Thursday, January 29, 2009

Evolution: Some further thoughts on radiation and mutation

Radiation is "in part responsible for the mutation that occurs in all organisms"*. In fact, I've heard little to suggest that there are any other significant [non-anthropogenic] causes of mutation (see previous post on mutation here).

Humans have happened upon this Earth about halfway through the planet's habitable lifespan. Putting aside terrestrial sources of radiation (both artificial and natural - they don't seem to figure significantly on the whole), it has been frequently noted that our atmosphere protects us from a large amount of cosmic radiation, solar and otherwise. The implication is that our atmospheric and solar characteristics dictate the "steady" rate of mutation experienced by life on this planet, which facilitates a stable - or life-fostering - evolutionary pace. It's interesting to speculate on the different radiation scenarios, and their possible outcomes. Too much cosmic radiation and mutation rates may go too high for good species cohesiveness; higher life forms may not develop. Too little radiation may mean insufficient adaptability to the planet's changing environment - Earth's environment for one has varied quite substantially in many directions over its history.

Given that we inhabit one of a very large number of solar systems in the outer reaches of our galaxy, it's plausible that other planetary systems may have developed along a similar path to ours. Speculation on how likely it is for there to be life anywhere near us would be a function of the density of our galactic neighbourhood, the likelihood of a similar solar system developing, and the range of tolerance of radiation for viable mutative life to evolve.

On an anecdotal basis (given the results of SETI to date), the suggestion is that there is nothing close by. But it would remain interesting to attempt the sums on the range of radiation that would foster an evolving biosystem.

*101 Key Ideas: Genetics, Jenkins, M (2000); Hodder & Stoughton, London.
This book has got some surprisingly sloppy writing and at least one incorrect diagram. But from time to time its descriptions give particularly useful insights.

Tuesday, January 27, 2009

rebirth of rationality in America

"Science, science, science" - summary from Nancy Pelosi, Speaker of the US House of Representatives, when asked about priorities in a plan for reviving the US economy (quoted in New Scientist, 24 Jan 2009).

"I believe in evolution, scientific enquiry, and global warming" - Barack Obama, The Audacity Of Hope (p17).

"I refuse to believe the majority of people believe this malarky" - Joe Biden, now Vice President, when asked about intelligent design in 2006.

Monday, January 26, 2009

Practical astronomy lessons

I was never interested in astronomy: those patterns of stars never made any sense to me. But recently I spoke to an astronomer, and he helped put a lot of pieces together for me.

Stephen works for the Anglo Australian Telescope, a joint venture between those two governments (although it looks like the English are planning to pull out).

The telescope itself is situated near Coonabarabran, in the west of New South Wales; however Stephen is located in Sydney, sending requests out west, receiving data back, and sometimes travelling out to be there in person. In stark contrast to me, he had always loved astronomy, has a PhD, and seems to be working where he wants to be. he painted several dichotomies which helped me understand the discipline. He was really on top of his subject, so any error here is due to my effort in understanding.

One of those dichotomies is between the practical and the theoretical astronomer. The practical astronomer will do all the practical work in aligning the telescope, identifying the items of interest, and taking the images. The work is then handed over to a theoretical astronomer, who tries to work out what it all means. If anything, I would be that theoretician; the practical side would scare me, but the maths and physics would fascinate.

He also clarified for me the difference between optical and radio telescopes. Although I should have had an inkling, I never did join the dots: there is quite a distinction between the two. The first, of course, scans space for what can be seen in visible light, using what we traditionally understand a telescope to be, lenses and all. But a radio telescope picks up radiation in the spectrum beyond ultraviolet light, thus needing non-optical radio receivers to pick up data from space. They're both picking up information from the EM spectrum, but representing and analysing it differently. Radio telescopes can be as in the film The Dish, which has an enormous parabolic dish that concentrates signals to a point which records them.

This is the Parkes observatory (again in western New South Wales), which is part of the CSIRO (Australia's scientific research organisation) whereas the AAT is not part of the CSIRO at all.

Radio telescopes can also be set up in an array of smaller ones, as in the film Contact - in fact, there is a site in Western Australia that is in the running for global funding to develop an array of dishes that would be one of the largest in the world, running to an area of square kilometres.

Stephen said that, in a very broad sense, optical telescopes took images that represent a (relatively) static view of the universe - as it was at a single point in time (so to speak - the light from distant objects, of course, would date back further in time than that from closer objects). In contrast, radio telescopes recorded data from events - a more dynamic picture being built up of suns flaring, galaxies colliding, black holes, gas clouds, etc. My guess is that images we see that are built from radio telescopes are colour coded to depict the intended narrative that is not otherwise representable visually, whereas optical images may at times be enhanced to also provide clarity to the narrative. Unfortunately, this means some people would be misled into thinking that at a macro level, the universe is more colourful than it really is.

Stephen told me much more about the subject than I have reproduced here, and I am very grateful to him for helping me fill so many gaps in my understanding.

