an autodidact meets a dilettante…

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

exploring spermatogenesis

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Canto: So If Charles Darwin was alive today, he’d be gobsmacked at the facts derived from the ‘random variation’ end of his theory of natural selection from random variation. I’m talking about genes, DNA, genetic recombination and all that we know about meiosis and mitosis, spermatogenesis and oogenesis, genomics and epigenetics, mitochondrial DNA, ribosomes, mRNA, proteins and the like, none of which I’m particularly knowledgeable about – but surely even what I know about it all would make Darwin’s head explode.

Jacinta: Yes, and of course Darwin did all his studies on phenotypes, a term he would never have heard. He studied pigeons, finches, barnacles, fossils and a wide variety of plants. But he was never able to ‘crack the code’ of random variation. Why did offspring differ from parents? Why did those offspring vary from the utterly dysfunctional to the super-functional? For a time he considered pangenesis, his coinage, as a solution. This involved ‘gemmules’ inherited from both parents, blended together and somehow modified by the environment, presumably in a Lamarckian way. So Darwin never quite cracked the code of inheritance as we understand it today, but the work with plants which occupied his last years – allowing him to avoid the acrimony around human origins surrounding the publication of On the origin of species – produced important results for the understanding of plant reproductive biology. Take this quote from the Smithsonian magazine:

Darwin designed highly rigorous experiments and made predictions—which turned out to be correct—using his theory of natural selection. For example, he predicted that the myriad floral adaptations he saw existed to ensure that flowers were outcrossed, or fertilized by individuals other than themselves. He then tested this hypothesis with over a decade of pollination experiments and found that self-pollination leads to lower fitness and higher sterility. Inbred plants, like inbred animals, don’t fare well, at least over time—a phenomenon that’s now known as inbreeding depression.

Canto: Right, but let’s not get bogged down in the history of reproductive biology and the birth of genetics here, as it’s hard enough for me to comprehend meiosis and mitosis, gametes and zygotes and all the rest, as we understand it all today. We’ve previously written about meiosis, but I want to understand, or to begin to understand, in this post, how the process of producing gametes is so different in male and female mammals.

Jacinta: Okay, so we’re talking about gametogenesis. The male gametes are called sperm, the female gametes are called eggs, and so have two forms of gametogenesis, spermatogenesis and oogenesis. In this post I’ll focus on the male, saving the best for another post. So sperm is formed in the testes…

Canto: The ballsacks?

Jacinta: Uhh, well, the sack is just the sack, also known as the scrotum. Inside, you’ll find a testicle, hopefully. And as you well know there are, ideally, two of them. That is, two sacks, each with its testicle. And a testicle is about as complex as any other piece of biological machinery – a lifetime’s learning worth. Take this illustration, courtesy of ken hub.com:

Note the seminiferous tubules above. That’s where the sperm is formed, first by the mitotic division of a spermatogonial stem cell…

Canto: Eh what? How did they get in there?

Jacinta: Okay let me try to understand this for myself, but I may get more and more bogged down. It all begins at the beginning, during the early stages of male foetal development. The primordial germ cells differentiate in the testis, in these seminiferous tubules… But let me first fast forward to the end of the process and describe a complete, mature sperm cell or spermatozoon. That’s an active, motile sperm – plural spermatozoa, or just plain sperm. It’s divided into three parts, essentially, the head, the midpiece and the tail. At the head we find the acrosome and the tightly packed nucleus. The midpiece contains the mitochondria. which provides energy for the sperm’s motility, and the tail is essentially the flagellum, the sperm’s outboard motor, so to speak.

Canto: Okay, so that’s the end product – get back to the spermatogonial stem cells and the seminiferous tubules.

Jacinta: Fine. Spermatogonia are undifferentiated male germ cells, or sperm cells. It’s hard to find a simplified, but not overly simplified, explanation of how pluripotent or totipotent stem cells become germ cells, or any other cells for that matter, but it begins in the embryo. A cell signalling process in the embryo induces a small, transient proportion of the cell mass, the primitive streak, to become primordial germ cells (PGCs), along with other cells. This process is called gastrulation, in which the embryo begins to differentiate into distinct cell lineages. For the PGCs, according to a paper cited in Wikipedia, ‘The specification of primordial germ cells in mammals is mainly attributed to the downstream functions of two signaling pathways; the BMP signaling pathway and the canonical Wnt/β-catenin pathway’. This is essentially about regulatory proteins, I think.

Canto: This is getting too complicated for me. How come that second pathway is canonical?

Jacinta: See, you are paying attention. That Wnt/beta-catenin pathway gets a lot of attention in scientific papers, because we know that its deregulation is a problem in serious diseases and cancers. Basically these pathways are essential for embryonic development. The terms ‘canonical’ and ‘noncanonical’ are terms of art used to describe the standard production of Wnt proteins for development or homeostasis, and less well-known, or later-discovered pathways. I think. Anyway, let’s get back to spermatogonia, of which there are three types – A dark, A pale and B. The A dark spermatogonia are the reserves, and they don’t generally go through the mitosis process – they remain dormant. The A pale cells (so called because they have pale nuclei compared to the A dark cells) undergo mitosis to become the type B cells, which grow and develop to become primary spermatocytes, a process called spermatocytogenesis, truly. All of this occurs, as mentioned, in the seminiferous tubules of the testes, and begins at puberty.

Canto: Okay so how do these primary spermatocytes differ from spermatozoa, or how do they become spermatozoa?

Jacinta: The primary spermatocytes are diploid cells, so they need to undergo meiosis to become gametes. After meiosis 1, two haploid cells are formed, called secondary spermatocytes. And of course, being diploid cells undergoing that first process of meiosis, there’s this crossing over or recombination that occurs, shuffling the deck so to speak. And this is followed by meiosis 2, replicating the haploid cells, and so forth. But you ask how the spermatozoa are formed as an end product, so I need to take us back to those tubules in the testes. They’re packed with particular cells called Sertoli cells, and just outside the tubules are Leydig cells, which produce testosterone. Anyway, once these sperm cells have developed further they travel up to the epididymis via the rete testis, where they continue to mature, ready for ejaculation. They reach the rete testis, and presumably also the epididymis, by means of peristalsis, which you’ll know about from the intestines and other parts of the body.

Canto: Sort of. You think you know about stuff until you find out what you don’t know, which is overwhelmingly vast. Mais, continue..

Jacinta: So the last transformations, making them those mobile little tadpole-like critters, occur in the epididymis. But returning to those tubules. There are lots of Sertoli cells in there, and the sperm is developed in the gaps between them, strangely enough, but they acquire nutrients from those cells to help them along. Their journey between the cells takes them from the outer membrane of the tubule to the lumen. At the beginning of this journey they’re called spermatogonia. They’re going to go through this differentiating process to finally become spermatozoa. Now I’ve already partially described the first step, when a spermatogonium divides by mitosis, into two cells, one of which is kept in reserve, the Ad or ‘dark’ cell. The Ap or ‘pale’ cells continue on the pathway between the Sertoli cells towards the lumen, somehow becoming B cells – don’t know how that happens, but it involves mitosis, perhaps with nutrients from the Sertoli cells. I think, because the process of mitosis is continuous, those reserve cells are left behind all along the pathway. Or maybe not. But that pathway is obstructed along the way by ‘tight junctions’ between the Sertoli cells, which create separate compartments as they open and close before and behind the sperm cells (which are now called primary spermatocytes) like locks in a canal. Now these compartments, called basal and lumenal compartments, aren’t empty, they’re full of chemicals, signalling proteins and such, a different mix for each compartment, which add to the spermatocyte’s development. So the sperm grows as it travels along this pathway, accumulating more cytoplasm. And the junctions close very tightly after the sperm moves through, to prevent leakage into the next chemical environment. Now, somewhere along this pathway between the Sertoli cells, the primary spermatocyte is ready to divide into two secondary spermatocytes via meiosis, a very different form of cell division from mitosis.

Canto: Yes, meiosis has those two parts, ending with four haploid cells from one diploid cell, and genetic recombination to make us all unique.

Jacinta; Okay, moving right along, so to speak, those four haploid cells are now called spermatids, and they continue to mature in the lumen. They’re still not motile, they’re rounded cells at first, but they go through lots of changes, to the conformation of the DNA, for example, with histone proteins being replaced by protamines. We’re now entering the final processes, known as spermiogenesis, which I think occurs after transportation to the epididymis. The cytoplasm is removed, the acrosomal cap is formed, and the other structures I mentioned at the outset, the mitochondrial spiral and the fibres that form the flagellum, all take shape. This whole process, from spermatogonia to spermatozoa, takes about 65 days.

Canto: Okay, that’s enough of all that, I don’t particularly want to learn about seminal fluids and ejaculation at this point, fascinating though that might be – I’m more interested in the female stuff, the generation of eggs, known as oogenesis.

Jacinta: So that for you to detail in a future post.

