Thursday, June 12, 2008

Climate change and oil: an ironic confluence

It could be speculated that if the current oil shock had come about fifteen years earlier - say when Bush senior was waging his war - our global environment would not have such a drastically unhealthy prognosis.

Aside from the effects of maintaining war in Iraq the American way, this incredible rise in oil prices has other roots, particularly in the rapid rate of industrialisation in China (and to a lesser extent India). The irony of timing remains: if a few factors in the course of human history - or planetary composition - were tweaked, we might be switching from fossil fuels before the irrevokable global damage that we are busy causing.*

But we're caught unaware. Due to soaring petrol prices, Sydney's seeing a sudden strain to public transport infrastructure, after decades of favouring cars at the expense of rail. In Spain, the government shows signs of bowing to pressure from truck drivers. And despite governments across the world turning around on the issue, the pace of policy change is far too slow to match the urgency of the problem.

Belatedly, this shock has slightly increased the rate at which we are moving away from fossil fuels. But it's not enough, and precious lead time has been lost. Further, despite some arbitrary claims that we have reached a time of "peak oil" (which would deliver its own shocks), in reality the science and the economics is not incontrovertibly there, as it is with climate change. The surge in prices only makes it more lucrative to explore for and extract fossil fuels.

If the stars were in fully fortuitous alignment, we'd experience our current rapid technological spurt first, followed by an oil shock, followed by global warming danger. These factors are strongly intertwining, but the timing is off, and our mettle is being tested so harshly that one might stop to think there were no heavens to guide us. Our leaders are tested, but just as culpably we ourselves, who vote in those leaders and who wait around for others to take action or for governments to legislate to force our hand.

The Iraq-specific factor in the oil shock is temporary. But the galloping industrialisation of China is not.

*When I say our damage to the planet is irrevokable, I mean that the Earth has recovered several times in the past, however recovery doesn't happen on the scale of human history - it's in the millions of years. So this human-caused event is an "in our lifetimes" type situation.

Wednesday, June 11, 2008

Kids: communication, learning, imagination

I asked my seven-year-old how it looked, when she was staring at a pencil pine.

"Confused", she said.

"Untidy? Like it needed its hair brushed?"


I think her metaphor was the best.

I often find myself explaining to the kids the meaning of an English expression (eg "put a sock in it" which has no literal meaning). We do it all the time, using common expressions as shorthand to convey meaning. But they are not literal, not obvious, and have to be learnt. In this way, as we get older we become more adept at communicating, via such coded phrases.

The standard codebook of expressions (with regional variations) is very useful. But this is at the expense of imaginative thought, and imaginative expression. My daughter's description needed verification to ensure understanding. But at least it wasn't cliche, which is what most of the codebook becomes.

Perhaps this is an inevitable part of the processes of maturing. We learn to communicate more clearly with the aid of a common lexicon, but this is at the expense of imagination, in thought and in expression. And we end up talking in cliches, perhaps also thinking in cliches.

Monday, June 09, 2008

Evolution: DNA basics

It's been difficult to grasp the subtleties of some of the discourses on evolution without having a precise grasp of genetic biology. A general understanding can only help so far. In fact, I've found that some of the reason for my difficulties has been that much of the terminology has been used quite loosely, particularly when discussion escapes into the realms of mass communication such as journalism. In particular, the term 'gene' has been tossed about with such reckless abandon that it's all but lost useful meaning in the popular press.

Ideally, Wikipedia would always be a clarifying resource, but I've found that it's often not as clear as one might expect. In days to come, I hope to nail down some basics, starting with DNA.

Deconstructing the term DNA
Schematically, the shape of Deoxyribonucleic acid is the well-known double helix. To be literal, the name is broken down thus. An Acid by definition has hydrogen ion activity greater than that of pure water - this corresponds to a pH of less than 7 (which is neutral). Nucleic acid - mostly either DNA or RNA - is typically located within a cell's nucleus, although there are exceptions. The ribose part of the name refers to the backbone spirals - they are made of repeating groups called nucleotides, each of which is built on a nitrogen base, a phosphate, and ribose sugar. Further, in DNA the ribose sugar has an oxygen atom removed, thus the sugar is effectively deoxyribose.

These molecules are long - about 1.8 metres in humans! - but 46 of them are wrapped into each cell nucleus in our body - these are the 23 pairs of chromosomes.

The two spirals of repeating nucleotides are just infrastructure. The true value lies in the rung that connect one nucleotide to its opposite. Each nucleotide contains one of four bases, at their simplest C, G, A and T. They are paired (via hydrogen bonds) with their opposite number in one of four combinations: C with G, G with C, A with T, and T with A. There are up to 220 million of these base pairs in a human chromosome. Three base pairs in a row, called a codon, provides the blueprint for an amino acid, the building block of a protein. One codon sequence denotes the end of the DNA strand. (There are 64 possible codon sequences but only 20 amino acids, so some redundancy exists in ways of describing them.) A somewhat involved process uses the whole sequence in the manufacture of proteins, which are ultimately responsible for the development of an organism.

