Presidental decrees not so easy

Sahotra Sarkar has linked to a Newsday story that gives a slightly different account of events than John Rennie's blog castigating university presidents for not supporting the theory of evolution in public.

It seems that some, particularly the University of Texas at Austin president Larry Faulkner, a chemist, did indeed stand up and be counted. But the political issue is somewhat more complex.

American universities rely for their funding from political sources, such as states. This is something that we in Australia also deal with. But unlike Australia, and I am guessing universities in the UK and elsewhere, American universities can be subjected to political pressure to revise or restrict what is taught. There is, for example, that really stupid piece of legislation in Florida designed to "stamp out leftism" and force teachers to include any theory a student might like to see taught, in particular Intelligent Design. [If it gets up, I really hope a Holocaust denier uses it to sue for a change in curriculum.]

A university president is first and foremost a political beast under such constraints. They are there to see education given at the best level they can, and to see academic work done the best it can be, and this involves a fight for resources. While I am sure some presidents behave in a less than idealistic manner, to assert that it is policy that a university "believes" in evolution is to take at best a self-defeating stance in areas where the presumption is that education is something that can be squeezed for political purposes.

And on reflection, I am not sure that Rennie is right anyway. Suppose that a university did declare that it supports "evolutionary theory". Which kind? Does it support neo-Darwinian theory as revised by Richard Lewontin? John Maynard Smith? Ernst Mayr? Does that mean evo-devo is not to be taught? Shall we condemn ideal morphologists as schismatics and heretical? Science is all about changing ideas to suit evidence and experience, not asserting doctrinaire assent.

Universities ought to acclaim the right to teach the best ideas in a field, and that is all. If an idea is popular outside a university, but it has been closed off by scientific and scholarly research as a viable option, like phrenology, platygaeanism, or phlogiston, then it ought not to be taught. If that offends the agendas of religious or political figures, then they have the same rights to argue their case as anyone else. Who knows? Perhaps some of them will actually change the scholarly debates for the better. But they have no right to impose doctrine on scholarship, and neither do university presidents.

I'm going to come down all Millian liberal on this one.

Yet another missing link

New evidence supports the claim to being a hominid of the Toumai skull found in Chad, which gave its name to Sahelanthropus tchadensis. The find is regarded by some as having a "a puzzling combination of human and chimp traits".

Transitional forms between two modern groups are sometimes called "missing links", but this is a misnomer based on the pre-Darwinian idea that there should be an unbroken series of gradual changes over time from simple organism to modern organism. A "missing link" would be an unfound member of that series, which is like a morphing graphic with a missing frame.

But species, while they have a history from their ancestors, do not fill in all the possible intermediates. Speciation involves greater or lesser modification, and the sequence is not a simple consistent morph. It is thought that much modification in speciation occurs early on, and the species tends to remain stable for the remainder of its "lifespan". While the modification is gradual in one way (there will not be massive adaptive change in a single or few steps, and so from the point of view of a human observer, change would be extremely gradual. But evolution happens on geological, not sociological, time scales), in terms of what will be preserved, it will be episodic.

The type of "transitional form" here is of a species that probably evolved in its own way such that we think it is like both groups: apes and hominids. It is a twig between the two main branches. But they only became main branches after the fact. At the time, tchadensis was probably just another ape species, one of many, like the ancestor of modern hominids (i.e., us). Neither the African Great Apes nor Hominids were at that time a main branch.

A lot of the problem people have with conceptualizing evolution is that so much of what seems "significant" or "different" is assignable only after the fact. When evolution is happening, it is not aiming to deliver Apekind and Humankind. It just delivers apes that survive, or not, leaving greater or less record in the living and preserved organisms we have found.

When we are growing up and learning language, the words apply to "obviously different" groups. But from the perspective of the evolutionary tree, they are not so different, and other things we think are less different, like the many species of bats or ants that we naively group into a single "kind", are recognizable as massively diverse. Bats form 1100 or so species, out of the total of around 4000 species. 1 in 4 mammal species is a bat species. But most of the time, we are happy to say "It's a bat!"

