Archive for the ‘biology’ Category
bonobo society, sex and females
sexual dimorphism – a difference on average, but massive individual variation
Men are bigger than women, slightly. That’s how things evolved. It’s called sexual dimorphism. It happens with many species, the genders are different in size, shape, coloration, whatever. With humans there’s a size difference, and something of a shape difference, in breasts and hips, but really these aren’t significant. Compare, say, the deep-water triplewort seadevil, a type of anglerfish, in which the female is around 30 cms long, and the male a little over a centimetre. The difference in mass would be too embarrassing to relate.
Among our primate cousins the greatest sexual dimorphism, in size as well as other features, is found in the mandrills, with the male being two to three times the size of the females. In some gorillas there’s a substantial size difference too in favour of the males, and in fact in all of the primate species the male has a size advantage. But size isn’t everything, and the bigger doesn’t have to always dominate.
Female bonobos are smaller than the males, even more so than in humans, yet they enjoy a higher social status than in any other primate society, probably including humans, though it’s hard to compare, since humanity’s many societies vary considerably on the roles and status of women. So how have females attained this exalted status within one of the most highly socialised primate species?
Bonobos and chimpanzees are equally our closest living relatives. It isn’t clear when exactly they separated from each other, but some experts claim it may have been less than a million years ago. Enough time for them to become quite distinct physically, according to the ethologist Franz De Waal. Bonobos are more gracile with longer limbs and a smaller head, and they have a distinctive hairstyle, with a neat parting down the middle. They’re also more easily individuated by their facial features, being in this sense more like humans. And there are also major differences in their social behaviour. Male chimps are dominant in the troupe, often brutally so, whereas bonobo society is less clearly hierarchical, and considerably less violent overall. De Waal, one of the world’s foremost experts on both primates, became interested in bonobos primarily through studies on aggression. He noted that sometimes, after a violent clash, two chimps would come together to hug and kiss. Being interested in such apparent reconciliations and their implications, he decided to look at reconciling behaviours in other primates. What he discovered in bonobos (at San Diego Zoo, which in 1983 housed the world’s largest captive colony) was rather ‘shocking’; their social life was profoundly mediated by sex. Not that he was the first to discover this; other primatologists had written about it, noting also that bonobo sex was far more human-like than chimp sex, but their observations were obscurely worded and not well disseminated. There are other aspects of the physical nature of sexual relations in bonobos that favour females, such as female sexual receptivity, indicated by swelling and a reddening of the genital area, which pertains for a much longer period than in chimps. Female bonobos, like humans and unlike other primates, are sexually receptive more or less all the time.
This isn’t to say that bonobos are oversexed, whatever that may mean. Sexual relations are far from constant, they are casual, sporadic and quickly done with. Often they’re associated with finding food, and it seems likely that sexual relations are used to reconcile tensions related to food availability and other potential causes of conflict.
So how does this use of sex relate to the status of females in bonobo society. I’ll explore this further in the next post.
bonobo relations – more than just sex
Abiogenesis – LUCA, gradients, amino acids, chemical evolution, ATP and the RNA world
Jacinta: So now we’re thinking of the Earth 4 billion years BP, with an atmosphere we’re not quite sure of, and we want to explore the what and when of the first life forms. Haven’t we talked about this before?
Canto: Yeah we talked about the RNA world and viroids and abiogenesis, the gap between chemistry and biology, inter alia. This time we’re going to look more closely at the hunt for the earliest living things, and the environments they might’ve lived in.
Jacinta: And it started with one, it must have. LUA, or LUCA, the last universal common ancestor. Or the first, after a number of not-quite LUCAs, failed or only partially successful attempts. And finding LUCA would be much tougher than finding a viroid in a haystack, because you’re searching through an immensity of space and time.
Canto: But we’re much closer to finding it than in the past because we know so much more about what is common to all life forms.
Jacinta: Yes so are we looking definitely at the first DNA-based life form or are we probing the RNA world again?
Canto: I think we’ll set aside the world of viroids and viruses for now, because we want to look at the ancestor of all independently-existing life forms, and they’re all DNA-based. And we also know that LUCA used ATP. So now I’m going to quote from an essay by Michael Le Page in the volume of the New Scientist Collection called ‘Origin, Evolution, Extinction’:
How did LUCA make its ATP? Anyone designing life from scratch would probably make ATP using chemical reactions inside the cell. But that’s not how it is done. Instead energy from food or sunlight is used to power a protein ‘pump’ that shunts hydrogen ions – protons – out of the cell. This creates a difference in proton concentration, or a gradient, across the cell membrane. Protons then flow back into the cell through another protein embedded in the membrane, which uses the energy to produce ATP.
