Saturday, March 29, 2008

Æon Flux - an improvement?

Æon Flux was a series of short animations that had a memorable style, but made hardly any sense.

Little did I know the creator, Peter Chung, had made some deliberate moves to subvert the concept of narrative. There was little to no continuity between the episodes I saw. The two central characters had a relationship, but that relationship seemed to be completely different from one episode to another, veering between lovers and enemies at the slightest whim, sometimes within a single episode.

This creative sensibility was taken to Hollywood where, lo and behold, they made something of it.

True, it doesn't retain all the stylistic elements of the original series, but I'm finding it's captured what I liked about the series - the minimalist dialogue, the tone, the acrobatics - while adding structure.

And while that structure
brought sufficient intrigue, not only did it have a sorely-needed coherency, but it provided a vehicle to make sense of the contradictory scenarios of the original animations.

At that same time it took away some of the more angular aspects - both in narrative and visual style - which to my mind weren't much more than a hindrance.

To read an altogether more scholarly take on the animation series, it's worth reading this overview and recap by an aficionado, in a blog called the Concept Den. It also contains some of the original animations for comparison. The writer may argue me wrong, but I'm happy enjoying the Hollywood version.

Thursday, March 27, 2008

Life On Mars: Bring You Back Home

"Not your fault he got off.

"Hang in there.

"Bring you back home."

Life On Mars is a real mind-twister. Just when you think you have a handle on it, a few simple words throw your whole paradigm off kilter.

What other tv series has done that?

The initial premise doesn't sound simple enough. It's something one has to try to work out. And try again. Sam Tyler, a present-day Manchester police detective, is hit by a car and apparently finds himself back in 1973, newly assigned to a station that is equivalent, but 30 years out of whack. Cars, colours, attitudes are all different. Cases are not watertight, methods are not ethical, analysis is not sophisticated.

He can't get out. The world is consistent unto itself, so he has to make his way at face value. Work with his new team, solve problems in an old world with a contemporary sensibility that sometimes helps, sometimes roughs him up badly.

Consistent. Bar a couple of jarring, juddering sets of incongruity.

First, he keeps meeting people with a strong connection to his life in the future, albeit from 30 years in the past. He has to play this straight, because he's in a world he can't escape, except by being locked up for a lunatic.

Second, once in a while he is exposed to a feed from a world which he may never have left: one in which he is clinging tenuously to life support in a hospital bed. His 1973 world relays the occasional sound or image from that viewpoint - via radio, television set, telephone - with people passing comment on his likelihood of survival. What to think?

Is he really transported to the past? Is he really on life support?

You'd think it's just a transport of the consciousness. But at one point he traces back a call he got from the future, only to be told angrily: "you know you're not to ring this number."

Now in this, the penultimate episode, his boss, the guv, is fingered for a murder and on the run. Upon resolution, when he is cleared and helps collar the culprit, Sam asks his stand-in boss "are we all right?" Is it okay between us?

Then this is misconstrued, leading to the quote at top. Rounded off with the absolutely cryptic remark "Bring you back home". What is happening?

Who is playing what role? Who is on whose side, and who is just a figment?

One week to go.

(On a final note, no less jarring, and rather bamboozling in a completely different direction: the music played as soundtrack is often enough 1973: Hellraiser, Goodbye Yellow Brick Road, etc. But often enough it's 1972: How Can I Be Sure?, Virginia Plain, and so on. Sometimes it's putatively on the cusp - Cindy, Incidentally (arguably). But why would one expect radio of 1973 to be playing so much 1972? Yet there has not been anything anachronistically later...)

Wednesday, March 26, 2008

Surviving early mammal lineages

Researching mammals seems to be a particularly popular occupation. Most of that research relates to extant species and their evolutionary history. So it's mostly eutherians (placentals), metatherians (marsupials), and monotremes. It's hard to find much detail about extinct lineages such as New Zealand's mysterious SB mammal fossil.

I'm currently browsing with curiosity a hefty tome called Mammals From The Age Of Dinosaurs. It's about as comprehensive as one can get, and is destined to be the reference book for early mammals. Written by three of the leading experts (and most widely quoted) in the field of mammal paleontology: Zofia Kielan-Jaworowska, Richard Cifelli, and Zhe-Xi Luo. It's dated 2004; to get anything more current, you'd have to be constantly scouring the journals (which is not a bad thing, as these are times of rapid change in knowledge and understanding in this field.)

The book contains many seminal reference points, including a full survey of distribution by location and period (to just past the Mesozoic boundary), and a fully detailed survey of each major lineage of the Mesozoic.The diagrams I find particularly useful are - two (alternative) cladograms of all major mammal taxa up to eutheria (pp521 & 522); - an overview of the changed view of the evolution of the major lineages (p5); - most importantly, a diagram of the temporal distribution (through the Mesozoic) and relationships of the main lineages (p3); - a clade table (listing) of all lineages down to family level (pp 14-15).

Of major interest is the comment (p13) that only four major lineages have a significant presence after the KT boundary (end of the Mesozoic, and the dinosaurs).

