Category Archives: Systematics

by John S. Wilkins | August 26, 2012

Phylogeny and the history of language and culture

Increasingly, work is being done using the methods of phylogenetic systematics to uncover cultural and linguistic evolution. A leading lab on this work is Russell Gray’s lab at the University of Auckland in New Zealand. He and his collaborators have looked at the evolution of language, particularly Pacific languages, and other cultural trends (like canoe decoration) in evolutionary terms.

Now they have published a paper in Science (Bouckaert et al. 2012), “Mapping the Origins and Expansion of the Indo-European Language Family”. The media of course published this under headlines like “English language originated in Turkey”, thereby demonstrating that journalists understand no evolutionary thinking as well as they understand no economics. Basically by using word forms of many extant and extinct Indoeuropean (IE) languages, and a Bayesian analysis, they established that IE originated in Anatolia, or the central regions of modern Turkey.

This is not unlikely, for certain values of “began”. They locate the origination event around 9500 years ago, which is not long after agriculture began more or less in the same region. Previous hypotheses were that IE began around 5000 years ago in the central Asian steppes, along with the domestication of horses and the invention of the stirrup.

However, how good is this thesis? The BBC article with the silly headline is actually pretty well sourced and written. They quote Prof. Petri Kallio from the University of Helsinki as saying that “Unlike archaeological radiocarbon dating based on the fixed rate of decay of the carbon-14 isotope, there is simply no fixed rate of decay of basic vocabulary, which would allow us to date ancestral proto-languages.” He remains skeptical.

This is a matter of methodology and epistemology, and it goes to the very foundation of phylogenetic method itself. At best a sample of an organism or artefact from within C14 radioisotopic dating ranges only shows that an instance of that type was around at that time and place. It does not show whether it was the earliest or latest; it merely sets up a single anchor point that all hypotheses must account for.

Likewise, a document or monument with written language shows only that a language type was there at a time. And since writing per se did not arise until around 3500 years ago, even that cannot help. All we know are where recorded languages are or were found. They are anchor points, but not fixed ones. These anchors can and do move.

And Kallio is right: there are no fixed decay rates, or molecular clocks. In fact there aren’t such things in biology either. Molecular rates of change are not universal or constant, and inferences based upon them are at best hypotheses based hypotheses. Phylogeny is a tool, but what does it show?

In my last post I noted that phylogenetic reconstructions show only relatedness. What they do not show, without some extensive ancillary assumptions, is how that relatedness arose. The increasing awareness of lateral transfer and hybridisation between taxonomic lineages indicates that there can be some complex histories even if the taxonomic relationships are treelike. NB: to head off the most common error about this, lateral transfer does not undercut the treelike structure either of evolution or phylogenetic diagrams. It makes them harder to detect, but a certain admixture can be accommodated in a standard tree classification. Of course, if the rate of lateral transfer approaches equality, then you no longer have separate taxa, and so that would count as a single lineage that temporarily separated like populations either side of a geographic barrier that are brought back into contact.

In the case of sociocultural evolution, such lateral transfer is often assumed to be rife. This is thought by some to undercut the importance of phylogenetic method in cultural contexts. I want to argue that it doesn’t, but that the inferences from phylogeny are not so obviously historical as some seem to think.

First of all if some lateral transfer is possible in biological contexts between “good species” (the term used by biologists when they know it’s a species but it doesn’t follow some set of strictures they think species must), then some must be permissible in sociocultural contexts to. A loan word in French from English doesn’t make English and French the same language, no matter what the Academie Française might think. In biology it is the entire shared developmental system, including the genome, that makes a species a species. In culture a tradition has more than just a few elemental objects; it has a functional structure, and in language a grammar.

So phylogenetics can apply nicely in contexts where traditions (or species) are well behaved. If they are relatively stable (i.e., not so transitory that they cannot be tracked), and distinct (i.e., the rate of lateral transfer is not so high they aren’t recognisable traditions any more), then you can do a phylogenetic analysis of them. It’s not so surprising really. Willi Hennig, whose Phylogenetic Systematics (1966) set up modern phylogenetics, took some of his ideas out of the discipline of stemmatics, or tracking manuscripts by differences in transcription (Platnick and Cameron 1977, Atkinson and Gray 2005)

However, there are limitations when using this to reconstruct history. For a start, suppose you have two manuscripts that differ. You cannot reconstruct the last version they share historically. Suppose you have three, and two agree mostly. Can you reconstruct the last version from that? Well the two copies that agree might be from a large copy centre, but the one that disagrees might be from a minor monastery that actually had better copying procedures and a more original version, and so on. These issues are well known to historians and biblical scholars, for example.

Now consider the argument put forward by Bouckaert et al. They look at the frequencies of cognate words and conclude from their analysis that IE began in a particular location at a particular time. Such reconstructions rely on assumptions, like a relatively constant rate of diffusion in all directions. What if the language was blocked by a cohesive language and culture in one direction? What if one population into which it diffused was more conservatively structured? What if a small military power managed to spread through large territories? Each of those shifts the “weight” of the diffusion pattern and means we might think something other than the conclusion that Anatolia was the centre of origin. There are many contingencies and possibilities allowed just by a phylogeny, in culture and language as in biology.

