Friday, February 27, 2009

Effective, easy exercise!

These days, my preferred form of exercise is swimming. I came back to it after at least ten years of exercise machines, running, or - in the main - little exercise beyond a reasonable amount of walking.

I determined to do a form of exercise where the bar to making an excuse is so high that it is easier to just do it. Based on past inhibitors, this has to be:

  • close to home;
  • not too strenuous as to make me tired all the time;
  • not take up too much of my time;
  • no significant financial hurdle;
  • not too tedious;
  • easy to keep it very regular.
So I no longer do 1000 to 1500m swims - it's a relatively quick 650m per time, every two days, at a humble local pool.

After about a year of this, I noted that it didn't seem to be doing me any good. Yet a short time later, I realised I did have somewhat better well-being, and in fact my muscles were now getting restless for exercise - a sure sign of success.

In fact, recently I've found my swimming is surprisingly vigorous - to the extent that my muscles are demanding to be tested pretty much all the way through.

Not long ago, I decided I should be doing more realistic stretching exercises beforehand. This might have made some difference to the benefit I was getting - but I'm still not stretching all that much. Maybe the helpful minimum is small.

And now I find that my muscles are restless only a couple of hours after the swim. I'm not convinced that I'm the sort of person that experiences a noticeable endorphin rush with a good dose of exercise. But I'm now at the point where I do need the exercise to feel good - at least, for my muscles to feel better. And the walking I do is dead easy now - feels good even.
I hope this is a salient lesson. 650 metres is not really all that much - I feel apologetic to mention it - but it has become effective.

Telstra turbulence to subside sans Trujillo

And now... the seamier side of the business world.

Sol Trujillo is departing Telstra's helm after a particularly turbulent four years. He says he's looking forward to "reconnecting with his family" - which tends to be code for being fired (otherwise, he'd already have an announcement on his new position). There had been ruminations in the press for the past few weeks about this, so it's not unexpected.

Although Telstra is no longer in government hands, it is still Australia's largest telco by a good margin. Trujillo's plan was to shake up Telstra's "ossified" structures, but I'm not convinced that he achieved much in the end. Doubtless, obituaries on his tenure will be written in the next few days. These should include the fact that he was a big stakes bluffer - I'd be very surprised if he doesn't play poker.

Throughout his tenure, he was using Telstra's market dominant position to attempt to leverage advantage from the government for the organisation. He drove Telstra into more or less constant litigation to attempt to protect its privileged position. But he didn't seem to understand the political paradigm that had developed in Australia over the past 20 years: that legislation and structures had been put in place to foster strongly competitive over monopolistic practices, and a one-man band wasn't going to change that, even when flexing the muscle of one of Australia's largest organisations.

In reality, now that it is effectively not a publicly-owned utility, there has long been a strong case for breaking up Telstra into separate infrastructure and communications service organisations. Trujillo strongly resisted this, as he would, but I can't see this not happening over time. The synergies of a unified company are only as useful as the competitiveness of the services provided, and there's a good argument that Telstra has effectively held back sorely-needed development of Australia's telecommunications - quite apart from the issue of encouragement/discouragement of capital investment.

Trujillo's last gasp was to put in Telstra's bid for the government telecomms infrastructure spend - a non-compliant bid. Trujillo was gambling that the government wouldn't realistically want to do anything but go running to Telstra.

He lost. I can't see that he'll be missed when he leaves. At a time when the share price is, of course, at a long-term low, estimates of total payment for his time there range from $30m to $40 million. I haven't heard of any intention of his to give any of it away.

Thursday, February 26, 2009

Banker shares his bonus

Leonard Abess Jr is a banker who, when faced with a $60 million payout, went against type. He shared it all out amongst the bank's employees. And former employees. To 471 people all told, for an average of $127,000 each.

Digging deeper into the story, it's even more interesting, with a few unexpected twists.

Abess' father started the bank in 1946. Abess Jr started out in the print shop, and worked his way up. The bank was sold in the 1980's, but eventually got bought by a businessman who was convicted of fraud, and the bank fell into bankruptcy. Abess Jr then bought out the bank for $27 million, most of it borrowed. He built it back up to a profitable level, and didn't require any federal bailout funds. When he sold the bank for $927 million, he shared his $60m profit amongst current and former employees. "I knew some of these people since I was 7 years old. I didn't feel right getting the money myself."

