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, December 15, 2005

Modes of speciation - organising the mess

So, I have started to consider how the various kinds of speciation relate to each other. The traditional approach is to conceive of speciation as something that happens in sympatry or in allopatry; that is, in the same locale or isolated locales respectively. A third form of speciation is named by Mayr peripatry, in which peripheral populations, almost but not quite detached from the main distribution of the species, evolve independently of the rest like an isolated population would.

Mayr showed allopatric speciation with a diagram that has become iconographic in evolutionary textbooks:

The sequence is to be read from top to bottom over time. The global range of the species, called a metapopulation, fragments as conditions change, perhaps due to geological processes like mountain building or river formation. One part becomes detached, or geographically isolated, it evolves in its own way, incidentally causing reproductive isolation (RI) to evolve. Note that RI is not itself the subject of selection, but happens as a side-effect of other change. This means that being a species formed through RI is not something "functional", but this can change when species that have formed allopatrically come back into contact.

Sympatric populations that are RI will tend to reinforce this isolation through lowered hybrid fitness, since several mechanisms will mean that hybrids actually are less-fit: sexual selection, adaptive traits, chromosomal structure. In the first case, preferential mating may mean that the new-comers find it harder to find willing mates. In the second, the newcomers may be adapted to some resource or condition, while the oldtimers are adapted to a different resource or condition. The hybrids will be neither - sorry - fish nor fowl, and so it will mean they are less viable. In the third case, inversions, translocations, fusions and fissions [see these lecture notes for details] make it harder for the chromosomes of the sex cells to pair up and continue development.

This led Mayr to define species, effectively, as gene pools protected against introgression (the influx of genes from other population):
... species are reproductive communities. The individuals of a species of animals recognize each other as potential mates and seek each other for the purpose of reproduction. A multitude of devices insure intraspecific reproduction in all organisms ... . The species is also an ecological unit that, regardless of the individuals composing it, interacts as a unit with other species with which it shares the environment. The species, finally, is a genetic unit consisting of a large, intercommunicating gene pool, whereas the individual is merely a temporary vessel holding a small portion of the contents of the gene pool for a short time (Mayr, 1963 p21)
RI itself became the focus of a lot of research, most recently summarised in Coyne and Orr's book Speciation. RI was divided into subcategories, versions of which found their way into the textbooks. The primary division was between prezygotic and postzygotic or between those mechanisms that prevented the fusion of the sex cells, and those which prevented the fused sex cell, the zygote, from developing through to further reproduction. The most complete list is this one:
A classification of Reproductive Isolating Mechanisms (RIMs)
From (Littlejohn 1969: 461)

Reduction of contact
(a) temporal
(b) ecological

Reduction of mating frequency
(c) ethological
(d) morphological


3. Reduction of zygote formation
(e) gametic and reproductive tract incompatibility


4. Reduction of hybrid survival
(f) hybrid inviability

5. Reduction of gene flow through hybrids
(g) hybrid ethological isolation
(h) hybrid sterility
(i) hybrid breakdown
Note that the barriers here are not absolute - the RIMs only produce a reduced frequency of successful breeding.

So, what is the debate? For years now, biologists working in the domain of speciation have argued whether speciation occurs in allopatry, or sympatry or some intermediate peripatry. Much of the debate has been about terms. For example, if the Rhagoletis fruitfly that has speciated by moving from one host (Hawthorns) to another (Apples) is not in sympatry, then nothing is, but it is claimed that the host species is a kind of allopatry. And so on. It's a messy debate, needing some conceptual clarity.

Enter Gavrilets. In the Introduction to his 2004 book Fitness Landscapes and the Origin of Species, he defines these different modes of speciation in ways that - finally - make sense, relating them to each other. In my next post, I will list these and then try to organise them into a "conceptual space".


Mayr, Ernst. 1963. Animal species and evolution. Cambridge MA: The Belknap Press of Harvard University Press.

Littlejohn, Murray J. 1969. The systematic significance of isolating mechanisms. In Reflections on systematic biology; Proceedings of an international conference, University of Michigan, June 14–16, 1967. Washington, DC: National Academy of Sciences.

Wednesday, December 14, 2005

The narwhale's tusk

Why would a whale have an 8 foot long tooth growing out of it's head? Answer: to sense salinity. More here.

More on chromosomal rearrangements

RPM, at evolgen, has more links and interesting comments on the rearrangements of chromosomes in various organisms, to follow up my King Kong post.