References

https://embryo.asu.edu/pages/charles-darwins-theory-pangenesis

https://www.smithsonianmag.com/science-nature/charles-darwin-botanist-orchid-flowers-validate-natural-selection-180971472/

https://sciencing.com/difference-female-mammals-male-mammals-8092368.html

Spermatogenesis | Reproductive system physiology | NCLEX-RN | Khan Academy (video)

https://en.wikipedia.org/wiki/Germline_development#Germ_line_development_in_mammals

https://www.biologyonline.com/dictionary/spermatid

Written by stewart henderson

June 28, 2022 at 3:21 pm

still bitten by the bonobo bug…

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Having written quite a few essays on a future bonoboesque world, I’ve found myself in possession of a whole book on our Pan paniscus relatives for the first time. All that I’ve gleaned about these fellow apes until now has been from the vasty depths of the internet, a gift that will doubtless keep on giving. My benefactor apologised for her gift to me, describing it as a coffee-table book, perhaps more pictorial than informative, but I’ve already learned much that’s new to me from the first few pages. For example, I knew from my basic research that bonobos were first identified as a distinct species in the late 1920s or early 1930s –  I could never get the date straight, perhaps because I’d read conflicting accounts. De Waal presents a more comprehensive and interesting story, which involves, among other things, an ape called Mafuka, the most popular resident, or inmate, of Amsterdam Zoo between 2011 and 2016, later identified as a bonobo. The zoo now features a statue of Mafuka.

More important, though, for me, is that everything I’ve read so far reminds me of the purpose of my bonobo essays, but also makes me wonder if I haven’t focussed enough on one central feature of bonobo society, probably out of timidity. Here’s how De Waal puts it:

It is impossible to understand the social life of this ape without attention to its sex life: the two are inseparable. Whereas in most other species, sexual behaviour is a fairly distinct category, in the bonobo it has become an integral of social relationships, and not just between males and females. Bonobos engage in sex in virtually every partner combination: male-male, male-female, female-female, male-juvenile, female-juvenile, and so on. The frequency of sexual contact is also higher than among most other primates.

In our own society, definitely still male-dominated but also with a legacy of religious sexual conservatism, this kind of all-in, semi-masturbatory sexual contact is absolutely beyond the pale. I’m reminded of the Freudian concept of sublimation I learned about as a teen – the eros or sex drive is channelled into other passionate, creative activities, and, voila, human civilisation! And yet, we’re still obsessed with sex, which we’re expected to transmute into sexual fulfilment with a lifelong partner. Meanwhile, the popularity of porn, or what I prefer to call the sex video industry, as well as the world’s oldest profession, indicates that there’s much that’s not quite right about our sex lives.

This raises questions about monogamy, the nuclear family, and even the human concept of love. This is ancient, but nevertheless dangerous territory, so for now I’ll stick with bonobos. As with chimps, female bonobos often, though not always, move to other groups at sexual maturity, a practice known as philopatry. Interestingly, this practice has similarities to exogamous marriage practices, for example among some Australian Aboriginal groups. It’s interesting, then, that female-female bonds tend to be the strongest among bonobos, considering that there’s no kinship involved.

Needless to say, bonobos don’t live in nuclear families, and child-care is a more flexible arrangement than amongst humans, though the mother is naturally the principal carer. And it seems that bonobo mothers have a subtly closer relationship with their sons than their daughters:

the bond between mother and son is of particular significance in bonobo society where the son will maintain his connection with his mother for life and depend upon her for his social standing within the group. For example, the son of the society’s dominant female, the strong matriarch who maintains social order, will rise in the ranks of the group, presumably to ensure the establishment and perpetuation of unaggressive, non-competitive, cooperative male characteristics, both learnt and genetic, within the group.

Considering this point, it would be interesting to research mother-son relations among human single-parent families in the WEIRD world, a situation that has become more common in recent decades. Could it be that, given other support networks, rather than the disadvantages often associated with one-parent families in human societies, males from such backgrounds are of the type that command more respect than other males? Particularly, I would suspect, from females. Of course, it’s hard to generalise about human upbringing, but we might be able to derive lessons from bonobo methods. Bonobo mothers rarely behave punitively towards their sons, and those sons remain attached to their mothers throughout their lives. The sons of high-status females also attain high status within the male hierarchy.

Yet we are far from being able to emulate bonobo matriarchy, as we’re still a very patriarchal society. Research indicates that many women are still attracted to high-status, philandering men. That’s to say, they’ve been ‘trained’ to climb the success ladder through marriage or co-habitation than through personal achievement. They’ve also been trained into the idea of high-status males as dominating other males as well as females. It is of course changing, though too slowly, and with too many backward moves for the more impatient among us. Two macho thugocracies, Russia and China, are currently threatening the movement towards collaboration and inclusivity that we see in female-led democracies such as Taiwan, New Zealand and a number of Scandinavian countries. It may well be that in the aftermath of the massive destruction wrought by these thugocracies, there will come a reckoning, as occurred after the two ‘world wars’ with the creation of the UN and the growth of the human rights movement and international aid organisations, but it is frustrating to contemplate the suffering endured in the meantime, by those unlucky enough to be born in the wrong place at the wrong time.

Now of course all this might be seen as presenting a romanticised picture of bonobos (not to mention female humans), which De Waal and other experts warn us against. The difference in aggression between bonobos and chimps is more a matter of degree than of type, perhaps, and these differences can vary with habitat and the availability of resources. And yet we know from our studies of human societies that male-dominated societies are more violent. And male domination has nothing to do with simple numbers, it is rather about how a society is structured, and how that structure is reinforced. For example I’ve written recently about how the decidedly male god of the Abrahamic religions, originally written as YWH or Elohim, emerged from a patriarchal, polygamous society in the Sinai region, with its stories of Jacob and Abraham and their many wives, which was reinforced in its structure by origin myths in which woman was created out of a man’s rib and was principally responsible for the banishment from paradise. The WEIRD world is struggling to disentangle itself from these myths and attitudes, and modern science is its best tool for doing so.

One of the most interesting findings, then, from modern neurology, is that while there are no categorical differences between the male and the female brain in humans, there are significant statistical differences – which might make for a difference in human society as a whole. To explain further: no categorical difference means that, if you were a professional neurologist who had been studying the human brain for decades, and were presented with a completely disembodied but still functional human brain to analyse, you wouldn’t be able to assert categorically that this brain belonged to a male or a female. That’s because the differences among female brains, and among male brains, are substantial – a good reason for promoting gender fluidity. However, statistically, there are also substantial differences between male and female brains, with males having more ‘grey’ material (the neurons) and females having more ‘white’ material (the myelinated connections between neurons), and with males having slightly higher brain volume, in accord with general sexual dimorphism. In a 2017 British study involving some 5,000 subjects, researchers found that:

Adjusting for age, on average… women tended to have significantly thicker cortices than men. Thicker cortices have been associated with higher scores on a variety of cognitive and general intelligence tests.

This sounds promising, but it’s doubtful that anything too insightful can be made of it, any more than a study of bonobo neurophysiology would provide us with insights into their culture. But, you never know…

References

Frans De Waal & Frans Lanting, Bonobo: the forgotten ape, 1997.

https://www.humancondition.com/freedom-the-importance-of-nurturing-in-bonobo-society/

https://www.science.org/content/article/study-finds-some-significant-differences-brains-men-and-women

on the origin of the god called God, part 2: the first writings, the curse on women, the jealous god

Written by stewart henderson

June 13, 2022 at 2:43 pm

exploring meiosis

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Canto: So I’m trying to get my head around meiosis in general, and how the parental chromosomes get assorted in the process. I understand that Mendel arrived at his law or principle of independent assortment by noting the resultant phenotypes from particular crosses, especially dihybrid crosses. He knew nothing about gametes and meiosis, an understanding of which didn’t get underway until a decade or more after his 1865 experiments…

Jacinta: Well, meiosis is a v v amazing process that deserves lots of attention, because if not for, etc….

Canto: But what is meiosis for, I don’t even understand that.

Jacinta: It’s for the production of gametes – the sperm and egg cells in mammals. And that’s interesting, because, according to Medical News Today, ‘Females are born with all the eggs they will ever have in their lifetime. The amount decreases until a person stops ovulating and reaches menopause’. According to a graph they present, the number of egg cells produced is at its peak long before birth, and has reduced about tenfold by the time of birth, to about one or two million. This number continues to reduce through life, though it remains relatively stable during the period of ‘optimum fertility’ from about ages 18 to 31, when the number of eggs is around 200,000, with a lot of individual variation.

Canto: So, meiosis occurs entirely while the infant is in the womb? For females at least. And what exactly is ovulation?

Jacinta: Yes, egg cells don’t regenerate like other cells. Remember, tens of billions of our somatic cells die every day, and are being replaced – mostly. As to ovulation, this occurs as part of the menstrual cycle, which occurs with females at puberty. During menstruation, mature eggs are released from the ovaries, which are on the left and right sides of the uterus and connected to it by the fallopian tubes.

