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

Saturday, June 03, 2006

Evolution and irony in the yard

A funny story on a site called Community Press about one woman's struggle against dandelions in the yard makes a nice followup to my piece on lawns a while back. In case the link changes, I will give the story here (and here is the direct link):
Tales from the imperfect rural wife: Chuck had it all wrong in the survival game

by Paula Cassidy

I had just chopped off their heads, but by the next morning, this lawn full of infiltrators resurrected to full attention, awaiting the next bloody battle, standing there semi-headless, taunting me with their “Darwinian survival of the fittest chant.” Chemical warfare crossed my mind, but my heart leans ever so tenderly to the possibility of a happy, healthy planet and Kyoto Protocol and such—unlike our glorious western leaders who live in some confused environmental denial bubble. The low tech war was on. May the most stubborn species win.
History tells of a carpenter that forever changed our lives. Although golf courses and manicured suburban homeowners may deem him the messiah, this carpenter didn’t wander the lands guiding the spiritual walk of the multitudes. Edwin Beard Budding invented the first lawn mower. His 1830’s patent even touts that country gentlemen would not only be amused by his invention, but would also reap the rewards of a little healthy exercise. Country gentlemen. Right then. To the present, where women rule the powerful motorized riding lawn mower, no longer sitting pretty on the sidelines, sipping lemonade in tight corsets and poofy dresses. Vanity mirror? Forget about it. Who wears lipstick to battle?

I roll my engineless reel mower about thirteen times over the same dandelion stem. The mower was a Mother’s Day gift, but before a mob of sympathetic mothers disperse to lynch my husband, it should be noted that it was a gift I had requested; hindsight brought on by frustration, finds me pining for the sapphire ring or a new toaster. No fuel. No noise. No environmental impact. Great cardio workout. The concept was great on paper, but the reality stood before me, relentlessly clinging to life and limb on acres of grass. I roll over the dandelion one more time, and one more time it bends, side stepping its fate. Stubbornness is something we both had in common. It refused death and I refused the effort to bend over and pull it out. Stalemate.

And without warning, like a trumpet sounding in the high afternoon, I hear the call of the machine—the lure of the green John Deere, parked alone and abandoned in the barn, inside the mechanical perimeters of my husband’s fleet of un-environmentally friendly toys and gadgets. Now the dilemma. Stick to my ecological and heart healthy guns, or cave like a hypocritical jellyfish so I can kill me some dandelions real fast-like, and get on with my day. What’s a girl to do?

“You want to use the riding mower, don’t you? Taking too long, eh?” Ah, thank goodness for sarcastic husbands, because without them, how would we women justify our intrinsic stubbornness. Farewell green champion, may you sit idly in the barn, for destiny calls me to the front yard. My clipping shears in hand, I head into battle, the last samurai, facing each adversary one-on-one, with the mutual respect of a true warrior. Snip. Snip. Snip. Our man Charles Darwin got it all wrong, because he failed to consider the female fight for equality. Fittest? No way. Survival of the “stubborn-est” is the best insurance for species predominance.
The irony comes from the fact that Chuck did actually consider female choice in evolution, in a rather different context, but more from the fact that dandelions have no sex. They are clonal organisms that reproduce from parts if disturbed. Slash them as much as you like, they will keep coming back. Survival of the most stubborn indeed.

Moreover I sometimes suspect that the reason why humans have culture is because they have mothers who insist that there is only one right way to do things (even when you are in your 50s), acting as a cultural brake against change. Think of mothers as a kind of memetic repair mechanism...

Friday, June 02, 2006

The Synthesis and historiography

In an execrable display of taste, Rob Skipper at hpb etc. has linked to this blog, and discussed the Michael Ghiselin quote I put up a few days ago. He rightly notes the standard story is a bit harsh, and suggests some extra reading (to which I would add the series of papers from a special issue of Journal of the History of Biology last year, in particular Jon Hodge's article).

