Thursday, February 28, 2008

Convergent evolution

This is always such a fascinating subject. Earth's natural history is positively littered with examples of different species that develop remarkable similarities to each other in complete evolutionary isolation.

An easy example is the body shapes of sharks (fish), cetaceans (mammals: whales, dolphins, etc), and ichthyosaurs (porpoise-like reptiles): all evolved fairly similar adaptions for swimming, although a notable difference is the tailfins of cetaceans, giving rise to an up-and-down tail movement, rather than side-to-side for the others. A ready observation would be that they show similar vertebrate adaptions to the similar demands of the environment.

There are so many other examples: similar-shaped and/or similar-functioned animals around the world. Try unrelated fish in the arctic and antarctic waters each with an equivalent anti-freeze-like chemical in their blood, with genetic origins quite unconnected.

Try re-invention of the eye several times. Albeit the squid's, for example, is better engineered than ours, since our retinal nerve endings emerge between lens and retina, making for less efficient vision that the squid's whose nerve endings sensibly emerge behind the retina. Moving ahead of myself in Richard Dawkins' The Ancestor's Tale (currently at p344), Dawkins mentions on p602 an expert in comparative zoology of eyes, Professor Michael Land, who identifies nine independent principles of optical mechanics, "each of which has evolved more than once".

Try the proliferation of parallels between eutherian (placental) mammals and metatherian (marsupial) equivalents. Thylacine and timber wolf skulls, for example are said to be nearly identical, despite being completely unrelated.

It sounds like a rash of grossly unlikely coincidences, ready-made for creationists to fan argumentative flames. Yet in some ways it makes perfect sense: evolution is about species expanding to fill environmental niches, and
a) Over many times and locations, there are sets of all but identical niches
b) What developed and survived was what was most successful in the environment, so the directive forces of nature operated in a similar way on what was often a relatively similar genetic material.

This is obviously quite a source of frustration for taxonomy. Whereas in the relatively recent past, classification was based largely on morphology (body shape and features), modern molecular analysis has demonstrated that many of the connections drawn in the past were examples of convergence.

Dawkins also describes three different moles. The African golden mole (Chrysochloridae) was grouped with the Eurasian mole (Talpidae) in the defunct order Insectivora on the basis of such close similarity as burrowing machines: forepaws modified as spades; atrophied eyes (superfluous underground) and no visible ears. Then there's the marsupial mole: Wikipedia says they are so similar to golden moles that they were once thought to be related despite the marsupial/placental divide. Of course, all three are now classified quite separately; molecular analysis has in fact torn down the whole disputed Insectivora order altogether.

Interesting to note convergent evolution depicted as a criticism of Stephen Jay Gould. One of Gould's consistent themes was the contingent nature of evolution: how randomness played such a role that any slight re-alignment would have resulted in totally different outcomes.

I don't see these concepts as being entirely in opposition. Gould's theme plays out on a much larger tapestry than the micro-evolutionary outcomes. Convergence doesn't necessarily mean, for example, that had the K-T meteor not wiped out non-avian dinosaurs, reptilian humans would have evolved. In the absence of that meteor, dinosaurs could have remained successful in their niches for many millions more years given no other environmental pressures.

I suspect that certain paths are available only for species at a certain level of complexity; yet evolution is not specifically directional towards complexity (merely towards variation in complexity)...

How convergence does and doesn't work, what it does do and what it doesn't, is a fascinating area of study.

Dawkins, R (2004): The Ancestor's Tale. Phoenix, London.

Wednesday, February 27, 2008

Garnaut on emission changes: too late?

In commenting on the Garnaut report, the Herald's Ross Gittens points to the obvious elephants in the room: the economic growth of India and China.

Yes, we knew this. But he also provides an breakdown of carbon emissions increase.

Garnaut notes that global carbon emissions grew at an average rate of 1.1% per year through the 1990s. This would have been what was taken into the 1997 Kyoto talks.

However, from 2000 to 2006, the rate of increase surged to 3.1% per year.

This change has been attributed to the following:

  • Global economic growth was 5% per year rather than the anticipated 3.3%
  • Growth became more energy intensive. In the 1990s, the "energy intensity" of global gross domestic product fell (improved) by 1.4% per year; however this decade, the energy intensity has been falling by only 0.2%
  • Energy use became more emission-intensive. Through the 1990s, cleaner fuels were used and the emission-intensity of energy use dropped 0.2% per year; however this emission-intensity increased by 0.4% per year this decade.

And all of this is said to be due to India and China coming on-stream in the economic world.

It remains difficult to begrudge those countries their due, although it makes the job that much harder.

Simulations run for Garnauts team require global emissions to peak by 2010 if atmospheric carbon is to stabilise at 450ppm.

Unlikely? It needs leadership from the developed world: to cut emissions by example, and to forge partnerships with those emerging nations to tip the balance in the right direction.

Two years is too short. Ten years might have done it. And that's what we lost with George Bush being declared winner in the 2000 presidential election. And officially, that's 537 Florida votes.

You couldn't write fiction like this.

Mass extinctions in earth's past, when due to climate change, have taken much longer than we're taking.

Sunday, February 24, 2008

End of life: sooner than you think

Stephen Jay Gould was fond of emphasising the contingent nature of life - and in particular the emergence of humans.

The earth is 4.5 billion years old, and it had been estimated that we are at about the halfway point in the planet's existence.

