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Einstein, science and the natural world: a rabid discourse

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Einstein around 1915

Einstein around 1915

Canto: Well, we’re celebrating this month what is surely the greatest achievement by a single person in the history of science, the general theory of relativity. I thought it might be a good time to reflect on that achievement, on science generally, and on the impetus that drives us to explore and understand as fully as possible the world around us.

Jacinta: The world that made us.

Canto: Précisément.

Jacinta: Well, first can I speak of Einstein as a political animal, because that has influenced me, or rather, his political views seem to chime with mine. He’s been described as a supra-nationalist, which to me is a kind of political humanism. We’re moving very gradually towards this supra-nationalism, with the European Union, the African Union, and various intergovernmental and international organisations whose goals are largely political. Einstein also saw the intellectual venture that is science as an international community venture, science as an international language, and an international community undertaking. And with the development of nuclear weapons, which clearly troubled him very deeply, he recognised more forcefully than ever the need for us to take international responsibility for our rapidly developing and potentially world-threatening technology. In his day it was nuclear weapons. Today, they’re still a threat – you’ll never get that genie back in the bottle – but there are so many other threats posed by a whole range of technologies, and we need to recognise them, inform ourselves about them, and co-operate to reduce the harm, and where possible find less destructive but still effective alternatives.

Canto: A great little speech Jas, suitable for the UN general assembly…

Jacinta: That great sinkhole of fine and fruitless speeches. So let’s get back to general relativity, what marks it off from special relativity?

Canto: Well I’m not a physicist, and I’m certainly no mathematician, but broadly speaking, general relativity is a theory of gravity. Basically, after developing special relativity, which dealt with the concepts of space and time, in 1905, he felt that he needed a more comprehensive relativistic theory incorporating gravity.

Jacinta: But hang on, was there really anything wrong with space and time before he got his hands on them? Why couldn’t he leave them alone?

Canto: OMG, you’re taking me right back to basics, aren’t you? If I had world enough, and time…

Jacinta: Actually the special theory was essentially an attempt – monumentally successful – to square Maxwell’s electromagnetism equations with the laws of Newton, a squaring up which involved enormous consequences for our understanding of space and time, which have ever since been connected in the concept – well, more than a concept, since it has been verified to the utmost – of the fourth, spacetime, dimension.

Canto: Well done, and there were other vital implications too, as expressed in E = mc², equivalating mass and energy.

Jacinta: Is that a word?

Canto: It is now.

Jacinta: So when can we stop pretending that we understand any of this shite?

Canto: Not for a while yet. The relevance of relativity goes back to Galileo and Newton. It all has to do with frames of reference. At the turn of the century, when Einstein was starting to really focus on this stuff, there was a lot of controversy about whether ‘ether’ existed – a postulated quasi-magical invisible medium through which electromagnetic and light waves propagated. This ether was supposed to provide an absolute frame of reference, but it had some contradictory properties, and seemed designed to explain away some intractable problems of physics. In any case, some important experimental work effectively quashed the ether hypothesis, and Einstein sought to reconcile the problems by deriving special relativity from two essential postulates, constant light speed and a ‘principle of relativity’, under which physical laws are the same regardless of the inertial frame of reference.

the general theory - get it?

the general theory – get it?

Jacinta: What do you mean, ‘the initial frame of reference’?

Canto: No, I said ‘the inertial frame of reference’. That’s one that describes all parameters homogenously, in such a way that any such frame is in a constant motion with respect to other such frames. But I won’t go into the mathematics of it all here.

Jacinta: As if you could.

Canto: Okay. Okay. I won’t go any further in trying to elucidate Einstein’s work, to myself, you or anyone else. At the end of it all I wanted to celebrate the heart of Einstein’s genius, which I think represents the best and most exciting element in our civilisation.

Jacinta: Drumroll. Now, expose this heart to us.

Canto: Well we’ve barely touched on the general theory, but what Einstein’s work on gravity teaches us is that by not leaving things well alone, as you put it, we can make enormous strides. Of course it took insight, hard work, and a full and deep understanding of the issues at stake, and of the work that had already been done to resolve those issues. And I don’t think Einstein was intending to be a revolutionary. He was simply exercised by the problems posed in trying to understand, dare I say, the very nature of reality. And he rose to that challenge and transformed our understanding of reality more than any other person in human history. It’s unlikely that anything so transformative will ever come again – from the mind of a single human being.

Jacinta: Yes it’s an interesting point, and it takes a particular development of culture to allow that kind of transformative thinking. It took Europe centuries to emerge from a sort of hegemony of dogmatism and orthodoxy. During the so-called dark ages, when warfare was an everyday phenomenon, and later too, right through to the Thirty Years War and beyond, one thing that could never be disputed amongst all that disputation was that the Bible was the word of God. Nowadays, few people believe that, and that’s a positive development in the evolution of culture. It frees us to look at morality from a broader, richer, extra-Biblical perspective..

Canto: Yes we no longer have to even pretend that our morality comes from such sources.

Jacinta: Yes and I’m thinking of other parts of the world that are locked in to this submissive way of thinking. A teaching colleague, an otherwise very liberal Moslem, told me the other day that he didn’t believe in gay marriage, because the Qu-ran laid down the law on homosexuals, and the Qu-ran, because written by God, is perfect. Of course I had to call BS on that, which made me quite sad, because I get on very well with him, on a professional and personal basis. It just highlights to me the crushing nature of culture, how it blinds even the best people to the nature of reality.

Canto: Not being capable of questioning, not even being aware of that incapability, that seems to me the most horrible blight, and yet as you say, it wasn’t so long ago that our forebears weren’t capable of questioning the legitimacy of Christianity’s ‘sacred texts’, in spite of interpreting those remarkably fluid texts in myriad ways.

Jacinta: And yet out of that bound-in world, modern science had its birth. Some modern atheists might claim the likes of Galileo and Francis Bacon as one of their own, but none of our scientific pioneers were atheists in the modern sense. Yet the principles they laid down led inevitably to the questioning of sacred texts and the gods described in them.

Canto: Of course, and the phenomenal success of the tightened epistemology that has produced the scientific and technological revolution we’re enjoying now, with exoplanets abounding, and the revelations of Homo floresiensis, Homo naledi and the Denisovan hominin, and our unique microbiome, and recent work on the interoreceptive tract leading to to the anterior insular cortex, and so on and on and on, and the constant shaking up of old certainties and opening up of new pathways, all happening at a giddying accelerating rate, all of this leaves the ‘certainty of faith’ looking embarrassingly silly and feeble.

Jacinta: And you know why ‘I fucking love science’, to steal someone else’s great line? It’s not because of science itself, that’s only a means. It’s what it reveals about our world that’s amazing. It’s the world of stuff – animate and inanimate – that’s amazing. The fact that this solid table we’re sitting at is made of mostly empty space – a solidity consisting entirely of electrochemical bonds, if that’s the right term, between particles we can’t see but whose existence has been proven a zillion times over, and the fact that as we sit here on a still, springtime day, with a slight breeze tickling our faces, we’re completely oblivious of the fact that we hurtling around on the surface of this earth, making a full circle every 24 hours, at a speed of nearly 1700 kms per hour. And at the same time we’re revolving around the sun at a far greater speed, 100,000 kms per hour. And not only that, we’re in a solar system that’s spinning around in the outer regions of our galaxy at around 800,000 kilometres an hour. And not only that… well, we don’t feel an effing thing. It’s the counter-intuitive facts about the natural world that our current methods of investigation reveal – these are just mind-blowing. And if your mind doesn’t get blown by it, then you haven’t a mind worth blowing.

Canto: And we have two metres of DNA packed into each nucleus of the trillions of cells in our body. Who’d’ve thunkit?



Written by stewart henderson

November 23, 2015 at 11:33 pm

this one’s for the birds

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Canto: If anybody doesn’t appreciate the beauty and complexity and general magnificence of birds they should pee off and never darken this blog again.

Jacinta: Right. Now what brought that on, mate?

Canto: Oh just a general statement of position vis-à-vis other species. Charles Darwin, an old friend of mine, was pretty disdainful of human specialness in his correspondence, but he kept a low profile – on this and everything else – in public. I want to be a bit more overt about these things. And one of the things that really amazes me about birds, apart from their physical beauty, is how much goes on in those teeny noggins of theirs.

