Somehow, I got minions/The first biological species concept revisited


It’s late in Real Time so I can only do a brief one now…

I made the mistake of noting on Twitter that I lacked minions after PZ accused me of hating his. Of course I don’t hate them. It’s just that, as an agnostic I am superior to them in every way. Anyhoo, several Agnostic Wilkins Minion Volunteers popped up. Welcome to the possible future autarchy, folks: @shanemuk @tynk_ and @HomunculusLoikm – I am carving up the spoils of conquest now, to save time.

On more serious subjects (what is more serious than conquering the world?), in teaching Blumenbach today I came to see that I was wrong to think he was the source of the interbreeding criterion for specieshood. Instead he says of species that

… animals belong to one and the same species, if they agree so well in form and constitution, that those things in which they do differ may have arisen from degeneration

He thinks that races, or subspecific varieties, are caused by environmental deviation from the original species stock, which he calls “degeneration”.

He contrasts this with the views of Johann Leonhard Frisch (1666–1743; I think – there’s no citation):

The immortal Ray, in the last century, long before Buffon, thought those animals should be referred to the same species, which copulate together, and have a fertile progeny. But, as in the domestic animals which man has subdued, this character seemed ambiguous and uncertain, on account of the enslaved life they lead; in the beginning of this century, the sagacious Frisch restricted it to wild animals alone, and declared that those were of the same species, who copulate in a natural state.

I think the reference is either to Frisch’s Wörterbuch, which he prepared as a philologist, or to his Vorsstellung der Vögel in Deutschland (1733-), but as I have access to neither I can’t say for sure. Anyone got a microfilm copy in their library? He’s overinterpreting Ray, I think. Ray said that a species was when similar forms are reproduced through seed. Buffon thought that what a Linnaean would call a genus or family was a natural species and the Linnaean species were like Blumenbach’s “varieties”, degenerated from the premiere souche (original stock).

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.

Arseholes! Systematics, phylogenetics and HPS


There’s been some developments this day.

First of all a defunct blog on history and philosophy of science has revived with a new skin and as a group blog: AmericanScience: A Team Blog. I keep wanting to say “F&*k yeah!” It used to be the Forum for the History of Science in America. Some nice pieces there already (but horrible horrible font choices: I say this as a quandam graphic artist and compositor, okay?)

Second we have, courtesy of Softpedia (which turns out to be a useful science news feed) some developments in systematics and phylogeny. Or perhaps I should say, some phylogeny FAIL.

The first one is that – as the headline screams – ‘Mosaic of Life’ May Replace ‘Tree of Life’ – why? because it turns out genes cross taxonomic boundaries. Which we knew already. Gene trees are not species trees, and it is a category error to think that they should be the same. In fact, in order to identify lateral transfer of genes, we already need to have a species tree, or (to be consistent with my prior arguments) a relationship statement of taxa, which turn out to be something you can represent as a tree. This is on a par with the awful New Scientist article from a while back.

The second one is that a cricket Species Found Unchanged After 100 Million Years – except that the species are not the same, only the whole group, which is only the same if you ignore changes at the species level. The genus has remained the “same” for values of the “same” that include species evolution. And “genus” is an artificial construct at any rate, defined largely by traits that do not change much. Hence, the title of the press release should have read: “Things which do not change much by definition haven’t changed much, if you squint”.

Finally Bjørn Østman at Pleiotropy points out problems with a recent reassignment of Acoels (arsehole lackers) from a basal node on the evolutionary tree to a within-deuterosome node. The problem? Deuterosomes have arseholes, so this guy, which everybody wanted to be a kind of surrogate for the common ancestor of all bilaterans, is in fact a vastly reduced version of us. But…

They used microRNAs as their character set. They ignored, in other words, morphology and development, the traditional criteria for inferring relationships, in favour of a single test criterion. And this is because RNA is a “magic molecule”.

But there’s even a problem with Bjørn’s objection: why should we think that the morphology and development of these guys should be placed at the base anyway? The answer is simple: it makes evolutionary sense. No-arseholes come before arseholes, right? Well now this is an interesting question. How do we know that? Are we using hypotheses as evidence here? Why can’t a group be greatly reduced, evolutionarily? Even Darwin noted this among his barnacles. The presumption of what Hennig called transformation series is not supported by direct evidence, and so wanting these guys to fall anywhere in an evolutionary tree is fraught, although not, I think, beyond overcoming. It’s just that we had better be testing things as closely to the evidence as we can, and not rely on “what everybody knows”, or as J. B. S. Haldane called it, Aunt Jobisca’s Theorem.

<end of rant>

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 What is systematics and what is taxonomy?

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.

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.

Intelligent designoids are unsure about me


Normally I wouldn’t link to these guys, but I’m having a kind of odd week with the ID crowd. On the one hand the ever reliable Casey Luskin has declared I am condescending for suggesting we teach science free of religious overtones to young children (but Kelly Smith is more condescending). And on the other, Michael Behe says my species book is great! I’m so conflicted.

I suspect Behe thinks that because I am critical of the standard or received essentialist story I am undercutting evolutionary thinking. I am not, of course, but maybe he just thinks it’s a damned good read.

My talk online


The Australian Broadcasting Commission, or ABC, radio show on science, Ockham’s Razor (named after some philosophy guy), has finally played my talk on species concept history and the death of essentialist stories. You can go listen to it here.

The recording process was fraught. I have reduced lung capacity due to decades of smoking (I stopped a while back, but lungs don’t regenerate), and so I kept swallowing the ends of the sentences, so the sound editor is to be congratulated for making it sound natural, as each sentence took several takes.