As we saw previously, life emerged about 3.5 billion years ago, about as soon as it theoretically could. However, it was not until around 540mya that complex multicellular animal life (as we know it) appeared.

A new paper by a University of Sussex astronomer, Dr Robert Smith, actually calculates that the Earth has another 7.6 billion years to go. But now for the bad news. According to Smith's team, the slow expansion of the sun will cause temperatures to rise well before that: "the oceans will boil dry and the water vapour will escape into space. In a billion years from now the Earth will be a very hot, dry and uninhabitable ball."

So, we actually have less than a billion years left on this planet. We're here near the end of its cycle, not the middle.

Of course, a billion years is a long time for us to come up with other means of survival. If we don't kill the planet earlier.

But the point is, in the great contingent nature of our planet's history, there's effectively only a small window of time in which such complex life as ours could have developed.

Lucky our war against prokaryotes (see previous entry) has been balanced as much in our favour as this. But are we already starting to tip the balance back the wrong way?

Mass Extinctions explained: prokaryotes vs eukaryotes

An article in the New Scientist points to an important way to trace evolution through the sedimentary rock record.

In the development of life into multicellular organisms, there is some difference of opinion on the most significant step: whether it's from simple single-cellular organisms (prokaryotes) to complex ones with nuclei (eukaryotes), or the evolution of single-cellular life to multicellular. Most seem to favour the former.

Whereas stromatolites give a record of when the earliest lifeforms first emerged 3.5 billion years ago (according to Stephen Jay Gould this was just about as early as it could) there has been no way to trace back first emergence of eukaryotes - until now.
Peter Ward reports on chemical biomarkers in rock. Certain biological molecules break down under heating, cooling and pressure into highly stable organic compounds that could not be made by any known inorganic process. That last phrase is the kicker, which indicates that any such occurrence of the relevant compound would be an indicator of life. Moreover, some of the compounds are unique to particular groups of organisms. For example, C28 to c32 polyenoic fatty acids have been found to be unique biomarkers of sponges.

In the late 1990s, two Australians found steranes - biomarkers for eukaryotes - in Australian rock dating back to 2.7 billion years (but no older). This gives a good indication of the first emergence of lifeforms with cell nuclei.

By 800 mya, the biomarkers indicated multicellularity.

By 542 mya, the biomarkers indicated animal life - but we know this already as the Cambrian explosion.

In 2005, a Japanese team investigating the K-T extinction event (65 mya) they found, as expected, biomarker indicating a deluge of dead plant material. One study then found a decreased abundance of land plants for the next 7000 years.

Then to the Permian mass extinction event, the biggest of the lot. In 2005 a biomarker called isorenieratene was found at this point. These indicate green and purple sulpher bacteria, which cannot tolerate oxygen in water, in turn suggesting the oceans were [largely] devoid of oxygen and "saturated with hydrogen sulphide". A poisonous balance. A suggestion since (by Lee Kump) has been that hydrogen sulphide as the primary cause of the Permian extinction: so much in the ocean that it escaped into the atmosphere, poisoning land-based life and depleting the ozone layer.

The cause of this was in turn traced to global warming triggered by greenhouse gases from the Siberian Traps - the biggest ever volcanic eruption episode. The coinciding of the Permian extinction with the Siberian Traps has long been identified. although not all the mechanisms had been strung together: the global warming lessened the temperature differential between polar and tropic regions, in turn slowing ocean currents, causing stagnation (deoxygenation) then a buildup of anaerobic (oxygen-shunning) bacteria.

Via that biomarker isorenieratene, the same mechanism is seen to have happened - on a smaller scale, obviously - with the Devonian and Triassic extinctions. Ward comments that "it is beginning to look as if the K/T mass extinction was unique in having been caused by an impact [meteor]".

Ward's ultimate comment is that the planet is effectively a battleground between the early-emerging prokaryote life and the later-emergent eukaryotes (including us).

These periodic patterns seem only to serve to delay the emergence of tail-end complex life. And, as Gould would say, we just happened to get our chance due to that preceding history. Otherwise, it would have been down to the descendants of more advanced creatures than were our ancestors of the time.

Thingodonta: a salient lesson in analysis

So much to do, so little time. I would do more on non-paleontological subjects, but they keep getting crowded out...

New Zealand's SB mammal fossil has been interpreted as more archaic than therians (marsupials and 'placentals', referred here as metatherians and eutherians), although on a relatively similar par with monotremes, Australia's earliest known mammals and the world's most ancient extant lineage.

Mike Archer (et al)'s book Australia's Lost World includes a relevant anecdote about mammal classification.

The mammal is now called Yalkaparadonta, but started out as Thingodonta, because the teeth, uncovered first, were unlike any known clades of mammals.

A few months later, a jawbone turned up. It demonstrated three molars, where all plesiomorphic (both primitive and derived) metatherians had four [apart from some specialised groups] but eutherians properly had only three. Further, dental action was much more akin to that of eutherians, ie this would be the first early 'placental' in Australia.

In the third step, a skull turned up. Evidence now suggested it was a metatherian albeit quite primitive, and with a front section unlike any other.

Classification had switched back and forward; fortunately publication hadn't happened until the fuller story had emerged.