Jacinta: Yes, but what really brought this on? I haven’t heard you rhapsodising about birds before.

Canto: You haven’t been inside my vast noggin mate. Actually I’ve been taking photos – or trying to – of the bird life around here; magpies, magpie-larks, crows, rainbow lorikeets, honeyeaters, galahs, corellas, sulphur-crested cockies, as well as the pelicans, black swans, cormorants, moorhens, coots and mallard ducks by the river, not to mention the ubiquitous Australian white ibis and the masked lapwing.

Jacinta: Well I didn’t know you cared. Of course I agree with you on the beauty of these beasties. Better than any tattoo I’ve seen. So you’re becoming a twitcher?

Canto: I wouldn’t go that far, but I’ve been nurturing my fledgling interest with a book on the sensory world of birds, called, appropriately, Bird sense, by a British biologist and bird specialist, Tim Birkhead. It’s divided into sections on the senses of birds – a very diverse set of creatures, it needs to be said. So we have vision, hearing, smell, taste, touch, and that wonderful magnetic sense that so much has been made of recently.

Jacinta: So we can’t generalise about birds, but I know at least some of them have great eyesight, as in ‘eyes like an eagle’.

Canto: Well, as it happens, our own Aussie wedge-tailed eagle has the most acute sense of vision of any creature so far recorded.

Jacinta: Well actually it isn’t ours, it just happens to inhabit the same land-form as us.

Canto: How pedantic, but how true. But Birkhead points out that there are horses for courses. Different birds have vision adapted for particular lifestyles. The wedge-tail’s eyes are perfectly adapted to the clear blue skies and bright light of our hinterland, but think of owl eyes. Notice how they both face forward? They’re mostly nocturnal and so they need good night vision. They’ve done light-detection experiments with tawny owls, which show that on the whole they could detect lower light levels than humans. They also have much larger eyes, compared with other birds. In fact their eyes are much the same size as ours, but with larger pupils, letting in more light. They’ve worked out, I don’t know how, that the image on an owl’s retina is about twice as bright as on the average human’s.

Jacinta: So their light-sensitivity is excellent, but visual acuity – not half so good as the wedge-tailed eagle’s?

wedge-tailed eagle - world's acutest eyes

wedge-tailed eagle – world’s acutest eyes

Canto: Right – natural selection is about adaptation to particular survival strategies within particular environments, and visual acuity isn’t so useful in the dark, when there’s only so much light around, and that’s why barn owls, who have about 100 times the light-sensitivity of pigeons, also happen to have very good hearing – handy for hunting in the dark, as there’s only so much you can see on a moonless night, no matter how sensitive your eyes are. They also learn to become familiar with obstacles by keeping to the same territory throughout their lives.

face of a barn owl - 'one cannot help thinking of a sound-collecting device, quoth researcher Masakazu Konishi

face of a barn owl – ‘one cannot help thinking of a sound-collecting device’, quoth researcher Masakazu Konishi

Jacinta: So they don’t echo-locate, do they?

Canto: No, though researchers now know of a number of species, such as oilbirds, that do. Barn owls, though, have asymmetrical ear-holes, one being higher in the head than the other, which helps them to pinpoint sound. It was once thought that they had infra-red vision, because of their ability to catch mice in apparently total darkness, but subsequent experiments have shown that it’s all about their hearing, in combination with vision.

Jacinta: Well you were talking about those amazing little brains of birds in general, and I must say I’ve heard some tales about their smarts, including how crows use cars to crack nuts for them, which must be true because it was in a David Attenborough program.

Canto: Yes, and they know how to drop their nuts near pedestrian crossings and traffic lights, so they can retrieve their crushed nuts safely. The genus Corvus, including ravens, crows and rooks, has been a fun target for investigation, and there’s plenty of material about their impressive abilities online.

seeing is believing

seeing is believing

Jacinta: So what other tales do you have to tell, and can you shed any light on how all this cleverness comes in such small packages?

Canto: Well Birkhead has been studying guillemots for years. These are seabirds that congregate on cliff faces in the islands around Britain, and throughout northern Europe and Canada. They’re highly monogamous, and get very attached to each other, and thereby hangs another fascinating tale. They migrate south in the winter, and often get separated for lengthy periods, and it’s been noted that when they spot their partner returning, as a speck in the distance, they get highly excited and agitated, and the greeting ceremony when they get together is a joy to behold, apparently – though probably not as spectacular as that of gannets. Here’s the question, though – how the hell can they recognise their partner in the distance? Common guillemots breed in colonies, butt-to-butt, and certainly to us one guillemot looks pretty well identical to another. No creature could possibly have such acute vision, surely?

Jacinta: Is that a rhetorical question?

Canto: No no, but it has no answer, so far. It’s a mystery. It’s unlikely to be sight, or hearing, or smell, so what is it?

Jacinta: What about this magnetic sense? But that’s only about orientation for long flights, isn’t it?

Canto: Yes we might discuss that later, but though it’s obvious that birds are tuned into their own species much more than we are, the means by which they recognise individuals are unknown, though someone’s bound to devise an ingenious experiment that’ll further our knowledge.

Jacinta: Oh right, so something’s bound to turn up? Actually I wonder if the fact that people used to say that all Chinese look the same, which sounds absurd today, might one day be the case with birds – we’ll look back and think, how could we possibly have been so blind as to think all seagulls looked the same?

Canto: Hmmm, I think that would take a lot of evolving. Anyway, birds are not just monogamous (and anyway some species are way more monogamous than others, and they all like to have a bit on the side now and then) but they do, some of them, have distinctly sociable behaviours. Ever heard of allopreening?

Jacinta: No but I’ve heard the saying ‘birds of a feather flock together’ and that’s pretty sociable. Safety in numbers I suppose. But go on, enlighten me.

Canto: Well, allopreening just means mutual preening, and it usually occurs between mates – and I don’t mean in the Australian sense – but it’s also used for more general bonding within larger groups.

Jacinta: Like, checking each other out for fleas and such, like chimps?

Cant: Yeah, though this particular term is usually reserved for birds. Obviously it serves a hygienic purpose, but it also helps calm ruffled feathers when flocks of colonies live beak by jowl. And if you ever get close enough to see this, you’ll notice the preened bird goes all relaxed and has this eyes half-closed, blissed-out look on her face, but we can’t really say that coz it’s anthropomorphising, and who knows if they can experience real pleasure?

Jacinta: Yes, I very much doubt it – they can only experience fake pleasure, surely.

Canto: It’s only anecdotal evidence I suppose, but that ‘look’ of contentment when birds are snuggling together, the drooping air some adopt when they’ve lost a partner, as well as ‘bystander affiliation’, seen in members of the Corvus genus, all of these are highly suggestive of strong emotion.

Jacinta: Fuck it, let’s stop beating about the bush, of course they have emotions, it’s only human vested interest that says no, isn’t it? I mean it’s a lot easier to keep birds in tiny little cages for our convenience, and to burn their beaks off when they get stressed and aggressive with each other, than to admit they have feelings just a bit like our own, right? That might mean going to the awful effort of treating them with dignity.

Canto: Yyesss. Well on that note, we might make like the birds and flock off…

how the flock do they do that?

how the flock do they do that?

Written by stewart henderson

November 13, 2015 at 12:06 pm

exoplanets – an introduction of sorts

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Jacinta: So do you think we’ve hauled ourselves out of ignorance sufficiently to have a halfway stimulating discussion on exoplanets?

Canto: I think we should try, since it’s one of the most exciting and rapidly developing fields of inquiry at the moment.

Jacinta: And that’s saying something, what with microbiomes, homo naledi, nanobots and quantum biology…

Canto: Yes, enough to keep us chatting semi-ignorantly to the end of days. But let’s try to enlighten each other on exoplanets…

Jacinta: Extra solar planets, planets orbiting other stars, the first of which was discovered just over 20 years ago, and now, thanks largely to the Kepler Space Observatory, we’ve discovered thousands, and future missions, using TESS and the James Webb telescope, will uncover megatonnes more.