He didn't publicise this himself either, and apparently hasn't been returning media calls.

One of the beneficiaries was a retiree who started at the bank as janitor, and worked his way up to vice president. Not something that might easily happen these days.

Abess was lauded in Obama's recent speech to congress. More reports here and here.

Answer to yesterday's puzzle: ebullient.

Wednesday, February 25, 2009

The brain and background problem-solving

How the brain works remains a fascination for me. Two of the tales that stay in my mind over the last few years are:
- the man with severe brain degeneration who simply experienced a certain loss of complex functionality - because he did exercise his brain well (mentioned here);
- Daniel Tammet, autistic savant who can memorise long strings of numbers - and perform complex calculations - by visualising them as shapes. (Discussed here.)

The one spoke to the capacity of the brain to rewire; the other possibly illustrated what can be achieved when the brain is rewired - or short-circuited - in some way.

Today's thought is somewhat more trivial, but an interesting question about how the brain works.

One good way to exercise the brain is with regular puzzles. A common one in daily newspapers is Target. Today, your goals range from 12 to 18 to 24 words in the following letters:


- but all words need to be at least four letters, include the middle letter, and you need to find the nine-letter word.

I can usually get between the middle and the top target, beyond which point the words can become arbitrary - dependent on the dictionary used.

Today I tried to work out the nine-letter word, but I just couldn't get it. I walked away, but in the next 30 seconds it just came to me.

This has happened from time to time, and so is not a coincidence. Is it something to do with the ability of the "subconscious mind" to keep processing in the background - and then feed the results to the "conscious mind"? Is it something to do with the forced foreground train of thought, which needs to be relaxed to allow the processing to better happen?

Thoughts welcome.

Answer (to the nine-letter word) tomorrow.

Tuesday, February 24, 2009

Sculptures by the Sea - 2008

I know this is rather late, but I can record at least a couple of items that struck me in last November's exhibition of sculptures placed on the walk between Tamarama Beach and Bronte Beach.

First up is the one that made the biggest impression on me. I liked its strength, and its unexpectedness.

Interface by Michael Lipman

"my aim is to create the interface between the ocean and man. The ocean is turning back the iron road as its force cannot be controlled."

My wife's vote (and my next favourite):

Mongrel country - nil tenure by Amanda Stuart

My six-year-old son's vote: Poroplastic 2 [an exploded motorcycle] by Richard Goodwin

My seven-year-old daughter's favourite:

Humpback gunship by Benjamin Gilbert

Monday, February 23, 2009

A mynah with a tail feather

Yes, the common mynah does normally have tail feathers. We see a lot of them in our back yard. But this morning I saw one with an extra tail feather.

It's a large white feather, attached to the mynah's tail. I figured the feather came from a cockatoo - they're they only white birds abundant in this area.

And the feather was firmly stuck - I saw the mynah fly up to a tree a couple of times, and the feather stayed with it, more or less straight in alignment. I daresay the extra baggage must have either helped or hindered the mynah's flight, but I didn't see any evidence either way.

So, the question is: was it an accident, self-decoration, or did someone put it there? I would guess the former, although it seemed so firmly attached as to suggest the latter. Then again, has any ornithologist heard of a mynah decorating their own tail?

Sunday, February 22, 2009

The dearth of documentaries

When I was a child, documentaries were anathema, getting in the way of the fun stuff of tv. There seemed to be a lot of them.

Now that I'm too old to have time to watch tv, the death knell seems to already have been sounded for documentaries. There are a few, scattered here and there, but the only consistency I can find is the mixed bag that both SBS and ABC run on Sunday nights. Even then, I will not usually have the opportunity to watch, since their timing coincides with the maelstrom of running the kids through the processes of getting them to bed.

By documentary, I seem to be referring to history and science. On reflection. The kids are quite happy with nature programmes, and I'm happy when they learn something of evolution from that, which they do.

Australian regulations mandate a certain number of hours per week to be devoted to "non-fiction" type programming. But that has traditionally allowed the commercial channels to indulge in little more than tabloid journalism. And the market seems to have lurched decidedly towards the tabloid end in more recent times. This became epitomised by the uber-tabloid reality tv programming, which is in vogue not least because it is so cheap to produce. And which, while they may for some provide an able source of material for certain sociological analysis, are not really the stuff of great insight.

