an autodidact meets a dilettante…

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

Archive for the ‘science’ Category

The bonobo world: an outlier, but also a possibility: part 1

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To say that culture is an important part of our lives doesn’t do the word justice. Culture is not a part of our life. We are a part of it.

Carl Zimmer, She has her mother’s laugh.

bonobos refusing to physically distance at San Diego zoo – what are they planning?

I plan to turn the following into a book.

I think it was 1984, some 36 years ago now, that I first heard about bonobos on an episode of The Science Show, still running on Australia’s ABC Radio National. I was living in just another share-house amongst students, student-types, misfits like myself. It had been my life for several years. I wasn’t a student myself, in the formal sense. I was a sometime kitchen-hand with a patchy history of work in factories, offices, restaurants, and, briefly, a hospital. My favourite activity, my daily need in fact, was to write. In those pre-computer days I filled up foolscap journals with crabbed writing in blue ink. I wrote about the things I read, the people I met, imitations of favourite writers, and, too often, elusive, admirable, mysterious and ever-unattainable women. I still have those journals, mouldering in old boxes, covering 15 years or so before I bought my first computer.

I was ever a hopeless case when it came to the opposite sex. It wasn’t quite that they all hated or were indifferent to me. I sometimes made female friends but they were never the ones I was attracted to. In fact I rarely made friends, and my obsession with writing didn’t help. As one of my housemates once bluntly told me ‘you’re always living alone no matter how many people you’re sharing with.’

So I wrote about my failures with women and congratulated myself on my literary abilities. I was of course my own worst enemy vis-a-vis the opposite sex. Whenever a woman I was interested in showed signs of repaying that interest, I ran the other way, figuratively and sometimes even literally. There were all sorts of excuses, even some good ones. I was perennially penniless, I had a chronic chest or airways condition that meant my voice would get caught in the ‘wet webs’ as I called them, and which made me naturally anxious about my breath, and there were other problems I’d rather not go into. In fact I was intensely shy and self-conscious, but good at putting on an air of intellectual disinterestedness. This had generally disastrous consequences, as when I encountered a female ex-housemate and told her that now our share-house was all-male. ‘Oh yes, that would suit you down to the ground,’ she said with some disdain. I was mortified.

In fact I was obsessed to what I felt was an unhealthy degree with women and sex. My fantasies went back to childhood, or adolescence, when I imagined doing it with every attractive girl within my purview. Now I assume this was relatively normal, but I’m still not sure. But my thoughts on sexuality and gender went further. I recall – and all memories are unreliable, as they share most of the same neural processes as our imaginations – standing during assembly in a line with my classmates, looking up and down the line, assessing their attractiveness and overall likeability. It occurred to me that the most ‘interesting’ boys were girlish and the most interesting girls were boyish. I remember being struck by the thought and how smart I was to think it. I returned to this thought again and again.

Before I ever had a girlfriend (and I had few) I imagined an ideal, embodied by one of the pretty ones around me, with another brain inserted, more or less like my own. Someone funny, thought-provoking, inspiring, freewheeling, exhaustingly fascinating – and yes, I really did think of myself that way! And yet – I did worry that I might not be able to hold onto such a scintillating prize. And that set me thinking – such an extraordinary girl couldn’t be mine, or anyone’s. She would own herself. To maintain her interest in me, I’d have to be constantly proving myself worthy, which might be a thrilling challenge, but then – a change is as good as a haircut. What if I had to share her? My adolescent answer was – so be it. The key, if I found her so valuable, so inspiring, would be not to lose her. Not to be cut off from her. To prove myself so valuable that she wouldn’t want to lose me either, while seeking out others.

I won’t pretend that they were so clear-cut, but these were certainly the sorts of ideas swirling around in my head when I thought about love, desire and relationships as a youngster, and they hadn’t changed much – perhaps due to little actual experience – when I listened to the scientist extolling the virtues of our bonobo cousins many years later. I still remember the warm tones of his signing off – ‘Long live bonobos – I want to be one!’

Since then, my thoughts, my reading and my writings have taken a more scientific and historical turn, perhaps as something of an escape from the tribulations and disappointments of the self, and the bonobo world has always been a touchstone. Of course I don’t want to be a bonobo, anymore than the researcher-reporter on the Science Show really would’ve happily exchanged his amazing human brain for that of a rather less intelligent mammal eking out a threatened existence on the banks of the Congo River, but I have no doubt that we can learn from this remarkable species, and that it would be to our great benefit to do so.

Written by stewart henderson

July 13, 2020 at 12:07 pm

the male and female brain, revisited

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Culture does not make people. People make culture. If it is true that the full humanity of women is not our culture, then we can and must make it our culture.

Chimamanda Ngozi Adichie

An article, ‘Do women and men have different brains?’, from Mysteries of the human brain, in the New Scientist ‘Collection’ series, has persuaded me to return to this issue – or perhaps non-issue. It convincingly argues, to me, that it’s largely a non-issue, and largely due to the problem of framing.

The above-mentioned article doesn’t go much into the neurology that I described in my piece written nearly 7 years ago, but it raises points that I largely neglected. For example, in noting differences in the amygdalae, and between white and grey matter, I failed to significantly emphasise that these were averages. The differences among women in these and other statistics is greater than the differences between women and men. Perhaps more importantly, we need to question, in these studies, who the female and male subjects were. Were they randomly selected, and what does that mean? What lives did they lead? We know more now about the plasticity of the brain, and it’s likely that our neurological activity and wiring has much more to do with our focus, and what we’ve been taught or encouraged to focus on from our earliest years, than our gender. 

And this takes me back to framing. Studies designed to ‘seek out’ differences between male and female brains are in an important sense compromised from the start, as they tend to rule out the differences among men and among women due to a host of other variables. They also lead researchers to make too much of what might be quite minor statistical differences. To quote from the New Scientist article, written by Gina Rippon, author of the somewhat controversial book The gendered brain:

Revisiting the evidence suggests that women and men are more similar than they are different. In 2015, a review of more than 20,000 studies into behavioural differences, comprising data from over 12 million people, found that, overall, the differences between men and women on a wide range of characteristics such as impulsivity, cooperativeness and emotionality were vanishingly small.