Canto: Yes, and you know, about the Kepler scope, l was blown away – this might be veering off topic a bit, but I was blown away in researching this by the fact that Kepler orbits the sun. I mean, I knew it was a space telescope, but I just assumed it was in orbit around earth, probably at a great distance to avoid interference from our atmosphere, but that we can position satellites in orbit around the sun, that really sort of stunned me, more I think than the exoplanet discoveries. Am I being naive?

Jacinta: No, not at all. Well, yes and no. Everything is stunning if you haven’t followed the incremental steps along the knowledge pathway. I mean, if you think, hey the sun’s a way away, and it’s really big and dangerous, best not go there, or something like that, you might be shocked, but think about it, we’ve been sending satellites around the earth for a long time now, and we know how to do it because we know about earth’s gravitational field and can calculate precisely how to harness it for satellite navigation. We’ve currently got a couple of thousand human-made satellites orbiting the earth and trying more or less successfully to avoid colliding with each other. So the sun also has a gravitational field and we’ve known the mathematics of gravitational fields since Newton. It’s the same formula for a star, a planet or whatever, all you need to know is its mass and its radius. And look at all the natural objects orbiting the sun without a problem. Can’t be that hard.

Canto: Okay… so how do we know the mass of the sun? Okay, forget it, let’s get back to exoplanets. What’s the big fuss here? Why are we so dead keen on exploring exoplanets?

Jacinta: Well the most obvious reason for the fuss is SETI, the search for extra-terrestrial intelligence, but to me it’s just satisfying a general curiosity, or you might say a many-faceted curiosity. And it’s all about us mostly. For example, is the solar system that we inhabit typical? We’ve mostly thought it was but we didn’t have anything to compare it with, but now we’re discovering all sorts of weird and wonderful planetary systems, and star systems, with gas giants like Jupiter orbiting incredibly close to their stars – it’s completely overturned our understanding of how planets exist and are formed, and that’s fantastically exciting.

Canto: So you say we discovered the first exoplanet about 20 years ago, and now we know about thousands – that’s a pretty huge expansion of our knowledge, so how come things have changed so fast? You’ve mentioned new technologies, new space probes, why have they suddenly become so successful?

Jacinta: Well I suppose it’s been a convergence of developments, but let’s go back to that first discovery, back in 1992. Two planets, the first ever discovered, were found orbiting a pulsar – a rapidly rotating neutron star. First discovery, first surprise. Pulsars with planets orbiting them, who would’ve thought? Pulsars are the remnants of supernovae – how could planets have survived that? But that first discovery was largely a consequence of our ability to measure, and the fact that pulsars pulse with extreme regularity. Any anomaly in the pulsing would be cause for further investigation, and that’s how the planets were found, and later independently confirmed. Now this was big news, in a field that was already becoming alert to the possibility of exoplanets, so you could say it opened the floodgates.

Canto: Really? But they didn’t discover any more for two or three years.

Jacinta: Well, okay it opened the gates but it didn’t start the flood, that really happened with the second discovery, the first discovery of a planet orbiting a main-sequence star like ours.

Canto: Main sequence? Please explain?

Jacinta: Well these are stars in a stable state, a state of balance or equilibrium, fusioning hydrogen – basically stars not too different from our own, within much the same range in terms of mass and luminosity. So 51 pegasus b was the first planet to be discovered by the radial velocity method, and radial velocity means the speed at which a star is moving towards or away from us. We can measure this, and whether the star is accelerating or decelerating in its movement, by means of the Doppler effect – waves bunch up when the object emitting them is moving towards us, they spread out when the object is receding from us, and the degree of the bunching or the spreading is a measure of their speed and whether it’s accelerating or decelerating. Now we can measure this with extreme accuracy using spectrometers, and that includes any perturbations in the star’s movement caused by orbiting bodies. That’s how 51 pegasus b was discovered.

Canto: So… how long have we had these spectrometers? Were they first developed in the nineties, or to the level of accuracy that they could detect these perturbations?

Jacinta: Well I don’t have a precise answer to that apart from the general observation that spectroscopes are getting better, and more carefully targeted for specific purposes. The French ELODIE spectrograph, for example, which was used to find 51 pegasus b, was first deployed in 1993 specifically for exoplanet searching, and since then it’s been replaced by another improved instrument, but of the same type. So it’s a kind of non-vicious circle, research leads to new technology which leads to new research and so on.


Canto: So – we’ve gotten very good at measuring perturbations in a star’s regular movements…

Jacinta: Regular perturbations.

Canto: And we know somehow that these are caused by planets orbiting around them? How do we know this?

Jacinta: Well we will know from the size of the perturbation and its regularity that it’s an orbiting body, and we know it’s not a star because it’s not emitting any light (though it may be a low-mass star whose light isn’t easily separated from its parent star). We also know – we knew from the results that it was a massive planet orbiting very close to its star – a hot Jupiter as they  call it. And that was another surprise, but we’ve developed different techniques for discovering these things and we often use them to back each other up, to confirm or disconfirm previous findings. The ELODIE observation of 51 pegasus b was confirmed within a week of its announcement by another instrument, the Hamilton spectrograph in California. So there’s a lot of confirmation going on to weed out false positives.

Canto: So radial velocity is one technique, and obviously a very successful one as it got everyone excited about exoplanets, but what others are there, and which are the most successful and promising?

Jacinta: Well the radial velocity method was initially the most successful as you say, and hundreds of exoplanets have been discovered that way, but this method actually led to a kind of bias in the findings, because it was only able to detect perturbations above a certain level, so it was best for finding large planets close to their stars. But of course that was good too because we had never imagined that large gassy planets could exist so close to their stars. It’s opened up the whole field of planet formation. Then again, if the main aim is to find earth-like planets, this method is less effective than other methods. So let’s move on to the Kepler project. Kepler was launched in 2009, and since then you could say it has blitzed the field in terms of exoplanet detection. It uses transit photometry, which means that it measures the dimming of the light from a star when an orbiting planet passes between it and the Kepler detector.

Canto: So I get the idea of transit, as in the transit of venus, which we can see pretty clearly, but it’s amazing that we can detect transiting planets attached to stars so many light years away.

Jacinta: Well this is how we’ve expanded our world, from the infinitesimally small to the unfathomably large, from multiple billions of years to femtoseconds and beyond, through continuously refining technology, but let’s get back to Kepler. It orbits around the sun, and has collected data from around 145,000 main sequence stars in a fixed field of view – stars that are generally around the same distance from that dirty big black hole at the centre of our galaxy as our sun is.

Canto: Is that significant – that we’re focusing on stars in that range?

Jacinta: Apparently so, at least according to the Rare Earth Hypothesis, which puts all sorts of unimaginative limits on the likelihood of earth-like planets, IMHO, but no matter, it’s still a vast selection of stars, and we’ve reaped a grand harvest of planets from them – some 3000-odd, with over 1000 confirmed.

Canto: So… promising earth-like planets?

Jacinta: Yes, but I must point out that earth-like planets are difficult to detect. You see, Kepler was a kind of experiment, and we’ve learned from it, so that our next project will be much improved. For various reasons due to the photometric precision of the instrument, and inaccurate estimates of the variability of the stars in the field of view, we found that we needed to observe more transits to be sure we’d detected something. In other words we needed a longer mission than we’d planned for. And of course, Kepler has suffered serious technical problems, especially the failure of two reaction wheels, which have affected our ability to repoint the instrument. Having said that, we’ve been more than happy with its success.

Canto: Okay I just want to talk about these exoplanets. Can you summarise the most interesting discoveries?

Jacinta: Well, Kepler has certainly corrected the view we might’ve gotten from the earlier radial velocity method that large Jupiter-like planets are more common than smaller ones. We’ve had a number of reports from the Kepler group over the years, and over time they’ve adjusted downwards the average mass of the planets detected. And yes, they’ve discovered a number of planets in the ‘habzone’ as they call it. But that’s not all – only this year NASA confirmed the existence of five rocky planets, smaller than earth, orbiting a star that’s over 11 billion years old. I’m just trying to give you an idea of the explosion of findings, whether or not these planets contain life. And we’ve only just begun our hunt, and the refinement of instruments. It’s surely a great time to study astrophysics. It’s not just SETI, it’s about the incredible diversity of star systems, and working out where we fit into all this diversity.