I would like to add, though, that the Synthesists themselves were pretty good at mythmaking when it came to history. In particular, but not restricted to, Ernst Mayr's history of biology. Although this may sound harsh, Mayr has referred to his “precursors” as “prophetic spirits” (Mayr 1996: 269), noting “how tantalizingly close to a biological species concept some of the earlier authors had come” (Mayr 1982: 271), and claimed that “Buffon understood the gist of it” and the early Darwin also (Mayr 1997: 130), thus claiming authoritative precursors. Mayr spends considerable ink defending himself from the charge of reinterpreting history in a whiggist manner in chapter 1 of his 1982 (pp11-13) and yet he is still perhaps the best example of this kind of progressivist triumphalism.

And that is why I quoted Ghiselin.

Smocovitis, Vassiliki Betty (2005), "'It Ain't Over 'til it's Over': Rethinking the Darwinian Revolution", Journal of the History of Biology 38 (1):33.
Ruse, Michael (2005), "The Darwinian Revolution, as seen in 1979 and as seen Twenty-Five Years Later in 2004", Journal of the History of Biology 38 (1):3.
Hodge, Jonathan (2005), "Against "Revolution" and "Evolution"", Journal of the History of Biology 38 (1):101.
Herbert, Sandra (2005), "The Darwinian Revolution Revisited", Journal of the History of Biology 38 (1):51.
Ghiselin, Michael T. (2005), "The Darwinian Revolution as Viewed by a Philosophical Biologist", Journal of the History of Biology 38 (1):123.
Mayr, Ernst (1982), The growth of biological thought: diversity, evolution, and inheritance. Cambridge, Mass.: Belknap Press.
——— (1996), "What is a species, and what is not?" Philosophy of Science 2:262–277.
——— (1997), This is biology: the science of the living world. Cambridge, Mass.: Belknap Press of Harvard University Press.

Not cooking frogs

Talking Points Memo links to a number of debunkings of the myth that a frog will stay in a gradually heated pot and so boil. Yet Another Thing Everybody Knows that is false. J.B.S. Haldane called this the Aunt Jobisca Theorem: it is a thing that everyone knows.

Possible cause of the Permian extinction

Researchers have found a 300 mile (that's around 480km in real money) crater beneath the Antarctic ice sheet that dates to around the time of the Permian extinction. Bolides seem to be at or near most of the major extinctions. I wonder, idly*, if the impacts themselves aren't the killer blow but rather the subsequent tectonic vulcanism.

* Idly = "wild eyed guess with no evidence or real understanding. Just for future reference, OK?

Invade America, and establish democracy there!

A while back I was at a dinner sitting next to Pete Richerson, a lovely guy who is an ornithologist who has written with Robert Boyd (who I haven't met, but I'm sure he's just as nice) some of the most sophisticated and sensible material on cultural evolution - it figures anyone who has to deal with the hyperintelligent Corvidae and other passerine birds would be interested in that. But the talk turned, being mid 2005, to what was going on in Iraq, which had been invaded to bring democracy to Iraqis (or were we still dealing with weapons of mass imagination then? I forget).

In the course of it I happened to elicit a sharp laugh from Pete when I suggested that we should invade the United States - it sorely needed democracy (not having much of it at present) and it certainly had weapons of mass destruction. I was joking, of course. Right?

But today, Leiter Reports link to an article in Rolling Stone that indicates that not only the 2000, but also the 2004 presidential election, was systematically stolen by deliberate fraud and vote rigging. Gore should have won, and Kerry should have won, but the GOP appartchiks made it harder for Democrats to vote, by closing booths, sending voter registration forms too late, or miscounting. Read the article. It's frightening.

