Archive for the ‘DNA’ Category
could I ever manage to get my head around epigenetics?
Nessa Carey’s book, The epigenetics revolution, was published in 2011, and discusses, and introduces, to many of us, gene methylation, histones, a number of different types of RNA, the names of specific genes, karyotypes, selective serotonin re-uptake inhibitors (SSRIs), phosphorylation, the Waddington epigenetic landscape and much else besides. Wikipedia’s account of epigenetics is no doubt more up-to-date, and is just about book-length (how long does a book have to be?), with over 200 references to scientific papers and such. Although the term was coined in the 1940s, the study of epigenetics is very much a 21st century thing, Our current knowledge of the area, like our knowledge of neurophysiology, has been one of the great developments in modern science. To read about it is exasperating, because there’s just too much to learn, to explore, to get your head around, and yet it’s vital to an understanding of who and what we are. When I think of SETI, for example, the Search for Extra-Terrestrial Intelligence, I wonder – how could such ineffable super-complexity have developed more than once in the universe, even given its incalculably massive extent?
I wish I was young and gifted with the opportunity to work in such a field, one which explains us, or tries to. How we manage to replenish all the cells in our bodies throughout our lives – not perfectly, for then we could live forever – but for a period extended enough for us to learn our own history, to fall in love, to learn from our many mistakes, to experience, delight in and suffer through all the stages of life, to observe all its amazing variety – the birds and the bees as they say, and the flowers and the trees, all of which have their genetic blueprints.
To think we had virtually no idea of this only a century ago, and we are 300,000 years old as a species, and DNA-driven creatures have existed for millions, maybe billions of years on this planet. We only worked out the structure of this molecule in the 1950s, and now we know for example that a spruce tree contains about six times more DNA than a human, and that it’s likely that our world was preceded by an RNA world, which still enlivens the viruses that plague us with influenza, hepatitis, polio, COVID-19 and so much else.
And all this epigenetic stuff – which is mainly about DNA methylation and histone modification – has been going on beneath our awareness, and certainly without our permission, since our life began as an embryo. That’s how our cells differentiate into some 200 different types. It has much to do with whether we’re tall or short, sickly or healthy, extroverted or introverted – even before we’ve ever met another soul. All of these goings-on in our growing bodies, as well as the inter-connections, disconnections and reconnections in our growing brains, in the time spent connected to a placenta and the subsequent years being buffeted by parents, relatives, strangers and frenemies, are what shape us for a lifetime.
So where am I going with all this? Those who know me might guess, and be much annoyed, or much heartened.
To return to Carey’s book, which explores, inter alia, how laboratory creatures like rats and mice show specific patterns of behaviour for a lifetime after early deprivation, stress and other conditions, I was struck by this passage:
The human brain possesses sufficient flexibility to generate adult outcomes in response to similar childhood experiences. Our brains contain one hundred billion nerve cells (neurons). Each neuron makes links with ten thousand others to form an incredible three dimensional grid. This grid therefore contains a thousand trillion connections – that’s 1,000,000,000,000,000 (a quadrillion). It’s hard to imagine this, so let’s visualise each connection as a disk that’s 1mm thick. Stack up the quadrillion disks on top of each other and they will reach to the sun (which is 93 million miles from the earth) and back, three times over.
That’s a lot of connections, so it’s perfectly possible to imagine that our brains have a lot of flexibility. But the connections are not random. There are networks of cells within the giant grid which are more likely to link to each other than to anywhere else. It’s this combination of huge flexibility, but constrained within certain groupings, that is compatible with a system that is mechanistic but not entirely deterministic.
Nessa Carey, The epigenetics revolution, pp 235-6
This is, I believe, the only passage in Carey’s 300-page book that refers to determinism, and of course it struck me enough to write one word in the margin.
‘Really?’
I don’t often write in the margins of my books these days. Decades ago I had a girlfriend who expressed shock and great disapproval at finding margin notes in some of my books. She apparently found this behaviour to be sacrilegious in some way. Texts were sacred even if they were reproduced in their thousands. So, though I respectfully disagreed, I’ve reduced my sacrilegious behaviour, maybe to honour her memory. But this time I couldn’t resist.
