Friday, October 26, 2007

Neandertals: pale skin

I'm going to do something different, and pull something verbatim.

The radio report suggested red hair/pale skin was of Neanderthal origin, and that the original humans were more like modern Africans: Black hair and dark skin.
(Neanderthal, of course, has been reclassified to Homo sapiens neanderthal, and us as Homo sapiens sapiens. Here's the BBC report from the web (which is slightly different from the [world] radio version):

Some Neanderthals were probably redheads, a DNA study has shown.
Writing in Science journal, a team of researchers extracted DNA from remains of two Neanderthals and retrieved part of an important gene called MC1R.
In modern people, a change - or mutation - in this gene causes red hair, but, until now, no one knew what hair colour our extinct relatives had.
By analysing a version of the gene in Neanderthals, scientists found that they also have sported fiery locks.
"We found a variant of MC1R in Neanderthals which is not present in modern humans, but which causes an effect on the hair similar to that seen in modern redheads," said lead author Carles Lalueza-Fox, assistant professor in genetics at the University of Barcelona.
Though once thought to have been our ancestors, the Neanderthals are now considered by many to be an evolutionary dead end.
They appear in the fossil record about 400,000 years ago and, at their peak, these squat, physically powerful hunters dominated a wide range spanning Britain and Iberia in the west, Israel in the south and Siberia in the east.
Our own species, Homo sapiens, evolved in Africa, and displaced the Neanderthals after entering Europe about 40,000 years ago. The last known evidence of Neanderthals comes from Gibraltar and is dated to between 28,000 and 24,000 years ago.
Selective pressure
Until relatively recently, scientists could turn only to fossils in order to learn what Neanderthals were like. But recent pioneering work has allowed scientists to study DNA from their bones.
In Neanderthals, there was probably the whole range of hair colour we see today in modern European populations, from dark to blond right through to red
Dr Carles Lalueza-Fox
Genetics could shed light on aspects of Neanderthal biology that are not preserved in fossils. These include external appearance - such as hair, skin and eye colour - cell chemistry and perhaps even cognitive ability.
This will help scientists address key questions, such as why we inherited the Earth and not them.
Genes for skin colour and hair colour are obvious early targets for scientists engaged in these efforts.
In modern people from equatorial areas, dark skin and hair is needed to guard against skin cancer caused by strong UV radiation from the Sun.
By contrast, pale skin - along with red or blond hair - appears to be the product of lower levels of sunlight present in areas further from the equator such as Europe.
"Once you go out of Africa, the selective pressure from UV radiation disappears. So any mutation that falls into the MC1R gene is allowed to survive and spread through a population," said Dr Lalueza-Fox, speaking at the Climate and Humans conference in Murcia, Spain.
But people with fair skin are able to generate more vitamin D, which may have given them an evolutionary advantage in northern regions.
Altered chemistry
The latest research suggests that similar adaptations were evolved independently by Neanderthals and modern Europeans in response to similar environmental circumstances.
All humans carry the MC1R gene, but modern redheads possess an altered, or mutated, version of it.
This rare variant doesn't work as effectively as more common forms of the gene. This loss of function alters the chemistry of the cell, producing red hair and pale skin.
In the latest study, the authors retrieved fragments of the MC1R sequence from Neanderthal bones found at Monte Lessini in Italy and from remains unearthed at El Sidron cave in northern Spain. DNA is notoriously difficult to obtain from very old specimens such as these.
"This was a bit like finding a needle in a genomic haystack. I couldn't believe we found it the first time. I asked my friends to repeat the results. Eventually the variant was found in two separate Neanderthals in three different labs," said Dr Lalueza-Fox.
Unique variant
The researchers found that Neanderthals carried a unique variant of the gene not present in modern humans.

