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The Roman Catholic Church: how to slowly kill off a seriously patriarchal institution

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Catholic patiarch, tastefull and elegantly dressed in a classical red 33-buttoned cassock of watered silk with matching baretta and sash. For simplicity's sake he appears to have eschewed the traditional laced undergarments, and his gold cross with tastefully inlaid jewels is clearly a mark of humility and servitude. Only one kissable ring is on display

Catholic patiarch, tastefully and elegantly vested in a classical red 33-buttoned cassock of watered silk with matching baretta and sash. For simplicity’s sake he appears to have eschewed the traditional laced undergarments, and his gold cross with tastefully inlaid jewels is clearly a mark of humility and servitude. Only one kissable ring is on display

The Roman Catholic Church is one of the few institutions in the western world permitted to discriminate, in terms of employment, on the basis of gender. Recently it announced that it would allow women to become deacons. The term deacon comes from ancient Greek, meaning servant, which of course accurately expresses the RCC attitude to women. There’s no upward employment pathway for women who become deacons, and I’d strongly advise any woman against applying for such a position. Of course I’d also strongly advise them to reject Catholicism altogether, as the religion, or business organisation, whatever it is, clearly has an attitude towards women which should have no place in modern society.

So given the outrageous discrimination practised by the RCC, why do so many women sheepishly accede to its restrictions? Well, maybe they don’t. I know this is anecdotal, but in a recent trip around Europe I took a few tours of major European cities. These unsurprisingly involved visits to quite a handful of historic cathedrals, featuring tombs of popes and sculptures of saints and such, but what impressed me more was that each of our tour guides felt obliged, apparently, to say that though their city was nominally Catholic, few of its residents actually practised the religion today. Maybe there was collusion among the tour guides, maybe they were all keen not to frighten the many Asian tourists, but they were surely speaking the truth. Roman Catholicism is the largest non-practiced religion in the world (though of course in some parts it’s practised fervently).

So since the RCC isn’t yet dead from indifference, perhaps something should be done to kill it off legally, and mounting legal challenges to its discriminatory policies on employment and other matters would be a good way to speed up the dying process. Sadly, I can’t find any legal or rights-based organisations keen to take up the challenge. The influential American Civil Liberties Union has many strong statements about Catholic and other religious charities and health providers discriminating against the women they serve, on issues such as abortion, family planning and homosexuality, but nothing about employment within the religious orders of the RCC. Of course the RCC doesn’t discriminate against women in their welfare arm, because to serve is a woman’s vocation. And of course the ACLU only highlights issues, it doesn’t have the resources to go any further, nor would it succeed, as religious groups are routinely exempt from anti- discrimination laws.

In Australia, the Sex Discrimination Act, particularly sections 37 and 38, provides the legal backing to religious sex discrimination. The sections are written with ‘religious freedom’ in mind, and with an eye to Article 18 of the International Covenant on Civil and Religious Rights. These freedoms, though, aren’t absolute and are to be balanced against other human rights, such as equal opportunity based on gender.

There are of course good reasons why nobody is legally challenging the RCC on this issue. Women as priests, bishops, cardinals, popes – this is hardly low-hanging fruit, it’s the heart of the Catholic system. Better to focus on discrimination against homosexuals and LGBT individuals employed in, or just attending, RCC schools. This chips away at the edges of this dreadful patriarchy and slowly weakens it. Every concession the RCC makes to modernity is like another gulp of poison it’s forced to take. Its strength will ebb away…

Written by stewart henderson

August 22, 2016 at 7:11 am

Abiogenesis – LUCA, gradients, amino acids, chemical evolution, ATP and the RNA world

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chemical-evolution-1

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

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.

 

Written by stewart henderson

July 29, 2016 at 8:51 am

clever Charlie Darwin

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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

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?

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.