Canto: Okay, I can see this an appropriately massive subject. Maybe we can revisit it from time to time?

Jacinta: Absolutely.

Some very useful sites:


Written by stewart henderson

October 30, 2015 at 10:05 pm

HIT, mitochondria and health

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and for a gentler form of exercise...

and for a gentler form of exercise…

Jacinta: Well now, I know you’re dying to explore the recently touted benefits of your favourite exercise, so let’s have it.

Canto: Yes, I’m very much a HIT man, that’s high intensity interval training, highly recommendable because it takes so little time and only requires an exercise bike. I was put onto it by one of Michael Mosley’s documentaries, though I’ve been a rather theoretical enthusiast in recent times, having trouble overcoming my laziness and my pain-avoidance tendencies, because though it’s short exercise it is a little painful.

Jacinta: So the recent Catalyst episode has brought your enthusiasm surging back?

Canto: Naturellement, especially as it brings with it some new research to focus on. Mitochondria – what do you know about them?

Jacinta: That they are organelles in our cells, believed to have originated as bacteria but to have united with our eukaryotic cells way back in time in a process known as endosymbiosis. They’re also responsible for producing ATP, the energy molecules… though I’ve no idea how, or what an energy molecule actually is.

Canto: That’s music to my ears.

Jacinta: The dulcet tones of ignorance?

Canto: In the country of the blind the one-eyed science pundit is king, and I’d rather be a king than a commoner, so hear ye, my subject.

Jacinta: I may be blind but I’m all ears, Your Majesty.

Canto: Well, as the Catalyst program tells us, mitochondria are about a billion times smaller than a grain of sand, but the world at nanoscales has really opened up to us in recent decades. Mitochondria are good for us, and the more the merrier. And the evidence is that HIT exercise can not only increase the production of mitochondria but increase their function.

Jacinta: So how do we produce mitochondria?

Canto: Are you going to keep interrupting me with questions? Okay, the production of mitochondria relies on our oxygen intake. The story goes that we fill our lungs with oxygen and it enters the bloodstream for a specific purpose…

Jacinta: Hang on, we fill our lungs with air, not just oxygen, so how does the oxygen get separated, and how does the blood take up the oxygen? Aren’t you skipping a few steps here?

Canto: Yes, go and research it yourself and you can report on it next time. The destination of this inhaled oxygen is the mitochondria. There are billions of these mitochondria in our musculature, though the more fit and trained up you are, the more you’re likely to have. Mitochondria apparently comprise some 10% of our body mass, which I’m sure will come as a surprise. Now oxygen, as you know, acts as a corrosive through the process known as oxidation, which involves the loss of electrons…

Jacinta: Hang on…

Canto: Please shut up. So oxygen can have a negative effect on proteins, enzymes and even our DNA, but mitochondria uses this corrosive electron-stripping power to break down nutrients and to create energy in the form of adenosine triphosphate (ATP). Don’t ask! Of course this doesn’t just happen in humans but in all other mammals and complex creatures, and in plants. And that brings us to physical fitness, and the VO2 Max, which is, essentially, the measure of the fitness of our mitochondria. The term stands for volume (V), oxygen (O2), and of course maximum, though generally those concerned with aerobic fitness don’t make the association with mitochondria, they’re just looking at increasing their maximum oxygen consumption levels. Now it’s not an easy thing for impoverished nonentities like us to find out what our VO2 Max is, but it’s probably pretty pathetic. It’s something that endurance athletes tend to obsess about as they try to improve their performance – I believe rowers in particular have some of the highest levels. I notice there’s at least one VO2 Max app on the market – going very cheap too – but I’d be very sceptical about its reliability. In the testing facility shown on Catalyst they measure it via a version of HIT. They get the subject to ride an exercise bike, building up speed till she’s going as fast as she can, and she can go no faster and starts slowing down. That peak represents her VO2 Max. She will be tested 16 weeks later, after a mere 6 minutes of HIT a week, and you can bet your rented house that her VO2 Max will have substantially improved.

Jacinta: So for us low-lifes – excuse my interruption – who can’t easily or cheaply measure improvements in our VO2 Max or, say, our fat to muscle ratio, we just have to feel the difference in aerobic fitness, mitochondrial health and the like…

Canto: Yeah, and your weight will go down too, if you’re carrying a bit extra, as we both are. And the exertion will make you feel better and healthier, I guarantee it. We all know that the placebo effect is real after all. But seriously, I’m sure if we keep to a regime of HIT – say 3 bursts of 20-second full-pelt pedalling interspersed with a minute or so of more relaxed pedalling, or even if we start with 10-second bursts and then 15-second bursts, maybe eventually getting up to 30-second bursts, we’ll feel it getting easier, and it won’t be purely subjective even if we have no way of objectively measuring it.

Jacinta: But shouldn’t we consult a doctor beforehand? I already feel a heart-attack coming on.

Canto: I know you’re joking, but certainly anyone who has any kind of heart condition, or are diabetic or pre-diabetic or have any other serious chronic condition should discuss it with their GP, but really, apart from your couch potato tendencies, there’s nothing wrong with you.

Jacinta: You’re right, and I’m looking forward to the challenge, even though I’m already a to-die-for, effortlessly slim, perpetually twenty-two year old intellectual beauty..

Canto: And I’m the ultimate metrosexual hipster of indeterminate age and shoe size, discreetly tattooed and tucked…

Jacinta: Ah, yuck, you stupid twat, tattoos are the most repugnant fashion development of all time. At least you’re not a spornosexual, yuk, stay away from the gym or I’ll never speak to you again .

Canto: Promise? Anyway, around 35 is the average VO2 Max, but that’s a bit meaningless for us low-lifes as you say. Top athletes have levels in the 60s and 70s, with the highest ever recorded being around 96 or 97 for humans, but some mammals – like racehorses and Siberian sled dogs – can reach much higher levels. But there’s also going to be a big improvement in your fat-to-muscle ratio with regular bouts of HIT. In the Catalyst episode, the reporter took a DEXA body composition scan to measure this ratio. It also measures bone density. DEXA stands for Dual Energy X-ray Absorptiometry, that means you’re subjected to 10 minutes of very low-dose x-radiation at two different energy levels. It measures the relative densities of the different tissues. You can get this scan done in Adelaide, for a baseline measure, but it’ll probably cost an arm and a leg.

Jacinta: One way to lose weight. Cheaper to just take it for granted that you’re getting more muscular with every HIT.

Canto: Spoken like a true scientist. But generally, inactivity itself is a health problem, and anything that raises your metabolism, as HIT most definitely does, will be good for you, if it doesn’t kill you. And of course one of the most exciting findings in recent times is that your VO2 Max can be raised, with all the associated health benefits, without spending crazy amounts of time and money at the gym.

Jacinta: So how did they make this discovery?

Canto: Well I suppose they were doing a lot of experimenting and testing around the health benefits of exercise, but one test, a Wingate test, involved 30 seconds of all-out pedalling on an exercise bike, repeated a few times between periods of rest, to make up to two or three minutes of full-on exercise per session.

Jacinta: And this was for already-athletic types, right?

Canto: Yes – not advisable for middle-aged or post-middle-aged couch potatoes to start on that regimen. I’m currently doing three fifteen-second bursts, building up to 20-second bursts, then up to 30 seconds and no more. So researchers found that endurance levels can be dramatically improved after just six minutes or so of this kind of exercise. A doubling of endurance capacity, no less. Compare this to the current recommendations of 150 minutes a week. Who ever does that, apart from gym junkies?

Jacinta: So, it’s like this incredible short-cut to health.

Canto: Well of course it isn’t the solution to all ills, but among other things such a quick turn-around is a great motivator towards a healthier lifestyle all round. And it doesn’t have to be an exercise bike – you can adapt it, for example you can get yourself outside and do interspersed 30-second sprints, but I hate running and I’ve got a gammy knee so I’ll stay on the bike.

Jacinta: So, have they looked more into the actual science of this? What’s happening here?