Until now, information on hair colour has been sparse
In order to test what effect it had on hair and skin colour, the researchers inserted the Neanderthal variant into a human cell called a melanocyte.
Melanocytes produce the dark pigment called melanin which gives skin, hair and eyes their colour.
The researchers saw the same loss of function in the Neanderthal form of MC1R as they did in modern variants of the gene which produce red hair.
"In Neanderthals, there was probably the whole range of hair colour we see today in modern European populations, from dark to blond right through to red," Dr Lalueza-Fox told the BBC News website.
To Dr Lalueza-Fox, the observation that the Neanderthal version of the gene is not found in modern humans suggests they did not interbreed with each other, as some scientists have proposed.
Primitive speech
Dr Clive Finlayson, director of the Gibraltar Museum, commented: "It's extremely interesting - it makes us understand a bit more about who the Neanderthals were.
"It suggests there may be a propensity towards the reduction of melanin in populations away from the tropics. If the Neanderthal and modern variants are different, it may be a good example of parallel, or convergent evolution - a similar evolutionary response to the same situation."
"Neanderthal genetics is going to give us a lot more information. This is the tip of the iceberg."
In a separate study, published in the journal Current Biology, Dr Lalueza-Fox and colleagues extracted the DNA sequence for a gene called FoxP2 from Neanderthals.
Modern people have several changes in this gene that are absent in our relatives the chimpanzees. This suggests that FoxP2 may have been an important gene in the evolution of language, something which separates us from the great apes.
The researchers found that Neanderthals shared these key mutations in FoxP2 with modern humans, suggesting they had some of the prerequisites for language and speech.
An ongoing project to sequence the entire Neanderthal genome was recently hit by the discovery that samples had been contaminated with modern human DNA.

Tuesday, October 23, 2007

Refinement of evolutionary theory

A quick summation of evolutionary theory might be in order. Different books tend to make up different equations on what constitutes current thinking, so I might just take the flattened versions, in the main, of Wikipedia.

Darwinism: Evolution by natural selection (I find "survival of the fittest" a particularly misleading phrase - and it's not really used by those in the know anyway). The generally accepted use excludes some misconceptions Darwin had or didn't rule out [not having a handle on genetics at the time], including Lamarckianism, the fallacy that acquired characteristics could be inherited. However, this general use is more strictly neo-Darwinism (below)

neo-Darwinism: Not correctly in current use; refers to refinements of Darwinism to about 1895. Wikipedia redirects this to the following (modern evolutionary synthesis), although there is an extant article on neo-Darwinism if you have the link - here. Incorporates refinements from Alfred Wallace (often mentioned along with Darwin when books are in the mood to be more correct), which specifically exclude Lamarckianism.

Modern evolutionary synthesis: the general basis of evolutionary thought since the 1940s. Genetic variation happens through chance mutation (and recombination in sexual interaction/selection); evolution happens through changes in the frequency of alleles (variants within a species) between one generation and the next, through natural selection and genetic drift. You can see how Wikipedia puts it here.

There's some subsequent argument on the unit of evolution: is it the gene (Dawkins)? The individual? The Species? or the Clade? (Gould seems to argue for some combination or synthesis of these.)

Some books put together an equation, with many incomplete variants such as:
reproduction + natural selection + mutation = evolution

From my readings, I would add some attendant concepts that help round out conceptualisation of evolution.
anthropocentrism - the great barrier to clarity in understanding is our own location at this point in evolutionary time and space. We too easily see things to our own scale and bias. The path to modern human has been, as one writer said "zigzaggy" over a period of time that is impossible to properly place in perspective.
the environmental niche - that is, an environment and its attendant organisms, whether it is isolated or experience some movement in or out of the environment
genetic drift (as mentioned above) - that is, even aside from mutations that are more favourable within the environment, there are changes (mutations) that have no nett effect on the individual or species survivability within that environment. The smaller the population, the more prone to drift, where isolated from other members of the same species and even when the environmental niches are equivalent. Change still happens.
redundancy and multiple use - a great engine for evolutionary change is available when two body parts can fulfil the same function, or one part can serve two functions. For example, a swim bladder in a marine creature that eventually facilitates air-breathing and develops into a lung; or bones in the jaw that help perform rudimentary auditory functions, then over time become exclusively used for hearing.
environmental change - more of a fundamental than most people admit, in my reckoning. Even aside from catastrophes that result in mass extinctions, environmental niches are never static in geological time scales. The whole planet is not static: plate techtonics, over time, affect global and local environments.

On another note, it's too easy to pretend environments don't change, and that without human interference, the planet would be a happy little paradise of biodiversity. That's simply not true - on geological time scales. But on the time scale of human history, it's sad but true: we have rocked the boat far too quickly.

Monday, October 22, 2007

Warsaw: No Love Lost

I was thoroughly annoyed with the Joy Division compilation Substance. Not because it overlooked one of my favourites, the perennially ignored Atrocity Exhibition, but because it included a patently inferior version of No Love Lost.

