# an autodidact meets a dilettante…

‘Rise above yourself and grasp the world’ Archimedes – attribution

## kin selection – some fascinating stuff

Canto: So we’ve done four blogs on Palestine and we’ve barely scratched the surface, but we’re having trouble going forward with that project because, frankly, it’s so depressing and anger-inducing that it’s affecting our well-being.

Jacinta: Yes, an undoubtedly selfish excuse, but we do plan to go on with that project – we’re definitely not abandoning it, and meanwhile we should recommend such books as Tears for Tarshiha by the Palestinian peace activist Olfat Mahmoud, and Goliath by the Jewish American journalist Max Blumenthal, which highlight the sufferings of Palestinian people in diaspora, and the major stresses of trying to exist under zionist monoculturalism. But for now, something completely different, we’re going to delve into the fascinating facts around kin selection, with thanks to Robert Sapolski’s landmark book Behave.

Canto: The term ‘kin selection’ was first used by John Maynard Smith in the early sixties but it was first mooted by Darwin (who got it right about honey bees), and its mathematics were worked out back in the 1930s.

Jacinta: What’s immediately interesting to me is that we humans tend to think we alone know who our kin are, especially our extended or most distant kin, because only we know about aunties, uncles and second and third cousins. We have language and writing and record-keeping, so we can keep track of those things as no other creatures can. But it’s our genes that are the key to kin selection, not our brains.

Canto: Yes, and let’s start with distinguishing between kin selection and group selection, which Sapolsky deals with well. Group selection, popularised in the sixties by the evolutionary biologist V C Wynne-Edwards and by the US TV program Wild Kingdom, which I remember well, was the view that individuals behaved, sometimes or often, for the good of the species rather than for themselves as individuals of that species. However, every case that seemed to illustrate group selection behaviour could easily be interpreted otherwise. Take the case of ‘eusocial’ insects such as ants and bees, where most individuals don’t reproduce. This was seen as a prime case of group selection, where individuals sacrifice themselves for the sake of the highly reproductive queen. However, as evolutionary biologists George Williams and W D Hamilton later showed, eusocial insects have a unique genetic system in which they are all more or less equally ‘kin’, so it’s really another form of kin selection. This eusociality exists in some mammals too, such as mole rats.

Jacinta: The famous primatologist Sarah Hrdy dealt something of a death-blow to group selection in the seventies by observing that male langur monkeys in India commit infanticide with some regularity, and, more importantly, she worked out why. Langurs live in groups with one resident male to a bunch of females, with whom he makes babies. Meanwhile the other males tend to hang around in groups brooding instead of breeding, and infighting. Eventually, one of this male gang feels powerful enough to challenge the resident male. If he wins, he takes over the female group, and their babies. He knows they’re not his, and his time is short before he gets booted out by the next tough guy. Further, the females aren’t ovulating because they’re nursing their kids. The whole aim is to pass on his genes (this is individual rather than kin selection), so his best course of action is to kill the babs, get the females ovulating as quickly as possible, and impregnate them himself.

Canto: Yes, but it gets more complicated, because the females have just as much interest in passing on their genes as the male, and a bird in the hand is worth two in the bush…

Jacinta: Let me see, a babe in your arms is worth a thousand erections?

Canto: More or less precisely. So they fight the male to protect their infants, and can even go into ‘fake’ estrus, and mate with the male, fooling the dumb cluck into thinking he’s a daddy.

Jacinta: And since Hrdy’s work, infanticide of this kind has been documented in well over 100 species, even though it can sometimes threaten the species’ survival, as in the case of mountain gorillas. So much for group selection.

Canto: So now to kin selection. Here are some facts. If you have an identical twin your genome is identical with hers. If you have a full sibling you’re sharing 50% and with a half-sibling 25%. As you can see, the mathematics of genes and relatedness can be widened out to great degrees of complexity. And since this is all about passing on all, or most, or some of your genes, it means that ‘in countless species, whom you co-operate with, compete with, or mate with depends on their degree of relatedness to you’, to quote Sapolsky.

Jacinta: Yes, so here’s a term to introduce and then fairly promptly forget about: allomothering. This is when a mother of a newborn enlists the assistance of another female in the process of child-rearing. It’s a commonplace among primate species, but also occurs in many bird species. The mother herself benefits from an occasional rest, and the allomother, more often than not a younger relation such as the mother’s kid sister, gets to practice mothering.

Canto: So this is part of what is called ‘inclusive fitness’, where, in this case, the kid gets all-day mothering (if of varying quality) the kid sister gets to learn about mothering, thereby increasing her fitness when the time comes, and the mother gets a rest to recharge her batteries for future mothering. It’s hopefully win-win-win.

Jacinta: Yes, there are negatives and positives to altruistic behaviour, but according to Hamilton’s Rule, r.B > C, kin selection favours altruism when the reproductive success of relatives is greater than the cost to the altruistic individual.

Canto: To explain that rule, r equals degree of relatedness between the altruist and the beneficiary (aka coefficient of relatedness), B is the benefit (measured in offspring) to the recipient, and C is the cost to the altruist. What interests me most, though, about this kin stuff, is how other, dumb primates know who is their kin. Sapolsky describes experiments with wild vervet monkeys by Dorothy Cheney and Robert Seyfarth which show that if monkey A behaves badly to monkey B, this will adversely affect B’s behaviour towards A’s relatives, as well as B’s relatives’ behaviour to A, as well as B’s relatives’ behaviour to A’s relatives. How do they all know who those relatives are? Good question. The same researchers proved this recognition by playing a recording of a juvenile distress call to a group of monkeys hanging around. The female monkeys all looked at the mother of the owner of that distress call to see what she would do. And there were other experiments of the sort.