Canto: Well again it seems to be about sucking in oxygen and providing a drug hit to the mitochondria. They did this rather nasty experiment with mice, genetically modifying them so that their mitochondrial DNA wasn’t functioning properly – their mitochondria were getting worn out. They looked pretty sorry-looking compared to the control mice, prematurely ageing as evidenced in their fur, their neural activity, heart function and sensory abilities. Their life-span was about half that of normal mice, and no drugs improved the situation.  Then they set them on a treadmill regularly, 3 times a week, at a brisk pace, for 45 minutes each session, which you might think would’ve killed them off all the more quickly, but the result was a spectacular improvement in mitochondria production and overall health and energy levels.

Jacinta: And this was in genetically modified mice?

Canto: Apparently so. The program didn’t go into detail about that, except to say that the bad mitochondria were apparently being selected against. Now of course we’re talking about mice here, and this was looking at endurance fitness rather than HIT, but it’s been shown that HIT does all the right things, and in some areas performs better than endurance training. Reductions in blood pressure, improvements in insulin sensitivity, in muscle to fat ratio, in VO2 max all in a matter of weeks, but the really interesting finding was that with HIT, improvement in mitochondrial function was significant – which wasn’t the case after endurance training.

Jacinta: How do they know that?

Canto: They took muscle samples and measured the ability of the muscles to produce oxygen – basically a measure of mitochondrial function. After just four weeks of HIT, mitochondrial function improved by up to 30%, while endurance training over the same period showed little or no change.

Jacinta: Wow. Doesn’t say much for endurance training.

Canto: Well endurance training does improve your VO2 max and it’s hardly bad for you. But the thing with these quick sprints is the difference at the muscle level. Sports medicine distinguishes between fast-twitch, slow-twitch and intermediate muscle fibres. HIT uses a wider range of muscles and muscle types than endurance work, and that seems to be the key. Improvement in mitochondrial function confers a heap of benefits, so this kind of exercise wards off neurological and other conditions, including muscle weakness and epidermal deterioration, the tell-tale signs of ageing. In fact all exercise does this. Ever heard of the stratum corneum?

Jacinta: Mmmm, corneum, cornea, isn’t that part of the eye?

Canto: Excellent guess but wrong in this case. The stratum corneum is the top layer of the epidermis, the skin. It starts to thicken as you age, and the layer underneath gets thinner as your mitochondrial function reduces. You can slow down that process quite significantly with regular exercise. They did skin biopsies of sedentary people over 65 before and after endurance training. After just 3 months the skin showed great improvement – a 20 to 30 ‘youthening effect’, according to one researcher. The dead outer layer thinned, and the dermis, full of collagen fibres, thickened. So, clearly, you’re never too old to start.

Jacinta: Or never too young. So okay I’ll start.

Canto: Great, but let me describe one more impressive study, being done on menopausal women using HIT. Menopause is about a major decline in estrogen, which has serious vascular, heart and metabolic effects, as well as insulin resistance. You tend to produce a lot of bad visceral fat which negatively affects the liver, due to the over-production of cytokines – but that’s another story. Anyway, the women were given a sprint regime, of just a short period of fast peddling interspersed with more relaxing peddling, amounting to eight minutes of fast but not hard exercise all up. The results of this research haven’t been published yet, but the women’s self-reporting is all very positive, which isn’t surprising. The research is also based on previous research with obese young men, and the exercise proved very effective. Visceral fat is generally much easier to reduce than subcutaneous fat.

Jacinta: Okay, so we’re going to do this?

Canto: Absolutely. And finally, here are some links.


The Catalyst episode,

High-Intensity Training and Changes in Muscle Fiber, []

Written by stewart henderson

October 16, 2015 at 8:34 am

Is Malcolm Turnbull a libertarian?

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Jacinta: Okay so here’s a topical topic. I was listening with baited breath – I can do that, I’m a multi-tasker – to Malcolm Turnbull’s post-election speech the other day, and along with the whole nation I heard him extoll three ‘roolly good things’, in his estimation. The holy trinity – freedom, the individual and the market. Did y’all hear that? And I thought, Jeez, the libertarians among us will be doing cartwheels right now. And I further thought ‘hang on a minute Malcolm, turn that bull around’.

Canto: I see, so you prefer slavery, group-think and state control?

Jacinta: Ah very good, but let’s prise ourselves out of the straightjacket of ideology and slip into something more comfortable, like reality. Of course freedom’s a good thing, but of course it has its limits. And of course individuals are great, but as any mathematician will tell you, all individuals are members of a set, that’s actually what makes them individuals, and the market..

Canto: That’s not a very good analogy, I don’t think – that one about individuals.

Jacinta: That wasn’t an analogy.

Canto: Well… maybe, but bringing maths into it isn’t very helpful.

Jacinta: Okay. Okay, let me focus on the individual thing, because that’s probably my biggest gripe – it all flows from a misconception of the individual, IMHO.

Canto: What flows?

Jacinta: The horrors of libertarianism. I’ve been bottling this up for years, now I’m going to let it all seethe out. And it just so happens that ‘All hail freedom, the individual and the mighty market’ is essentially the libertarian mantra. Of course I don’t take Malcolm’s mellifluencies too seriously, but libertarianism really shits me.

Canto: But really – politics? Can’t we talk about water on Mars? Or Homo naledi?

Jacinta: Well, there is world enough, and time…

Canto: Bullshit.

Jacinta: Ok I’ll try to be the soul of wit. Libertarians – and I know they come in all shapes, sizes and political colours – tend to believe in small government, minimal regulation and the invisible, wonderfully shaping and fixing hand of the market. I got my first dose of libertarianism years ago when I read – or tried to read – Anarchy, State and Utopiaby the American philosopher Robert Nozick. I could barely comprehend it, but I could see it was underpinned by a sacrosanct notion of rights, particularly the rights of the individual. It was also, I thought, an overly rational analysis of how individuals might aggregate. Or rather, that’s how I’ve come to think of it since. I had no idea what to think of it at the time.


Canto: So how do you think individuals aggregate?

Jacinta: No no what I think doesn’t matter, it’s more about what history and psychology and sociology tells us. And they tell us about families and extended families and kinship groups and trade affiliations, becoming ever more extended and convoluted as societies grow. And all this without any concept of rights.

Canto: Okay I think I see where you’re coming from. You think the individual shouldn’t be seen as the central human unit, or political unit, you’re wanting to emphasise social connections.

Jacinta: Of course! We didn’t get where we are now, the top predators of the biosphere for better or worse…

Canto: The fat controllers of the planet…

Jacinta: We didn’t get to this situation as individuals, we got here because we’re the most socially-oriented mammals around. Our language, our technology, our superior brainpower, these are all socially constructed. And our systems of government are just ways of organising and trying to get the best out of this dynamic, interactive, co-operative and competitive society.

Canto: So there are legitimately diverse views about the role of government. So what’s wrong with that? Libertarians just happen to lean towards the individualist, unregulated, small-government side.

Jacinta: Well, as I’ve said, I’m not so much interested in opinions as in what actually works to create the most effective society…

Canto: You’re trying to be scientific, but the question of what makes for an effective society will have different answers, not based on science. Some will say an effective society is one that looks after its minorities and its disadvantaged, others will say that diversity and dynamism is key, and this means inevitably that there will be winners and losers. How can there be an objective, scientific definition of an effective society?

Jacinta: Okay, I concede your point that there are a range of legitimate views on this, but I would be guided by what works, and that would reduce the range of legitimacy. Extreme libertarianism – of the ‘there is no society, only individuals’ kind – seems to me to be paradoxically an outcome of the success of certain societies in educating and empowering their members, so that they start to fantasise about themselves as ‘self-made’ and owing nothing to anyone. It’s delusional and would result in scrapping all history has taught us about the communities of language and shared knowledge and values which have shaped us. It’s an ahistorical ideology which has never been instantiated anywhere. Not to mention its arrogant (and ultimately self-defeating) selfishness. Of course the other extreme is also unworkable, that of communism with an equal share of communal goods, which would stifle innovation and diversity and would have to be imposed from above.

wtf? Most people don't give a tinker's toss about the state when they act. But they do think about the consequences for others

wtf? Most people don’t give a tinker’s toss about the state when they act. But they do think about the consequences for others

Canto: Which would be self-contradictory because in communism, there is no ‘above’, presumably absolute equality is just meant to happen naturally…

Jacinta: There’s no perfect or perfectly fair society, just some are fairer than others, and it’s an endless balancing act, it seems to me, between encouraging the freedom to develop ideas and ‘get ahead’, and protecting others from being exploited and done down. So to me it’s a matter of pragmatism and endless adjustment rather than gung-ho ideology. Individuals are pretty well infinitely complex so you would expect society to multiply that complexity to to a new level of infinity.