Coincidentally, my family (without me) passed by Parkes a couple of weeks after our conversation, which is why I have this magnificent picture. The dish is 64m in diameter, covers 3216 square metres, and weighs 300 tonnes. Operating frequencies range from 440 MHz to 23 GHz.

Sunday, January 25, 2009

Obama on politics

Barack Obama's book The Audacity Of Hope is a very pleasant read. It's easy, lively and thoughtful, and gives an impression of grace.

The chapter on politics gives a few interesting insights into his experiences. He discusses the danger of "transformation into the stock politician of bad tv movies", and every politician's fear of losing an election - more, a fear therein of "total, complete humiliation". Winner takes all. He compares this to the business executive who can prosper by coming second, year after year.

He also discusses the burgeoning need for money to fund campaigns. He is aware of the process of increasingly spending one's time in the company not of ordinary people, but those who are well off enough to donate thousands to one's next campaign. Despite efforts to maintain one's stands on particular issues, the voices one hears become increasingly slanted to those people and their interests: "the problems of ordinary people... become a distant echo rather than a palpable reality, abstractions to be managed rather than battles to be fought". On the other hand, Obama says: "One of my favourite tasks of being a senator is hosting town meetings... my time with them is like a dip in a cool stream."

He recognises the tangible difference in motivation between lobbyists who represent profit-making interest and those that represent public issues. Yet he mentions filling in 50 questionnaires from interest groups in his senate primary campaign, and the difficulty in ticking all of any one set of boxes. For example: "I might agree with a union on the need to enforce labor and environmental standards in our trade laws, but did I believe that NAFTA should be repealed". He says he lost some endorsements on his answers, although on occasion he was surprised in getting an endorsement despite a "wrong answer".

And he goes into some detail on the convoluted practices of the Senate and the House of Representives, which of themselves are a demoralising indictment on the subversion of political processes.

The chapter exhudes integrity - but of course, words written by a politician about politics can very easily be seen as self-serving, whether they are or not. He rounds off the discussion about the demerits of the system with a set of ideas for campaign reform. They include: "nonpartisan districting, same-day registration and weekend elections" to increase participation (and thus scrutiny) levels. "Public financing of campaigns or free television and radio time could drastically reduce the constant scrounging for money and the influence of special interests. Changes in the rules in the House and the Senate might empower legislators in the minority, increase transparency in the process, and encourage more probing reporting".

He frames this challenge in terms of the willingness of those in office to yield some of their power base: a change in attitude, an amount of courage, and - implicity - a generosity, a harkening back to the reasons for public service.

He now has his best opportunity to influence some of these adverse political practices. He has already made a start, in mandating a greater distance between serving in his administration and joining the lobbyists on the other side of the fence. Let's see how far he can get.

Neil Young and My Morning Jacket

Seldom can I go to a concert and look forward to anything the band plays. Usually I have a level of anticipation for certain high spots; usually the band has some rather average moments.

Neil Young has behind him 40-odd years of experience in his craft, and just as much material to draw upon. Appreciating his guitar style alone is enough to appreciate the whole of his concert. He can improvise with consummate ease; and he clearly loves what he does.

I don't remember too much of the song list: much of it wasn't immediately familiar to me. He played Everybody Knows This Is Nowhere; one of the more trivial songs from the eponymous album, but possibly something that he simply enjoyed playing. He played a rousing Cinnamon Girl too, and The Needle And The Damage Done, but to my memory nothing more from his first seven albums. The centrepiece was an extended take on Cortez The Killer, which was truly mesmeric. Four Strong Winds was also included but again, as an acoustic song it seemed to be no match for those where he was electric. It's also worth mentioning an instrumental piece he played solo, on a miniature pipe organ and harmonica. Haunting; very well done.

There are few concerts to match such an experience that was captivating from beginning to end. Most of those for me have been guitar bands (The Clean, The Verlaines, Sonic Youth and The Church), but to that list I would add Solomon Burke, whose secular gospel style was truly spiritual.

My Morning Jacket was quite a surprise. They have (to me) a somewhat shoegazer ethic, but their guitar work is ultimately a mark of respect for Neil Young. Yet the guitarist is also a singer, with a voice that aspires to the heights of Thom Yorke. It is a wonder to see the two talents in one person, but it is unsurprising that he doesn't do both at the same time. Definitely a band to watch out for.

Thursday, January 22, 2009

Obama is sometimes black

In reading the headlines in Australian newspapers, it's easy to get the impression that the only notable feature of Barack Obama as president is that he is black. Never mind his ethics, intelligence, insight, vision, coherency - and praxis. As a letter-writer took glee in pointing out in two Australian papers, Martin Luthor King said "[I have a dream that my four little children will one day live in a nation where] they will not be judged by the color of their skin, but by the content of their character." That writer didn't notice anything particular about Obama; he had already missed the boat.