Canto: What do you mean by mature eggs? Aren’t they always mature?

Jacinta: Hmmm. Detour after detour. Four phases are recognised in the menstrual cycle – menstruation, the follicular phase, ovulation and the luteal phase. It’s the follicular phase that produces mature eggs, through the release of follicle stimulating hormone (FSH) by the pituitary gland. Do you want me to go into detail?

Canto: No, let’s get back to meiosis – but I always knew there was something fshy about the menstrual cycle. So meiosis is about haploid cells producing more haploid cells? You mentioned that egg cells, which are haploid cells, are at their peak long before the birth of a female child, a peak of around 10 million. But where does the first haploid cell come from, when a child starts as one fertilised egg – a diploid cell? Haploid cells combining to form diploid cells is one amazing process, but diploid cells separating to form haploid cells?

Jacinta: Okay so here’s what I think is happening. A human being starts as a diploid cell, a fertilised egg. As cells differentiate, which happens quite early, some become germ cells. But they’re diploid cells, like all the others, not haploid cells. So meiosis starts with diploid cells.

Canto: Okay, so what differentiates a germ cell from other somatic diploid cells?

Jacinta: I don’t know, just as I don’t know what makes a pluripotent or totipotent cell become a brain cell or a blood cell or whatever. This presumably has a lot to do with genetics, epigenetics and the production of endless varieties of proteins that make stuff, including germ cells. Which presumably are not egg cells or sperm cells, which are haploid cells, or gametes. And these germ cells can undergo mitosis, to reproduce themselves, or meiosis, to produce gametes. So now, at last, we describe the process, and much of this comes from Khan Academy. There are two ’rounds’ of meiosis – M1 and M2 – each of which has a number of phases. In M1 the diploid cell is split into two haploid cells each with 23 chromosomes, and in M2 the haploid cells reproduce as haploid cells, so that at the end of the cycle you have four haploid cells. And in each of these ’rounds’ there are the four phases, prophase, metaphase, anaphase and telophase. PMAT is how to remember it. And then there’s interphase, where cells just going on being themselves and doing whatever they do – though it’s important to know what happens during interphase for these other stages.

Canto: The complexity of it all is fairly mind blowing. Molecules that have a code for making proteins that perform all these functions that produce a huge variety of cells every one of which – apart from the gametes – has a nucleus containing 23 chromosomes from your mother and 23 from your father. Trillions of them!

Jacinta: Yes, it’s certainly amazing – and billions of those cells die and are replaced every day. And not just in humans but in dogs and bonobos and cetaceans and whatnot.

Canto: But here’s a thing – we’re talking about gametes, also known as germ cells, which may be female or male – sperm cells or egg cells. But sperm are also known as spermatazoa, and they’re much tinier and less complex than egg cells, and also far more numerous. Is a spermatozoon a sperm cell, or do lots of spermatozoa live in one cell, or what? One ejaculation releases – how many of these tiddlers?

Jacinta: Well sperm counts can range from about 15 million or less per millilitre of semen (that’s a low sperm count) to somewhere between 200 and 300 million. An ejaculation can vary in volume of course – generally about a teaspoon, which might be as much as 5mls. And, yes, a single sperm or spermatozoon is a male gamete, much smaller than the female ovum. So, yes, male sperm, like male political leaders, make up in numbers for what they lack in complexity.

Canto: Okay so let’s get started with PMAT and all that.

Jacinta: Well it’s all very miraculous or mind-blowing as Salman Khan rightly emphasises – to think that this complexity comes from mindless molecules and all. But here goes, and it cannot help but be a simplified description. So we start with a germ cell – and I’m not sure how this particular type of diploid cell is distinguished from other diploid cells…

Canto: Or whether, even though it’s called a germ cell, it is essentially different in male bodies as compared to female bodies, since they produce such different gametes…

Jacinta: Yeah well I’ll keep that in mind as we progress. Now we start with the interphase, during which time the chromosomes in the nucleus are synthesised. Interphase is generally subdivided into three phases, Gap 1 (G1), Synthesis (S) and Gap 2 (G2). The cell itself experiences a lot of growth during interphase.

Canto: Too vague.

Jacinta: Well I’m just getting started, but I’m not writing a book here.

Canto: Are you going to explain how the chromosomes are ‘synthesised’?

Jacinta: Probably not, this is just a summary.

Canto: I want to know about chromosome synthesis.

Jacinta: Sigh. You’re right, it sounds pretty important doesn’t it. So let’s focus in detail on interphase, which I think is much the same whether we’re looking at mitosis or meiosis.  If you consider a whole cell cycle, from its ‘birth’ – usually through mitosis – to its ‘death’ (through mitosis again? I’m not sure), 95% of its time is spent in interphase, during which it doubles in size. It is, in a sense, preparing itself for chromosomal replication and cell division. Here’s a quote from a text book, Concepts of Biology, which I found online, describing the first stage of interphase:

The first stage of interphase is called the G1 phase, or first gap, because little change is visible. However, during the G1 stage, the cell is quite active at the biochemical level. The cell is accumulating the building blocks of chromosomal DNA and the associated proteins, as well as accumulating enough energy reserves to complete the task of replicating each chromosome in the nucleus.

Canto: So it’s a clever cell, actively accumulating the material to build and replicate its particular and unique DNA – I mean unique to the particular soma that it somatically serves, along with several trillion others.

Jacinta: Actually, another source tells that the G stands for growth, which I think makes more sense. The next stage is the S or synthesis phase. Now at this stage, or the beginning of it, the chromosomes exist largely as chromatin, a kind of mixture of DNA and proteins. Histones, in particular are important proteins for packaging the DNA into a tight enough space to fit in the nucleus. I mean, 23 pairs of chromosomes doesn’t really tell you how much DNA and other molecules it all amounts to. Now, this S phase is really complicated, and summaries don’t do it justice. Here’s a quote from yet another source to kick things off:

The S phase of a cell cycle occurs during interphase, before mitosis or meiosis, and is responsible for the synthesis or replication of DNA. In this way, the genetic material of a cell is doubled before it enters mitosis or meiosis, allowing there to be enough DNA to be split into daughter cells. The S phase only begins when the cell has passed the G1 checkpoint and has grown enough to contain double the DNA. S phase is halted by a protein called p16 until this happens.

So you’re asking how these chromosomes are synthesised. Note how this says ‘synthesis or replication’, so it’s presumably about the same sort of process that occurs when cells and their chromosomes are replicated during mitosis? Here’s another passage from the same source, and I don’t pretend to understand it:

The most important event occurring in S phase is the replication of DNA. The aim of this process is to produce double the amount of DNA, providing the basis for the chromosome sets of the daughter cells. DNA replication begins at a point where regulatory pre-replication complexes are attached to the DNA in the G1 phase. These complexes act as a signal for where DNA replication should start. They are removed in the S phase before replication begins so that DNA replication doesn’t occur more than once.

Canto: Wow. That explains not much. Obviously the key to it all is the ‘regulatory pre-replication complexes’ previously attached. How could I not have known that?

Jacinta: Well let’s just say that there are known mechanisms by which DNA replication is regulated, and prevented from occurring more than once in the S phase. I’m sure all those ‘pre-replication complexes’ have been named and studied in detail by scores of geneticists. So that’s enough for now about chromosome synthesis/replication. The S phase also involves continued cell growth and the production of more proteins and enzymes for DNA synthesis. Always looking to the future. And so we move to the next phase.

Canto: Ah yes, reading ahead I see that DNA synthesis is always much the same. The DNA double helix is kind of unzipped by an enzyme called helicase, and the two single strands can be used as templates to form new and identical double strands. I’m over-simplifying of course.

Jacinta: Yes there are different processes going on to ensure that everything goes more or less smoothly, as well as to maintain cell growth outside of the genetic material. A key enzyme, DNA polymerase, binds nucleotides to the template strands using the base pairing code – A binds to T, C to G. This creates an identical new double helix of DNA.

Canto: Apparently there’s a difference between DNA replication and chromosome replication. Please explain?

Jacinta: I’m not sure if I can, but we’re talking about the replication of chromosomes in the S phase, after which each chromosome now consists of two sister chromatids (halves of a chromosome), as you see below.

 

In the first circle, A and B are homologous pairs. That’s to say, they’re segments of DNA, chromosomes, from each parent, though they might code differently – they might be different alleles. This is a bit complicated. Sal Khan in his video puts it this way:

Homologous pairs means that they’re not identical chromosomes, but they do code for the same genes. They might have different versions, or different alleles for a gene or for a certain trait, but they code essentially for the same kind of stuff.