I am not denying the conclusions reached here. I think it likely (the use of Bayesian analysis here is significant) that Anatolia was indeed a centre of many cultural novelties. We certainly think that agriculture arose near or around there. But it doesn’t follow that because Anatolia is novel in one respect (farming) it is novel in another (language). We should avoid confirmation bias in science.

In more general terms, what counts as evidence in any historical and evolutionary process? Can we say that passerine birds first evolved in Austronesia? Can we say that writing began once and was diffused or whether there were many independent inventions? Where did the Etruscans come from? Can we make any origin claims at all? We certainly would like to. The trouble is that information gets lost over time, and the best we can do is anchor events based on actual data. All process hypotheses based on these anchoring events are at best consistent with the data, not proven or even necessarily made more likely by them (to avoid confirmation bias and affirming the consequent style inferences when unwarranted).

It may sound like I am being contrarian here. I am not. This is the standard view in palaeontology (see for example Smith 1994), for example. History is hard to find, and we never have much confidence in our extensions beyond the data. It might be that we can reasonably think IE arose in Anatolia; knowing that is a lot harder.

References

Atkinson, Quentin D., and Russell D. Gray. 2005. Curious Parallels and Curious Connections—Phylogenetic Thinking in Biology and Historical Linguistics. Systematic Biology 54 (4):513-526.

Bouckaert, Remco, Philippe Lemey, Michael Dunn, Simon J. Greenhill, Alexander V. Alekseyenko, Alexei J. Drummond, Russell D. Gray, Marc A. Suchard, and Quentin D. Atkinson. 2012. Mapping the Origins and Expansion of the Indo-European Language Family. Science 337 (6097):957-960.

Hennig, Willi. 1966. Phylogenetic systematics. Translated by D. D. Davis and R. Zangerl. Urbana: University of Illinois Press.

Platnick, Norman I., and H. Don Cameron. 1977. Cladistic Methods in Textual, Linguistic, and Phylogenetic Analysis. Systematic Biology 26 (4):380-385.

Smith, Andrew B. 1994. Systematics and the fossil record: documenting evolutionary patterns. Oxford, OX; Cambridge, Mass., USA: Blackwell Science.

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Filed under Epistemology, Evolution, History, Natural Classification, Social evolution, Species and systematics, Systematics

by John S. Wilkins | August 25, 2012

A periodic table of insects? More thoughts on classification

Seen by Malte Ebach at the XXIV International Conference of Entomology in South Korea:

Entomology classification

What’s fun about this (to a philosopher of taxonomy) is why a periodic table doesn’t serve to classify taxa in biology like this. Instead we get this:

Hexapoda
[From here]

The answer is that elements are, and taxa aren’t, a series. That is, elements fill every available spot on a timeless sequence, whereas organisms (and other historical objects, like institutions, cultures, and planets) do not. So a periodic table works for elements. It doesn’t work for historical taxa. They fill the available space extremely sparsely (in fact the available taxonomic space is so large we couldn’t represent it – how many possible characters or traits could organisms have?), and do so in an irregular and contingent manner. So a tree diagram, representing the actual taxa and their relations, is formally the better way to classify them. Other ways to classify them graphically include Venn diagrams and indented lists, but they all end up doing the same formal job.

That formal job is to indicate that of any three arbitrarily chosen taxa, two are more closely related than either is to a third, a view that goes back at least to Aristotle (doesn’t everything?). The explanation of that relationship is historical: the two more closely related taxa share a more recent common ancestor than either does with the less closely related taxon. However, the classification logically precedes the explanation, in that it sets up the explanandum for the historical explanans. Once the classification (and explanation) are in play, we refine and extend it inductively to other taxa. This is called “phylogenetics”.

Classification is a crucial and almost inescapable function in science, not merely at the early stages of a discipline but throughout its lifespan. We neglect it at our peril. Unfortunately it has been so deprecated recently that even those who are doing classification have to pretend they are in the business of hypothesis generation and testing, when in fact they are setting up the things hypotheses are needed to account for.

The difference between classification by series and classification of sparsity, however, is even less well appreciated. Everyone is taught in biology, for example, that we abandoned the former (the great chain of being) in favour of Darwinian tree thinking, but few seem to appreciate what that means. We are so taken by adaptationist stories (which are, by nature, series-style classifications; adaptive landscapes represent some fictive space of possible states in which we are locating this or that trait-bearer) that we tend to forget how sparsely we have filled it (by “we”, I mean, organisms on earth, of course). Classifying in terms of adaptive traits is a very limited form of classification, entirely dependent upon what the investigator happens to think is critical or significant. Nature has no such cognitive limitations and arranges things as it wills, without regard for series or orderly behaviour. We either keep up, or we spend our time classifying our own mental contents.

