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Axiomatic Panbiogeography

offers an application of incidence geometry to historical biogeography by defining collection localities as points, tracks as lines and generalized tracks as planes.
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This vicariance model can be applied to other taxa.  Side-necked turtles, some anurans, seem to be usual suspects.



Below is a blog post on MPT which points to the reason for a need of Vicariant TIME.


http://evolvingthoughts.net/2012/03/bayes-evolutionary-clocks-and-biogeography/

Gareth Nelson's review is here.

Head's paper on "transmorgification" is here.

"He does not continue the long-standing dispute over dispersal versus vicariance but rather commits to a consistent mode of interpretation (p. 7):In the vicariance approach, the focus is on tracing the originary breaks between groups, not on locating a point center of origin within a group. In a dispersal analysis, the first question is: Where is the center of origin? In a vicariance analysis, the first question is: Where is the sister group? The focus is not on the group itself or on details of its internal geographic/phylogenetic structure, but on its geographic and ecological relationship with its sister group and other relatives."

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.

Ankersmit, Frank. 2010. The Necessity of Historicism. Journal of the Philosophy of History 4 (2):226-240.

Griffiths, Paul E. 1999. Squaring the circle: Natural kinds with historical essences. In Species, New interdisciplinary essays, edited by R. A. Wilson. Cambridge, MA: Bradford/MIT Press:209-228.

 

 

 

Nelson, Gareth J., and Norman I. Platnick. 1981. Systematics and biogeography: cladistics and vicariance. New York: Columbia University Press.

 

Toulmin, Stephen. 1970. Does the distinction between normal and revolutionary science hold water? In Criticism and the Growth of Knowledge, edited by I. Lakatos and I. Musgrave. Cambridge UK: Cambridge University Press:39–48.