Make of that what you will. I suppose it means that the homologous pair might have, say, genes for eye colour, but mum’s will code for blue, dad’s for brown. But the same kinds of genes are paired. Anyway, after replication in the S phase, you get, as above, two male and two female chromosomes, joined together in a sort of x shape. They’re joined together at that circular sort of binding site called a centromere (it’s not actually circular). The images above are misleading though, in that there are short arms and long arms leading off the centromere. You could say the centromere is off-centre. So the whole of this new x-shaped thingy is called a chromosome and each half – the right and the left – is called a chromatid. And at the four ends of the x-shaped thingy – I mean the chromosome – is a cap of repetitive DNA called a telomere.

Canto: Ah yes, I’ve heard of those and their relation to ageing…

Jacinta: Let’s not be diverted. So all of this is occurring in the nucleus, and there’s also replication of the centrosomes. Okay they’re a new structure I’m introducing, one that seems to only occur in animal-type or metazoan eukaryotic cells. They serve as microtubule organising centres (MTOCs), according to Wikipedia, which is never wrong, and which goes into great detail on the structure of these centrosomes, but for now the key is that they’re essential to the future separation of the chromatids via microtubules during prophase I. And that’s the next phase to describe. And it’s worth noting that the developments described up to now could be preliminary to meiosis or mitosis.
So, in prophase I the nuclear envelope starts to disintegrate and the pair of centrosomes are somehow pushed apart, to opposite sides of the chromosomal material, and microtubule spindles start extending from them – presumably by the magic of proteins. And another sort of magical thing happens, though I’m sure that some geneticists understand the detail of it all, which is that the homologous pairs line up on opposite sides of a kind of equator line, guided by these spindles, forming a tetrad, and this is where a process called crossing over or recombination occurs, in which the pairs exchange sections of genes. And this recombination somehow manages to avoid duplication and to maintain viability, and indeed to increase diversity. The recombination occurs at points in the chromosomes called chiasmas.
So that’s the end of prophase I. Now to metaphase 1. In this phase the nucleus has disappeared, the centromeres have completed their move to the opposite sides of the cell, and the spindle fibres of microtubules become attached to chromosomes via the kinetochores – protein structures connected to the centromeres. Here’s an interesting and useful illustration of a kinetochore.

All of this is similar to metaphase in mitosis. Then in anaphase I the homologous pairs, which remember had come together and recombined, are separated, or pulled apart, which is different from anaphase I in mitosis, where the chromosomes are split into their separate chromatids. Next comes telophase I, when the separation is complete, the facilitating microtubules break down and cytokinesis, the final separation of the chromosomes and the cytoplasm into two distinct cells, occurs. Telophase I ends with two cells and two nuclei, each containing 23 chromosomes, half of those in the original cells. They’re called daughter cells, for some reason.

Canto: Probably because son cells sounds silly.

Jacinta: Good point. So now these daughter cells start on a whole new PMAT process, which is a lot more like mitosis. Prophase II involves the disintegration of the nucleus once more, the two centrosomes start to move apart as microtubules are formed – and remember this is happening simultaneously in the two daughter cells – and then we’re into metaphase II, where the centrosomes have migrated to opposite ends of the cell, and the chromosomes line up at the ‘equator’, and the spindle fibres attach to the kinetochores of the sister chromatids. Next comes anaphase II, in which the spindle fibres draw the chromatids away from each other, as in anaphase during mitosis. And at the end of this journey they’re now treated as sister chromosomes. And all of this is happening in those two daughter cells, which start to stretch and cleave, which of course means that, in telophase II, you have cytokinesis, and the creation of new nuclear membranes, and the cytoplasm – remember that all the cytoplasm and its organelles have to be replicated too, to make, in the end four, complete haploid cells, or gametes. So that’s the potted version. There’s lots of stuff I’ve excluded, like the difference between centrosomes and centrioles, and lots of details about the cytoplasm, and there’s no doubt much more to learn (by me at least) about the crossing over that’s so essential to provide the variation that Darwin searched for in vain. Anyway, that was sort of fun and thank dog for the internet.

Canto: But I’m still confused about sperm cells and egg cells… If sperm cells are just those little tadpole things – a bunch of DNA with a flagellum, they don’t have any cytoplasm to speak of, do they?

Jacinta: Ah yes, something to look into. There’s spermatogenesis and there’s oogenesis… for a future post. It just never ends.

References

https://www.thoughtco.com/stages-of-meiosis-373512

https://www.albert.io/blog/what-occurs-in-the-s-phase/
https://en.wikipedia.org/wiki/Centrosome
https://www.thoughtco.com/kinetochore-definition-373543
https://opentextbc.ca/biology/chapter/6-2-the-cell-cycle/
https://www2.nau.edu/lrm22/lessons/mitosis_notes/meiosis.html
https://www.genome.gov/genetics-glossary/Chromatin
https://sciencing.com/difference-between-centriole-centrosome-13002.html

Written by stewart henderson

June 8, 2022 at 10:25 pm

exploring genetics – Mendel, alleles and stuff

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Canto: So I’d like to know as much as I can about genetics before I die, which might be quite soon, so let’s get started. What’s the difference between genetics and genomics?

Jacinta: Okay, slow down – but I suppose that’s as good a place to start as anywhere. I recently listened to a talk about the human genome project, which was completed around 2003, and the number I heard the guy mention was 3 billion genes, or something. But according to videos and other sources, each human has between 20,000 and 25,000 genes – though I’ve found another FAQ which estimates 30,000. So I gather from this that our genome is the number of genes we might possibly have – in the whole human population? Which raises the question, how do we know that the human genome project has captured or mapped all of them.

Canto: So there’s an individual genome, peculiar to each of us, and a collective genome?

Jacinta: Errr, maybe. We’re 99.9% genetically identical to each other, supposedly. And if this sounds very paradoxical, we need to zoom in on the detail. And with that, I’ve discovered that the 3 billion refers to base pairs, sometimes called ‘units of DNA’. So what’s a base pair? Well, we need to start with the structure of DNA, the genetic molecule. That’s deoxyribonucleic acid, which is made up of basic components called nucleotides. A nucleotide of DNA consists of a sugar molecule, a phosphate group and a nitrogenous base. The bases come in four types – adenine, guanine, thymine, and cytosine (A, T, G and C). The sugar and phosphate groups provide structure, allowing the bases to form a long string of DNA. Bonds form between the bases to create a double strand of DNA – hence base pairs.

Canto: Here’s how the World Health Organisation defines genomics, obviously from a health perspective:

Genomics is the study of the total or part of the genetic or epigenetic sequence information of organisms, and attempts to understand the structure and function of these sequences and of downstream biological products. Genomics in health examines the molecular mechanisms and the interplay of this molecular information and health interventions and environmental factors in disease.

Now you might think that this definition could cover genetics too, and maybe we shouldn’t be too worried about the distinction. Maybe, in general, genomics is about sequences of genes, especially in detailing whole organisms, while genetics is more about individual genes.

Jacinta: Genomics is the much more recent term, first coined in the 1980s, whereas genetics and genes date back to before we knew about DNA as the genetic molecule. Going back to Mendel and all, though I don’t think he used the term, he talked about ‘factors’ or some such.

Canto: So we know that there’s DNA, and there’s also RNA, another building block of life. How old are they, and which came first? And can species replicate without these molecules?

Jacinta: Oh dear – we’ll get there eventually, maybe. Genomics deals with the whole complement of genes in an organism, which we’ve gradually realised is necessary to evaluate, say, how prone that organism is to contracting a disease, or developing some immuno-deficiency, because individual genes often don’t tell us much. And there’s also the matter of dominant and recessive genes. Which takes us to inheritance. All those genes are combined together on chromosomes, of which there are 23 pairs in humans, which we inherit from our parents, 23 chromosomes each.

Canto: Combined together? Can you  be more specific?

Jacinta: Okay, a chromosome is a thread-like structure, in which DNA is coiled around structural proteins called histones. Each chromosome has two ‘arms’, flowing from a constriction point called a centromere. These arms are labelled p and q. The p arm is shorter than the q. And these chromosomes contain genes, which may or may not code for proteins. The genes, as mentioned, consist of base pairs, which vary in number from hundreds to millions.

Canto: Okay, so what’s the difference between a gene and an allele?

Jacinta: Well, genes are codes for making proteins – and those proteins affect all sorts of things, to do with taste, smell, hair colour and type, height, and predisposition to various diseases, among many other things. You can call these things ‘traits’, which show up in our phenotype, our physical characteristics. And it should be pointed out that many of these traits are the results of not just one gene but different genes in combination. Now, as mentioned, these genes are in pairs of chromosomes – 23 pairs in humans. Now, say we isolate an area in a chromosome that codes for a particular trait. What about the other chromosome in that pair? Remember, each chromosome comes from a male or female parent, and they are different, genetically – or likely to be. That’s where alleles come in, and it takes us back to Mendel, who found that with pea plants, traits such as colour, or the alleles that carried those traits, could be dominant or recessive. So, for that trait, they could carry two dominant alleles, or two recessive alleles, or one of each. If one or both of those alleles is dominant, the trait will be expressed, but if both are recessive, it won’t be. But as I say, it’s more complicated than that, as traits expressed in phenotypes are generally carried by many genes.

