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

Wednesday, February 07, 2007

The Voltage Gate: Basic Concepts: What Is Ecology?

Wednesday, September 13, 2006

The last ever post here

Dear folks. I have defected to Seed Blogs on a promise of fame, fortune and women. So this will be my last ever post at this site. The new link is here, and the news feed in Atom form is here. It's been fun, so drop by for a chat.

I will repost some oldies from here to begin with, and continue our discussions.

Friday, June 09, 2006

A blogging delay

Dear readers, for reasons that will shortly become clear, there is a blogging delay here. Hmm... "blogging" in that context sounds like a swear word... "another blogging delay! Dammit!"

Stay tuned and in a day or so All Will Be Revealed.

Monday, June 05, 2006

Biologically feasible political systems

I often wonder what goes through the minds of those who propose utopian political ideals that turn out to become the worst of all possible dystopias, like Leninism or Maoism, or for that matter the extreme laisse faire capitalist conservatism. For it appears to me that these systems would work just fine, if only they didn't involve any human beings. And that raises an interesting question in my mind, and I hope, yours too. What sorts of political systems are biologically feasible for human beings? As Aristotle said, Man is a Political Animal, but what sort of political animal?

Any political system that relies upon purely rational behaviours, for example, is right out. It is often noted that economic and political behaviours are like the games of game theory - any system that relies on a rational outcome, is vulnerable to the free rider effect, as in Garrett Hardin's Tragedy of the Commons. Here's a case in which a shared common resource (the commons, on which each farmer may graze on sheep) is systematically destroyed. One farmer (the freerider) thinks to get an edge on his competitors and graze two sheep. The other soon find that to keep up, they must do this also. Eventually, the commons is overgrazed, but every participant in its destruction has acted in a rationally self-interested manner.

But worse than this, it may pay not to be rational. Suppose you have a Vulcan society. Each is given according to ability calculated rationally, and each accepts this, in that, as Spock said channelling James Mill and Jeremy Bentham, the needs of the many outweigh the needs of the few. All it takes to subvert that little society, in the absence of draconian sanction, is for one member to act irrationally, and take their own needs as paramount. They will cause others to rationally reflect that if that is happening, there will be a point at which it pays individually to subvert the rational society.

Others, such as Marx, Engels and Lenin have argued that society should be just. A just society does not permit one person to own or control others or their means of production. But it turns out that the ordinary person doesn't see it that way (because of "false consciousness") and so there needs to be an elite (the political proletariat) that judges how things should go on their behalf. Good intentions. It led to the Gulag.

One could multiply examples almost indefinitely. The French Revolution. Jonestown. Finnish utopian colonies, the Philadelphians, the Colonia Dignidad, and a range of American experiments.

Why don't these work? Well, for one thing, it seems that they rely on a particular anthropology - of humans as rational, or spiritual, or open to free love, and so on, all of which are simply implausible as depictions of real humans. But it has for a long time been a Bad Thing to talk about Human Nature, which leads to Essentialism, Racism, Fascism (itself a utopian vision) and ultimately Blindness. But while there are a large number of apologetics for the status quo in the application of ethology to human society, sure enough, most of the time this has relied upon taking distant analogies from, among other things, gazelles, geese, wasps, bees, and caricatures of apes in order to argue that way. Few seem to have tried to argue from the observed and actual human ethological traits to what is a feasible human social structure.

Since I have no internal warning systems of professional suicide, I am going to try to sketch, very roughly, what I think these traits might be, and to discuss how this might affect our quest to form a decent and sustainable society. Feel free to chip in, either with criticisms or suggestions.

Our questions are these:

1. What sort of social animal are human beings? What are the basic social structures of the human animal "in the wild"? We might indeed wonder if there is such a beast as "in the wild" for humans.

2. How do these traits affect us in large societies? Is there something novel in our sedentary and urbanised lifestyles that we did not previously express?

3. Is our social nature constrictive? That is, can we establish a social order that escapes, modifies or completes our biological dispositions?

Others will come to mind.

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.

Saturday, May 27, 2006

How not to apply evolution to culture

Here is a small piece in the Korea Herald, by Arne Jernelov on how evolution explains cultural excellence. It's all about sexual selection, you see - if you do something that is very hard and very costly, you are attracting mates, and this explains sports, painting, literature and science. It is only coincidental that the author is a scientist (an environmental biochemist). I bet he also plays sport competitively.

Friday, May 26, 2006

Microbial species 4: degrees of sex

When we attempt to apply to organisms that are not obligately sexual (that is, which don't have to have sex to reproduce) concepts that were specified to use with those that are, we have problems. The Recombination Model is one such attempt. Sure, some microbial species exchange genes. Others do it more frequently and more completely. There appears to be a continuum of gene exchange all the way from almost never to almost every time. So why should we expect that gene transfer will provide us with the sort of homogeneity of lineages and quasispecies that it does in obligate sexuals?

In part I believe this is because we always start from what we know. As I mentioned, the existence and ubiquity of asexual organisms has been resisted from a long time, and treated as exceptional rather than the rule, because biology began with large scale plants and animals, where the paradigm cases were encountered for the biospecies concept. As exceptional cases were encountered, these concepts were stretched, and modified, to serve the increasingly "deviant" cases, until now we realise that deviance is relative to the paradigm conceptions rather than a fact about the organisms. What should we say instead?

I believe we should treat this continuum idea more seriously and as the basis from which the metazoan and metaphyte conceptions are drawn out. And we should consider how the two factors of the Templeton conception - exchange and ecological niche - play differing roles according to the degree of sex a lineage has.