Diversity is not a subjective fact about biology. It's real. So if we do biology, rather than teach third grade children the meanings of ordinary words like "bat" or "cat" (36 species, including 9 tiger species), then we need to pay attention. Evolution explains why the diversity is there. It also explains why it has the distribution over space and time it does. We find the transitionals we expect to find, like tchadensis. But we don't find "missing links". That's just journalistic hyperbole. Ignore the headlines and look at the information. It's much more interesting.

Editorial Activism

The editor of Scientific American, John Rennie, has attacked the unwillingness of US University Presidents to defend evolutionary theory in a rather blistering blog. Go read it. Of course, he's just an unrepresentative editor, unelected. I gather this makes a difference in the USA.

How is classification started?

Here's my problem. Classification, these days, in systematics is not founded upon morphological or functional similarity so much as on the residues of history. In philosophese, these groups are not made by equivalence classes or similarity relations, but by processes that we recover, as best we can, from the characters or traits of organisms living or dead.

But these characters or traits (there is a difference - characters are abstact representations of biological facts about organisms; traits are actual physical features of organisms - ah... but which ones?) have to be chosen. They get put into an "instance matrix" for processing by the various black boxes of systematics, but if you add homoplasious characters, or characters that have been arrived at independently by different pathways in evolution, you will get a false "signal" of the past. All this is discussed in the standard texts; I suggest Elliot Sober's Reconstructing the Past (MIT Press 1988) as a primer to the philosophical issues.

So, here's my problem: how are the characters, particularly at the molecular level as molecular-based phylogenies become the predominant mode of classification, arrived at? I once asked an ichthyologist of note how he chose the characters for this purpose (we were talking about morphological characters, but the point remains), and his reply was, "Well, I should damned well hope I knew my organisms by now!" (or words to that effect). And he should, and so should all systematists, but if we want to avoid the "Cynical Species" problem ("A species is whatever a competent systematist calls a species", see McOuat's paper for why this is not so cynical as it has been painted), we need to know how these characters/traits are selected.

In short, how are they classified, so that they can be compared to recover history? I am not asking how homoplasy is identified compared to homology - that's a fish of a different river - but how classification proceeds before systematics, that is, classification of taxa, begins.

I thought to find some comfort and information among the bioinformatics literature. But all I found was reference to classifying by function or structure. Most structural classification of molecules appears to be done on the primary sequence, that lineal series of bases or monomers. Functional classification relies, by contrast, on the secondary, tertiary and later structures, as the molecules fold, because the functional role of a molecule in a cell or organism depends on the attachment sites it has for other biomolecules, and that depends on the shapes the three dimensional (and, if it changes over time, four dimensional) molecules form.

But classifying molecules in terms of their structure gets us back to the older problem of classifying by morphology, only now it is the morphology of molecules, and the consequent problem of molecules being that way for reasons of simple form - it can't fold any other way no matter what its past history is. And classifying molecules in terms of their function is context-dependent - in one organism a molecule has one function because other molecules have the shapes and parts to play in the cycles of biology in that species; in another species, it may have a different function. It's a bit like teeth. History can be lost or confused if we classify by function.

More on this later. Joe Felsenstein just gave me some refs to chew over...

McOuat, Gordon. 2001. Cataloguing power: delineating 'competent naturalists' and the meaning of species in the British Museum. The British Journal for the History of Science 34:1-28.

Sober, Elliott. 1988. Reconstructing the past: parsimony, evolution, and inference. Cambridge, Mass.: MIT Press.

The real me

Some people have cast doubt that I truly do look like an albino silverback lowlands gorilla. They are right. My gravatar is actually the late Snowflake, of the Barcelona zoo. He was 40 years old when he died of skin cancer in September 2003, the equivalent of 80 human years old. He left many descendents.

But just so that you know what I truly look like, and I am slightly less hairy than Snowflake, I am taking a leaf out of Pharyngula's and De Rerum Natura's books, and using the Flash application they linked to to devise a self-portrait in South Park style.

Click here to see me in all my gory, I mean glory. It's just luck that the body type of South Park characters is pretty much mine...