Biological Essentialism and the Tidal Change of Natural Kinds
Category Archives: Systematics
In my last post, commentator DiscoveredJoys raised the question of abductive reasoning and how it relates to my claim that classification is basically pattern recognition. It’s a fair question. First I’ll repeat my response, and then go into it a little more.
In my view, abduction is larger in scope than pattern recognition (PR). PR provides the foundation, but abductive reasoning leaps (usually on the basis of very few observations) to a causal argument or inference, while I am merely talking about the PR itself. PR presents the explicandum for inductive, abductive and deductive explanation.
So I have a much smaller target here. However, I should have thought (and written) about abductive reasoning more. Let me now. Abduction is sometimes called “inference to the best explanation”. Recognition of species, for example, is not, I think, explanatory, but it sets up a problem for the pattern recogniser: why is that pattern there? The usual answer (leapt to immediately on the basis of prior knowledge) is that there is some reproductive power that makes progeny resemble parents. This is the abduction, not the recognition of a pattern. It is the “best explanation” based on a host of prior assumptions and knowledge claims. If we had never seen a living thing (if we were a Matrix style computer), we might not leap to the explanation, but I think we would still recognise the pattern.
Of course the economic argument would not apply, and would rely upon other criteria of salience (maybe the Matrix needs to categorise objects that have functional roles in the simulation).
First of all, what is abduction? The Stanford entry is quite complete and comprehensible (see this also), but basically it is leaping to an explanation from a single or few observations. It is called by the late Peter Lipton Inference to the Best Explanation (IBE). IBE is a principle that you should choose to explain an observation based on the best causal explanation, the most likely based on background knowledge. My commenter suggested that pattern recognition is a form of IBE. I think it is not.
For a start, to make a pattern recognition-based classification does not require positing an explanation. It requires explanation once you have one, which is to say, it sets up an explicandum. To make an IBE, one needs already to know enough to make some explanations more likely than others. Lipton (1991) calls this assessing the “loveliness” of competing hypotheses. But while pattern recognition involves prior knowledge – of the domain and its general properties, mostly what to look for – it doesn’t involve assessing the loveliness of hypotheses. Instead it involves assessing the salience of differing stimuli.
In order to make an IBE, you have to recognise things. Take for example an IBE about what made footprints in the snow. First you have to recognise the pattern of footprints. This is something you have learned to do, not least by making footprints. Second, in order to make an IBE that a deer made these particular tracks, you need to recognise the difference between bipedal and quadrupedal tracks (gotten from years of observing them), and between claws and hoofs (likewise) and so on. With all that categorical apparatus in play, you “leap” to the hypothesis that of the likely animals in the area, it was a deer, not a cat or horse.
But classification is different to that, at least initially when the domain under investigation (DUI) is unexplored. You know about the wider domains in which the DUI is situated, so you are primed to see some sorts of things. But you get an idea of what is in the DUI by looking, a lot. Experience trains you to see patterns, and then, and only then, can you make IBEs. Hence my response above.
There are those who think taxa are explanations. One author, Kirk Fitzhugh (2005, 2009) thinks species are explanations, a view I cannot make sense of. An explanation of why a species is a species is something independent of recognising the species. Others have argued that phylogenies are explanations or hypotheses, in a Popperian fashion. Again, I cannot make sense of this. In the case of phylogenies, the explanation is the theory of common descent (or, in some cases, lateral transfer and introgression through hybridisation), but the phylogenies themselves are patterns in data. If a systematist works out a phylogeny of a group, then there is an IBE of common ancestry (or perhaps a Bayesian inference, which is distinct in the eyes of IBE advocates from abductive inferences), but common ancestry is not the same thing as working out the phylogeny, again, at least initially. Then background information can come into play to revise and refine the phylogenetic systematics, for instance by using molecular clocks or distributional properties, but again, these are further inferential activities to classification.
The relations of different kinds of cognitive activities here are not simple. While it helps us to classify them as distinct activities, in practice we shift and change from one to another, or do them simultaneously. Science is not done by recipe. However, it pays to be clear about the differences between them.
Fitzhugh, Kirk. 2005. The inferential basis of species hypotheses: the solution to defining the term ‘species’. Marine Ecology 26 (3-4):155-165.