This creature isn't even listed on Paleos, although there's an entry at the Australian Museum site Australia's Lost Kingdoms and Wikipedia has some good (sourced but broken-linked) discussion on the classification difficulties. That discussion ultimately placed it in its own order, with some dissent from one Frederick Szalay who placed it as a (primitive) diprotodontan metatherian.

Some distinctiveness, some alignment with metatherians and with eutherian insectivores, with a good dose of convergent evolution thrown in.

Ah, convergence. Must be the bane of a taxonomist's life. But the lesson is that classification can be disrupted by hitherto unseen characteristics. For example, in the SB mammal, the femur suggests an abducted, or sprawling gait, although not as much so as monotremes. Yet that abduction must help place it, as it is placed, close to monotremes.

One must easily accept that the paper on the mammal brings together all current knowledge - at the time of publication. Yet it's understandable if there's much keenness to uncover more evidence, as a femur and two jaw fragments tell a tantalisingly curtailed story.


Archer M, Hand S J, Godthelp H (1991): Australia's Lost World: Riversleigh, World Heritage Site. Reed, Sydney.

Thursday, February 21, 2008

Garnaut's climate change report IS the hard call.

Written Thursday 21-Feb-08:

The interim Garnaut report was released today. Ross Garnaut spoke to it, and said all the right words: climate change is happening faster than had been envisaged; the cost of doing nothing is more expensive than the cost of doing nothing; emission cuts have to be bigger; and solar is the way to go.

And he warned that low incomes households would be hit worst as electricity supply costs inevitably rose.

Therein lies the rub for the Rudd government. They had hidden behind the writing of that report, saying they wouldn't act until released. Sounded to me like they knew the outcome, but they didn't. So far (today Thursday), they said it would be business as usual for emission cuts, which meant sticking to a 60% reduction by 2050. Yet Garnault had said it needed to be more.
No problem for those of us who are already on 100% solar-sourced electricity? Think again - of the flow-on costs from other goods and services: the inflation costs. This when inflation is the thorniest issue this year as far as the government is concerned.

Lateline tonight: it was announced they could not get a government minister to interview, which is highly unusual. They must be hunkering down. They could have foreseen this, but that doesn't mean they have the answers.

It's going to take imagination and radical action on the part of any government. I'd like to be optimistic, but I'm not. Worst case scenario: policy that causes pain but doesn't achieve the climate change objectives.

Update: Greg Hunt, opposition environment spokesman, was on Lateline just now. It's easier to be in opposition and support doing the right thing, but Hunt did come across as a sincere believer in the urgency of the issue facing us. If nothing else, that will help keep the blowtorch on the government's response. (Gosh, I never thought I'd be barracking for the Liberals to press Labor to act on climate change!)

Update 22-Feb-08: According to one report, Climate Change Minister Penny Wong says she is now deferring action until the release of Treasury modelling in June.

Seaweed linked to parasites

A brief article on the Herald's website heralds the discovery of a type of brown algae whose closed relatives include a couple of parasites, cryptosporidium and plasmodium.
This is the closest yet to linking those parasites to algae.

The link is already understood in general terms, because the parasites contain relics of chloroplasts, the mechanism for photosynthesising sunlight into energy. The parasites thus evolved from feeding off sunlight to feeding directly off hosts, leaving residual traces of their origins.

Previously, the closest link between those parasites and algae was a group of dinoflagellates (some parasitic simple algae); this discovery brings the link much closer.

The resonance with Sydney is that they were found in Sydney harbour, while seeking algae living in coral.

Brown algae tends to manifest as seaweed.

Cryptosporidium and plasmodium are both single-cell eukaryotes of the phylum Apicomplexa (classes Aconoidasida and Conoidasida respectively - differing in the absence/presence of the conoid, an organelle comprised of a "funnel of rods").

Brown algae are distinguished by chloroplasts with four membranes, suggesting an origin in symbiosis between two eukaryotes. While Brown algae, dinoflagellates and those parasites are all eukaryotes, in the kingdom chromalveolata. Brown algae are multicellular; the parasites are unicellular, and dinoflagellates are... _mostly_ unicellular.

The online report raises more questions than answers. It refers to the print edition, but it's not been published there. What is the name of this new algae? Which dinoflagellates? The findings are said to be published in Nature, but maybe the paper hasn't been published yet, because a search of Nature's archive doesn't turn it up.

And finally... hello to Dee Carter, microbiology Associate Professor at Sydney University, quoted in the report. Based on this photo (not so much the current one at the university!), looks like the same Dee Carter who was in my class at school (Onslow College). Small world.

Other references: Wikipedia [beware, however, there are inconsistencies in classifying organisms: some use unhelpful paraphyletic groupings such as protista.]

Wednesday, February 20, 2008

The Devil frog and Gondwana

It’s worth noting recent news reports of a fossil from Madagascar: the Beelzebub frog (ie Beelzebufo), about the shape and size of a "squashed beach ball".

Noteworthy specifically because of its resemblance to South American frogs, and consequent claim that South America and Madagascar had Gondwanan connections until well into the late Cretaceous. (Madagascar only diverged from the fast-moving India comparatively recently).

There are two competing claims: the traditional view is that South America and Madagascar diverged about 120 million years ago; a more radical one (supported by this finding) gives a more recent 80mya (around the same time New Zealand split from Antarctica).
Most news reports gloss over the incongruity of Madagascar being directly connected to South America, but some indicate the path - via Antarctica.
The relevant scientific paper is at PNAS - but it's sufficiently recent that it requires subscription or payment.