Four? To the extant lineages mentioned above, the book adds multituberculates (p15). In a footnote, they elaborate the list with the multituberculate suborder Cimolodonta (lasting to the Eocene), and one dryolestoid from the Paleocene of South America. However, that note is not complete, as there are scatterings of other multituberculate taxa that are mentioned as passing through to the Paleocene. These include Ptilodontidae, and Gondwanatheria. The latter are admitted as uncertain placement (Incertae sedis) - somewhere between monotremes and (metatherians plus eutherians) - but discussed with multituberculates.

Ptilodus, a Ptilodontid

[Update 27-Mar: Dryolestes is Trechnotherian - a clade (a superset of both eutherians and metatherians) which covers all mammals that give birth to live young. I'll now exclude these from the discussion, since I'm focusing on egg-laying mammals, which it looks like the SB mammal is.]

So far, then, we have three non-therian - egg-laying - groupings surviving into the Paleocene (which ended 55 million years ago): Monotremes, multituberculates and, arguably, Gondwanatherians. To this, we now add the even more enigmatic SB mammal, surviving all the way to the Miocene, 19mya.

So what does this say about the SB mammal?

On the one hand, Worthy et al place this mammal in an unresolved trichotomy with multituberculates (which it says are more basal) and the more derived clades that include (Tinodon + the viviparous therians). In effect, pretty close to multituberculates, but no match. On the basis of the femur fragment (specifically, the greater trochanter), it's more primitive than the latter - but that's predicated on the femur and jaw fragments matching. Parsimony suggested so, but it's not a guarantee.

On the other hand, the paucity - and piecemeal nature - of the book's references to non-therian KT survivors is a good reminder that we are dealing with a matching scarcity of pertinent fossils. What has been reported so far should not be taken as a complete and reliable guide to what did survive. New Zealand has, after all, sheltered such oddities as the lizard-like Tuatara and the Leopelmatid frog, no less surprising in their uniqueness.

Next up: more on multituberculates.

Kielan-Jaworowska Z, Cifelli R L, and Luo Z-X (2004): Mammals from the age of dinosaurs : origins, evolution, and structure. New York, Columbia University Press.
Worthy T, Tennyson A, Archer M et al (2006): Miocene mammal reveals a Mesozoic ghost lineage on insular New Zealand, southwest Pacific in PNAS vol 103 no 51.

Alternative Sydney 6: Circular Quay+

Following straight on from yesterday's comment on the clearing of Circular Quay, the Herald splashes just such a proposal on the front page:

This out of the office of Mayor Clover Moore, from Danish urban planner Jan Gehl. The text to go with the picture says that in this proposal, the expressway would be torn down (and presumably the railway line underneath, which would be sunk underground as per earlier suggestions), and the ferry terminals "streamlined and moved to the east". Current vista below.

It's admirable to open it up from the water to the Custom House to the cityscape; but I'm not convinced the new proposal is sufficiently dramatic, or ultimately much different from the current situation. Moving the ferries gives it much better impact, but retaining a barrier - so to speak - between city and water... it doesn't really complete the vision.

This is actually part of the council's city vision for 2030; the Herald's website has quite a bit more of it on display, including removing all traffic from George Street, reducing car parking, removing the Western Distributor, increasing park space in Darling Harbour, replacing the (apparently inadequate) Convention Centre with apartments, and hiding the whole Central railway land area under a mass of shops, apartments, and entertainment and convention facilities. The Herald has befores and afters for George Street, Darling Harbour and Central. There's also a slide show. All definitely worth a look.

Tuesday, March 25, 2008

Alternative Sydney 5: more Opera House

Sydney Opera House is iconic on the outside, but unfunctional inside. According to the Sydney Morning Herald, the original brief for a large hall combining operatic and symphonic functions was doomed from the start. As a result, opera ended up in the smaller of the two shells, which was never entirely satisfactory.

There are now plans to rebuild the opera theatre - for $700m. The Herald suggested that price could buy a whole new building, and now the Herald reports a proposal by architect Ken Woolley to build an opera theatre next to the Opera House.

Former PM Paul Keating now expresses his dislike for that proposal, suggesting another site altogether. He calls the idea an "all too proximate appendage to the great composition". The issue is the Opera House as a collaborative product of both design and site.

This speaks to the outcry over the Opera Quays building ("the toaster") which was seen as sullying the land next to Bennelong point. The opprobium is muted with the accomplished fact of the building, which doesn't really lessen the original criticism.

Ideally, the Opera House would house opera - that is how this 20th century landmark is known throughout the world - with no building close by. Unfortunately, I think this vision has already been abrogated by the toaster. Yet that doesn't mean it needs to be abandoned altogether.

Previous posts on an alternative Sydney have included two early designs for the Opera House (here and here) and one for the Harbour Bridge, as well as a vision for the future of the area in front of the Town Hall.

A substantial remaining issue is the removal of the Cahill Expressway, a blight on Circular Quay (and the transformed Custom House).

Monday, March 24, 2008

A red rose

A few years ago, I gave my wife an Alice-in-Wonderland present: a rose bush with red and white roses.*

After a year or so, the white roses predominated, and we saw only the occasional red rose, then just some pink flecks on the white roses from time to time.