Before a cell divides, the two arms of the spiral separate and unwind. This requires the DNA molecule to spin at several hundred turns per second. I can't say my reading has given me a clear understanding of this process, although DNA molecules are located in specific areas of the cell nucleus, so there's unlikely to be any entanglement (and thus interference) between the different strands of DNA in a cell.

Junk DNA
Better described as non-coding DNA, this term refers to coding sections of DNA for which no function has been detected. This currently constitutes about 80% to 90% of the information stored in DNA. There's a variety of thoughts on the reason for this non-coding information. Most of it may be repetitive elements. A lot of it may be historical artifacts of evolution. It's plausible that the function of some of these sequences simply remains to be discovered. Some consider the sequences as stored away for potential future use. This is an interesting puzzle that may speak volumes on evolutionary processes. The evolutionary narrative finds demonstrated that redundant features of an organism don't tend to survive too long: carrying extra baggage costs, and the mutations that ditch unneeded baggage tend to be more successful. Either this precept doesn't apply at the DNA level, or there is some evolutionary benefit in this "junk" being maintained, which we just haven't yet fathomed.

There is some to suggest organisms habitually absorb DNA from other sources (as seen recently, bdelloid rotifers seem particularly good at this), although it's hard to say what part this plays in the mystery.

Other DNA
Mitochondrial DNA is that located outside the cell nucleus, in an organelle (an organ of the cell) called mitochondria, which are used to produce energy. This DNA is circular in shape, as is that of bacteria. In fact, it's thought that it originated from bacteria absorbed by eukaryotic cells. mDNA is inherited entirely matrilinearly; it has been found that mDNA in sperm cells have been marked for deletion. There are hundreds to thousands of copies per human cell, each with around 16,000 base pairs, which correspond to the same set of functions in most higher organisms.

Jones, S & Van Loon B (1993): Genetics For Beginners. Icon, Cambridge.
Lafferty P & Rowe J (eds, 1994): The Hutchinson Dictionary Of Science. Helicon, Oxford. [of the sources, this one has proved the most lucid, despite the brevity.]
Wikipedia: DNA, Base Pairs, Junk DNA and Mitochondrial DNA.

Music: Maladies

Sunday 8th June at the Annandale Hotel, headliners were Front End Loader and Spurs For Jesus, two longtime Sydney bands. But the band that really impressed was The Maladies.

They're a relatively young band. Daniele, the singer/guitarist, told me they'd been in existence for two years, although he'd been playing for five. They have not yet released a CD, although they are recording at the moment.

The music? Very lively, passionate, very rock. Reminds me somewhat of Nick Cave, although there's no way Cave and co would be this energetic. All the musicians were very accomplished. The drummer, who sometimes beat drums with rather unusual sticks, including a maraca at one stage; the singer's delivery was riveting, his voice fluid, and his talent on acoustic guitar good enough to stand out on its own; guitarist and bassist both noticeably skilled, as well as having the musical ideas to make it all interesting and exciting.

They have a MySpace page here. The guitarist, also a Daniel, apparently teaches guitar in Sydney - here. But ignore a website called - that's some US band unfortunately sharing the name.

An exciting and thoroughly impressive band. I'm eagerly awaiting a CD.

Thursday, June 05, 2008

Evolution: what are microbes?

Once biology terminology breaks out into the world of popular press, the sense of a word is often lost or misconstrued, or never well understood in the first place by either communicator or recipient.

Soon I hope to dive into the sordid mess of genetic terminology. Right now, it's microbes.

Microbe is simply a synonym for micro-organism, or microscopic organism. However, therein lies a welter of misinformation; much of the time, it's rendered synonymous with bacteria - but that's only part of the story. Here is a list - not necessarily complete - of microbes.

Bacteria. Domain: Bacteria - yes, they're a whole grouping unto themselves, which animals, plants and fungi are not, being of domain eukaryote. Bacteria are unicellular with no nucleus (thus prokaryotic). They reproduce by binary fission. There are ten times as many bacteria cells in the human body as human cells, although as prokaryotes they are an order of magnitude or so smaller than human cells.

Archaea: Domain: Archaea. Also prokaryote, reproducing by binary fission. It was thought until relatively recently that they were restricted to extremophilia - that is, only living at the extremes of tolerable ranges of temperature, acidity, etc. Since then, they've been found to be far more common. Possibly the most ancient lineage (hence the name), although there's whole worlds of debate in that issue.

Protists: a paraphyletic grouping (a Kingdom), ie a bucket for things that don't belong together, but don't fit elsewhere. They include unicellular animals (protozoa), plants (protophyta), and fungi (slime molds, water molds).

