Evolving Thoughts

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.

Epistemology Evolution History Natural Classification Philosophy Species and systematics

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Comments (13)

  1. Makes sense to me. We sometimes, instead of “similarity”, refer to “special similarity”, meaning, more or less, homology.

    Quibble: “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.” How are these two different? If data Y are explained by theory X (as opposed to theory Z, which can’t explain Y), aren’t data Y evidence favoring theory X, and thus useful in defending X against claims of Z?

    2. Now if I’d been clever, I should have said “it’s a species of inference, yes”. But I wasn’t clever.

  3. Apparently there is not yet a genus Modus. I will keep this in mind during my taxonomic endeavours. It would be a great taxon in which to place the species operandi, tollens and vivendi.

  4. Poor Darwin! When I first studied biology decades ago, we looked at modern theories of evolution and just nodded towards Darwin, in the same way that physicists nod towards Newton. That is, we knew they were great scientists worthy of respect, but we also knew that science had moved on, and it was better to engage with modern knowledge.

    The most amazing thing (to me) about Charles Darwin’s work is how much of it was correct even though he didn’t have a good theory of heredity to work with, so he was working half-blind. Some of his speculations might have been wrong, but I think he knew this and clearly indicated when he was on dodgy ground.

    I feel uncomfortable with the way his writings are sometimes picked over as holy writ. I almost wish he had been clearly wrong occasionally, so people would say “this brilliant idea came from Darwin, but we’ve moved on beyond his mistakes”. Social sciences (and philosophy!) may have schools of thought where the eponymous sensei is revered: Marx, Durkheim, Hegel, but one of the characteristics of modern science is that it is not built on leaders and their schools. The “masters” of science are respected for their skill, knowledge and insight, but they are not placed on pedestals as secular saints. There is no Feynmannian school of physics and there is no Mendeleevian school of chemistry; there is physics, and there is chemistry.

    OK, this is history of science, which is an interesting and worthy subject, but aren’t there better things for Sober to study than trying to find fault with the minutiae of the century old writings of a pre-genetics biologist, however great he was?

    That said, thanks for standing up for Old Beardy. Don’t want no Sober dissin’ our man. Respeck to Chas.

  5. Similarity is evidence of relationship is sometime called Darwinian parsimony. My major professor corrected me whenever I said I had evidence of relationship, that I only had evidence of similarity. I finally caught on to what he was telling me. I think it was Steve Farris who said, “A similarity is only a similarity. A difference is really a difference.”

  6. I recently wrote (yet unpublished):
    The Connection between three ideas, resemblance as evidence of ancestry, was made long ago by Denis Diderot (1713-1784), a notable figure of the French enlightenment, the siècle des lumières (Lovejoy, 1904:325). In 1753 he provided an example of what today is termed “transformational homology” (Patterson, 1982:36): “If one considers the animal kingdom, and particularly the mammals, there is not one that lacks the functions and the parts, particularly internal ones, that are entirely similar to the others; so much so that it is easy to believe that there was a first prototype for all of them, for which nature merely elongated, shortened, transformed, multiplied, or obliterated certain organs. Imagine the fingers of the hand united, and the substance of the nails so abundant that it extends over the whole; then in place of the hand of a man, you have the foot of a horse.”
    He concludes: “Regardless if this philosophic conjecture be considered true as does Doctor Baumann [Pierre-Louis Moreau de Maupertuis, 1698-1759], or false as does Buffon [Georges-Louis Leclerc, Compte de…, 1707-1788] one cannot refuse to embrace it as an hypothesis essential for progress in experimental science, in rational philosophy, and in the discovery and explanation of the phenomena displayed by living things” (1994:565, Thoughts on the interpretation of nature no. 12, translated). And elsewhere he presciently comments: “exact classification of organisms will be achieved only through successive efforts of a large number of naturalists; it will be only painfully and very slowly achieved” (1994:1261-1262, Elements of Physiology par. 7, translated).

  7. John, I have numerous worries here. As for the logical point, the modus darwin inference is quite obviously meant in the context of phenotypes of organisms. You say that Sober doesn’t guard, but that just makes no sense. The whole 99 paper and section in chapt 4 of E&E is a discussion of the conditions under which this inference is a good inference. And the answer is NOT ALWAYS but often. Sober isn’t applying the inference uncritically, he is investigating the question of whether it is a good inference. In the book, he ends up laying down 9 conditions which are jointly sufficient for similarity of a dichotomous trait to be evidence of CA vs. SA (I think it might be fewer, slightly different conditions in the paper). Then things are generalized to continuous traits, to multiple independent traits, and to correlated traits. Each new section of course introduces new worries and complications. Also, you seem to be saying that of course this isn’t a good inference by concluding that it common ancestry is sometimes false. But the claim isn’t that you should INFER CA but rather than similarity is evidence of CA. It sounds like you are talking about posteriors in which case go to the Bayesian decomposition section where he points out that of course priors matter here. But evidence for doesn’t not mean sufficient evidence for. So for example, you say he doesn’t discuss things like convergent evolution (wrong, he does). For example, the torpedo shape of dolphins and sharks is evidence for CA though only small evidence because the trait is under selection. This is in fact exactly what Darwin says about the case. Convergent evolution (and all homoplasies) are just cases of misleading evidence from the standpoint of common ancestry (relative to another group – of course they all related at some level). Yes, they are evidence. Homoplasies aren’t eliminated by methodology, they are outweighed. Some similarities are less evidence than others but to say no evidence whatsoever (in the context of looking at just that trait and not a collection of traits) is to say that this similarity is at least as likely to come about from something other than CA. This is false on any reasonable model of evolutionary change we have.

    As for Darwin being much more sophisticated, yes, of course he used plenty of other arguments for common ancestry and of course Sober points this out. Obviously showing how Darwin infers CA in some cases does not imply that he does not ever just rely on pure similarity. Sure, groups within groups is great (Darwin says the best). But he clearly did not have this in the finch case (just looking within the finches, Darwin had no idea of the structure within them. Yet he thought they were all closely related). And of course when you start to look at multiple traits at the same time everything changes and you don’t just do a straight averaging over traits as you seem to imply. On a “statistical” view like Sober where likelihoods measure evidence, you specifically don’t just do some kind of crude counting. For example, in theory, one trait could trump all the rest. For example, Sober’s example is the stronger evidence taken from neutral traits (or even stronger, traits selected against) as opposed to traits that could reasonably be under positive selection. And at the phenotype level, obviously traits like teeth have different likelihoods than traits like color pattern.

    I read your post as saying ‘we have this really good way of inferring CA which Darwin used – affinities – which goes beyond mere similarity’. Okay fine, but is mere similarity also evidence? You seem to say no but I can’t see why not. — Joel

  8. I am moving right now and have no access to my library. In a while I shall respond. For now, I note that planets and rubber balls are similar in phenotype.

  9. Joel, I’m glad that you had the patience to defend against a pretty violent misreading of Sober. Given how careful Sober is to consider just the issues that here we’re told he doesn’t consider, I was too shocked for patience.

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