Tuesday, February 19, 2008

SB Mammal: notes for a review, pt 1

Further notes to an earlier discussion on the discovery of a unique New Zealand mammal.  To recap:

The SB mammal (or "waddling mouse") is represented by a set of fossils found in New Zealand in December 2006. Found were two partial jawbones (mandibles) and a partial femur, dated to 19mya. Quite small - the bar on the photo represents 2mm. By the looks of the front incisors (picture C), it would have been quite mean - if it was bigger.
(jawbone views from the paper, referenced below.)

The reason the femur and mandible are linked is simply one of parsimony - nothing else like them has been found. A fair assumption, although it remains falsifiable.

Some of why it intrigues me so much:
- the proliferation of unique NZ bird life (including several flightless birds) had been suggested to be due to the lack of native terrestrial mammals
- it's a "ghost lineage" - no links to living mammals, yet it survived until very recently (19mya)
- how did it get there? - NZ split from Antarctica about 85 mya
- in particular, it has been characterised as non-therian, suggesting it was an egg-layer, unrelated to any other mammalian species extant in the Miocene epoch. Archaic, out of time.

The paper itself: Miocene mammal reveals a Mesozoic ghost lineage on insular New Zealand, southwest Pacific

APP (Acta Palaeontologica Polonica), a Polish publication in English, has a particularly significant reference from the paper: In quest for phylogeny of Mesozoic mammals - this links to the abstract and full 78 page text by three very significant names in the field: Luo, Kielan-Jaworowska, and Cifelli.

Also recommended: An Early Cretaceous Tribosphenic Mammal and Metatherian Evolution (Luo, Ji, Wible, Yuan), available from Science magazine with free registration.

The only vaguely useful blog discussions I've found on this mammal are at Tet Zoo, and one at WebWeaver's World.
News reports mainly rehash, but perhaps the one at New Scientist is best.

Monday, February 18, 2008

Mammals 3: mammaliformes

Again: What is a mammal?

Of course, it's hard to draw the line. Any line is arbitrary, and doesn't reflect the incremental nature of evolution.

Taxonomists must be particularly grateful that the fossil record is gappy. The result is more harmonious: the appearance that ancestor and descendant species are somehow separate, whereas each evolutionary lineage is best represented as a continuum.

There are a number of characteristics that go towards making an animal distinctly mammal. The "canonical" signs include:
- the movement of the articular and quadrate bones from the jaw to the ear (as anvil and hammer)
- hair
- secondary palate (which enables mammals to eat and breathe at the same time).

Colin Tudge reckons homiothermy is a defining characteristic. This allows mammals to simply burn heat to keep warm, and is seen as a particular evolutionary advantage.

In a previous post, I mentioned the definition that mammals are the common ancestors (and all descendents thereof) of monotremes, marsupials, and placentals.

Other relateds are thereby referred to as mammaliformes. However, this is quite arbitrary, as the line is drawn at those currently living. Egg-laying monotremes are thus admitted in somewhat anomalously. They are non-therian mammals.

The split between mammals and reptiles occurs from the amnoite level. Reptiles (and birds and dinosaurs) are sauropsids. The mammal line of descent from amniotes runs through synapsids (from the Carboniferous period) to therapsids (mid-Permian) to cynodonts (late Permian). Synapsids through to cynodonts have been at various times in the past referred to as "mammal-like reptiles".

From there, we have the mammaliformes. The oft-cited Paleos is a fairly authoritative web site, referenced in Wikipedia (amongst many others) and with copious primary references (Paleos itself is being slowly expanded as a wiki here). The journey from cynodonts to mammals is detailed here.

Only trouble is, it's not quite in harmony with the paper on New Zealand's SB mammal (aka "waddling mouse"). The paper describes them as "more derived than morganuconodonts, and more primitive than multituberculates". However, the cladogram in the paper differs from that in Paleos. Both quote a nearly-identical set of sources, one of the main of which is a Chinese paleonotologist called Zhe-Xi Lou, who has done extensive work on early mammalian taxonomy.

More to come.

Friday, February 15, 2008

I'm Kevin, I'm here to help, part 1: East Timor

I can think of no useful sporting analogy. But Kevin Rudd has made three great moves, but faces two brick walls.

His first act as Australian Prime Minister was to ratify the Kyoto treaty. This is not simply symbolic: there are binding commitments behind it.
On Wednesday in parliament, he apologised on behalf of Australia to the Stolen Generations. This wasn't symbolism either: he made important commitments in his speech (on health, education and housing for aboriginals).

Today he's off to East Timor. This, directly after attempts on the lives of both Timor's President and Prime Minister (looks like Horta will pull through). He has also commited more troops to the UN peacekeeping force there. On last night's Lateline, Rudd put his actions squarely in the context of safeguarding Timor's democratic processes. Resource commitment, and personal.

[A welter of half-truths surround the Timor situation, not in the least helped by Murdoch's Australian newspaper, which immediately claimed the rebels only wanted to talk, but were mown down. Facts so far seem to be that Timor's leadership had in the past replaced their Australian guards with locals, so no international forces were on the scene at the time. Although it's been claimed the rebels "only" wanted to kidnap the leaders, which begs the question why they indulged in a shootout with Gusmao's guards.]

Rudd's headlining occasional catchphrase is more one of bravura than bravado - he's used it a few times when the situation's done and dusted.