Achondroplastic_sheep

Written by stewart henderson

June 4, 2016 at 11:00 am

night flight to Dubai

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imageIf you’ve come here looking for Bondesque hijinks click off now. The plane was a Boeing 777, with I think 10 passengers abreast, 3x4x3 with 2 aisles. I take this from Dr Google as much as from unreliable memory, there are apparently many ways of fitting out a 777. Our seating was on the left side facing forward, my TC had the aisle seat, I took the centre, and the window seat was taken up by a late-comer, who thus dashed our hopes of moving up one and gazing into the outer dark. This gangly young Englishman’s trials in clambering over and around us to get to his seat were a promise of discomfort to come.

It was a 14-hour flight to Dubai, starting at around 2200 but due to time zones and date-lines etc we’d be arriving at 0530 the next morning. As mentioned, I’ve had plenty of advice about pills or treatments for whatever might ail me on the flight but in truth I prefer remaining unmedicated as far as possible, and in my sixtieth year I’m pretty well drug-free, if you except life’s absolutely necessary pleasures, caffeine and alcohol, and I’m ever alarmed by and resistant to the collections of meds many of my peers feel forced to take against Alzheimer’s, anaemia, angina, anxiety, apnoeia, arthritis and let’s not get started on the rest of the alphabet. So all I took was some nasal spray and chewing gum as a defence against ‘plane brain’, aka aerosinusitis, and this worked a treat.

I didn’t sleep a wink in those 14 hours, though my reliable but argumentative TC insisted I had some winks, possibly as many as 40. Of course I was wide awake as I could possibly be for the take-off, but I mustn’t exaggerate my terror, it was nothing compared to the Mad Mouse. What made sleep impossible was the discomfort, the novelty and the anticipation, a mèlange of unbeatable distractions. My window-side neighbour was asleep within minutes of take-off, which didn’t stop him jabbing and kicking me when he shifted positions. There was a dearth of space between me and the seats in front and I felt timid about leaning my seat back too far. As time went by I became obsessed with my legs, which didn’t have room to straighten. I tried pushing my arse right back in the seat, I raised it up awkwardly, but just couldn’t get my angles right. My TC on seeing me squirm suggested I take some exercise in the aisle, as per the advice of all experts, but I perversely refused such an easy solution, and didn’t leave my seat until just before touch-down. Which turned out to be one of the highlights of the flight – possibly the longest pee in my peeing career.

Of course it’s hard to look back over so many years of peeing and pick out some, or any, of the great ones, and in any case peeing is such a subjective thing. For example, we’ve all experienced the agony of desperately needing a pee but being nowhere near a publicly sanctioned pee-place. In such circs your distressed state will disable you from conducting pee-stream studies of any kind; the last thing on your mind will be your PB in this activity. I’d go so far as to say that the physical release, the sense of near-weightless joy caused by these outpourings has been probably my most spiritual/religious experience. A true feeling of Salvation, as far from mere bean- or pee-counting as can be had.

Anyway what was intriguing about this mighty slash after 13 hours or so of being plied – necessarily, given the arid aircraft atmosphere – with coffee, fruit juice, and more pure unadulterated water (my least fave drink) than I usually consume in a month, was that, until my legs finally communicated to me that they really had to be stretched, I felt no great urge to relieve myself. Even after several minutes of quite exhilarating straightening and muscle-rubbing in the aisle, my loo visit seemed more after-thoughtful than necessary, so I was in a kind of neutral, clear-headed state when I observed my pee go on and on, leading me to thoughts of PBs and such. If it wasn’t my longest ever, was it in my top 10 (or top 5 if it was in the top half of the 10)? How could I tell? Clearly there is one pee I’ve had in my life that is my longest. Is this in any sense important? Well, maybe. Interesting, certainly. Though on reflection it isn’t so much the longest but the largest by volume that’s important* (or merely interesting) for presumably sometimes the pee runs more feebly than at others; the valve, so to speak, being plus ou moins open – constricted or dilated due to the vagaries of the weather, state of health, age perhaps or even just state of mind. Maybe one day scientists will hatch a device to be implanted in the midriff to measure the highs and lows of pee-flow. Maybe they already have, it wouldn’t suprise me, the utility of such is clear. But it would also allow some champion to claim the Biggest Pee, another entry to add to the Guiness Book of Perhaps Not so Pointless Records. And as I sat back in my now more comfy seat readying myself for Dubai, I thought of another perhaps not so pointless PB that I might just have broken, in that at some point during this flight I may have reached a higher distance above sea-level than ever before. Now how could that be monitored in our monitor-loving age? But then again, sea levels rise and fall, so….

