an autodidact meets a dilettante…

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

Archive for the ‘Eve’ Category

understanding genomics 1 – mitochondrial DNA

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Canto: So maybe if we got humans to mate with bonobos we’d get a more promising hybrid offspring?

Jacinta: Haha well it’s not that simple, and I don’t mean just physiologically…

Canto: Okay those species wouldn’t be much attracted to each other – though I’ve heard that New Zealanders are very much attracted to sheep, but that just might be fantasy. But seriously, if two species – like bonobos and chimps, can interbreed, why can’t bonobos and humans? And they’d don’t have to canoodle, you can do it like in vitro fertilisation, right?

Jacinto: Well, bonobos and chimps are much more closely related to each other than they are to humans. And if you think bonobo-human hybridisation will somehow create a female-dominant libertarian society, well – it surely ain’t that simple. What we see in bonobo society is a kind of social evolution, not merely a matter of genetics. But having said that, I’m certainly into exploring genetics and genomics more than I’ve done so far.

Canto: Yes, I’ve been trying to educate myself on alleles, haplotypes, autosomal and mitochondrial DNA, homozygotism and heterozygotism (if there are such words), single nucleotide polymorphisms and…. I’m confused.

Jacinta: Well, let’s see if we can make more sense of the science, starting with, or continuing with Who we are and how we got here, which is mostly about ancient DNA but also tells us much about the past by looking at genetic variation within modern populations. Let me quote at length from Reich’s book, a passage about mitochondrial DNA – the DNA in our mitochondria which is somehow passed down only along female lines. I’ve no idea how that happens, but…

The first startling application of genetics to the study of the past involved mitochondrial DNA. This is a tiny proportion of the genome – only approximately 1/200,000th of it – which is passed down from mother to daughter to granddaughter. In 1987, Allan Wilson and his colleagues sequenced a few hundred letters of mitochondrial DNA from diverse people around the world. By comparing the mutations that were different among these sequences, he and his colleagues were able to construct a family tree of maternal relationships. What they found is that the deepest branch of the tree – the branch that left the main trunk earliest – is found today only in people of sub-Saharan African ancestry, suggesting that the ancestors of modern humans lived in Africa. In contrast, all non-Africans today descend from a later branch of the tree.

Canto: Yes, I can well understand the implications of that analysis, but it skates fairly lightly over the science, understandably for a book aimed at the general public. To be clear, they looked at the same stretches of mitochondrial DNA in diverse people, comparing differences – mutations – among them. And in some there were many mutations, suggesting time differences, due to that molecular clock thing. And I suppose those that differed most – from who? – had sub-Saharan ancestry.

Jacinta: Dating back about 160,000 years, according to best current estimates.

Canto: The science still eludes me. First, how does mitochondrial DNA pass only through the female line? We all have mitochondria, after all.

Jacinta: Okay, I’ve suddenly made made myself an expert. It all has to do with the sperm and the egg. One’s much bigger than the other, as you know, because the egg carries nutrients, including mitochondria, the only organelle in your cytoplasm that has its own DNA. Your own little spermatozoa are basically just packages of nuclear DNA, with a tail. Our mitochondrial DNA appears to have evolved separately from our nuclear DNA because mitochondria, or their ancestors, had a separate existence before being engulfed by the ancestors of our somatic or eukaryotic cells, in a theory that’s generally accepted if difficult to prove. It’s called the endosymbiosis theory.

Canto: So mitochondria probably had a separate, prokaryotic existence?

Jacinta: Most likely, which could take us to the development, the ‘leap’ if you like, of prokaryotic life into the eukaryotic, but we won’t go there. Interestingly, they’ve found that some species have mitochondrion-related organelles with no genome, and our own and other mammalian mitochondria are full of proteins – some 1500 different types – that are coded for by nuclear rather than mitochondrial DNA. Our mitochondrial DNA only codes for 13 different types of protein. It may be that there’s an evolutionary process going on that’s transferring all of our mitochondrial DNA to the nucleus, or there might be an evolutionary reason for why we’re retaining a tiny proportion of coding DNA in the mitochondria.

Canto: So – we’ve explained why mitochondrial DNA follows the female line, next I’d like to know how we trace it back 160,000 years, and can place the soi-disant mitochondrial Eve in sub-Saharan Africa.

Jacinta: Well the term’s a bit Judeo-Christian (there’s also a Y-chromosomal Adam), but she’s the matrilineal most recent common ancestor (mt-MRCA, and ‘Adam’ is designated Y-MRCA).