Canto: So alleles are? – how to define them?

Jacinta: Google it mate. Here’s a quickly found definition: “each of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome”. So let’s continue with the work of Mendel. When we find a dominant trait, we use a capital, T. It might be paired with another dominant trait, TT, or with a recessive trait, Tt. On the other hand, both traits might be recessive, tt, and that’s all the combos you have, for single traits. Now, in noting this, and the way that alleles combine, Mendel came up with a ‘law of segregation’. Or rather, he noticed a process, which later became recognised as a law. In fact, he observed three fundamental processes, ‘segregation’, ‘independent assortment’, and ‘dominance’, which we now describe as laws. Now, I’ve used the term ‘trait’ but perhaps I should’ve used the term ‘allele’. So TT combines two dominant alleles. The law of segregation has been stated thus:

During gamete formation, the alleles for each gene segregate from each other such that each gamete formed carries only one allele for each gene.

Canto: Right. Uhhh, what’s a gamete again?

Jacinta: Sex cells, which carry only one copy of each chromosome. They’re created during meiosis, after which we end up with four cells each with only one allele for each gene. So indeed, alleles are segregated during gamete formation.

Canto: Oh dear. I’ll have to brush up on meiosis.

Jacinta: So now we have these segregated alleles, which will be recombined. The law of independent assortment comes next. This also occurs during meiosis. In the fourth or metaphase period of cell division, the chromosomes align themselves on the equatorial plane, also called the metaphase plate. This alignment is random, and that’s the key to the law of independent assortment – ‘genes for different traits assort independently of each other during gamete formation’. But obviously Mendel knew nothing about meiosis, though it was first observed in his lifetime, in sea urchins . Anyway, this law allows for many different combinations of alleles depending on how chromosomes become aligned on the metaphase plate. A dihybrid cross will provide more such combinations.

Canto: A dihybrid cross? Please explain.

Jacinta: Well, a monohybrid cross will be like this – TT x tt. Not much to be assorted there. A dihybrid cross might be like this – TtCc x TtCc, creating four different assortments for each cross. So now to the third law, of dominance. This law simply states that ‘some alleles are dominant while others are recessive. An organism with at least one dominant allele displays the effect irrespective of the presence of the recessive one’. So the phenotype will present the dominant allele regardless of whether it’s double-dominant or single-dominant. Though the terms used are homozygous (TT), or heterozygous (Tt).

Canto: So are we going to look at punnett squares now? I’ve heard of them…

Jacinta: Well it might help. They were named after a bloke called Punnett back in 1905, the early days of Mendelian genetics. They’re neat little tables, that can start to get quite complicated, for determining the genotypes of offspring, when you breed dominant with recessive, heterozygous with homozygous and so on. It’s useful for simple genotypes, but when genotypes are multifactorial, as they often are, other methods are obviously required.

Canto: Okay, that’s more than enough to absorb for now.

Jacinta: I think, since we’ve started with Mendel, we might do a historical account. Or maybe not….

References

https://www.google.com/search?client=safari&rls=en&q=alleles&ie=UTF-8&oe=UTF-8

https://byjus.com/biology/mendel-laws-of-inheritance/

https://www.yourgenome.org/facts/what-is-meiosis

 

 

Written by stewart henderson

May 29, 2022 at 8:04 am

Posted in alleles, Mendel

Tagged with , , , ,

vive les bonobos

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I’ve written a lot about a bonobo future for humans, but what about the future of real bonobos? How long will they have one in the wild?

It’s likely the bonobo population has never been large. Their range has always been limited, presumably because they’ve inhabited a fertile niche south of the Congo River, and have had no reason to stray from it. All wild bonobos happen to inhabit one human country, the Democratic Republic of the Congo. The geographic range of chimpanzees, of which there are four sub-species, includes nineteen countries throughout west and east-central Africa. Both species are on the endangered list. The World Wildlife Fund has estimated the population at between 10,000 and 50,000 and declining. It’s a large margin for error, due to the difficulties of trying to track numbers in one of the most dangerous locations on the planet. It’s probable that the numbers today are well to the lower end of that spectrum. They have a slow reproduction rate, poaching and habitat loss are a perennial issue, and there’s the common notion in faraway regions such as China and South-East Asia that these ‘exotic’ creatures make for prestigious pets or that their body parts provide miraculous remedies. The live trade is generally in infants, which more often than not involves killing their parents. They’re not all being shipped overseas however – bonobo ‘charms’ (whatever they are) are quite common in the Congo itself, according to WWF and other sources.

Many of the DRC’s humans are fighting for survival themselves, and are competing with bonobos for forest resources, so deforestation is an issue. But the live trade is much more lucrative than that for bushmeat. Most of their habitat is unprotected, and the natives are not necessarily aware that they’re breaking the law, if in fact they are, in capturing these animals. Here’s a grim description of the situation from the wildlife website Mongabay:

Dead apes are chopped up and sold for meat and body parts. Meat is generally consumed by middle- to upper-class urban families, as well as foreigners living there. … On average, a kilo of such meat would cost between $20 to $40 in local markets … prices vary according to species and size. Body parts such as the skin, hands, and head are used as medicine and in spiritual rituals… The head takes the highest price at between $500 and $1,500, and hands between $20 and $50 each.

Trying to save and defend bonobos in the DRC is a dangerous business. The war-torn country is over-supplied with deadly weaponry, and it’s difficult to win people over to conservation when they are so impoverished and the trade is so lucrative. Improving the lives of the native human population is probably more important than education, but little appears to be happening in that regard. The natives have formed gangs to facilitate the trade, and conservationists have received death threats. The general corruption of the government is obviously a problem too, though international exposure may help to turn things around. The first nationally announced arrest of hunters only occurred in 2019.

Still, there are many conservationists working for a brighter future for bonobos. The Bonobo Conservation Initiative has for a long time been promoting indigenous leadership in land management for biodiversity in bonobo habitats, in particular the Kokolopori Bonobo Reserve. The plan is to extend this reserved area into a Bonobo Peace Forest, ‘a constellation of community-based reserves in the Congo rainforest supported by sustainable development’. Ecotourism is seen as a key to providing a future for both the bonobos and the human communities of the region, but this is a delicate issue, as the natural life-style of our cousins needs to be maintained. The DRC itself needs international support – it has suffered devastation in the past from the worst forms of colonialist exploitation, and it has never been properly compensated. Now, the nation is, hopefully, beginning to realise what a treasure lies within its forests. Vive les bonobos!

References

Images from a dropped phone reveal the ugly truth behind bonobo trafficking

https://www.awf.org/blog/endangered-bonobo-africas-forgotten-ape

https://www.worldwildlife.org/magazine/issues/spring-2018/articles/charting-a-future-for-bonobos

https://www.bonobo.org/news-and-knowledge/appeal-2019

Click to access projdoc.pdf

 

Written by stewart henderson

May 15, 2022 at 5:11 pm

Posted in bonobos, conservation

Tagged with

omicron omicron omicron

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So I haven’t written about Covid for some time, and it hasn’t gone away, though I’ve managed to avoid it myself. I’m recovering from a bacterial infection which played havoc with my bronchiectasis, and had me coughing and sneezing so much that I felt for a few days that my usually life-saving course of antibiotics, together with steroids, wouldn’t be enough. I asked for a referral to a pulmonologist/respiratory specialist, but discovered that, due to Covid, they’re almost impossible to access. Anyway, I’m on a puffer and on the mend.

So according to worldometer’s coronavirus website, which I’ve regularly used, there have been about 6 and a quarter million deaths from Covid19, but the latest New Scientist podcast (118) informs me that there have been nearly 15 million deaths. That’s a huge discrepancy, and I suspect these rubbery figures will be a feature for years. What’s certainly true is that the various forms of this virus are going to be with us for some time. The latest Omicron sub-variants emanating from South Africa, BA.4 and BA.5 are still being monitored for their infectivity. Omicron in general (first discovered in Botswana) is a variant of concern, which has led to a new spike in cases, but it generally appears to be less lethal, though whether this is because most people, here in Australia at least, have been immunised, I’m not sure. Anyway, winter is on its way here, and I’m a bit worried. New covid cases are up by 127% in the USA in the last month, with hospitalisations up by 28% according to their ABC news. Omicron is mostly the culprit. Numbers are probably under-reported because effective testing has gone out the window. They’re testing waste water to measure the prevalence. In New Zealand, the Director-General of Health is warning of a new winter peak. Case numbers have bottomed there at a higher level than expected, and are now slightly on the rise. And of course not all cases are being reported, which would be expected with mild cases. In fact the DGH suggests that might amount to about half the cases. Influenza A is also on the rise there.