But the signal challenges are pace-stopping. First, he's trying to keep a lid on inflation while stubbornly meeting his election promise on tax cuts. Second, he has to manage meaningful action on climate change. There is no clear way forward.

Thursday, February 14, 2008

The past impacts the future

“we are the bearers of many blessings from our ancestors; therefore we must also be the bearer of their burdens as well.”

- something that people too often forget when there is a responsibility to fulfill.

Wednesday, February 13, 2008

Sorry: A historical act of reconciliation

When the band Midnight Oil played at the Sydney Olympics in 2000, they wore costumes emblazoned with "Sorry". Many watching from overseas wouldn't have known that it was a gesture of reconciliation to Aboriginal Australia, the Stolen Generations in particular.

Today, Oils singer Peter Garrett was in parliament as a Minister in the government that brought about a historical event.

When Kevin Rudd said sorry on the first full day of parliament sitting under his leadership, it brought much of Australia to a standstill. Many workplaces, mine included, watched live.
I didn't think I would be so moved, but tears came to my eyes several times in the course of his apology and his speech on the matter immediately afterwards. The cameras cut to audiences in the public gallery and outside parliament, and it was very moving to hear the words and see the reactions.

All Australia's living Prime Ministers from both sides were present - bar the last, John Howard, whose 11 years of obduration made this moment that much more poignant.

Opposition leader Brendon Nelson gave a reply that started off well, according to aboriginal people watching, but sank into partisanship and defending the previous government. The response was boos and backs turned, around the country. One news commentary: "Dr Nelson spent the first half of his speech apologising for the removal of Aboriginal children, and the second half implicitly suggesting that there should be more of it today."

Nevertheless, it was a historical moment, and Rudd's words will live on - particularly his subsequent speech outlining initiatives to turn around the appalling housing, health, and education situation of many aboriginal people.

Rudd's performance wasn't great oration, but the words mattered. At a reception afterwards for representatives of the stolen generations, he relaxed more and was much warmer.

The words were not actions, but what they symbolised was welcomed around the country, a very important step in aboriginal reconciliation. And they came with commitments.

The reactions of Aboriginal Australians to this day were warming. Their expressions and gestures, their words afterwards, demonstrate the real power in this act.

Some background stories on the eve of the apology.

One-time Aboriginal tennis player Yvonne Goolagong's response.
Other comments include: Maureen Riches, who travelled to Canberra from Shepparton, Victoria: it is "by far, the most momentous day" in Australia's history.
"I've been working for this for 11 years, ever since [John] Howard refused to apologise," she said.

Elder Beryl Gambrill said Mr Rudd was sincere and respectful.
"It brought back memories of what happened to our people when Kevin Rudd was talking about saying sorry to families," she said.
"I didn't think it was going to be that powerful. But I thank Kevin Rudd for what he said in his speech and thank him for all Aboriginal people."

Tuesday, February 12, 2008

some Paleontology sites

A few useful references:

Tet Zoo - Tetrapod Zoology blog. Always something of interest. Somewhat skewed to dinosaurs?

Palaeos - A very good reference for cladograms and geological times

Paleo news - A reasonable summary of recent news, generally stuff that's broken through to mainstream media. - an "unofficial archive"

Paleoring - for a bit of a trawl

Monday, February 11, 2008

Evolutionary oddities 2: Giant tube worm

Riftia pachyptila, the Giant tubeworm, is a marine annalid (the phylum, or body type, most familiar to us as the earth worm).

These creatures appears to be sessile, which means they latch on to a rock (or somesuch) and stay there (in the adult form at least). They live near black smokers, geothermal vents in the ocean floor. The emissions of these vents are particularly hot and acidic.

They have no digestive system as such: no mouth, no gut, no anus. They do, however, have specialised bacteria inside them, which make up perhaps 35% of the tubeworm's weight. The red plume you see is an organ used for absorbing a number of chemicals, including oxygen, carbon dioxide, and hydrogen sulphide. These chemicals are fed to the bacteria, which then metabolises them into nutrients for the worm.

I'd note that this is one of the few food cycles that doesn't rely on the sun's emissions, directly or indirectly. Such cycles will typically involve bacteria.

My research thus far hasn't been able to answer a few questions: are the juvenile forms of the tubeworm non-sessile? (that is frequently the case.) How does it excrete waste products? (if there are any.) And how do the bacteria get inside them in the first place? (in the juvenile stage?)

It's likely this worm was able to adapt to a niche that was otherwise unoccupied. It would have few predators either, so over time it was probably able to strip back its organs to the bare essentials.

The other thing of note is that whenever an evironment is found on earth that is hostile to life, you're likely to find bacteria adapted to it.

Evolution oddity #1 was: the anglerfish.

Sunday, February 10, 2008

Evolution: Size change may not be what you think

In his book Life's Grandeur, Stephen Jay Gould has a salutory point to make about evolution and size. In typical Gould fashion, he knocks on the head a "conventional wisdom" that is not really so.

Foraminifera are small, single-celled marine organisms that form shells. Their abundance is such that they have been used as fossil markers that help in dating sedimentary rock. Mostly, they are fairly small, less than a millimetre.

Gould details three episodes in their evolution: their emergence in the Mesozoic (dinosaur-dominated) era; in the following Paleogene period; then subsequently in the Neogene period to the present day.