———. 2009. Species as Explanatory Hypotheses: Refinements and Implications. Acta Biotheoretica 57 (1):201-248.
Lipton, Peter. 1991. Inference to the best explanation. London: Routledge.
It occurs to me as I read Rosenberg’s Philosophy of Science (2005), that we tend in that field to classify epistemic activities into two kinds: induction (about which we have many arguments as to its warrantability) and deduction (with many arguments about its applicability). But I believe there is something else that we do to learn about what exists in the world. In my forthcoming book, The Nature of Classification, coauthored with Malte Ebach, I argue that this is classification, but typically classification is seen as either of the other two kinds of inference. I think it is a third kind.
So what happens when we classify in the absence of theory? We aren’t yet inductively constructing theory, and we aren’t able to deduce from theory (since there isn’t any yet) the classes of objects in the domain we are investigating. We argue that what is happening here is pattern recognition (Bishop 1995). We are classifier systems. It is one of the distinguishing features of neural network (NN) systems such as those between our ears that they will classify patterns. They do so in an interesting fashion. Rather than being cued by theory or explanatory goals, NNs are cued by stereotypical “training sets”. In effect, in order to see patterns, you need to have prior patterns to train your NN.
Where do these come from? I think that there are several sources. One is evolution: we are observer/classifier systems of a certain kind. This gives us a host of cue types to which we respond by training our stereotype classifier system. For example, we respond to movement of large objects, to differences in colour and shade, and so on, in our optical system. Quine (1953) referred to this as our “quality spaces” – these are fields of discriminata, to which we (in Quine’s view, behaviouralistically) react. They are adaptations to the exigencies of survival for organisms of the kind that we are. The problem is that so long as our survival and reproductive success is ensured, evolution cannot guarantee us access to the way things “really” are. At best it gives us a good balance between false positives and false negatives. It is good enough, as it were, for government work (Godfrey-Smith 1991). But is it good enough for science and metaphysics?
One of the standard accounts of the success of science is that it increasingly approaches the truth. This is called the Ultimate Argument for Scientific Realism by van Fraassen (1980) and the Miracle Argument by Putnam (1975, that unless science does converge on reality, science would be a miracle). It is quite clear that the received dispositions evolution has bequeathed our cognitive capacities is not enough. While one might reject the Plantingan argument against all naturalism based on this insufficiency of our evolved cognitive powers (Plantinga 2002), there is a problem. How do we come to identify aspects of the world reliably and properly?
Science proceeds by refining its categories of what exists in the world based on two main sources. These are evidence, and explanatory force. In the case of a domain of investigation for which there is as yet no explanation, all we have is evidence, but apart from our evolved dispositions to respond to certain stimuli, how do we identify the salient aspects of evidence? There is an almost infinite amount of possible information we might make use of, and so we must glean the right sources of information. One source is economic necessity. Over time, farmers and hunters will tend to respond to the features of the things they are engaged in acquiring and using that are more or less important for success, because those features which are not salient will impose a cost of time and effort that tends to reduce success. This is a process very like natural selection, and has been the basis for what came to be known as evolutionary epistemology, in which a parallel process to biological evolution occurs in the domain of knowledge. Cognitive traditions become better at acquiring reliable knowledge because ideas and approaches that do not aid this goal are costly and are abandoned.
However, we have a superfluity of cognitive and conceptual resources. We can retain ideas and practices that are not really relevant for social reasons, such as rituals and “explanations” that have no counterpart with the reality being dealt with. So the fact that a particular culture is successful at farming by relying upon a ritual calendar (as in pre-Indonesian Bali) doesn’t warrant belief in Hindu gods. The functional aspects of the rituals acts to transmit the information even if nobody in the culture (or in Western agribusiness) fully understands why those rituals make farming successful (Lansing 2007).
So when a classifier recognises patterns in economic circumstances, what counts is not the conceptual superstructure, the theories and ideologies, but the categories of what matters – in this case of water, soil, and landscapes. How might this explain the success of science?