This is all quite a pity, as I've found the new technologies are a marvellous way to supplement broadcast documentaries: whenever the narrative veers on a tangent, or moves on while leaving potent questions unanswered, I can immediately explore the topic further on the web.

Unfortunately, the best chance I get for decent documentary tv these days is via videos at the local library.

Saturday, February 21, 2009

Apartheid and Israelis

Dubai, an oil-rich emirate that wants to become a significant part of the world - or rather, bring the world to it - caused headlines recently when it barred an Israeli female tennis player from attending a tournament.

It subsequently relented, and made special provisions to allow Andy Ram, an Israeli male tennis player, to compete.

That reminds me of the days of apartheid in South Africa, where everyone was classified on the basis of perceived races. This frequently arbitrary system fell apart when it was tested at the fringes - for example, some VIP visitors being given temporary 'white' status. This just showed how the whole system stank, since it wasn't based on a rigorous logic.

Likewise Dubai's actions stink - in particular in granting Ram a special status visa. Of course, they're caught between the desire for global status and their righteous sympathy for the plight of all Palestinians. Unfortunately, the two goals clash at times like this. In an ideal world this would not happen, but in an ideal world the US would not bankroll an Israel that continued to support Israeli settlements in the occupied territories - much less condoning occupation at all.

One can only hope that the new administration has the capacity to force meaningful resolution for the Palestinians.

Friday, February 20, 2009

Chris Pyne is a Liberal, after all.

Whenever an MP of the Liberal Party of Australia refers to the party as a "broad church", you know there's disunity in the parliamentary ranks.

Although it is one of the few right-wing Liberal parties in the world, its founding basis (in the 1940s) means it sometimes attracts what is known in Australia as "small-L liberals", ie those that are not really right wing.

Former Prime Minister John Howard recently referred to the party as "centre right" - which is ironic, given he led it on a lurch to the right over his 11-year tenure.

As it happens, Malcolm Turnbull, who is currently warming the leadership seat, is a small-l liberal. In a few bouts of turmoil over the past week, he elevated a couple of colleagues who were of the same ilk, Joe Hockey - now shadow Treasurer - and Chris Pyne. The latter in particular rankled the hard right and conservatives, including Pyne's fellow South Australian and factional opponent Cory Bernardi. Bernardi published a newsletter in which he mentioned that an unnamed Liberal MP once mentioned to him that he could easily have joined the Labor Party instead, but he joined the Liberals because he lived within a Liberal seat.

The nameless one was quickly identified as Pyne, and Bernardi was seen (by Turnbull at least) as fanning the flames of disunity, and was asked to apologise. Of course, what he said was true, and he hadn't named the MP, so Bernardi stood his ground, and for his sins was forced to resign from the front bench.

The point of it all is that, yes the Liberal Party is a broad church. And Labor, too, has left and right - it's easy to call it more right than left. However, in the dichotomous spectrum of Australian politics, Liberal is clearly the party of the conservative/right, and Labor is clearly more the party of the left. If you join the Liberals, you should expect to be working with, and to, a right-wing agenda.

My political sympathies see a stark delineation between left and right. And from that perspective, someone who is out of step with that is simply a quisling. Having said that, it's easy to see that in the wake of the Liberals' electoral defeat, there would inevitably be forces trying to bring the party back from the hard right, and I can't complain about that.

Thursday, February 19, 2009

Not flattering Hillary

When a photo of Hillary Clinton was mentioned to me yesterday, I said "I bet it's unflattering". Yep.

And sure enough, in today's paper, another bad photo.

Now I have my own gripes with her, but I have to say that she's very intelligent, and her heart's in the right place. I can only speculate that news editors are deciding that unflattering photos of her are more arresting than standard ones. Anything for attention.

Wednesday, February 18, 2009

Australia's Minister for Defence - who?

Up until tonight, I could not have told you the name of Australia's Defence Minister. Names of the senior cabinet members have certainly been bandied about, yet after 15 months in the position, his profile has remained particularly low.