The boundaries between those three episodes are marked by extinction events, where most foram species died. In each case, the foundation (or surviving) species were relatively small; conventional wisdom goes that they increased in size over the course of each episode.
There is a generality called "Cope's Rule" that observes that most taxons tend to increase in size over the course of evolutionary history. In this case, "most" is around two-thirds, and foram evolution would seem to follow that form.

However, Gould argues (rather successfully, I'd say) that this apparent trend is not so, as such. Evolutionary changes occur through random mutation (with environmental* selection being the winnowing process). One might expect that of mutations that affect size, if they are random then a change could equally be an increase or a decrease in size. However (and this is Gould's point), if the starting point is close to the small end of the range of viability for that organism, then over time the spread of size changes would favour increases over decreases. This would lead to the appearance of an increase in size, if one measured the mean (average) size. Also true, of course, if one measured the upper limit of size. If size was displayed in a standard bell curve distribution, the change in form of the curve over time would illustrate a "wall" at the lower end - a lower limit against which size movement would not be able to penetrate. The figures Gould used showed minor change over time in smallest size, but much more marked change in largest size.

When you think about it, it makes intuitive sense - an organism cannot simply dwindle away at the lowest end of the size range. The lesson is to avoid taking at face value any narrative that includes an increase in lineage size over time.

I do have a couple of comments to make on this. The first is that it has certainly been demonstrated that colder climates lead to larger size (on an evolutionary time scale) in animals that have over time adapted to such changes. There is some intuitive sense here, in that a larger body has a smaller surface-to-mass ratio, which is more efficient for heat retention.

The other comment is that one could also try Gould's measurements on a sort of logarithmic index, to see if size changes (from a starting point based to 1) would demonstrate some evenness of logarithmic change.

*Clearly the standard term here is "natural selection". My preference for "environment selection" is intended to make clear the encompassing of selection not just on the basis of inter- or intra-species competition, but environmental changes and also the human hand.


Gould, S J (1996): Life's Grandeur. Jonathan Cape, London

Friday, February 08, 2008

Odds and ends: Evolution and climate change

I accumulate bits and pieces of information far faster than I can download here. So I'm going to clear up a little backlog.

The Tree Of Life is a project to collate evolutionary links to all species. (unfortunately, like many sources, it's not so good on extinct taxa.)

An apposite comment on taxonomical placement (University of Michigan): “Mophological, reproductive, and developmental evidence overwhelmingly supports a sister relationship between marsupials and placentals to the exclusion of the more primitive monotremes. Recently, comparisons of mitochondrial DNA sequences among mammals have supported the alternative hypothesis that monotremes and and marsupials form a clade exclusive of the placentals. Cladistic analyses using large segments of nuclear DNA have supported the more traditional view, however. Relationships among higher mammalian taxa (including both inter-subclass and inter-ordinal relationships) are currently very much in question”

Another comment on classification (from Wikipedia): "Traditionally, membership in Mammalia is diagnosed by the presence of a single dominant jaw joint, in which the dentary contacts the squamosal. However, taxonomists debate whether established names, such as Mammalia, should correspond to the clade which is closest to the traditional definition or, alternatively, should be restricted to the 'crown-group' (which includes only descendants of the most recent common ancestor shared by all living member species and excludes any fossil forms which diverged at an earlier stage, even if they meet the traditional criteria). Supporters of the crown-group approach refer to the broader grouping as the Mammaliformes or Mammaliaformes, whereas traditionalists describe the entire assemblage as "mammals". For a summary of the argument and issues, see Benton 2005: 289

However, a consensus accepted by most scientists states that mammals as a group are defined by the possession of a special, secondarily evolved jaw joint between the dentary and the squamosal bones, which has replaced the primitive reptilian one between the articular and quadrate bones in all modern mammalian groups. Morganucodon is special in this respect, because apart from still having the primitive hinge, it has also evolved the derived mammalian one and thus features a double jaw joint. It is for this reason, and additional evidence pointing to diphyodonty and determinate growth, that Morganucodon is now usually considered a true mammal."

Global warming:“The most recent figures show Australians emit more than 17 tonnes of carbon per person, compared with an OECD average of just over 11 tonnes. The ABS says that is driven by the high use of coal in electricity generation and the reliance on cars. "

Aus Govt Environment department to get a "senior treasury official" - as part of a beef-up of climate change initiatives.

Aus liver transplant patient takes on her donor's immunity system and blood group.

Wednesday, February 06, 2008

Evolution: NZ prehistory: another narrative

The University of Waikato has an interesting and detailed narrative on New Zealand's natural history, based on its geological and fossil record. I'll summarise some of the main points here. (A reminder that this whole exercise is aimed at better understanding the circumstances surrounding the appearance of a non-therian mammal fossil in the south of NZ.)

Speaking specifically about the parts of New Zealand that are above water now, parts of NZ first rose from the sea in the Mesozoic era (dinosaur times), in the Triassic period (250 million years ago to 201 mya). Fossils are found in this period of early forms of kauri, rimu, and kahikatea trees; no terrestrial vertebrates.

In the Jurassic period (145mya to 201 mya), NZ was uplifted as part of a larger land mass ("Tasmantis"); the narrative strongly implies it was connected to Gondwana. In any case, it says that due to NZ's subsequent isolation, it is likely that this point saw the arrival of "archaic frogs, large land snails, tuatara, and peripatus".