Before I deal with this in detail, let me note for the record that there can be, and must certainly often be, other reasons why the carpet is not smooth, but is patchy. Extinction can cause there to be patches in genome space. Some varieties die out. While this can be because of selection, often it will be due to plain old genetic drift, and contingency. A lineage of asexuals can stochastically drift due to random biases in the direction of mutation, for instance, while earlier forms can go extinct simply because of random drift or random termination of that clone. Moreover, if a genome evolves in a habitat that is sensitive to sudden changes in climate or even geological change that degrades it, then that genome and its neighbours will become extinct. Evolution doesn't explore the same coordinates in genome space all the time and everywhere. This is similar to the phylogenetic trends that occur through simple stochasticity, because clonal evolution is phylogeny.

So, back to the notion that sex is not an all-or-nothing affair, so to speak. If the continuum ranges from 0% gene exchange (total asexuality) to 50% gene exchange (total sexuality), then it follows that at the asexual end, exchange can have only limited to no effect on maintaining homogeneity, while at the sexual end, it can have a very great role in maintaining homogeneity. Likewise, at the asexual end, homogeneity not due to stochastic effects will be due largely to ecological selection (fitness peak tracking), while for sexuals this will not be so great a cause. I have given a schematic graph to illustrate this.

This will be why we find that gene exchange doesn't have a simple relationship to genomic homogeneity. It will depend on the rate and amount of genes shared across lineages case by case, as well as the degree to which the quasispecies is maintained by ecological interchangeability. Following on from my discussion about speciation earlier, and my 2001 paper on species concepts, where I employed this evolutionary aspect of the nature of sex to argue that being a species is an evolved trait, not a natural kind, we ought to expect that each species and group of species has its own unique evolutionary history and therefore properties, just as limbs and lungs and livers do. There will be a more general theoretical context of adaptive landscapes, genetic dynamics, and so on, but given that each evolutionary group has encountered different conditions, this means that each modality will be shared in a fairly limited way.

Moreover, this means that biospecies is not the most basal notion of species. In fact, biospecies, or reproductive conceptions of species in general, are derived modalities. The basal notion is quasispecies. All species are at least quasispecies; some are in addition reproductive cohesion or isolation conceptions. This means that some standard requirements for biospecies, such as reciprocal monophyly, do not need to apply to all species. But there is one rather interesting aspect to this approach that I find illuminating, although your mileage may vary: a simple quasispecies is cohered by more or less one adaptive peak (if it is cohered; stochastic clustering does not imply this), while a biospecies famously can be and often is adapted as a generalist or have polytypic traits for differing adaptive peaks.

What maintains a sexual species in this case will be, therefore, the combination of extrinsic selection, and internal or intrinsic cohesion, due to selection for reproductive compatibility with potential mates. I have a paper forthcoming in Biology and Philosophy which argues this in detail. Microbial species will tend to depend on adaptive peak cohesion inversely to the degree that they do share their genes and directly to what functional value of those genes they share have ecologically.

Enough for now. I'll wrap up this series next post.

Microbial species 3: Quasispecies and ecology

The second main approach to a natural conception of microbial species (by which I mean, as opposed to operational, practical or conventional ones, collectively called "artificial" conceptions) is what I will call the Quasispecies Model. According to the concept developed by Manfred Eigen for viral species, a quasispecies ("as-if-species") is a cluster of genomes in a genome space of the dimensionality the number of loci. A quasipecies is in effect a cloud of genomes, with a "wild-type" coordinate (that is, genome) that may or may not actually have an extant or extinct instance.

A genetic cluster of the quasispecies kind is therefore not unlike James Mallet's Genotypic Cluster Concept (1995), although this is primarily an operational definition than a substantive underlying account of species. We still need to account for quasispecies existing in the first place. We have considered one possible mechanism - gene sharing by lateral transfer - and found it to be insufficient. Is there something else we might make use of?

There is one proposal by Alan Templeton (1989), devised for sexual organisms, which defines a species as a genetic cluster, as Mallet's does, but accounts for it either by genetic exchange, as in the recombination model, or ecological interchangeability. This latter notion is what we might call the "Fitness Peak Conception" of quasispecies.

Each coordinate in genome space, that is to say each genome, has a fitness value associated with it that is imposed by ecological factors. If the adaptive landscape is relatively smooth, which means that adjacent coordinates are correlated in their fitness values, we should expect in the absence of all other causes of clustering that the cloud of genomes will tend to centre upon the most adaptive genome. Of course, this is an abstraction and a gross simplification - genomes are not independent of each other, or from fitness values. Organisms create their ecological conditions to a degree, and how fit a genome is depends also upon what other genomes exist in a population (at least, in sexual organisms), but we can leave these complications to one side for the moment.

So one potential reason why quasispecies exist, why genomes cluster, is that they track local fitness peaks. Let's flesh this out, so to speak. Take a pathogen that is clonal. It needs to employ certain features of the host species in order to infect and exploit that host. Assuming these don't change - say they are recognition molecules on a cell surface - the quasispecies will cluster about those point in the genome space that are more effective than others with respect to the capacity to infect and exploit.

So now we have the two cohesion mechanisms proposed by Templeton - cohesion due to shared genes, and cohesion due to the need to exploit the environment better than competitors. Anything that can do well at the latter will tend to be better represented in the average population. Hence quasispecies.

But fitness peaks typically do not remain constant or decoupled from the populational structure, as I said. Does this mean that quasispecies are not real species because they are ephemeral? Of course not - all species are, over a suitably extended timescale, ephemeral. That is in the nature of evolution. What the fitness peak conception means is that a quasispecies will remain homogeneous so long as there is a more or less unitary fitness peak. If the peaks shift, there will be "speciation". Oh heck, let's stop the pretense that quasispecies aren't real species. There will be real speciation.