Dubai lights. We watched the perfect landing on the screen before us. The airport was pale in the breaking dawn and glittering with artificial light. There were planes everywhere. Already it was 28 degrees outside.

 

*Just as the Nile is the longest river but the Amazon is by far the largest by volume. The Amazon wins.

TRIP HIGH/LOWLIGHTS

– The food was plentiful, varied and delicious IMHO, and the service was excellent, under sometimes difficult conditions.

– You need to see things from a baby’s perspective. As they’ve not yet developed sophisticated means of either conveying or receiving info, their instinct is to make as much noise as possible to make absolutely sure that others know they’re suffering horrendous agonies or experiencing the most frabjous joy. So nature has furnished them with the most impressive noise-making equipment for this purpose. It’s highly adaptive, another fine example of evolution at work. Ear plugs next time, though simple perspective taking can be sufficient.

– Not having a tech-savvy 13-y-o as my TC it took most of the flight to work out the functioning of the on-board entertainment (the first 2 hours just to get the headphones plugged in and operational). The movies were mostly boorish but I found one, Carol, based on a Patricia Highsmith novel I actually read some 20 years ago, a book/film about longing, desire and hope, regardless of sexual preference really, very much the sort of thing I’m drawn to. Reminds me of my fave Jane Austen novel, Persuasion. Highly recommended – I got teary. Fine performances by Cate Blanchett and Rooney Mara. Also recalls to my mind my fave line from the KJ Bible, perhaps my fave line in all litt: ‘Hope deferred makes the heart sick’.

Couldn’t settle to anything else much, though I did find a silly thriller very much starring Olga Kurylenko, the Most Beautiful Woman Who Has Ever Lived according to my ever-changing judgment (OK is always more than OK, I like to say), but not even her loveliness and her formidable ball-breaking superhero role could force me to see the shamefully silly shenanigans to the end. Better to watch L’Annulaire again, and again.

– Aerosinusitis. I did feel a painful buid-up after take-off but then came a sudden but sort of slow uncorking and brightening of sound, rather pleasurable, and I had no further problems on the outbound flights.

 

Une presence francaise at Dubai airport

Une presence francaise at Dubai airport

 

 

Written by stewart henderson

May 2, 2016 at 12:13 pm

why are our brains shrinking?

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my own brain, squeezed of alcohol

my own brain, squeezed of alcohol

Jacinta: So you know that the average human brain mass, or is it volume, has reduced by  – is it 15%, I can’t remember – over the past 20,000 years or so, right? And there’s this theory that it’s somehow related to domestication, because the same thing has happened to domesticated animals…

Canto: How so..?

Jacinta: Well, we don’t know how so, we just know it’s happened.

Canto: How do we know this? Who says?

Jacinta: Well I’ve heard about it from a few sources but most recently from Bruce Hood, the well-known psychologist and skeptic who was talking on the SGU about a recent book of his, The Domesticated Brain. 

Canto: So the idea is that humans have somehow domesticated themselves, in the same way that they’ve domesticated other species, with a corresponding decrease in brain mass in all these species, which signifies – what?

Jacinta: Well it raises questions, dunnit? What’s going on?

Canto: It doesn’t signify dumbing down though – I read in Pinker’s big book about our better angels that our average IQ is rising in quite regular and exemplary fashion.

Jacinta: Yes, the Flynn effect. Though of course what IQ measures has always been controversial. And they do reckon size isn’t the main thing. I mean look at all those small critters that display so many smarts. For example, rats, octopuses and corvids (that’s to say crows, ravens and some magpies). They all seem to be fast learners, within their limited spheres, and very adaptable. But getting back to the human brain, it seems to be something known mainly to palaeontologists, who have a variety of theories about it, including the ‘we’re getting dumber’ theory, but I’m not convinced by that one. It seems more likely that our brains are getting more organised, requiring less mass.