But Obama is sometimes black. Meaning, there is sometimes some particular significance [beyond what his experiences have fed into his character]. This even apart from those around the world who are now infusing his ethics and asking themselves in a given situation "what would Obama do?"

BBC World Service radio recorded and reported some personal experiences from some people who had made the trek to Washington to experience the inaugeration in person. One African American woman expressed how he was a personal inspiration to her, his example encouraging her to a greater level of personal responsibility in her life. (Not that she, from her discourse, seemed to lack any particular sense of responsibility. It seemed, more, that she felt that connection, and felt duty-bound to take her sense of responsibility to a higher level.)

It is not my intention to purvey any sort of condescension here, but rather to convey a sense of the inspiration he has provided to so many people that would not have otherwise been engaged were he not African American.

Obama is black when it has particular significance. But for the most part, he is more than that.

Tuesday, January 20, 2009

Early extinctions in New Zealand

New Zealand had a special environment. From the time it split from Antarctica about 80 million years ago, it was one of the larger, more isolated land masses in the world*. The fact that it was mostly free of terrestrian mammalian predators** eems to have, of itself, fostered a unique panoply of ground-based wildlife.

A recent article in American Scientist (The Rat's Tale) paints a picture of ecological destruction that followed the first wave of predatory mammals - although the second wave (Europeans) would ultimately have been more destructive.

The article details the laborious scientific process - and debate - in establishing the date for that first wave, which last year was settled with a period range of 1290 to 1380AD for the arrival of the Maori and the Polynesian rat, kiore or Rattus exulans.

The rats ate "plants, fruits, seeds, insects, lizards, snails, eggs, and the nestlings of ground-breeding birds".

Maoris were apparently responsible for the extinction of the largely predator-free [ostrich-like] moa, and the reduction in forestation of New Zealand from about 85-90% to 25-27% (according to the article). Good evidence suggests this latter was due to significant burn-offs - for various reasons, including living space, ease of travel, and fostering food sources, specifically the bracken root, a starchy staple.

From that first wave, human and rat between them precipitated a 50% decline in bird species and the extinction of bat, frog, and numerous lizard species.

The oldest verified archeological site in NZ is Wairau Bar in the South Island, dating to 1285 to 1300. Amongst many artifacts are the bones of 8000-odd moas and 2000 moa eggs - suggestive of the ease with which they were killed.

The Polynesian rats apparently took less than 80 years to spread throughout the North and South Islands - about the same time as it took the European rat, Rattus norvegicus, once introduced.

This is not a tale of Maori destruction - rather, it's the familiar one of human destruction: "The first duty of colonisers is to survive. That requires rapid population growth sustained by consuming the richest resources" (Atholl Anderson, Australian National University).

The main reference for the article is: Wilmshurst, J. M., A. J. Anderson, T. F. G. Higham and T. H. Worthy. 2008. Dating the late prehistoric dispersal of Polynesians to New Zealand using the commensal Pacific rat. Proceedings of the National Academy of Sciences 105:7676–7680.

*Albeit some theories (discussed earlier, here) posit complete submergence of the land mass for a period of time. I'm not convinced of this, particularly given the continued existence of the flightless ratite moa, discussed here.
**The recently discovered 'waddling mouse'/'sb mammal' -see here and here - notwithstanding. There doesn't seem to be any evidence that it impacted the significant and burgeoning terrestrial habiting bird population.

Saturday, January 17, 2009

Flight Of The Conchords

Belatedly due to a pointer from my New Zealand sister, I have become addicted to a duo of annoying New Zealand musicians and comics, Flight Of The Conchords.

The premise for this Emmy-nominated no-budget sitcom is a pair of New Zealanders trying to hit it big in New York.

Buried within a costume of weak humour is a truly engaging, dry wit, and a surprising depth of musicianship that could score all the points on its own.

I find it particularly funny that they see all Australians as their natural enemies.

Aggrevating and engaging, deceptively talented.

Obama before inaugeration

Obama's "last interview before inaugeration" was another good insight into the man who, having already cemented his pivotal status in this epoch must also be, in some part of his mind, aware that eight years is a drastically short time to put in place sound building blocks for the world's future.

Despite the questions being inevitably located within the same melange of pressing issues of the era, and despite his charactistically easy loquatiousness echoing themes largely previsited, there remained room - as always - to gain further understanding of his capacity to chart the maelstroms.

He mentioned discussing with his daughters Lincoln's inaugeration addresses and their personal expectations of him to achieve so much, in a human sphere. He has consistently been able to weave any and all of the varying strands of ideas to a broader, nobler narrative. The clarity and strong coherency of his vision, humanity and intelligence is always stunning. Although that is all too often proven inadequate unto itself, he also clearly articulates action that is already underway as concrete reality. It's fortunate that the opportunity is here: There are truly few who could face these times like Obama.

Friday, January 16, 2009

Patrick McGoohan: The prisoner is free at last

Patrick McGoohan has died.

He will always be known for his work on The Prisoner, where he was captured by an unknown agency, and placed in a surreal village with the aim of extracting unidentified information.