In the next blog, I will discuss a way to bring these two notions together, and to link quasispecies with biospecies (sexual species).

Eigen, Manfred (1993), "The origin of genetic information: viruses as models", Gene 135 (1-2):37–47.
——— (1993), "Viral quasispecies", Scientific American July 1993 (32-39).
Mallet, J (1995), "The species definition for the modern synthesis", Trends in Ecology and Evolution 10 (7):294-299.
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.

Thursday, May 25, 2006

Microbial species 2: recombination

The cluster of genomes of asexual organisms forms what is called a "phylotype" (Denniston 1974, a term coined by C. W. Cotterman in unpublished notes dated 1960; I like to track these things down). Phylotype is a taxon-neutral term, though, that is determined entirely by the arbitrary level of genetic identity chosen. For example, "species" in asexuals might be specified as being 98%+ similarity of genome, or it might be 99.9%+ (I have seen both in the literature). A phylotype of, say 67% or 80% might be used for other purposes (such as identifying a disease-causing group of microbes).

The phylotype concept, while useful in other respects, reinvents (or preinvents - 1960 predates the work of Sokal and Sneath) phenetics. A phenetic taxon was called the Operational Taxonomic Unit (OTU) and it used an arbitrary measure of similarity and difference: an 80% "phenon line" was the arbitrary measure for species based on phenotypic similarities. The problem was that the distances changes as you chose different principal components, and I warrant the same is true for phylotypes.

One solution to the Problem of Homogeneity for asexuals is what I will call the Recombination Species Concept. Proposed by Dykhuizen and Green in 1991, it basically the Biological Species Concept for lineages that occasionally share genes or gene fragments through lateral transfer.

There are several mechanisms by which lateral transfer of DNA can occur among "prokaryotes". One is DNA fragment reuptake, in which DNA from a cell that has lysed (its membrane or wall has disintegrated, releasing the cell contents into the medium) is taken up by another cell, and rather than being digested it becomes active. There are variations on this. Entire chromosomal rings, called plasmids can be taken up this way. Or a cell can "bleb", forming vesicles or compartments of lipids, containing DNA (including plasmids), which then attach to the receiving cell, opening up to the interior.

I mentioned prokaryotes before. This refers broadly to a paraphyletic group of organisms that are basically not-eukaryotes. Nowadays we refer instead to several groups: Bacteria, Archaea (which is sometimes decomposed into several other groups), and Eukaryota. One thing the not-Eukaryotes have in common, though, is a lack of a nuclear membrane, allowing the transfer of genetic material between genomes.

So the Recombination model of microbial species is based on the claim that the greater the genetic distance between strains, the less likely it is that the genes will be functional and useful in the receiving strain, and this is what serves to maintain the homogeneity of bacterial and other microbial species. One of the claims is in fact that the differences in genetic structure, and in some cases differences in restriction enzymes, that break DNA sequences, will make a nonsense of the DNA fragment or insert it in a nonfunctional location in the target genome.

These compatibility issues act like sex does to maintain the overall "location" in genome space of the population. Those strains that deviate too far from the mode will be unable to take up the functionally useful lateral genes, and so will be more susceptible to extinction through genetic load.

So the Recombination model is a mix of Maynard Smith's theory of sex, and Mayr's notion of biological species. The only problem is that it isn't consistently true. A beautiful explanation is spoiled by ugly facts. Recombination via lateral transfer appears to be rather more profligate than first appeared (Beiko, et al. 2005), and there are some "species" of bacteria, such as the Lyme Disease-causing spirochete Borrelia burgdorferi, that appear not to share genes much, if at all (as Dykhuizen himself observes, Dykhuizen and Baranton 2001). So if in those cases clustering occurs, it is not due to lateral transfer, but some other processes.

I failed to mention a process that is directly analogous to sex in bacteria - conjugation. This is a case where part of the genetic component, usually plasmids, which are secondary small chromosomes (B), or the main nucleoid (A), can be inserted into another cell via processes called pili, which are part of the Type IV secretory system used for other purposes and which is homologous to flagella. The typical mode of conjugation is that one mating type (often called the "male") is activated by pheromones from another mating type ("female") to attach the pilus to the recipent, and insert the genetic material.

Now this is "almost-sex", because there is no genetic reassortment, but other processes will tend to shuffle genes into the nucleoid, as well as utilising the taken-up plasmids. But again, while the mating types seem to act as cohesive mechanisms, conjugation can be profilgate across large, even vast, phylogenetic distances (and hence genetic distances). It has been observed between bacteria and yeast, bacteria and plants, and there has even been a case in which it was observed between bacteria (E. coli) and mammalian (hamster) cells (Waters 2001).

So while it may be that recombination of lineages through partial genetic transfer operates as a reason for some phylotypes, it does not account for all, and is therefore not a sine qua non of specieshood, or homogeneity, among microbes.

Next, we'll consider ecological accounts, as well as drift, migration and geographical isolation.

Beiko, Robert G., Timothy J. Harlow, and Mark A. Ragan (2005), "Highways of gene sharing in prokaryotes", Proceedings of the National Academy of Sciences, USA 102 (40):14332-14337.

Denniston, Carter (1974), "An extension of the probability approach to genetic relationships: One locus", Theoretical Population Biology 6 (1):58-75.