What all the research seems more and more to be pointing to is that there’s no such thing as a male or a female brain, and that our brains are much more what we make of them than previously thought. Stereotyping, as the article points out, has led to ‘stereotype threat’ – the fact that we tend to conform to stereotypes if that’s what’s expected of us. And all this fuels my long-standing annoyance at the stereotyped advertising and sales directed at each gender, but especially girls and women, which, as some feminists have pointed out, has paradoxically become more crass and extreme since the advent of second-wave feminism.

And yet – there are ways of looking at ‘natural’ differences between males and females that might be enlightening. That is, are there informative neurological differences between male and female rats? Male and female wolves? Are there any such differences between male and female bonobos, and male and female chimps, that can inform us about why our two closest living relatives are so socially and behaviourally different from each other? These sorts of studies might help to isolate ‘real’, biological differences in the brains of male and female humans, as distinct from differences due to social and cultural stereotyping and reinforcement. Then again, biology is surely not destiny these days. 

Not destiny, but not entirely to be discounted. In the same New Scientist collection there’s another article, ‘The real baby brain’, which looks at a so-called condition known as ‘mummy brain’ or ‘baby brain’, a supposed mild cognitive impairment due to pregnancy. I know of at least one woman who’s sure this is real (I don’t know many people), but up until recently it has been little more than an untested meme. There is, apparently, a slight, temporary shrinkage in the brain of a woman during pregnancy, but this hasn’t been found to correlate with any behavioural changes, and some think it has to do with streamlining. In fact, as one researcher, Craig Kinsley, explained, his skepticism about the claim was raised in watching his partner handling the many new tasks of motherhood with great efficiency while still maintaining a working life. So Kinsley and his team looked at rat behaviour to see what they could find:

In his years of studying the neurobiology underlying social behaviours in rats, his animals had never shown any evidence of baby brain. Quite the opposite, actually. Although rats in the final phase of their pregnancy show a slight dip in spacial ability, after their pups are born they surpass non-mothers at remembering the location of food in complex mazes. Mother rats are also much faster at catching prey. In one study in Kinsley’s lab the non-mothers took nearly 270 seconds on average to hunt down a cricket hidden in an enclosure, whereas the mothers took just over 50 seconds.

It’s true that human mothers don’t have to negotiate physical mazes or find tasty crickets (rat mothers, unlike humans, are solely responsible for raising offspring), but it’s also clear that they, like all mammalian mothers, have to be more alert than usual to any signs and dangers when they have someone very precious and fragile to nurture and attend to. In rats, this shows up in neurological and hormonal changes – lower levels of stress hormones in the blood, and less activity in brain regions such as the amygdalae, which regulate fear and anxiety. Other hormones, such as oestradiol and oxytocin, soar to multiple times more than normal levels, priming rapid responses to sensory stimuli from offspring. Many more connections between neurons are forged in late pregnancy and its immediate aftermath.

Okay, but we’re not rats – nothing like. But how about monkeys? Owl monkeys, like most humans, share the responsibilities of child-rearing, but research has found that mothers are better at finding and gaining access to stores of food than non-mothers. Different behaviours will be reflected in different neural connections.

So, while it’s certainly worth exploring how the female brain functions during an experience unique to females, most of the time women and men engage in the same activities – working, playing, studying, socialising and so forth. Our brain processes will reflect the particular patterns of our lives, often determined at an early age, as the famous Dunedin longitudinal study has shown. Gender, and how gender is treated in the culture in which we’re embedded, is just one of many factors that will affect those processes.

References

New Scientist – The Collection, Mysteries of the human brain, 2019

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

https://ussromantics.com/2013/10/06/what-do-we-currently-know-about-the-differences-between-male-and-female-brains-in-humans/

Written by stewart henderson

June 25, 2020 at 10:50 pm

reading matters 2

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The beginning of infinity by David Deutsch (quantum physicist and philosopher, as nerdy as he looks)

Content hints

  • science as explanations with most reach, conjecture as origin of knowledge, fallibilism, the solubility of problems, the open-endedness of explanation, inspiration is human but perspiration can be automated, all explanations give birth to new problems, emergent phenomena provide clues about other emergent phenomena, the jump to universality as systems converge and cross-fertilise, AI and the essential problem of creativity, don’t be afraid of infinity and the unlimited growth of knowledge, optimism is the needful option, better Athens than Sparta any day, there is a multiverse, the Copenhagen interpretation and positivism as bad philosophy, political institutions need to create new options, maybe beauty really is objective, static societies use anti-rational memes (e.g gods) while dynamic societies develop richer, critically valuable ones, creativity has enabled us to transcend biological evolution and to attain new estates of knowledge, Jacob Bronowski The Ascent of Man and Karl Popper as inspirations, the beginning….

Written by stewart henderson

June 18, 2020 at 11:46 pm

the male violence thing: why deny it?

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I’ve written a few pieces on women, power and such things, from a position of frustration that there haven’t been enough women in power, and that women, and men, have suffered too much from male abuses of power – and that of course includes violence. At the beginning of last year I attended a vigil of sorts on the steps of our state parliament, which involved a solemn roll call of all the women who died violently in Australia (not including those who died in vehicle accidents, of which more later), and the sad circumstances of their passing. I noted that not all the women were victims of male violence – only 90-95% from memory – but clearly male violence was the principal problem. I was also aware, from research, that most victims of male violence are other males.

Around 95% of all victims of violence, whether women or men, experience that violence from a male perpetrator.

White Ribbon Australia, citing the Australian Bureau of Statistics

So I was a bit disconcerted when, some time ago, I brought up the obvious issue of male violence, in the context of sport (as opposed to the relative lack of violence, on and off the field, or court etc, in female sports) and I received pushback, as the Yanks say, from someone who more less completely denied that there was any imbalance. In fact he appeared to argue that women were just as violent as men, in every way.

So, to be clear, this is a question of fact, not of opinion, and in order to be factual we need to define violence precisely. I’m defining it as an act which results in death or physical injury, to the self and/or others. This isn’t to deny that psychological or emotional violence exists, of course it does, but it’s virtually impossible to measure. Any conversation between two people could be seen as profoundly coercive by one, totally benign by the other, or anything between these extremes by observers. It’s very subjective. Nor am I denying that psychological violence can be totally life-destroying. It just isn’t measurable in any clear way, unlike physical violence. And it was physical violence that our conversation was about.