Under the Cretaceous (65mya to 145 mya) heading, it mentions a single vertebra of an upright carniverous land dinosaur. It also mentions waterways developing around 120mya between Gondwana and the land mass that included NZ. A consensus from other sources is that that split was final by about 82mya. The dinosaur extinction event was 65mya; the iridium boundary marker has been noted in NZ.

Other points of note:

- Oligicene epoch (23-37mya): two thirds of NZ was submerged (it notes the continued survival of frogs, tuatara, snails, peripatus and ratites (flightless Gondwanan birds);

- Miocene (5-23mya): bat, gecko and takahe ancestor appeared from Australia...

And we're back where we started: the SB mammal from around 19mya: Miocene, but non-therian. Appearing from Australia relatively recently (despite no equivalent fossil found there), or surviving from Gondwanan days.

Evolution: Gondwana vs New Zealand

Gondwana* was a large land mass that tended to reside in the southern hemisphere from Cambrian times to mid-Jurassic times (c.500 million years ago to c.160mya). It consisted, in the main, of Antarctica, Africa, South America, India, Australia, and New Zealand. For part of its existence, it was united with its northern equivalent into the supercontinent Pangea.

Through this time, Gondwana experienced a number of climate changes, due in part to the movement of Earth's techtonic plates which formed then ultimately broke up the continent.
Africa moved away first, followed by South America and India (the latter has been a particularly fast mover, crashing spectacularly into Asia to form the Himalayas).

Of course, disintegration took many millions of years, so the dates are approximate. The dispersal (and later speciation) of fauna is not entirely stopped by such splits. For some time after complete separation, islands are typically scattered between the land masses. This more or less allows for some island hopping from one land mass to another, typically through "rafting" - the carriage of fauna across on masses of vegetation, often after storms. Richard Dawkins treats this well in The Ancestor's Tale, and makes the point that even if such an event sounds unlikely, given the time scales involved - millions of years - it's unlikely that it wouldn't happen. And all it takes for a population to be established is one pregnant female.

I always thought that New Zealand broke away from Australia, because they seem to be such a neat fit. However, New Zealand is usually cited as splitting from Antarctica/Australia earlier. Ultimate separation was achieved around 82mya. Dawkins says Australia was finally sufficiently free of Antarctica to obviate island hopping around 55mya, although estimates vary a fair bit; Wikipedia suggests it was still freeing itself at 40mya.
The point about this is that New Zealand was isolated for substantially longer than Australia. At the time of the dinosaur-extinction K-T meteor - 65mya - New Zealand was already isolated, and Australia probably was not.

Various sources suggest New Zealand eroded since isolation, by up to 80% - some claim it disappeared below the waves altogether for a time, although this seems unlikely. The question is around the sustainability of populations in isolation. This is mainly relevant for large terrestrial tetrapods. Conventional wisdom is that the number of unique flightless birds in New Zealand reflects the absence of terrestrial predatory species until human introduction in the past thousand years.

There remains a few species in New Zealand's islands that are "anomalous" to the global narrative, including:
  • the living Tuatara - only lizard-like - actually a distant lizard relative called a sphenodont.
  • fossil dinosaurs and crocodilia from well before NZ's isolation
  • and the newly-discovered sb mammal or "waddling mouse" from NZ's very recent evolutionary past, c.16 million years ago (main discussions here and here), interpreted as non-therian, ie egg-laying.

These need to be drawn into the narrative one way or another.

Related discussions:

*Gondwana means "land of the Gonds"; the term Gondwanaland is both redundant and obsolete.


Dawkins, R (2004): The Ancestor's Tale. Phoenix, London.

Tuesday, February 05, 2008

Evolution: Mammals 2: Monotremes

Odd fact of the day: echidnas derived from platypus-like creatures.

Monotremes are the only group of extant mammals that are non-therian, i.e. non-placental. (The name refers to their peculiar single opening for intestinal/urinary/reproductory functions.)

There are five identified species: four are echidna, and one is a platypus.

I happen to be reading Richard Dawkins' Ancestor's Tale. Dawkins mentions platypus fossils (Obdurodon) older than the point at which echidna and platypus diverged, along with molecular analysis that strongly implies the echidna is derived from a platypus! - effectively, over time its ancestors gradually abandoned water, changed the form of their feeding appendage (duckbill to tubular) and acquired protective quills.

Monotremes are non-therian mammals, which would mean they lay eggs. I am casting aside the oft-used term Prototherian ('first animals') as not being truly cladistic, since it excludes descendant Eutherians ('placentals') and Metatherians (marsupials).

So to other non-therians: early mammals and their non-placental descendants.
Research is hard. The situation is not as simple as Tudge's statement (dated 2000) that there are eight types of non-therian mammals - that takes a judgment call, and a lot has happened since then.

Non-therians are typically taken to include at the least: monotremes, multituberculates, Morganucodonts, Triconondonts, Doconondonts... and a few others.
How they're grouped is a matter of current debate. It would take several posts, so I intend to lay this aside for the moment.

Most of the names above are based on characteristics of their teeth - I imagine for several reasons:
- teeth are often all that remains
- they're a useful differentiating characteristic
- they give some indication of diet, and thus niche, adaption, selectivity.