Canto: But I notice that many libertarians tend to avoid going on about ‘society’, they prefer to focus their ire on ‘the state’, as if it’s the enemy of society.

Jacinta: Oh yes, good point, the rhetoric goes that the state is this abstract, inhuman monster that steals our money, stifles our initiative and makes a mess of everything it touches. Insofar as it consists of people, it consists of really dumb or power-mad types who haven’t seen the light and just don’t realise that society functions better either without the state or with a minimalist one. They’ve never been able to point to any evidence to support their claims though. Essentially, the libertarian ‘state’ has been trialled in the real world even less than the communist state, its polar opposite, has been.

Canto: So how is it supposed to work?

Jacinta: Well, clearly there are libertarians of many different types and degrees who would argue endlessly about that. But many of them seem to think it would grow ‘organically’ through adherence to certain basic principles, one of which has to do with the primacy of private property, though I’m not sure how to articulate it. Another is that no law or imposition should be applied that interferes with an individual’s liberty, the idea being I think, that you’re free to do what you like as long as it doesn’t interfere with everybody else’s right to do what he or she likes, which when you think about it is a recipe for disaster, because who decides between competing claims – for example my right to enjoy the peace and quiet of my own residence versus my neighbour’s right to play shite music all night with the volume up to eleven?

Canto: Aww, is that neighbour still bothering you Jass?

Jacinta: Fuck off. Actually what really bothers me is the obsession with private property and ownership. Coming from a pretty impoverished background, I was always more fond of the ‘property is theft’ mantra. And that reminds me of a story from my youth. I was living in a share-house very close to the spacious grounds of Saint Peter’s College, the biggest and most exclusive private school in South Australia. It must’ve been school holiday time, and we decided to take our racquets and balls and have a hit around on one of their tennis courts. There was no fence or anything, we just walked in and started playing. There was no net either, so it wasn’t a particularly serious hit-out, but we were absorbed enough not to notice a fellow scurrying across the greensward to tick us off. The look of outrage on the face of this fellow was unforgettable, it was as if he’d caught us pissing on the altar…

Canto: Which is exactly what you were doing mate.

Jacinta: His get-up was unforgettable too, he had this bright orange cravat, and sort of pantaloons with braces as I remember…

Canto: You’ve forgotten the candy-striped jacket and the Old Boys’ cap…

Jacinta: No, it was too hot for that. Anyway, I remember his words, more or less. ‘What are you doing here? Don’t you know this is private property!!’

Canto: Ah yes, a defining moment in the Great Australian Class War. So you made mince-meat out of him with your graphite, carbon-fibre and kevlar weaponry?

Jacinta: Well, we were just teenagers. I remember we stood our ground for a while, more out of shock than anything. So he went on haranguing us about our outrageous behaviour and threatening to call the police, so we wandered off. But I was so infuriated when I realised what was happening. I wish I’d confronted the guy, and I ran though imaginary narratives in my head many times afterwards. It was a defining moment for me, actually, it crystallised for me my attitude to private property…

Canto: Which is?

Jacinta: Well, it’s never been very important to me – I mean, as part of his harangue, this guy said something like ‘how would you like it if someone came into your garden and started..’, and my honest answer would’ve been that it wouldn’t have bothered me, certainly nothing like the way it bothered him. And the comparison was odorous anyway, I didn’t own any spacious grounds, I wasn’t born into that world. The way this guy mentioned private property, as if it was his Lord and Master, to be protected and fought for with life and limb, it just sickened me.

Canto: You were outraged?

Jacinta: Yeah, I suppose our intellectual positions are just post-hoc rationalisations of some basic feelings.

Canto: Reason is but the slave of the passions and all that. Anyway, I’m keen to get on to some of those more interesting topics. So let’s get back to the original question – is Malcolm Turnbull a libertarian?

Jacinta: Well the correct answer is that he didn’t say enough, in that first Prime Ministerial speech, for us to make that inference. He believes strongly in freedom. So do I, of course. He believes in the individual. So do I, and I believe individual expression and effort should be nurtured. He believes in the market or markets. I most certainly do too, as sources of exchange, cross-fertilisation, community and growth. The devil or delight is in the detail. I mean, I’ve called his statement a libertarian mantra, which it is, but it’s also classical liberalism. In the end, though, we need to judge governments on their actions, not their words. We’ll have to wait and see.

Written by stewart henderson

October 4, 2015 at 10:06 am

how did life begin?: part 2 – RNA, panspermia, viroids and reviving the blob

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Jacinta: So you’re going to talk about RNA, I know that stands for ribonucleic acid, and DNA is deoxy-ribonucleic acid, so – RNA is DNA without the oxygen?

Canto: Uhhh, you mean DNA is RNA without the oxygen.

Jacinta: Whatever, they’re big complex molecules aren’t they, but RNA is simpler, and less stable I think.

Canto: Okay, I’ll take it from here. We haven’t really known for very long that DNA is the essential material for coding and replicating life, and it’s a very complex molecule made up of four chemical bases, adenine, guanine, thymine and cytosine, better known as A, G, T and C. They connect to form base pairs, A always pairing with T and C with G.

Jacinta: What the hell are chemical bases? Do you mean bases as opposed to acids?

Canto: Well, yes. These bases, also called nucleobases, accept hydrogen ions, which have a positive charge. It’s all about pair bonding. The nucleobases – A, G, C and T, as well as uracil, found in RNA – are nitrogen-containing compounds which are attached to sugars… but let’s not get bogged down too much. The point is that DNA and RNA are nucleic acids that code for life, and most of the researchers chasing down the origin of life believe that RNA is a precursor of DNA in the process of replication.

Jacinta: And presumably there are precursors to RNA and so on.

Canto: Well presumably, but let’s just look at RNA, because we have a fair amount of evidence that this molecule preceded DNA as a ‘life-engine’, so to speak, and really no solid evidence, that I know of, of anything before RNA.

Jacinta: Okay so what is this evidence, and why did DNA take over?

Canto: Right, now the subject we’re entering into here is abiogenesis, the process by which life emerged from the inanimate. RNA is probably well down the chain from this emergence, but better to start with it than to dive into speculation. Now as you probably know, RNA has a single helical structure, and today it’s heavily involved in the process whereby DNA ‘creates’ proteins. In fact, all current life forms involve the action and interaction of three types of macromolecule, DNA, RNA and proteins…

Jacinta: But of course these complex molecules didn’t spring from nowhere.

Canto: Well we don’t know how they were built up, and many pundits think they may have been seeded here from elsewhere during the late heavy bombardment, which came to an end about 3.8 billion years ago, around the time that those Greenland rocks, with their heavy load of organic carbon, have been dated to. It seems plausible considering how quickly life seems to have taken off here.

Jacinta: Okay so tell us about RNA, how does it relate to the other two macromolecules?

Canto: Well, RNA is able to store genetic information, like DNA, and in fact it’s the genetic material for some of our scariest viruses, such as ebola, SARS, hep C, polio – not to mention influenza.

Jacinta: Wow, I didn’t know that. But one thing I do know about viruses is that they can’t exist independently of a host, so is RNA the basis of any truly independent life forms?

Canto: Not currently, on our planet, as far as we know, but the evidence is fairly strong that RNA has been central to life here from the very beginning, as it is still key to the most basic components of cells such as ribosomes, ATP and other co-enzymes. This suggests that RNA was once even more central, but in some areas it’s been subordinated to, and harnessed to, the more complex and recent DNA molecule. But, yes, since we can’t look at RNA coding for independent life-forms, we need to wind the clock back still further to look at precursors and other constituents of life, such as amino acids and peptides.