Omicron reproduces in the airways much much more rapidly than previous variants so it will pass quickly between people before they even know it, plus the mutation upon mutation will probably have rendered previous vaccines, and the antibodies they produce, less effective. Its precise infectiousness is hard to calculate because so many who are infected either aren’t aware of it or don’t report it. Animal studies of Omicron are showing that it goes into the lung less readily than previous variants, which is a relief to me at least, and probably a relief to most. But we shouldn’t describe it as a mild variant. There’s also the long Covid issue, which, being long, will take a long time to get a handle on. And there’s also the unvaccinated, who are more likely to be hospitalised. Of course, if you survive infection this will boost your immunity in future, at least for that particular variant. But it may well be the case that the virus will become endemic, that it’s on its way to being so.

It’s worth knowing some of the terminology regarding viruses and their mutations. They mutant constantly of course, though not always viably. Viable mutations will mutate further, and once they’ve gone further from the original they’re classed as a different lineage. That’s steps away from being classed as a variant, which is a lineage that has enhanced capability of infecting and causing damage to hosts. Omicron, because of its increased infectivity, is producing more lineages, and subsequently more variants. So we’re seeing reinfections, almost regardless of vaccination – depending no doubt on number and timing of vaccinations. The situation in South Africa is being watched, because they seem to be ahead in new infection rates. But there are concerns everywhere – at the end of April a new Omicron sub-variant, BA 2.12.1, was found in wastewater here in Australia (in Victoria). It’s deemed more transmissible, but no more severe, than previous variants. It should be noted, though, that influenza viruses still mutate more than four times faster than these Omicron variants, on average. However, some variants seem to have a brief ‘sprint’ period of high tranmissibility. Also, variants can arise through recombination. This appears to have occurred with the Omicron XE variant, the result of ‘two omicron strains merging together in a single host and then going on to infect others’. The genes of one variant can combine successfully with another infecting the host at the same time, and then spread to other hosts. There’s also been a ‘Deltacron’ recombinant variant.

Some 60 mutations have been identified since the original SARS-Cov2 virus was detected in Wuhan. 32 changes in the spike protein have been identified. This is the protein that attaches to human cells, and has been the principal target of vaccines.

The latest worry is the Omicron BA.4 and BA.5 sub-variants, which ‘threaten to trigger a new wave of COVID-19 infections in South Africa’, according to the VaccinesWork website, but the good news is that antibodies produced by those who had been vaccinated against COVID-19 were more effective than those from people who had recovered from natural infection. Vaccines work indeed. Still, the number of cases are rising. It may be due to waning immunity or increased infectivity or both. We can only continue to monitor the situation – it’s certainly not over yet. What an incredible journey this has been, and the fallout from reduced food production and other economic constraints is another problem for the future.

References

https://theconversation.com/whats-the-new-omicron-xe-variant-and-should-i-be-worried-180584

https://www.theguardian.com/world/2022/may/06/why-are-there-so-many-new-omicron-sub-variants-like-ba4-and-ba5-is-the-virus-mutating-faster

https://www.gavi.org/vaccineswork/five-things-weve-learned-about-ba4-and-ba5-omicron-variants

 

Written by stewart henderson

May 15, 2022 at 4:36 pm

democracy, women and bonobos

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Jacinta Ardern, Prime Minister of New Zealand

Some people out there might not think that democracy is the best system, but I’d say that, given the crooked timber of humanity and all that, it’s probably the best we can come up with. One of its major problems, as I see it, is its adversarial, or partisan nature. Modern democracies are generally about two major parties, left and right, with power swinging on a more or less regular basis from one side to another. On the other hand, many European nations have evolved multi-party systems, with fragile coalitions always threatening to break apart, and negotiations often bogging down and ending with decisions nobody is particularly happy about, or so it seems. While this can be a problem, so can the opposite, when one party’s decisions and initiatives are swept aside holus bolus by a new government with a polar opposite ideology.

When I occasionally check out social media, I’m disheartened by the number of commentators for whom party x can do no right, and party y can do no wrong. It almost seems as if everybody wants to live in a one-party state – their party. This is a problem for a state which is diverse and necessarily interconnected. That’s to say, for any modern state. And of course there are other problems with representative democracies – generally related to wealth and power. Parliamentarians are rarely truly representative of their constituents, each vote rarely represents one value, and cronyism has always been rife.

And then there’s the maleness of it all. It’s not just that the percentage of women in parliament is always less than the percentage in the general population, but the movers and shakers in the business community, notorious for their pushy lobbying, are invariably male. And then there’s the military, an ultra-male bastion which must have its place…

So here’s a ridiculous thought experiment. Imagine a cast-iron law comes in, dropped from the heavens, that for the next 200 years, no male is allowed to be part of any government of any stripe. Women must, and will, make up every political decision-making body on the planet. Sure they can have the odd male advisor and helpmeet, but they seem to find female advice more congenial and useful. And let’s imagine that in this thought experiment, the males don’t mind their secondary roles at all. They just see it as the natural order of things. After two hundred years, from the point of our current ever-expanding technological and scientific knowledge (which women and men will continue to fully participate in), where will be in terms of war and peace, and our custodianship of the biosphere?

I told you this was ridiculous, but you don’t have to be a professional historian to realise that a more or less unspoken ban on female participation in government has existed historically in many countries for a lot more than a couple of centuries. And we’ve survived – that’s to say, those of us that have survived. Sorry about the tens of millions of Chinese that Mao starved to death in his Great Leap Forward. Sorry about the genocides of Stalin, Hitler, Leo Victor, Talaat Pasha, Pol Pot and Suharto, not to mention Genghis Khan and countless other known or unknown historical figures, again invariably male.

So returning to that thought experiment, we could take the easy option and say we don’t know how things would turn out – certainly not in any detail. But that’s surely bullshit. We know, don’t we? We know that the world, and not just the human world, would be a far far better place in the event of female leadership than it is today.

The evidence is already coming in, as creepingly as female leadership. I recently learned of the Democracy Index, a sophisticated worldwide survey of nations conducted by the Economist Intelligence Unit, the people who publish the Economist magazine, among other things. The survey annually measures and ranks 168 nations according to their democratic bona fides, or lack thereof. According to Wikipedia, ‘The index is based on 60 indicators grouped in five different categories, measuring pluralism, civil liberties and political culture’. The nations are divided broadly into four ‘types’. The top 21 are described as ‘full democracies’, the second category are the ‘flawed democracies’, the third are ‘hybrid regimes’ and the last and largest grouping are the ‘authoritarian regimes’. But when I looked at the very top ranking countries I found something very interesting, which prompted me to do a little more research.

In 2017, just under 10% of the world’s leaders were female. The percentage may have grown since then, but clearly not by much. We could be generous and say 13-14% at present. There are some difficulties in defining ‘nation’ as well as ‘leadership’, but let’s go with that number. So I had a look at the rankings on the Democracy Index, and the leadership of various countries on the index and what I found was very enlightening. Of the 21 countries rated as full democracies on the Democracy Index, seven of them were led by women. That’s 33%, quite out of proportion to the percentage of female leaders in general. But it gets better, or worse, depending in how you look at it. Of the top ten democracies on the list, six were led by women. Sixty percent of the top ten. Narrow it down still further, and we find that four of the top five democratic nations – which, in order, are Norway, New Zealand, Finland, Sweden and Iceland, are led by women – 80 per cent. It’s almost ridiculous how successful women are at making things work.

So what about the bottom of the barrel – the Afghanistans, the Burmas, etc. Of the 59 nations characterised as authoritarian by the Democracy Index, (though I prefer to call them thugocracies), zero are led by women. That’s nothing to crow about.

So, bonobos. The females, who are as small compared to their male counterparts as female humans are, dominate through solidarity. The result is less stress, less fighting, less infanticide, less killing and rape, less territoriality, and more sharing, more togetherness, more bonding, more love, if you care to call it that.

We don’t know anything much about the last common ancestor we share equally with chimps and bonobos. We don’t know about how violent Homo erectus or Homo habilis or the Australopithecines were, within their own species. We may never know. We do know that chimp troupes have gone to war with each other, with unbridled savagery, and we have evidence, from sites such as the Pit of Bones in northern Spain, of human-on-human killing from near half a million years ago. Our supposedly great book of moral teaching, the Hebrew Bible, describes many scenes of slaughter, sometimes perpetrated by the god himself. So it seems obvious that we’ve gone the way of the chimpanzee. Our worst leaders seem determined to continue the tradition. Our best, however, are making a difference. We need to make their numbers grow. Let’s make those female leaders multiply and see what happens. It may just save our species, and many others.

References

A bonobo world and other impossibilities 25: women and warfare (2)

Number of women leaders around the world has grown, but they’re still a small group

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

Written by stewart henderson

May 13, 2022 at 10:48 am

on the origin of the god called God, part 2: the first writings, the curse on women, the jealous god

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2500 years of this BS? Time for a change

 

So now we come to the writings on the god we’ve come to call God, and his supposed activities, nature and purpose.