Reliable statistical data on this topic is available everywhere on the internet. It tells us a sad, but fairly obvious truth. Men are more violent than women in every country and in every culture on the planet, without exception. And men have been more violent than women in every age of which we have record, since the appearance of Homo sapiens some 300,000 years ago.

Looking at the matter historically, there’s a certain amount of controversy, due to the patchy evidence as to whether hunter-gatherers were more ‘prone to violence’ than humans in a more ‘civilised’ state. Certainly it’s true that after the establishment of expansionist states, war was more often than not a central component of politics, and war was carried out by men, generally young men from their late teens into their late twenties. This state of affairs was the norm for centuries, and one could reasonably argue that warfare as policy was only abandoned when weaponry became so devastating that it was too costly for each state to engage in it, though I think Enlightenment values, a more scientific understanding of universal human nature and the subsequent development of trans-national treaties and organisations have all played a role.

But even in hunter-gathering societies the pattern of male violence was set. The hunters were of course more or less exclusively male, and, with rewards going to the best hunters, fierce competition was bound to arise within hunter-gathering tribes. It’s quite likely that the most successful competitors would have high status, even chieftain status, within the group. And with the division into groups, or tribes, with their more or less self-appointed hunting territories, rivalry and competition between groups would have arisen, the precursors of later, more destructive forms of aggression. We see exactly this pattern, of course, in our closest living relatives, chimps – battles between males of different groups over territory and resources, and battles between males within groups over hierarchy and access to females.

It might be argued that the modern world is quite different. But there’s a pattern in modern society that needs to be accounted for, though it’s not exactly a modern pattern, even if it’s given a modern spin. Men – and boys -tend to join gangs. Of course, not all young men do this, but a substantial proportion do. Women tend not to do so, or not nearly to the same extent. I’m talking about street gangs, crime gangs, ethnic gangs, ‘football hooligan’ gangs, bikie gangs, neo-nazi gangs, white supremacist gangs etc. I even joined one myself as a teenager, and we roamed the streets looking for trouble but rarely managing to find it.

not my gang

What drives this behaviour amongst this section of the male population (from the mid-teens to the mid-twenties, roughly speaking)? Hormones appear to play a primary role, and it’s no coincidence that exactly the same aggressive, show-offy group behaviour is to be found in the young males of other complex, highly social mammals, including chimps, dolphins and elephants. I have mixed feelings for those who scoff at all comparisons between homo sapiens and other mammals, because of course science has taught us about our profoundly mammalian nature, while our development of scientific explanations and understandings is precisely what marks us off from other mammals, and provides us with the potential to transcend our mammalian nature. Biology doesn’t have to be destiny.

The preponderance of male violence in our society is a problem for which we need to find solutions. But first we need to admit that there’s a problem. Let me give one compelling statistic as proof. The major cause of violent death and injury in peaceful countries – those not engaged in internal or external warfare – are males between the ages of approximately 17 and 25 behind the wheel of a motor vehicle. On a per capita basis, males cause 1.5 to 2 times more vehicle accidents than females, regardless of country, and it’s entirely that 17-25 age group that causes the disparity. It’s of course no coincidence that this is the same age that young males join gangs or the military. It’s the hormonal age.

In presenting this brief account of male risk-taking, aggression and violence, I’m not pretending that females are passive victims of all this. Of course the picture is enormously complex (in humans and in other mammals). In the cyber-age, female teenage bullying has become a serious problem – and of course it was a problem in the schoolyard before that. People in general can be brutal and malicious to their neighbours in times of stress, but we’ve emerged from, or are trying to emerge from, a highly patriarchal culture in which being a physically tough male is still a source of respect – in my own schoolyard, everyone knew who the toughest kid was, the ‘best fighter’, not the ‘brainiest’.

So, to return to my conversation, which was about sport and violence, and the claim that men are no more violent on and around sporting arenas than women. It amazes me that, given all the evidence about male violence, someone would think that sporting arenas would be an exception to the well-attested facts about male violence, in comparison to that of women. The sport I follow most by far is soccer, and I’ve particularly enjoyed the rise in women’s soccer in the last few years. It’s of course fiercely competitive, full of rough and tumble, with plenty of pushing and shoving at corners and free kicks, but having watched a lot of female matches over the years, I’ve rarely seen an example of the face-to-face, ‘I’m tougher than you’ behaviour shown at the top of this post, which is very common in the male game. The image prompts more or less amusing comparisons with wildlife programs, with rival males competing to be the pack leader. Men are too often like that, but of course not all men, and with the broad societal changes that have occurred in recent decades and centuries, there’s no need for men to think and act like this today – though the profound inequality that persists still sanctions and rewards this behaviour in poorly resourced, embattled parts of the world.

Where I see most progress and feel most hopeful is, again, the enterprise of science. In reading, for example, Venki Ramakrishnan’s book The gene machine and Meredith Wadman’s The vaccine race, I find the mix of competition and collaboration in fields of research to be favourable to both genders (or should I say all genders these days), and its success will hopefully flow on to politics, sports and other aspects of life.

Written by stewart henderson

June 12, 2020 at 2:03 pm

gods, science and explanation

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If you think that it would be impossible to improve upon the Ten Commandments as a statement of morality, you really owe it to yourself to read some other scriptures. Once again, we need look no further than the Jains: Mahavira, the Jain patriarch, surpassed the morality of the Bible with a single sentence: ‘Do not injure, abuse, oppress, enslave, insult, torment, torture, or kill any creature or living being.’ Imagine how different our world might be if the Bible contained this as its central precept.

Sam Harris, Letter to a christian nation

Reading David Deutsch’s The beginning of infinity, together with a collection of Stephen Jay Gould’s essays, Dinosaur in a haystack, has reminded me of my critique of Gould’s bad NOMA argument, which I reread lately. So here’s a revisiting and a development of that critique.
Put very simply, Gould argued that religion was about moral and spiritual matters, and that science was about causes and effects in the natural world, and that these spheres of interest didn’t overlap, so co-existence was not only entirely possible but mutually beneficial.

