Evolving Thoughts

Evolution, culture, philosophy and chocolate! John Wilkins' continuing struggle to come to terms with impermanence... "Humanus sum, nihil humanum a me alienum puto" - Terence

Thursday, September 08, 2005

Crossing the line - HGT and [Paul] Nelson

For some time now, there has been an increasing awareness that evolution is not always tree-like in structure. Lyn Margulis and her collaborators identified cases of endosymbiosis, where one life form was captured by another and integrated into the cell. Our organelles are examples. Mitochondria were once free living organisms. Same with chloroplasts in plants, which photosynthesise light. Moreover, retroviruses can copy parts of the DNA of one organisms and then infect the sex cells of another, entirely distinct species. As much as 45% of mammalian genomes are the end result of such "horizontal transfer", including ours, and who knows how much of this ends up providing useful genetic material for the new host?

And hybridisation of sexual species has been known since Aristotle - it is a common source of new species, and looks, in the genetic "fossil record" just like crossover. Genes can also "introgress" from one species into another, a process that's common also in plants.

So lateral transfer is not exactly something "paradigm breaking" in evolutionary biology. In fact, it is one of the oldest of all known ways in which novel hereditary material is added to an evolving lineage. But it does tend to undercut the "textbook" view of evolution, which gets taught to undergraduates, that evolution is a branching tree. It is only nearly always a branching tree. There is resistance to the idea, though, and so advocacy of this is sometimes thought to be an indicator of crackpottery amongst biologists (rarely amongst those who study it, though). The leading names here are Carl Woese, Ford Doolittle, and their collaborators.

One person who has advocated this since the mid 1980s is Mike Syvanen, a professor of molecular genetics at UC, Davis. So, since we evilutionists are often accused of not "teaching the controversy" with respect to ID and creationism, I suggested that it might be a good idea for him to discuss an actual controversy in evolution - this one - in a guest article at the Panda's Thumb blog. This he did. All that there was left was to wait for the IDevotees to quote mine and spin it. And so they did.

Most concerning was not that this happened - in the blog discussion list it was predicted that it would. The worry is that this was done by one of the few IDevotees who I had some respect for, Paul Nelson. Paul s a graduate of Chicago's excellent history and philosophy of science program, and, if memory serves, his advisor was Bill Wimsatt, one of the most influential, if underpublished, philosophers of biology out there.

Paul has a history of being a nice guy - in email he is polite and respectful, unlike the less pleasant Wells and Dembski, whose idea of debate is to make dismissive insults. But this piece is abysmal. It is simple misdirection, and knowing what Nelson knows, it can only be put down to a deliberate attempt to lie.

It's in the context of another article by Mooney and Nisbett in the Coumbia Journalism Review, on how journalism ought not take a "fair and balanced" view when one side is incompetent or wrong, in debating evolution. Nelson tries to make the existence of a tangled root and occasional vine in the evolutionary tree reason to think there is no tree. He cites, misleadingly and quoteminingly, the Syvanen article. It's pure deception, and nicely dissected on the evolutionblog.

Meanwhile, Carl Zimmer's Loom trumpets lateral evolution as interesting science (with a fascinating picture). Oh what a tangled web we weave, Paul...

Tuesday, September 06, 2005

The origins of species... errr... concepts

So, after about 8 years of work and study, I finally completed my book, whimsically entitled The origins of species concepts: the history and philosophy of a living idea last night. Well, that's the title until the more sensible and less punnish publishers get hold of it. They probably won't like my suggestion of using the duck rabbit in a thought bubble on the cover either. Bastards.

In this book I argue a few rather contrary-to-received-wisdom views. One is that there never was essentialism about biological species before Darwin - it's a later development. Of course, people had essentialistic views of diagnoses or definitions of particular species - this was part of taxonomic practice following Linnaeus. But nobody thought species had actual material essences until around 1880, and nobody I can find used that as an argument that species were immutable until after that, early in the 20thC. There's an interesting story there, too, about (I think) the influence of Catholic philosophy in reaction to Haeckel's atheism. That's for later.

Another is that nobody thought what we now call "species" were freely mutable prior to Linnaeus. They all seemed to implicitly and occasionally explicitly deny that species changed their mode of generation much, if at all (hybrids excepted). Of course, they use the word species, but it seems to have no more meaning that an English speaker using the word sort.

A third claim is that the default, widely accepted with few exceptions, notion of living kinds, was something like "the generation of like or similar forms of living beings". I find this in Aristotle, Epicurus, and all through the modern era right up to the present day, although there is a strong move away from "form" as a definiens after Mendelian genetics was rediscovered.

Philosophically, I am reiterating my claim that species just means any lineage that is maintained over time as separate from other lineages but differences in shared properties. I call this the Synapomorphic Species Concept. A sexual species is a mode of being a species. So is an asexual species, an ecological species, and so on. These modes evolved, just like having four limbs or feathers.

I distinguish between three kinds of "individuals" that species might be - ontological particulars, historical cohesive systems, and phenomenally distinct objects.

What else? I have a slew of claims and treatments of existing concepts (which are better called conceptions - species is the concept, that a species is a protected gene pool, for example, is a conception of species), but my major claim is that scientists are entitled to use as many concept[ion]s as they need to do accommodate the (biological) ways in which lineages are held apart. This is a limited pluralism, or as I call it in my paper already published, a "chaste" rather than a promiscuous pluralism.

Much fun will be had by all, I am sure. I still need the publishers to accept it for publication, but as this is a revision (and roughly doubling) of a previously reviewed manuscript, I am very hopeful.

Now on to other papers. I've been a historian long enough. Some philosophy!

Sunday, September 04, 2005

ID in Australian Schools?

Well, it looks like Intelligent Design is finding its way into at least religious schools. And worse, it is getting a conditional approval from (who else?) Cardinal George Pell, who has previously attacked "Darwinism" in print a few years back. Pell at least has the good sense to admit that ID was not established science, although the way he put it was that he was "agnostic" about ID as a school subject. But nevertheless it's finding its way into Catholic school texts.

But Paul Davies, who has used the word "God" in titles and articles to indicate the nature of the universe (thereby giving all kinds of aid and comfort to the new age nitwits) didn't avail himself of that temptation this time. "God has never been a part of science" he said. That's correct. And ID is, despite occasional denials, all about God.

I quite like the Australian National Science Teachers' Association formulation, though:
While Intelligent Design has no status as a scientific theory, teachers of science may wish to contrast it to other belief systems with scientific theories like evolution, as a means of assisting students to understand better the nature of science.
Although... there are only so many ways you can say "this is also not science" before you have to wonder if you hadn't better get going actually teaching it.

We ought not to panic. ID is a very marginal movement here in Australia, pushed by the religious for political reasons. It's very worrying that idiots like Brendan Nelson, who continues to deflect attention on his handling of Australian tertiary education by appearing on TV to denigrate State-based primary and secondary education, over which he has no control at all, give their unqualified approval of ID (I finally got to see what he said at the National Press Club a few weeks back. There was no hedging.). But teachers, curriculum developers, and those who really do control the content of science teaching, aren't calling for it.

If it is to become a problem, expect to see political-religious interference in the makeup of those curriculum advisory boards at the State level. Fortunately the less-religiously inclined Labor Party is in power in those states (although I can think of a lot of other reasons why that isn't such an unmitigated good, either) and is unlikely to be corrupted in that particular manner. But if the Liberals keep going the way they are going, as a Liberal MP said it was this week, when they finally get in power, it might happen. One can only hope that the Australian public sees this as a malign thing, and that eventually the Liberals learn this is not an electable way to go.