Then last year some shoots started zooming up. I installed a garden arch to support them, and they've been quite vigorous in the rains of the recent season, growing more than double the height of the previous years.

And then: a solitary red rose in the middle of the trellis, isolated high above the bush of white roses. Quite a sight. The photo below is an indication, but doesn't do it sufficient justice.

* A product of grafting, of course.

Friday, March 21, 2008

Obama: ethics, intelligence, inspiration

Hunter S Thompson once wrote about a speech Jimmy Carter gave on the stumps running up to the 1976 presidential election. It was delivered, I believe, at a minor venue and was not widely reported.

Thompson was sparse on details, but his pivotal point was that the speech enormously impressed him and greatly increased Carter's stature in his mind. Soon after, he asked Carter for a text of the speech. Carter responded that it had been given off the cuff, and that nobody had kept a record of it.

Whatever you think of Carter or Thompson, the sentiment has to be admired. When in the course of a cliche-strewn, jading, saturation-reported, safe-rhetoric-laden election season, there is anything at all that raises the spirits, it must stand out like an oasis in the desert.

Barack Obama has given such a shining beacon of a speech.

I read it yesterday, and gave it a strong recommendation to the first two people I met (for the first time), minutes later.

The sentiment, ethics, and intelligence of the speech reflect enormously on the man. Until I read it, I suspected Obama of potentially empty rhetoric. But he dealt with a controversial situation (his association with a divisive firebrand preacher) not by distancing himself as any other candidate would, but by speaking to the wider issues with a ringing clarity.

My personal feeling is there has not been a candidate of such intelligence and ethics since at least Jimmy Carter (and I would be very surprised if Carter does not endorse him) - and probably much further back.

I can only hope that Obama lasts the distance to election day, because the world needs him.

BBC mentioned the speech is available on YouTube and Obama's web site. I reproduce below the text as I read it yesterday. The full text is here; the video is on Obama's web site (YouTube's copy is not in sync).

I recommend you read below for a taste, then watch the full 30 minute speech. I cannot recall ever being held by a political speech for more than five minutes; this lasts the distance and is most rewarding.

"The fact that so many people are surprised to hear that anger in some of Reverend Wright's sermons simply reminds us of the old truism that the most segregated hour in American life occurs on Sunday morning. That anger is not always productive; it keeps us from squarely facing our own complicity in our condition, and prevents the African-American community from forging the alliances it needs to bring about real change.
But the anger is real; it is powerful; and to simply wish it away, to condemn it without understanding its roots, only serves to widen the chasm of misunderstanding that exists between the races.
In fact, a similar anger exists within segments of the white community. Most working- and middle-class white Americans don't feel that they have been particularly privileged by their race. Their experience is the immigrant experience - as far as they're concerned, no one's handed them anything, they've built it from scratch. They are anxious about their futures, and feel their dreams slipping away; in an era of stagnant wages and global competition, opportunity comes to be seen as a zero sum game, in which your dreams come at my expense.
Like the anger within the black community, these resentments aren't always expressed in polite company. But they have helped shape the political landscape for at least a generation. Anger over welfare and affirmative action helped forge the Reagan coalition.
Just as black anger often proved counterproductive, so have these white resentments distracted attention from the real culprits of the middle class squeeze - a corporate culture rife with inside dealing, questionable accounting practices, and short-term greed; a Washington dominated by lobbyists and special interests; economic policies that favour the few over the many. And yet, to wish away the resentments of white Americans, to label them as misguided or even racist, without recognising they are grounded in legitimate concerns - this too widens the racial divide.
This is where we are now. It's a racial stalemate we've been stuck in for years. Contrary to the claims of some of my critics, black and white, I have never been so naive as to believe that we can get beyond our racial divisions in a single election cycle, or with a single candidacy.
But I have asserted a firm conviction that working together we can move beyond some of our old racial wounds, that we have no choice if we are to continue on the path of a more perfect union.

In the end, then, what is called for is nothing more, and nothing less, than what all the world's great religions demand - that we do unto others as we would have them do unto us.
For we have a choice in this country. We can accept a politics that breeds division, and conflict, and cynicism. We can tackle race only as spectacle - as we did in the O. J. trial - or in the wake of tragedy, as in the aftermath of Katrina - or as fodder for the nightly news. We can play Reverend Wright's sermons and talk about them from now until the election, and make the only question in this campaign whether or not the American people think that I somehow sympathise with his most offensive words. We can pounce on some gaffe by a Hillary supporter as evidence she's playing the race card, or we can speculate on whether white men will all flock to John McCain in the election regardless of his policies.
That is one option. Or, at this moment, in this election, we can come together and say, "Not this time".
This time we want to talk about the crumbling schools that are stealing the future of all our children. This time we want to reject the cynicism that tells us that these kids can't learn; that those kids who don't look like us are somebody else's problem.
This time we want to talk about how the lines in the Emergency Room are filled with whites and blacks and Hispanics who do not have health care; who don't have the power on their own to overcome the special interests in Washington, but who can take them on if we do it together.
This time we want to talk about the fact that the real problem is not that someone who doesn't look like you might take your job; it's that the corporation you work for will ship it overseas for nothing more than a profit.
This time we want to talk about the men and women of every colour and creed who serve together, and fight together, and bleed together under the same proud flag. We want to talk about how to bring them home from a war that never should've been authorised and never should've been waged, and we want to talk about how we'll show our patriotism by caring for them, and their families, and giving them the benefits they have earned."