For my money, the best Joy Division album was the canned Warsaw. According to Wikipedia, it was scrapped because the band was "disappointed with the post-production" work. Well, bully. Maybe because it sounded more rock than punk? Too slick? In any case, it is a very solid album, for rock of any type. The anger of punk fused onto some great guitar music.

The track No Love Lost was recorded on at least two occasions. December 1977, later surfaced on Ideal For Living, and, later, the dreadful compilation above. May 1978 was the Warsaw album, finally released in 1994. (To my ears, there was a third recording of this track, also inferior, but I could be wrong.)

Why was the album named Warsaw? I understood it was eponymous - Warsaw was Joy Division's earlier name. But they changed their name in 1977, well before the recording. I guess it was named for the eponymous song, Warsaw.

The tone of the album was more anger than despair, uncharacteristic for Joy Division's work. No Love Lost was the peak of the album: a very long intro that reached a crescendo of guitar fury before the vocals even started, subsequently the two interplaying to great effect.

The version that matters doesn't include the words "no love lost". It's the one whose near-spoken bridge begins "two way mirror in the hall/they like to watch everything you do". Ah yes, good old punk paranoia on a hard rock riff.

I just had to mention this track. No Love Lost is right up there in the pantheon of Great Overlooked Music.

Why did this come up in the first place? My wife was invited to a premiere of the film Control, a biopic of Ian Curtis. I reckoned she wouldn't like the subject matter (and she's no particular fan of rock, punk or new wave), but she came back and said the film was actually very good. So there you go.

Saturday, October 20, 2007

Surprising Mike Bailey

Sky News had a debate today between North Sydney candidates Mike Bailey and Joe Hockey.

Industrial Relations Minister Joe Hockey is in trouble.

His opponent Mike Bailey, weatherman(!), comes across as a particularly sincere, thoughtful candidate; Joe Hockey comes across as simply an experienced politician.

The polls don't give a flavour for this.

Thursday, October 18, 2007

Unsafe abortions

The Herald reported a study on abortions worldwide, published in Lancet recently. It found that abortions occurred at about the same rate in countries where it was legal as in countries where it was legally restricted.

Inter alia, lead author Gilda Sedgh said that whether an abortion was safe or unsafe depended largely on whether it was legal; there was a higher incidence of unsafe abortions in countries with higher legal restrictions.

Sedgh: "The findings presented here indicate that unrestricted abortion laws do not predict a high level of abortion, and by the same token highly restrictive abortion laws are not associated with low abortion incidence."

The report summary also said:"Overall abortion rates are similar in the developing and developed world, but unsafe abortion is concentrated in developing countries. Ensuring that the need for contraception is met and that all abortions are safe will reduce maternal mortality substantially and protect maternal health."

Wednesday, October 17, 2007

Election: the Green Scorecard

The Australian Conservation Foundation has released a green Election Scorecard. Their press release headline is that both major political parties failed.

The score is:
Liberal/National 21%
Labor 49%
Greens 93%
Democrats 90%
Family First 31%

Now it might seem a tad unfair to say they both failed when Labor is streets ahead of the Liberals. But it should be borne in mind that the election is the only real, major opportunity to have any effect on environmental issues. It's a stepwise change only, with few supsequent gains possible. So it pays to put pressure on Labor while there is that opportunity.

The Greens' score is unsurprising - the difference between 93% and 100% can be ascribed simply to difference of opinion between environmental groups. That the Democrats scored 90% may be a bit surprising. But then, I recall somewhere around 1991 helping out the Democrats (scrutineering for them, even) through The Wilderness Society, who felt that neither main party had sufficient integrity on the issue. This was not too long before the enviromental movement coalesced into the Greens as an actual political party.

That the Scorecard is intended to goad Labor more than anything else can be gleaned from the stats. Although a Newpoll showed that more people were aware that Labor was better at managing the environment than Liberal (39% to 25%), it still means that 61% don't really have a clue. In fact, an earlier poll of marginal electorates showed that those swinging voters who will decide the election aren't actually aware at all which party is better for the environment. And if the political processes haven't filtered through to them by all this time, then they're hardly about to notice a headline lumping togerther the Liberals and Labor on the issue.

Thus, the best tactical move is to put the frighteners up Labor at a time where they should be most amenable to the electorate's concerns.