Jacinta: And even when we can’t prove knowledge of kin relations (kin recognition) among the studied animals, we find their actual behaviour tends always to conform to Hamilton’s Rule. Or almost always… In any case there are probably other cues, including odours, which may be unconsciously sensed, which might aid in inclusive fitness and also avoiding inbreeding.

Canto: Yes and It’s interesting how this closeness, this familiarity, breeds contempt in some ways. Among humans too. Well, maybe not contempt but we tend not to be sexually attracted to those we grow up with and, for example, take baths with as kids, whether or not they’re related to us. But I suppose that has nothing to do with kin selection. And yet…

Jacinta: And yet it’s more often than not siblings or kin that we have baths with. As kids. But getting back to odours, we have more detail about that, as described in Sapolski. Place a mouse in an enclosed space, then introduce two other mice, one unrelated to her, another a full sister from another litter, never encountered before. The mouse will hang out with the sister. This is called innate recognition, and it’s due to olfactory signatures. Pheromones. From proteins which come from genes in the major histocompatibility complex (MHC).

Canto: Histowhat?

Jacinta: Okay, you know histology is the study of bodily tissues, so think of the compatibility or otherwise of tissues that come into contact. Immunology.  Recognising friend or foe, at the cellular, subcellular level. The MHC, this cluster of genes, kicks off the production of proteins which produce pheromones with a unique odour, and because your relatives have similar MHC genes, they’re treated as friends because they have a similar olfactory signature. Which doesn’t mean the other mouse in the enclosure is treated as a foe. It’s a mouse, after all. But other animals have their own olfactory signatures, and that’s another story.

Canto: And there are other forms of kin recognition. Get this – birds recognise their parents from the songs sung to them before they were hatched. Birds have distinctive songs, passed down from father to son, since its mostly the males that do the singing. And as you get to more complex species, such as primates – though maybe they’re not all as complex as some bird species – there might even be a bit of reasoning involved, or at least consciousness of what’s going on.

Jacinta: So that’s kin selection, but can’t we superior humans rise above that sort of thing? Australians marry Japanese, or have close friendships with Nigerians, at least sometimes.

Canto: Sometimes, and this is the point. Kinship selection is an important factor in shaping behaviour and relations, but it’s one of a multiple of factors, and they all have differential influences in different individuals. It’s just that such influences may go below the level of awareness, and being aware of the factors shaping our behaviour is always the key, if we want to understand ourselves and everyone else, human or non-human.

Jacinta: Good to stop there. As we’ve said, much of our understanding has come from reading Sapolsky’s Behave, because we’re old-fashioned types who still read books, but I’ve just discovered that there’s a whole series of lectures by Sapolsky, about 25, on human behaviour, which employs the same structure as the book (which is clearly based on the lectures), and is available on youtube here. So all that’s highly recommended, and we’ll be watching them.

References

R Sapolski, Behave: the biology of humans at our best and worst. Bodley Head, 2017

https://www.britannica.com/science/animal-behavior/Function#ref1043131

https://en.wikipedia.org/wiki/Kin_selection

https://en.wikipedia.org/wiki/Eusociality

Written by stewart henderson

February 24, 2019 at 11:17 am

## on luck, and improving environments

I’m in the process of reading Behave, by Robert Sapolsky, a professor of neurology and biology at Stanford University, who has tried in his book to summarise, via the research literature, the seconds, then minutes, then hours, then days, then lifetimes and more, that precede any particular piece of behaviour. It’s a dense but fascinating book, which aligns with, and provides mountains of evidence for, my view that we’re far less in control of ourselves than we think.

It seems we think this because of what might be called conscious awareness of our behaviours and our decisions. This consciousness is something we sometimes mistake for control. It’s interesting that we consider it obvious that we have no control over the size of our nose or the colour of our eyes, but we have more or less complete control of our temper, appetites, desires and ambitions.

Humanistically speaking, this understanding about very limited control needs to have massive implications for our understanding of others. We don’t get to choose our parents, our native country or the immediate environment that most profoundly affects our early life and much of our subsequent behaviour. The flow of hormones and neurotransmitters and their regulation via genetic and epigenetic factors proceed daily, hourly, moment by moment, and all we’re aware of, essentially, is outcomes.

A lot of people, I note, are very uncomfortable about this kind of talk. For example, many of us want to treat each other as ‘equal before the law’. But is one person ever ‘equal’ with another? We know – it’s obvious – that we’re all different. That’s how we distinguish people, by their smiles, their voices, their fingerprints, their DNA. So how can we be different and equal at the same time? Or, to turn things around, how can a legal system operate if everyone is treated as different, unique, a special case?

Well, in a sense, we already do this, with respect to the law. No two bank robberies, or rapes, or murders are the same, and the judiciary must be highly attuned to the differences when applying punishments. Nowadays, and increasingly, the mental state of the offender – particularly at the time of the offence, if that can be ascertained – is considered when sentencing.  And this is surely a good thing.

The question here is, considering the exponential growth of our neurophysiological knowledge in the 21st century, and its bearing on our understanding of every kind of negative or positive behaviour we engage in, how can we harness that knowledge to improve outcomes and move from a punitive approach to bad behaviours to something more constructive?

Of course, it’s one thing to identify the release or suppression of glucocorticoids, for example, and its effect on person x’s cognitive faculties, it’s entirely another thing to effect a remedy. And to what effect? To make everyone docile, ‘happy’ and law-abiding? To have another go at eugenics, this time involving far more than just genes?