Gaining power by vote fraud is a mark of totalitarian regimes subverting democracy. It happened in Russia, in Germany, in Spain and a host of other places. Here's my dilemma - I like America enormously. My visits there have been marked by the richness of the culture, the diversity of places, and the hospitality of the people. I even got to like their accents a bit. But I hate the way its polity is developing and fear not only what will happen when the 200lb gorilla starts throwing its weight around to force its quandam allies to conform to its narrow minded policies (as it has with the previous war on abstract notions, the expensive War on Drugs), but also when likeminded totalitarians in my and other countries start to gain support and comfort from the rise of the totality in the US.

To prevent this, the entire rest of the world needs to invade the US and establish democracy. I'm joking, right?

Thursday, June 01, 2006

Cooking up a species

Here's one I was going to leave until I could read the actual paper, because I am both suspicious and skeptical on the one hand and sympathetic to the underlying rationale on the other. And on the gripping hand...
Writing this week in the Proceedings of the National Academy of Sciences, scientists say higher temperatures near the equator speed up the metabolisms of the inhabitants, fueling genetic changes that actually lead to the creation of new species.

The finding — by researchers from the University of Florida, the National Center for Ecological Analysis and Synthesis, Harvard University and the University of New Mexico at Albuquerque — helps explain why more living species seem to exist near the equator, a scientific observation made even before naturalist Charles Darwin set sail to South America on the H.M.S. Beagle nearly two centuries ago.

It may also have a bearing on concepts such as global warming and efforts to preserve diversity of life on Earth.

“We’ve shown that there is indeed a higher rate of evolutionary change in the form and structure of plankton in the tropics and that it increases exponentially because of temperature,” said James Gillooly, an assistant professor of zoology with the UF Genetics Institute. “It tells us something about the fundamental mechanisms that shape biodiversity on the planet.”

Speciation — when animals or plants actually evolve into a new species — occurs when life forms with a common ancestor undergo substantial genetic change.

Using a mathematical model based on the body size and temperature-dependence of individual metabolism, the researchers made specific predictions on rates of speciation at the global scale. Then, using fossils and genetic data, they looked at rates of DNA evolution and speciation during a 30-million-year period in foraminifera plankton, a single-celled animal that floats in the ocean. Researchers compared arrivals of new species of this type of plankton with differences in ocean temperatures at different latitudes ranging from the tropics to the arctic. The results agreed closely with predictions of their model.
There are many errors in this release, not the least being the definition and explanation of a new species, but one ought not attack scientists for the inability of a journalist (or in this case, PR maven) to express themselves properly.

The sympathy I have is that there truly must be an energy budget involved in speciation. Life is, after all, applied thermodynamics, but there is something (please excuse me!) fishy about this. The thermodynamic budget of a species will depend entirely upon context - its trophic level (position in the food web), the complexity of the ecosystem, its distribution and abundance. You can't tell me that a population of 10,000 fishes speciating over time is energetically equivalent to 100 million fishes of the same overall body size speciating. The energetic cost to speciation depends crucially on a number of individual and contingent parameters.

But, as I say, I'll have to wait to see the paper. Last time I looked it wasn't there, either in this week's edition or early edition.

The good that men do

is oft interred with their bones. The evil lives on after them in their posts and papers...

The Explanatory Filter is being revived for SETI. See the post by Pim van Meurs at Panda's Thumb linked above.

Microbial species 5: A new beginning

Well after reading many papers by various bacteriologists, mycologists, and other non-vertebrates specialists, I have come to the conclusion that there is no single set of conceptions or criteria (that much abused word!) for something being a species in non-sexual organisms, which I am here calling "microbial". Of course, as I noted, microbes can be "sexual" in various ways. They can share genes via cross-species viral infection (transfection or transduction), via gene fragment uptake (transformation), via sharing in a protosexual way (conjugation), and so on, with it being occasional and rare through to being frequent. They can do this across many clades or only a few. As Butch Cassidy's opponent Harvey Logan observed, there are no rules in a knife fight...