Monday, October 15, 2007

Election: try the World's Smallest Political Quiz

The election date has finally been announced (24 November), and the "phony" election campaign is over. The government can't spend money on political ads now, nor take any startling new initiatives.

And the first promise the Liberals made was $34 billion in tax cuts over the next three years. They understand well the response to tax cuts, but this cuts across what's been shown (in several surveys) as the electorate's key concerns:
  • economic management
  • industrial relations
  • environment
  • health
  • education

- in that order, I believe. In this context, a tax cut would seem to go against all those - it's called disinvestment. But it's aimed at people who aren't very engaged in the political debate, and at the margins there are people who don't make the connection between tax cuts and disinvestment. (In contrast, the ALP are talking about reinvesting in infrastructure, health and education, while maintaining a budget surplus.)

I mentioned it in passing six months ago, but it's worth making a point of it: the world's smallest political quiz. Ten questions, and it positions you on a two-axis chart, from liberal to conservative, from "big government" to small. It should be enough to allow any swinging voter to see through the bribery, and identify where one's sympathies really lie, and where one's votes should really go.

But if you're not a swinging voter, you probably already know.

Sunday, October 14, 2007

Where is the danger in creationism?

Yesterday I had the privilege of talking to a couple of creationists face to face.

They had set up a stall at the Surry Hills Festival. One said he had a degree in philosophy; the other had not done any post-secondary school study. If I recall correctly, both said they had studied evolution for decades. At least one was well aware of Stephen Jay Gould's paradigm-shifting work on punctuated equilibrium.

It's is ipso facto hard to gain traction in a discussion where the perspectives are pretty much orthogonal. Perhaps with more thought I could have established more points at which our perspectives overlap, and can agree or disagree.

They both cherished the fact that their perspective was published in peer-reviewed journals. What journals? "Journal of Creation". Who are the peers? Creationist scientists. (You may view that as oxymoronic, but they adhere to scientific method to a degree. At what stage it becomes non-scientific is a matter of disagreement.)

Of course, their viewpoints aren't given scientific credence, and specific examples wouldn't survive peer review in the wider, fully scientific community.

Or would they?

Three cases demonstrate some of their limitations.

The first is a finding by Mary Schweitzer of blood cells and soft tissue with a Tyrannosaurus Rex bone. Now it made absolutely no sense to me that this could be, but one of the creationists said it demonstrated that dinosaurs didn't die out as long as 65 million years ago. I asked what was the science community's response to Schweitzer's finding. He said they rejected it because their mindset couldn't handle it (well, he would say that, wouldn't he?)

I asked what it said on Wikipedia, but he didn't trust Wikipedia. I looked it up when I got home. In fact, it said Mary Schweitzer characterised herself as a "complete and total Christian", but that she resented Young Earth Creationists hijacking her work, and said they "twist your words and manipulate your data".
(I remain blown away by her finding, and will make further investigations.)

The second example was the Peppered Moth. This is the standard biology textbook case of the moth in England during the industrial revolution, which started out a light colour, but the successful mutations were the ones that had darker colouring, and so were better camoflaged against predators in an environment that rapidly became dirtier, darker, more polluted. The creationist said that Kettlewell was the bloke who made that finding, and his results were subsequently shown to be fraudulent.

Apparently, it is accepted that there were "errors and oversights" in his work. But crucially, subsequent study has confirmed the findings.

Thirdly, discussion came to global warming. The creationist admitted he hadn't formed a viewpoint yet, but noted that a judge in England had found eight errors in the film An Inconvenient Truth.

This brings me to a central issue in the politicised climate of the global warming debate. If there are errors, are they sufficient to invalidate the whole conclusion?

In this case, the answer is no, of course, but the general lack of understanding of scientific method is specifically what enabled vested interests to cruel the general population's appreciation of the urgency of the issue for the past twenty years. Twenty years in which action could have been initiated before it is too late. And it is too late, in the sense of the recent findings that carbon emissions to date are already sufficient to raise global temperatures. Whatever action we take right now.

Al Gore ably demonstrated the gulf between the understanding of the scientific community and that of the wider community, when he noted that in a survey of hundreds of peer-reviewed scientific literature, not one paper doubted the issue was real, whereas over 50% of media articles surveyed included expressions of doubt.