Jacinta: Which are chemical molecules, not biological ones. It seems to me we’re still a long way from working out the leap from chemistry to biology.

a peptide or amide bond - a covalent bond between two amino acid molecules

a peptide or amide bond – a covalent bond between two amino acid molecules

Canto: Yes, yes but we’re bridging various gaps. Peptides are created from amino acids, as you know. They are chains of amino acids linked by peptide bonds, and proteins are only distinguished from peptides in that they’re bigger versions of them, and bonded in a particular biologically useful way. You’ll notice when you read about this stuff that the terms ‘chemistry’ and ‘biology’ are used rather arbitrarily – a chemical compound can be referred to as a biological compound and vice versa. But various experiments have cast light on how increasingly ‘biological’ constituents are formed from simpler elements. For example, you may know that meteorites and comets, which bombarded the early earth in great numbers, contained plenty of amino acids – we’ve counted more than 70 different amino acids derived from meteorites, such as the Murchison meteorite that landed in Victoria in 1969. Another probable source of these amino acids, and even more complex and ‘biological’ molecules is comets, which also contain a lot of water in frozen form, but this has raised the question of how these molecules could have survived the impact of these colossal objects, which released enormous energy, some of them partially vaporising the earth’s crust. But an ingenious experiment, described in this video, and elsewhere, was able to simulate a comet’s impact, creating pressures many times greater than that experienced in our deepest oceans, to see what would happen to the amino acids. It was expected that they would barely survive the impact, but surprisingly they not only survived but forged bonds that created complex peptides.

a fragment of Murchison meteorite - of which there are many. This carbonaceous chondrite is still being analysed for organic compounds. Up to 70 amino acids identified so far

a fragment of Murchison meteorite – of which there are many. This carbonaceous chondrite is still being analysed for organic compounds. Up to 70 amino acids identified so far

Jacinta: Mmmm, that is interesting. So, the gap between peptides, or proteins, and RNA, what do we know about that?

Canto: Well, now you’re getting into highly speculative territory, but it’s certainly worth speculating about. Firstly, though, in trying to solve this origin of life problem, we have to note that the earth’s atmosphere was incredibly different from what it is now. In fact it was probably quite different from the way Haldane and Oparin and later Miller and Urey envisaged it. It was predominantly carbon dioxide, with hydrogen sulphide, methane and other unpleasant gases – unpleasant to us, that is. That, together with the continual bombardment from outer space has led some scientists to suggest that the place to find the earliest life forms isn’t the open surface but in hidden nooks and crannies or deep underground, in more protected environments.

Jacinta: Yeah the discoveries of so-called extremophiles has made that idea fashionable, no doubt, but presumably these extremophiles are all DNA-based, so I don’t see how investigating them will answer my question.

Canto: Okay, so it’s back to RNA. The thing is, I don’t want to go into the properties of RNA here, it’s just too complicated.

Jacinta: I believe it was Richard Feynman who said something like ‘to fully understand a thing you have to build it’. So there’s still this leap from polypeptides or proteins, which don’t code for anything, they’re just built by ribosomes – RNA structures – from DNA instructions, to sophisticated coded replicators. We have no idea how DNA or RNA came into being, and nobody has successfully created life apart from Doktor Frankenstein. So it’s all a bit disappointing.

Canto: You must surely be joking, or just playing devil’s advocate. You know very well that this is an incredibly difficult nut to crack, and we’ve made huge progress, new discoveries are being made all the time in this field.

Jacinta: Okay, impress me.

Canto: Well, only this year NASA scientists have reported that the nucleobases uracil, thymine and cytosine, essential ingredients of DNA and RNA, have been created in the laboratory, from ingredients found only in outer space – for example pyramidine, which they’ve hypothesised was first created in giant red stars – and they’ve found pyrimidine in meteors. So, another step towards creating life, and further evidence that life here may have been seeded from elsewhere. And if that doesn’t impress you, what about viroids?

Jacinta: Uhhh… what are they, viral androids? Which reminds me, what about the artificial intelligence route to creating life? Intelligent life, what’s more exciting.

Canto: Another time. Viroids are described as ‘sub viral pathogens’. We were talking about viruses before, as a kind of halfway house between the living and the lifeless, but really they’re much more on the side of the living. The smallest known pathogenic virus is over 2000 nucleobases long, and the biggest – well, a megavirus was famously identified just last year and revived after being frozen in Siberian permafrost for something like 35,000 years…

Jacinta: An ancient megavirus has been revived…? WTF? Who thought that was a great idea? Wait a minute, the Siberian permafrost, wasn’t that where Steve MacQueen and his mates dropped The Blob? Megadeath, not just a shite band! We’re doomed!

Canto: Well, strictly speaking it’s a virion, a virus without a host, which means it’s in a kind of dormant phase, like a seed. But I don’t want to talk about megaviruses, fascinating though they are – and very new discoveries. I want to talk about viroids, which are plant pathogens. They consist of short strands of RNA, only a few hundred nucleases long, without the protein coat that characterises viruses, and their existence tends to support the ‘RNA world hypothesis’. It was the discoverer and namer of viroids, Theodor Diener, who pointed out that they were vitally important macromolecules for explaining essential steps in the evolution of life from inanimate matter. That was back in 1989, but his remarks were ignored, and only rediscovered in 2014. So viroids are now a big focus in abiogenesis. They’ve even been called living relics of the pre-cellular RNA world.


Jacinta: Okay, I’m more or less impressed. We’ll have to do more on abiogenesis in the future, it’s an intriguing topic, with more breakthroughs in the offing it seems. ..



Written by stewart henderson

September 28, 2015 at 11:23 pm

how did life begin? part 1 – Greenland rocks, warm little ponds and unpromising gunk

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the basics of the Miller-Urey experiment: sparking interest

the basics of the Miller-Urey experiment: sparking interest


Jacinta: Well, we need an antidote to all that theological hocus-pocus, so how about a bit of fundamental science for dummies?

Canto: Sounds great, I just happened to read today that there are three great questions, or areas of exploration for fundamental science. The origin of the universe – and its composition, including weird black holes, dark matter and dark energy – that’s one. The others are the origin of life and the origin of consciousness. Take your pick.

Jacinta: I’ll choose life thanks.

Canto: Not a bad choice for a nihilist. So life has inhabited this planet for about three and a half billion years, or maybe more, while the planet was still cooling from its formation…

Jacinta: Isn’t it still doing that?

Canto: Well, yes of course. An interesting study conducted a few years ago found that around 54% of the heat welling up from within the earth is radiogenic, meaning that it results from radioactive decay of elements like radium and thorium. The rest is primordial heat from the time of the planet’s coalescing into a big ball of matter.

Jacinta: Gravity sucks.

Canto: Energetically so.

Jacinta: You say three and a half billion years or more – can you be a bit more specific? Are we able to home in on the where and the when of life’s origin on this planet?

Canto: Well, that would be the pot of gold, to locate the place and time of the first homeostatic replicators, to wind back history to actually witness that emergence, but I suspect there would be nothing to actually see, at least  not on the time-scale of a human life. I think it’d be like the emergence of human language, only slower. You’d have to compress time somehow to witness it.

Jacinta: Fair enough, or maybe not, it seems to me that the distinction between the animate and the inanimate would be pretty clear-cut, but anyway presumably scientists have a time-frame on this emergence. What allows them to date it back to a specific time?

Canto: Well, it’s an ongoing process of honing the techniques and discovering more bits of evidence, a bit like what has happened with defining the age of our universe. For example, you’ve heard of stromatolites?

Jacinta: Yes, those funny black piles that stick out of the water and sand, somewhere in Western Australia? They’re made from really old fossilised cyanobacteria, right?

Canto: Well, that’s a start, they’re rather more complicated than that and we’re still learning about them and still discovering new deposits, all around the world, both on the shoreline and inland. But the Shark Bay stromatolites  in WA were the first to be identified, and that was only in 1956. More recently though, there’s been an entirely different discovery in Greenland that’s raised a lot of excitement and controversy…

Jacinta: But hang on, these stromatolites, they say they’re really old, like more than 3 billion years, but how do they know that? As Bill Bryson would say.