So the Problem of Homogeneity stands in need of explanation. One way it can be explained is in terms of a Branching Random Walk (BRW) with extinction (Pie and Weitz 2005). This generates heterogeneity in the absence of selection even if the extinction is stochastic. If developmental entrenchment is permitted (that is, the longer a gene has been in the lineage, the more tightly developmentally integrated the lineage is to that gene, making change likely to disrupt viability of the organisms, the less heterogeneous the genome distribution, but arguably that involves prior selection for genetic harmony. Still, the "null model" here allows for some heterogeneity just from random events.

As selective pressures are introduced, we get a range of homogeneity-causing processes. Endogenous selection for harmonious genes, which occurs in sexual species through reproductive compatibility, also occurs in microbial species through developmental entrenchment, and possibly also via lateral transfer, although this while sometimes sufficient, appears not to be necessary nor always sufficient. As the frequency and degree of genetic exchange increases, so too does the contribution of exchange to maintaining homogeneity, and this I call endogenous selection.

Ecological selection, or tracking fitness peaks, is, I think, going to be a much stronger "force" in maintaining genomic homogeneity, and this I call exogenous selection. However, given that stochastic "forces" can cause both differentiation (heterogeneity) and clustering (homogeneity), we might expect that ecological selection is indistinguishable from the BRW model, unless there is both a strong signal of ecological adaptation and functionality of the shared genes, and a relative stability of the genome itself. Of course, sometimes neither information is available, but that is an epistemological problem rather than an ontological or causal one.

Note that this is not going to specify exact and constant criteria for microbial specieshood. There are sexual species that are ephemeral, and there are microbial species that have all the "right" preconditions for being a species in place and yet do not behave like them. This is a first-approximation conception of microbial species, and deviants are highlighted by its adoption, so that the reasons why each one is not a species, or species that fail to meet these conditions are, can be further investigated.

That the basic notion of species is a quasipsecies model is not exactly to return to a phenetic or "typological" notion of species*. Rather it is the recognition that there has to be some phenomenally salient clustering of properties for something to be a species. What we do with it afterwards, how we explain it, or identify it, is a matter of empirical work.

Now to sum up the lessons. I argued that the best way to think of microbial, and by extension all sexual, species is twofold: Templeton's Cohesion concept, and Mallet's Genetic Cluster concept. We need to add to this something like de Querioz's General Lineage concept as well. Templeton gives us a causal requirement. Mallet' gives us a phenomenal requirement. De Querioz gives us the evolutionary, or phylogenetic, precondition. We might therefore specify that a species, microbial or otherwise, is this:
A species is a lineage or set of closely related lineages [De Querioz] that clusters genomically [Mallet] through either stochastic [Pie and Weitz] or cohesive [Templeton] mechanisms and processes, which can be due to exogenous selection tracking fitness peaks or endogenous selection for compatibility with genetic exchange, or some admixture of both.
Add to this my Synapomorphic Species Concept, which is a general specification of the notion of biological species rather than a particular conception:
A species is a lineage separated from other lineages by causal differences in
and you have more than enough from me on species definitions for now...

* I object to the caricature of types that one finds in the biological literature. Types were always more-or-less notions, and they were rarely, if ever, identified with static entities. It's time to put that notion to bed (Winsor 2003)


de Queiroz, Kevin (1998), "The general lineage concept of species, species criteria, and the process of speciation", in Daniel J Howard and Stewart H Berlocher (eds.), Endless forms: species and speciation, New York: Oxford University Press, 57-75.

Mallet, J (1995), "The species definition for the modern synthesis", Trends in Ecology and Evolution 10 (7):294-299.

Pie, Marcio R., and Joshua S. Weitz (2005), "A Null Model of Morphospace Occupation", Am Nat 166 (1):E1-E13. [This paper is not specifically about species concepts, but it transfers nicely to phylogenetic clustering of asexuals.]

Templeton, Alan R. (1989), "The meaning of species and speciation: A genetic perspective", in D Otte and JA Endler (eds.), Speciation and its consequences, Sunderland, MA: Sinauer, 3-27.