Taxonomists are classifiers in a particular economic situation: professional science. When a taxonomist encounters organisms in the wild, they are in the same situation as when a hunter hunts in that ecology. To succeed at taxonomy, as to succeed at hunting, the agent must know the right things about the target objects. A hunter that doesn’t know what different species of bird look like and how they behave and where they live is in exactly the same economic conditions as a taxonomist who also lacks knowledge. Neither will end up with dinner on the plate (qua hunter or taxonomist). In the case of the taxonomist, the gap between failure and hunger is somewhat more distal than for the hunter (but hunters typically get most of their food from foraging rather than hunting anyway, courtesy of the non hunters, mostly women, in their village), but ultimately economic success depends directly upon correct pattern recognition.
Ernst Mayr was fond of telling the story of how when he visited Papua in the 1930s, he and the local hunters identified the same species of bird, with an exception where western ornithologists also disagreed, and he used this as justification for the reality of those (and all) species. He made the inference that science was able to discover kinds of things that were real in the world, and he may have been right (many biologists and philosophers believe species are not real), but it was not, I think, because of the pattern recognition abilities of humans per se to see species. When Ed Wilson tried the same experiment about ants, a subject he knows intimately, instead of the locals counting the same species he did (several dozens) he got something like “the black ones, the bitey ones and the red ones”. Why did Mayr’s informants know their birds while WIlson’s did not know their ants? The answer is that birds, but not ants, were of economic importance to the locals, while ants were of economic importance to Wilson and entomologists only.
By “economic” I do not mean fiscal, but the acquisition of resources, success at which gives the person investigating a living. What distinguishes scientific success is a unique socioeconomic system of professionalism, credit in society, and access to funds and resources like labs, students, and equipment. The motivations of the individuals concerned are several, often (but not always) based on personal curiosity, but curiosity is not enough if you don’t get the resources to do the work.
So we are very good at turning our perceptual pattern recognition systems to scientific work. What evolution provides, science refines. It happens that pattern recognition and the subsequent classificatory activities can deliver reliable knowledge of the world when it matters. But being as it is parasitic upon those evolved capacities, and being as scientists are social organisms, this is not without its failures. Social influences, particularly the inherited traditions of ritual and conception that history bequeaths, can skew and bias our categories about the world. This is where theory and experiment come in.
Science, by way of its historical accidents, also seeks to explain things in ways that can be tested. Here the ordinary philosophical issues come into play – we inductively generalise based on the patterns we have recognised, and form hypotheses, and from those hypotheses we derive deductive consequences, which we can test in ways that are not circular, which do not rely upon our original observations. As T. H. Huxley once said, nature whispers yes, but shouts NO! And so we can eliminate hypotheses that are not fit to the facts, more or less. This is what the evolutionary epistemologists, and philosophers like Popper, built their views upon. What evolutionary epistemology never explained, nor Popper, was how we came up with those hypotheses in the first place. Pattern recognition does.
For a half century or more we have had the view that observation is theory laden. As I have argued before (and which is part of our forthcoming book), observation need not be laden with theory of the domain under investigation. And what evolution has bequeathed need not be in the slightest theoretical, nor even reliable (as the massive literature on illusions shows us). We can naively observe things that we know little about, but we never start knowing, or at least being disposed to know, nothing.
So can we say that science is adequate to tell us the true nature of the world? Putnam’s miracle argument indicates a reason for thinking the world is knowable. If we could not know the world, there would be no reason to think that success indicated anything. And while success is not a guarantee of truth, it is as good as fallible knowers can ever achieve. In the end, I think that truth is, as the pragmatists said, what works. More than that is restricted to gods, demons and mathematicians.
Bishop, Christopher M. 1995. Neural networks for pattern recognition. Oxford, New York: Clarendon Press; Oxford University Press. [Sorry, I forgot to put this in]
Van Fraassen, Bas C. 1980. The scientific image. Oxford: Clarendon Press.
Godfrey-Smith, Peter. 1991. Signal, decision, action. Journal of Philosophy 88:709-722.
Lansing, J. Stephen. 2007. Priests and programmers: technologies of power in the engineered landscape of Bali. Princeton NJ: Princeton University Press.