Dykhuizen, D. E., and G. Baranton (2001), "The implications of a low rate of horizontal transfer in Borrelia", Trends in Microbiology 9 (7):344-350.

Dykhuizen, D. E., and L. Green (1991), "Recombination in Escherichia coli and the definition of biological species", Journal of Bacteriology 173 (22):7257-7268.

Waters, V. L. (2001), "Conjugation between bacterial and mammalian cells", Nature Genetics
29 (4):375-376.

Wednesday, May 24, 2006

On microbial species

OK, this is one of a series of posts in which I will play with ideas that might become a paper.

The problem is this: usually we define a species as a group of related organisms that share genes (or a gene pool, which amounts to the same thing). Sometimes we include also ecological considerations (either in the form of natural selection, or in terms of sharing a niche).

But many microbial species either do not share genes to reproduce, or they can but do not need to. So, the question is sometimes raised whether microbes (of this kind) form species at all, or if there is some replacement term or concept for microbial taxonomy.

Historically, it took a long time to even accept that there were asexual organisms. Darwin discussed hermaphroditic species, but they still had mating types or genders; it was just that a single individual had both kinds. It was long recognised that some plants could propagate vegetatively. But the notion that there were obligately asexual organisms was doubted, for instance, by Fisher as late as 1958 (in the second edition of the Genetical Theory of Natural Selection). George Gaylord Simpson, the famous joint architect of the synthesis and paleontologist, simply denied that asexuals formed species. Call them something else, he said.

But bacteriologists, mycologists, and virologists all continued to name and describe species, even though they could not really make use of the Biological Species Concept of Dobzhansky and Mayr. They relied on their staining properties, the colony shape, the microscopic morphology of the cells, and of course the ecological conditions under which they lived. There was lacking, though, a clear definition of what a species could be for these organisms.

Part of the problem is this: if a species were obligately clonal, then each mutation would make a new clonal lineage:

and we would expect to find not clusters but a carpet of strains more or less evenly distributed. How can we account for this? I will call this the Problem of Homogeneity: why are asexual lineages ever found as groups at all? Why are they homogeneous over time, and stable enough to be called "species"?

I will follow this up in the next post, but I want to get your feedback first.

Monday, May 22, 2006

What, if anything, is a rabbit?

Darren Naish [via Pharyngula] has a lovely article about the morphology and taxonomic and phylogenetic relationships of Lagomorpha, rabbits and hares. In the course of the piece, Naish quotes one Albert Wood, from 1957, whose paper with the title of this post starts out
The title of this paper is slightly modified from that of an article I encountered some years ago, which appeared to be approaching the problem of the relationships of the Lagomorpha, or rabbits and their relatives, from the most basic point of view. This paper, entitled “Gibt es Leporiden?”, seemed to be questioning the very existence of such animals. Investigation showed, however, that the question involved was not whether members of the family Leporidae existed, but whether rabbit-hare hybrids did. Since then, I have met no one who questions the existence of rabbits and hares, and I have been reluctantly forced to accept them.
They don't write papers like that any more. I, too, question the reality of rabbits. Just because.

Sunday, May 21, 2006

Islamist paradise: selling children

The Times is reporting that 20 young boys were bought from an Islamist leader, Gud Khan, in Pakistan, who runs a "pure Islamic environment" at a centre initially funded by al-Qaeda, by Osama bin Laden directly. The sale was made to a Christian missionary who was freeing them and returning them to their parents, from whom they had been kidnapped. Khan apparently knows that the children will be used for sexual and illegal activities, and doesn't care, because they are Christian. The proceeds are used to support his Islamic paradise, free from the corruption and degradation of the West. Oh irony!

The obvious inference to draw here is correct but insufficient. Islamism is not based on some morally pure foundation. It is political, pure and simple. Sure, this is true, but a much better inference is that religion makes for a very bad foundation for morality. Not only Islamists, but Christians, Jews, Hindus and every other religious movement, privileges believers over unbelievers morally. It's OK to kill abortionists or gays, to disenfranchise Jews or Arabs, and so on, because They Aren't The Same As Us.

And Christians in the US and here (Australia, in case you forgot) will often criticise those who think that all human beings deserve the same rights and privileges in society as "humanists". In fact, humanism has become the all-purpose bogey among religious circles. Of course it is - it undercuts the basic moral intuition of all religions: that rights are given based on conformity to their, and only their, standards of behaviour.

I am proud to be a humanist. I think that Jews, Muslims, Hindus, Catholics, Scientologists and even those evil atheists (spelled athiest by fundamentalists) have exactly the same rights as any other person. That means they can run for office, vote as they wish, take any course of action even if it contravenes the "deeply held moral standards" of some religious majority so long as it is not illegal, and live wherever they like. This is a measure of civilisation. The covert prejudices and bigotry of religion need to be opposed openly by a civilised state.

To my religious friends, who are not at all like this, most of the time, I can only say that your morality is civilised in spite of, not because of, your religious traditions. It was but an eye blink since your own traditions, if they are enlightened now, were treating those who differed as subhuman. Christians, Muslims, Jews, it doesn't matter. The underlying social function of religion is to exclude, not include. Thus it ever has been.

Humanism is not a religion. It is a general principle - that human life is equally valid no matter the social status, ethnicity, religious belief, or sexual orientation of the individual. Somebody should found a country on these principles...

Friday, May 19, 2006

Ian McKellen - bigger than Jesus?

Famously, the Beatles lost a lot of customers when John Lennon said that they (the group) were "bigger than Jesus" (meaning they had more fans than Jesus did at that particular moment). British litotes and irony failed to register with Americans, and so there were the famous LP burnings (and damn, aren't the people who kept their original LPs in good order happier now).