It could be said to be a work of paranoia: living in a bizarre village where nobody could be trusted, and the only aim was to escape. But it was, on the other hand, a subversive work: the prisoner had to function - live - within the Village even as he would want to subvert the paradigm, which only seemed to exist to ensnare him.

His creative control over that work was bought off the back of his great success in a tv series called Secret Agent. Ironically, The Prisoner was the less successful work at the time, but better remembered now. And it imprisoned him from then on. His later roles were minor at best, risible at worst.

But he will always be remembered for that contentious, infuriating, quirky, imaginative ouevre.

Thursday, January 15, 2009

Saudi Arabia's tragic human rights

Of course, when a society treats half its population like chattels at best (liabilities at worse), it stunts the full development and realisation of the whole's potential.

That is not - yet - enough of a problem in Saudia Arabia.

The headline (here) is that the 'most senior' Saudi cleric said "A female who is 10 or 12 is marriageable and those who think she's too young are wrong and are being unfair to her."

In what sense is he using the word unfair? Unfair to the perceived honour of the girl's father and family? It can only have meaning in a society where the dominant culture views a girl as no more than a burdensome responsibility.

The context beyond the headlines relates to the Saudi government's Human Rights Commission, which condemned marriages of girls as an inhuman violation [of them and their rights].

Some comfort could be taken from the fact that such a body exists. Yet it's a long haul if both government and courts lag far behind.

A Saudi court recently dismissed a divorce petition emanating from a girl's mother, saying that only the girl could file - once she reached puberty. Meaning: today's courts are only conducting trivial argy bargy around the fringes of the issue.

As much as anything else, two fundaments should apply to anyone who considers that children, and childhood, should be respected as tantamount to sacred.

First, if there were such a concept as 'informed consent' in Saudi Arabia, a child clearly couldn't give such consent until reaching a deemed level of maturity - and that age being 16 in most countries could be argued to be not protective enough, in this context. Second, the reproductive cycle is impact enough on any woman's body, but going through it before the body is fully matured is potentially quite dangerous.

Wednesday, January 14, 2009

Evolution: causes of mutation

Mutagens are those factors that cause mutation. Most sources list radiation and chemicals as the two types of mutagens. Some sources also add that there is a steady (background) amount of "natural" or "spontaneous" mutations. I haven't read enough about it to know whether this can be ascribed to a "natural" [terrestrial] amount of background radiation.

It is important to note that the implications of mutation - change in the original DNA base sequences of an organism - differ depending on whether the cell affected is a somatic or a germ cell. A mutation that occurs in a somatic, or body, cell will not affect heredity; the most notable outcome for a somatic mutation is cancer.

A mutation can be inherited if a) the DNA change has no significant impact on the viability of the cell, and the reproduction process, and b) it occurs in any of several types of germ cells - ie those cells that eventually give rise to the gamete egg or sperm.

Radiation in the ultraviolet wavelength can sometimes penetrate cells, and get absorbed by DNA, causing structural damage. Ionising radiation, which has a shorter wavelength than UV, is so called because it can knock electrons out of atoms, producing ions - which are more easily capable of taking part in chemical reactions. All organisms experience a small level of background radiation, which in origin can be either cosmic, solar or terrestrial (from either naturally occurring radioactive material or, more recently, human-originated).

At the DNA level, mutations can result in insertions of extra information (as base pairs), deletion of some pairs, or miscopying, such as transposition of sequences of base pairs.

Again, I wonder if "background" levels of ionising radiation are responsible for "background levels" of mutation. I would be interested to hear if any experiments have been done to establish causality: this could, for example, involve sufficiently shielding from background ratiation a sample of DNA-bearing organisms with a reasonably short generational span.

Tuesday, January 13, 2009

Zuma may still face the music

There remains a strong expectation that Jacob Zuma will be South Africa's next president.

Fortunately, however, he has been put back on the hook of corruption charges (NY Times report here). An appeals court has reinstated the charges against him; BBC radio also reported that the judgment criticised political interference in the original trial. A very salient and salutary comment, but it remains to be seen whether the judge presiding over the retrial will be sufficiently resolute. Tricky times for judicial independence in South Africa.

Lucy Kellaway on unemployment

Although many economic indicators around the world are at their worst measure since the Great Depression, there is one that beats them all. The Bank of England's interest rate has sunk to its lowest level in over three hundred years.*

Meanwhile, the ultra dry Lucy Kellaway, financial/management commentator for the BBC and Financial Times, gives her take on advice for employment and unemployment (reported here in the Irish Times). As always, she's well worth a read**.

She reports with great bemusement the three tips from the Harvard Business Review on how to keep your job: act like a survivor, show empathy to your boss, and be a good "corporate citizen". Her response: it would make your job so loathsome that you wouldn't mind losing it.

Kellaway herself looks at being unemployed. She derides the standard philosophies of "networking like crazy", assessing strengths and weaknesses, and beefing up one's web presence: "It is too late to do sensible things".

