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, March 23, 2006

Welcome to Daily Kos readers

Hi ya'll. Thanks for reading the interview on Daily Kos. Darksyde said you'd be dropping by. To give you a hint of this blog, apart from the puns and cartoons, here's a list of some of the more substantial posts from the last six months:

Species and Speciation

A series of posts on the ideas of Sergey Gavrilets
Enjoy, and do look around. Comments welcomed, so long as you don't try to convert me to a religion or sell something.

Update on Hayes and that show

FOXNews.com - not the most reliable source - is denying that Isaac Hayes ever quit South Park, but someone else did it for him. Apparently Hayes is presently recovering from a stroke, and did and said nothing about the show.


Botany gets a "C" for species

Nature has a paper in this week about the nature of plant species. It's an interesting claim - according to Loren Reiseberg, Troy Wood and Eric Baack at Indianan University, around 70% of the species identified through traditional taxonomy are, in fact, reproductively isolated lineages, somewhat better than animal species, at around 40%. So much for the vertebrate bias... (although of course animal species also include annelids, arthropods, and molluscs, to mention only a few). Does this mean botanists get a "C", while zoologists get an "F"? Here's the abstract:
Many botanists doubt the existence of plant species, viewing them as arbitrary constructs of the human mind, as opposed to discrete, objective entities that represent reproductively independent lineages or 'units of evolution'. However, the discreteness of plant species and their correspondence with reproductive communities have not been tested quantitatively, allowing zoologists to argue that botanists have been overly influenced by a few 'botanical horror stories', such as dandelions, blackberries and oaks. Here we analyse phenetic and/or crossing relationships in over 400 genera of plants and animals. We show that although discrete phenotypic clusters exist in most genera (> 80%), the correspondence of taxonomic species to these clusters is poor (< 60%) and no different between plants and animals. Lack of congruence is caused by polyploidy, asexual reproduction and over-differentiation by taxonomists, but not by contemporary hybridization. Nonetheless, crossability data indicate that 70% of taxonomic species and 75% of phenotypic clusters in plants correspond to reproductively independent lineages (as measured by postmating isolation), and thus represent biologically real entities. Contrary to conventional wisdom, plant species are more likely than animal species to represent reproductively independent lineages.
One reason why this is an interesting result is that there is what I call a species denialism trend of recent years, which argue that species are merely arbitrary constructs, and should be replaced by terms like "evolutionarily significant group" or "least inclusive taxonomic unit" or "smallest monophyletic taxon", and so forth. Yet it seems there is something there that answers to "species".

My feeling is this: taxonomists have more than a set of definitions and protocols to go by. When they observe phenetic* clusterings in the world, they do so on the basis of a broad range of background knowledge about that general class of organisms. Nobody just picks up a barnacle and says, "hey! this is a species!" unless they already know a hell of a lot about barnacles and biology in general.

There is a formal class of classifier systems in computing known as neural nets (NNs). These are based roughly on the structure of the human cortex, and one of the interesting things about NNs is that they can train on a set of exemplary data, and then make classifications on that basis. Humans are much more complex and adaptable, and for that matter trainable, than NNs in a computer. Consequently, when a suitably informed taxonomist says something is a species, it is very likely she was trained on all the other species in that group known so far, and has a complex classifier system in place. It is no surprise, therefore, that she can identify, using fairly sparse hints, a naturally reproductively independent group.

Even back in the medieval herbals and encyclopedias, species that were identified turn out to mostly be natural (see Stannard's works cited below). In many cases humans can be remarkably accurate at identifying real things with training (which is, I think, the explanation of the oft-cited agreement between Ernst Mayr and the Foré Mountains peoples who both distingusihed the same species of birds, with one exception).

So, why the failure among animals? What's wrong with zoologists? I can't say for sure, but I warrant that it is the nature of the identifying marks or characters used to distinguish them under classical zoology. Most species names and character descriptions date from before phenetic, let alone phylogenetic, classification techniques. Consequently there may be a bias to split when the discriminators are close to the sorts of discriminators that work well in human and mammalian, or even ornithological, cases, and a tendency to lump when you are dealign with velvet worms or mites. Anyone else have any ideas?