Jacinta: You understand that?
Canto: Sort of.
Jacinta: ‘Energy from food or sunlight is used..’ that’s a bit of a leap. What food? The food we eat is organic, made from living or formerly living stuff, but LUCA is the first living thing, its food must be purely chemical, not biological.
Canto: Of course, not a problem. I believe the microbes at hydrothermal vents live largely on hydrogen sulphide, and of course sunlight is energy for photosynthesising oganisms such as cyanobacteria.
Jacinta: Okay, so your simplest living organisms, or the simplest ones we know, get their energy by chemosynthesis, or photosynthesis. Its energy, or fuel, not food.
Canto: Semantics.
Jacinta: But there are other problems with this quote re abiogenesis. For example, it’s talking about pre-existent cells and cell membranes. So assuming that cells had to precede ATP.
Canto: No, he’s telling us how cells make ATP today. So we have to find, or synthesise, all the essential ingredients that make up the most basic life forms that we know – cell membranes, proteins, ATP and the like. And people are working towards this.
Jacinta: Yes and first of all they created these ‘building blocks of life’, as they always like to call them, amino acids, in the Miller-Urey experiments, since replicated many times over, but what exactly are nucleic acids? Are they the same things as nucleic acids?
Canto: Amino acids are about the simplest forms of organic compounds. It’s probably better to call them the building blocks of proteins. There are many different kinds, but generally each contain amine and carboxyl groups, that’s -NH2 and -COOH, together with a side chain, called an R group, which determines the type of amino acid. There’s a whole complicated lot of them and you could easily spend a whole lifetime fruitfully studying them. They’re important in cell structure and transport, all sorts of things. We’ve not only been able to create amino acids, but to combine them together into longer peptide chains. And we’ve also found large quantities of amino acids in meteorites such as the Murchison – as well as simple sugars and nitrogenous bases. In fact I think we’re gradually firming up the life-came from-space hypothesis.
Jacinta: But amino acids and proteins aren’t living entities, no matter how significant they are to living entities. We’ve never found living entities in space or beyond Earth. Your quote above suggests some of what we need. A boundary between outside and inside, a lipid or phospho-lipid boundary as I’ve heard it called, which must be semi-permeable to allow chemicals in on a very selective basis, as food or fuel.
Canto: I believe fatty acids formed the first membranes, not phospho-lipids. That’s important because we’ve found that fatty acids, which are made up of carbon, hydrogen and oxygen atoms joined together in a regular way, aren’t just built inside cells. There’s a very interesting video called What is Chemical Evolution?, produced by the Center for Chemical Evolution in the USA, that tells about this. Experimenters have heated up carbon monoxide and hydrogen along with many minerals common in the Earth’s crust and produced various carbon compounds including fatty acids. Obviously this could have and can still happen naturally on Earth, for example in the hot regions maybe below or certainly within the crust. It’s been found that large concentrations of fatty acids aggregate in warm water, creating a stable, ball-like configuration. This has to do with the attraction between the oxygen-carrying heads of fatty acids and the water molecules, and the repulsion of the carbon-carrying tails. The tails are forced together into a ball due to this repulsion, as the video shows.
fatty acids, with hydrophobic and hydrophilic ends, aggregating in solution
Jacinta: Yes it’s an intriguing video, and I’m almost feeling converted, especially as it goes further than aggregation due to these essentially electrical forces, but tries to find ways in which chemical structures evolve, so it tries to create a bridge between one type of evolution and another – the natural-selection type of evolution that operates upon reproducing organisms via mutation and selection, and the type of evolution that builds more complex and varied chemical structures from simpler compounds.
Canto: Yes but it’s not just the video that’s doing it, it’s the whole discipline or sub-branch of science called chemical evolution.
Jacinta: That’s right, it’s opening a window into that grey area between life and non-life and showing there’s a kind of space in our knowledge there that it would be exciting to try and fill, through observation and experimentation and testable hypotheses and the like. So the video, or the discipline, suggests that in chemical evolution, the highly complex process of reproduction through mitosis in eukaryotic cells or binary fission in prokaryotes is replaced by repetitive production, a simpler process that only takes place under certain limited conditions.