Wednesday, March 19, 2008

Milk is for... egg wetting?

The transition from egg-laying to viviparous (live) birth is a fascinating one, a transition point in mammal history that was arguably involved in the current dominance of the lineage.

Where does milk - an essential part of the viviparity equation - come into it?

Henrik Kaessman from the University of Lausanne says it was originally used for keeping the egg moist. He says mammalian eggs were originally soft, parchment-like, as seen in reptiles today.

This from PLoS Biology [Public Library of Science], reported today in New Scientist.

The argument revolves around a calcium-rich protein, casein, which is in mammalian milk. Monotremes - the only living egg-laying mammals - also produce milk. It was confirmed through genetic analysis that platypus milk had casein-like proteins, which leads Kaessman to suggest milk arose in a common ancestor to mammals, up to 310 million years ago.

platypus egg

Further, he analysed genes for a protein called vitellogenin, which sends nutrients into egg yolk. These are active in chickens, and inactive in mammals, yet one is active in the platypus. Thus, according to Kaessman lactation came long before eggs disappeared in (eutherian) mammals.

This is of interest particularly in describing the transition from eggs to viviparity as a process that went through a series of stages - exactly as one should expect in such an evolutionary process.

Sunday, March 16, 2008

Paucity of useful books on mammals

A quote from a 1993 book called Mammal Phylogeny:

"Prior to the advent of phylogenetic systematics... the influence of environment over natural selection was virtually the only mechanism invoked to describe morphological patterns discovered in the history. It was argued that similar environmental demands... led to the convergent evolution of 'mammalian' characters in many different lineages. Implicit in many discussions is the thought that convergence was so prevalent that the true genealogy could never be known with any precision.Phylogenetic systematics has turned our attention from many of these issues. The discovery of monophyletic taxa replaced definitions of grades as the central issue in understanding early mammalian history." (pp130-131; my emphasis).

It goes on to say there is no doubt mammalia is monophyletic. Further: "Previous views saw taxa as classes defined by characters, while contemporary phylogenetics views taxa as individuals defined by common ancestry".

This gives some context to the difficulty I had in finding useful books on mammalian evolution in the university library (UNSW). Most of them were not recent enough to encompass the revolution in evolutionary analysis. One of the more promising titles had an unpromising date from the 1960s, last updated 1972.

The quote above suggests the cladistic approach to analysis has cleared the decks, so to speak. On the one hand, the attempt to group all species into equivalent hierarchical sets was obviously thoroughly doomed. This, even apart from the quite vexed issue of delineating evolutionary lineages into species in the first place.

On the other hand, systematic phylogeny has immeasurably clarified evolutionary relationships, which to my mind should be rather paramount.

On the other, other hand, I can greatly empathise with adherents of Linnean taxonomy, whose tidy world is so greatly threatened. But they should acknowledge the appropriateness of the threat: phylum, order, class, family, and species were always arbitrary, and give unhelpful illusions of equivalence that just do not exist.

Another difficulty for me with libraries is the sort of books I'm looking for: non-therians, that is mammals that are not placental (which also excludes marsupials). Most evolutionary biologists happen to be very much focused on extant species and lineages. Thus most books on mammalian history treat eutherians or metatherians - or monotremes at a pinch.

Szalay, F, Novacek, M and McKenna, M (eds.) (1993): Mammal Phylogeny. Springer, New York.

Friday, March 14, 2008

Birds, ratites, moas, kiwis, predators

This is a story about native New Zealand birds and animals, one that gets more interesting as it goes.

First, I'll start by drilling down through the origin of birds.

Birds are members of the taxonomical class Aves, and are the only living descendants of dinosaurs.  The earliest recognised Ave is the archaeopteryx, dates from the Jurassic period, about 250 million years ago (mya). As a result of the dinosaur-killing KT meteor 65 mya, most near relatives are gone: apart from birds (as descendants), the closest remaining relatives to dinosaurs are the crocodilians. In fact, what we now know as birds are the Avian sub-class Neornithes, and are not direct descendants of the archaeopteryx.

The earliest division of modern birds is between the two superorders Palaeognathae - nearly all are ratites - and Neognathae - the rest. Ratites (properly, the order Struthioniformes) are effectively one of the oldest surviving avian lineages - and they're all flightless, descending from a flying ancestor but at some point no longer needing to fly.

Not all flightless birds are ratites. Many different bird families have evolved flightlessness on islands, where they have found themselves with no predators. Richard Dawkins notes that rails in particular "lend themselves to island-hopping followed by flightlessness".

Why lose flight? Colin Tudge: "flight ... exacts an enormous price. It requires commitment from the entire anatomy, and a huge input of energy".

Ratites are the most well-known of the flightless birds, encompassing the ostrich, emu, cassowary, rhea, kiwi, moa, and extinct elephant bird. Between them, they represent pretty well all the current pieces of the old southern land mass Gondwana. That suggests survivability of this grouping, even when exposed to predators. Some were pretty large, though, but perhaps ironically the largest ones, Madagascar's elephant bird and New Zealand's moa, survived only until the last millenium - finally a victim of the greatest predators, humans. The elephant bird was the heaviest bird ever, at up to 500kg and three metres tall.