Tonight I heard a radio interview with the Minister - Joel Fitzgibbon. The interviewer was trying to draw out information and thoughts about Australia's engagement in Afghanistan. As does happen, the interviewer was trying to extract more information than he felt he needed to give or was wise to give. So he wasn't saying anything meaningful in the first part of the interview. However, he got to the point where he was willing to enumerate a set of (four) principles for Australia's involvement in Afghanistan, and he let flow. They were rather a complex set of principles on strategy - where often enough you hear just a few tactical comments. And when pressed on particular points - naming names, so to speak, he was clearly not going to give away anything that could be diplomatically sensitive.

He could have simply fobbed off the interviewer with a few bland comments - but ultimately he made some meaningful points. Although I can usually tell which side one's ideological bread is buttered, it's not so easy with Afghanistan, because a strong case can be made for an involvement that helps that nation gain some stability and infrastructure that it scarcely ever seems to have had. That issue aside, I have to be impressed with Joel Fitzgibbon's capabilities. And he hasn't said anything yet to give me cause for alarm in a political sense, but it is still early days.

Tuesday, February 17, 2009

Automating comparison of unlike products

Oded told me today about a friend who had developed an application to identify your best mobile phone plan.

You set it to access your call pattern from your current provider; it then trawls through the web for the plans on offer from all providers, and recommends the best to you.

That in itself would be a great help, but I can see a variety of uses for this in the realm of consumer selection, particularly where service providers seem to deliberately obfusticate by ensuring their products aren't directly comparable.

Oded mentioned it in the context of evolving algorithms. I'm not sure of the exact connection, but I understood him to refer to the necessity to cater for products such as this change that change subtly over time. Parameter changes are nothing new, but if this refers to the ability to integrate new features (characteristics) into the algorithm, and learn how they interact, that would be something. If I hear anything further etc.

Monday, February 16, 2009

Not all good bacteria are alike

Research on gut bacteria has turned up some interesting and somewhat unexpected results.

Certain bacteria are necessary for humans to digest food. But we don't all have the same bacteria. Although the research found people possessed the "same core group of bacterial genes" needed for digestion, those genes in common were provided by different ranges of bacteria species.

The study also found people who were related shared a similar set of species of gut bacteria. There are several possible explanations for that including, I presume, inheritance via shared environment.

Analysis also indicated that obese people had a greater proportion of bacterial genes for digesting fat, protein and carbohydrates - ie they were better able to extract and store energy from food. If this proves significant, it has strong ramifications for the management of obesity.

The study, written up in Nature, was headed by Jeffrey Gordon of Washington University School of Medicine (Missouri), reported in New Scientist, 8-Dec-08.

Saturday, February 14, 2009

Carter on the Middle East

Heard some comments from Jimmy Carter on the radio overnight - probably a BBC interview. He seemed to be very aware of the issues and points of contention in the middle east. Some of what emerged from that interview follows.

He mentioned that Obama consulted him on the middle east, and indicated it was one of his big priorities. Carter expressed strong optimism for the new administration's capacities to reduce tensions (his words on Obama in the past included: "honesty, intelligence, and politically adept"). He was especially praiseful for Obama's middle east envoy, George Marshall, who had a significant part in easing tensions in Ireland. Carter stressed Marshall's neutrality to the situation, with words that suggested a) previous envoys had been too pro-Israel to achieve solutions; and b) Israel probably wouldn't like him. Carter also noted that Israel seemed headed to a one-state solution, which was patently unviable, not the least because the arab population (Israeli? or Israeli+Palestinian?) was set to outnumber the Jewish.

Carter did not mention Hillary Clinton at all, which suggests that either Obama has no intention for her to play a significant part (wise), or that Carter had little confidence in her capacity to bring about peace. Certainly, Hillary's words prior to inaugeration sounded like a death-knell to peace, substantially the same attitude as past US administrations had had. I think it's possible for her to be a successful Secretary of State, but clearly not in this area.

The interviewer also made mention of Carter's upcoming book We Can Have Peace in the Holy Land: A Plan That Will Work. A promising title, and now, hopefully, a government with the capacity to achieve it.

Evolution: Darwin's modification by descent

There's something of a flood of media relating to Darwin, as it is the bicentennary of his birth and 150th anniversary of his book On The Origin Of Species. Even something in it for me, as I heard on the radio part of a 1987 event featuring successive addresses by Richard Dawkins and Stephen Jay Gould. They both downplayed any beatup notion that there was any fundamental dispute between them, while emphasising their different perspecitives on their field. Still it was fascinating to listen to them both.