Canto: So under the right conditions the balls of fatty acids grow in number and themselves accumulate to form skins, and further forces – I think they’re hydrostatic forces – can cause the edges of these skins to fuse together to create ‘containers’, like vesicles inside cells.
Jacinta: So we’re talking about the creation of membranes, impermeable or semi-permeable, that can provide a safe haven for, whatever…
Canto: Yes, and at the end of the video, other self-assembling systems, such as proto-RNA, are intriguingly mentioned, so we might want to find out what’s known about that.
Jacinta: I think we’ll be doing a lot of reading and posting on this subject. I find it really fascinating. These limited conditions I mentioned – limited on today’s Earth surface, but not so much four billion years ago, include a reducing atmosphere lacking in free oxygen, and high temperatures, as well as a gradient – both a temperature gradient and a sort of molecular or chemical gradient, from more reducing to more oxidising you might say. These conditions exist today at hydrothermal vents, where archaebacteria are found, so researchers are naturally very interested in such environments, and in trying to replicate or simulate them.
Canto: And they’re interested in the boundary between chemical and biological evolution, and reproduction. There are so many interesting lines of inquiry, with RNA, with cell membranes….
Jacinta: Researchers are particularly interested in alkaline thermal vents, where alkaline fluids well up from beneath the sea floor at high temperatures. When this fluid hits the ocean water, minerals precipitate out and gradually create porous chimneys up to 60 metres high. They would’ve been rich in iron and sulphide, good for catalysing complex organic reactions, according to Le Page. The temperature gradients created would’ve favoured organic compounds and would’ve likely encouraged the building of complexity, so they may have been the sites in which the RNA world began, if it ever did.
a hydrothermal vent off the coast of New Zealand. Image from NOAA
Canto: So I think we should pursue this further. There are a lot of researchers homing in on this area, so I suspect further progress will be made soon.
Jacinta: Yes, we need to explore the exploitation of proton gradients, the development of proton pumps and the production of ATP, leaky membranes and a whole lot of other fun stuff.
Canto: I think we need to get our heads around ATP and its production too, because that looks pretty damn complex.
Jacinta: Next time maybe.
clever Charlie Darwin
A photo taken by me! King Charles seated in state in the Musuem of Natural History, London. It was a thrill to be granted an audience
I recently decided to reread Darwin’s Origin of Species, which was really reading it for the first time as my first reading was pretty cursory, and I could barely follow the wealth of particular knowledge he used for cumulative effect to adduce his theory. This time I’ve been doing a closer reading, and becoming increasingly impressed, and I’ve only read the first chapter, ‘Variation under Domestication’.
Darwin’s argument here of course is that domesticated horses, dogs, birds and plants have been artificially selected over long periods of time, and often unconsciously, to suit human needs and tastes. This might seem screamingly obvious today, and to a degree it was recognised in Darwin’s time, but because of an inability to take the long view, and also because of the then-prevalent paradigm of the fixity of species, breeders and nurserymen tended to under-estimate their own cumulative powers, and to claim, for example, that dogs and pigeons had always come in many varieties. Even Darwin was uncertain, and was willing to concede – writing of course before the advent of Mendelian genetics, never mind the revolution wrought by the identification and analysis of DNA as the molecule of inheritance – that in some cases the breeders might be right:
In the case of most of our anciently domesticated animals and plants, I do not think it is possible to come to any definite conclusion, whether they have descended from one or several species.
He was even prepared to concede that it was ‘highly probable that our domestic dogs have descended from several wild species’, while at the same time arguing that the breeding of dogs, in Egypt, other parts of Africa and Australia (where, in his Beagle travels, he observed dingoes, which he may have seen as semi-domesticated by the Aborigines) extended back far further in time than most people suspected. We now know that Darwin’s concession here was ‘premature’. The latest research strongly suggests that our domesticated dogs trace their ancestry to a group of European wolves dating from 19,000 to 32,000 years ago, and probably now extinct. That’s a time-frame Darwin would’ve baulked at, and it’s both funny and kind of tragic that this is something I’ve ‘discovered’ after 30 seconds of selective internet searching. There’s no doubt, though that Darwin’s bold but always informed speculations were heading in the right direction.