Stannard, Jerry (1968), "Medieval reception of classical plant names", in, Actes du XIIe Congrès International d'Histoire des Sciences, 21-31 Août 1968, Paris, Paris.
——— (1979), "Identification of the Plants described by Albertus Magnus' De vegetabilibus lib. VI", Res Publica Litterarum 2:281-318.
——— (1980), "The botany of St. Albert the Great", in Gerbert Meyer and Albert Zimmerman (eds.), Albertus Magnus, Doctor Universalis, Mainz: Matthiàs Grünewald Verlag, 345-372.
——— (1999), Pristina medicamenta: ancient and medieval medical botany. Aldershot: Ashgate.
Stannard, Jerry, Richard Kay, and Katherine E. Stannard (1999), Herbs and herbalism in the Middle Ages and Renaissance. Aldershot ; Brookfield, Vt., USA: Ashgate Variorum.

Hat tip to Nick Matzke for both bringing the paper to my attention and suggesting the post title.

* Phenetic: meaning that the group is defined by a mathematical clustering technique in a Cartesian graph of some chosen variables. Also called numerical taxonomy.

Wednesday, March 22, 2006

Essentialism revisited

In my long-delayed book on the species concept, I find myself concurring with historians like Polly Winsor and Ron Amundson that there never was an "essentialist" view of species before Darwin. In fact it is my opinion that essentialism in biology postdates Darwin, and was in fact due to the revival of Thomism among German and French speaking Catholic biologists who were reacting to the metaphysical views of people like Herbert Spencer and Ernst Haeckel. Thomism, or neo-scholasticism as it was called at the time, relied upon the doctrines of Aristotle as interpreted by Thomas Aquinas, particularly in his text
De ente et essentia (On being and essence). As such the essence of a thing was that which was necessary to be that sort of thing. So species had, said these revisionists, an essence that could not change, and so they denied evolution. This was not a majority view even among Catholic scholars, but it is the first appearance of essentialism as a justification for species fixism I can find.

So why did the story arise that prior to Darwin everyone was an essentialist? There are two reasons - one a matter of history, the other a matter of, well, the uses of history by biologists. Ernst Mayr, the main architect of this essentialist myth, studied in Germany as an undergraduate in the early 1920s, under an ornithologist named Erwin Streseman. This was the high water mark of Thomist inspired essentialism and anti-evolutionism, although I have a book dated 1955 by a Jesuit arguing this line. It's my opinion that Mayr overgeneralised his undergraduate experience, and then read the prior literature through those spectacles.

The second reason is that biologists often use history in a triumphalist manner, to indicate that they or their school is the apex of thinking on a topic. In this case, Darwin acts as the John Baptist of biology, and before him, all was in darkness. The apex is, of course Ernst Mayr (he's rather shameless about declaring this).

But were there essentialists before Darwin? Why does this myth seem to hold up? The reason is that history-plundering evolutionists misread the literature. There most certainly was a diagnostic essentialism before Darwin - if you specify a set of identification key characters, then that is a kind of essence. It's just not a substantive one. Even Darwin himself contributed to that, although it derives basically from the way Linnaeus set up the "definitions" of species in Systema Naturae and other works. Darwin was a member of the so called Strickland Committee, which determined how classification was to be done in 1842, and from which modern taxonomic codes derive. It's a very harmless kind of essentialism, based on practice rather than scientific ontology. And every systematist who had a number of specimens had to deal with the increasing problem of variation, code or no code.

The reason why I mention this is that there have been a number of interesting blogs lately on the matter, based on what psychologists like Susan Gelman call "essentialism". This is a matter of cognitive behaviour - we tend to select a single criterion or property as the way to identify kinds, and deal with the variation later, as the early nineteenth century systematists did.

The first blog is from Mixing Metaphors, on a paper by Andrew Shtulman on the differences between naive and informed views of evolution. The conclusion is (rightly) that our predilections to average across variation to generate a "type" inhibits our ability to understand class concepts like species and their evolution.