Canto: But both of these characters had parents and grandparents – who would be somehow just as common in their ancestry but less recent? I want to know more.

Jacinta: To quote Wikipedia…

… she is defined as the most recent woman from whom all living humans descend in an unbroken line purely through their mothers and through the mothers of those mothers, back until all lines converge on one woman.

… but I’m not sure if I understand that convergence. It clearly doesn’t refer to the first female H sapiens, it refers to cell lines, haplogroups and convergence in Africa. One of the cell lines used to pinpoint this convergence was HeLa, the very first and most commonly used cell line for a multiplicity of purposes…

Canto: That’s the Henrietta Lacks cell line! We read The Immortal Life of Henrietta Lacks! What a story!

Jacinta: Indeed. She would be proud, if she only knew… So, after obtaining data from HeLa and another cell line, that of an !Kung woman from Southern Africa, as well as from 145 women from a variety of populations:

The published conclusion was that all current human mtDNA originated from a single population from Africa, at the time dated to between 140,000 and 200,000 years ago.

Canto: So mt-MRCA is really a single population rather than a single person?

Jacinta: Yeah, maybe sorta, but don’t quote me. The Wikipedia article on this gives the impression that it’s been sheeted home to a single person, but it’s vague on the details. Given the way creationists leap on these things, I wish it was made more clear. Anyway the original analysis from the 1980s seems to be still robust as to the time-frame. The key is to work out when all female lineages converge, given varied mutation rates. So, I’m going to quote at length from the Wikipedia article on mt-MRCA, and try to translate it into Jacinta-speak.

Branches are identified by one or more unique markers which give a mitochondrial “DNA signature” or “haplotype” (e.g. the CRS [Cambridge Reference Sequence] is a haplotype). Each marker is a DNA base-pair that has resulted from an SNP [single nucleotide polymorphism] mutation. Scientists sort mitochondrial DNA results into more or less related groups, with more or less recent common ancestors. This leads to the construction of a DNA family tree where the branches are in biological terms clades, and the common ancestors such as Mitochondrial Eve sit at branching points in this tree. Major branches are said to define a haplogroup (e.g. CRS belongs to haplogroup H), and large branches containing several haplogroups are called “macro-haplogroups”.

So let’s explain some terms. A genetic marker is simply a DNA sequence with a known location on a chromosome. A haplotype or haploid genotype is, as the haploid term suggests, inherited from one rather than both parents – in this case a set of alleles inherited together. SNPs or ‘snips’ are differences of a single nucleotide – e.g the exchange of a cytosine (C) with a thymine (T). As to the rest of the above paragraph, I’m not so sure. As to haplogroups, another lengthy quote makes it fairly clear:

A haplogroup is…. a group of similar haplotypes that share a common ancestor with a single-nucleotide polymorphism mutation.More specifically, a haplogroup is a combination of alleles at different chromosomal regions that are closely linked and that tend to be inherited together. As a haplogroup consists of similar haplotypes, it is usually possible to predict a haplogroup from haplotypes. Haplogroups pertain to a single line of descent. As such, membership of a haplogroup, by any individual, relies on a relatively small proportion of the genetic material possessed by that individual.

Canto: Anyway, getting back to mt-MRCA, obviously not as memorable a term as mitochondrial Eve, it seems to be more a concept than a person, if only we could get people to understand that. If you want to go back to the first individual, it would be the first mitochondrion that managed to synthesise with a eukaryotic cell, or vice versa. From the human perspective, mt-MRCA can be best conceptualised as the peak of a pyramid from which all…  but then she still had parents, and presumably aunts and uncles…. It just does my head in.



Written by stewart henderson

February 11, 2023 at 5:56 pm

a bonobo world: the ascent and fall of man

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                                  devil woman, with evil on her mind

Bonobos obviously evolved from some earlier type, along with chimps, but we’re not as interested in their evolution as we are in ours, understandably enough. What wouldn’t we give to fill in the gaps in our rise – the where and when of the first use of fire, the first spoken language, the beginnings of religious practice and so on? And of course none of us will live long enough to find out if bonobos, left alone (which they won’t be), become more gynocratic or less in the distant future, let alone whether we humans will eventually manage to live for as long as some tortoises I’ve heard about.