Her thoughts on four things needed:
- a tidy pile of savings
- character ("backbone and level-headedness")
- perseverance (it may take time and shoe leather)
- luck

[However, in contrast to her also recommending a holiday, I would suggest a different change: training. The world is constantly changing, and such a time is ideal for improving skills and employability.]

*Still not the evolutionary upheaval of capitalism outlined by Marx. Globally, capitalist development clearly hasn't yet run out of expansion room.

**Her latest annual awards for management twaddle give a good read too. Her award for Best Term for Sacking People: "upgrade", as in "we're going to upgrade you: allow you to move on so you can upgrade your career elsewhere".

Sunday, January 11, 2009

Atheists lack information

A letter to the editor (SMH) yesterday inter alia said athiests were "ill informed". It looks like all they need is a bit more information, and everything will be hunky dory.

Yet it was pointed out that the letter writer was a Reverend Green, and those who know Cluedo may find him a bit suspicious.

Saturday, January 10, 2009

The big bang was a bounce?

A recent article in New Scientist posited the idea that the big bang was really a bounce.

It details a computer simulation, based on Loop Quantum Theory, that runs time backwards to the big bang, which demonstrates a bounce back to a previous(ly collapsing) universe. This is apparently one up on general relativity, which breaks down at the big bang.

Having only completed undergraduate physics and maths, the article will take some time for me to absorb properly. But there is a certain neatness to the concept of a universe continuously expanding and collapsing. I would imagine that in that case, there would be no state memory retained from the previous incarnation, so all prior information/knowledge (both about and within the prior universe) would be lost. There is sufficient unevenness to the expansion after a big bang that successive universes would not develop identically.

I have previously drawn a depiction of how time could work going backwards to the big bang. It's a conceptualisation, rather than based on hard physics. The above theoretical paradigm would be closer to hard physics, but still just theory at this point.

In the process of conceiving a universe running backwards to the big bang, most people might imaging a large box, with the matter filling a decreasing amount of space in the middle of the box. Fewer would imagine space as being a contracting 'box', with nothing 'outside' it, because it's hard to think of a space without automatically extending one's thoughts beyond the limits. Likewise with time. Is 'what happened before the start of time' a valid construct?

There is no certainty yet, but I think the ultimate solution would have a satisfying neatness and symmetry.

Thursday, January 08, 2009

Pirates have a "Golden Age"

Speaking of pirates, today my son got a pirate book and model ship for his 7th birthday (thanks, sis).

It's one of the many kids' themes that just seems to knock around eternally*. Dinosaurs seem to be particularly overdone, but there I can weave into the kids' interest some meaningful narrative around evolution. Pirates, fairies, unicorns,... less useful but mostly harmless as kiddie themes, and our children have a good grip on the line between fact and fiction.

Anyway, the book characterises a "Golden Age of Piracy", from 1690 to 1730. It also distinguishes pirates from privateers, those who were granted licence by their country's rulers to attack ships from nations they were at war with.

In depicting a mythologised era, such books are fostering interest in themes that are harmless when seen from a distance. Yet in this case, we are now noticing that these narratives are not so far removed, and we are not fully innoculated from the effects.

Of course, piracy has never entirely disappeared from the earth - for example, it has long existed around the shipping lanes separating southeast Asian mainland from the archipelagoes (such as the Strait of Malacca). And of course, the Gulf of Aden has currency for the Somali pirates operating there.

Not so far removed. Australia is now considering a request to provide naval resources to patrol the seas around Somalia. And my son has a friend whose father is in the navy, which could bring the issue very close to home indeed.

"Golden Age" pirates in the West Indies sometimes found berth in the more lawless ports where they were less likely to be hounded by authorities. Those ports have their mirror in modern-day Somalia, and however freewheelin' it may sound, they are today places that few can feel safe.

It's a minor point perhaps: my beef is with the sanitisation, the stripping of meaning then in particular the romanticisation of something that is not romantic at core, which still has the potential - however latent - to render the trivialisation hypocritical.

* Is piracy as kiddytheme traceable to Stevenson's Treasure Island?

The worst security threats are cyber

The FBI warned yesterday that cyber attacks posed a bigger threat to the US than physical threats.

It's a little far fetched to claim that whole infrastructures are at stake - for the US, at least. But all large organisations (government, capital or community sector), have a heavy reliance on computerised processes, and those processes - and key organisational assets - are facing the entire world via their online presence. It is almost axiomatic that much of these assets aren't fully secured against determined and knowledgeable cyber attacks - let alone compromise from within.