Winsor, Mary Pickard (2003), "Non-essentialist methods in pre-Darwinian taxonomy", Biology & Philosophy 18:387-400.

Quote: Ghiselin on the Synthesis

The notion that "the" Synthesis was somehow complete at one time or another in its history implies that the participants were aiming at some culminating event, like the Resurrection of Christ.The canonical texts are being treated as if they were The Gospel according to Saint Doby, The Gospel according to Saint Ernst, The Gospel according to Saint G. G., The Gospel according to Saint Julian, The Gospel according to Saint Bernhard, and The Gospel according to Saint Ledyard. Scientists are explorers, not prophets. For them to display themselves otherwise is as dishonest as it is misleading.
Ghiselin, Michael T. (2001), "Evolutionary synthesis from a cosmopolitan point of view: a commentary on the views of Reif, Junker and Hossfeld", Theory in Biosciences 120:166-172.
Can I get an amen!? Amen, brother.

Hobbits and tools

In a hole in the ground there was found a hobbit...

The Independent is reporting objections to the recent claims by the Microcephaly Proponents that the hobbits (Homo floresiensis) had brains that were too small to make the stone tools found with them.

James Phillips, professor of anthropology at the University of Illinois at Chicago, said that it was wrong to suggest that the stone tools could have been made by earlier species of humans, such as Homo erectus, a creature that evolved more than 1.8 million years ago and predated modern humans by many hundreds of thousands of years.

"These tools are so advanced that there is no way they were made by anyone other than Homo sapiens," Professor Phillips said.

Now, however, another team of stone-tool experts has cast doubt on this judgement, saying that similar stone tools have been uncovered on the island that clearly predate the arrival of modern Homo sapiens.

Adam Brumm of the Australian National University in Canberra and his colleagues report in the journal Nature that they have found hundreds of almost identical stone tools at a site called Mata Menge just 30 miles away from the Liang Bua cave. They say the tools are between 700,000 and 840,000 years old - too old to have been made by Homo sapiens - and that the production techniques are practically identical to that used at Liang Bua 18,000 years ago.
Good to see this line being taken. If the evidence suggests they did make stone tools, then intuitive preconceptions about brain size and tool making have to go by the wayside. As Grissom says, the evidence does not lie.

The objections of those proposing that the hobbits were microcephalics strike me as being special pleading in the truest sense - we humans are so special, nothing else could have made these tools. But the ANU team seem to have shown that tools were made by the prior hominid erectus along the same style and method, and that the hobbits probably retained that technology when isolated. It takes big brains perhaps to invent the technology, but it takes only the normal mimetic repertoire of hominid brains to learn how to do this. I'm not even convinced it takes much brain power to invent Acheulian or Olduwan style tools anyway. In fact, given the right circumstances I would think chimps could do it.

Argument by imagination (I can/can't imagine it, therefore it does/doesn't happen that way) is completely bankrupt, in science or out of it. There are more things in heaven and earth than are dream't of in your philosophy, Horatio...

New cave species found in Israel

Israeli researchers have described eight new species of crustaceans and invertebrates in a recently discovered limestone cave isolated from the external world. They live in and around an underground lake fed by deep water sources rather than rainfall from above.

Creationist UK school expels anyone who doesn't conform

The Guardian reports that parents of students at Sir Peter Vardy's Trinity school, the school that gained some notoriety for being partially government funded but also teaching creationism, are complaining that it is expelling students for any kind of religious or cultural nonconformity, thereby selecting both academically and religiously. The school denies this.