This is why I have a serious problem with creationists. The general lack of understanding of scientific method has hampered action on a world-changing issue. At the most generous reading, creationists' selectivity in the use of science, and lack of commitment to objectivity (which - in totality - is key to the advance of scientific knowledge), have only served to perpetuate a level of ignorance that has been very damaging to the world.

I return to the comment in New Scientist that the beauty about science is that it doesn't matter what you or I believe, the world is as it is. Scientific method, over time, uncovers that truth. Creationist dialectics helps keep the truth at bay.

Friday, October 12, 2007

Al Gore, Nobel Peace Prize

Congratulations, Al Gore. I've been saying this for the past year, but the issue's been on the table for 15 years, quite clearly. The Nobel Peace Prize is a challenge for the whole world, to action.

Immediate refugees from Climate Change

From Aim High, the newsletter of Australian Ethical Investment (supplemented from Friends of the Earth Australia, whom AIE helps sponsor):

The Carteret Islanders, located off the coast of Papua New Guinea, are amongst the world's first cliamte change refugees. An entire cultural group is facing relocation due to rising seas and flooding.

The Carterets are a scattering of low lying islands in a horseshoe shape stretching roughly 30 kilometres in a north-south direction, with a total land area of 0.6 square kilometres and a maximum elevation of 1.2 metres above sea level.

While the islanders have fought for more than twenty years against the rising ocean, by building sea walls and planting mangroves, storm surges and high tides continue to wash away homes, destroy vegetable gardens, and contaminate fresh water supplies.

On November 24, 2005, the Papua New Guinean government authorised the evacuation of the islands, 10 families at a time, to Bougainville. The evacuation started in early 2007 and this could continue up until 2020, depending on how inhabited the islands remain. However, it has also been estimated that by 2015, the Carteret Islands could be largely submerged and entirely uninhabitable.

There are significant cultural issues in relocating an entire people from atolls to the mainland where different food, livelihood and living conditions will affect the identity of the people.

This situation is but one example of the impacts being felt in our region. It highlights the need for rich countries like Australia to stop harming, by significantly reducing their emissions, and start helping, by supporting adaptation and resilience building in climate affected communities.

The Carteret Islands (also known as Carteret Atoll, Tulun or Kilinailau Islands/Atoll), are part of Papua New Guinea (PNG) and located 120 kilometres northeast of Bougainville in the Pacific Ocean.

All of the islands are on the edge of the lagoon and the population of the Carterets is about 2,500 people. Han is the largest island, with a population of about 1,000. All of the islands have tree cover, except where small clearings have been made for crop gardens.

Impacts of climate change
Salt water intrusion is becoming a growing problem and appears to be a result of climate change induced sea-level rise mixed with the natural variation in elevation of atolls. This natural movement or variation in islands exacerbates the vulnerability of the Carterets to the climate change impacts of sea-level rise because it allows salt water intrusion during times of storm surge behind houses and gardens.

Thursday, October 11, 2007

Sources, and the value in going offline

A few days without internet access gives quite a different perspective on information absorption.

When I found myself with some research to do and some time to do it, Internet access was kaput. So I spread out a number of books around me: Britannica, Stephen Jay Gould, two evolution primers, two academic books, and an evolution atlas. I also consulted my mother, since she'd done a geology degree some years back.

It's rather different from the lazy person's guide to everything, Wikipedia:
a) Within each source, the information was less well structured, and less lucidly presented. I had to do more work to extract the information;
b) I had a variety of viewpoints in toto, as opposed to ground down and polished within Wikipedia;
c) I found errors in most sources.

Britannica is often dreadfully opaque, and rambles on in whatever fashion it chooses to ramble on about, making it difficult to gain an overview in the context I was seeking. My mother gave the best overview of geology - because the investigation process was interactive. However, as with everyone there are gaps.

Looking through five books for that standard diagram of geological time, I found five different pictures. It's expected that there will be some differences: time periods definitions have traditionally differed between the Europe and the US, and have changed over time. Yet I found actual errors (or egregious omissions) in each one. Except Britannica - because the diagram I found was sparse on detail.

- Wikipedia is certainly less time consuming to consult. Yet although it gives different perspectives, they're not usually well fleshed out; and while the detail is generally good, it lacks the depth of a dedicated work. And you can chase down the sources when necessary;
- Britannica is a substitute for internet access; no more authoritative than Wikipedia (in general), but harder to navigate and less up to date;
- comparing and contrasting different sources can provide extra insights;
- indepth narrative often provides extra insights too;
- trust yourself, and if something doesn't sound right, chase it up rather than accept it;
- consult your mother.

