See the book at the right entitled The Nature of Classification? According to the website you go to when you click on the cover, it has now been published. I haven’t seen a copy yet, but I’m hopeful… anyway, there’s your stocking filler for the philosopher of science in your life.
Category Archives: Natural Classification
[Note: this is a paper that has sat in my drawer for a while now. I am posting it to follow from my last post on the theological origins of species. If species are not ranks in biology, what are they?]
It is often claimed that species are the units of evolution, but this is not defined or clearly explained. In this paper I will argue that species are phenomenal objects that stand in need of explanation, but that they are not objects required by any theory of biology. I further define, or rather describe, species as the genealogical cluster of various lineages at the genetic, haplotype, genomic, organismic, and population level, in keeping with my previous discussions.
It takes a while for the implications of one’s own work to sink in. In my 2009 book Species, a History of the Idea (see here), I argued that the notion that before Darwin people were essentialistic and fixist about species was false. A recent paper by Jack Powers about Mayr’s misreading of Plato complements an earlier paper about the essentialism mythos by Carl Chung. It is becoming widely accepted that there was no essentialism before Darwin to speak of.
But what I didn’t ask was this question: given that there was no concept of species before the late 17th century in natural history, and that the prior logical and metaphysical notions had nothing much to do with natural history, why did we get a concept of species in the first place? What is “species” needed for?
I answered this in a talk I gave at Berkeley earlier this year, and repeated last night (and which, yes, will become a paper). The reason we have a notion of species in biology at all is because of Noah’s Ark…
The word species, as John Locke noted, is just a Latin word that means a kind or sort of things, and it is entirely appropriate to use that word to denote kinds of things in biology, as in other domains, if you happen to be a Latin speaker or writer, as most educated people were in that time. Does it have any further or deeper meaning?
Try this: whenever you see the word species, replace it as Locke suggested with sort or kind. Likewise, in ordinary life, try out using species every time you want to use sort or kind or similar terms. See how the vernacular deflates that technical term and how the Latin elevates it to a technical terminology. Before long you find yourself wondering what the ontology of, say, ice cream flavours might be. If species is used as a vernacular word, it means just that botanists and others were simply talking about kinds of things.
Actually in the late Latin of the post-renaissance period, there were two words that meant a kind: genus and species, and as far back as the Greek writings of Aristotle and Theophrastus (Aristotle’s pupil who extended his mentor’s natural historical principles to botany) the correlate terms in Greek – genos and eidos – these were used interchangeably, as any good writer would vary their words to avoid repetition.
What is ironic about that is that in Aristotle’s technical philosophy, and in European discourse up until our target period, a genus was the more general (general being the adjective of genus) and a species was more special (special being the adjective of species), so in ordinary work in natural history neither Aristotle nor his student used the terms as logical terms. Likewise, when they are used in early modern taxonomy, neither are they used in the same manner as they are in logical and metaphysics, contrary to the essentialist story.
So what is at issue is not that scholars of the late 16th century talked about kinds or species, as botanists had since the herbalist tradition became botany and the zoologists had since bestiaries became Historia Animalia. What is at issue is why there had to be a rank or level of organisation that all and only species occupied in natural history. Why did we think there were most basic kinds of organisms? The answer lies in a theological problem: given that there was a trend towards literalism in biblical interpretation in the period from the Reformation through to the Counter-reformation, and given that the number of species described by naturalists was increasing rapidly as exploration of the Americas and the Orient uncovered them (and still is, by the way), how could the story of Noah’s Ark be true?
A German-born Jesuit, the youngest of nine children, Athanasius Kircher (c.1602–1680), working out of Rome but in correspondence with explorers and scholars around the known world, attempted to provide a “scientific” solution. I put scientific in quotes because it is anachronistic: there was no distinction to be had between theology and science in the 16 century, or for some time to come, so this does not imply somehow that science and religion were in conflict here. Kircher is doing what any good naturalist would do – appeal to all lines of evidence, including the Bible.
Kircher tried to work out how many of each kind would fit on the Ark, and so determine what the basic kinds were. He didn’t give them a special (sorry) name, though; he just used the ordinary word species.