One of the points constantly hammered home in Sapolsky’s book is the effect of environment on everything that goes on inside us, so that, for example, genes aren’t quite as determinative as we once thought. Here are some key points from his chapter on genes (with apologies about unexplained terms such as epigenetic, transcription and transposons):

a. Genes are not autonomous agents commanding biological events.

b. Instead genes are regulated by the environment, with environment consisting of everything from events inside the cell to the universe.

c. Much of your DNA turns environmental influences into gene transcription, rather than coding for genes themselves; moreover, evolution is heavily about changing regulation of gene transcription, rather than genes themselves.

d. Epigenetics can allow environmental effects to be lifelong, or even multigenerational.

e. And thanks to transposons, neurons contain a mosaic of different genomes.

And genes are only one component of the array of forces that influence or control our behaviour. We know, or course, about how Phineas Gage-type accidents and brain tumours can alter behaviour, but many other effects on the brain can alter our behaviour without us and others knowing too much about it. These include stress, malnutrition, and long-term cultural and religious influences which permanently affect our attitudes to, for example, women, other species and the food we eat. Domestic violence, drug use, political affiliations, educational outcomes and sexual affinities are all more inter-generational than we’re generally prepared to admit.

The first thing we need to do is be aware of all this in our judgment of others, and even of ourselves. There’s just so much luck involved in being who we are. We could’ve been more or less ‘good-looking’ than we are -according to the standards of the culture around us – and this would’ve affected the way we’ve been treated throughout our whole lives. We could’ve been born richer or poorer, with more or less dysfunctional parents, taller or shorter, more or less mentally agile, more or less immune to the pathogens that surround us. On and on and on we could go, even to an extreme degree. We could’ve been born in Algeria, Argentina or Azerbaijan. We could’ve been born in 1912, 1412 or 512, or 150,000 years ago. We could’ve been born a mongoose, a mouse or a mosquito. It’s all luck, whether good or bad is up to us to decide, but probably not worth speculating about as we have no choice but to make the best of what we are.

What we do have is consciousness or awareness of what we are. And with that consciousness we can speculate, as we as a species always have, on how to make the best of ourselves, given that we’re the most socially constructed mammalian species on the planet, and for that reason the most successful, measured by population, spread across the globe, and what we’ve done for ourselves in terms of social evolution – our science, our technology, our laws and our politics.

That’s where humanism comes in, for me. Since we know that ‘there but for the randomness of luck go I’, it surely follows that we should sympathise with those whose luck hasn’t been as lucky as our own, and strive to improve the lot of those less fortunate. Safe havens, educational opportunities, decent wages, human rights, clean environments, social networks – we know what’s required for people to thrive. Yet we focus, I think, too much on punishment. We punish people for trying to improve their family’s situation – or to avoid obliteration – by seeking refuge in safer, richer, healthier places. We punish them for seeking solace in drugs because their circumstances are too overwhelming to deal with. We punish them for momentary and one-off lapses of concentration that have had dire consequences. Of course it has always been thus, and I think we’re improving, though very unevenly across the globe. And the best way to improve is by more knowing. And more understanding of the consequences of that knowledge.

Currently, it seems to me, we’re punishing people too much for doing what impoverished, damaged, desperate people do to survive. It’s understandable, perhaps, in our increasingly individualist world. How dare someone bother me for handouts. It’s not my fault that x has fucked up his life. Bring back capital punishment for paedophiles. People smugglers are the lowest form of human life. Etc etc – mostly from people who don’t have a clue what it’s like to be those people. Because their life is so different, through no fault, or cause, of their own.

So to me the message is clear. Out lives would be better if others’ lives were better – if we could give others the opportunities, the health, the security and the smarts that we have, and if we could have all of those advantages that they have. I suppose that’s kind of impossible, but it’s better than blaming and punishing, and feeling superior. We’re not, we’re just lucky. Ot not.

Written by stewart henderson

December 4, 2018 at 2:22 pm

## more about ozone, and the earth’s greatest extinction event

Ozone, or trioxygen (O3), an unstable molecule which is regularly produced and destroyed by the action of sunlight on O2, is a vital feature in our atmosphere. It protects life on earth from the harmful effects of too much UV radiation, which can contribute to skin cancers in humans, and genetic abnormalities in plant life. In a previous post I wrote about the discovery of the ozone shield, and the hole above Antarctica, which we seem to be reducing – a credit to human global co-operation. In this post I’m going to try and get my head around whether or not ozone depletion played a role in the so-called end-Permian extinction of some 250 mya.

I first read of this theory in David Beerling’s 2009 book The emerald planet, but recent research appears to have backed up Beerling’s scientific speculations – though speculation is too weak a word. Beerling is a world-renowned geobiologist and expert on historical global climate change. He’s also a historian of science, and in ‘An ancient ozone catastrophe?’, chapter 4 of The emerald planet, he describes the discovery and understanding of ozone through the research of Robert Strutt, Christian Schönbein, Marie Alfred Cornu, Walter Hartley, George Dobson, Sidney Chapman and Paul Crutzen, among others. He goes on to describe the ozone hole discovery in the 70s and 80s, before focusing on research into the possible effects of previous events – the Tunguska asteroid strike of 1908, the Mount Pinatubo eruption of 1991 and others – on atmospheric ozone levels, and then homes in on the greatest extinction event in the history of our planet – the end-Permian mass extinction, ‘the Great Dying’, which wiped out some 95% of all species then existing.

According to Beerling, it was an international team of palaeontologists led by Henk Visscher at the University of Utrecht who first made the claim that stratospheric ozone had substantially reduced in the end-Permian. They hypothesised that, due to the greatest volcanic eruptions in Earth history, which created the Siberian Traps (layers of solidified basalt covering a huge area of northern Russia), huge deposits of coal and salt, the largest on Earth, were disrupted:

The widespread heating of these sediments and the action of hot groundwater dissolving the ancient salts, was a subterranean pressure cooker synthesising a class of halogenated compounds called organohalogens, reactive chemicals that can participate in ozone destruction. And in less than half a million years, this chemical reactor is envisaged to have synthesised and churned out sufficiently large amounts of organohalogens to damage the ozone layer worldwide to create an intense increased flux of UV radiation.