Wednesday, May 31, 2006

A quote

Francis Bacon wrote of those
that have pretended to find the truth of all natural philosophy in the Scriptures; scandalizing and traducing all other philosophy as heathenish and profane. But there is no such enmity between God's word and His works; neither do they give honour to the Scriptures, as they suppose, but much imbase them. For to seek heaven and earth in the word of God, (whereof it is said, Heaven and earth shall pass, but my word shall not pass,) is to seek temporary things amongst eternal: and as to seek divinity in philosophy is to seek the living amongst the dead, so to seek philosophy in divinity is to seek the dead amongst the living: neither are the pots or lavers, whose place was in the outward part of the temple, to be sought in the holiest place of all, where the ark of the testimony was seated. And again, the scope or purpose of the spirit of God is not to express matters of nature in the Scriptures, otherwise than in passage, and for application to man's capacity, and to matters moral or divine.

Advancement of Learning, Bk II.XXV.16, p216-7 in the Everyman edition.

I'll get back to microbial species, I promise...

Monday, May 29, 2006

Microbial species 4a: monophyly and species

Here is a nice image that shows that even among eukaryotes, reciprocal monophyly is not always the case for species. It's from a paper in PLOS Computational Biology critical of the DNA Barcoding proposal.

Each version shows two species, X and Y. In A, X and Y are reciprocally monophyletic, which means that the coalescent (or last common shared genomic node in the tree, shown by the open stars) is different for each of them and is not nested within either. In B, Y is nested in X, and so X is paraphyletic, although Y is monophyletic. In C, X and Y are interspersed, phylogenetically, in each other, and so each species is polyphyletic and share a coalescent.

Of course in sexual species this raises the question of what makes X and Y species in the latter two cases (that is, why do we think they are different species? The usual answer is either based on mating behaviours, ecology or morphology, or some mix of these) but in asexuals this will occur when the two species cluster genomically as quasispecies in different ways despite being convergently evolved.

Evolving Thoughts up a tree

Well, everybody's doing it (doing it, doing it) so I have to. Yes, if everybody else jumped off a cliff I would too, mum. This is what the HTML tags look like for this site when run through the websitesasgraphs Java Applet. It is also what the mental contents of my my brain look like when viewed through any medium at all.

I can't believe Pharyngula's was so tidy. Maybe his HTML is cleaner than mine, or maybe he cheated by not including the 6000 year archive from his old site; his brain is certainly no tidier than mine, I warrant...

State religion encroaching on military freedoms to believe

While I'm working through the conceptual tangle I've gotten myself in over microbial species. allow me to mention this item from Mike Dunford's The Questionable Authority: apparently the US Army National Cemetery Administration will not permit Wiccans to use a symbol for the headstones of dead veterans.

Guys, the reason why there's a separation of church and state in the first place is because of just this sort of encroachment. If you aren't of an "approved" religion (and note that despite the present President's prior comments about Wiccans in the military, Wicca is an approved religion in the US military anyway), you get sidelined. Doesn't matter that you gave your life for your nation (or for the policies of the same Administration at least). You can't be remembered as the person that you were.

Religion in public affairs has an inbuilt disposition to encroach upon the freedoms of others, whether they are religious or not. It seems to me this is conveniently overlooked by those of the majority religions when it suits them, and they scream loudly when it harms their own interests, perceived or otherwise, or goals and aims. But one never sees atheism or agnosticism encroaching on religion in a secular society (I think that the Soviet and Maoist communisms were not secular, but a form of state religion). This must be why all those majority Christians claim there is a war on religion, when agmostics, atheists and members of minority religions don't like being subsumed under the ruling majority.

How does a religion even get approval? Is there a Senate standing committee that reviews applications for state approval of religion? I thought that was the sort of thing that the Cold War was notionally about...

Good thing I'm not in the US military (well, actually, there are many reasons why that is a good thing, not least for those who might have had to rely on me in combat). If I died in service I'd want to be buried under a very large question mark. That would be appropriate for an agnostic. Although if I died in combat, I'd probably also want a large exclamation mark too. Not for nothing do compositors call it a "shriek", "screamer", or "bang".

Late note: see this post from Dispatches from the Culture Wars for more background.