All that from a joke poster…

New publications

I have added some under-review drafts of my papers to the PhilPapers archive:

Essentialism in Biology. Essentialism in philosophy is the position that things, especially kinds of things, have essences, or sets of properties, that all members of the kind must have, and the combination of which only members of the kind do, in fact, have. It is usually thought to derive from classical Greek philosophy and in particular from Aristotle’s notion of “what it is to be” something. In biology, it has been claimed that pre-evolutionary views of living kinds, or as they are sometimes called, “natural kinds”, are essentialist. This static view of living things presumes that no transition is possible in time or form between kinds, and that variation is regarded as accidental or inessential noise rather than important information about taxa. In contrast it is held that Darwinian, and post-Darwinian, biology relies upon variation as important and inevitable properties of taxa, and that taxa are not, therefore, kinds but historical individuals. Recent attempts have been made to undercut this account, and to reinstitute essentialism in biological kind terms. Others argue that essentialism has not ever been a historical reality in biology and its predecessors. In this chapter, I shall outline the many meanings of the notion of essentialism in psychology and social science as well as science, and discuss pro- and anti-essentialist views, and some recent historical revisionism. It turns out that nobody was essentialist to speak of in the sense that is antievolutionary in biology, and that much confusion rests on treating the one word, “essence” as meaning a single notion when in fact there are many. I shall also discuss the philosophical implications of essentialism, and what that means one way or the other for evolutionary biology. Teaching about evolution relies upon narratives of change in the ways the living world is conceived by biologists. This is a core narrative issue.

Gods Above: Naturalizing Religion in Terms of Our Shared Ape Social Dominance Behavior. To naturalize religion we must identify what religion is, and what aspects of it we are trying to explain. In this paper religious social institutional behavior is the explanatory target, and an explanatory hypothesis based on shared primate social dominance psychology is given. The argument is that various religious features, including the high status afforded the religious, and the high status afforded to deities, is an expression of this social dominance psychology in a context for which it did not evolve: high density populations made possible by agriculture.

Naturally these are unreviewed, unedited and probably under-thought.

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Filed under Cognition, Evolution, Metaphysics, Natural Classification, Race and politics, Religion, Social evolution, Systematics

by John S. Wilkins | July 6, 2012

How not to give a keynote

So we finally managed to get things going for the Poland keynote. It took over half an hour to get the sound working, after a fashion, and the connection was blocky at best. The hardest part was that I kept trying to hear what people were saying at the other end, but got only feedback and delayed echoes. Most disconcerting. It would have been almost easier to fly to Poland.

Here’s the slides if anyone is interested:

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Filed under Cognition, Epistemology, Evolution, Natural Classification, Philosophy, Religion, Social dominance, Social evolution, Systematics

by John S. Wilkins | May 1, 2012

Carnival of Evolution 47: All the Evolution News that’s Fit to Blog

Newspaper 300x225

Welcome to the 47th edition of the Carnival of Evolution. We have had our science reporters out in force hunting down the best of the blogosphere on evolution and related subjects, and here they are for your delectation and delight and other d-words.

First some links I encountered in my random walk through the webbies: Face to face with primate facial diversity at Wild Mammal Blog gives information about the evolution of facial colouring in South American primates. Social evolution in mole rats at the same blog discusses the adaptive niches of naked mole rats (not all of which are social or eusocial, by the way). And the agony column Molecular Love asks The evolution perspective: Do antidepressants do more harm than good?; and the answer is not clear.

Reporter Bradley Alicea at Synthetic Daisies tells the story of Recent Advances Towards a Truly Darwinian Neurodynamics, which is a good review of an emerging area at the interface of artificial and natural evolutionary systems (based on a recently-published paper). He also gives an excellent overview of The Neuromechanics and Evolution of Very Slow Movements, in sloths and turtles, but also fast movements in woodpeckers.

Humorist David Morrison at The Genealogical World of Phylogenetic Networks (there’s a mouthful) notes that Steven Jay Gould was wrong: You can find Copes’ Rule in manufactured objects. Cars, for instance, tend to get bigger… Almost as humorous if it were not so serious, reporter Troy Britain offers a human interest story about a silly creationist who can’t get anything right about horse evolution at Playing Chess with Pigeons, in a story entitled Open mouth, insert hoof.

The science reporter at Bytesize Biology discusses recent research in It’s a smORF world, after all? Small open reading frames are everywhere (in Drosophila, anyway)

The living rainbow: In budgies, same-sex courting isn’t practice for wooing the ladies: Essayist Jeremy Yoder at Denim and Tweed observes that the gay rainbow is found in budgies and it isn’t just practice for hetero mating. In Notes from the field: What’s Chris doing to that Joshua tree? he also discusses why Joshua trees have two distinct phenotypes. It’s all about what fertilises them. Sex, sex, sex; it’s all the young folk think about these days! I’m tempted to write a letter to the Times.