However, Beerling questions this hypothesis and considers that it may have been the eruptions themselves, which lasted 2 million years and occurred at the Permian-Triassic boundary 250-252 mya, rather than their impact on salt deposits, that did the damage. There’s evidence that many of the eruptions originated from as deep as 10 kilometres below the surface, injected explosively enough to reach the stratosphere, and that these plumes contained substantial amounts of chlorine.

More recent research, published this year, has further substantiated Visscher’s team’s finding regarding genetic mutations in ancient conifers and lycopsids, and their probable connection with UV radiation enabled by ozone destruction. The mutations were global and dated to the same period. Laboratory experiments exposing related modern plants to bursts of UV radiation have produced more or less identical spore mutations.

The exact chain of events linking the eruptions to the ozone destruction have yet to be worked out, and naturally there’s a lot of scientific argy-bargy going on, but the whole story, even considering that it occurred so far in the past is a reminder of the fragility of that part of our planet that most concerns us – the biosphere. The eruptions clearly altered atmospheric chemistry and temperature. Isotopic measurements of oxygen in sea water suggest that equatorial waters reached more than 40°C. As can be imagined, this had killer effects on multiple species.

So, we’re continuing to gain knowledge on the ozone shield and its importance, and fragility. I don’t know that there are too many ozone hole skeptics around (I don’t want to look too hard), but if we could only get the same kind of apparent near-unanimity with regard to anthropogenic global warming, that would be great progress.

Written by stewart henderson

October 10, 2018 at 3:15 pm

## about ozone, its production and depletion

with one comment

People will remember the ‘hole in the ozone’ issue that came up in the eighties I think, and investigators found that it was all down to CFCs, which were quite quickly banned, and then everything was hunky dory….

Or that’s how I vaguely recall it. Time to take a much closer look.

I take my cue from ‘An ancient ozone catastrophe?’, chapter 4 of David Beerling’s The emerald planet, in which he looks at the evidence for a previous ozone disaster and its possible relation to the great Permian extinction of 252 millions years ago. I’ll probe into that matter in another post. In this post I’ll try to answer some more basic questions – what is ozone, where is the ozone layer and why does it have a hole in it?

Ozone is also known as trioxygen, which gives a handy clue to its structure. Oxygen can exist in different allotropes or molecular structures which are more or less stable. O3, ozone, is much less stable than O2 and has a very pungent chlorine-like odour and a pale blue colour. It’s present in minute quantities throughout the atmosphere but is most concentrated in the lower part of the stratosphere, 20 to 30 kilometres above the Earth’s surface. This region is called the ozone layer, or ozone shield, though it’s still not particularly dense with ozone, and that density varies geographically and seasonally. Ozone’s instability means that it doesn’t last long, and has to be replenished continually.

In 1928 chlorofluorocarbons (CFCs) were developed as a seemingly safe form of refrigerant, which, under patent as Freon, came to be used in air-conditioners, fridges, hair-sprays and a variety of other products. As it turned out, these CFCs aren’t so harmless when they reach the upper atmosphere, where the chlorine reacts with ozone to form chlorine monoxide (ClO), and regular O2. This reaction is activated by ultraviolet radiation, which then breaks up the unstable ClO, leaving the chlorine to react with more ozone in a continuing cycle.

By the eighties, it had become clear that something was going wrong with the ozone layer. Studies revealed that a gigantic hole in the layer had opened up over Antarctica, and without going into detail, CFCs were found to be largely responsible. There was the usual fight with vested business interests, but in 1987 the Montreal protocol against the use of ozone-depleting substances (ODS) was drawn up, a landmark agreement which has been successful in starting off the long and far from completed process of repair of the ozone shield.

As a very effective oxidant, ozone has many commercial applications, but the same oxidising property makes it a danger to plant and animal tissue. Much better for us to keep most of it up above the troposphere, where its ability to absorb UV radiation has made it virtually essential for maintaining healthy life on Earth’s surface.

So here are some questions. Why does ozone proliferate particularly at the top of the troposphere, in the lower stratosphere? If it’s so reactive, how does it maintain itself at a particular rate? Has the thinning or reduction of that layer seriously influenced life on Earth in the past? From my reading, mainly of Beerling, I think I can answer the first two questions. The third question, which Beerling explores in the above-mentioned chapter of his book, is more speculative, and more interesting.

Sidney Chapman, a brilliant geophysicist and mathematician of the early twentieth century, essentially answered the first question. He realised that ozone was both formed and destroyed by the action of sunlight, specifically UV radiation, on atmospheric oxygen. He calculated that this action would reduce and finally stop at a point approximately 15 km above sea level, because the reactions which had produced the ozone higher up had absorbed the UV radiation in the process. No activation energy to produce any more ozone. That explained the lower limit of ozone. The upper limit was explained by the lack of oxygen in the upper stratosphere to produce a stable layer – for production to exceed destruction. This was interesting confirmation of observations made earlier by the meteorologist and balloonist Léon-Phillippe Teisserenc de Bort, who noted that, contrary to his expectations, the air temperature didn’t fall gradually with altitude but reached a point of stabilisation where the air even seemed to become warmer. He named this upper layer of air the stratosphere, and the cooler more turbulent layer below he called the troposphere. It’s now known that this upper-air warming is caused by the absorption of UV radiation by ozone.

