog to project properties is insufficient to make the taxon natural (that is, in philosophical terms, a projectible class), since the class (the taxon) is formed from the overall suite of homological relations (which my coauthor and I are calling the affinity, following early 19th century taxonomic use). Affinity acts to set up taxonomic kinds, and these act as a “straight rule”, as they do tend to converge upon projectible properties.

In taking inference from homology to be a kind of “straight rule”, the question is why it works. If the universe were such that properties correlated by chance, it would not work, but in the cases of the special/paletiological sciences, properties correlate due to a shared productive cause. If the universe lacked appreciable structure of this kind, then no search method would deliver knowledge (consider Wolpert’s and Macready’s “No Free Lunch” theorem [5]). Assuming that properties can be correlated, the epistemic question is how to identify those that are and to distinguish them from those that aren’t, which in biological systematics is the distinction between homology and homoplasy. If there’s knowledge to be had, then one way to acquire it is to iteratively refine one’s classifications in an attempt to maximize the homological relations on which they are based.

Such inferences are, of course, quite defeasible. It should not be thought we are supposing that natural classifications are in any way certain, or that any given homolog will exemplify the same states in each taxon or object classified. Of course this will not apply. On the one hand this is probabilistic [6] inference, in the sense that there is some likelihood or confidence that the projection will succeed for each property, and a high confidence that it will succeed for most properties. [This is akin to selection on a smooth landscape versus on a rugged landscape; selection can act on traits in a highly correlated “smooth” landscape (where adjacent coordinates are not too different in value from each other), but it fails on an uncorrelated, or “rugged” one. [7] The progress of science has been compared to an adaptive walk, [8] and similar considerations apply to inference in science as apply to selective searching of the adaptive landscape; both are special cases of a search procedure of the kind Wolpert and Macready discuss.]

Systematics in biology, and classification in science generally, resolves much of the practical issues of gruesome induction by, as Godfrey-Smith says, ensuring that the right class is sampled by finding the right dependence relations through a process of iterative refinement. These are what we are generally calling homologies.

  • If you count what a pigeon does as lactation, which, technically, it isn’t.
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My present work

Life can be … interesting, for Chinese values thereof. No, I don’t mean the Nobel Prize, although good choice. I mean that I’m presently undergoing some kind of curse. I think it’s called “work” .

Work!?
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So what I’m doing doesn’t translate to meaningful blog posts. Not always (but eventually, sure). I’m going to be doing this in the near future:

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