The ostrich is hard to place, but Dawkins reckons it was with the elephant bird when India and Madagascar became isolated from the rest of Gondwana then, like other species, took the fast "Indian ferry to Asia", later to take a slow way back to Africa.

Moas diverged from the rest only about 80 mya - when New Zealand split from Gondwana. A couple of notes about their traditional representation in New Zealand: first, they did not tend to hold their heads fully erect, as you see in the museums. Rather, the head was closely level with the body, for browsing. Second, one of their predators was something called Haast's Eagle, the largest eagle that ever lived. This extinct giant eagle is something I certainly never heard about growing up in New Zealand. Intriguing.

Anyway, given the robust ratite's story, you'd expect the kiwi to be closely related to the moa. Well, it's not. It's closer to the emu and cassowary, both from Australia and New Guinea. Dawkins suggests the kiwi arrived in New Zealand via New Caledonia.


It's worth considering the effects of predation over time.  For the elephant bird and moa, size was a boon, but ultimately the source of their demise as they became relatively fearless. For the kiwi, nocturnalism may have been a recent survival mechanism; yet Wikipedia notes that in predator-free sanctuaries, the notoriously nocturnal kiwi is often seen in the daytime. For others, speed has been on their side.

I mention all this to help give context to the unusual 19myo mouse-size SB mammal fossil (discussed here and here) recently found in NZ. Predation has to be a significant issue in the story. How did it survive 60 million years in NZ? What size changes might have happened to avoid predation in a land of bird seeking small morsels? Why did they ultimately disappear? This species doesn't seem to have had any impact on the NZ story as it is known so far...

Dawkins, Richard (2004): An Ancestor's Tale. Phoenix, London.
Tudge, Colin (2000): The Variety of Life. Oxford University Press, Oxford.

Thursday, March 13, 2008

A chimeric cure: donor takeover

A unique medical case reported in the New England Journal of Medicine in January is seen as an example of chimerism: that is, one body with genetic components of two distinct entities.

Around 2002, a nine-year-old girl from south of Sydney "contracted a virus that destroyed her liver". With less than two days to live, she was given a replacement liver. Normally, it would be expected that she would need to take immunosuppresant drugs for the rest of her life - which would leave her susceptible to opportunistic illnesses.

Nine month later, when she fell ill, it was discovered that her blood type had changed from O negative to O positive - that of her donor.

Effectively, the blood stem cells of the donor's liver penetrated the bone marrow, performing a bone marrow transplant. As a result the new liver was no longer treated as foreign. The girl's immune system had been almost totally replaced.

The story from Westmead Hospital's haematology head (Julie Curtin) was that the patient's remaining white blood cells (responsible for immunity) started breaking down the new O positive red blood cells, a process called haemolysis. This resulted in the patient being very sick for a while. The medical staff, in trying to recover the situation, tried the risky step of stopping the course of immunosurpressant (anti-rejection) drugs. The situation stabilised, and the patient recovered. Blood tests also showed she no longer had immunity to measles or mump, despite immunisation as a baby.

There is no recorded precedent for this, and no easy explanation. Some factors mooted include that the donor was young (12 years old), the recipient having a low white blood cell count, the original type of liver failure - and the original virus, cytomegalovirus, which can suppress the immune system.

Four years down the track, the situation appears to be permanent and stable; anti-rejection drugs are not needed.

Interesting to note some irony between the mythic history of chimeras and this actual outcome: this is a complete reversal of the traditional, perjorative depiction of monsters.

Knowing the answers would be a giant boon to medical treatment. I note that there is some research into inducing chimerism to achieve just such an outcome. However, as it stands I suspect most doctors would be extremely reluctant to replicate some of the risky situations involved.

Wednesday, March 12, 2008

Dolphins are human too

I must recap on a recurring theme of this blog: a meaningful study of evolution requires a continual process of re-orienting oneself away from the human perspective.

Deanthropocentrism. No other discipline mandates this. The nearest one gets is the physics of vast (and minute) scales of time and/or space, but this becomes an academic exercise with little direct meaning to the observer.

Not so evolution: the ramifications are often direct and clear. We are not the most successful form of life, from the perspective of either a lengthy run, or the most numerous or ubiquitous, or the greatest mass (that's bacteria). We have shaped our environment like none before, achieved consciousness, left artifacts. But all that can fade with the ravages of time. We are here strictly by lucky contingency. As but one example: if the K-T meteor hadn't struck, we would not have developed this body shape and would still be huddling under the shadow of dinosaurs.

All of which must be anathema to creationists. Ah, but that's their lot.

I'm reminded of another dent to our pedestal today, by a news report of a friendly dolphin. Moko, in New Zealand, is apparently at ease with humans, playful even. This dolphin let a stranded mother and baby sperm whale back out to sea, at Mahia Beach in Northland.