Tuesday, December 13, 2005

Who bashed Mirecki?

I have been thinking some more about the confiscation of Mirecki's computer by the Lawrence police. This is very suspicious. Apart from the possibility that he is being, in Australian and British parlance, "fitted up" (I wonder if kiddy porn will surface on his computer and be "leaked" by the police?), it suggests that the motives of the police here are far from pure. And this leads to a speculation...

Now I'm not usually a fan of conspiracy theories, but if anything generates them, it's religious conflict (vide the Gunpowder Plot against James I). The religious right-wing have been happily dancing around doing a Swift Boat attack on Mirecki in various blogs and no doubt media outlets. They suggest that Mirecki faked it, or got caught in some other dispute and blamed it on the fundamentalist backlash.

I'm going to hypothesise here. It's just musing, hypothetically, you know? But suppose the evidence, that is, Mirecki's testimony, is correct. Who might the police be protecting this way? It couldn't have been ... themselves, could it? A couple of off-duty cops couldn't have followed Mirecki or known his license plate, and decided to teach that atheist sumbitch a lesson, could they?

Is this likely? Well to decide this, we need to do a Bayesian analysis, and it will depend on what we know about Kansas police. And as I know nothing (which seems to be rather more than the ideologues who are claiming he faked it know) about them, all I can do is generalise from my knowledge of police generally when they are in a monocultural society. Yes, they could have done this. Yes, there is past history of such things.

Is it likely Mirecki faked his assault given that (i) he is a respected academic, and (ii) the behaviour of the police subsequently? I say it is unlikely. Equally likely or more so is that he was assaulted by cops. Or by friends of cops. Much more likely still is that the cops share the opinions of whoever beat Mirecki up, and so would love for there to be a reason to dismiss his testimony.

We'll see. But this exposes one thing about such cases - no matter what the evidence, if you really want to, you can make any kind of case you like. Or, you can just take the evidence as it comes and draw the obvious conclusions.

The Kong Love Interest

The New York Times has a piece by Clive Wynne on a possible inspiration for the King Kong love interest - the attempt by a Soviet biologist to "prove evolution" by cross breeding humans with chimps in the 1920s.
The young Soviet Union, in its effort to stamp out religion, was determined to prove that men were descended from apes. In 1926, a Soviet scientist named Ilya Ivanov decided the most compelling way to do this would be to breed a humanzee: a human-chimpanzee hybrid.

Ivanov set off for a French research station in West Africa. There he inseminated three female chimpanzees with human sperm. Not his own, for he shared the colonial-era belief that the local people were more closely related to apes than he was. He stayed long enough to learn that his experiment had failed.

Next Ivanov wrote a Cuban heiress, Rosalia Abreu. Abreu was the first person to breed chimps in captivity and had a large menagerie outside Havana. Ivanov asked if any of her male chimpanzees might be available to inseminate a Russian volunteer known to posterity only as 'G."

Now why anyone would think that cross-breeding humans and chimps would prove evolution is beyond me. Buffon, back in the 1780s had tried cross-breeding species to show that the concept species was arbitrary, and that a limited form of common descent united all cats, as it did all cattle, sheep and goats, and various fowl. Buffon was prior to evolutionary ideas, with one exception of no influence (Pierre Maupertuis). He wasn't trying to show that evolution happened, but that local climates and soils affected species more widely than had previously been considered (he also hated and opposed Linnaean ideas, especially the taxonomic ranks).

Hybridisation has always been known. Aristotle discusses it in the History of animals, Book VIII, chapter 28 (605b22-607a7). Aristotle considers what will produce variety in animal life - the main cause is locality, including climate. In Africa ("Libya"), "animals of diverse species meet, on account of the rainless climate, at watering-places, and there pair together; and such pairs will breed if they be nearly of the same size and have periods of gestation of the same length". He goes on to say, "Elsewhere also offspring are born to heterogeneous pairs; thus in Cyrene the wolf and the bitch will couple and breed; and the Laconian hound is a cross between the fox and the dog." He then reports that "they" say that the Indian dog is a bitch-tiger third
generation hybrid.