Particularly informed – and bold – were his speculations about pigeons. This is hardly surprising as he spent several years studying and breeding them himself. Interestingly, he started doing so because he’d become convinced that all the fancy pigeons then on show were most likely derived from one common species, the rock pigeon or rock dove (Columba livia), a view already held by some naturalists but few breeders. He devotes several pages in Chapter 1 to arguing his case, for example pointing out that the ‘several distinct species’ argued for by breeders can be crossed with complete success, that’s to say with no signs of sterility or more than usually defective offspring.
So, as with dogs, I decided to look up what the latest research was on the ancestry of English carriers, short-faced tumblers, runts, fantails, common tumblers, barbs, pouters, trumpeters and laughers, to name some of the pigeons Darwin mentions in the chapter, and was excited to find that a piece of research published as recently as 2013 has confirmed Darwin’s hypothesis. Cheaper and faster genome sequencing technologies have enabled researchers to sequence the genomes of many wild and domesticated birds, and they’ve found that all of the latter are clearly closer to C livia than to any other wild species. It only took just over 150 years for Darwin to be proven correct.
Close reading like this really does reap some fun rewards, and I’ll finish with two more examples. Darwin wrote of how in the world of breeding, quite a drastic change can be brought about in one breeding step, as in the case of the fuller’s teasel with its hooks. He goes on:
So it has probably been with the turnspit dog; and this is known to have been the case with the ancon sheep.
Not knowing wtf he was talking about, I irritatedly decided to look up these unknown creatures. The turnspit dog is a now-extinct breed, bred specifically from around the 16th century to provide the dogpower to turn meat on a spit, the only conceivable way of cooking large joints of meat in your average fancy household for a couple of centuries. The dog, or dogs, because the system worked better if you had two of them engaged in shift work, turned a wheel by running inside it, rat-like, until the meat was cooked. They were known to be long-bodied and short-legged, but details of how they were bred aren’t known, as they were apparently beneath scholarly consideration. They certainly weren’t seen as cuddly pets – if you treat creatures as slaves it heightens your contempt for then (cf Aristotle) – and they were even taken to church as foot-warmers. They’d disappeared entirely by the end of the 19th century.
It’s a dog’s life?
The ancon sheep was a short-legged type, apparently bred from a single individual in the USA in the late nineteenth century, its short legs having the singular advantage, to some, of curtailing its hopes of freedom by jumping the fence. The term ‘ancon’ has since been used by breeding researchers to describe strains of creatures arising from an individual with the same phenotype.
What is a trisomy?
Canto: So I happened to watch an excellent video from the Royal Institute recently, a talk by the beautifully named and beautifully voiced Irish geneticist, Aoife Mclysaght…
Jacinta: How do you pronounce that?
Canto: It’s pronounced Aoife Mclysaght…
Jacinta: Oh right.
Canto: So the theme was that everything in biology makes sense only in the light of evolution, and she was illustrating this through her area of interest and research, gene duplication. And along the way she talked about trisomies, particularly trisomy 21, usually referred to as Down Syndome.
Jacinta: A trisomy involves having an extra copy of a chromosome, in this case chromosome 21.
Canto: Very good, and the extra copy is a perfectly good copy, but having that extra copy causes major problems, obviously.
Jacinta: The term ‘trisomy’ refers of course to three – having three rather than two sets of a particular chromosome. Humans normally have two sets of 23 chromosomes. I have a relative who has a rare and unnamed form of trisomy, or at least a rare form of chromosomal disorder, which, when looking into it, I decided must be a trisomy. But since then I’ve discovered that Williams syndrome – which I learned about from another person I know with that condition – isn’t a trisomy, but the result of genes missing from chromosome 7. So now I’ve gone from thinking that trisomies accounted for all or most sorts of genetic intellectual disabilities to… I don’t know.
Canto: To a position of deeper ignorance. So people with trisomies have 47 chromosomes, with Down syndrome being the most common. Others include Edward syndrome (trisomy 18) and Patau syndrome (trisomy 13). Interestingly, though, there’s another rarer form of Down syndrome that’s due to translocation – that’s when a part of a chromosome – in this case chromosome 21 – migrates to another chromosome, usually chromosome 14, during cell division
Jacinta: That complicates matters… So do we know what causes these trisomies, and these translocations? They seem to be very specific, occurring for only particular chromosomes, or bits of them.