Volunteers had failed in four attempts to direct the whales back out to sea. The whales were visibly distressed, adjudged doomed, but "as soon as the dolphin turned up they submerged into the water and followed her". They never came back, but an hour later Moko returned.

A Conservation Department official speculated the dolphin had heard the whales' distress calls.

Plan, purpose, altruism, compassion. Some of the traits we typically, erroneously, ascribe to higher-functioning humans only.

Such a story - about dolphins in particular - is not new. But it's a timely reminder that we are blindly self-centred, pay too little heed to the world around us. We don't have a monopoly on these advanced qualities. In fact, some of our more basal capabilities are notably absent in dolpins.

Tuesday, March 11, 2008

Linking us to starfish

More precisely, this post is about the connection between vertebrates and echinoderms (starfish, sea urchins, and so on).

The New Scientist article mentioned in the last post describes this connection, which seems fairly uncontentious on the whole, with broad agreement in the sources I've consulted (Tudge, Dawkins, Palaeos, Wikipedia).

It goes like this, according to the article: echinoderm -> hemichordate -> sea squirt -> lancelet -> vertebrate.

By phylum, the latter three are all chordates, but sea squirts and lancelets are more basal than the vertebrates we know and love.

Tunicates (sea squirts) - © Martin Riddle

They constitute the three sub-phyla of the Chordata phylum: respectively Tunicata (Urochordata, until recently), Cephalochordata, and Vertebrata. Wikipedia lists the number of species for each as approx 3000, 30, and 58,000 respectively.

The article suggests lancelets were probably neotenous tunicate larvae. Funny to see sessile marine creatures (pictured above) related to vertebrates. But from what I've read, most sessiles seem to have a motile juvenile phase. So the above is what we could have looked like if we'd continued developing, rather than reproducing early then trundling off down a different path. Rather a plank in the eye for creationists, I'm afraid, but an object lesson in deanthropocentrism.

I recommend this entry in a blog about tunicates (it's where I got the nice picture). Eerie.

Sunday, March 09, 2008

On classifying velvet worms

New Scientist had an article recently on evolution, by Donald Prothero, a geology professor in California. It was trying to smooth the understanding of evolutionary relationships with ten examples of linkages between taxa at various levels. It seems to be based largely on Prothero's recent book "What the fossils say and why it matters" (Columbia Press). Prothero is often described as a paleontologist (including by Stephen Jay Gould); his books include the paleontological and the geological, although heavily weighted towards the latter.

Yet the first evolutionary example in his article is rather contentious. Additional research on the matter gives some insight into the difficulties of phylogeny and taxonomy.

This example was Onychophora - the velvet worm. This is a phylum with just two families - tropical and southern hemisphere - and 80 to 90 species. Their mode is the damp forest floor; it is hard to know how prevalent they are; they are difficult to count, and when this has been done, they're proven endangered. Yet most species are described only very local to where the type specimen (the official sample against which the species is measured).

Prothero depicts Onychophora as the link between two phyla: arthropods (insects, spiders, crustacea) and nematode worms. The former is unremarkable; they are consistently grouped near arthropods. Yet how near, and the closeness of their relationship to nematodes, seems to be still up for grabs.

Tudge puts them in an unresolved trichotomy between Tardigrada and Arthropoda, which grouping is in turn unresolved against nematodes and nematophora (hair worms). gives three alternatives. The first posits them as a sub-phylum of Arthropoda, sometimes lumped with Tardigrada as Lobopoda - yet this is not such a common approach, and they acknowledge the polyphyletic questionmark over that. They also list a 2001 source (Peterson and Eernisse) placing instead another obscure phylum, Chaetognatha (marine worms) between Arthropods and Onychophorans. Thitdly, they mention an alternative (Halanych, 2004) that agrees with Tudge.

Wikipedia puts Onychophora between the nematodes and arthropods, with tardigrades closer to the arthropods.

One thing they all agree on: it was wrong to portray Onychophora as the intermediate between annalids and arthropods. Panarthropoda has been used (as recently as Tudge) to lump Onychophora, Tardigrada, and Arthropoda, but it seems a more currently-accepted super-phylum is Ecdysozoa - which adds a few other phyla, including nematodes as closest to the 'panarthropoda'.

I like a clean cladistic diagram. But the jury's still out, so it won't happen yet. The article's a little simplistic, but a rough consensus does seem to place our two lobopods between arthropods and nematodes.

Halanych, KM (2004): The new view of animal phylogeny. An Rev. Ecol. Evol. Syst. 35: 229-256.
Prothero, D (2008): What Missing Link? in New Scientist, 1-Mar-2008.
Tudge, C (2000): The Variety of Life. Oxford University Press, Oxford.

Saturday, March 08, 2008

Phylogenetic wallpaper

Amira told me about her vision for what would be a phylogenetic wallpaper: that is, one that lists all organisms cladistically around the wall, showing the evolutionary relationships (and degree of closeness) of everything.