I’m no biblical scholar, and this is a daunting prospect, but here are some questions I need to ask myself. When? What language? Who? How many authors? Is ‘the Torah’ the same as ‘the Pentateuch’? Don’t look for too many answers here.

The first five books of the Bible, and presumably all of the Hebrew Bible, or Old Testament, was written in Biblical Hebrew, and this is important to always keep in mind for English readers, who so often fail to realise they’re reading translations of translations. The first traces of Biblical texts discovered, the Ketef Hinnom scrolls, date back about 2600 years. They are fragments from Numbers, the fourth book. Of course we may never know if these are the oldest texts, but it’s unlikely they’ll find anything too much older. They date, therefore, from a little before the Babylonian exile, written up in various books (Jeremiah, 2 Kings, 2 Chronicles, Ezra and Daniel). According to Wikipedia and its sources:

The final redaction of the Pentateuch took place in the Persian period following the exile, and the Priestly source, one of its main sources, is primarily a product of the post-exilic period when the former Kingdom of Judah had become the Persian province of Yehud.

There were multiple authors, it seems. Famously, there were two origin stories, written presumably by separate persons. They’re designated as Gen 1 and Gen 2, and they each use a different name for the creator. The first, starting at Genesis 1:1, uses the Hebrew word Elohim, whereas the second, starting at Genesis 2:4, uses a tetragrammaton, YHWH, for Yahweh. Stylistically, they’re also very different. The first is fairly tightly organised and brief. Importantly from my perspective, the god, though male, is described as creating ‘man’ in its two forms, male and female, together. Here’s the the King James English version:

And God said, Let us make man in our image, after our likeness: and let them have dominion over the fish of the sea, and over the fowl of the air, and over the cattle, and over all the earth, and over every creeping thing that creepers upon the earth. So God created man in his own image, in the image of God created he him; male and female created he them (Genesis 1:26-27).

The second story begins immediately after the first story ends, and it is more detailed and lyrical, describing the garden of Eden, the river out of it, the tree of life, the tree of knowledge of good and evil, and the lands fed by the rivers, divided from the original, flowing from the garden. God spends a lot of time chatting with Adam (the name suddenly pops up), getting him to name all the beasts of the fields and the fowl of the air that he, the god, conjures up. He also tells him that he will create a help-meet for him, but Adam has to remind him of this later. So, the great moment arrives:

And the Lord God caused a deep sleep to fall upon Adam, and he slept: and he took one of his ribs, and closed up the flesh instead thereof; And the rib, which the Lord God had taken from man, made he a woman, and brought her unto the man. And Adam said, This is now bone of my bones, and flesh of my flesh: she shall be called Woman, because she was taken out of Man (Genesis 2:21-23).

So the male has the naming rights, and the woman provides unspecified help, and they quickly notice that they’re both ‘naked’ – though what might that mean? – but it didn’t apparently bother them – because, it seems, they hadn’t eaten from the Tree of the Knowledge of Good and Evil (TKGE), a useful tree for any garden. Clearly, none of this makes sense from a modern perspective, but the story goes on, with a talking serpent, who addresses the as-yet unnamed woman, convincing her that she should eat from the TKGE, to become wise. This sounds like good advice, and the woman judges the fruit of the tree to be good, and so she eats, and gets the man to eat, and they’re ashamed, and they hide from the god, who, being omniscient, eventually finds them. He asks why they’re hiding and Adam explains that they’re naked – sophisticated language already! – to which the god asks the very interesting question, Who told you you were naked? There’s no answer, and the god assumes that they’ve eaten from the TKGE. But he doesn’t appear to be sure, he has to ask them. So Adam blames the woman, who blames the serpent, though of course there’s no explanation as to why ignorance is bliss and devouring knowledge is bad.

Most important for my purposes here is the god’s treatment of the woman:

Unto the woman he said, I will greatly multiply thy sorrow and thy conception; in sorrow thou shalt bring forth children; and thy desire shall be to thy husband, and he shall rule over thee (Genesis 3:16)

So that sets the pattern of male-female inequality in Judaism. Pretty flimsy, needless to say.

Now to turn to the warrior god, who is also a jealous god (which is certainly not the same thing). The god of the Israelites, essentially YHWH, is deliberately mysterious, and amorphous. He must not be represented (this is called aniconism, against icons), to make a graven image is toto forbidden. The religious historian Christophe Lemardelé, in an essay of great complexity, finds that the tension between a jealous god, who seems in some kind of marital relation with his people, and a warrior-god seeking to save his people and fight for them, as in the books of Exodus and Judges, can best be resolved by examining the anthropology of the peoples who created this god:

The figure of the patriarch Abraham echoes a pastoral population located in Hebron and therefore leads to suggesting that the patriarchal ideology of Genesis—a book of Judean and rather late origin (Persian period, around the 5th century)—would have its background in the family and kinship structures of these nomadic groups. It seems difficult to us to envisage, without any migration, a late Iron age diffusion, however slow, of the Yahweh’s religion from south to north through these groups. The divine covenant with Abraham, Isaac and Jacob is not at the origin of God’s privileged relationship with Israel but rather one of its final elaborations.

It seems the god evolved with an increasing patriarchy – the origin stories were by no means the first written, and their misogyny, such as it is, is partial witness to an increasingly endogamous patrilineal society. This god, through the stories of Judges, Deuteronomy and Exodus, becomes more tightly bound to his chosen people, increasingly jealous of other gods, and increasingly demanding and unforgiving. Such is the legacy of the Abrahamic religions, if you want it.

There is of course a great deal more to say and learn, but the WEIRD world continues to move away from these tales and life examples, into hopefully something more bonoboesque, something more in keeping with our actual and potential human nature. The religion that reinforced over a millennium of misogyny is failing, all too slowly, in its Western European heartland, and it would be nice if we could speed that up. We understand our world now well enough to know that keeping women out of positions of power, demeaning them, pretending that they are inferior, or that their roles should be circumscribed, has been disastrous. Nothing short of disastrous. I want to argue for a worldwide release of female power, and a promotion of female dominance. It’s happening slowly, but I’m impatient. I want to present the evidence and I want to continue to see changes bearing fruit. There are parts of the world that are going backwards, certainly – in Afghanistan, in Burma, in China and many other regions. We need to show them by example how good it can be. We need to work to reduce the macho thugocracies (the majority of the world’s nations), and find ourselves in a less brutal, more collaborative, more caring, inclusive and thoughtful world. The rise of female power, I believe, is absolutely central to that transition. Without which not.

References

https://www.bibleodyssey.org/en/passages/related-articles/two-creations-in-genesis

Click to access the-jealousy-of-god.pdf

Written by stewart henderson

May 12, 2022 at 11:50 am

On the origin of the god called God, part one – on the Judean need for a warrior god

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It has long irritated me that people ask the question ‘Do you believe in God?’ or ‘why don’t you believe in God?’, assuming that there’s only one deity, a cultural assumption that reveals a fair degree of ignorance. Obviously there are many gods, or spirits, or powers or forces, because many many cultures have developed over many thousands of years in isolation to each other. 

For example, I’ve been reading Cassandra Pybus’ book Truganini, which relates the horrors suffered by the Aboriginal inhabitants of what was then Van Diemen’s Land in the 1820s and 30s. One particular spirit – Raegewarrah – was considered mostly responsible for the disaster that had befallen them with the advent of Europeans, but there were many other gods and spirits associated with places, activities and so on. Speaking more generally, I recall one spiritually inclined friend saying that these different gods or spirits are all different interpretations of God, or the godhead or some such thing, but it doesn’t take much anthropological research to discover that so many of these creatures have different characters, powers, relationships and fields of agency. There are malevolent and benevolent gods, there are capricious, unpredictable gods, there are regional gods, seasonal gods, gods of love and gods of war, gods of the sea, gods of the forest, squabbling and/or incestuous families of gods, hierarchies of gods, and gods of the other peoples over the mountains or on faraway islands.

It’s stated on some websites that there are between 8000 and 12000 gods on record, but records require writing, and religious beliefs surely predates writing, as for example those of Aboriginal Australians. And we have as little idea of when religious belief in humans began as we do of the beginning of human language. It’s likely though, at least to me, that the origins of human language and religion are connected.

But returning to God, rather than gods, this is a reference to the Judeo-Christian god, as I live in a country colonised by Christians. He (and he’s very male) is also referred to as the Abrahamic god, who unites the three associated religions, Judaism, Christianity and Islam in monotheism, or sort of. Christianity differs from the others in that there’s two gods, father and son, who sort of compete with each other for the attention of belevers, being, apparently, quite different characters. 

Anyway, this Judaic god wasn’t, strictly speaking the first monotheistic god, though he was at the foundation of the first successful monotheistic religion that we know of. We can’t of course be certain of how many monotheisms have been tried in history or ‘prehistory’ but we do know of the attempt by the Egyptian pharaoh Akhenaten, some 3,300 years ago – some 750 years before the rabbis of Judah got together to institute their monotheism. Akhenaten tried to compel his subjects to worship the Aten, the Sun God, but only through him, the pharaoh. It was an attempt to impose monotheism in a very hierarchical way, to consolidate the pharoah’s power, and it would’ve entailed the essential abolition of over a hundred other Egyptian gods, so it didn’t survive Akhenaten’s death – in fact, there was a fierce reaction to it afterwards.