Canto: Well you’re right in that trisomies 21, 18 and 13 are relatively common – I mean rare but more common than a trisomy 9 or 15 or 19, just to pick out any numbers less than 23. We do know that trisomies become more common with older egg cells. As you know, your egg cells are as old as you are, and they become a little decrepit with age like yourself.
Jacinta: We’re both slouching to oblivion.
Canto: It’s also the case that most trisomies don’t survive to term, in fact they mostly miscarry so early that the mother doesn’t even know she’s been pregnant. So presumably those trisomies I just picked at random, if they occur at all, have more fatal consequences. It seems in any case that a trisomy occurs when cells divide but one chromosome somehow sticks to its homologue and is carried with it into the new cell. So maybe some chromosomes are more ‘sticky’ than others?
Jacinta: I think we need to do a deeper dive, as one pundit likes to say, into meiosis and aneuploidy.
Canto: Aneuploidy?
Jacinta: That’s just when you have an abnormal number of chromosomes per cell: it could be less or more. Actually trisomy 16 is the most common form, but fatal in its full-blown version. It can exist in mosaic form – when not all the cells have it.
Canto: So can you explain meiosis for us?
Jacinta: A long story but fascinating of course. It’s the basis of sexual reproduction for all eukaryotes. So before eukaryotic germ cells or gametes divide they need to replicate their chromosomes so that the resulting pair of cells has an equal share. This period of replication is known as the S phase.
Canto: Wait a minute, does this mean that in the S phase humans have 92 chromosomes per cell instead of 46?
Jacinta: Don’t bog me down with clever questions. Taking another step back, we have this whole process called the cell cycle, which we divide into phases. We can start anywhere, since it’s a cycle, if you know what I mean, but if you need a beginning it’s the prophase. Anyway, the S phase comes after the G1 phase and before the G2 phase. S, by the way, stands for synthesis, and G here stands for gap. Together these three phases make up the interphase, at the end of which we have the prophase of a new cell cycle, though actually meiosis isn’t a cycle the way mitosis (non-sexual reproduction or cell division) is. To be accurate, the next phase is called prophase 1, which is followed by metaphase 1, anaphase 1 and telophase 1 before we have prophase 2….
Canto: Stop cycling I’m getting dizzy.
Jacinta: Well yes believe me it’s complicated, and I haven’t begun yet. But you did ask for it.
Canto: Can you give the simplified version?
Jacinta: Not really.
Canto: Okay, we’ll leave that for another day. Focusing in on the part of meiosis when these trisomies and other anomalies occur, it seems that the problem isn’t so much stickiness as non-stickiness. Think of gametes. In mammals such as humans there are two types, egg and sperm cells. They’re differentiated by their sex chromosomes, chromosome 23…
Jacinta: And also by the fact that the egg cell is like the sun and the sperm cell is like the earth.
Canto: Well, sort of, in terms of volume. Now, after meiosis – which occurs in phases, meiosis 1 and meiosis 2, creating two daughter cells then four grand-daughter cells, so to speak – each of these grand-daughter gametes should be haploid. That’s to say, they should contain only one of each of the 23 chromosomes. But nothing’s perfect and sometimes there are errors, and we’re not clear about why, though the chances of error rise with the age of the female as mentioned before. Mostly the problem is that the chromosomes didn’t properly separate, a state called chromosome nondisjunction. Something to do with the spindle apparatus not functioning properly due to a lack of cohesion of the chromosome. This occurs rather more frequently in female meiosis, or oogenesis, than in male meiosis, or spermatogenesis, they’re not sure exactly why.
Jacinta: Well I must say that’s all very enlightening, and salutary, as it’s made me aware of how little I know about genetics in general. Now I know a teensy bit more. As to trisomies and other such chromosomal problems, what they know just makes me keen to know more about how we might detect them and possibly in the deep future rectify them at source. But the science is clearly a long way from that…
Canto: Well you never know. Genetics is a fast-moving field.
Jacinta: we must explore it more. It’s serious fun.
this one’s for the birds
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
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
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
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?
HIT, mitochondria and health
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, http://www.abc.net.au/catalyst/stories/4319131.htm
https://newsroom.unsw.edu.au/news/health/sprint-fight-fat
High-Intensity Training and Changes in Muscle Fiber, [www.springerlink.com/content/1137px7x66667132]
how did life begin?: part 2 – RNA, panspermia, viroids and reviving the blob
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
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
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. ..
how did life begin? part 1 – Greenland rocks, warm little ponds and unpromising gunk
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
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
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
something to send you to sleep
sleep apnoea mask – looks great, feels even worse?