At Nothing in Biology Makes Sense, our intrepid observer devindrown argues that hosts can survive parasitism in Multidimensional coevolution, no oscillation overthruster required. At the same blog, embedded journalist Hird shows how critically endangered species used illegally in Traditional Chinese Medicine can be identified by Genetic Auditing.

In breaking news, David Winter talks about Flightless Flies (not Walks – dad joke) at Sciblogs. Many of them are bloodsuckers.

Our man in the lab, Kevin Zelnio, discusses my favourite topic, Species Concepts at the Scientific American blog. Michael Ryan, senior correspondent at Paleoblog, mentions the father of cladistics, Willi Hennig’s, birthday.

Womens’ Affairs Reporter (it had to be a man, didn’t it?), Zen Faulkes, sensei at Neurodojo, covers the question of why women wear red. Answer: It’s sexy but not sexual, and he returns to the issue to consider how cultural bias might influence such evolutionary psychological explanations.

Occasional science reporter (he usually covers the religion beat) PZ Myers at little known blog, Pharyngula, shows how modular gene networks can place eyes in all kinds of places, and just generally be the source of evolutionary novelties.

In the features page, politics reporter Joachim D asks who coined the term “social Darwinism” at Mousetrap. [He missed William Graham Sumner, though.]

Hidden in the classifieds, Bug Girl gets onto one of my pet peeves with Taxonomy Fails, in this case cochineal insects not being beetles. She works up a useful metric for taxonomy fails.

The education pages cover the question of whether there is a biology of metaphysics (as opposed to a metaphysics of biology?) via reporter Ken Weiss at The Mermaid’s Tale in Metaphysics in science, Part II: Life in a cave. Are philosophical objects blind in caves? Thanks to Anne Buchanan for the notice.

The cookery pages editor, Katie Sorene at The Flying Fugu, asks Was the Caveman Diet Healthier than Our Own? What did ancient humans eat during the paleolithic era? Was their diet healthier than our own? What we can we learn from evolutionary nutritional standards and could we benefit from adopting the Paleo diet today?

Suzanne Elvidge at Genomic Engineering reports on news on Stickleback genetics and evolution, and on how Athletic frogs have faster-changing genomes, and how Synthetic genetic material, XNA, can replicate and evolve and DNA data: Polar bears evolved 600,000 years ago. This is a good blog to subscribe to for the news front page.

~~Danielle Whittaker~~ Tyler Hether at the evolution consortium BEACON reports on work done there on The effect of landscapes and ecology on gene flow and speciation in amphibians.

Finally some video: TV reporter Donald Forsdyke at Queens University, Ontario, has a series of Youtube talks on various aspects of evolution worth looking at. In particular check out the one on Mendelian inheritance and Speciation under Branching Evolution.

Last and least, I have an editorial on reconstructing the past in evolution in Bayes, Evolutionary Clocks and Biogeography. Rupert won’t be happy. Until next time at some little known blog by the name of Pharyngula, this is the news…

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Filed under Ecology and Biodiversity, Evolution, Genetics, History, Natural Classification, Species and systematics, Systematics

by John S. Wilkins | April 7, 2012

The Knight’s Song, or What is a [scientific] theory?

“Or else it doesn’t, you know. The name of the song is called ‘Haddocks’ Eyes.’”
“Oh, that’s the name of the song, is it?” Alice said, trying to feel interested.
“No, you don’t understand,” the Knight said, looking a little vexed. “That’s what the name is called. The name really is ‘The Aged Aged Man.’”
“Then I ought to have said ‘That’s what the song is called’?” Alice corrected herself.
“No, you oughtn’t: that’s quite another thing! The song is called ‘Ways and Means’: but that’s only what it’s called, you know!”
“Well, what is the song, then?” said Alice, who was by this time completely bewildered.
“I was coming to that,” the Knight said. “The song really is ‘A-sitting on a Gate’: and the tune’s my own invention.”
[Through the Looking-Glass, chapter 8]

Few words carry the weight that the Greek word theoria carries today. It is a word that applies to everything from politics to philosophy to mathematics, art, economics, psychology and of course, the natural sciences. Usually contrasted to another Greek word praxis, meaning practice or doing, it is the mental view one has of some aspect of the world. Beyond that, there is almost nothing in common with all uses of the term, especially now that it has been extended to apply to all of our general dispositions to observe and learn.

It comes as something of a surprise to me that the philosophy of science does not have a neat discussion I can locate of what counts as a theory in science. There are two general metalevel views – the traditional or “syntactic” notion and a structural or “semantic” notion – but these do not tell us what theories are, only what they entail in a more general philosophical sense. The syntactic notion holds that theories are logical theorems and their derivations, while the semantic view holds that theories are models that have real world interpretations. The slogan for the semantic view is

SEM: A theory is a collection of models (cf. McEwan unpublished)

There seems not to be an equivalent slogan for the syntactic view, but we can invent one:

SYN: A theory is an axiomatic system in some formal language

However, neither of these slogans make clear either what the difference between the two actually is, or what scientific theories, the things scientists take themselves to be using, making and testing, are. Instead we are dealing with logical objects – sentences, sets, classes and axioms. This is a dispute between philosophers (indeed, between schools of philosophy, the logical positivists supposedly holding SYN, following Carnap, and the post-positivists holding SEM (two originators of this view are Frederick Suppe and Bas van Fraassen).