A little before Kircher, and possibly influencing him (although I have no evidence of that [late note 1]) my namesake Bishop John Wilkins (no close relation) published his Essay on a Real Character and a Philosophical Language, where he tried to capture all facts about the world in a universal system of logic and an invented language to go with it. While Wilkins (ncr) used genus and species in the usual logical sense (that is, rather in the way we would use set and subset), he did seek to do for the Ark what Kircher shortly afterwards did, to establish what species would fit onto it. He gave this page:
wherein he specified not only the “species” but also that a Mule was not a true species, because it is “a mongrel production”; that is, a hybrid. Likewise various kinds of cattle (“Beeves”) and sheep are varieties of the original species.
Now Wilkins (ncr) employed the young John Ray and Francis Willughby, a botanist and his patron, who was also a zoologist, to draw up the lists of species used in the Essay, and Ray and Willughby (who died young, unfortunately) were gently mocked by their peers for the artificiality of Wilkins’ (ncr) system. So he began to do the hard empirical work of classifying plants directly. Later, he gave a definition of what he meant by species, or rather, what test there was for identifying them:
“In order that an inventory of plants may be begun and a classification (divisio) of them correctly established, we must try to discover criteria of some sort for distinguishing what are called “species”. After long and considerable investigation, no surer criterion for determining species has occurred to me than the distinguishing features that perpetuate themselves in propagation from seed. Thus, no matter what variations occur in the individuals or the species, if they spring from the seed of one and the same plant, they are accidental variations and not such as to distinguish a species … Animals likewise that differ specifically preserve their distinct species permanently; one species never springs from the seed of another nor vice versa.” [Historia plantarum generalis, in the volume published in 1686, Tome I, Libr. I, Chap. XX, page 40 (Quoted in Mayr 1982: 256). The Latin of the definition is nulla certior occurit quam distincta propagations ex semine.]
This was the first definition or operational criterion for identifying these fundamental units of natural history. In short, and in modern terms, it was the first biological definition of species.
Why did natural history need units? After all, people had been using and identifying kinds in botany and other areas of natural history for a great many years, and some of the species of plants identified in the century before this are still held to be “good” species. The sole answer that I can find is that species were required by theology, using philosophical techniques and distinctions.
And one has to wonder if, as a rank, species are still statements of faith, in conservation, genetics and taxonomy in general (ironically, measuring diversity using phylogenetic measures for conservation is called the “Noah’s Ark Problem“; see this on species and this problem). While individual species seem to be real objects occasionally, a good many aren’t (they have subspecific structure or are foldable into larger groups). This leads some, like my colleague and friend Brent Mishler, to deny their existence. Like him, I deny their rank. There is no “unit” of evolution or rank of biological ontology. But I think that there is a reality to phenomenological species: we really do see the patterns in the world we name species. The mistake arises, I believe, in thinking that our perceptual biases somehow give us the structure of the world. Sometimes they do, sometimes they don’t, and the question can only be resolved by finding the actual structure of the biological realm. More to follow on this. For now it is enough to note that species are articles of belief…
[You can see the slides here: now works...]
[In case that doesn't work, I'll try to embed it below]
Late edit: I added the final comment to the title, as it seemed to fit.
Late note 1: Further reading, especially via William Poole’s The World Makers, has led me to understand that Johannes Buteo (Jean Borrel) first started this tradition, and that both Wilkins and Kircher were working off his Arca Noe, published in 1554. Ray regarded Buteo as credulous, and Wilkins noted that he included several fabulous creatures on the Ark. His term for kinds was genera.
Much later note: A version of this post, much shortened and better edited, will appear on The Conversation soon.
Much much later note: Here it is.
As readers may have noticed, I have been pretty inactive here lately. This is because I have been finishing a book and sending it off to the publishers, which was achieved about 8 hours ago. The book is titled The Nature of Classification, and it will come out from Palgrave Macmillan. I coauthored this with Malte Ebach.
When I have done a few things, I will return to the Living With Evolution series. The next series of posts will be on Evolution and Morality. If you have questions you would like to see discussed, drop them in the comments below.
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.