Wednesday, October 10, 2007

Recovery from mass extinction

Douglas H Erwin (Dept Paleobiology, Smithsonian Institute) - Lessons from the past: Biotic recoveries from mass extinctions

This paper, for a 2000 colloquium, "The Future of Evolution", is essentially a literature review in the area of recovery from mass extinction.

Although it's the extinctions that capture the imagination, environmental and species recovery can be seen as more pertinent, since this defines the pathway to the present.

Erwin characterises two types of extinction event: pulse extinction, which is too rapid to see adaptive organic response, and press extinctions, where the environment gradually turns sour (so to speak) for a large number of existing species, but for which steady adaption to environmental change is possible.

For pulse extinctions in particular, recovery is characterised as gradual expansion from more sheltered environments, best exemplified by deep water (below continental shelf) niches, which would be most resilient to changes in temperature or atmospheric oxygen.

Initial post-extinction fauna typically consists of a limited variety of widespread species. It's not obvious to me whether this is due to opportunistic expansion or good suvival of prevalent species, but the paper suggests the former. However, there's a cautionary note that that shouldn't be taken as global spread.

There is some support for the intuitive notion that more ["morphologically"] complex species suffer more in mass extinctions - ie the evolutionary clock is reset or wound back somewhat. That in itself should give pause for thought.

The paper makes several mentions of "Lazarus taxa" - species which apparently disappear at the event's boundary, only to subsequently reappear. These are often simply an illustration of the gappiness in the fossil record, but Erwin suggests this can often be due to biogeographic differentiation, ie local geography. For example, he says that extinction is less apparent in the southern hemisphere after the K/T event - the meteor in the shallow waters of Yucatan, Mexico.

A couple of minor extinction events are mentioned: the early Jurassic Toarcian event and the Late Cretaceous Cenomanian-Turonian event. In the descriptions given, I see both as bearing putative symmetry with current conditions: both are press extinctions involving marine anoxia (oxygen depletion) during relatively high sea levels and a greenhouse climate. Adaption (by anoxic-adapted species such as bivalves) is suggested rather than opportunistic expansion [by a few remaining species].
Lest this breed complacency, it's worth noting that recovery of the terrestrial (and thus atmospheric) carbon cycle took a mere 130,000 years!

From peak of extinction rates to peak of speciation (diverse and specialised fauna) is at one point set to about 3 million years - but I would find it hard to accept generalisations on this. Some interesting phenomena in the interval include:
- clades on the wane as others gradually take over, which is reversed by the extinction event, simply because of the greater resilience to the specific event. Erwin mentions cheilostome bryzoans taking over from cyclostomes, only to have the latter triumph over the conditions of the event;
- other lineages that survive the event, only to disappear as (re)speciation hits its peak.

Overall, the suggestion is that there is no clear relationship between the magnitude of an extinction and its evolutionary impact. Modelling has shown 80% of phylogenetic structure to survive a 90% overall species loss. That is, most body types survive, and subsequent speciation is only a matter of variants.

Which would bring us back to the question of the Cambrian Explosion: why a short period of evolutionary activity resulted in pretty much all the body types in existence today.

Tuesday, October 09, 2007

Election: still postponing the inevitable

The last election was held three years ago today. It was called August 29 for October 9.

Of course, this year's election has been delayed because the Liberals are so far behind in the polls that they're giving themselves as much time as possible to catch up. Not that it's helped: the last couple of opinion polls have not moved a jot in their favour.

Howard has claimed he'll call the election before Christmas, but given the necessary lead time, the available Saturdays are rapidly slipping away.

Apparently, he doesn't have to call the election until January. And if the omens aren't propitious, it's not too long a call to say he might drag it out that long. If nothing else this year, Howard has readily demonstrated his grim determination to hang on to the Prime Ministership as long as humanly possible. His accession to handing over the reins to his deputy at some time in the next term is just such a sign. The vagueness in that pronouncement could be seen as a sop to the voters who aren't enamoured with Costello, but it's entirely within character that he would hang on until just before the following election. Howard has at several points in the past stated that his life's ambition had been to be Prime Minister. Not "statesman", no focus on what he would achieve. Just to have that top job.