SEM is about “model-theoretic models”, which is to say “an interpretation which satisfies some set of sentences (or sentential formulae). An interpretation specifies a set of individuals (the domain or universe of discourse) and defines of all the appropriate symbols (i.e., constant, function and predicate symbols) of the language on that set” (McEwan). SYN is a set of sentences in a formal (that is a logico-mathematical) language. Very roughly, a SEM theory is a structural representation of the world, while a SYN theory is a set of formal statements, each of which has some truth value. Both of these are highly abstract objects.

At the other end of the scale, we find scientists talking about theories as laws, prediction techniques, intellectual schemes, descriptions (sometimes) and even extended hypotheses. The Folk, on the other hand, treat “theory” as a special kind of guess. Creationists and other dissemblers regarding some science or other they object to play very strongly on these ambiguities and polysemies.

So I am left to wonder what a theory is (as opposed to how philosophers explicate theories in philosophy). We can consider a few senses for a theory in some domain of investigation:

The Mathematical Sense: A theory is some class of mathematical axioms and all their formal implications. This is sometimes called the axiomatic sense of theory – a theory, the real thing, is a class of mathematical theorems taken to be axioms.
The Interpretation Sense: A theory is a set of mathematical statements or structures together with rules for interpreting those statements. If you have a mathematical equation that purports to describe how things fall, you need to know what to interpret the variables in that equation as referring to.
The Representation Sense: A theory is a description of the way things are in some domain. It allows the theorist to explain, predict, and manipulate those things.
The Worldview Sense: A theory is the set of beliefs that enables the theorist to engage with the world, structuring observation, action, reasoning and expression. This is effectively Thomas Kuhn’s notion of a “paradigm” or his later explication “exemplar”, some conceptual scheme that guides everything in the discipline.
The Practical Sense: It seems a bit odd to call a theory “practical” when it is usually contrasted with practice (praxis), but in this sense a theory is the set of conceptual commitments that the theorist employs to do things in the domain. So having a theory enables one to identify the relevant objects under study.
The Causal Sense: A theory is an explanation in terms of the causes of objects in the domain

Each of these senses appeals to some intellectual activity or state, but they vary greatly: the mathematical and interpretation senses involve mathematical equations or statements, the representation and worldview senses appeal to linguistic objects such as statements, sentences or logical formulae. The worldview and practical senses involve action-guiding stances. The causal sense is common but not universal. At best we can say they all involve beliefs (in the sense of mental stances, not faith statements necessarily). Of course, an actual theory may exhibit many or even all of these senses.

When we look at actual theories, they typically involve formal models – equations, simulations, algorithms – but this is not true of some older theories prior to the flowering of mathematisation of all science. It is also often not true of theories in domains that lack well-elaborated accounts. For example, theories in psychology are often verbal. Darwin’s theories (I count seven of them) were not mathematical at all, although he clearly intended them to be filled out later (as they were, apart from his theory of heredity). Freud’s theories remain unmathematised. So it doesn’t follow that for something to be a theory, it must be a mathematical structure, even if the philosophical analysis of theories develops a mathematical view. The reason is that “theory” in philosophy is a different beast to “theory” in science, and the relation is more like the relation between “concept” in philosophy and my concept of a television, for example.

So we might entertain the heresy that there is actually no “natural kind” in science that answers to “theory”, or, if you like, there’s no such thing as a theory, just lots of individual and particular intellectual constructs that get called theories. P. D. Magnus has argued that the term “theory” is a “family resemblance predicate” in which there are multiple meanings that overlap and cluster, but which have no necessary and sufficient definienda for all theories (Magnus unpublished), in an analogy with my favourite term of science, “species”. I think that this is correct, but I would go one further, and say that “theory” (unlike “species”) is a term that lacks any substantial meaning in science, and is really an assertion of the sociological status that some ideas have attained in a discipline, which can be for programmatic, political, or educational reasons as well as explanatory. A good theory will exhibit the majority of the cluster properties, but it doesn’t follow that theory is a category that stands alone, as it were, from the psychological, historical and social aspects of science.

What gets called a theory depends on no unique set of inherent properties of the theories themselves. This has some deep implications for thinking about science, if correct. Let’s consider some of them: the scientific process, domain specificity, and theory-dependence of observation.

The scientific process

Scientists are introduced to their disciplines in various ways, but nearly all of them are taught at some point that there is a scientific method. This methodism is, however, itself indefinable. Some accounts introduce a cycle of conjecture, testing, formulation, further testing and then publication as a law or generalisation. Others focus on the use of statistical adequacy. Yet others make consilience (abductive reasoning) a key virtue – many lines of investigation must coincide.