In his argument, I noted, Gould generally avoided mentioning gods, or God. It seems to me now, that this is more of a problem than I thought at the time, because religions are all about gods. While I don’t want to be hard and fast about this, religions really don’t exist without gods. In that sense, you might call Buddhism a spiritual belief system or worldview or discipline, but it isn’t a religion. It doesn’t use gods to explain stuff. And Confucianism even less so. Certainly in earlier times, in a more god-besotted world, Buddhism and even Confucianism were associated with or could be easily assimilated with local deities in China, Korea and Japan, and the world of morality was generally associated with portents and god-induced ‘disasters’, but that was to be expected in a pre-scientific climate, which prevailed globally for most of human history.

This is the point. For century upon century, gods, their behaviour, powers and attitudes or natures, were the explanations for war, famine, disease and the everyday accidents that humans suffered from. Even as some medical and other knowledge developed, the will of the gods was always there as a background explanation for the otherwise inexplicable. And so it shouldn’t be surprising, in a world teeming with god-explanations, that the pioneers of more earthly, measurable and testable explanations for phenomena still clung to this background of god-explanations for so much of what they saw around them – the birds in the sky, the food that sprang from the ground or hung from the trees, the life-giving rain, the failed harvests, the floods, the plagues, the invasions and so on.

Nowadays, what we call science can provide better explanations in every area we can think of than do god-explanations, and this is a major blow to religion and its relevance in the modern world. I would describe it as a death-blow. Indeed gods aren’t just bad explanations, they’re not really explanations at all. Why gods, after all? What are they, and where do they come from? No coherent explanation can be offered for them. Of course the obvious answer is that they come from the human imagination, as is evidenced by the human qualities they display – the beauty of the love-goddess, the long-bearded father-god, the thunderous dyspepsia of the war-god and so forth – but such an explanation is anathema to religion, as it collapses the house of cards. So an attempt is made to divert attention from inquiring into the ineluctable mystery of the god’s existence – sometimes by making such inquiries a kind of sacrilegious abomination – and to focus more on the god’s commandments. This is a move made by many a staunch Catholic.

I’ve heard such people say that the ten commandments of the Old Testament are clearly the basis of all our laws and morality. I’d like to have a look at them, particularly in terms of explanation. As young children, we’re often given commands – do this, don’t do that – by our parents. These commands generally have an explanation supporting them, which we learn later. But the explanations are essential, and commands without effective explanations to support them are surely a form of tyranny – at least that’s how I see it.
So let’s have a look at these commandments, which are so essential to ‘western’ or ‘civilised’ morality, according to some. I’ve put them in my own words.

  • 1. I’m your god, you mustn’t have other gods before me.
    This has nothing whatever to do with morality as far as I can see. This god says elsewhere that he’s a jealous god, and this is further proof. Catholics gloss this commandment as a commandment against idolatry, but that’s highly problematic because it makes the enormous assumption that the god called God is not an idol. If he’s saying ‘I’m the true god, all the others are fake’, he needs to provide proof. He doesn’t – and presumably makes the arrogant claim that he doesn’t need to.
  • 2. You mustn’t take my name in vain.
    So what is this god’s name? God, apparently. It’s like a marketing ploy, as if MacDonalds got to change their name to Hamburger and could take action against anyone else who used the name. In reality the god now called God was an amalgam of Hittite and Armenian gods, forged into a monotheistic being by elites of the region somewhere around the 7th century BCE. The idea of the commandment is that you should speak his name respectfully. Why? Because he’s God. The only way to avoid a circular argument here is to provide proof of this god’s existence, which hasn’t been done and can’t be done. There’s no morality on display here.
  • 3. The sabbath day should be kept holy.
  • This is fairly arbitrary, the word coming from the Hebrew sabbat, meaning rest, and it’s based on God’s rest day, as he created the universe or multiverse or whatever in six days and rested on the Saturday, according to Judaic tradition, but Christians arbitrarily changed the day to Sunday. Of course no educated person today thinks the world, universe, or whatever, was created in a week, whatever you define a week as, by an ethereal being. Again, this could only have moral effect if you believe in this creation story and the god at the centre of it (and if you believe the god is egotistical enough to want to be eternally remembered and acknowledged in this way).
  • 4. Honour your parents.
  • As a heuristic, this makes sense, but it is not a given. Some parents kill their children, others do irreparable damage to them. The vast majority, of course, don’t. This is a matter of individual cases and analyses. The complexity of parent-child relations is dealt with most profoundly by Andrew Solomon in his great book Far from the tree. I would refer everyone to that book as a response to the fourth commandment.
  • 5. You mustn’t kill.
  • This again is too vague, as it doesn’t deal with self-defence and other exculpating circumstances. It’s also fairly commonplace, and common-sense. It’s easy to find supporting explanations. Nobody needed this commandment to create laws regarding murder and unlawful death.
  • 6. You mustn’t commit adultery.
  • A lot can be said here. At the time that these commandments first appeared, and for a long time afterwards, women and girls were treated as chattels and very often married off against their will, sometimes as children, to men twice or thrice their age. Considering such a context, and considering that contraception was essentially non-existent in those days, adultery was generally treated differently depending on wealth, social status and gender. There might have been an explanation for the law of adultery, but it probably had more to do with property and the status of offspring than morality per se.
  • 7. Don’t steal
  • The concept of private property would have emerged slowly, and would have been interdependent on other cultural developments in the move from horizontally to more vertically based cultural systems. Even so, it’s unlikely that a prohibition on stealing would’ve been novel when this commandment was formulated.
  • 8. Don’t lie
  • the telling of lies to advantage oneself and disadvantage others would have been a problem at least since effective languages developed, and we have little evidence as to how long ago that happened. We certainly know it was long before the 6th or 7th centuries BCE, so there’s nothing new here. Again, though, the commandment is too vague to be particularly effective.
  • 9. Don’t covet (lust after) your neighbour’s wife
  • These last two commandments are about thoughts, which makes them particularly ineffectual. They might be interpreted as advice, which would leave us with fewer commandments to criticise, but even as advice they seem like so much pissing into the wind. And of course the fact that wives and not husbands are singled out is an indication of the particularism of the patriarchal society this commandment addresses.
  • 10. Don’t covet (hanker after) your neighbour’s goods.
  • Again, hardly a profound or memorable commandment, and barely relevant to today’s society. If you’re impressed by your neighbour’s car, for example, you might ask her about it, check out its performance and decide to get something similar yourself. What’s the big deal?