There's a particularly good reason for not announcing the date, as the Herald pointed out yesterday. Once announced, the government is in caretaker mode and spending has to stop. In particular, this means a halt to the tens of millions of dollars worth of current advertising campaigns (on a wide variety of fronts) that are posing as "government information" yet are undeniably party political.

And they haven't finished yet. In addition to taxpayer-funded political advertising, they're spending our money on expensive market research to test how effective that political advertising has been. When you think about it, that's quite a rational thing to do: if you've still got access to the money, it makes sense to test how effective that spend is. Rational, but clearly piling one unethical behaviour on top of another.

Opposition leader Kevin Rudd would have political ads banned three months out from an election. Yes, he would say that. But that is not unethical behaviour.

The calendar is such that if Howard doesn't call the election this weekend, parliament would have to sit again next week, which recall would again cost millions of dollars (albeit not in the same league as the above advertising spent). Would he suffer that cost - and opprobium?

News reports suggest he would. He has indicated he plans to attend a Pacific Islands Forum in Tonga next week. There's no way he would be away in the first week of an election campaign, so it looks like we're going to have to wear at least a week's worth of parliament - with no business scheduled.

And the election date is dragging towards Christmas.

Friday, October 05, 2007

Evolution, diversity, and Gould vs Dawkins

In the book Wonderful Life, Stephen Jay Gould made a subtle point about species diversity. While accepting that life over the past few million years "is more diverse than it has ever been" (Sterelny, p71), he characterises this as not the peak of "disparity" - diversity in a different sense, thus requiring application of a different term.He refers to disparity as the number of different types of body form or plan. So, for example, the large number of types of beetle contributes to the overall species diversity, but not disparity.

He attributes the peak of disparity to the time of the Cambrian explosion (530-odd million years ago), where a large number of multicellular animals with substantially different body types "came into being" so to speak. Specifically, it looks like he's referring to the the number of different phyla. (the animal kingdom is made up of 25 to 80 different phyla, depending on who you talk to. Most of the animals we are aware of come from just a handful of phyla, eg vertebrates, invertebrates, etc; most phyla are obscure, unnoticed, and with just a handful of representatives.)

The disparity of life forms never again matched that of the Cambrian era, which Gould says is one of the key issues of evolution that needs to be explained. Conversely, he says that the remaining lineages show - by comparison - "profound evolutionary conservatism".

As Sterelny (see below) points out, by analysing and comparing at the genetic level (DNA/RNA) two species, it's possible to make some observations on the length of time since they diverged from a common ancestor. Yet the technique is silent on the rate of divergence, for example whether they made key changes regularly, or all at once close to either the beginning of the divergence, or to the period contemporary to the species.

The Cambrian explosion presents little evidence of earlier formations, yet it is the time of (sudden) record of the greatest disparity of species ever.

Sterelny's book is called Dawkins Vs Gould: Survival Of The Fittest. Here's where he paints Richard Dawkins in opposition to Gould (and although I can't be sure how much of his dichotomisation is a straw man, it is clear there has been divergence of perspective - and opinion - at times). Sterelny portrays Dawkins and his adherents as "cladists". In this context, it means they are relatively blind to disparity (as opposed to diversity in general). Sterelny says the true cladist says morphology (the comparison of similar features between species) is unimportant compared to the genetic distance between two species. As mentioned before, in one sense this is true. But this well illustrates one definited divergence in perspective between Dawkins and Gould. It is one thing to say that taxonomy (and cladograms) should be wholly based on genetic proximity (and thus break down reptilia as a grouping). But genetic analysis only works on _our_ timescale, that is, what DNA can be extracted today. Morphology as paleontology is the only possible approach where the DNA evidence is unavailable, and is thus the only appropriate tool for analysis at large time scales. In any case, morphological taxonomy or cladistics must ultimately incorporate the findings of genetic analysis, so the two perspectives must converge.
So in Sterelny's terms, Dawkins would not regard the Cambrian explosion as particularly noteworthy. In the history of life on earth, those diverse phyla _must_ have been more closely related than many that exist today. However, this is where I see the straw man in Sterelny's argument, because I simply can't see someone of Dawkins' experience writing off the Cambrian experience thus.