It's also likely that jurisdictions that are less technologically sophisticated could face greater threats to computer-based assets, particularly from concerted attack from countries with a stronger base of technical skills. The article above mentioned cyber attacks on Estonia and Georgia that emanated from Russia - just one illustration of the possibilities for unofficial warfare to gain advantage in standoff situations. Such attacks can be worse than physical war because:

- it is often difficult to ascertain the size of an attack: as mentioned in the article, it is much easier to see and gauge the extent of a physical conflagration;
- it is often difficult to ascertain the source of an attack. The general location can be hard, but the originating organisation is much more difficult;
- adequate security requires a level of sophistication to plug all the gaps that most organisations simply don't have;
- at best, the attacker may be located physically, which knowledge may not help.

I can see nothing to suggest this situation will substantially change over time. Security may get more sophisticated for many organisations, but more gaps will always emerge, attackers will in turn improve skills and tools, and the stakes will get higher as organisational assets become more intrinsically tied to the digital economy. Soldiers, pirates and privateers will all circle around each other's forts, barely seen.

Wednesday, January 07, 2009

Keith Windschuttle, hypocrite historian

Keith Windschuttle is the Australian equivalent of a holocaust denier. His publications on history (especially 2002's The Fabrication of Aboriginal History, Volume One) claimed there were no massacres (let alone genocidal) by white settlers of aboriginal Australians. He has claimed that oppositional historians have fabricated evidence, misrepresented facts, and insufficiently researched the sources.

Since that book's publication, Windschuttle has repeated promised imminent publication of a Volume Two, which has never emerged, no doubt due at least in part to the extensive rebuttals that have been published of Volume One.

Of course, Windschuttle's heyday was in the era of Australia's arch-conservative Prime Minister John Howard (1996 - 2007). Howard warmly embraced Windschuttle's views (both railed against a purported 'black armband' view of history), to the extent of appointing him - a contemporary at Canterbury Boys High School - to the board of the ABC, Australia's national broadcaster (previously mentioned here).

Windschuttle was also appointed editor of the conservative journal Quadrant. And he has now fallen victim to his own vituperations. Without checking sources - or the author's bona fides - he published an article on genetic engineering that turned out to be a deliberate hoax. This was more Sokal than Ern Malley - the writer followed Alan Sokal's temptation to an editor: does it sound good, and does it reinforce the editor's ideological preconceptions?

Enthusiasm for such an article is not a hanging offence. But the bait was too good for Windschuttle, and he published on sympathy rather than rigour.

So what does he do now? Hang on in case the Quadrant board doesn't boot him out? It'll be hard for him to fall back on Volume Two: his work would be subject to fine scrutiny. Shame he remains festering like a carbuncle on the ABC. But it can't last forever.

A footnote on bad science: both climate change sceptics and creationists are these days clutching at straws, rather than engaging in rigorous analysis (SMH Columnist Michael Duffy is a case in point, often arguing with incomplete understanding of the presentation of facts of climate change). It can't take much to tempt such people to hang their hat to anything that sounds to them plausible. They would be more deserving of this treatment than scientists, since they do not foster debate by constant analysis and refinement through exchange and testing of ideas - more by grabbing at plausibility that suits a perspective.

Tuesday, January 06, 2009

Evolution: genes as base sequences (DNA part 3)

Introductory narratives on genetics - and evolution and paleontology, for that matter - are often quite perilous. For every five sources that discuss the same concept, two can be incompletely informative, two can be actually misleading (frequently enough due to sloppy language), and one can be sufficiently lucid to cover the concept well. We didn't evolve from monkeys (as we know them), birds didn't evolve from dinosaurs (not the ones we know), and there isn't a 'gene for breast cancer' (as such; there has been identified a genetic mutation that can increase the risk of breast cancer).

My previous posts on DNA and genes have been somewhat meandering, on the whole. In DNA basics, I discussed DNA as the physical mechanism for storing genetic information. In part two, I discussed different types of DNA, and how genetic material can be shared through means other than species reproduction. I also discussed DNA exchange pertaining to both bacteria, and viruses (here and here).

DNA is the physical medium, and a fairly robust one it is, despite mutation. Its purpose is to store genetic information, express it, and reproduce it. This is about expression: the actual use made of the information store.

The DNA strand has combinations of four different bases, normally known as A, C, G, and T. Three consecutive bases (called a codon) can together direct the formation of an amino acid. There are 20 standard amino acids that codons can make, but at 64 possible combinations of three bases (4 x 4 x 4), several different codons can make up the same amino acid.

An amino acid schematic (analine)

These amino acids are typically combinations of about 10 to 20 carbon, oxygen, hydrogen and nitrogen atoms. Further chemical processes within a cell unite amino acids (in a process called translation, which is also directed by DNA-originated instructions) into polypeptides, which are the building blocks of proteins. The proteins are an end product of the expression of a consecutive set of bases within a DNA strand; those proteins then form an essential part in metabolic processes.