I’ve spent too much time on this, but I simply wanted to point out that, while gods are what religion is all about, they are, or were, also used as explanations. That’s in fact what they were for. And a ‘commandment’ is simply an explanation once removed, because they represent the god’s will. The explanation, therefore, for bad tidings or bad karma or whatever, becomes failure to follow the will and the commandments of some particular god or other.

Nowadays we have better explanations, based on what we know of human psychology and neurophysiology, and of how we work together in societies, as the most socially constructed mammals on the planet. We also know much more about how the physical world works, which has resulted in technological developments of increasing reach and sophistication. The idea that knowing so much more about what we are has no relationship to what we should do – the moral sphere – has always struck me as preposterous. This old is-ought separation was key to Gould’s NOMA thesis. But it’s not only that science’s increasingly far-reaching accounts of ourselves and the universe we live in is essential to our decisions about what we should do. It’s also true that religion keeps trying to tell us what we are. And its account s just don’t stack up, from the broadest scientific perspective. It just fails comprehensively as an explanation.

Written by stewart henderson

March 20, 2020 at 2:58 pm

random thoughts on progress and culture

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random pic of one of the Andaman Islands, I think

 

I seem to have a mind geared toward progress. I look forward (as I’m just beginning to feel my age) towards electric vehicles increasing market share in the ‘backward’ land of Oz. I look forward to governments here throwing their weight behind renewables without the usual reservations. I look forward to the James Webb telescope finally being launched, learning more about exoplanets, and of course genomics, epigenetics, neurophysiology, human origins, and much more. I look forward to the collapse of the Kim monarchy in North Korea, the demise of the current batch of macho political thugs worldwide, and the continuing rise to power of women in politics, business, science and technology. I’ve read Pinker’s two big books on the virtues of progress and enlightenment, I’m reading David Deutsch’s book on the beginning of an infinity of knowledge and discovery and technological improvement, and I’m wishing I could live at least another hundred years to watch the two-steps-forward-one step-back dance into the future. 

And yet. 

I generally describe myself as a humanist, and I’m drawn to those expressing suspicion and a degree of disdain toward nationalism – but, why is that? Am I free to have those feelings, which have been more or less with me since childhood, or have they been imposed on me by experiences I didn’t choose to have? After all, I’m human but I’m thoroughly localised in time and space. I’m a product, of a particular culture, often described as the dominant culture, white (though my skin is light brown and variable as I tan easily), Anglo-Saxon (though being born in the north-east of Scotland I may have Pictish and/or Scandinavian forebears, and frankly I’m not interested in tracing my ancestry) and protestant (though I’m not religious in any sense). Clearly, if I was born in the same place but several hundred years earlier, I wouldn’t be banging on about progress. I wouldn’t have ended up in Australia and I would likely never have travelled more than a few miles from the town of Dundee, where I was born. Whatever occupation I had wouldn’t have differed greatly from that of my father or my son, if I had one. 

So much for time. Think of place. Had I been born in Australia a few hundred years ago, I would’ve been what Europeans call an Aborigine or an indigenous Australian – but I should get with the program, they’re called first nations people now, presumably because we now know that we’re all actually indigenous to the African continent. In any case, my world would’ve been unimaginably different. Or I might’ve been born to first nation parents, but in the fifties (that’s to say, on my actual birth date), in which case I would’ve experienced a mixture of Aboriginal and Western/European/White Australian culture. Again, an experience nigh impossible for me to imagine. How, in that case, would I think of nationalism, as someone linked to a ‘nation’ with an ancient, resilient culture, or complex of different cultures, but surrounded by an innovative, progressive, dominant culture that I would never quite belong to. Would I want to belong to it? Who can say – I’m mixing generalisations with particular experiences here, and it’s not making sense.   

So it’s perhaps better, or certainly easier, to take the self out of the picture and think of cultures in the way we think of species and sub-species. Some species have found a niche, in the depths of the oceans, say, which has allowed them to survive and even thrive in a basic sort of way for eons, pretty well unchanged. Others, like rats and pigeons, have adapted to a variety of conditions, allowing them to spread across the globe, in tandem with ever-urbanising homo sapiens. Do we value all these species equally? Do we value all human cultures equally? We’re generally encouraged to think positively about biodiversity and cultural diversity. Yet we know that by far the majority of species mothered by this planet are now extinct. Many cultures, too, have been obliterated, by war, climate change, absorption into more dominant cultures and so forth. Which brings me back to progress. There seems to be a tension between the drive to preserve and the drive to transcend. There appears to be room for both drives much of the time, but what if they clash?

I recently had cause to learn a little more about the Andaman Islanders, who have a distinct and clearly self-sustaining culture developed over millenia. They don’t want to be disturbed and they’ve largely been granted that wish. After all, our progressive culture has no great need of their small scraps of land and what, from our perspective, are their meagre resources. However, imagine that something was discovered, via the latest in sophisticated computer technology, not too far beneath the soil of those islands – some mineral with extraordinary properties, valuable beyond measure to the dominant society’s continued technological advancement, but the extraction of which would massively disrupt the everyday life and compromise the spiritual beliefs of the islanders?

Perhaps this is a far-fetched scenario – it’s highly unlikely that, with our multi-faceted ingenuity, we would need to rely on some particular item from a remote set of islands for our juggernaut progress. And yet – I’ve read, in Simon Winchester’s book Pacific – of the fate of the Marshall Islanders in the forties and fifties, as the USA chose to use their region as the site of scores of nuclear tests, causing widespread and more or less permanent radioactive contamination – the price of a particular kind of progress. As Wikipedia puts it:

The testing concluded in 1958. Over the years, just one of over 60 islands was cleaned by the US government, and the inhabitants are still waiting for the 2 billion dollars in compensation assessed by the Nuclear Claims Tribunal. Many of the islanders and their descendants still live in exile, as the islands remain contaminated with high levels of radiation

Mistakes were made…

The ‘new world’ (meaning new to Europeans) and its first nations cultures have paid a heavy price for largely European colonisation, domination and progress. My position, as a somewhat low-ranking beneficiary of the dominant culture, makes it hard to judge the costs and benefits of these developments. We will go forward, but we need to look back at what we’ve done, and to look around at what we’re doing now. Preservation and progress is an uneasy balancing act which we’ll probably never quite master, but we need to keep trying, for humanity’s sake.