Nearly all of them work on conceptual elements: statements in ordinary, formal or mathematical languages. Some domains or disciplines are more formalisable than others, but independently of this, scientists work with “hypotheses”, which, when sufficiently well established, become “theories”. In short, a theory is what a hypothesis wants to be when it grows up.

If there is no common property for theories, apart from properties held by things that aren’t theories by any estimation, then this picture of science, while not false, is misleading. There can be no singular method, because there is no singular destination for scientific ideas (see Magnus’ paper for a good discussion about what count as scientific ideas). And as famously expressed by Feyerabend:

It is clear, then, that the idea of a fixed method, or of a fixed theory of rationality, rests on too naive a view of man and his social surroundings. To those who look at the rich material provided by history, and who are not intent on impoverishing it in order to please their lower instincts, their craving for intellectual security in the form of clarity, precision, ‘objectivity’, ‘truth’, it will become clear that there is only one principle that can be defended under all circumstances and in all stages of human development. It is the principle: anything goes. [Against Method pp27-28]

If there are no essential features for theories, then there are no essential methods for attaining them. On the other hand, I think that the simple view that anything is or can be science is equally mistaken. Feyerabend did not actually argue that anything goes, but instead that there is no fixed method; this is a reductio. He knew perfectly well that disciplines have canon of reasoning and methods, and that some methods are inadequate or unfruitful (no aid and comfort to creationists in this argument, at any rate).

Domain specificity

One assumption often made about science is that it is divided into fields of inquiry that are themselves more or less natural. We think, for example, of biology as a natural subset of natural processes where we do not think of medicine that way (because medicine uses techniques and ideas that also apply to veterinary science). One standard view about domains in science is that they are effectively defined by the best attested theory of the phenomena in the domain. As theories develop, and as some parts of a domain are explained by theories in other domains, the scope of the domain is refined and revised (consider how much biology has been relegated to organic chemistry, or psychology to neurobiology).

If, however, we find that there are no such privileged conceptual constructs as theories, what does this mean for domains? How do we anchor domains (like biology) in natural ways? We can always give institutional arguments for domains, like saying that there is a Biology faculty in universities, or a course of educational requirements in schools. Or we can argue that it is easier to teach techniques when bundled together (microscopy, field observation, etc.) but it may just as easily have turned out a different way. Arguments about “what is “life”, for example, presuppose the naturalness of that domain (as do the NASA attempts to locate evidence of “life” elsewhere than earth), but if there is nothing that ties life together but human practical considerations and a collection of theories that are not entirely connected or commensurate, why bother? Why not just further divide the domains into groupings that are natural? Why, for example, does biology consider both evolution by natural selection and biochemistry, the Krebs cycle and ecology, behaviour and biogeography?

Attempts to formulate ontologies of domains also typically derive from the theoretical commitments of the domain (atoms are part of the domain of physics, while pain sensations aren’t); so if the theoretical commitments are sui generis to the domain because the nature of “theory” in that domain is unique also, we have a problem of ontological relativity, which may or may not be a problem, depending on how you think ontologies should be handled.

This is, in effect, an argument for a descriptive pluralism. Pluralisms are often thought of as some kind of failure or postmodern relativism, but I see them rather differently. We start our investigations of things based on the phenomena that present themselves to our inspection. Since we have prior sensory, social and conceptual commitments which may or may not be reliable guides to the structure of the world, we very often have to revise our concepts to fit what we learn by investigation. So, “fish” no longer means any thing that lives in water and moves of its own accord, and humans are now apes. Pluralism is a necessary aspect of discovering that the world wasn’t structured the way we naively thought it was. It is a recognition that words matter less than the world they describe.

But this indicates something about science that is so obvious as to almost not need saying: evidence – observation, measurement and experiment – takes priority over theory. That is perhaps a dumb thing to say, or perhaps it is so dangerous as to be obviously false, depending on what you think about our ways of knowing and explaining (theoretical constructionists would take the latter tack). But I think that theories, and domains demarcated by theories, are definable solely in terms of their being something other than evidence. In short, a theory is what evidence isn’t. That leads naturally to the next point.

Theory dependence of observation revisited

I have previously discussed the “theory-dependence of observation thesis (TDOT)” in detail, so I will be brief. If theory itself is not a natural kind, the claim that observation relies upon it falters. Of course our conceptual furniture affects how we observe – this follows from the mere existence of trained observers – but the nonexistence of Theory (that is, as a natural kind) means that the sting of the TDOT is largely removed. It resolves down to the view that we observe things that we have learned to observe. This is not, I think, so deep as the TDOT5 claim defended by Kuhnians at one time. It certainly does not license the sorts of claims that are sometimes made that science is a self-contained hermeneutic bubble just like any other world view.

Conclusion

I think this is significant in part because it helps up to understand how science really proceeds. The notion of “law” in science has been deprecated recently amongst philosophers (e.g., Cartwright et al. 2005); it is time to deprecate “theory” also.