Canto: So this has happened only in the last 20,000 years?

Jacinta: Or perhaps even less – between 10 and 20 thousand.

Canto: Isn’t that a phenomenally short time for such a substantial change?

Jacinta: I really don’t know. They say it might be partly related to a decrease in overall body size, so that the brain to body ratio remains much the same.

Canto: A decrease in body size? What about the obesity epidemic? And I remember way back when I was a kid reading about how we’d been getting taller with each generation since the Great Depression – or was it the Industrial Revolution? Anyway our improved diet, our era of relative abundance, has led to a change in height, and presumably in mass, in only a few generations.

Jacinta: So now you’re saying that substantial changes can occur in a few generations, let alone 10,000 years?

Canto: Uhhh, yeah, okay, but I wasn’t talking about brain size.

Jacinta: Well why not brain size? Anyway, although there have been those recent changes, at least in the west, the story goes that the planet has warmed since the last ice age, favouring less bulky bodies, less fat storage, more gracile frames.

Canto: So what about domestication, why has this led to decreased brain sizes?

Jacinta: Well this is very complex of course…

Canto: I can think of a reason, though it might not be called domestication, more like socialisation, and outsourcing. You can see it in very recent times, with smart phones – it’s even become an already-stale joke, you know phones are getting smarter so we’re getting dumber. But then we always tend to exaggerate the short-term and the present against the longer view. And yet…. I was on the tram the other night, sitting across from this couple, locked into their phone screens, I mean really locked in, earplugs attached, heads bent, utterly fixated on their little screens, completely oblivious, of each other as well as of the outside world. I was reading a book myself, but I became distracted by my irritation with these characters, while wondering why I should be irritated. It just went on so long, this locked-in state. I leaned forward. I waved my hand in front of their bowed heads. I wanted to tell them that the tram had rattled past all the stations and was heading out to sea…

Jacinta: There are some problems with the whole argument. How do we know that domesticated animals have smaller brains? Domesticated cats have a wide range of brain sizes no doubt, but what wild cats are you comparing them with? Even more so with dogs and their immense varieties. Okay they’re descended from wolves so you compare a wolf brain with its modern doggy-wolfy counterpart, but who’s going to agree on type specimens?

Canto: So you brought the subject up just to dismiss it as a load of rubbish?

Jacinta: Well if we shelve the domestication hypothesis for the moment – I’m not dismissing it entirely – we might consider other reasons why human brains are shrinking – if they are.

Canto: So you’re not convinced that they are?

Jacinta: Well let’s be sceptical until we find some solid evidence. In this Scientific American site, from November 2014, palaeontologist Chris Stringer states that ‘skeletal evidence from every inhabited continent’ suggests – only suggests – that our brains have become smaller in the past 10 to 20 thousand years. No references are given, but the article assumes this is a fact. This piece from Discovery channel or something, which dates back to 2010, relies in part on the work of another palaeontologist, John Hawks, whose website we link to here. Hawks also talks about a bucketload of evidence, but again no references. The original research papers would likely be behind a paywall anyway, and barely intelligible to my dilettante brain….

Canto: Your diminishing brain.

Jacinta: Okay I’m prepared to believe Hawks about our incredible shrinking brains, but is domestication the cause, and what exactly is domestication anyway? Hawks doesn’t go with the domestication hypothesis. In fact the Discovery article usefully covers a number of alternative hypotheses, and of course the shrinking may be due to a combo. In fact that’s more than likely.

Canto: So what’s Hawks’ hypothesis, since we’re supposedly admirers of his?

Jacinta: Well Hawks decided to look more closely at this brain contraction – which is interesting because I was thinking along the same lines as he was, i.e. has it been a uniform contraction, or was there a sudden, quick development, followed by a stagnant period, as you would expect?

Canto: Anyway isn’t brain organisation more important than brain mass? Sorry to interrupt, but haven’t we already established that?