References

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

S Winchester, Pacific: the ocean of the future, 2015

Written by stewart henderson

February 4, 2020 at 2:35 pm

A DNA dialogue 2: the double helix

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Canto: Ok we talked about base pairs at the end of dialogue 1. A (nucleo)base pair is, duh, a pairing of nucleobases. There are four types of base in DNA – adenine and thymine, which always pair together, and the other pairing, cytosine and guanine.

Jacinta: Please explain – what’s a nucleobase, what do they do, and why do they come in pairs?

Canto: Well, let’s see, how do we begin… DNA stands for deoxyribonucleic acid…

Jacinta: So it’s an acid. But bases are like the opposite of acids aren’t they? So how can an acid be constructed of its opposite?

Canto: Look, I can’t answer that right now – I haven’t a clue – but let’s keep investigating the structure and function, and the answers might come. So, you’ll know that there was a battle in the 1950s to elucidate the structure of DNA, and it was found to form a double helix two strands of – I don’t know what – connected to each other in a twisted sort of way by, I think, those base pairs connected by hydrogen bonds. Anyway, here’s a fairly typical explanation, from Nature Education, which we’ll try to make sense of:

The double helix describes the appearance of double-stranded DNA, which is composed of two linear strands that run opposite to each other, or anti-parallel, and twist together. Each DNA strand within the double helix is a long, linear molecule made of smaller units called nucleotides that form a chain. The chemical backbones of the double helix are made up of sugar and phosphate molecules that are connected by chemical bonds, known as sugar-phosphate backbones. The two helical strands are connected through interactions between pairs of nucleotides, also called base pairs. Two types of base pairing occur: nucleotide A pairs with T, and nucleotide C pairs with G.

Jacinta: So I think I have a problem with this description. I think I need a picture, fully labelled. So the two strands themselves are made up of nucleotides, and the connections between them are made up of bonded sugar and phosphate molecules? But the strands are connected, via sugar and phosphate, in particular ways – ‘through interactions’ – which only allow A to pair with T, and C to pair with G?.

Canto: I think that’s right. Maybe we can find a picture.

Jacinta: Ok, so we got it completely wrong. The backbone, of sugar-phosphate, is the outer, twisted strand, or two of them, like the vertical bars of a twisted ladder, or the toprails of a spiral staircase, and the base pairs are like the stairs themselves, made of two separate parts, the bases, bonded together by hydrogen…

Canto: Forget the description, the picture above is worth all our words. It also tells us that the DNA molecule is around 2 nanometres wide. That’s two billionths of a metre. And 3.4 nanometres long for a full twist of the double helix, I think.

Jacinta: Whateva. There’s also this claim that the two strands are ‘anti-parallel’. It looks to me as if they’re simply parallel, but twisted. What does this mean? Is it significant?

Canto: I don’t know – maybe we’ll find out next time. I’m already exhausted.

Jacinta: …….

Written by stewart henderson

January 16, 2020 at 5:13 pm

Posted in biochemistry, DNA, science

Tagged with , ,

thoughts on smoking, cancer and government

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a simple and provenly effective solution

Recently I was talking about unhealthy habits to my students – I teach academic English to NESB students – and smoking came up. A student from Saudi Arabia piped up: ‘smoking isn’t unhealthy’.
Now, considering that this same student, a married man aged around thirty, had previously told me that, in ancient times, humans lived to be over 900 years old – ‘it says so in the Bible’ – I wasn’t entirely surprised, and didn’t waste too much time in arguing the point. Actually, I think now he probably mentioned the Bible to show or suggest that Moslems and Judeo-Christians might agree on some things!

Of course, this student was a smoker. Many of my male students are. These students are predominantly Chinese, Vietnamese and Arabic speakers, that’s to say from countries whose governments have acted less forcefully in dealing with smoking than has the Australian government. I myself smoked. albeit lightly, until the age of 24 (a long time ago). Now, having been diagnosed with bronchiectasis, I’m extremely intolerant of cigarette smoke, not to say smokers.

I’m currently ploughing though Siddhartha Mukherjee’s classic Emperor of All Maladies, and have just finished the section on smoking and cancer, and the battle with tobacco companies in libertarianism’s heartland, the USA. 

Cigarette smoke contains a number of carcinogens – but what is a carcinogen? It’s basically a product or agent that has a reasonable likelihood of causing cancer, which doesn’t of course mean that it will cause cancer in every instance. You can play Russian roulette with the 60 or more well-established carcinogens in cigarette smoke, and risk-taking young men in particular will continue to do so, but it’s a massive risk, and the dangers increase with age and length and frequency of use. Lung cancer is the most regularly cited outcome, but as the US surgeon-general’s 2010 report shows in vast detail, cancers of the larynx, oral cavity, pharynx, oesophagus, pancreas, bladder, kidney, cervix, stomach and liver can all be induced by this inhaled chemical cocktail. And cancer isn’t the only issue. There is the problem of nicotine addiction, as well as cardiovascular and pulmonary disease, and fertility and foetal developmental effects. 

With all this evidence, why do people still smoke, and why don’t governments step in? Drugs with far less devastating effects are illegal, so what gives?

Of course the role governments should play in determining or influencing public health has always been debated, as has the efficacy of banning particular substances and practices. The situation isn’t helped by the facts on the ground, an ad hoc regime in which relatively harmless substances such as marihuana are banned almost worldwide, while proven carcinogens like tobacco, costing millions in treatment, are merely ‘discouraged’ to varying degrees. Similarly, in some countries you have ‘cults’ like falun gong being treated as highly dangerous and criminal while more mainstream ‘cults’ such as christianity, no less or more nonsensical, being given a free ride. None of which promotes faith in government decision-making regarding our physical or psychological health.
Even so, I believe governments should play a role. We pay taxes to government so that it can organise our particular state more effectively for all of its citizens – and that means subsidising education, health and general welfare, to reduce inequalities of opportunity and outcome. Democratic government and an open society helps to reduce government ineptitude, ignorance and corruption. The science and technology sector in particular – a proudly elitist institution – should play a more significant role in government decision-making. But a real weakness of capitalist democracy is that political leaders are too often swayed by business leaders, and the money and influence they bring to the table, than by knowledge leaders. This obeisance paid to business success, with insufficient regard paid to scientific evidence, is possibly the greatest failing of modern political society.