Ian McKellen nearly got himself into similar hot water just recently in this interview. From beginning a sentence with "The Bible ought to have a disclaimer that it is fiction" he got to "it takes an act of faith" - great save! Every so often the rest of the English-speaking world has to realise there are gaps in the rhetorical education of Americans...

[From the commenter cm on Pharyngula]

Sorry for the silence, and chimp hybrids

I apologise for the lack of posts. My hindbrain (Powerbook G4 12") was out being serviced, and I (i) was stuck on a PC (*shudder* How do people work on those things?), and (ii) I got busy with other stuff, which may find its way here anyway.

So while I was incommunicado (is anyone ever communicado?) the "news" that humans and chimps were hybridising for several millions of years appeared in the New York Times, presaging an article in Nature. John Hawks has a nice takedown of this paper, although it has been hysterically dealt with by the media.

But what's the big deal? Hybrids occur between greatly differentiated lineages all the time. They aren't, though, common, and while many are sterile like the mule, many are also fertile and can back-breed into one of the parent species. Hawks mentions the lion-tiger crosses in genus Panthera, the tigon and the liger, which are fertile and not, respectively. Tigers (nine species or subspecies) and lions separated about 2 million years ago. Similarly, horse evolution has allowed a considerable amount of cross breeding between species that separated about 4 to 2 million years ago. When such things occur, the resulting process of genes crossing species boundaries is called introgression, and it is more common than we might think.

So why would the discovery, if it is, that genes occasionally cross from chimp to hominid lineages be any more unusual than the horse or Panthera hybrids? Obviously because we are involved. Our evolution is, after all, just ordinary evolution, no matter how unusual our brain size or other phenotypic traits. All species are unique (which is why we call them "species"). And the rate of introgression looks to be pretty rare anyway. It's not like Greatn Grandfather was out for a bit of chimp tail every Saturday night.

Now, some housekeeping. In the near future I will be travelling a fair bit, so I'll be reviving some old posts from the dusty archives. Moreover, this blog is moving. Stay tuned for an announcement. I'll leave this site up indefinitely, but you'll need to revise your RSS feeds and bookmarks when it does.

Monday, May 15, 2006

A guide to Christianity, for sports fans

Via Uncertain Principles via Jim Henley, at last a guide to terms and types of Christianity for those whose idea of an education is reading the Sports Page. In particular, I find the description of fundamentalism enlightening:
The belief that basic elements of play - like passing, ball handling, and defense - are the essential building blocks of a winning basketball team is generally referred to as "fundamentalism." The fundamentalists formulated their doctrine in the 1980s against the showy, heretical play of Magic Johnson's Los Angeles Lakers. Leading fundamentalist institutions include Bob Jones University and Syracuse. Larry Brown's failure to get the Knicks into the playoffs has been seen as a major setback for the cause of fundamentalism.

A question to my readers

Folks, I've been invited to join the Seed Magazine Science Blog site that Pharyngula, Aetiology, Evolgen, Stranger Fruit and others have joined. If it's good enough for PZ Variablename, it has to be good enough for me. But I wonder how this might affect the fifteen readers who aren't part of my family. So please, let me know what you think. Should I? Or shouldn't I?

Later: Well the ayes have it. Once I get things sorted out with Seed, we'll start there. I'll leave this blog up indefinitely, but I'll probably intersperse new posts with old ones for a while. Thanks guys. I had no idea my mother paid so many people to read this blog...

Saturday, May 13, 2006

Evolution and truth

One of the problems in having a philosophy related blog is that ideas are hard things to generate on demand, so often you need someone to raise the problems for you to think about. Being naturally (and preternaturally!) lazy, I don't go out looking for problems (of a philosophical nature; the ordinary kind seem to find me like flies find rotting garbage). Hence, this blog is sporadic.

Well, I just tripped over an interesting question raised by Certain Doubts: can we reconcile the Platonic value of truth with an evolutionary view of epistemology? That is, if we think that our knowledge is the outcome of evolution (which I do), can we still think that knowledge is about the getting of truth? Absolute truth, that is, not the purely "good enough for government work" kind that we all rely upon in daily life.

The conundrum is this: evolution (natural selection, anyway) serves only to optimise that which is satisfactory to the past environments of the organism's ancestors. To use a memorable phrase of Hull's, evolution is like the Prussian military academy that turns out officers admirably suited to winning past wars. But our cognitive capacities were not designed to deal with such matters as subatomic physics, comparative biology, or risk analysis in complex economic systems. We were designed to deal with living in certain environments and social groupings that we no longer mostly live in, and the ideal of truth-gathering is well out of that environment. In short, can we trust modified monkey brains, as Darwin posed in another context?

One way to rescue some form of naturalised epistemology f this kind might be to say that we can rely upon our native cognition in cases where they are closely similar to those ancestral conditions, whatever they might have been. But even this fails, since evolution is not, generally speaking, a global optimiser, but a general satisficer. That is, so long as the animal is viable enough, relative to other candidates, then it will procreate its kinds. Some sort of induction is good enough for hominids in their usual environment - as Quine said, "Creatures inveterately wrong in their inductions have a pathetic, but praiseworthy, tendency to die before reproducing their kind". I don't know about the praiseworthiness, which remains to be seen, but Quine's claim was that we have an innate "quality space" honed by selection, which refers because it works.