Our picture of ozone still had some holes in it, however, as it seemed there was a lot less of it around than the calculations of Chapman suggested. To quote from Beerling’s book:

… there had to be some as-yet unappreciated means by which ozone was being destroyed. The fundamental leap required to solve the problem was taken comparatively recently, in 1970, by a then young scientist called Paul Crutzen. Crutzen showed that, remarkably, the oxides of nitrogen, produced by soil microbes, catalysed the destruction of ozone many kilometres up in the stratosphere. Few people appreciate the marvellous fact that the cycling of nitrogen by the biosphere exerts an influence on the global ozone layer: life on Earth reaches out to the chemistry of the stratosphere.

Now to explain why the hole in the ozone shield occurred above the Antarctic. My understanding and explanation starts with reading Beerling and ends with this post from the USA’s National Oceanic and Atmospheric Administration’s Earth System Research Laboratory (NOAA/ESRL).

The ozone hole over Antarctica varies in size, and is largest in the months of winter and early spring. During these months, due to the large and mountainous land mass there, average minimum temperatures can reach as low as −90°C, which is on average 10°C lower than Arctic winter minimums (Arctic temperatures are generally more variable than in the Antarctic). When winter minimums fall below around −78°C at the poles, polar stratospheric clouds are formed, and this happens far more often in the Antarctic – for about five months in the year. Chemical reactions between halogen gases and these clouds produce the highly reactive gases chlorine monoxide (ClO) and bromine monoxide (BrO), which are destructive to ozone.

Most ozone is produced in the tropical stratosphere, in reactions driven by sunlight, but a slow movement of stratospheric air, known as the Brewer-Dobson circulation, transports it over time to the poles, so that ozone ends up being more sparse in the tropics. Interestingly, although most ozone-depleting substances – mainly halogen gases – are produced in the more humanly-populated northern hemisphere, complex tropospheric convection patterns distribute the gases more or less evenly throughout the lower atmosphere. Once in the stratosphere and distributed to the poles, the air carrying the halogen-gas products becomes isolated due to strong circumpolar winds, which are at their height during winter and early spring. This isolation preserves ozone depletion reactions for many weeks or months. The polar vortex at the Antarctic, being stronger than in the Arctic, is more effective in reducing the flow of ozone from tropical regions.

So – I’ve looked here briefly at what ozone is, where it is, and how it’s produced and destroyed, but I haven’t really touched on its importance for protecting life here on Earth. So that, and whether its depletion may have had catastrophic consequences 250 million years ago, will be the focus of my next post.

References

The Emerald Planet, by David Beerling, Oxford Landmark Science, 2009

https://www.esrl.noaa.gov/csd/assessments/ozone/2010/twentyquestions/Q10.pdf

https://en.wikipedia.org/wiki/Ozone

https://en.wikipedia.org/wiki/Brewer–Dobson_circulation

Written by stewart henderson

October 3, 2018 at 9:24 pm

## exploring oxygen

I’ve been reading David Beerling’s fascinating but demanding book The Emerald Planet, essentially a history of plants, and their contribution to our current life-sustaining atmosphere, and it has inspired me to get a handle on atmospheric oxygen in general and the properties of this rather important diatomic molecule. Demanding because, as always, basic science doesn’t come naturally to me so I have to explain it to myself in great detail to really pin it down, and then I forget. For example, I don’t have any understanding of oxidation right now, though I’ve read about it, and probably written about it, and more or less understood it, many times. Things fall apart, and then we fall apart…

Okay, let me pull myself together. Oxygen is a highly reactive gas, combining with other elements readily in a number of ways. A bushfire is an example of oxidation, in which free oxygen is ‘consumed’ rapidly, reacting with carbon in the dry wood to produce carbon dioxide, among other gases. This is also called combustion. Rust is a slower form of oxidation, in which iron reacts with oxygen to form iron oxide. So I think that’s basically what oxidation is, the trapping of ‘free’ oxygen into other gases or compounds, think carbon monoxide, sulphur dioxide, hydrogen peroxide, etc etc. Not to mention its reaction with hydrogen to form water, that stuff that makes up more than half our bodily mass.

Well, I’m wrong. Oxidation doesn’t have to involve oxygen at all. Which I think is criminally confusing. Yes, fire and rust are examples of oxidation reactions, but so is a reaction between hydrogen and fluorine gas to produce hydrofluoric acid (it’s actually a redox reaction – hydrogen is being oxidised and fluorine is being reduced). According to this presumably reliable definition, ‘oxidation is the loss of electrons during a reaction by a molecule, atom or ion’. Reduction is the opposite. The reason it’s called oxidation is historical – oxygen, the gas that Priestley and Lavoisier famously argued over, was the first gas known to engage in this sort of  behaviour. Basically, oxygen oxidises other elements, getting them to hand over their electrons – it’s an electron thief.

Oxygen has six valence electrons, so needs another two to feel ‘complete’. It’s diatomic in nature, existing around us as O2. I’m not sure how that works – if each individual atom wants two electrons, to make eight electrons in its outer shell for stability, why would it join with another oxygen to complete this outer shell, and then some? That makes for another four electrons. Are they now valence electrons? Apparently not, in this stable diatomic form. Here’s an expert’s attempt to explain this, from Quora

For oxygen to have a full outer shell it must have 8 electrons in it. But it only has 6 electrons in its valence shell. Each oxygen atom is actively seeking to get more electrons to complete its valence shell. If no other atoms except oxygen atoms are available, each oxygen atom will try to wrestle extra valence electrons from another oxygen atom. So if one oxygen atom merges with another, they “share” electrons, giving both a full outer shell and ultimately being virtually unreactive.