Written by stewart henderson

January 5, 2020 at 10:47 am

How did we get language?

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a most persuasive hypothesis

                                          a most persuasive hypothesis

According to National Geographic there are, or were, at least 7000 languages globally. That was a few years ago and they say the numbers are dwindling, so who knows. There may also be a lumpers v splitters issue here – are they all unique languages or are some just variants of the same language?
There are organisations out there dedicated to preserving rare and endangered languages via recordings and analyses, but is this such a vital project? After all, when a language dies out it’s not because their speakers have gone dumb, it’s because they’ve died and their offspring are speaking one of the more common, viable languages of their region. And this of course raises the question of whether language diversity is a good in itself, in the way that species diversity is seen to be, or whether we’d be better off speaking fewer languages globally. It’s actually quite a dangerous topic, since language is very much a cultural artefact, and cultural suppression, often of the most brutal kind, is currently going on in various benighted parts of the world.

The diversity of language also raises another fascinating question – did it evolve once or many times? Was there an ‘ur-language’ or proto-language from which all these diverse languages sprung? Take for example, the Australian Aboriginal languages. Anthropologists claim that there were some 250 of them around when Europeans arrived with their much smaller number of languages. And Aborigines arrived here about 50,000 years ago. But how many, and with how many different languages? These are perhaps the unanswerable questions that Milan Kundera liked so much. However, linguists have been studying surviving Aboriginal languages intensively for some time, and are mostly agreed that they can be ‘lumped together’ in a small number of dispersed family groups with distinctive features, which suggests that, on arrival, the number of languages was much smaller.

Added to this evidence (if you can call this evidence), is the recent understanding that our species, Homo sapiens, spread out from the African continent in separate waves, from 250,000 years ago to 70,000 years ago. So it seems to me more likely that there was a proto-language, developed in Africa and moving out with one of those waves, and taking over the world, through breeding or cultural exchange, and diversifying with those migrations and their growing cultural diversity. Then again, maybe not.

We used to to describe the world before the emergence of writing as ‘prehistoric’, which seems rather arrogant now, and the word has fallen out of favour. And yet, there is some sense in it. Writing (and drawing) always tells us a story. It provides a record. That’s its intention. It’s the beginning of the modern story, and so, history, in a sense. All of what comes before writing, in the story of humans, is unrecorded, accidental. Scraps of stuff that require a lot of interpretive work. That’s what makes the development of writing such a monumental breakthrough in human affairs. It happened in at least three separate places, only a few thousand years ago. Human language itself, of course has a much longer history. But how much longer? Eighty thousand years? A hundred thousand? Twice that long? Currently, we haven’t a clue. The origin of language is regarded by many authorities as one of the toughest problems in science. It isn’t just a question of when, but of how, where and why. Good luck with answering that lot.

Written by stewart henderson

December 17, 2019 at 11:37 pm

how statins work 3: the beginnings of cholesterol, from Acetyl-CoA

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Coenzyme A – an acetyl group attaches to the -SH shown in red

So how is cholesterol made in the body? We need to know this in order to understand how statins inhibit or interfere with this process.

I’ve shown the actual structure of cholesterol in part 1 of this series, but remember it’s a sterol, which is a steroid – four carbon rings with hydrogen atoms attached – in which one of the hydrogens is replaced by an alcohol group. The particular form of sterol called cholesterol, with a 7-carbon chain attached to the end-carbon ring (the D ring), and three methyl groups attached to specific carbons in the rings and chain (it’s better to look at the skeletal structure in part 1). There are precisely 27 carbon atoms specifically placed within the molecule.

I’m using a set of videos to understand how cholesterol is synthesised – it might be best to look at them yourself, but I’m writing it all down to improve my own understanding. So we start by understanding something about acids and their conjugate bases. Apparently an acid is a molecule which is capable of donating protons into solution. Take pyruvic acid and its conjugate base pyruvate. Here’s what Wikipedia says about them:

Pyruvic acid (CH3COCOOH) is the simplest of the alpha-keto acids, with a carboxylic acid and a ketone functional group. Pyruvate, the conjugate base, CH3COCOO, is a key intermediate in several metabolic pathways throughout the cell.

I don’t understand the first sentence, but no matter, pyruvic acid is a 3-carbon molecule with a carboxylic acid at one end and a ketone group in the middle of the molecule (according to Britannica, a ketone is ‘any of a class of organic compounds characterized by the presence of a carbonyl group in which the carbon atom is covalently bonded to an oxygen atom. The remaining two bonds are to other carbon atoms or hydrocarbon radicals)’. The proton that comes off the oxygen of the alcohol group of the pyruvic acid can be donated into the surrounding solution, increasing its acidity. The pyruvic acid is thus transformed into its negatively charged conjugate base (it’s no longer capable of donating protons but it can receive them). This is the case with all acids in the cytoplasm of cells. As inferred in the quote above, conjugate bases are vital components of biosynthetic pathways. Most of the molecules in the cytoplasm will exist as pyruvate at a physiological pH of around 7.5.

Next – and hopefully this will become clear eventually – we’re going to look at two molecules, NAD+ (nicotinamide adenine dinucleotide) and NADP+ (nicotinamide adenine dinucleotide phosphate). They transport electrons, and are capable of accepting a hydride anion, which is a hydrogen atom with a negative charge. The normal hydrogen atom, called protium, has a proton and an electron only. When it donates away its electron it becomes a hydrogen cation, and when it gains an electron it becomes a hydride anion.