Plantinga, Alvin. 2002. The Evolutionary Argument against Naturalism. In Naturalism Defeated? Essays on Plantinga’s Evolutionary Argument against Naturalism, edited by J. K. Beilby. Ithaca, NY: Cornell University Press:1-13.
Putnam, Hilary. 1975. Mind, language, and reality, His Philosophical papers v. 2. Cambridge Eng. ; New York: Cambridge University Press.
Quine, Willard Van Orman. 1953. From a logical point of view: 9 logico-philosophical essays. Cambridge MA: Harvard University Press.
Rosenberg, Alexander. 2005. Philosophy of science: a contemporary introduction. 2nd ed, Routledge contemporary introductions to philosophy. New York; London: Routledge.
[A segment of my new book, coauthored with Malte Ebach]
The classification of clouds
Clouds were regarded as so subjective, fleeting and resistant to classification that they were a byword for the failure of empirical classification, until Luke Howard in 1802 proposed the foundation for our present system of cloud classification (in competition, although he did not know it, with others in Europe, and on the heels of Hooke and later meteorological language proposals including one by Lamarck the same year.
Howard’s proposal, like Lamarck’s, was driven solely by empirical observations. No experiment was possible with clouds (although there were some schemes for building cloud producing machines early on), and there was no real theory as such, just a desire to, as Lamarck said, note that “clouds have certain general forms which are not at all dependent upon chance but on a state of affairs which it would be useful to recognise and determine” (Hamblyn 2001: 103. This section is taken mostly from Hamblyn’s excellent book). In short, this is an example of a classification scheme without much if anything in the way of Theory.
Howard proposed seven classes (genera) of clouds – three “simple modifications”, cirrus, cumulus, and stratus, two “intermediate modifications”, cirro-cumulus, and cirro-stratus, and two “compound modifications”, cumulo-stratus and cumulo-cirro-stratus, or nimbus. His criteria used apparent density, elevation, height, and whether it produced rain. Particular types of clouds were called, following the logical and Linnaean examples, “species”. He also devised our present system of signs for these cloud types, and proposed a correlation with certain types of rain and clouds. Now meteorologists could communicate and seek explanations and presently the International Cloud Atlas is the global standard for identifying clouds (World Meteorological Organization 1975).
This is a classic example of an empirical passive classification. Although the hydrological cycle was of ancient vintage, the direct Theory of clouds, such as it was, had to await the hypothesis of the thermal theory of cyclones and cloud formation (Kutzbach 1979). Similar passive classifications were done for wind, resulting in the Beaufort Scale.
Howard’s scheme outcompeted Lamarck’s largely because of its technical terminology and signs. Lamarck’s was too French and odd even for them. It gained great acceptance. Johann Wolfgang von Goethe, had written a poem in Howard’s honor, as well as contribute “Towards a Study of Weather” in which he briefly discusses Howard’s categories of clouds and a basic law of weather (Goethe 1825 (1970)).
Goethe, Johann Wolfgang.von. 1825 (1970). Versuch einer Witterungslehre. In Die Schriften zur Naturwissenschaft, edited by D. Kuhn and W. von Engelhardt. Weimer: Hermann Böhlaus Nachfolger:244-268.
Hamblyn, Richard. 2001. The invention of clouds: how an amateur meteorologist forged the language of the skies. London: Picador.
Kutzbach, Gisela. 1979. The thermal theory of cyclones: a history of meteorological thought in the nineteenth century. Boston: American Meteorological Society.
World Meteorological Organization. 1975. International Cloud Atlas. Secretariat of the World Meteorological Organization:155 pp.
The following letter, from this site with permission, was written by Thomas Jefferson in 1814. Apart from demonstrating how low American political life has fallen from its high commencement point, Jefferson shows he was up on the latest disputes in taxonomy. It was written to a Dr John Manners.