Sirus takes this up and develops what he calls Minimum Classificatory Essentialism. In the first of four blogs, he starts by discussing the difference between type essentialism and shared-nature essentialism. It is the latter that Mayr targeted, incidentally, but it is the former that was actually employed by pre- and post-Darwinian biologists. In the second, he discusses the nature of creationist kinds attacked by Darwin. I actually think Darwin chose this target to make the line of argument easier - the competing Platonist morphology of Owen and Oken was a harder target to identify, let alone attack. In blog three, Sirus discusses whether Darwin was an essentialist, and notes a confusion between type and essence in Mayr.

I'd like to comment on this for a minute. A "type" can be a number of things. It can be a definition. It can be a generalised description. or it can be an exemplar. Mayr often attacked cladism as being "typological" (I don't have my notes to hand, but I think this was a term introduced by George Gaylord Simpson, and adapted by Mayr). It is - it uses a single instance as a type for the species. So what? The likelihood is that if you select enough characters, the specimen/s used will cover the consensus characters of the species (or taxon), so individual idiosyncracies will average out. Types are pretty harmless. If you use types as exemplars, then you might be led to make poor inferences, I guess, but there are all kinds of safeguards used by biologists, and they have been with a few failures all the way back to Linnaeus. Most of the time type specimens were pretty representative of the taxon, even if sexual morphs got mistaken once in a while for different species or, like (my favourite case) the seal Arctocephalus pusillus, so named because the type specimen was small, turn out to be a juvenile.

Types do not need to, and did not have as far back as they were used, essences. Everybody was aware of deviation from the type. Locke even has a discussion in the Essay for heaven's sake, and when philosophers know this, it isn't secret specialist knowledge. The book by Peter F. Stevens, The development of biological systematics: Antoine-Laurent de Jussieu, nature, and the natural system (New York: Columbia University Press 1994) discusses how types were not fixed or essentialistic in some detail.

Enough. Back to Sirus' discussion. He mistakenly claims that Darwin was a "type" essentialist. He was not. But he was a typologist, as were and are all biologists, even those who study variation (or else how do you know you are studying variation in the same taxon?).

The remainder of the series, blog four, discusses how Shtulman investigated attitudes of people to evolution based on (psychological) essentialism, and it is a worthy study. I'll let you go read it for yourself. Sirus graciously links to my presentation on the history of essentialism. I only add self-servingly that you can listen to my talk as well.

How to conclude? I believe that essentialism is not the boogieman it is claimed to be. It is even philosophically respectable to say that species have essences in Aristotle's sense of the what-it-is-to-be that the Latins gave the translation of "essentia" to. Of course they do (although I think it is more likely to be the nature of the species as a whole rather than a shared essence in each organism). And this doesn't thereby make species intensional classes of the kind that cannot evolve. Individuals have essences too (contra Aristotle) - I am whatever it is that makes me who I am. So are species. And like them I can change...

The fat lady sang, already

In one of my favourite films, Donnie Darko, there is a scene where a teacher loses her job for teaching poetry that is ever so slightly subversive. Now comes a story where a teacher in Bennett, Colorado, has lost her job, wait for it, for showing an opera to her students. The teacher, who is herself an opera singer, showed a clip from the school library of Charles Gounod's Faust. She showed a 12 minute segment featuring Dame Joan Sutherland, Australia's major contribution to opera (until Caitlin Hulcup gets better known, that is*) to her elementary school students in preparation for them performing it.

Like the wonderful Drew Barrymore in Donnie Darko, Tresa Waggoner was accused of promoting non-Christian ideas, and of being in league with the devil, rather like Faust himself. The mayor of Bennett had the grace to resign over the incident, declaring that the town had a "mean streak".

The legend of Faust has an interesting history. Although probably a historical figure who ran afoul of the Lutherans for practising alchemy, his story has earlier precursors, some going back to the middle ages. He is also very like John Dee, the Queen's Alchemist, who was also a noted mathematician and member of the Cambridge Platonists from which sprang Locke, and the Royal Society.