For a while this didn’t make sense to me, mathematically. Atomic oxygen has eight electrons around one nucleus. Six in the outer, ‘valence’ shell. Molecular oxygen has 16 electrons around two nuclei. What’s the configuration to make it stable? Presumably both nuclei still have 2 electrons configured in their first shells, that makes 12 electrons to make for a stable configuration, which doesn’t seem to work out. Did it have something to do with ‘sharing’? Are the shells configured now around both nuclei instead of separately around each nucleus? What was I missing here? Another expert on the same website writes this:

[The two oxygen atoms combine to] create dioxygen, a molecule (O2) in which both oxygen atoms have 8 valence electrons, so they are happy (the molecule is stable).

But what about the extra electrons? It seems I’d have to give up on understanding and take the experts’ word, and I hate that. However, the Khan academy has come to the rescue. In video 14 of his chemistry series, Khan explains that the two atoms share two pairs of electrons, so yes, sharing was the key.  So each atom can ‘kind of pretend’, in Khan’s words, that they have eight valence electrons. And this is a covalent bond, unlike an ionic bond which combines metals with non-metals, such as sodium and chloride.

Anyway, moving on. One of the most important features of oxygen, as mentioned, is its role in water – which is about 89% oxygen by weight. But how do these two elements – diatomic molecules as we find them in our environment – actually come together to form such a very different substance?

Well. According to this video, when H2 and O2, and presumably other molecules, are formed

electrons lose energy to form the new orbitals, the energy gets away as a photon, and then the new orbitals are stuck that way, they can’t undo themselves until the missing energy comes back.

This set me on my heels when I heard it, I’d never heard anything like it before, possibly because photon stuff tends to belong to physics rather than chemistry, though photosynthesis rather undoes that argument…

So, sticking with this video (from Brigham Young University Physics Department), to create water from H2 and O2 you need to give them back some of that lost energy, in the form of ‘activation energy’, e.g by ‘striking a match’. The video turns out to be kind of funny/scary, and it again involves photons. After the explosion, water vapour was found condensing on the inside of the glass through which hydrogen was pumped and ignited…

Certainly the demonstration was memorable (and there are a few of these explosive vids online), but I think I need more theory. Hopefully I’ll get back to it, but it seems to have much to do with the strong covalent bonds that form, for example, molecular hydrogen. It requires a lot of energy to break them.

Once formed, water is very stable because the oxygen’s six valence electrons get two extras, one from each of the hydrogens, while the hydrogens get an extra electron each. The atoms are stuck together in a type of bonding called polar covalent. Oxygen is more electronegative than hydrogen, meaning it attracts electrons more strongly – the negative charge is polarised at the oxygen, giving that part of the molecule a partial negative charge, with a proportional positive charge at the hydrogens. I might explore the effects of this polarity in another post.

The percentage of oxygen in our atmosphere seems stable at 21% – that’s to say, it appears to be the same now as when I was born, but that’s not a lot of time, geologically. The issue of oxygen levels in our atmosphere over geological time is complex and contested, but the usual story is that something happened with the prokaryotic life forms that had evolved in the oceans billions of years ago, some kind of mutation which enabled a bacterial species to capture and harness solar energy. This green mutation, cyanobacteria, gave off gaseous oxygen as a waste product – a disaster for other life forms due to its highly reactive nature. The photosynthesising cyanobacteria, however, multiplied rapidly, oxygenising the ocean. Oxygen reacted with the ocean’s iron, creating layers of rust (iron oxide) on the ocean floor, later visible on land through tectonic forces over the eons. Gradually over time, other organisms evolved that were adapted to the new oxygen-rich atmosphere. It became an energy source, which in turn produced its own waste product, carbon dioxide. This created a near-perfect cycle, as cyanobacteria required CO2 as well as water and sunlight to produce oxygen (and sugar). Other photosynthesising water-based and land-based life forms, plants in particular, emerged. In fact, these life forms had harnessed cyanobacteria as chloroplasts, a process known as endosymbiosis.

I’ll end this bitsy post with the apparent fact, according to this Inverse article, that our oxygen levels are actually falling, and have been for near a million years, and that’s leaving aside the far greater effects due to human activity (fossil fuel burning consumes oxygen and releases CO2). Of course oxygen is very vastly more abundant in the atmosphere than CO2, and the change is minuscule on the overall scale of things (unlike the change we’re making to CO2 levels). It will make much more of a difference in the oceans however, where the lack of dissolved oxygen is creating dead zones. The article explains:

The primary contributor to these apocalyptic scenes is fertilizer runoff from agriculture, which causes algal blooms, providing a great feast for bacteria that consume oxygen. The abundance of these bacteria cause O2 levels to plummet, and if they go low enough, organisms that need it to survive swim away or die.

Just another of the threats to sea-life caused by humans.

Written by stewart henderson

September 16, 2018 at 4:20 pm

Posted in environment, science

Tagged with , ,

## an assortment of new technology palaver

I like the inset pic – very useful for the Chinese

Western Australia lithium mining boom

I’m hearing, better late than never, that lithium carbonate from Western Australia is in big demand. The state already provides most of the world’s lithium for all those batteries used to run smart devices, electric vehicles, and large-scale storage batteries such as South Australia’s Tesla-Neoen thingy at Jamestown (now 80% complete, apparently). Emissions legislation around the world will only add to the demand, with the French and British governments planning to ban the sale of petrol and diesel vehicles by 2040, following similar plans by India and Norway, and the major investments in EVs in China. Australia’s government, of course, is at the other end of the spectrum re EVs, but I’ve no doubt we’ll get there eventually (we’ll have to!). Tesla, Volvo, Nissan, Renault, Volkswagen and Mercedes are all pushing more EVs into the marketplace. So now’s the time, according to Money Boffins Inc, to buy shares in lithium and other battery minerals (I’ve never bought a share in my life). This lithium mining boom has been quite sudden and surprising to many pundits. In January of this year, only one WA mine was producing lithium, but by mid-2018 there will be eight, according to this article. The battery explosion, so to speak, is bringing increased demand for other minerals too, including cobalt, nickel, vanadium and graphite. Australia’s well-positioned to take advantage. Having said that, the amount of lithium we’re talking about is a tiny fraction of what WA exports in iron ore annually, but it’s already proving to be a big boost to the WA economy, and a big provider of jobs.