Linnaeus famously found hybridisation in the genus Peloria, forcing him to revise his species fixism somewhat. This was widely known in the early 19thC - and yet nobody thought that it was "proof" of the recent evolutionary views of Lamarck. If anything, it would have been proof of Buffon's views, before Lamarck. At the end of the 19thC, Flaubert could write, satirically, of two muddle headed amateurs seeking to breed and eat anything they could:
They opened Buffon again and went into ecstasies at the peculiar tastes of certain animals.
They wanted to try some abnormal mating.
They made fresh attempts with hens and a duck, a mastiff and a sow, in the hope that monsters would result, but quite failing to understand anything about the question of species. This is the word that designates a group of individuals whose descendants reproduce, but animals classified as different species may reproduce, and others, included in the same species, have lost the ability to do so.
[Flaubert 1976, 87]
So why would Ilya Ivanov think this would prove evolution (and even worse, disprove God)? It has to do with the nature of Marxist dialectic. Marx was, like Darwin, a philosopher of change, but the basis for change he used wasn't the undirected and tree-like change of evolution; rather it was the progressive and linear change taken by Hegel from Christian providentialism. For Marx and his followers, there was a necessary sequence that had to be followed by historical necessity. For Darwin, there simply wasn't. But in Stalin's Russia, biology was subordinate to political theory, and so evolution had to occur in the same manner as the predicted (and already falsified even then!) evolution of human society.

So hybridising a chimp and human would show that the dialectic of history had formed humans from prior apes. And this view of history, in which apes like chimps are less evolved than humans, is linear, progressive and much more like Lamarck's view of evolution than Darwin's, in which humans and chimps represent independent branches of the evolutionary tree, and in which neither is more evolved than the other except with respect to some particular traits.

Whether Wynne is correct that this inspired King Kong (one of my favourite childhood movies, just like Peter Jackson) or not is irrelevant (although I think it's a long bow). But in no way did Ivanov's experiment test evolution as we know it. Instead, it was perhaps another test of a failed theory, of the dialectic of history.

[That said, there's a lot in Marx of value. But not, it seems to me, for biology.]

Flaubert, G. (1976). Bouvard and Pécuchet, with the Dictionary of Received Ideas. Harmondsworth, Penguin.

Extinction, conservation, and the vertebrate bias

A new paper in PNAS [Note: it's not up as yet] suggests that we can stave off extinction of 794 endangered species by safeguarding 594 epicentres of extinction around the world. The Alliance for Zero Extinction believes that by protecting these regions we can prevent anthropogenic (that is, human-caused) extinction from progressing any further.

While I think it is a useful thing to identify these furry and feathered vertebrates under threat, it is yet another example of the vertebrate bias in much modern biology. What about all the plants that will die if their habitats are destroyed? What about the fungi, the algae, the bacteria? Life is more than big, mobile, things that have some sort of thermal protection. Ecosystems rely on all these things.

It might be argued that vertebrate species are surrogates for biodiversity in the round, but this cannot be right. The animals might persist for a while by migrating long after the viable populations of trees or nitrogen-fixing nodes in the soil are endangered in a region, and might go extinct well after their "infrastructure" has become unsupportable.

I have similar problems with the use of "genetic diversity" as a measure, in for example, the WORLDMAP project. What is it about genes that matters? Clearly it is the ability of those genes to contribute to the ecological behaviour of systems via whole organisms. Otherwise we might just as well say we should keep a genetic sample on dry ice as a way to "save" biodiversity. But nobody would suggest something that silly, would they? I mean, genes are just part of a developmental machinery, without which they'll just sit there and slowly decompose. To utilise genes properly, you need, you guessed, the organism. And to utilise the organism you have to have the ecosystem that supports it. So this is no solution either.

I wish I understood what was the solution - there is something that we measure in biodiversity measures, no matter whether it's species or population sizes or genetic diversity. But whether these things are surrogates for the "vitality" of the ecosystem, or are important in themselves, is something we need to work out. Species of things with backbones merely represents our own biases, not the biases of Nature. If we try to save things because they are obvious to us, then we may fail rather badly...

Sunday, December 11, 2005

Mirecki's V-C had a history of folding

The Vice-Chancellor of Kansas University, Paul Hemenway, had a history of folding to religious pressure, reports Bartholomew's notes of religion. A previous freethinker was fired after 21 years for objecting to the Medical Center supporting religious and faith-healing "treatments". Things look very suspect at Kansas.

I'm going to go out on a limb here, in a Bayesian sort of way: No matter how unlikely Mirecki's assault may seem, it is far less incredible than the documented anti-skeptical attitudes of KU and the locals.