There's an obvious problem with this, or rather, several obvious problems. First of all, we often make mistakes. The problems of optical illusions have a long history in philosophy of indicating the unreliability of vision, and similar issues arise with our cognition. We are very bad at deductive reasoning, for example, when the variables are abstract or unnatural, as the Wason test shows. We are bad at risk assessment - people are afraid of flying but not of riding in a car, although you have a much higher danger of death or injury in cars than planes. We fear home invaders far more than family, although you are more likely to be attacked by a family member than a stranger, and so on. Our cognitive skills are based on whether or not they contribute to reproduction rather than individual knowledge. Evolution, if we envisage it as a designer, cares nothing for truth, just progeny.

Another problem is that our quality spaces are, if they exist from evolution, very domain specific. While it explains why we have a priori concepts - Kant's synthetic a prioria are evolutionary a posterioria, as Lorenz said - it doesn't guarantee their applicability outside those domains. A third problem is the one of satisfaction; if a concept works most of the time, it doesn't make it reliable all the time, just satisfactory so far. Consider what will be better - the ability to spot a predator if and only if there is a predator, or a jumpiness that works most of the time if there is a predator, but also makes us jump at sudden noises and shadows. There is a cognitive cost to being right all the time, and evolution won't burden us with an expensive solution that in any case would take time to employ, while the leopard is leaping at your throat. Better to startle and run, and be embarrassed, than to be right and dead.

So, can we have absolute truth and natural evolved cognition? I think, as Putnam said, that evolutionary epistemology fails to explain the core problems of epistemology. Or does it?

We often focus on individual cognition as the locus of selection, and in one way this is right, because we are considering the reason we have big brains, and the cognitive apparatus they make possible. But there is another level of analysis - that of the tradition or culture. These, too, evolve, only not biologically but culturally. A society that learns how to use local resources to flourish has knowledge even if the "explanations" given involve ritual magic or religious etiology. It doesn't matter how the efficacy of Amazonian poisons derived from frogs is explained by the local tribes - it matters that the tribes know that it works.

But that brings with it implications of the magical explanations, and so on, which are formed largely in the context not of the physical world as such, but the social world in which explanations asked and offered play functional roles in establishing and maintaining social structure. In short, these explanations are not about adapting to the "world" but to "society". And throughout human history, such cultural evolution has been both minimally adaptive in a given environment (or not, as in the Anasazi case where they overexploited local resources), allowing the society to remain viable, and adaptive in social functional terms allowing agents within the culture to interact in various ways. What it does not do is offer truth, or if it does, this is a truth of pragmatic virtue and convention.

But around 1700 or so, a movement finally took off in which several factors combined to permit human cognition to overcome the limitations of biology and society to an extent. In this movement, specialisation ensured that the explanations given were satisfactory in each domain to those who were best acquainted with the material. It recorded the work in detail, and made a virtue of discovery and theory. I am talking about science, of course.

The prior commitment to Platonic or Aristotelian truth had, in 2000 years, made almost no progress of any real kind. While the logical and theological domains were transformed, actual knowledge of the extra-social world was thin on the ground. When advances were made that did relate to physical facts, such as engineering and manufacturing technologies, before this point, they could easily be lost because that knowledge was held only by a small family tradition or a guild that might be banned or become uneconomic at any time. Yes, truth was a virtue, but one more honoured in the breech than the observance.

It wasn't even enough to be empirical. Many, such as Roger Bacon, Nicholas Oresme, Frederick II, and others had done good empirical observation in the middle ages, but the habit didn't take. With the appearance (in fact the evolution) of specialisation and above all communication of results and the availability of the records to all, science took on the role of cognitive system. Subsequent adaptation of scientific institutions made it more able to generate knowledge than at any time in human existence.

But what is science adapting to, exactly? A naive answer might be that it is adapting to the data. This is a nice simple answer - we can rely upon science because hypotheses are tested and proven (in the Old English sense of "proven", meaning well tested and found reliable, as in the "exception that proves the rule" by testing it). Add a dash of falsificationism, and you are on your way. I think this is grossly mistaken.

Science is adapting to the real world, in some manner. It might help to think of it like this - a model builder invites you to guess what he has made, but it has a sheet of some thickness over it. You can see the points that support the sheet well enough, but the identifying details are hidden behind the cover. How can you find out what it is? You have a stick to poke it with, and ten seconds. Go...

Well, it's a large model, and in ten seconds you can't feel all of it, so you poke at the supported bits in the hope that the shape will become clear. At the end of ten seconds, you guess that it's a model of some guttering. It's actually the Vallis Marinaris on Mars.

Science, like you, has a limit on what it can measure, and there's a a cost to that activity, so some conceptual triage is needed. If something is measured, then within measurement error you have knowledge of that data point alone. The rest is inference, interpolation and generalisation. How do you choose what to measure, and what to infer? Some of these choices are influenced by your personal dispositions and predilections, some by the conventions of the discipline. Others are mostly due to social context, government policies, religious beliefs, and so on. Science has some social functional adaptation after all.

This has led some to claim that science is just another worldview, a claim seized upon by antiscience movements like creationism and intelligent designism. But it isn't. Is is not just another worldview. It is an enterprise that is parallel to worldviews, creates worldviews, and shares a multiplicity of disparate worldviews amongst its practitioners. Worldviews aren't what makes science special.

What makes it special is that the institutions themselves tend to make claims that can be challenged and do get challenged, if there is any reason to. And given that the resources of science as limited like any other, there is always reason to do so. Of course, not everything gets tested in the usual sense, but there is sufficient selection for consonance with prior work, for empirical adequacy, for explanatory power and the ability to generate research programs, that in the medium to longer term, science generates pretty adapted results. Adapted to the empirical world, that is.