NAD+ is an adenine organic base bound to a ribose sugar. Then there are two phosphate groups coming off the ribose sugar, the second of which attaches to another ribose sugar. This second ribose sugar has nicotinamide attached to it (see below),

in which the phosphate groups are magenta-coloured circles. To explain something about ribose sugars, here’s something from Pearson Education:

The 5-carbon sugars ribose and deoxyribose are important components of nucleotides, and are found in RNA and DNA, respectively. The sugars found in nucleic acids are pentose sugars; a pentose sugar has five carbon atoms. A combination of a base and a sugar is called a nucleoside. Ribose, found in RNA, is a “normal” sugar, with one oxygen atom attached to each carbon atom. Deoxyribose, found in DNA, is a modified sugar, lacking one oxygen atom (hence the name “deoxy”). This difference of one oxygen atom is important for the enzymes that recognize DNA and RNA, because it allows these two molecules to be easily distinguished inside organisms.

So, just for my own understanding, nucleotides include phosphate groups. NAD+ is a dinucleotide, with two nucleotides (ribose sugars with phosphate groups attached), attached to adenine and to nicotinamide molecules. Also, NAD+ has a positive charge around the nicotinamide – on its nitrogen atom.

NAD+ becomes neutralised by accepting a hydride anion (one proton and two electrons) and becomes NADH, or reduced NAD. Now, remembering NADP+, it has an extra phosphate group on the ribose sugar of the adenine nucleotide (also called an organic base, apparently). Like NAD+, NADP+ can accept a hydride anion (becoming reduced NADP) and then later exchange it in another reaction. Effectively these molecules are electron carriers, collecting electrons and transporting them to where they’re needed for other reactions.

Now to introduce something else completely new for me – Acetyl-CoA (acetyl coenzyme A). A quick grab again, this time from Wikipedia:

Acetyl-CoA is a molecule that participates in many biochemical reactions in protein, carbohydrate and lipid metabolism. Its main function is to deliver the acetyl group to the citric acid [Krebs] cycle to be oxidized for energy production

Acetyl-CoA is found, and presumably produced, in mitochondria, and as part of this cholesterol-synthesising pathway it needs to be removed from the ‘mitochondrial matrix’. What’s that, I ask. So here’s a bit about the mitochondrial matrix, from yet another source, this time Study.com:

The mitochondrion consists of an outer membrane, an inner membrane, and a gel-like material called the matrix. This matrix is more viscous than the cell’s cytoplasm as it contains less water. The mitochondrial matrix has several functions.It is where the citric acid cycle takes place. This is an important step in cellular respiration, which produces energy molecules called ATP. It contains the mitochondrial DNA in a structure called a nucleoid. A mitochondrion contains its own DNA and reproduces on its own schedule, apart from the host cell’s cell cycle. It contains ribosomes that produce proteins used by the mitochondrion. It contains granules of ions that appear to be involved in the ionic balance of the mitochondrion.

So basically this matrix is like (or equivalent to) the cell’s cytoplasm, only more viscous, and contains ribosomes, one or more nucleoids and ionic granules, inter alia.

Acetyl-CoA is essential to the biosynthesis of cholesterol, and is found initially in the mitochondrial matrix, and we need to look at the pathway for its removal from that matrix into the cytoplasm, where all the action occurs.

Intruding into the mitochondrial matrix from the (quite impermeable) inner cell membrane are the cristae, which give the membrane more of a surface layer for interactions. This inner membrane is the site of oxidative phosphorylation. What’s that, I ask. Well, it’s key to the production of ATP, and at least I know that ATP is the ‘energy molecule’, and that it’s produced in mitochondria. Here’s something about the process from Khan Academy:

Oxidative phosphorylation is made up of two closely connected components: the electron transport chain and chemiosmosis. In the electron transport chain, electrons are passed from one molecule to another, and energy released in these electron transfers is used to form an electrochemical gradient. In chemiosmosis, the energy stored in the gradient is used to make ATP.

So a strong proton gradient is built up across the inner membrane of the mitochondrion. It’s a concentration gradient but also an ‘electrical potential difference’ gradient, so that the electrical potential within the matrix is lower, by some 160 millivolts, than that across the inter-membrane space. The protons within this space are unable to pass back into the matrix. The only way they can get back into the matrix is by means of ATP synthase which can harness the energy from the protons as they move down the chemical and electrical gradient, and use that energy to bind ADP to inorganic phosphate to create ATP.

I don’t fully understand all that, but the main point here is that the mitochondrial inner membrane is very ‘tight’, which makes it difficult to transfer Acetyl-CoA out of the matrix and into the inter-membrane space, from which it can more easily diffuse through the more permeable outer membrane into the cytoplasm.

The structure of Acetyl-CoA: it consists of an acetic acid molecule (CH3COOH) with a thioester link to the thiol group of a coenzyme A molecule. The importance for us here is this thiol (HS) group, which is similar structurally to an alcohol (HO) group, as sulphur has similar properties to its periodic table neighbour, oxygen. So thiol groups can be linked to carboxylic acid groups as alcohol groups can. Acetyl essentially means acetic acid with the alcohol removed. To get this Acetyl-CoA out of the matrix, it is first bound to oxaloacetate, a four-carbon molecule, to create citrate, the first molecule of the citric acid cycle. This citrate can be passed through the mitochondrial inner membrane and into the cytoplasm where it can be converted back into Acetyl-CoA.

So the conjugate base, oxaloacetate, has carboxylic acid groups, attached to the first and fourth carbon atoms, that have lost their protons into solution. An enzyme within the matrix is able to combine oxaloacetate with Acetyl-CoA and water to create citrate…

Okay, this is proving to be a much longer story than I might’ve hoped, but I like to be thorough – and in reality I’m still not being thorough enough. There’s a lot of rubbish on the internet about statins, much of it self-serving in one way or another, so I’ll just keep plodding along until I feel at least halfway informed about the matter. Meanwhile, you just keep getting on with your work, and don’t mind me.

References

Cholesterol biosynthesis part 1, by Ben1994, 2015

Cholesterol biosynthesis part 2, by Ben 1994, 2015

https://www.britannica.com/science/ketone

http://www.phschool.com/science/biology_place/biocoach/bioprop/ribose.html

https://en.wikipedia.org/wiki/Acetyl-CoA

https://study.com/academy/lesson/mitochondrial-matrix-definition-function-quiz.html

https://www.khanacademy.org/science/biology/cellular-respiration-and-fermentation/oxidative-phosphorylation/a/oxidative-phosphorylation-etc

Written by stewart henderson

October 14, 2019 at 5:26 pm