I went to a Science in the Pub talk last night, not knowing what to expect. The three speakers were all researching sleep, and the focus was mainly on insomnia and sleep apnoea. How fortunate, for I’m having a problem with insomnia at the moment. I may well have a problem with apnoea too, but because I sleep alone I can’t monitor it. Sleep apnoea is about blocked airways that reduce the intake of oxygen, causing sleep disturbance. Here’s an extract from the Better Health Channel on the subject:
In most cases, the person suffering from sleep apnoea doesn’t even realise they are waking up. This pattern can repeat itself hundreds of times every night, causing fragmented sleep. This leaves the person feeling unrefreshed in the morning, with excessive daytime sleepiness, poor daytime concentration and work performance, and fatigue. It’s estimated that about five per cent of Australians suffer from this sleep disorder, with around one in four men over the age of 30 years affected.
So it’s much more common among older males, and it correlates with excessive weight and obesity. Some years ago, when I had a sleeping partner, she expressed a concern about what she thought might be my sleep apnoea, but since then I’ve lost a lot of weight, and my overall health – apart from my bronchiectasis – has improved, so I don’t intend to worry needlessly over that, but it was interesting to hear about the CPAP mask and other treatments being offered, including the possibility of surgery to the uvula and tongue. Also that the evidence is mounting about the long-term effects of sleep apnoea, upon the heart particularly, though not surprisingly with obesity, confounding factors are hard to control for. The problem I’m having at the moment, though, is ‘advanced circadian rhythm’ insomnia, which has only been happening over the past few weeks and which I’m hoping will sort itself out. Our roughly 24-hour circadian rhythms, our body clock, when running at its best, gives us at least eight hours sleep, optimally between 11pm and 7am, though there is enormous individual variation, and huge variation in tolerance of sleep deprivation, possibly due to genetic factors. Amongst the many varieties of body clock-related sleep disorder, two were focused on last night; delayed-phase and advanced-phase circadian rhythms. The terms are largely self-explanatory. In the delayed-phase type, you stay up late and find it hard to get up in the morning, a common teenage problem (or habit). In the advanced-phase type, which I’m now experiencing for the first time in my life, you find yourself falling asleep alarmingly early, and then waking up – and being alarmingly wide awake, at 4am or sometimes even earlier.
The Circadian Sleep Disorders Network is a great place to learn about the problems, and possible solutions for having a body clock that’s out of synch with the day-night cycle or with your work or other commitments. These problems can lead to all sorts of stresses, but what I took from last night’s session, though it was never explicitly stated, was that your attitude to wonky sleep patterns might be causing more stress than the patterns themselves. In my case, though it’s irritating, I tell myself I needn’t stress over it as I have to get up around 6am for work anyway, and as long as I’m awake and fully operational until 5pm, or 7pm for cooking and eating dinner, it’s no big problem. I’ve not noticed excessive daytime sleepiness or poor concentration (but maybe I’m not concentrating enough). Though I do hope it will right itself, just because being abnormal feels – abnormal. Then again, I’m abnormal in so many other ways that are far more stressful.
Advanced-phase sleep disorder is apparently much less common than delayed phase, though that might just be that it’s less often reported precisely because it doesn’t disrupt work routines. The main treatment is the use of bright light, though I’ve found myself falling asleep in the bright light of the lounge room, or in my bedroom with a bright reading lamp left on. But there’s more to it than just leaving the light on. Here’s a summary from the Sleep Health Foundation:
Bright light visual stimulation should occur in the evening before you go to bed. The light should be brighter than normal indoor lighting. You can obtain it from specialized light boxes, or portable devices that you can wear, e.g. eye glasses. A few examples can be found by a web search for “bright light therapy”. You may need an hour or two of bright light therapy before bed. Some will benefit from nightly use for a week. Others will need longer, sometimes several weeks, to get maximum benefit. It is best used late in the evening, perhaps turning the bright light device off half an hour before bed.
Something to think about if this keeps up. Another treatment is with melatonin, the ’sleep hormone’:
One option is to take a 2mg slow release melatonin tablet (Circadin™) as close to your new (later) bedtime as possible. A second option is to take a small dose of melatonin (0.5 mg), about half way through your sleep period. This could be at a time when you wake up on your own. To change your hours of sleep, you should gradually delay your bed time (e.g. 20 minutes later each night) until you get it to the time that you want. As you delay your bedtime, you will also be delaying the time of your bright light exposure and melatonin intake.