Thus a gene can be said to be "a sequence of nucleotide (base) pairs along a DNA molecule which codes for a polypeptide product [protein]" - this includes both sequences that code for the protein(s), and those that govern when it is expressed. However, calling it "the basic unit of heredity in a living organism" (as Wikipedia does) is vague enough to allow for multiple interpretations. I believe it is sufficient to refer to a sequence whose coding results in an outcome of protein(s) that then take part in other reactions. If the sequence is mutated, the protein outcomes may be slightly different or there may be no viable outcome. A 'gene for breast cancer' may refer to a sequence that, if mutated in certain ways, the end chemical outcomes could lead to cancer. Usually, however, there are multiple pathways to a cancer, and such loose talk refers to the discovery that mutation of a particular sequence has a statistically significant bearing on the cancer.

Monday, January 05, 2009

Top films of 2008 (#8 of 2008)

Personal picks, of those I have seen. I certainly can't claim to have seen the best: these days, I tend to make it only as far as the mainstream cinema up the road. Because of this, I saw plenty of very unedifying, average films. Roger Ebert offers a list of films I have largely missed, partly because of the above and partly because Australian release is behind the US, and some of his are still in the up-and-coming here. Ebert also favours Canadian director Guy Maddin - and I simply cannot stand his maddening work (the last I saw of his was largely incoherent, and I have no intention of testing the waters again).

I wanted to see Rock n Rolla, but it escaped me. I hope to see The Day The Earth Stood Still, despite quite poor reviews.

Those I can recall:

1. Michael Clayton. Marvellous thriller. And George Clooney.

2. Burn After Reading. Marvellous, George Clooney, and funny.

3. Indiana Jones And The Kingdom Of The Crystal Skull. Ham-fisted attempt to a) incorporate science fiction, and b) hand over to a new generation. But it is Indiana Jones.

4. Quantum Of Solace. The reboot works, despite remaining over the top.

5. The Dark Knight. Surprisingly good acting from Heath Ledger. (some media stupidly characterises him as an Oscar "hopeful".)

6. The Curious Case Of Benjamin Button. Wide in scope and technically impressive, however its philosophising is at best minor, and at worst pseudo-.

7. Prince Caspian. Very pleasant to see these books brought to life with competence. Dawn Treader is next, and despite it being one of my least favourites in the series, it should be a spectacle.

8. Australia. The flaws are minor quibbles (mine, unlike others, pertains to the artifice that remains characteristic of Luhrmann), but this is a very enjoyable epic.

9. The X-Files: I Want To Believe. Good to see them again.

10. I Am Legend. Will Smith is a credit.

Special mention to U2 3D (on a large screen) - I'm not sure I'd call a concert pic a film. Best of the older films seen for the first time: No Direction Home, Scorsese's Dylan biopic.

Sunday, January 04, 2009

The (temporary) collapse of spam - #7 for 2008

I'm not sure this can be counted as being of equal substance with other issues in this series. But it has been noticeable. The forced closure of a single US spam emitting enterprise has dramatically reduced the amount of email spam circulating - and the effects are still evident months later.

Spam is more than an annoyance, it is also a resource burner at a time we need to conserve resources. It's a surprise that the emission would turn out to be largely generated from one source. Possibility: they passed through the spammer community such an attractive offer of services that 80% of the business came their way. Another possibility: they offered massively bulked services to a relatively small bunch of miscreants. I cannot tell, but there were certainly several quite distinct lines of "service" that dried up. Most comprised offers of (Indian-sourced) pharmaceuticals that were either pirates of real medicines (I presume) or out and out snake oil. There seemed to be several separate variants on this. Another line that largely dried up purported to be Russian women offering themselves in the home of a better life overseas. That could well be a variant on the Nigerian scam though.

I should note that I have two email addresses. I don't know how each got infected - I'd sorely love to know about the second infection, since I was trying to keep it clear. Possibly I registered to a relatively legit website with lax security that allowed itself to be scraped for email addresses.

The first address dates back at least 10 years, and was mainly infected by poorly-grammared Nigerian scam offers. These died over time, replaced by a smattering of miscellaneous "offers". It attracts hardly any spam right now, so erstwhile spammers must have either not onsold my address, or the remnants were hooked to that US server.

On my main, newer email, they're mainly tempting me to click on a link. I don't know where they lead, since I don't know that my security protects me sufficiently from link-clicks. And there's only three a week now, effectively taken care of by SpamFighter, but quite frankly overwhelmed by the number of tech mailouts that I haven't bothered unsubscribing from. But at least I have that choice.

Update 13-Jan-09: The spam is back in volume. It took a matter of months to ramp up again. It's unclear whether it's one source that has finally found a new home, or whether it involves a distinct community of spammers which has collectively found a new home.

Saturday, January 03, 2009

Israel and the occupied territories (#6 of 2008)

The continually festering conflict between Israel and the Palestinians continues to define overall tensions in the middle east - and the world in general. It is deeper and more far-reaching than conflagrations in Iraq.

The Palestinians have lived for so long with war, stress, poverty and utter hopelessness that they have no incentive to do anything but vote for Hamas, which will avowedly fight Israel and reduce global support for them. Their missiles are borne simply of desparation and futility; their situation is thus entrenched in a vicious circle.