Sounds great - if you're that way inclined, which I am too. I said to Amira that you'd need one that could update - pretty much on the fly - because our understanding of evolutionary relationships is changing all the time. Whereas in the past, taxonomy was based largely on morphology - physical relatedness - this is being broken down by molecular analysis, which is showing up much of our morphological classifications to be "mere" cases of convergent evolution.
Visual technology is such that we're not too far away from being able to "paper" a room with very thin, bendable computer displays. The result would be garish but fascinating. Garish because the technology's not good enough to make it easy on the eyes. Fascinating in that at the fringes you'd be seeing more or less constant movement, ripples of change that reflect ongoing corrections in the tree of life. Then every so often there would be a major cracking like an earthquake, as a fundamental adjustment is made.

Sometimes there are hazes, where differences of opinion result in toggles between different states.

Tomorrow, Amira, I'll go into some of those hazes. A recent article on linkages between arthropods and nematodes, vertebrates and echinoderms, speaks to some top-level cladistic relationships - but these are not without contention.

Wednesday, March 05, 2008

Floresiensis claim: ivory tower science

A fresh claim had been made that the putative homo species Floresiensis (the so-called "hobbit" found in Flores in Indonesia) were actually modern humans suffering dwarf cretinism.

This from Peter Obendorf, Charles Oxnard, Ben Kefford, of Melbourne's RMIT and the University of Western Australia, published in the Proceedings of the Royal Society.

The claim is that the dimensions of the fossil specimens were exactly equivalent to those of dwarf cretins, and thus displayed iodine deficiencies [resulting in thyroid malfunction]. "Dwarf cretins grow not much more than one metre and their bones have distinctive characteristics very similar to those of the Flores hobbits," according to Obendorf.

skull size relative to human

The immediate impression from the article in today's Herald is that these are scientists from other disciplines, not paleontology. The suspicion that they're taking the evidence out of context is borne out by the fact that they haven't studied the actual relics, and they misconstrue aspects of the fossils including, an area of skull that was actually excavation damage, rather than evidence supporting the new thesis. (From the paper's abstract:"We find that the null hypothesis (that LB1 is not a cretin) is rejected by the pituitary fossa size of LB1, and by multivariate analyses of cranial measures.")

The press release on RMIT's own site illustrates how much of a speculative exercise it was, initiated by Obendorf spotting a superficial link between floresiensis and historical pictures of cretins(!) Obendorf is hard to find at RMIT, but he's described as a human ecologist, which can be somewhat helpful but ultimately not too encouraging from a paleontological perspective.

Amongst other things, Colin Groves from ANU said the new paper "also ignored the fact the hobbits had primitive chins unlike those of modern humans".

Incidentally, the Herald article seems to be sourced from two separate reports, one of which refers to Floresiensis descent from Homo erectus; the other from australopithecines. The former, from AFP, is the more usual lineage description. The latter, from the Herald's own reporting, is not really sufficiently precise: australopithecines are much older ancestors of erectus. Reporters are not usually trained in anthropology.

One curiosity: the abstract also says, inter alia: "We show... how remains of cretins but not of unaffected individuals could be preserved in caves." That's quite a claim, if it's based on chemical science. It could easily, however, be based on speculation of social circumstance. I don't know, not having read the full article, but since the paper somewhat reeks of speculative application of anotomical science, I'm not going to hold my breath on the outcome.

Tuesday, March 04, 2008

Create your own hi-tech life

Interesting article today about Jon Oxer, a bloke who's been up-teching his life - as a hobby. You know, electronicising his house, car, body, etc.

There's nothing too alarming about this: doubtless there's a lot of techy blokes (and a few women) around the world doing this.

Yet it's interesting to read about some of the things he's done.

He chipped his arm (injecting a rice-grain-sized gadget) to allow him to open the door without a key. He has electronically enabled all [accessible] doors and windows such that he can secure the whole house on command.

He even gets notified of every mail delivery - mostly junk, though, I'd imagine.

Imagine going to bed and forgetting to close/set/turn off something. Then being able to press a few buttons to sort it out without getting up. Presuming the remote is simple enough to remember how to do everything you need.

To his credit, he maintains a principle of getting everything to work invisibly - ie, wireless everywhere, and control mechanisms effectively hidden.

Throughout these projects, it's hard to escape the thought that when something goes wrong, it's going to create such inconvenience. Such as not being able to get in the house. Strongly advised to ensure there are reality override backups for everything - it's easy forget something like that, to dire consequence.

A couple more salient points emerge from the article. First, for someone sufficiently enthused, imagination is just about the only limit to what can be achieved, given the componentry available.

Second: some of the innovations will doubtless prove an expensive waste of time. But out of all this will probably emerge a number of ideas that doubtless have legs. Fertile ground for venture capital.

Interesting to keep abreast of his initiatives - and the bloke's got a blog, so it is possible to keep up. And he says the phone's been ringing off the hook since the article came out.

Monday, March 03, 2008

Evolutionary explanations with heterochrony

Neoteny is a very interesting concept in evolution. It's the process by which an animal [which differs between juvenile and adult form] becomes sexually mature in the larval (or juvenile) form. Thus can be set off a divergent evolutionary path.

The Axlotl (sic) is probably the most well-known example. It's a member of the salamander's order, Urodela.