– ‘mechanistic but not entirely deterministic’? What is the difference between these two terms? Aren’t these mechanisms determined by other mechanistic processes? Isn’t this what the book is all about? Isn’t this how we know about epigenetic processes, because they produce certain changes under certain specific conditions? Aren’t the determining factors precisely what we’re looking for, and what knowledge is all about. And yet there is, I find, a kind of fear or distrust of the word, even amongst those researchers who rely on mapping out the causal chain, often a complex and elusive one, to make good their discoveries. Whether we’re looking at the causes of cancer, or how one or two bees become queens while thousands more become workers, to mention just two topics explored in Carey’s book, we’re always trying to uncover and explain the determining conditions. It’s the sine qua non of all science.
Maybe I’m mis-representing Carey here. Maybe she meant, when she described the ‘huge flexibility’ of our neuronal system, the impossibility of trying to pin things down, cause-and-effect-wise, with absolute certainty. But then, that’s not what she wrote. She wrote ‘not entirely deterministic’, and that was a red flag to me. So what was the part that escaped determinism? It doesn’t actually make sense.
The idea, it seems to me, and the argument that most people try to use against determinism, is that complexity trumps it (sorry to use the word ‘trump’ here). If complexity was infinite, that might be so, but complexity isn’t infinite, it’s just complex.
So, that’s enough for now. Again, I wish I was fifty years younger, and a more disciplined person than I was in my youth, because I’d love to be working in the field of organic chemistry, or molecular biology, or neurophysiology, rather than peering at it over a vast stretch of ignorance, as I am today. But never mind…
References
Nessa Carey, The epigenetics revolution, 2011
abiogenesis – some amateur explorations
woteva
One of the greatest mysteries and challenges we face, as living beings – if we’re interested – is how living beings came to be. And we’re the only form of living beings, that we know of, asking this question. Hans Castorp, the central character of Thomas Mann’s The Magic Mountain, pondered the matter in his loggia while taking the cure in an alpine sanatorium. He even went further than the What is life question, asking What is matter? Why is there something rather than nothing?
It was a novel that changed my life. From that reading experience I turned, quite abruptly, to science. I bought Scientific American every month, until I switched to New Scientist, and started reading books by Richard Dawkins, Peter Atkins et al. Of course I’ve never undertaken any formal studies in science, and I’ve always preferred the informal to the formal, and not being subject to authorities telling me what to learn or know. That’s why Hans Castorp, reading and musing in his loggia, so appealed to me.
So what do we know on this subject? When did life begin on Earth, and how? It could have been close to 4 billion years ago, only half a billion years(!) after our planet was fully formed. We don’t have solid evidence, though. The earliest accepted evidence goes back 3.5 billion years, of ‘bacteria-like organisms’. That sounds pretty complex already, and presumably the ‘ingredients’, the intracellular material that sustained and motivated these beings, were around long before. Complexifying chains of molecules, formed out of the ‘primordial soup’, to use an unhelpful term. We think RNA and DNA of course, or at least nucleic acid chains. But what are nucleic acids, and what are the parts thereof? Other essential components include proteins and lipids, with the latter being essential to create more or less permeable boundaries between the organic and the inorganic (or proto-organic?). Lipid molecules, as the Arvin Ash video referenced below tells us, consist of a hydrophilic body, of sorts, and a hydrophobic tail. These molecules tend to come together to form spheres, with the outer, bulkier, hydrophilic ends joining together to protect or insulate the hydrophobic tails from the watery outer environment.
So there’s always a ‘what came before’ question. Where did these lipid molecules spring from, not to mention the other bits and bobs of life? Well, on lipids, I’m relying, for now, on the same video. Carbon monoxide (CO), hydrogen and minerals found in the Earth’s crust can combine to form lipids. All of these components can be found in the hydrothermal vents so recently found in the Pacific depths. But lipid structures break down in the presence of salt or magnesium ions, and these ions are essential for cellular and RNA development. Big problem, as the primeval oceans are believed to be more salty than those of today – though apparently we’re far from being certain about this. In any case, a 2019 paper from the University of Washington showed that lipid spheres remained intact in the presence of amino acids, the building blocks of protein molecules. To quote from the video,
The enclosing of amino acids within cell walls allows them to concentrate within those walls and interact with each other to form proteins, which are part of the ‘trinity’, one of the essential components of life.