battery recycling

Of course all of this also poses a problem, as mentioned in my last post, and it’s a problem that the renewable energy sector should be at least ideologically driven to deal with: waste and recycling. Considering the increasing importance of battery technology in our world, and considering the many toxic components of modern batteries, such as nickel, lead acid, cadmium and mercury, it’s yet another disappointment that there’s no national recycling scheme for non-rechargeable batteries. Currently only lead acid batteries can be recycled, and the rest usually end up in landfill or are sent to be recycled overseas. So it’s been left to the industry to develop an Australian Battery Recycling Initiative (ABRI), which has an interesting website where you can learn about global recycling and many other things batterial – including, of course, how to recycle your batteries. Also, an organisation called Clean Up Australia has a useful battery recycling factsheet, which, for my own educational purposes I’m going to recycle here, at least partly. Battery types can be divided into primary, or single-use, and secondary, or rechargeable. The primary batteries generally use zinc and manganese in converting chemical to electrical energy. Rechargeable batteries use a variety of materials, including nickel cadmium, nickel metal hydride and of course lithium ion chemistry. Batteries in general are the most hazardous of waste materials, but there are also environmental impacts from battery production (mining mostly) and distribution (transport and packaging). As mentioned, Australian batteries are sent overseas for recycling – ABRI and other groups are trying to set up local recycling facilities. Currently a whopping 97% of these totally recyclable battery units end up in landfill, and – another depressing factoid – Australia’s e-waste is growing at 3 times the rate of general household waste. So the public is advised to use rechargeable batteries wherever possible, and to take their spent batteries to a proper recycling service (a list is given on the fact sheet). The ABRI website provides a more comprehensive list of drop-of services.

2015 registrations: Australia’s bar would be barely visible on this chart

EVs in Australia – a very long way to go

I recently gave a very brief overview of the depressing electric vehicle situation in Australia. Thinking of buying one? Good luck with that. However, almost all motorists are much richer than I am, so there’s hope for them. They’re Australia’s early adopters of course, so they need all the encouragement we can give them. Journalist Timna Jacks has written an article for the Sydney Morning Herald recently, trying to explain why electric vehicles have hit a dead end in Australia. High import duties, a luxury car tax and a lack of subsidies and infrastructure for electric vehicles aren’t exactly helping the situation. The world’s most popular electric car, the Nissan Leaf, is much more expensive here than in Europe or the US. And so on. So it’s hardly surprising that only 0.1% of all cars sold in Australia in 2015 were electric cars (compared with 23% and rising in EV heaven, aka Norway, 1.4% in France and 0.7% in the US). Of course Australia’s landscape’s more or less the opposite of compact, dense and highly urbanised Europe, and range anxiety might be a perennial excuse here. We have such a long way to go. I expect we’ll have to wait until shame at being the world’s laughing-stock is enough of a motivation.

I’ve been vaguely aware of Adelaide’s ‘green bus’ for some years but, mea culpa, haven’t informed myself in any depth up until now. The bus is called Tindo, which is a Kaurna aboriginal word meaning the sun. Apparently it’s the world’s first and only completely solar powered electric bus, which is quite amazing. The bus has no solar panels itself, but is charged from the solar panels at the Franklin Street bus station in the city centre. It’s been running for over four years now and I’m planning to take a trip on it in the very near future. I was going to say that it’ll be the first time I’ve been on a completely electric vehicle with no internal combustion engine but I was forgetting that I take tram trips almost every day. Silly me. Still, to take a trip on a bus with no noisy engine and no exhaust fumes will be a bit of a thrill for me. Presumably there will be no gear system either, and of course it’ll have regenerative braking – I’m still getting my head around this stuff – so the ride will be much less jerky than usual.

So here are some of the ‘specs’ I’ve learned about Tindo. It has a range of over 200 kilometres (and presumably this is assisted by the fact that its route is fixed and totally urban, so the regen braking system will be charging it up regularly). It uses 11 Swiss-made Zebra battery modules which are based on sodium nickel chloride, a type of molten salt technology. They have higher energy density, they’re lightweight and virtually maintenance free. According to the City of Adelaide website the solar PV system on the roof of the bus station is (or was – the website is annoyingly undated) ‘Adelaide’s largest grid-connected system, generating almost 70,000 kWh of electricity a year’. No connection to the ‘carbon-intensive South Australian electricity grid’ is another plus, though to be fair our grid is far less carbon intensive than Victoria’s which is almost all brown coal. South Australia’s grid runs on around half gas and half renewables, mostly wind. The regen braking, I must remind myself, means that when decelerating the bus uses no energy at all, and the motor electronically converts into an electrical generator, which generates electricity with the continued forward motion of the bus. There are many more specs and other bits of info on this Tindo factsheet.

Written by stewart henderson

November 6, 2017 at 9:30 pm

## electric vehicles in Australia, a sad indictment

Toyota Prius

I must say, as a lay person with very little previous understanding of how batteries, photovoltaics or even electricity works, I’m finding the ‘Fully Charged’ and other online videos quite addictive, if incomprehensible in parts, though one thing that’s easy enough to comprehend is that transitional, disruptive technologies that dispense with fossil fuels are being taken up worldwide at an accelerating rate, and that Australia is falling way behind in this, especially at a governmental level, with South Australia being something of an exception. Of course the variation everywhere is enormous – for example, currently, 42% of all new cars sold today in Norway are fully electric – not just hybrids. This compares to about 2% in Britain, according to Fully Charged, and I’d suspect that the percentage is even lower in Oz.