Although I am largely not one for hero-worship, Darwin must be given strong credit for introducing ideas that were revolutionary and prescient. On the latter, he broadly predicted the existence of a mechanism for evolutionary inheritance with modification, without knowing what shape it would take, and decades before it was widely verfied and accepted.

As part of the radio programme, I heard someone give a Darwinian characterisation of genetic variation as "copious, small and undirected". One of Darwin's revolutionary points was that evolution is paradoxically "neither random nor intentional". Not intentional, in that there is no overarching will at play that can make decisions about the process. And although the fodder for variation is random mutation, the effects are not, as species survival is directed by the totality of its environment.

Someone in that broadcast commented drily that although Darwin was inspired by Adam Smith's economic theory of numerous single players in a market vying for their own survival, Smith's theory "didn't work". Now that may be a bone of contention for some, but the purity of Smith's vision relied on equal players in a market where no monopoly develops - and we all know that in the absence of a directed force (ie a government), the natural tendency of capitalistic markets is towards monopoly. The analogy was imperfect; nevertheless it is the mark of a significant mind to be able to associatively draw from other fields to forge new understandings of one's own.

Friday, February 13, 2009

My Morning Jacket and the different sound sydrome

I located another track by My Morning Jacket amongst my CDs.

They were the band that rapidly won me over as support for Neil Young in Sydney recently. Wonderful singing and wonderful guitar work - and I'm saying this as one who could easily be jaded by a lifetime of guitar music.

The two tracks are both from the 2005 album Z; Anytime, and Gideon, the latter of which was played at the gig. But the recorded music gives scant clues to the live feel of the music: uplifting and transfixing. Something that can't easily be squeezed out of a CD.

Honestly, a live band presents an altogether different music experience to a recording. Sometimes both work; sometimes only one does. Take Solomon Burke. His concert was a wonderful communal experience of secular gospel; neither the early or recent music of his that I've heard gives a clue to this. Sonic Youth's recordings give some indication of their live sound, but not the holistic experience. The Church have different virtues live and recorded, some of which certainly overlap; but the best of each are rather different experiences from each other.

There's a song by Shayne Carter (from Straightjacket Fits) and Peter Jeffries called Randolph's going home. In some ways it sounds so rough that you wonder how it could have taken drummer Jeffries ten hours to perfect his work. But in other ways it is a sublime work, a yearning, soaring paean to a dead friend of Carter's. It may have been wonderful live - if it had ever been performed - but it could equally have come out somewhat flat. It's so often hard to tell.

Ideally, the purity of good opera is something that can transcend the medium. But rock music is not the same. You have to take it as it comes, and enjoy the transcendent experiences wherever you find them.

Thursday, February 12, 2009

Obama on foreign policy

Obama's book (Audacity of Hope) give a very helpful understanding of his goals for the US into the future - but as well as the good, it also flags some areas to watch out for, and some areas where his capacity to achieve an ideal will be sorely tested.

His words place his ideological foundation squarely in the western liberal tradition. Yes, he is a "liberal" in the American understanding of the word - that is, about as near as they can get to left-wing - but I'm using the term in the philosophical sense. This means he is explicitly pro-capitalism: he says as much. In that context, his words paint a picture of government as being the mediator and director of capitalist forces for the benefit of the people. It has to be said, however, that Obama's expression of his ideals - and he does have a nobleness of spirit - at times verges on motherhood sentiment. With a politician's eye on appreciating the dichotomous perspectives of the everyman, it's easy to suspect his capacity to exercise a hard edge that is sometimes needed to force a lurch of society in the right direction. Still, in terms of both ethics and position on the left-right spectrum, he is the most promising president in a very long time, and it's hard to see America producing the likes of him very often at all.

His chapter on the American constitution gives a good insight into the basis for the general American vision; he looks to the constitution and founders as a kind of bible for the values of their political and social system - yet ultimately he recognises that the original model for government is not a perfect bedrock: more, a basis for an ongoing political discussion.

(His assessment might be reasonably accurate - unsurprisingly, he has taught constitutional law. However, it also reveals a flaw inherent in their model - that there is too little to stop the political discourse being hijacked by a sufficiently strong ideologue or power nexus, particularly in the face of plummeting public engagement in any political processes. Obama's personal credit, he has probably raised the political engagement of the general public to levels not seen in a few generations.)