Jacinta: We haven’t established anything, we’re just effing dilettantes remember. Hawks started looking at more recent data, over the past 4000 years or so, to see if he could detect any difference in the encephalisation quotient (EQ) – the ratio of brain volume to body mass – over that time. He found that indeed there has. The picture is complicated, but overall there has been a reduction in the brain compared to the body. His explanation for this though is quite different. He reckons that a series of mutations over recent history have resulted in the brain producing more out of less…

Canto: Right, just as a series of modifications have allowed us to produce smaller but more powerful and fuel-efficient cars.

Jacinta: Uhh, yeah, something like that.

Canto: But we know what those modifications were, we can name them. Can we name the mutations?

Jacinta: Clever question, but we know about cars, we built them and they’ve only been around for a bit more than a century. We know vastly less about the brain and we’re still getting our heads around natural selection, give us a break. Hawks points out that it’s a rule about population genetics well-known in principle to Darwin, that the larger the population the more numerous the mutations, and there was a surge in the human population back when agriculture was developed and large settlements began to form. So a number of brain-related mutations led to streamlining and, as you suggest, fuel efficiency.

Canto: But isn’t this compatible with the domestication hypothesis? I imagine that, if there really is a brain reduction for domesticated animals, it’s because they don’t have to rely on their brains so much for survival, and we don’t either, the collective has sort of magically taken care of it through farming and infrastructure and supermarkets.

Jacinta: Yes but they all have their own complicated networks and issues we have to wrap our brains around. The domestication hypothesis is really about aggression apparently. The argument goes that all animals under domestication become more varied in size, coloration and general build, with a tendency to become more gracile over all. Selection against aggression, according to the primatologist Richard Wrangham, favours a slowly developing brain – one that is, in a sense, in a perpetually juvenile state (think of cute cat and dog videos). Of course, all this assumes that juvenile brains are less aggressive than adult brains, which some might see as a dubious assumption.

Canto: Yes, think of school bullying, Lord of the Flies, youth gangs, the adolescent tendency to extremes…

Jacinta: Well, both Wrangham and Hood offer a particularly interesting example of ‘super-fast’ domestication to illustrate their hypothesis:

In 1958 the Russian geneticist Dmitri Belyaev started raising silver foxes in captivity, initially selecting to breed only the animals that were the slowest to snarl when a human approached their cage. After about 12 generations, the animals evidenced the first appearance of physical traits associated with domestication, notably a white patch on the forehead. Their tameness increased over time, and a few generations later they were much more like domesticated dogs. They had developed smaller skeletons, white spots on their fur, floppy ears, and curlier tails; their craniums had also changed shape, resulting in less sexual dimorphism, and they had lower levels of aggression overall.

Now, how does this relate to juvenilism? Well, in the wild, offspring grow up quickly and have to fend for themselves, which requires a certain ruthless degree of aggression. Cats and dogs, yes, they abandon their offspring soon enough, but those offspring continue to be tutored, tamed, domesticated under their human owners. We hear a lot about school bullying and gangs of youths, but they’re actually the exception rather than the rule, or a last ditch rebellion against the domestication pressure that’s exerted by the whole of society, and they’ll either succumb to that pressure or end up in jail, or worse. It’s a bit like the Freudian concept of sublimation, you channel your aggressive energies into creativity, competitive problem-solving, sports achievements and the like.

Canto: So you’re in favour of the domestication hypothesis?

Jacinta: Well, I’m not against it. It sounds plausible to me. Human domestication, or self-domestication if you want to call it that, is a social-contract sort of thing. You agree to outsource and comply with certain arrangements – laws, government, taxation and so forth, in return for certain benefits in terms of security and resources. So you don’t have to fend for yourself. And that affects the brain, obviously. Though it might not be the whole story.

Written by stewart henderson

April 15, 2016 at 8:42 am

What is a trisomy?

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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.

chromosome_nondisjunction_meiosis

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.