There’s so much to find out about and write about in this field it’s hard to know where to start, so I’m going to limit myself in this post to electric cars and the situation in Australia.

First, as very much a lower middle class individual I want to know about cost, both upfront and ongoing. Now as you may be aware, Australia has basically given up on making its own cars, but we do have some imports worth considering, though we don’t get subsidies for buying them as they do in many other countries, nor do we have that much in the way of supportive infrastructure. Cars range in price from the Tesla Model X SUV, starting from $165,000 (forget it, I hate SUVs anyway), down to the Toyota Prius C and the Honda Jazz, both hybrids, starting at around$23,000. There’s also a ludicrously expensive BMW plug-in hybrid available, as well as the Nissan Leaf, the biggest selling electric car worldwide by a massive margin according to Fully Charged, but probably permanently outside of my price range at \$51,000 or so.

I could only afford a bottom of the range hybrid vehicle, so how do hybrids work, and can you run your hybrid mostly on electricity? It seems that for this I would want a (more expensive) plug-in hybrid, as this passage from the Union of Concerned Scientists (USA) points out:

The most advanced hybrids have larger batteries and can recharge their batteries from an outlet, allowing them to drive extended distances on electricity before switching to [petrol] or diesel. Known as “plug-in hybrids,” these cars can offer much-improved environmental performance and increased fuel savings by substituting grid electricity for [petrol].

I could go on about the plug-ins but there’s not much point because there aren’t any available here within my price range. Really, only the Prius, the Honda Jazz and a Toyota Camry Hybrid (just discovered) are possibilities for me. Looking at reviews of the Prius, I find a number of people think it’s ugly but I don’t see it, and I’ve always considered myself a person of taste and discernment, like everyone else. They do tend to agree that it’s very fuel efficient, though lacking in oomph. Fuck oomph, I say. I’m the sort who drives cars reluctantly, and prefers a nice gentle cycle around the suburbs. Extremely fuel efficient, breezy and cheap. I’m indifferent to racing cars and all that shite.

Nissan Leaf

I note that the Prius  has regenerative braking – what the Fully Charged folks call ‘regen’. In fact this is a feature of all EVs and hybrids. I have no idea wtf it is, so I’ll explore it here. The Union of Concerned Scientists again:

Regenerative braking converts some of the energy lost during braking into usable electricity, stored in the batteries.

Regenerative braking” is another fuel-saving feature. Conventional cars rely entirely on friction brakes to slow down, dissipating the vehicle’s kinetic energy as heat. Regenerative braking allows some of that energy to be captured, turned into electricity, and stored in the batteries. This stored electricity can later be used to run the motor and accelerate the vehicle.

Of course, this doesn’t tell us how the energy is captured and stored, but more of that later. Regenerative braking doesn’t bring the car to a stop by itself, or lock the wheels, so it must be used in conjunction with frictional braking.  This requires drivers to be aware of both braking systems and how they’re combined – sometimes problematic in certain scenarios.

The V useful site How Stuff Works has a full-on post on regen, which I’ll inadequately summarise here. Regen (in cars) is actually celebrating its fiftieth birthday this year, having been first introduced in the Amitron, a car produced by American Motors in 1967. It never went into full-scale production. In conventional braking, the brake pads apply pressure to the brake rotors to the slow the vehicle down. That expends a lot of energy (imagine a large vehicle moving at high speed), not only between the pads and the rotor, but between the wheels and the road. However, regen is a different system altogether. When you hit the brake pedal of an EV (with hand or foot), this system puts the electric motor into reverse, slowing the wheels. By running backwards the motor acts somehow as a generator of electricity, which is then fed into the EV batteries. Here’s how HSW puts it:

One of the more interesting properties of an electric motor is that, when it’s run in one direction, it converts electrical energy into mechanical energy that can be used to perform work (such as turning the wheels of a car), but when the motor is run in the opposite direction, a properly designed motor becomes an electric generator, converting mechanical energy into electrical energy.

I still don’t get it. Anyway, apparently this type of braking system works best in city conditions where you’re stopping and going all the time. The whole system requires complex electronic circuitry which decides when to switch to reverse, and which of the two braking systems to use at any particular time. The best system does this automatically. In a review of a Smart Electric Drive car (I don’t know what that means – is ‘Smart’ a brand name? – is an electric drive different from an electric car??) on Fully Charged, the test driver described its radar-based regen, which connects with the GPS to anticipate, say, a long downhill part of the journey, and in consequence to adjust the regen for maximum efficiency. Ultimately, all this will be handled effectively in fully autonomous vehicles. Can’t wait to borrow one!

Smart Electric Drive, a cute two-seater

I’m still learning all this geeky stuff – never thought I’d be spending an arvo watching cars being test driven and  reviewed.  But these are EVs – don’t I sound the expert – and so the new technologies and their implications for the environment and our future make them much more interesting than the noise and gas-guzzling stink and the macho idiocy I’ve always associated with the infernal combustion engine.

What I have learned, apart from the importance of battery size (in kwh), people’s obsession with range and charge speed, and a little about charging devices, is that there’s real movement in Europe and Britain towards EVs, not to mention storage technology and microgrids and other clean energy developments, which makes me all the more frustrated to live in a country, so naturally endowed to take advantage of clean energy, whose federal government is asleep at the wheel on these matters, when it’s not being defensively scornful about all things renewable. Hopefully I’ll be able to report on positive local initiatives in this area in future, in spite of government inertia.

Written by stewart henderson

August 15, 2017 at 9:51 am