And there are clear problems with Obama's exposition on America's relationship with the world. Yes, he has a solid understanding of the nature of American foreign policy, and its all-too-often deleterious consequences. He knows very well how America has time and again fuelled the fires of emnity around the world - hardly more so than in the very recent past. He understands

But two broad principles emerge from his discussion that mitigate against soundness in peace and international co-operation. The first is the age-old issue of ceding sovereignty to external organisations. A nation does this rarely, but with the notion that the real and upfront concessions are repaid by the more real and longer-term benefits. (The gradually evolving European Union is a good example of this: a very slow process in which an amount of sovereignty is yielded every once in a while, as pluses slowly emerge.)

The other notion that emerges is one that America's fundamental values are simply right or, at least, better than anyone else's, and that foreign policy just needs some - sometimes major - adjustment. First, as my wife is fond of telling me, knowing I am right - or my values are right - does not make it so. Second, that is not the way to foster international rapprochement.

Having said all this, I still think American could not have produced a more promising president.

Wednesday, February 11, 2009

Death of the Gene pt 2 (what is a gene? pt 397)

Following on from yesterday is yet another discussion on the Gene. This constitutes a brief overview of the article Genomics Confounds Gene Classification (Michael Serenghaus and Mark Gerstein), from American Scientist (Nov 2008).

The article clarifies the concept of a gene by rendering it more complex. Which sounds somewhat perverse, but the notion of a gene has always been rubbery, possibly due to efforts to render simple something that is more complicated than taxonomically-inclined people would like to deal with.

Quickly recapping, the human genome consists of 23 pairs of chromosomes located in the nucleus of nearly every human cell. Those chromosomes - long strands of DNA - contain some three billion items of information. A sequence thereof is used to build up proteins which are the biochemical fundaments of metabolism and life. Thus comes the concept of "one gene - one protein" - that the most atomic process constitutes the encoding of a protein, which ultimately determines a human characteristic, and is thus a "basic unit of heredity".

Via Wikipedia comes the claim that there are an estimated 20,000 to 25,000 "protein-coding genes" in the human genome; the Wikipedia collaborators thus nail down the Gene between the articles on Human genome and Gene. This leaves a number of troubling questions, however, including the function of large swathes of the genome - (only) some of which may be "junk DNA" and may have been inserted by viruses into germ line cells (thus fostering inheritance).

Seringhaus and Gerstein's central premise is that the gene, as "biology's basic unit", is "not nearly so uniform nor as discrete as once was thought" - so "biologists must adapt their methods of classifying genes and their products".

Part of the problem is that the encoding process is more complicated than simply reading a contiguous strand of DNA data. That has been recognised already by conceptualising introns, segments of data that are removed from the ultimate coding process (both main strands of theory posits these as junk). There are also control sequences that govern, inter alia, the beginning and end of the transcription process. However, the overall coding process has been found to involve serious convolutions of the DNA strand. Transcription is not purely a sequential process: exons (coding strands) are non-adjacent and "important control regions can occur tens of thousands of nucleotide pairs away from the targeted coding region - with uninvolved genes sometimes postioned in between"... "the physical qualities of DNA, its ability to loop and bend, bring distand regulatory components close".

The other complication is over functionality of a "gene". Seringhaus and Gerstein: "Function in the genetic sense initially was inferred from the phenotypic effects of genes... but a phenotypic effect doesn't capture function on the molecular level. To really elucidate the importance of a gene, it's vital to understand the detailed biochemistry of its products." But each protein, each enzyme, can have a variety of biochemical effects. "Deciding which qualities of a gene and its products to record, report and classify is not trivial". This leads to the system of classification called Gene Ontology (GO). Much more complicated than a simple hierarchy, it uses a Directed Acyclic Graph structure, where each node can have multiple parents - resulting in a rather messy-looking chart of interconnected notes. This, and the "flood of new genomic data" mean a "large volume of data" which can "paralyze the most dedicated team. Precisely this problem is occurring in biology today".

The solution may be found in the semantic web project mentioned yesterday, where indefinite amounts of information and, importantly, relationships, can be stored. Simplicity vanishes, but information can be retained in toto, and compiled collaboratively that can be mined for meaning. And intuitively, such complexity makes more sense.