Obviously, neither of these treatments are simple or guaranteed to be effective. Cognitive behaviour therapy was suggested by the experts, if these approaches were unsuccessful, but I know next to nothing about that. For now I’m not too worried, I just hope the problem goes away without my noticing.
why is evolution true? (if it is): part one, the problem of fixity
some Galapagos finches
Much of my writing, especially about sciency stuff, is an attempt to own the knowledge. It’s perhaps never completely successful, especially for the non-specialist, the dilettante, who tries to own so much and to keep all those possessions together. You read about it, you cast it in your own words, you grasp it, you think you’ve grasped it completely, you move on to other things, and six months later you’re asked a curly question and in trying to answer it you find you’ve forgotten the half of it, and you wonder – did I ever really understand it after all?
So. We have the theory of evolution, or natural selection from random variation, and we have the theories of special and general relativity and quantum theory and so forth. And we have those in science who tell us that ‘theory’ is a technical term constantly misunderstood by the general public and deliberately misconstrued by those with particular agendas. And we have general talk and a lot of general ignorance about evolution.
Several years ago, when I was starting out as a teacher of ESOL (English to speakers of other languages) I observed a small community centre English class. The elderly teacher was asked by a well-dressed middle-aged African man, did she really think evolution – that we were descended from monkeys – was true? It was a polite, puzzled question. The teacher, understandably not wanting to dive down that rabbit hole, replied, ‘well, you know, it’s just a theory’, and the subject was changed. It unsettled me, to put mildly. It’s not how I would’ve dealt with the matter, and in fact I’ve twice since been placed in that position in recent times, and I’ve responded with ‘oh yes, it’s true, the evidence is in and it’s overwhelming,’ or words to that effect. Bam bam, take that and let’s back to grammar.
But of course, that response, too, is unsettling. After all, I could’ve given the exact same response to the question ‘Does God exist?’. It was just saying, an argument from my own authority.
Of course I had back-up from years of science and evolution-reading, but still I felt I was just imposing my authority as a teacher. I half-hoped for and half-dreaded being asked to elaborate.
The other night, at an atheist meet-up, the group was ‘invaded’ by three or four young street-preachers, self-confessed fundies who were apparently keen to debate evolution (they didn’t believe in it) and cosmology (the universe can’t create itself, ergo god). I didn’t engage with them myself, as I’m still recovering from a chest infection and want to avoid stress, but things got very heated over in their corner and I’ve since received an email asking for help to convince one of them of the evidence for evolution. It may be that the young man’s ignorance is wilful, but maybe not, and in any case it provides me with a useful opportunity to answer as best I can the title question.
Questions were raised about the fixity of species well before Charles Darwin was born. The most important figures in this early questioning of orthodoxy came from France. One of the founders of naturalism, Buffon, speculated that the earth might be much older than the standard biblical 6000 years, and that change, both geological and organic, might be endemic and constant. He mostly kept his views to himself, as the idea that the earth was maybe more than ten times older than the accepted figure was incendiary for the time. Lamarck, however, was the first to really go public with a theory of evolution. His essential view was that creatures adapted to their environment over time through the inheritance of acquired characteristics. Although he was generally incorrect as to his mechanism there is still some interest in his ideas today, but above all Lamarck strongly influenced future thinking on the subject as he was a first-rate scientist.
It should be noted though that all this speculation was brought on by the problems posed by evidence. The biblical fixity of species account was becoming increasingly difficult to reconcile with the discoveries of fossils of creatures not to be found anywhere, yet apparently related to current species. And then there were the fossils of ‘giants’, which had been discovered here and there for centuries, but which were not described scientifically until the nineteenth century. How could all these remains of ‘disappeared’ creatures be turning up in a world where creation was fixed? The most popular explanation was ‘catastrophism’, a view held by Cuvier, a younger contemporary of Lamarck and one of his strongest critics. It was an attempt to reconcile fixity with a conveniently biblical diluvian view, but it continued to move thinking in a scientific, evidence-based direction.