Canto: Well, good question Jass, in fact it’s highly relevant to this Greenland discovery so let me talk about radiometric dating, using this example. Greenland has been attracting attention since the sixties as a potential mineral and mining resource, so the Danish Geological Survey was having a look-see around the region of Nuuk, the capital, in the south-west of the island. The principal geologist found ten successive layers of rock in the area, using standard stratigraphic techniques that you can find online, though they’re not always easy to apply, as strata are rarely neatly horizontal, what with crustal movements, fault-lines and rockfalls and erosion and such. Anyway, it was his educated guess that the bottom of these layers was extremely old, so he sent a sample to Oxford, to an expert in radiometric dating there. This was in about 1970.

Isua rocks, Greenland. Oldest rocks discovered, showing plausible traces of 3.8 billion-year-old life

Isua rocks, Greenland. Oldest rocks discovered, showing plausible traces of 3.8 billion-year-old life

Jacinta: And doesn’t it have to do with radioactive isotopes and half-lives and such?

Canto: Absolutely. Take uranium 238, which if you’ve been watching the excellent recent ABC documentary you’ll know that it decays through a whole chain of, from memory, twelve nuclides before stabilising as an isotope of lead. That decay has a half-life of 4.5 billion years – longer than the life of this planet, or at least the life of its crust. So it’s a matter of measuring the ratio of isotopes, to see how much of the natural uranium has decayed. In this case, the gneiss, the piece of bottom-strata rock that was analysed, had the highest proportion of lead in it of any naturally occurring rock ever discovered.

Jacinta: So that means it’s likely the oldest rock? Aw, I thought Australia had the oldest. This is terrible news.

Canto: No time to be parochial when the meaning of life is at stake. May I continue? So this was an exciting discovery, but more was to come, and it’s continuing to come. The geological team were inspired to continue their explorations around the Godthaab Fjord in Greenland, and found what are called ‘mud volcanoes’, pillows of basaltic volcanic lava that had issued out into the seawater. These were again dated at about 3.7 billion years old, and this strongly suggested the existence of warm oceans at that time, with hydrothermal vents such as those recently discovered to be teeming with life…

Jacinta: Right, so that might be pushing the age of life back a few hundred million years, if it can be verified, but it still doesn’t answer the how question..

Canto: Oh, nowhere near it, but I’ve just started mate. May I continue? Not surprisingly this region is now seen as a treasure trove for those hunting out the first life forms and trying to work out how life began. It was soon found that the Isua greenstone to the north of Nuuk contains carbon with a scientifically exciting isotopic ratio. The level of carbon 13 was unexpectedly low. This is generally an indication of the presence of organic material. Photosynthesising organisms prefer the lighter carbon 12 isotope, which they capture from atmospheric or oceanic carbon dioxide. But the finding’s controversial. Many are skeptical because this is the period known as the ‘late heavy bombardment’, with asteroids crashing and smashing and vaporising and possibly even sterilising… and they haven’t discovered any fossils.

Jacinta: So, photosynthesis, that’s what created the great oxygenation, which created an atmosphere for complex oxygen-dependent organisms, is that right?

Canto: Well, that was much later, and it’s a vastly complex story with quite a few gaps in it, so maybe we’ll save it for future conversations…

Jacinta: Okay, fine, but couldn’t one of those asteroids have brought life here, or proto-life, or the last essential ingredient…?

Canto: Yes, yes, maybe, but you’re distracting me. May I please continue? Where was I? Okay, so let’s look at the various theories put forward about the origin of life – and it will bring us back to Greenland. You’ve mentioned one, called panspermia. That’s the idea that life was seeded here from space, maybe during the heavy bombardment…

Jacinta: Which isn’t an adequate explanation at all, because where did that life come from? I want to know how any life-form anywhere can spring from the inanimate.

Canto: Yes all right, don’t we all smarty-pants? One of the most interesting early speculators on the subject was one Charles Darwin, who wrote – very famously – in a letter to his good mate Joseph Hooker in 1871, and I quote:

It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present.— But if (& oh what a big if) we could conceive in some warm little pond with all sorts of ammonia & phosphoric salts,—light, heat, electricity &c present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter wd be instantly devoured, or absorbed, which would not have been the case before living creatures were formed.

Now this was pretty damn good speculation for the time, and a couple of generations later two biologists, Aleksandr Oparin of Russia and John Haldane of England, independently developed a hypothesis that built on Darwin’s ideas.

Jacinta: Oh yes, they had this idea that if you added a bit of lightning to the early terrestrial atmosphere, which was full of  ammonia or something, you’d get a lot of organic chemistry happening.

Canto: Well I think the ‘or something’ part is true there – their idea was that there was a lot of hydrogen, methane and water vapour in the early atmosphere, and that, combined with local heat caused perhaps by lightning, or volcanic activity or some sort of concentrated solar radiation, the combo created a soup of organic compounds, out of which somehow over time emerged a primordial replicator.

Jacinta: So far, so vague.

Canto: Okay, I’m just getting started. The Oparin-Haldane hypothesis was highly speculative, of course. The point being made was that this key event was all that was needed for natural selection to kick in. This replication must have been advantageous, and of course over time there would’ve been mutations,with the mutants competing with the originals, and the winners would’ve been the most efficient and effective harvesters of resources, and there would’ve been expansion and more mutations and modifications and so forth. And out of that would come the first self-sustaining homeostatic environment, the proto-cell, within which more sophisticated machinery for processing resources could be developed…

Jacinta: Okay so you’ve more or less succeeded in dissolving the boundary between the animate and the inanimate before my eyes, but it’s still pretty vague on the details.

Canto: In 1953, Stanley Miller took up the challenge of his supervisor, famous Nobel Prize-winning biologist Harold Urey, who noted that nobody had tested the Oparin-Haldane hypothesis experimentally. Miller created a mini-atmosphere in a bottle, using methane (CH4), hydrogen, water vapour and ammonia (NH3), and after sparking it up for a while, he managed, to the amazement of all, to produce amino acids, the building blocks of proteins. Surely the first step in producing life itself.

Jacinta: Ah yes, that was a famous experiment, but didn’t it turn out to be something of a dead end?

Canto: Well, yes and no. It has been replicated with different mixtures and ratios of gases, and amino acids, sugars and even traces of nucleic acids have been generated, but nothing that could be described as a primordial replicator. But of course this work has got a lot of biologists thinking.

Jacinta: But this was 60 years ago. That’s a lot of thought without much action.

Canto: Well, what has since been realised about the experiments of Miller and others is that they create an enormous complexity of organic molecules in a rather uncontrolled way, a kind of chemical gunk similar to what might be created when you burn the dinner. The point being that when you burn the dinner – which is something necessarily organic like a dead chook, or pig, or tragically finless shark or whatnot…

Jacinta: Or a pumpkin, or Nan’s rhubarb pie..

Canto: Yeah, okay – you get this messy complexity, all mixed with oil and vinegary acids and shite – you get this break-down into gunk, and that’s easy. What’s hard is to go in the other direction, to build up from gunk into a fully fledged chicken, or a handsomely finned shark. And that’s what these experiments were trying to do, in their small way. They were creating this primordial-soup-gunk and hoping, with a bit of experimental help, to spark life into it, and basically getting nowhere. The problem is essentially to do with randomness and order. How do we get order out of random complexity? It’s easy to go the other way, for example with explosions and machine guns and such. We see that everywhere. But building the kind of replicating order that you find even in mycoplasma, the smallest genus of bacteria, from scratch, and by chance – well, that’s mind-bogglingly improbable.

mycoplasma, one of the simplest life forms - but try making one from scratch

mycoplasma, one of the simplest life forms – but try making one from scratch

Jacinta: So we have to think in terms of intermediate stages.

Canto: Yes, well, there are big problems with that, too… But let’s give it a rest for now. Next time, we’ll discuss the RNA world that most biologists are convinced preceded and helped create the DNA world we live in.


N B – This piece owes much to many, but mainly to Life on the edge: the coming of age of quantum biology, by Jim Al-Khalili & Johnjoe McFadden

Written by stewart henderson

September 8, 2015 at 10:03 pm


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