If I've counted them correctly, Sterelny measures three chief points of convergence between the two evolutionary biologists, Richard Dawkins and Stephen Jay Gould. Foremost, Dawkins is a genetic biologist, and Gould is a paleontologist - that is, their analytical perspective begins at the micro versus macro level. Dawkins is further characterised as the arch-rationalist - as he has demonstrated - who believes that "the scientific description of outselves and our world... is true... beautiful and complete". Then Gould is the humanist who "does not think science is complete".

Being a rationalist and a humanist myself, I can vouch that the two are not mutually exclusive, despite that portrayal as diametric opposites. Science is science, and human sociology, per se, is not - it's humanity. Yet humanism can be brought into the sciences without in the least abrogating scientific method, as Gould readily demonstrates in all his books of essays.

(The third point of differentiation I will leave to another day. This relates to their divergent approach to ethical analysis, which Dawkins extrapolates from his work while Gould sees answers as outside the scientific paradigm.)

As a coda, I think it's important to remember that there is still _much_ to be discovered in both genetic analysis and paleontology. Sadly, both may be helped along by the greatest tragedy of our era, as climate change melts the Siberian permafrost, and unleashes both a torrent of field discoveries, and - if you credit some analyses - a vast reservoir of carbon that will superboost the climate changes already happening.

Thursday, October 04, 2007

Evolution: The sins of Cladism

I came across the term "cladist" as a term of derision, or at least "other" or "out there".

A clade is a "group of organisms evolved from a common ancestor" (Concise Oxford, 1988). [Interestingly, it's solely "a disaster, or plague", according to my 1933 Shorter Oxford; my Encyclopedia Britannica, 1974-88, doesn't acknowledge the word at all - which shows how recent this use is.]

Cladism is the branching off of species successively by "shared derived" features. Stephen Jay Gould describes cladistics as a "theory and philosophy of taxonomy" (with a history longer than the Britannica admits), about which he calls himself agnostic (p254).

However, Gould does find a great virtue - and some vices - in it. He describes a tradition of depicting evolution as a succession of improvements: we've all seen pictures of a parade of creatures, from fish to amphibian to landed reptile to mammal to primate to human. Gould's problem with the traditional approach is that it portrays humans as being at the absolute pinnacle of a succession of changes: here it goes, and no further. Any other evolutionary form is irrelevant: anthropocentrism rears its ugly head again.

Yet there have been changes, speciation, clades evolving subsequent to our own branching off. A cladogram is a diagram that depicts those changes by successive branchings on key characteristics. I find such a diagram can be somewhat arbitrary in terms of the species portrayed, but it can give a good feel for how speciation (the splitting into different species) can happen.

Gould's example from a museum depicts the following key branchings: synapsids, middle ear bones, placenta, stirrup-shape stapes, hooves, eye socket near the snout. On such a diagram, humans branch off just before the hooves, while the last group includes sea cows and elephants. Noteworthy is the little-known fact that whales branched off from ungulates - ie their ancestors had hooves!

So a cladogram can be more instructive - and realistic - than tradition preaches. But Gould's reservations on this are that it ignores: a) unique traits evolved by single lineages; and b) trends in groups that don't lead to branching.

This is a tool, though, a useful one but just part of a toolkit. I think it has useful instructive value, but I have a couple more problems with it. First, this "assessment of morphological characteristics" (Viking, p27) can ignore the fact that separate branches of life's evolutionary tree can evolve similar features independently. For example, whales are mammals, but share many outwardly similar features with fish. Sharks too, although they branched earlier. And memory tells me that there were at least two different branches of fish that separately developed the similar body forms that we know so well.

Secondly, such depictions are easily subject to substantial revision, in particular due to DNA/RNA analysis. Species that appear to have branched off together have been found to be far less related than external features suggest.

Sterelny, a Gould champion, confirms my misgivings in pointing out that true cladists would acknowledge mammals in a common clade from a shared ancestor, but wouldn't refer to reptiles at all, since there is no single leap-off point (p103).

Cladograms are useful, but subject to revision. Much of that revision will originate with DNA analysis, but that's only part of the story; fossils are not suceptible to this (Jurassic Park notwithstanding), and for that we need paleontologists such as Gould.

Brief references:
Australian Concise Oxford Dictionary, 1988
Shorter Oxford Dictionary, 1934Encyclopedia Britannica, 1988
Stephen Jay Gould, Dinosaur In A Haystack, 1996
Kim Sterelny, Dawkins vs Gould, 2001
Viking Atlas of Evolution (Consulting editor: SJ Gould), 1996