Israel suffers from a parliamentary system that relies too much on coalitions containing toxic elements; at the very least, appeasing those elements leads to hawkish action and insufficient rollback of Jewish settlements in Palestinian territory. Their current blitzkreig of Gaza is due to an exquisite confluence of timing: Obama has not yet been inaugerated, and an election is coming up in Israel. Globally, governments know that stoking the fires of divisiveness and security threats is an election-winner. [Israeli historian Tom Segev roots Israeli action to the long-time but fundamentally flawed Zionist assumption that punitive action - military or clampdown - against Palestinians would or could 'teach them a lesson'.]

As Israel's bankroller, the US has traditionally been a weak, junior partner. Come election time, there is a strong enough margin of Jewish voters to stop any US government from dictating terms to Israel. It is hard to see Obama's watch making any difference, particularly with Hillary Clinton as Secretary of State. Obama is a man of measure, but there is no indication his team will remove all Jewish settlements and force full Palestinian statehood. That is the minimum necessary to ease conflict. It will cost, in aid to Palestine, but that is small bikkies compared to current costs. It will cost, in terms of some continued conflict, but is hard to see that that conflict would be worse than it is now, or couldn't be contained.

It's still possible that Obama could bring about change in the middle east; unfortunately, his words have not flagged decisive action. (see here for his exact words. At the tail-end of a list of foreign policy priorities: "And seeing if we can build on some of the progress, at least in conversation, that's been made around the Israeli-Palestinian conflict will be a priority".) Nevertheless, in carrying out this action just ahead of inaugeration, Israel clearly sees Obama as less sympathetic.

To stop Israel, the US must threaten their supply of aid. To reduce Palestinian attacks on Israel, they need to be given sufficient incentive to opt for a better way. And that requires substantially addressing their poverty and lack of sovereignty.

Friday, January 02, 2009

Bush's final whimpers (#5 of 2008)

The Bush administration gave a coup de grace to 2008 in responding to the punitive Israeli attack on Gaza. When asked if they had been told of the attack in advance, a spokesman noted that a few days earlier the Israeli cabinet had flagged publicly that it could not tolerate the rockets from Gaza.

To date, neither Bush nor Rice have said anything about the assault on Gaza. One of Bush's signal goals of this term - peace for Israel and Palestine - has been quietly put out with the garbage.

Meanwhile, Laura Bush is making her own attempts at expiative rewrites of history. The Iraqi journalist who threw the shoe at Bush? It proves there is freedom in Iraq (never mind that he had his bones broken on arrest, and was tortured in jail). The "9/11" attacks: well, they didn't happen again under Bush's watch (never mind that they happened the first time, with clear warnings).

Bush doubled the US budget deficit in his tenure; the cost to the US of the Iraq occupation has been estimated at $3 to 5 trillion. That goverment spending deficit has been attributed almost entirely to security costs and tax cuts - see discussion here).

Bush's fondness for abstinence pledges over sex education and contraceptives has been a truly dismal failure. A study published in the journal Pediatrics (reported here) shows that those who took "the pledge" are equally likely to experience sex before marriage - but their use of condoms and other contraception is noticeably lower. The implication is that, in the US at least, this policy has simply resulted in more disease and unwanted pregnancy.

Spending any more time or energy on this is unwarranted. Frank Rich of the New York Times addresses this subject far more eloquently and rigorously than me (read in particular about Bush's own, risible, 'mission accomplished' publicity, which inter alia touts foreign disaster aid, while ignoring the Katrina fiasco in their own backyard).

2008 is simply the year that saw out a particularly bad and deeply unpopular president.

Thursday, January 01, 2009

NYE: The Shouties/Shout Brothers/Bernie Hayes

Well, my time with the Shout Brothers was 20 years ago, when Roaring Jack was de rigeur at the Sando every Thursday, and it might mean a hangover on Friday. The Shouties also played there on Sunday afternoons, always covers, always raucous and enjoyable.

The Shouties were back for New Year's Eve, and the only thing in common seemed to be me and Bernie Hayes (and brother Justin?). The pub was different (it was the Botny View, down the St Peters end of Newtown), the punters were younger, the covers were different, and of course brother Stevie was no longer there.

Before they played, there was a bloke wandering around with a T Shirt of the Byrds' country album Sweethearts Of The Rodeo. As a tenuous coincidence the Shouties later played a cover of Cowgirl In The Sand, a song the Byrds covered in country style (quite creditably, albeit rather different to Neil Young's original). Anyway, the Shouties' version was lengthy and blistering: Bernie just wasn't doing that sort of lead guitar 20 years ago.

Just before midnight, they played Only For Sheep*. Just after the new year, they played Freda Payne's Band Of Gold, a song about a marriage that failed on the wedding night. One had to wonder if there was a message in either of those choices.

Nice to see them again. Almost like reliving...

*An obscure song by The Bureau, a Dexys Midnight Runners offshoot. I thought I was clever to recognise it, but it had actually been a hit in Australia.