I can think of some constraints on science, though. One is, and I haven't seen this discussed anywhere so You Heard It Here First™ unless you didn't, that science cannot progress beyond the ability to teach the next generation how to proceed. If something requires a depth of study that is going to take fifty years to learn, it will be abandoned in favour of either some other more rapid payoff to the individual's career, or the field will be divided into more manageable chunks. What can't be, won't be investigated at all.

So science is not absolute truth. Is it truth at all? Are we being objective here? Who knows? But a truth that is unattainable is not a truth that does much hard work. If the truth we can get through science works enough, that's the best we can hope for. Fortunately we got sufficient of a leg up from evolution to get started, and fortunately we did get started. But the Platonic ideal of truth is a dream of a reality we will never get access to, and is thus an item of religious faith not needed.

Novelist reinvents ethology

Tom Wolfe, whose works often show a considerable pretentiousness in my opinion, has a piece in the New York Sun entitled "Darwin meets his match". In this he adduces Zola and Weber, and most of all the 1950s American sociologists whose works stressed status seeking and display, to show that there is something missing from Darwinian theory.

Like social dominance ethology and psychology never happened, right? Darwin talked about social dominance and submission several times, and much of Weber's dialectic comes from the tradition of social psychology one might suggest Darwin was influential in creating, if not being the originator (Hobbes has that honour in my view). The ethology of Lorenz and Tinbergen, and the creation of social dominance theory among various species (not often applied to our own species, although the sociobiologists of the 1970s tried, such as Lionel Fox and Robin Tiger, but were shouted down as being neofascists), explained how social animals form dominance hierarchies, and the theoretical apparatus of honest advertising (costly, and therefore hard to fake) of status explained why animals "spend" status advertising the way they do, from the peacock's tail through to conspicuous consumption of potlatch feasts.

What I especially object to here is Wolfe's implication that somehow evolutionary theory is inadequate to this task of social explanation. But the theoretical infrastructure of modern evolution not only is adequate to it, it requires it. If the fitness of an individual depends upon his or her (or its) position in the social group, then he/she/it will need to be able to badge that status to those from whom the organism is seeking aid or mating opportunities.

Humans are social animals. This is a point noted since Aristotle. We form social dominance hierarchies. But unlike many organisms, which have a single, often nontransitive, hierarchy, we humans are able to set up and maintain our status on several hierarchies at once. I suspect this is because we are (i) mobile, and can interact with different geographical bands of humans through trade, warfare, intermarriage and cultural exchange, and (ii) we are able to abstract and communicate status verbally. Yes, Tom, language is important, but you are wide of the mark if you think there is no work done on when we evolved it. The likelihood is that it evolved around 200,000 years ago in its present form.

So we have a rank hierarchy for our own tribe or community, as well as hierarchies of age cohorts, ethnic groups, and within-gender hierarchies (come on - you didn't think that jewellery or bling was to impress the opposite sex, did you?). We also have a rather more obvious hierarchy in sedentary urbanised cultures - class hierarchies. So what will the average human do to maximise his/her/its* status? Each individual will strive to maximise fitness on a vector sum of these hierarchical scales, based on the physical traits and inherited wealth they have at birth and maturation. It may pay to get much money irrespective of physical attractiveness (the Trump ploy), but mostly it pays to come to an optimal tradeoff. You might find it best to be the top dog in your class, or your ethnic group. You might find that aggression works for you. Or it might be that being a middle manager in a middle class is the best outcome for you.

We use status to increase our fitness, but it doesn't follow that this equates to mating opportunities. It may be that your inclusive kin benefit from being a warrior who dies. It may be that having status vicariously will mean others in your tribe or troop will look after the progeny who are left behind. Or it may be that favours are returned, and because Uncle Fred died in the War (a sacrifice to the common good), his nephew is helped through hard times. All that counts from an evolutionary perspective is that one's inclusive fitness is improved.

One point that is often overlooked when discussing this sort of thing, is that it means that our biological dispositions created modern society. Evolutionary psychologists often say that our evolved dispositions are maladaptive in modern society. I find that hard to accept - we are in our "natural environment", because we made it. So we ought to go looking for the adaptive benefit of our general tendencies in urbanised agrarian societies, and not naively assume that if only we lived like foragers of yore, we would all be much happier. Perhaps we would if things went well. But have a population explosion, or a change of climate, and we would be damned unhappy. I read recently that "traditional" forager societies have a murder rate around 2-5% over an adult lifetime. That's much worse than New York during the 1980s.

Wolfe's essay is entertaining, and has some nice case examples, but it's not exactly news...

Friday, May 12, 2006

They call him the Decider

The US has an endangered species day

or so I found out from Grrlscientist. Given the extreme focus of US conservation policies on individual species, and the Endangered Species Act itself, now under attack from conservatives, I suppose this is a good thing. But one wonders, when will they have National Endangered Ecosystems Day?

They'd need to have it every week, I should think.

Hybrids in the news

I have a long standing interest in hybridisation, one that appeared out of nowhere after I read Jan Sapp's Evolution by Association, which is about another intuition-breaking aspect of evolution, symbiosis.

Hybridisation as an explanation of biodiversity goes back at least to Aristotle's History of Animals (Bk VIII, ch 28).

As a general rule, wild animals are at their wildest in Asia, at their boldest in Europe, and most diverse in form in Libya; in fact, there is an old saying, ‘Always something fresh in Libya.’