Very often, in the early days of science, people accused them of being Satanists because they used techniques that were tainted, such as alchemical methods, and because they thought (before Newton) that mathematics and astrology were the same thing, pretty much. Accusations of heresy were commonplace. It is such a pity that we haven't progressed beyond this. At least she didn't suffer the fate of Giordano Bruno, who died for being both a scientist of sorts, and heterodoxy, by being burned at the stake at about the same time as the Faust legend was getting going in popular mythology. But this whole story fully drips with irony.**

* Declaration of interest - Caitlin is a friend, even if she does think qualia are real. So's her husband Malte Ebach, even if he thinks Goethe, who coincidentally wrote Faust: Eine Tragödie in 1808-1831, was a scientist.

** Note to Americans: Irony is not an isotope of iron.

[Late note: Matt Young tells me it's Gounod's Faust not Berlioz's, and that, as an American he knows what irony is and also thinks Goethe was a scientist. So do I but I'm ragging on Malte. Also picked up a typo with the town name. Picky audience, hey?]

Choosing a career in biology

The Daily Transcript has a description of various subdisciplines in biology that may help those considering a career in one of them. Help them running screaming in the other direction, that is...

Tuesday, March 21, 2006

Making ball lightning

When I was a kid, I used to go lie in the rain on the roof and watch the lightning. Hey, it was better than fireworks, free, and delivered to your door. What can I say?

One night I saw the most amazing thing - I was about 11 or 12. A glowing ball of light about 50 feet up (this was before they allowed meters into Australia) which was about half a meter across (OK, I give in) moved slowly through the air, silently, and leaving a trail behind it that faded rapidly. "Cool!" I thought, and wondered if I could essay this as a UFO experience to my friends. UFOs were so the rage back then...

It was, of course, ball lightning, although at that time physicists denied such a thing could exist. Now they don't, but it's a hard thing to explain. Which is why this research is so interesting.

A team at Tel Aviv have created ball lightning in the lab.
Eli Jerby and Vladimir Dikhtyar from the University of Tel Aviv in Israel created a laboratory version of ball lightning using a "microwave drill." The device consists of a 600-watt magnetron taken from a domestic microwave oven and uses a powerful microwave beam to bore through solid objects.

The researchers aimed the beam through a pointed rod and into a solid object made from glass, silicon and other materials.

The energy from the drill created a molten hot spot in the solid object; when the drill was pulled away, it dragged some of the superheated material along with it, creating a fire column [video] that then collapsed into a bright fireball that floated and bounced [video] across the ceiling of the metal enclosure.

"The fireball [looked] like a hot jellyfish, quivering and buoyant in the air," Jerby said.

The glowing object measured just slightly over an inch across and lasted only about 10 milliseconds. The work was detailed earlier this month in the journal Physical Review Letters.

It's pretty cool, but not a spot on my ball lightning. Still, interesting stuff going on with this lightning research, what with "sprites" and "elves" and "jets" and wotnot. It seems there's more to it than Ben Franklin knew...

Monday, March 20, 2006

Lagrange Points explained

Normally I'd leave this sort of thing to my friend Ian Musgrave at Astroblog to explain, but it's cool, so there. NASA explains Lagrange Points for the WMAP Observatory in an accessible and cool way. I particularly like the "contour" diagram of forces acting on a body in the system. L1, L2 and L3 are effectively unstable because they are at the "top" of the gravitational potentials, like marbles on top of saddles, while L4 and L5 are at the "bottom" of the gravitational potentials, and if they deviate from that point, they will end up in an orbit around those points rather than moving away.

This probably explains the behaviours of Near Earth Objects like 3753 Cruithne which has a "kidney bean" shaped orbit that is affected by earth's as well as the sun's gravitational pull. But that sort of math hurts my head.

The WMAP Observatory has hit the news lately with a more detailed background radiation map of the sky, indicating some interesting things about the Big Bang. One is that it supports the simpler inflation theories. Another is that there appears to be some bias in the polarisation of the radiation, which is odd. We would expect that it would be randomly polarised. I haven't heard of any interpretations of this yet, but expect some ID misconstrual (along the lines of the Designer is actually very neat).

Over to Ian...