Amoebae: or amoebas, also lumped in with protists, ie Domain: eukaryota; Kingdom: Protista; phylum: sarcodina. Unicellular.

Algae: again paraphyletic. United by their focus on photosynthesis, they can be either unicellular or multicellular. Cyanobacteria was once called blue-green algae, but this is not accurate.

Plankton: Not a grouping per se, but actually defined by their ecological niche: pelagic (nearer surface) oceans. They encompass animal, plant, bacteria, etc. The bottom of the ocean food chain, and what all other pelagic animals feed on - a mixed diet, but uniformly microscopic.

Virus: Don't really belong here, as they're not classified as living: just bags of DNA seeking hosts, and which cannot live without those hosts. There are viruses for every type of living organism, including those for bacteria (bacteriophages).

Interestingly, genetic information infiltrates and is exchanged in all sorts of ways between these and other, larger organisms. That's quite a story in itself, and hopefully will be tackled soon.

Wednesday, June 04, 2008

Politics: Carter endorsing Obama

Former US President Jimmy Carter is a Democrat superdelegate. It was announced (by the Carter centre) that after polls closed in the final two Democrat primaries (Montana and South Dakota), Carter would pledge for Obama.

One wonders why he didn't do this before the primaries were over. Various news reports (here as well) point to an earlier surrogate endorsement when he said his family [children and grandchildren] supported Obama. Yet the Republicans (their National Committee) is reported to be active on the anti-Obama campaign by passing to journalists a two-year-old video in which Carter was apparently critical. The problem? Obama didn't yet have the "proven substance or experience".

Well, if that's all they can dig up, the Republicans are in trouble.

Carter also apparently said he regarded Al Gore as the best candidate (he wasn't ever to run), but if Hilary Clinton nominated, he would support her. But that was two years ago.

I'm not convinced that that earlier pledge was all that was behind the timing of Carter's official backing Obama. It's plausible that more superdelegates would have got behind Carter if he'd endorsed earlier, to the point of tipping the balance earlier.

Was it equivocation in any sense? A sense of duty to an earlier commitment? Or were (at least some of) the Democrats strategically opting for a lengthy primary campaign, calculating that prolonged exposure would outweight any internecine negativity?

Monday, June 02, 2008

Evolution: life on Earth started earlier

I record the following recent news report, which has quite meaningful implications. Some questions on the reportage niggle me, which I will record below, hopefully addressed when I find out more.

Australian scientists have found that life on Earth begain much earlier - and progressed faster - than previously believed.

The scientists, from the newly-inaugerated Centre for Astrobiology at the University of New South Wales (a short walk from here) studied stromatolites in tidal pools in Shark Bay in Western Australia. Stromatolites are traces left by bacteria life (as opposed to fossilised remnants of organisms), composed of calcium carbonate, the same substance shells are made of.

Shark Bay stromatolites

Earth was formed 4.54 billion years ago; stromatolites dating from 2.5 billion years had previously been found - also from Western Australia.

The Shark Bay specimens are very recent, dating from 10,000 years ago up to the present - uncommon, because stromatolite formations usually date from carbon-dioxide-rich times, prior to the buildup of a relatively oxygen-rich atmosphere from about 2.4 billion years ago.

The study found that the Shark Bay microbe colonies - little different from the 3.5 billion year old samples - consist of hundreds of different species, which perform a range of different tasks that each contribute to the survival of the overall ecosystem. This mutual dependency, according to Dr Brett Neilan, demonstrates that Earth was "already teeming with diverse microbial life", and thus life was evolving at least "many ten of millions of years earlier" than the 3.5 billion year mark.

The announcement was timed to coincide with the launch of the new Centre. How significant is it? On the one hand, "many tens of millions of years" would not seem to add many percentage points to the origin of life. However, it could be said that every bit counts. As I recorded in February, a recent study calculated that there was only about a billion years' worth of viable life left in the planet - before the sun expands to the point Earth becomes uninhabitable.

The chief issue is how contingent - and thus unlikely - the appearance of life is. The further back the origin is pushed, the less contingent life is on chance conditions: the more inevitable it becomes if the circumstances are right - that is (as far as we know it), a star of our sun's size, plus planetary objects of the right size in the right range of distance from the star.

(I have no specific need to tear down idols - they're already down as far as I'm concerned, and life is already here. But it speaks to an increase in the odds of encountering signs of life within a detectable distance from our sparsely populated arm of the galaxy.)

The scientists reporting this study do stress the similarity of the stromatolite formations to those in WA's Pilbara that were dated to 2.5 billion. My first inclination would be to wonder if that necessarily means the Shark Bay colonies are no more evolved than those in the Pilbara. They're the experts, so I'd have to take their word for it. I'd like to know more about those issues, though.