Tuesday, February 10, 2009

The Semantic Web (Death of the Gene, part 1)

Two recent articles - in American Scientist and New Scientist - purport to sound the death knell of our understanding of genetics. Interestingly enough, the New Scientist article is the more sensationalist, whereas American Scientist has the more meaningful one.

First, however, a diversion into computer science.

I first encountered the concept of the Semantic Web about four years ago, through a seminar presented by the W3 Consortium. The Semantic Web was envisaged as a successor to the worldwide web, something to better enable collaboration.

Web pages, written in Hypertext Markup Language, represent a rather unstructured way to navigate information. True enough, linkages are made from one concept to another. But on the whole the effect is a rather unstructured journey, with no instrinic meaning underpinning one's meanderings.

In contrast, the Semantic Web is intended to be a network of information in which the navigational links are imbued with specifically defined relationships, such that they could be machine-read. Web pioneer Tim Berners-Lee has referred to this as a Global Giant Graph in contrast to the worldwide web. Descriptive relationships are facilitated by languages designed for depicting data: Resource Description Framework, Web Ontology Language (OWL), and particularly XML (Extensible Markup Language), which is already in heavy use for defining data in a very wide range of contexts.

Why do this?, was the question that occurred to me at that seminar. The applications proposed were restricted to scientific fields such as pharmaceutics and bibliographics, somewhat esoteric to me.

But this set of design and representational principles is starting to make sense in fields in which collaboration is necessary simply because it is too difficult to keep track of a field that is constantly burgeoning, updating faster than any traditional publishing method, and too large for any one person or group to maintain. Thus, an ontology: precise specifications for a knowledge-classification system.

That could easily be a description of Wikipedia. Such an endeavour is not possible without the web, simply because it calls for such a vast community of contributors.

The same could apply to a more structured discipline, where structured relationships may be just as important as the single instance or 'article'. The ensuing structures, spread out over a large number of web sites, could then be data-mined for meaning.

There is increasing need for this in genetics, as we start to see the concept of a gene break down, and the need to build a large number of relationships out of a genetic code with billions of letters.

Monday, February 09, 2009

Kenneth Clark's Civilisation

Kenneth Clark's vision of civilisation had a viscereal effect on me.

Not too long ago, I happened upon the 1973 BBC series The Ascent Of Man, a monumental dissertation by Jacob Bronowski. It is a scientist's view of the history of humanity, and Bronowski is very humanist and thoughtful - in both the philosophical and analytical senses - in his considerations. An intellectual pleasure to watch.

It was made as a complement to Clark's 1969 series Civilisation. Again, I happened on this - at the local library - and was interested in this art historian's view of history - also said to be monumental.

However, I found this work to be disturbing rather than thought-provoking. Clark had ideas and narrative too, and put a lot of thought into it. Yet he quite struck me as fascistic in his view of the progress of history. His was an elitist perspective, whereby the watchword was a specific romantic vision of the "hero" - a unique person in history who by force of will forged a part of civilisation.

This was not Bronowski's gentle but rousing celebration of achievement; more, a Nietzchean tale of the triumph of the spirit over mere mortals, while ignoring all those that provide the milieu in which the individual achieves. Not to decry the achievements of a Shakespeare or a Da Vinci, but a lack of celebration of the synergetics of a society is ignorant at best.

As a scientist, Bonowski knows the scientific dialectic is a marvellous example of the joy of collective achievement and the exciting exchange of ideas. Particularly insightful and imaginative individuals such as Charles Darwin are rightly lauded as leaving a full body of meaningful work. But we learn and foster ideas when we have a culture in which to express. And those who have contributed ideas that languish - such as Mendel - can be resurrected later when those ideas are discovered to contribute anew to the dialectic.

Clark's world is one in which an Albert Speer could have been lauded - if his creations had survived context. Success is its own justification; in this world, Carravagio could be seen as being rightly justified in torturing models to death in search of his muse.

On a personal level, I feel Clark has debased the legacy of some of those whose work I admire, such as Michelangelo and Da Vinci. And better celebrations of history through architecture and art can be found.

Sunday, February 08, 2009

Australia's bushfires

Undoubtedly, news of Australian bushfires has spread around the world. Despite the phenomenon being largely confined to Victoria, it might give the mistaken impression that Sydney is in imminent danger of conflagration. Nevertheless, it now ranks as Australia's worst natural disaster.