The opinion which, in your letter of January 24, you are pleased to ask of me, on the comparative merits of the different methods of classification adopted by different writers on Natural History, is one which I could not have given satisfactorily, even at the earlier period at which the subject was more familiar; still less, after a life of continued occupation in civil concerns has so much withdrawn me from studies of that kind. I can, therefore, answer but in a very general way. And the text of this answer will be found in an observation in your letter, where, speaking of nosological systems, you say that disease has been found to be an unit. Nature has, in truth, produced units only through all her works. Classes, orders, genera, species, are not of her work. Her creation is of individuals. No two animals are exactly alike; no two plants, nor even two leaves or blades of grass; no two crystallizations. And if we may venture from what is within the cognizance of such organs as ours, to conclude on that beyond their powers, we must believe that no two particles of matter are of exact resemblance. This infinitude of units or individuals being far beyond the capacity of our memory, we are obliged, in aid of that, to distribute them into masses, throwing into each of these all the individuals which have a certain degree of resemblance; to subdivide these again into smaller groups, according to certain points of dissimilitude observable in them, and so on until we have formed what we call a system of classes, orders, genera and species. In doing this, we fix arbitrarily on such characteristic resemblances and differences as seem to us most prominent and invariable in the several subjects, and most likely to take a strong hold in our memories. Thus Ray formed one classification on such lines of division as struck him most favorably; Klein adopted another; Brisson a third, and other naturalists other designations, till Linnaeus appeared. Fortunately for science, he conceived in the three kingdoms of nature, modes of classification which obtained the approbation of the learned of all nations. His system was accordingly adopted by all, and united all in a general language. It offered the three great desiderata: First, of aiding the memory to retain a knowledge of the productions of nature. Secondly, of rallying all to the same names for the same objects, so that they could communicate understandingly on them. And Thirdly, of enabling them, when a subject was first presented, to trace it by its character up to the conventional name by which it was agreed to be called. This classification was indeed liable to the imperfection of bringing into the same group individuals which, though resembling in the characteristics adopted by the author for his classification, yet have strong marks of dissimilitude in other respects. But to this objection every mode of classification must be liable, because the plan of creation is inscrutable to our limited faculties. Nature has not arranged her productions on a single and direct line. They branch at every step, and in every direction, and he who attempts to reduce them into departments, is left to do it by the lines of his own fancy. The objection of bringing together what are disparata in nature, lies against the classifications of Blumenbach and of Cuvier, as well as that of Linnaeus, and must forever lie against all. Perhaps not in equal degree; on this I do not pronounce. But neither is this so important a consideration as that of uniting all nations under one language in Natural History. This had been happily effected by Linnaeus, and can scarcely be hoped for a second time. Nothing indeed is so desperate as to make all mankind agree in giving up a language they possess, for one which they have to learn. The attempt leads directly to the confusion of the tongues of Babel. Disciples of Linnaeus, of Blumenbach, and of Cuvier, exclusively possessing their own nomenclatures, can no longer communicate intelligibly with one another. However much, therefore, we are indebted to both these naturalists, and to Cuvier especially, for the valuable additions they have made to the sciences of nature, I cannot say they have rendered her a service in this attempt to innovate in the settled nomenclature of her productions; on the contrary, I think it will be a check on the progress of science, greater or less, in proportion as their schemes shall more or less prevail. They would have rendered greater service by holding fast to the system on which we had once all agreed, and by inserting into that such new genera, orders, or even classes, as new discoveries should call for. Their systems, too, and especially that of Blumenbach, are liable to the objection of giving too much into the province of anatomy. It may be said, indeed, that anatomy is a part of natural history. In the broad sense of the word, it certainly is. In that sense, however, it would comprehend all the natural sciences, every created thing being a subject of natural history in extenso. But in the subdivisions of general science, as has been observed in the particular one of natural history, it has been necessary to draw arbitrary lines, in order to accommodate our limited views. According to these, as soon as the structure of any natural production is destroyed by art, it ceases to be a subject of natural history, and enters into the domain ascribed to chemistry, to pharmacy, to anatomy, &c. Linnaeus’ method was liable to this objection so far as it required the aid of anatomical dissection, as of the heart, for instance, to ascertain the place of any animal, or of a chemical process for that of a mineral substance. It