Written by stewart henderson

January 31, 2016 at 10:06 pm

group think revisited, or how to improve your mind

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Confirmation bias (and the benefits of social reasoning) in a nutshell:

How can you say to your brother, ‘Brother, let me take the speck out of your eye,’ when you yourself fail to see the plank in your own eye? Luke 6: 42 New International Version

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The argumentative theory of reason

The recent New Scientist collection, Being Human, includes an essay, ‘The argumentative ape’, by Dan Jones, which is worth reading and contemplating for any teacher involved in encouraging her students to think richly about current ethical or political issues. In my college, NESB students study ‘English for academic purposes’, which involves a lot of basic grammar and vocabulary at the lower levels, and academic presentations and essays at the higher levels. In these ‘discussion’ or ‘argument’ essays and presentations, students are required to examine the pros and cons of some chosen activity or decision, such as the proper driving age, the consumption of GM food, or even whether humanity has benefitted or blighted our planet.

However, there seems to be a contradiction in asking students to write, and be examined on, individually written ‘discussion essays’, when discussions and arguments are group rather than individual activities. More importantly, if we want to improve our students’ understanding of current issues, perhaps we should be placing more emphasis on group discussion than on individual analysis.

This is hardly a new idea. The ancient Athenians, founders of democracy – decision-making by the people – built their city around the agora, a gathering place for public talk and argument. This design was quite deliberate, as all Athenian citizens were required to contribute to discussions from which civic decisions were made.

‘The argumentative ape’, however, provides contemporary evidence about the evolutionary importance of argument in human society. It describes a thesis put forward by European researchers Hugo Mercier and Dan Sperber, that human reason evolved not so much to assist us in more clearly understanding our world, but to argue, to persuade, to convince others of our position, our right-ness. So, it evolved socially. And there appears to be some evidence for the more general ‘social brain’ hypothesis, in that a clear correlation has been found between the number of individuals in a primate group and the average brain size of that particular species.

Now one essential problem here should be obvious, as it was to Socrates in his battle with the sophists. The most persuasive arguments aren’t necessarily the best. So it’s natural that along with persuasiveness, skepticism would have developed, as humans sought to evaluate competing arguments.

Through scepticism we’ve identified many types of fallacious reasoning, and ways we have of convincing ourselves in the process of trying to convince others. Confirmation bias, or motivated reasoning, probably tops this list, as it is extremely pervasive if not universal. As Mercier points out, using confirmation bias seems counter-productive if you wish to arrive at correct results, for example in scientific research, but it can be highly effective in argument, as your bias commits you to garnering a multitude of arguments for your position while ignoring, and thus rendering insignificant, all arguments against. If we accept an argumentative theory of the evolution of reason, then, we will see confirmation bias not as a flaw, but as a device to strengthen our own arguments, and the ability to detect such biases would in turn be a device to undo or diminish the arguments of others.

how individual reasoning is affected by the larger group

Experimental psychologists have found many ways in which our reasoning can be affected or manipulated. Take, for example, the framing effect. It has been found, and regularly confirmed, that how the same problem is worded will affect our decision. Jones presents the scenario, used by psychologists, of a small village of 600 people threatened by a deadly disease. In scenario one, if Plan A is adopted, exactly 200 people will survive. If plan B is adopted, there will be a 1 in 3 chance that all will survive, and a 2 in 3 chance that none will survive. When this scenario is presented to subjects, the majority invariably choose Plan A. However when, in scenario two, Plan A is framed with the slight difference that exactly 400 people will die (with no change to Plan B), this is enough for the majority to flip over to Plan B. This consistent result has been explained in terms of ‘loss aversion’ – we prefer to avoid the explicit loss of life as expressed in the change to Plan A in scenario two. Significantly though for the argumentative ape hypothesis, this loss aversion bias is strengthened when we have to justify our decision to a larger group. We have a ready-made justification as expressed in the framing. It’s probable that we always have in mind what the larger group, or ‘society’ will think of our decision, but when this need to justify ourselves is made explicit, the ready rationalisation is more likely to be adopted.

Other effects of apparently faulty reasoning, such as the attraction effect and the sunk-cost fallacy, have been detected in psychological studies, and all have been shown to be enhanced when there is an explicit need for justification. The ‘argumentative’ thesis claims that we tend to choose the most easily justified option rather than what might be best.