Meanwhile, however, other fields of research, such as geology, were also becoming increasingly scientific, especially in Britain, with the work of Hutton and Lyell. Through inference from present conditions, they developed a gradualist, uniformitarian theory of physical change, with a more open-ended view of the earth’s age. This was the scientific background to Darwin’s naturalism. His own grandfather, Erasmus, dabbled in evolutionary ideas, and proposed that the earth had existed for ‘millions of ages’.
Now I know there’s a view out there among fundamentalists called ‘young earth creationism’, but I don’t know much about it. It would seem to be an absolutely crackpot notion, a denial of modern geology, astronomy and cosmology as well as biology and palaeontology, and I presume people who think this way consider the whole of modern science a massive conspiracy theory. How could they not? Yet the young man mentioned above has suggested we go and see a lecture by John Hartnett, an Adelaide University Associate Professor of Physics who’s also a young earth creationist. How could this be? Well I know something of cognitive dissonance and confirmation bias, but still I can barely imagine what he would say to justify his worldview, and I’m not really interested in trying to rebut his specific arguments, if he has them. These people tend to have martyr complexes about their positions, and I suspect they’d be happy to spend hours trying to bamboozle you. The main thing is to be clear about your own understanding of the evidence.
However, I also have an interest in the psychology of belief. Take the case of Hartnett, which I can only speculate about, but this is an obviously intelligent person who has apparently written scientific papers on dark matter and other aspects of cosmology and astrophysics. He knows, surely, how vast the universe is, that the Andromeda Galaxy, our nearest neighbour, is a barely-conceivable 2.5 million light years away, and there are billions of them beyond that, and yet he manages to square this with a six-day creation 6,000 years ago because it was written down by someone and collected much later with a whole mess of other writings by other people, compiled into a book and pronounced ‘holy’. Surely such thinking is more of a mystery than the gods themselves?
I can only speculate again, but Hartnett’s middle name is Gideon, a name inevitably associated with bible-bashing. Can it be that a person gets locked in, from earliest childhood, to a religious schema that they would never think to escape from, no matter how intelligent they are? Can cultural-familial influences have such a vice-like grip? Apparently so, but it’s unusual for someone to be regularly crossing the boundary between a rigid and dogmatic religious belief system and a highly speculative, often free-wheeling but rational and profoundly naturalist enterprise in the way that Hartnett must do. Ain’t people fascinating?
I’ve just read an article about rapid speciation among cichlid fishes in the African lakes. The authors note that this speciation, involving some 500 new species in Lake Victoria, has taken place over less than 15,000 years, unlike the famous speciation among ‘Darwin’s’ finches in the Galapagos (14 species, several million years). It’s called adaptive radiation, where ‘one lineage spawns numerous species that evolve specialisations to an array of ecological niches’, to quote Axel Meyer, writing in the April 2015 edition of Scientific American.
Yet this rapid speciation is still too much for young earth creationists, who believe the earth is less than 10,000 years old. What they make of stromatolites is anyone’s guess. Note that the term ‘earth’ is central, and presumably the universe or multiverse is of little concern to them, existing perhaps only as a fireworks show for our delectation.
As an Australian, this is all good for a laugh – though some Australians, such as John Hartnett, are full-on believers of a six-day creation a few thousand years ago – but apparently in the USA a substantial proportion of their very large population actually believes this (though to be honest, I can’t bring myself to believe the survey figures).
So, I wonder how I would deal with these young-turk young earth creationists who come to our atheist meet-ups spoiling for an argument. My hope is that I would have the wherewithal to ask these questions.
Is it your hope to convert the whole world to your view?
If you were successful, wouldn’t science classes be a lot shorter?
What would you do with those who insisted on being heretical? Preaching that the universe has existed for 13 billion years? Would you have them liquidated, or just permanently incarcerated? How about public recantations?
How come your god allowed us to be led astray by the evidence into getting it so wrong?
What would science be like if young earth creationists controlled all the levers of power? What would scientists do?
Of course I’m yet to hear what young earth creationists, many of whom are apparently highly intelligent, have to say about star formation, black holes and the big bang. They may well have the talent to bamboozle me with ingenious arguments. In the end, though, the best argument is to just keep doing the science, following the evidence. As long as we’re still allowed to.
Meanwhile, I haven’t yet answered the question – why is evolution (or more specifically, natural selection of random variation) true? But before I answer that, I believe that creationists do accept evolution of a particular kind, and distinguish between ‘micro-evolution’ and ‘micro-evolution’. I’ll pay some attention to that – but perhaps not too much – in my next post.