Now of course the rabbis of Judah knew nothing about this when they began to develop their monotheism. It’s likely that the Judaic religion existed centuries before it turned monotheistic. It was one of several Canaanite polytheistic religions of the region, and the various Semitic cultures probably shared their different deities, leading to confusion at times about their identities and roles. Much of this will always be speculative as we have few written records from the time, but the name El, from which the Arabic name Allah derives, comes up in slightly different forms in Ugaritic, in Aramaic and in so-called proto-Semitic languages to describe a god who may are may not be the same god in each case. Sometimes El seems to represent a special or supreme god among gods. Other times it seems like a prefix to some particular god, such as El-Hadad. So basically, the name El, and its derivatives, comes up in so many language-forms and in so many contexts that it’s virtually impossible to characterise the god in any coherent way. If you don’t believe me, look up the comprehensive Wikipedia entry on this god, or this descriptor. 

So during the Bronze Age (about 5300 to 3200 years ago) the land of Canaan, of which Judah was a a small part, was occupied or influenced by the Egyptians, the Hittites, the Hurrian Mitanni and the Assyrians, among others. So there were all sorts of cultural and religious influences and pressures that I’m not scholared enough to sort out, but the gods that most stuck with or appealed to the Israelite tribes of Judah and surrounding regions were Yahweh, a warrior-god, the aforementioned El, the mother goddess Asherah, and Baal, who by the time of Iron Age 1 (3200-3000 years ago) had come to replace El in parts of Canaan as the master god. Baal was particularly a fertility god, associated especially with rainfall, which was crucial to the region. The scholarly term is monolatristic worship – with many gods, but one god being more prevalent or important. 

However, over time, and probably due to the regular incursions into and occupation of Israelite regions by other cultures, Yahweh became the more favoured god, a being to rouse the embattled Israelites against their various oppressors. The most serious oppression came from the Babylonians during Iron Age II (about 2600 to 2550 years ago) when the Babylonian King Nebuchadnezzar II besieged Jerusalem and deported the most prominent Judeans, taking them captive to Babylon. Jerusalem, the city, was apparently destroyed, though much of the rest of Judah remained untouched. It was likely this trauma (much relieved a few decades later by the defeat of the Babylonians by Cyrus II of Persia, and the return from exile) that turned the Judean people inwards, and caused them to see Yahweh, their warrior-god, as their sole god, under whom they needed to unite as his chosen people. 

Which brings me to the complex writings of the Torah or Pentateuch, the first five books of the Hebrew Bible. I feel daunted at the thought, so I’ll focus mostly on Genesis, the origin. I have very little interest in the endless abstrusities of Judaism or any other religion, but the tight hold that ‘the one true God’ still has on millions of people has fascinated and disturbed me for decades, especially considering what we’ve come to know about our universe in the past few centuries. It seems knowledge percolates slowly, even when confined to the so-called ‘WEIRD’ world. 

I don’t believe that science and religion are in any way compatible – they offer completely different programs, if you will, for understanding the world and our place in it. The science program is endless, or opened-ended, if you will – with new facts or findings leading to new questions, which, when answered lead to further questions with no end in sight, whereas the religious program (and I’m specifically focussing on Abrahamic religions) has an end, in God, He who cannot be questioned. The old Stephen Jay Gould attempt to evoke NOMA (non-overlapping majesteria), the idea that science and religion can live happily together, (about which I’ve written here), always struck me as frankly ridiculous. 

Of course I understand that religion comes wrapped in culture, which comes wrapped in religion, and all this forms a great part of the identity of many people, and I have no wish to belittle or take from people their culture. It’s a vexed issue, and I don’t have all the answers. I do think there are heavy cultures, which can be damaging, and I notice this damage especially when it comes to gender. Bonobos again. And since the god called God is so very very masculine, I cannot help but feel great discomfort about the Abrahamic religions. 

So my next post will look at the Hebrew Origin myth and the nature of the god as shaped by the writers of the earliest texts.

References

https://www.newscientist.com/letter/mg19125641-200-how-many-gods-are-there/

Truganini: journey through the apocalypse, by Cassandra Pybus, 2020

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

https://en.wikipedia.org/wiki/El_(deity)

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

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

Stephen Jay Gould, NOMA and a couple of popes

 

Written by stewart henderson

April 29, 2022 at 1:29 pm

some more on hydrogen and fuel cells

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an electrolyser facility somewhere in the world, methinks

Canto: Our recent post on democracy and public broadcasting has made me turn to PBS, in order to be more democratic, and I watched a piece from their News Hour on clean hydrogen. Being always in need of scientific education, I’ve made this yet another starting point for my understanding of how hydrogen works as an energy source, what fuel cells are, and perhaps also about why so many people are so skeptical about its viability. 

Jacinta: Fuel cells are the essential components of hydrogen vehicles, just as batteries are for electric vehicles, and infernal combustion engines are for the evil vehicles clogging the roads of today, right?

Canto: Yes, and Jack Brouwer, of the National Fuel Cell Research Centre in California, claims that fuel cells can be designed to be just as fast as battery engine. Now according to the brief, illustrated explanation, diatomic hydrogen molecules enter the fuel cell (hydrogen occurs naturally in diatomic form, as does oxygen). As Miles O’Brien, the reporter, puts it: ‘A fuel cell generates electricity by relying on the natural attraction between hydrogen and oxygen molecules. Inside the cell, a membrane allows positive hydrogen particles [basically protons] to pass through to oxygen supplied from ambient air. The negative particles [electrons] are split off and sent on a detour, creating a flow of electrons – electricity to power the motor. After their work is done, all those particles reunite to make water, which is the only tailpipe emission on these vehicles.’  

Jacinta: He tells us that the oxygen is supplied by ambient air, but where does the hydrogen come from? No free hydrogen. That’s presumably where electrolysis comes in. Also, membranes allows protons to pass but not electrons? Shouldn’t that be the other way round? Electrons are much tinier than protons.  

Canto: Very smart. Maybe we’ll get to that. Brouwer talks of the benefits of fuel cells, saying ‘you can go farther’, whatever that means. Presumably, going farther with less fuel, or rather, you can have a lot of fuel on board, because hydrogen’s the lightest element in the universe. Clearly, it’s not so simple. O’Brien then takes us on a brief history of hydrogen fuel, starting with the conception back in 1839, and real-world application in the sixties for the Apollo missions. The Bush administration pledged a billion dollars for the development of hydrogen fuel cell cars in the 2000s, but – here’s the problem – they were producing hydrogen from methane, that infamous greenhouse gas. Ultimately the cars would be emission free and great for our cities and their currently dirty air, but the hydrogen production would be a problem unless they could find new clean methods. And that’s of course where electrolysis comes in – powered by green electricity. 

Jacinta: The splitting of water molecules, a process I still haven’t quite got my head around…. 

Canto: Well the PBS segment next focuses on the sectors in which, according to Brouwer, hydrogen fuel will make a difference, namely air transport and shipping. Rail and heavy vehicle transport too – where the lightness of hydrogen will make it the go-to fuel. It’s energy-dense but it must be compressed or liquefied for distribution. This makes the distribution element a lot more expensive than it is for petrol. So naturally Brouwer and others are looking at economies of scale – infrastructure. The more of these compressors you have, the more places you have them in, the cheaper it will all be, presumably. 

Jacinta: Right, as presumably happened with wind turbines and solar panels, and the more people working on them, the more people coming up with improvements… But how do they liquefy hydrogen?

Canto: Hmmm, time for some further research. You have to cool it to horribly low temps (lower than −253°C), and it’s horribly expensive. There was a bipartisan infrastructure bill passed recently which will fund the building of hydrogen distribution hubs around the USA through their Department of Energy. That’s where the action will be. The plan, according to mechanical engineer Keith Wipke of the National Renewable Energy Laboratory, is to do in ten years what it took solar and wind 3 or 4 decades to achieve. That is, to bring hydrogen production costs right down. He’s talking $1 per kilogram. 

Jacinta: Okay, remember that in 2032. 

Canto: Yeah, I won’t. They’re talking about improving every aspect of the process of course, including electrolysers, a big focus, as we’ve already reported. They’re connecting these electrolysers with renewable energy from wind and solar, and, in the bonobo-science world of caring and sharing, any new breakthroughs will quickly become globalised. 

Jacinta: Yeah, and Mr Pudding will win the Nobel Peace Prize…

References

Could hydrogen be the clean fuel of the future? (PBS News Hour video)

green hydrogen? it has its place, apparently

Written by stewart henderson

April 25, 2022 at 5:37 pm