Another debate also seem to revolve around the time frames that they each occupy. Of particular interest are those mammal-like creatures (mammaliformes) that existed before the K-T boundary - the 65mya dinosaur extinction event that enabled mammals to proliferate. True mammals were all shrew-sized before then, barely eking an existence in the dominant shadow of the dinosaurs.

All this is relevant because it traces the evolution of mammals, how they developed their features over time (and how fast), and how successful they were in their environmental niches against competition from non-mammals and from later developments.

More to come on non-therians. I might take a break, however, to discuss the formation of New Zealand.

Monday, February 04, 2008

Evolution: basic mammal classification

As Australians will know more than most other people, there are three rather different types of mammals living today: (so-called) placentals, marsupials (kangaroos, koalas, etc) and monotremes (only the platypus and echidna). Whereas placentals predominate everywhere else, marsupials do so amongst the native Australian fauna, and the living monotremes are exclusive to Australia.

When it comes to classifying them, you can only go so far before losing scientific consensus. Traditional classification (taxonomy) is being superseded by cladistic taxonomy, where groupings are based on ancestor-plus-all-decendant clades. This outcome is most pleasing to someone like myself, valuing as I do the logic and neatness that it brings. Yet it also breeds confusion, rethinks, and re-classifications – very much so in the past decade or two, where molecular analysis tends to reveal true relationships, and shows that intuitive morphology (physical attributes) can be misleading, because of convergent or parallel evolution. Reptiles, for example, should no longer be referred to as a specific taxon, more a description – since mammals arose from their midst. They’re now often referred to as Reptilia*, with the asterisk to signify that status.

Three significant features of mammals are that the have fur (in general), give birth to their young life (in general), and they’re endothermic – that is, temperature regulation by internal means, eg the fur. (Terminology such as warm- or cold- blooded is not really sufficiently precise.) A key diagnostic can be taken as the movement of a couple of small bones in the jaw to become the hammer and anvil of the ear.

Current classifications of mammals is less solid than, say, Wikipedia would have you believe. If you look at their talk pages on the matter, you’ll see disagreement; their consensus emerges from a very small number of votes (see this one, for example).

For the moment, I’m going with Colin Tudge. He offers logic and a full narrative, which you can’t guarantee from Wikipedia. He frequently cites disagreement, and explains why his decisions fall where they do.

Following from this, mammals can be split into Theria (a sub-class) and non-therians. Theria is a sub-class of mammals that gives birth to their young live (rather than as eggs). They can be divided into infraclasses Eutheria (so-called placentals) and Metatheria (marsupials). It should be noted, though, that marsupials also give birth to live young – although at a rather less mature stage. Tudge in fact refers to this issue as a “movable feast” overall, when it comes to timing.

Next up: non-therians.

Tudge, Colin (2000): The Variety Of Life. Oxford University Press, New York.

Sunday, February 03, 2008

Backing the unbackable for President

I can't see Obama getting the Democrat nomination.

All sorts of tripe is put in the mainstream media (and even more into the Blogosphere, I'd say). I read one opinion piece that said Clinton would be withdrawing pretty soon. But that's forgetting a) her determination (good on her); and b) her substantial campaign funds - she outguns the lot by a handsome margin.

Since this isn't the mainstream media, I'm happy to get hung for a sheep. I expect McCain to win Super Tuesday by a good margin, with only Romney left hanging out until the convention. I'm sure this would have surprised most people a month ago.

And I expect Super Tuesday to be rather inconclusive for the Democrats, with only Clinton and Obama remaining. I still can't see a black getting the nomination, although if anyone could, it's conceivably him.

So I would expect it to be McCain against Clinton. Both candidates being far more to the middle of the road is, I feel, happenstance. But at the very least, it would mean an unceremonious dumping of those neoconservative troglodytes currently bunkered in the Whitehouse. And it would mean no exit plan for the Iraq war, although on that score we can be grateful for new ideas - any.

I could be wrong about Obama. He's a candidate I'd like to back, but he'd quite a dark horse as far as his executive ability goes. His achievements so far, both inside the senate and out, have been very commendable, but that's not the same as running a presidency. Oh, what the heck. I'll go for him. Although I have much admiration for Clinton's commitment to reforms such as health care, she's relatively conservative. Edwards would be second, but oops I see he's already "suspended" his campaign.

Obama's sounding like a junior Kennedy. Could the Democrats go with him? Could he avoid the fate of the previous Kennedys? And would enough Americans be able to swallow their past and vote for him? Passing those hurdles, could he make the grade? So much in the way of true vision, but one can always hope...

I find it hard to place money on which of those three will get up. So, with the rider of slim margins between them, I'd guess McCain as most likely, with Clinton second and Obama third.

I don't worry about Clinton or Obama really. And McCain is not the worst the Republicans could throw up. At least that anti-science irrationalist Huckabee's not going to make a dent.

I'm not optimistic about action on climate change. Again, chucking Bush and his cronies will in itself achieve as much as it did in Australia when John Howard was dumped. On climate change alone, the only US politician I've heard in which I can have full confidence would be... Schwartzenegger. He's ineligible, being born outside the US. If Gore ever came back, you'd know the USA was starting to treat the issue seriously.

As far as watching horse races go, I'm less concerned about really bad outcomes than I have been in a long time. A really good outcome would be too much to ask for.

Update 04-Feb-08: I've been ignoring Mitt Romney by and large. Expect those Republicans who don't want McCain to coalesce behind Romney - especially all groupings to the right. So it's not really over yet.