It also means that what we call a theory and how we talk about the notion of theory is not unlike the Knight’s song. We often refer to philosophical accounts of representation, explanation and formalisation when we discuss “theory” (excluding the terminological arguments amongst other philosophical traditions, like Marxist or phenomenological schools) when we should be talking about the ways scientists use the terms, and then, and only then, consider the philosophical implications. And if “theory” lacks the sort of reality it is sometimes held to have, if it simply is whatever in science is not evidentiary or probative, then we should be more empiricist in our philosophy.

I take this line, of course, to defend the claim that one thing science often does is, independently of theory, classify the world as a way to investigate it. If theory is not a natural kind, then it becomes clear that we can do this, only what we rely upon, our conceptual commitments that make a trained observer a better systematist, is more complex than “theory” suggests it would be.

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Filed under Biology, Creationism and Intelligent Design, Ecology and Biodiversity, Epistemology, General Science, Metaphysics, Natural Classification, Philosophy, Science, Sermon, Species and systematics, Systematics

by John S. Wilkins | March 30, 2012

Bayes, evolutionary clocks, and biogeography

I just received a review by Gareth Nelson of Michael Heads’ book Molecular Panbiogeography of the Tropics (publishers’ site). I should have blogged this before, since I got a copy, being on the editorial board for this series (the same one I published with at Uni Calif Press), but I have been bogged down with personal troubles and other tasks. Also, I am not professionally competent to make much comment, so Gary’s review, forthcoming in Systematic Biology, is welcome.

However, the book and the review set me thinking about how historical inferences in biology are made. We use dating to establish how evolution occurred – whether, for example, a particular species is the ancestor of another, or when a particular trait evolved. These inferences are ubiquitous and somewhat doctrinaire. But there is even a website and app (TimeTree) that uses techniques like molecular clocks to absolutely date divergence times, and which draws inferences from it (such as that a particular species is not an ancestral species because it is found too late or too early). Molecular clocks are not so reliable as is sometimes presumed, however. Gary quotes this episode:

Here I am reminded of a scientific meeting in London (5 September 2001; published by Donoghue & Smith 2003). Francisco Ayala presented a paper on “Molecular clocks: whence and whither?” An audience member then asked: “Francisco, is there a molecular clock”? He gave a complex reply. The same member asked again: “Francisco, is there a molecular clock?” This time he gave a one-word answer: “No.”

Stratigraphy is another example. The earliest date given for a species in the fossil record is usually the date of the oldest specimen found, but as a well known book, Systematics and the Fossil Record, notes, species may persist well outside of that record (“Lazarus taxa“), or be misidentified as persisting when they haven’t (giving rise to “Elvis taxa“, my favourite technical term). At best we have relative dates, with some degree of credence in the absolute dates, and little if any direct knowledge of the path of actual evolution.

This sets up a problem or two. One of these is the problem of calibration: how do we match these relative dates with absolute time? Heads’ solution is to use plate tectonics:

The method of dating used in this book does not assume an evolutionary clock, even a relaxed one. Instead it fits multiple tectonic events (rather than multiple fossils) to a phylogeny. This indicates a chronology in which rates can show extreme changes within and among lineages and genes at different times and places. [p71]

Gary notes that this gives us at best a minimum age, and he and Heads both dispute that this will give us confidence in a maximum age of taxa. And he and Heads both note the problems with the “dispersal” method (or as it is better called in my view, a “presumption”) in trying to find the centres of origin, both in time and space, of taxa, instead adopting the “vicariance” method (“presumption”) in which the known distribution of taxa gives the “tracks” of a taxon, along which the origin may be said to be, either some location or across the whole track. Given the recent work on human origins and the multiple dispersal model interbreeding claims with existing species in Asia and Europe, this is a present concern.

I leave readers to find Gary’s review and read it, and then to read at least the first two introductory discussion chapters in Heads’ book (which at nearly 100 pages is almost a book in itself). Right now, however, I want to make a point about historical inference in the natural sciences (and indeed in any domain). One of the besetting issues in the philosophy of history is “historicism”, which is the view that we know the natures of things when we know their origins. This is reflected in the title of a book, The Poverty of Historicism by Karl Popper. It is regarded by historians as a sin, along the lines of Whiggism and the Great Man theory.

In this context we might ask whether we indeed do know biological taxa from knowing their origins at all. It seems to many that biological taxa are known independently of the explanations and origin stories given in evolutionary contexts; for example the discovery that the Leopard Frog (Rana pipiens) was several species was based, not on evolutionary considerations but on a knowledge of how frogs made mating calls. Evolution provided the explanation after that discovery.

But the temptation towards historicism is inevitable (Ankersmit 2010); we do think things are known by their origins, for all that this is a fallacy of reasoning (the so-called genetic fallacy). And even more than that, we insist upon trying to find these origins, in time and space, and nowhere more than in evolutionary biology. In fact, one of the modern philosophical views on what species are relies entirely upon their origins (Griffiths’ 1999 historical essentialist account).