We human apes, of course, have socially evolved, especially over the past few thousand years, as Jacob Bronowski pointed out regularly in the series so admired by Deutsch. Yet interestingly, there was a kind of evolution that Bronowski himself, and the producers of The Ascent of Man, seemed not to have arrived at by 1971. I haven’t watched the entire series, only the two episodes and other bits and pieces I’ve found on YouTube, because I’m too poor to pay for the entire series, but having watched the first episode more than once, I felt bugged by all this ‘man’ stuff. So I did a count. Bronowski utters the word ‘man’ 70 times, together with the pronouns ‘he’ (29 times), ‘his’ (23) and ‘him’ (12). The words ‘woman’ ‘she’ and ‘her’ are uttered zero times in toto by my count. In terms of imagery, only two human figures are focussed on apart from Bronowski, a male child learning to stand on two feet, and a male athlete running and pole vaulting. But of course, by ‘man’ he means ‘human’, right? And, hey, this was the beginning of the seventies, right? Which was almost the sixties, really quite close to the fifties…

I’m not even a woman but I felt like I was having my female irrelevance bashed into my face in listening to all this – a bit like a sleeping woman who only realises she’s being clouted when she wakes up. And all this man stuff didn’t suddenly end with the seventies – I’m reminded of a book, God, actually, which I read at the tail end of the New Atheism flare-up a few years ago. It was a dreadful piece of drivel seeking to prove the existence of the Judaeo-Christian god and to debunk evolution, which, against the advice of my betters, I managed to read to the end. Yet nothing in the male author’s specious arguments irritated me more than his deliberate use of ‘man’ as a generic term (though I was more irritated at the publisher, ABC books of all people). At one point, after reading the ‘man’ word about fifteen times in a couple of pages, I threw the book across the room in disgust. It seemed far more of an attack on women than on atheists.

But perhaps the title ‘The Ascent of Man’ was meant as a clever science-and-human development counterpoint to the religious ‘Fall of Man’ trope? Or at least, let’s pretend. The fall of man really was male, of course, and it was caused by woman. Or, if you like, by god, who should’ve left that spare rib alone. Not that this little fable was necessary to create a viciously misogynistic society, as witness the ancient Greeks (with apologies to the Spartans). Still it did a fine job of making life hot for women, long before the witch-burning frenzy of the fifteenth,  sixteenth, seventeenth  and eighteenth centuries (to be precise, the last woman known to have been burnt to death as a witch was Barbara Zdunk in Poland in 1811, and the first known execution of a witch, recorded by Demosthenes, was of Theoris of Lemnos, and her family, some time before 323 BCE, though it’s likely that witch-hunting, torture and execution predates this). Since all the early Christian writers and power-wielders were men with natural sexual desires, and since they’d gotten into their collective heads a fear and hatred of sexual desire as a straying from the endless and more or less brainless contemplation of the divine, women, the ‘daughters of Eve’ (though women were generally supposed, at least by the elites who pretended to understand such things, to be the carriers of the human seed without contributing to it) became the collective scapegoat. Basically, women were encouraged to be the objects of men’s desires, and exploited as such, and then blamed for it. Here’s the early Christian writer Tertullian, as memorably quoted by Beauvoir in The Second Sex:

And do you not know that you are (each) an Eve? The sentence of God on this sex of yours lives in this age: the guilt must of necessity live too. You are the devil’s gateway: you are the unsealer of that (forbidden) tree: you are the first deserter of the divine law: you are she who persuaded him whom the devil was not valiant enough to attack. You destroyed so easily God’s image, man. On account of your desert — that is, death — even the Son of God had to die. And do you think about adorning yourself over and above your tunics of skins?

As many feminist writers have pointed out, the exploitation of, and the ill-treatment, murder and general public opprobrium of sex workers of all varieties has never really abated, despite the so-called sexual liberation that began decades ago. What these religious and conservative types would think of bonobo shenanigans is an interesting question, but not particularly relevant for the future of humanity, whether it’s headed upwards or down. For the future lies with those who are open and attentive to the behaviour of our relatives. Bonobos’ use of sex isn’t obsessive, or particularly excessive. What is excessive and obsessive is our fear of sex, and our need to control it, to hide it, to wrap it in bonds of ownership, to weaponise it. We’re so  absurdly uptight about it, so incapable of normalising it as a need, a feeling, an appetite, a social bond, a pleasure.

The fall, indeed. We’ve fallen for so many myths about sex. When will be able to rise above all that, and be kinder to each other? Not until women are on top, I’m pretty sure.


The Ascent of Man, Ep. 01 “Lower Than the Angels” (YouTube video)

Roy Williams, God, actually, 2010, ABC Books & HarperCollins

Misogynistic Quotations from Church Fathers and Reformers

Written by stewart henderson

October 11, 2021 at 9:32 pm