Over about a week, a lengthly heatwave fired the southeastern states of Australia, delivering day after day of 40 degree plus heat to Melbourne (Victoria) and Adelaide (South Australia) in particular. The heatwave seems to have bypassed more northerly locations such as Sydney and Brisbane - and perversely, Queensland, far north of Sydney, has been experiencing major floods in this time.

The prolonged heat seared Victoria dry, and it was only a matter of time before it succumbed to flame. Sad to say, it was just as much arsonists as carelessness and lightning that set off the fires. In fact, there were reports of areas bursting into flame very soon after fires had first been put out - and that is not to decry the work of the (largely volunteer) firefighters, who are skilled and dedicated in protecting their own community.

ABC's national service Newsradio has this evening been given over entirely to Victorian local radio services, to reach and inform as much as possible the communities that are being affected or threatened. As it stands at the moment, nearly people have been accounted dead, and hundreds of homes have been destroyed.

Some explanation of the loss of life can be gleaned from advice I heard on the radio from someone on the ground. He suggested people either get out early or stay to protect their homes; running the gauntlet along the roads as the fire came was not a realistic option. Yet he seemed resigned to accepting there were people who would stay to save what they could, come what may.

Saturday, February 07, 2009

Film: Shyamalan's The Happening

I have watched most of M Night Shyamalan's films, and on the whole I have found them quite imaginative, with some thoughtful writing.

I watched his latest film, The Happening on DVD, apparently having missed any theatrical release.

And I have to say, this film is surprisingly woeful. He writes in a similar milieu to his other works, but for some reason imbues this one with a paucity of meaning and quite an off-putting context - that in which people are en masse imbued with fully-realised suicidal impulses.

The point was weak, the story development was correspondingly so - in all its few tangents - and the characters unsympathetic. Casting was quite shoddy, and the actors neither developed or were encouraged to develop any depth of experience. This was more akin to a cheap slasher film than an intricately woven supernatural thriller.

I'm quite surprised to see such a mainline release that is so poorly planned and executed. Not recommended.

8 Feb Note: although the derisive casting (and acting) are not emphasised enough, a review in Time magazine bears an eerie similarity to the set of feelings I have for this film. (I hardly ever see a review that so closely echo my own sentiments.)

Wednesday, February 04, 2009

Lucid dreams

Last night I experienced a series of dreams in which I became aware each time that I was dreaming.

In the first dream, I noticed that the detail in a patterned surface was elusive. It was not that the detail was hard to discern; rather, when I looked at it closely, it kept changing.

Thereafter, I had a succession of mini-dreams: in each one, I would find myself in a given environment, realise it was a dream, then I would try to do something specific - that is, influence my surroundings rather than simply experience them. The dream would then ebb away as I was trying to achieve my goal, and I would wake.

In successive dreams I was able to get further towards a given goal - that is, explore in a given direction. In one dream, my home was in the top floor of a small building. I realised I was dreaming and tried to get outside. I left the room, went downstairs and out onto the street; but it faded (I awoke) before I could try interacting with anyone. I was back in the same room in the following dream. This time, when I left to go downstairs, I noticed the bannister railing was missing. I got outside again, and was able to briefly interact with someone before I felt it all slip away from me.

Despite the frustration of having the experience melt away when I try to do something, I enjoy lucid dreams. I find them special, as are dreams in which I am flying. Only, in this case it's the extra sense of wonder that comes with the awareness that I am in a world that is not real, where normal rules don't apply.Such dreams don't happen often, and maybe only under special conditions, such as when I test the dream detail.

It has been said that lucid dreams can be invoked in that way. An example given is to practice counting people's fingers during the day, then see if you can do that in the dream to induce awareness.

As I found, prolonging a lucid dream can be quite a challenge. A couple of odd methods have been found to be rather effective: one is to spin around (in the dream), and the other is to rub one's hands together. My experience was that to exert conscious will in the dream was to shorten it, but if one could slip back into that state quickly enough, the dreams could be extended. Certainly, I've never before experienced such an extended sequence of lucid dreams.

Monday, February 02, 2009

The value of theorists

"A theorist can explain any correlation, and its inverse."

- attributed to Thomas Gold