Confirmation bias for me, scepticism towards you, and how it pans out

While this may seem a pessimistic outlook on our use of reason, the counterbalance lies in our ability, from clear evolutionary need, to identify and so counter the faulty arguments of others. This pattern follows a familiar evolutionary trajectory, in which a predator evolves a means to capture its prey, leading the prey to develop a defence mechanism to protect itself against the predator. Scepticism helps us to avoid being sucked in and ‘devoured’.

The result for group reasoning is that bias and the scepticism can balance each other out, leading to a greater recognition of the weaknesses in our own opinions and the strengths in those of others. And experimental evidence backs up this result. To quote from Jones’ article:

In one convincing study, psychologists David Moshman and Molly Geil at the University of Nebraska-Lincoln looked at performance in the Wason selection test – a simple card game based on logical deduction. When thinking about this task on their own, less than 10 per cent of people got the right answer. When groups of 5 or 6 people tackled it, however, 75 per cent of the groups eventually succeeded. Crucially for the argumentative theory, this was not simply down to smart people imposing the correct answer on the rest of the group: even groups whose members had all previously failed the test were able to come to the correct solution by formulating ideas and revising them in light of criticism (Thinking and Reasoning, vol 4, p 231).

He also points to research indicating that groups are more creative in their thinking than individuals (see sources below).

Implications for teaching, or how to best facilitate the best group thinking

Evidence from a series of studies by Anita Williams Woolley of Carnegie Mellon University in Pennsylvania suggests that a group’s individual skills are not the best predictor of the group’s overall performance in problem-solving. These studies were designed to measure the ‘collective intelligence’ of the group, in something like the manner of IQ tests for individuals. She found that those groups who scored highest were the most inclusive, allowing maximal participation within the group. Sensitivity to the moods and feelings of others helped groups to score highly, and the best groups were those with the greater number of female members, presumably because females have a greater social sensitivity.

Group thinking can, of course, backfire. Groupthink in fact has long been seen negatively, but this is because people with the same cognitive biases often congregate together, as with political parties and religious organisations, or gravitate towards similar professions, such as the police or the military. In such groupings it’s often the case that the group moves collectively to quite extreme positions. Where group thinking would be expected to work most effectively is precisely in a college for NESB students from different cultures and backgrounds, in which individuals are challenged by widely different but (hopefully!) cogent opinions.

As educators, we need to consider the best outcomes for our students. Clearly there is pressure, in an individualised results-based system, to push for individual skill in argumentation, with the resultant high test scores. However, the evidence for group interaction in improving students’ understanding of the many issues focused on in essays and seminars at the higher levels is clear. Of course the situation is complicated by the fact that many students at EAP2 and EAP3 levels still don’t have the  grammatical and lexical skills to present cogent arguments in English, so that it’s often hard to determine whether their difficulties are those of reasoning or of language. Even so, I believe it is vital to take advantage of the cultural diversity of students’ experience and knowledge (even within identical language groups) to encourage interaction that will challenge biases and create awareness of a variety of perspectives. Hopefully this will enliven their thinking both within the college and in their studies beyond Eynesbury.

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Some sources are found in the links. Here are others.

D Sperber and H Mercier,”Why do humans reason? Arguments for an argumentative theory”, Behavioural and brain sciences: Published online March 2011. http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1698090

http://edge.org/conversation/hugo_mercier-the-argumentative-theory. Mercer elaborates on the theory very interestingly in a video on this website

Williams Woolley, Anita, ‘Collective intelligence in human groups’, April 2012: Center for Collective Intelligence: http://cci.mit.edu/ci2012/plenaries/speaker%20slides%20ci%202012/Woolleyslidesci2012.pdf

D Moshman & M Geil, 1998 ‘Collaborative reasoning: evidence for collective rationality’. Thinking and reasoning V4 issue 3: http://www.tandfonline.com/doi/abs/10.1080/135467898394148

Written by stewart henderson

November 26, 2015 at 6:57 am

this one’s for the birds

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clevercrow1

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

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

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1280px-Difference_DNA_RNA-EN

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.

Viroid

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