Although salamanders look rather like lizards, that's just due to convergence (see previous evolution post), and they're actually amphibians. Colin Tudge refers to that shape as the "archetypal tetrapod" - albeit one whose legs sprawl out the side, as in many reptiles, as opposed to being positioned beneath the body as with most mammals.
The axlotl is effectively a salamander that never made it to land. The adult form retains a number of the features of the salamander's early water-based existence, such as gills, while having grown the limbs that would be expected in an adult salamander.

Richard Dawkins (The Ancestor's Tale) details experiments that verified this neotenous nature - separately conducted by Vilem Laufberger and Julian Huxley (brother of Aldous). They each used hormone injections (thyroxine, the absence of which is said to have set off the neoteny), and induced the axlotl to lose its gills and become a fairly normal salamander.

Neoteny is actually the slowing down of other aspects of development relative to sexual maturity. This is subtly different from the acceleration of sexual maturity relative to the rest of the body, called progenesis.

Dawkins refers to the general case as heterochrony, which is the change of pace (a slowdown or a speeding up) of one developmental process relative to other developmental processes. He suggests that this must be behind a high proportion of evolutionary changes in anatomical shape.

Dawkins then mentions the newt, a type of salamander which does this twice, so to speak. It matures to a land-based adult form, but doesn't reproduce. It only becomes sexually mature when it returns to the water, and reclaims some (but not all) of its larval features. Strangely enough, one aspect that doesn't roll back is the gills. It's easy to postulate that the land-based form is not as redundant as it seems: it may have been quite useful at some point to ride out dry seasons - or, more plausible to me, it may have been evolutionarily advantageous to be able to travel a fair distance between ponds or other such water bodies. And it may have been easier to retain water-based birth practices (a somewhat harder call at why it switched the second time - it may have just reverted).

It is also speculated that humans underwent several differeny kinds of heterochrony - for example, the human brain keeps developing for several years after birth, which doesn't happen with chimpanzees. In fact, Wikipedia's Heterochrony entry claims (based on Penin, Berge, Baylac, 2002 and Mitteroecker, 2004) that humans demonstrate 30 different neotenies compared to chimps.


Dawkins, B (2004): An Ancestor's Tale. Phoenix, London.
Mitteroecker, P et al (2004): "Comparison of cranial ontogenetic trajectories among great apes and humans" in Human Evolution (2004) Volume 46, pages 679-697.
Penin, X, Berge, C and Baylac, M (2002): "Ontogenetic study of the skull in modern humans and the common chimpanzees: neotenic hypothesis reconsidered with a tridimensional Procrustes analysis" in American Journal of Physical Anthropology (2002) Volume 118, pages 50-62.
Tudge, C (2000): The Variety of Life. Oxford University Press, Oxford.

Saturday, March 01, 2008

New ethics in Australian government?

It's easy to postulate that there's a clear pattern to the practical ethics of a government: when newly incumbent, it's easy to create distance with the previous administration by instituting a raft of new measures that speak to the ethics of rule. Later, as the government finds itself somewhat hamstrung by its own rules, it relaxes those standards. By the time the government is ready to be turfed out, it can be seen as positively venal, and an easy target for the next administration.

In 1996, although I don't recall any strong lapse in ethics of the Keating government, incomer John Howard promulgated a Ministerial Code of Conduct, only to relax it after seven (!) Ministers (Jull, Sharp, etc) were obliged to resign due to undeclared conflicts of interest and misuse of allowances. Peter McGuaran, for one, made it back to the cabinet.

Kevin Rudd sounds like a very principled man. He is sticking to a number of electoral promises that he'd probably rather not keep (eg tax cuts), and that others would prefer he didn't keep (eg retaining superlatively generous funding for a number of private schools as instigated by Howard).

His appointment of Harry Jenkins as Speaker of the House of Representatives made a stark departure from the previous office-holder, the partisan David Hawker. It could even be said that Rudd didn't know what he was in for: Jenkins has been particularly rigorous in keeping his own government in line (for example, requiring Ministers to answer the actual question that was asked of them!). Against that argument is the fact that Jenkins was Deputy Speaker in the last Keating government.

It remains that Rudd is highly principled. An article in today's Herald gives some insight into the man, which speaks of a significant break from the previous Prime Minister, and not just due to this "early days" syndrome.

And his government is also set to sign the Optional Protocol to the United Nations Convention against Torture, which Howard balked at, probably because the consequent laws may apply to "Australian officials overseas who co-operate with foreign intelligence agencies known to engage in torture".

I still have strong reservations about Rudd's ability to handle the reins of government. Of overriding importance is the setting of carbon emission caps as soon as possible - providing industry with clarity and leadership. And the commitments to tax cuts and those special private schools were wrong to make in the first place, campaign or no*.

Yet... it's early days.

Postscript 3-March: I've heard rumours from high-level public servants (across departments)that Rudd has been very difficult to get to commit to decisions. This would jibe with his apparent propensity to set up committees on a welter of issues. But it doesn't make sense in the context that it's his ministers that should be making the specific departmental decisions. One example given was in relation to the budget - yet I wouldn't be surprised if these ones take time to sort out. Still, something to watch out for.

*In mitigation is some analysis on the decreased commitment over time of the Australian public to a particular side of politics (mentioned last year). I would expect this to lead to an increased "what's in it for me" vote, which would make it hard to opt out of a tax cut auction at election time.