would certainly be better to adopt as much as possible such exterior and visible characteristics as every traveller is competent to observe, to ascertain and to relate. But with this objection, lying but in a small degree, Linnaeus’ method was received, understood, and conventionally settled among the learned, and was even getting into common use. To disturb it then was unfortunate. The new system attempted in botany, by Jussieu, in mineralogy, by Hauiy, are subjects of the same regret, and so also the no-system of Buffon, the great advocate of individualism in opposition to classification. He would carry us back to the days and to the confusion of Aristotle and Pliny, give up the improvements of twenty centuries, and co-operate with the neologists in rendering the science of one generation useless to the next by perpetual changes of its language. In botany, Wildenow and Persoon have incorporated into Linnaeus the new discovered plants. I do not know whether any one has rendered us the same service as to his natural history. It would be a very acceptable one. The materials furnished by Humboldt, and those from New Holland particularly, require to be digested into the Catholic system. Among these, the Ornithorhyncus mentioned by you, is an amusing example of the anomalies by which nature sports with our schemes of classification. Although with out mammae, naturalists are obliged to place it in the class of mammiferae; and Blumenbach, particularly, arranges it in his order of Palmipeds and toothless genus, with the walrus and manatie. In Linnaeus’ system it might be inserted as a new genus between the anteater and manis, in the order of Bruta. It seems, in truth, to have stronger relations with that class than any other in the construction of the heart, its red and warm blood, hairy integuments, in being quadruped and viviparous, and may we not say, in its tout ensemble, which Buffon makes his sole principle of arrangement? The mandible, as you observe, would draw it towards the birds, were not this characteristic overbalanced by the weightier ones before mentioned. That of the Cloaca is equivocal, because although a character of birds, yet some mammalia, as the beaver and sloth, have the rectum and urinary passage terminating at a common opening. Its ribs also, by their number and structure, are nearer those of the bird than of the mammalia. It is possible that further opportunities of examination may discover the mammae. Those of the Opossum are asserted, by the Chevalier d’Aboville, from his own observations on that animal, made while here with the French army, to be not discoverable until pregnancy, and to disappear as soon as the young are weaned. The Duckbill has many additional particularities which liken it to other genera, and some entirely peculiar. Its description and history needs yet further information.
In what I have said on the method of classing, I have not at all meant to insinuate that that of Linnaeus is intrinsically preferable to those of Blumenbach and Cuvier. I adhere to the Linnean because it is sufficient as a ground-work, admits of supplementary insertions as new productions are discovered, and mainly because it has got into so general use that it will not be easy to displace it, and still less to find another which shall have the same singular fortune of obtaining the general consent. During the attempt we shall become unintelligible to one another, and science will be really retarded by efforts to advance it made by its most favorite sons. I am not myself apt to be alarmed at innovations recommended by reason. That dread belongs to those whose interests or prejudices shrink from the advance of truth and science. My reluctance is to give up an universal language of which we are in possession, without an assurance of general consent to receive another. And the higher the character of the authors recommending it, and the more excellent what they offer, the greater the danger of producing schism.
I should seem to need apology for these long remarks to you who are so much more recent in these studies, but I find it in your particular request and my own respect for it, and with that be pleased to accept the assurance of my esteem and consideration.
Jefferson’s views on classification are tied closely into national pride; by adopting the Linnaean system, he manages to treat taxa in North America, like mastodons, as distinct from Eurasian taxa (a term not introduced until the early 20th century), contrary to Buffon’s tendency to classify in terms of apparent similarities. Buffon held that the North American taxa were “degenerate” forms of the Eurasian forms. Buffon, who followed the Jussieuan scheme (because it was, after all, the system of a Frenchman), tended to lump taxa because it was always possible to find similarities. The Linnaean system tended to identify species and higher taxa by the character essentialis, a unique set of characters for each taxon. However, Jefferson does concur with Buffon that taxa are just artificial, and that only “units” (individual organisms) exist.
While Jefferson is not entirely the paragon of enlightened virtue he is sometimes painted as, it’s not a bad thing for a politician to be intellectual enough to discuss such arcane matters. Even Obama couldn’t do this. Maybe Jeb Bartlett could.
I have been translated again (people never learn). My Macroevolution FAQ:
The translator is Vlad Brown, so any errors of fact can now be assigned to someone else… [Thanks Vlad]
Also, check out the special issue of the Geological Society of Lond Special Publication (143) from 1998, which was on Charles Lyell. It is now open access, and you can download the PDFs.