It would appear that in that country animals of diverse species meet, on account of the rainless climate, at the watering-places, and there pair together; and that such pairs will often breed if they be nearly of the same size and have periods of gestation of the same length. For it is said that they are tamed down in their behaviour towards each other by extremity of thirst.
"Libya" is the name for Africa, from the Hellene perspective, of course. Aristotle had another long standing account of biodiversity too - the effects of local water, soil and climate. This view wasn't abandoned until the early years of the 20th century. But it's hybrids that fascinate me and motivate this post.

Hybrids were accepted as a way to "fill in" the empty territory of the Great Chain all through the middle ages, through the renaissance and Reformation, by the translators of the King James Bible, and even by Linnaeus, the champion of species fixity. Mendel was in part attempting to work out how hybridisation generated the material for evolution, at a suggestion of von Nägeli, who was in effect his scientific mentor.

Oddly, though, hybridisation plays a largely negative role in modern evolutionary thought - a species is defined by its inability to hybridise, according to the Mayrian hegemony, at any rate. More positive conceptions like the Recogniton Concept or the Genetic Cluster concept focus on the cohesion of species rather than the isolation between them.

So I am going to post, whenever I become aware of a case, instances of hybridisation, both as a counterexample to the Mayrian Reproductive Isolation Conception of Species, and as an example of a process that we tend to overlook and which needs more attention.

The inaugural example is a hybrid between a grizzly bear father and a polar bear mother, taken from a note on John Hawk's site. It is often the case that when a species is stressed ecologically, and members find it hard to find mates of their own species, they will attempt to mate with closely related species. This has been seen with lions and tigers, ducks, and wolves and coyotes, to mention just a few cases. I wonder if this might be due to the warming effect reducing the hunting territories of the polar bear. The polar bear is sometimes regarded as a subspecies of the Brown Bear of which the grizzly, kodiak and Mexican Brown Bear are subspecies, though, so this might be just a case of introgression between locally adapted members of the same species.

Tuesday, May 09, 2006

A model scientific paper

Here is a model paper, the very paradigm of what a scientific paper should be...

Did the Neandertals jump, or were they pushed?

John Hawks is involved in a bit of a stir by suggesting that there was little or no overlap between sapiens and neanderthalensis occupation in the Near East and Europe. A Yahoo report today gives the claims of those for and against the idea of there being little overlap. It seems that Aurignacian culture, which ended around 29,000ybp, may have been Neandertal, rather than modern human. This may also put a dent in the view some have that Neandertals and modern humans interbred, although I gather that is not a popular hypothesis anyway. Fun to watch from the sidelines...

Monday, May 08, 2006

Poor creation scientists

Click on the comic to see it at home.

Sunday, May 07, 2006

The evolution of lawns

PZ Noun laments the need to mow his lawn. So do we all (I have a Darwinian view of gardening - anything that can survive my tender ministrations deserves to be there. I once killed a cactus by under-watering. I have a shriveled black thumb). But nobody asks the obvious question: why do we have lawns at all?

I have a theory. It is mine (ahem). Consider what lawns are - they are composed of early colonising plants that typically grow in patches of recently cleared ground. Later, longer grasses take over, and if the conditions are right, and there are no grazing animals, trees and forests. So it takes a considerable amount of energy to maintain a lawn. Why would we do this?

The English had lawns of camomile and herbs in the middle ages. Grass lawns began as part of the seventeenth century fashion, out of Italy, France and England, of bordered and hedged gardens, which were made by the rich aristocracy, who had plenty of land around their manors and palaces. A mown lawn was an indicator of wealth, disposable land, and servants to do the scything before mowers were invented in 1830. So it became the fashion for the middle classes, who were on the rise at the time in terms of wealth, to emulate the aristocracy. Lawns became particularly an English passion, and from there to America and the Commonwealth.

Why would we have lawns? To display our wealth and status. In other words, to behave as social dominance behaving apes. And the use of land is particularly interesting. We evolved as territorial nomads, not as landholders. What made us landholders was the coevolution of agriculture. When you spent most of your time sowing and nurturing crops, you needed to defend your territory (Rindos 1984), which gave rise to a warrior class from whom the rulers were chosen or arose through might and alliances.

One of the things that such wealthy rulers do is display their status through conspicuous consumption. Lawns were a case of "honest advertising" in that respect. Having land meant that you controlled power, such as military might, and could waste perfectly useful crop fields for a useless product that had nothing to recommend it other than it looked good.

Lawns also take an inordinate amount of water. In arid countries and places like Australia and the south western United States, to waste that much water is another signal of wealth. Of course, this requires that the signal is both differentially available (if everyone can grow one, it's not that much of a status symbol), and of course that the water is freely available. Unfortunately, now that the fashion is ensconced in our culture, we can't continue to do this, so the social selection pressure with rise to have them to display wealth. So something is going to have to give.

And none of that even begins to address the problem of ecosystems for native animals. PZ Thingy needs to grow his prairie.

Rindos, David (1984), The origins of agriculture: an evolutionary perspective. Orlando: Academic Press.

Late edit - south eastern to south western, as per reader's edit in comments.

Rick Pombo - the Gnostic gospeller of "wise use"

Here is an interesting item at Counterpunch on the anti-environmentalist Senator Representative Rick Pombo (R, CA). An opponent of the Environmental Species Act, Pombo wrote a book described here as "the book acquired the allure of a Gnostic gospel among the "Wise Use" crowd, whose concept of wise use derives from God's commandment to Adam in the book of Genesis to pillage the earth's natural resources as he thinks fit." Again, the use of religion by conservatives to support exploitation, in this case of ecological systems, for profit shines through.

Once upon a time "conservative" meant "one who desires to keep things stable". Now it means "one who tries to take whatever can be took". It's a peculiarly American definition of "conservative".