Here’s the problem I have here, and it is one that was raised many times in the history of post-evolutionary biology, in particular by the so-called Pattern Cladists (e.g., Nelson and Platnick 1981): if we do not know the history, how can we evaluate claims made based on the evolutionary process? That is, if we don’t already know how evolution in general proceeds (such as assumptions of molecular clocks or rates of change), how do we evaluate the claim that a particular lineage evolved in the absence of direct evidence? And how do we learn how evolution proceeds in the first place?

This circularity can be called the Creationist Objection, in a rather restricted sense: not that evolution does not happen, but that we do not know how it happens directly, but have to rely upon a “methodological creationism” (a term of Paul Griffiths’), in which the evidence takes priority over inferences, and in which inferences cannot be used as evidence. It’s an ironic take on the common creationist objection to anything that contradicts the account of Genesis: “were you there?” [Answer: well yes, in the relevant sense – observation – we were there.]

The Creationist Objection is based on an extreme empiricism; the view that evidence is only measurement and observation. Consequently, assumptions of molecular clocks is not evidence (but radioactive decay rates are, because they are fundamental laws of nature, and this argument applies only to historical observations). It is my view that the historicism of modern evolutionary biology is based on the faulty assumption that we can treat some prior hypotheses as Bayesian priors to estimate the likelihoods of some process occurring and evaluate claims of origins.

Now Bayesianism is a well-established theory of knowledge, and in one sense we are all Bayesians now, but that doesn’t imply we are actually using Bayes theorem; just that we know that we can’t make most inferences without assuming some prior hypotheses and likelihoods. However, when we do that, we are hostages to the correctness of those prior estimates. If we screw them up, all our subsequent reasoning will also screw up. So evidence should always trump our priors, and we need to do a kind of reality check from time to time, which is why Heads’ approach has merit; tectonics is a distinct domain from biology, and so the assumptions are relatively independent of our biases of evolutionary theory and narratives.

I once asked Gary, as a callow youth (well, I was still just a doctoral student; I was aged even then), whether he thought we could get some idea of ancestors, a question motivated by the refrain among some pattern cladists that ancestors are unknowable, and his answer surprised me. He replied that it was something we could have various degrees of confidence in, but yes. We could know ancestors just to the extent that we had evidence of various kinds. I recall thinking this was a kind of consilience view. It’s just that we cannot observe ancestors, and so from a purely empirical perspective, one has to represent them as “sister taxa” to their putative descendants in a cladogram. Today this is universally understood (although at no time have the process cladists conceded that they agree with the pattern cladists now, so far as I know). The question is not how we represent them or what the evidence actually indicates, but how we take evidence to guide inference.

Back in the 18th century, naturalists often debated what counted as “scientific reasoning” and many of them followed Lockean principles that knowledge is only ever got from observation, through the senses. This extreme empiricism led rather directly to positivism, and thence to logical positivism. The alternative view is something one might call a kind of Kantianism: one can only observe in the light of some theory. Empiricism and Kantianism are ever at war in the philosophy of science, and in science itself.

Depending on what you require of inference, either we cannot know ancestors, events and centres of origin in the past, or we certainly (or almost certainly) do know these things although we have yet to uncover some events. Or, you are somewhere in the middle there. This mediate view is a more common position than the rhetoric of the debate might indicate. Generally in science, when one side makes claims at one extreme and their opponents take the other extreme, you can get them to qualify and qualify until they approach each other in the middle and only words separate them (a point once made by Stephen Toulmin in 1970). Most pattern cladists and panbiogeographers will admit that you can at least estimate the ancestors and origins; most evolutionary biologists and dispersalist biogeographers will admit that no, we don’t know for sure, but that these are our best guesses. Almost nobody is either a true methodological creationist or darwinian fundamentalist.

And this is how it ought to be; science is about warrantable inferences, not doctrine. However, loose talk sinks inferences. We often assume that what we hypothesise is what we actually know, when instead we are multiplying uncertainty upon uncertainty, a problem with Bayesian inference. And yet… Bayes rules. It works well. We manage to navigate the world by assuming that what we hypothesise is true, so unless the world is simply bizarre and perverse, something about it must be right.

I think that the solution is to presume there is no solution. Both approaches – Locke and Kant – are necessary in a population of scientists to ensure both that neither the opposition to theory so common in the 18th century nor the total theory-dependence of various language-centric philosophies is in control of science, as neither is sufficient for science to proceed. We do different things when we observe than when we make inferences based on hypotheses. The only problem arises when we confuse and conflate these two things. Theories are not evidence, and evidence is not explanation.

The temptation of historicism is a kind of Kantianism, but Kant was not wrong, merely incomplete. Science requires that we are both empiricists ands theorists and that neither is dispensed with, nor takes on the role of the other in inference. The origins of species and traits in evolution are interesting topics, and we should try to work them out. But not by ignoring or trimming evidence.

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