So lipid cell walls and proteins, both of course non-living, require each other to survive in salty or iron-rich water. But what about the nucleic acids, DNA and RNA? These are the self-replicating molecules, the genetic material, or precursor genetic material. Today we know that RNA is created from DNA to build proteins according to DNA’s code, but the fact that RNA is the simpler of the two genetic materials suggests to most analysts that it came first. So there’s a hypothesis called the ‘RNA world’, which is generally well accepted by those in the field, but unfortunately we’ve made little progress in working out how RNA came to be formed.
RNA is made up of three chemical components – ribose (a sugar), the nucleobases, and phosphate. A ribose-base-phosphate unit links with other such units to form RNA polymer. But it’s not well understood how these links were formed, and they haven’t been successfully replicated in human experiments. The ribose-base link has proved particularly problematic. As Arvin Ash describes it, ‘this is because cells in your body require complex enzymes to bring RNA building blocks together before they combine to form polymers’. He describes one study, however, which found that today’s RNA could have formed on the surface of clays ‘which act like a catalyst to bring RNA bases together’. A later study showed that the building blocks of RNA could have polymerised in the early Earth, using organic molecules from meteorites and interplanetary dust in shallow ponds, where wet/dry cycles would have been conducive to such polymerisation. They considered that these polymers were probably present on Earth shortly after its formation.
So Ash describes a trinity – RNA, lipids and proteins. What about the proteins? We can go back to the Miller-Urey experiments of the 1950s, which showed that amino acids, the essential components of proteins, as well as other organic compounds, could be produced under particular atmospheric conditions, which they were able to replicate in the laboratory.
So, all these precursors might be explained, but they still need to combine for life as we know it, however basic. This is the big question that still needs to be answered. We haven’t discovered any precise mechanism, but oodles of time, and incremental steps are probably required, and there is surely a possibility of this in the first billions of our planet’s existence, wherein trillions of molecular interactions may have taken place. It’s something of a numbers game, something that many earlier theorists, and today’s creationists, have not taken sufficient account of. It’s also probable that the earliest life forms, those sparks, were so basic that they were quickly improved upon and rendered obsolete by – evolution. But that’s another story…
Needless to say, this piece was more or less wholly reliant on Arvin Ash’s excellent video, which I highly recommend.
References
Why is the Ocean So Salty?
understanding genomics 3: SNPs and other esoterica
Canto: So SNPs are pretty essential to modern genomics I believe, so why, and what are they? I know that they’re ‘single nucleotide polymorphisms’ and that nucleotides are A, C, G, T and U, each of which have a slightly different structure. They’re all based on sugar structures – ribose in the case of RNA and deoxyribose in the case of DNA – attached to a phosphate group and a nitrogenous base. Here’s a diagram of thymine (T) filched from the USA’s National Human Genome Research Institute:
So that’s a nucleotide, one of the building blocks of DNA and RNA, but the real problem, for me anyway, is the connection between single and polymorphic, if there is one. I know that poly means many and that morphology is about shape and size and such….
Jacinta: You can only get so far with interrogating the words themselves. An SNP is a genetic variation in a single nucleotide between one person’s genome and another (I think). But there are many of these variations, which is where the ‘poly’ comes in. I’ll quote this from a NIH website, and then try to make sense of it:
SNPs occur normally throughout a person’s DNA. They occur almost once in every 1,000 nucleotides on average, which means there are roughly 4 to 5 million SNPs in a person’s genome. These variations occur in many individuals; to be classified as a SNP, a variant is found in at least 1 percent of the population. Scientists have found more than 600 million SNPs in populations around the world.
Canto: So they’re called ‘variants’ because they vary from the ‘normal’ pattern in 1% or more of those whose genomes are mapped? So there’s such a thing as a ‘normal’ human genome, but perhaps everyone differs from that normal pattern due to different SNPs? And why is 1% the cut-off? Isn’t that a bit arbitrary? Also, it says that these variations occur in many individuals, which sounds a bit vague. Does this mean that there are many individuals where they don’t occur at all? I mean, what is a normal human genome, if there are so many variants? Is it just some kind of aggregated value?
Jacinta: Uhh, maybe. And note – but I’m not sure if this is relevant to your question – that these SNPs mostly occur in non-coding DNA, where they won’t be affecting the phenotype and its general functioning, though it seems to depend on how close they are to coding regions. Anyway, we’re just scratching the surface here. Look at this diagram, from Wikipedia.
As you can see, there are synonymous and non-synonymous SNPs. Synonymous with what, you might ask?
Canto: As a language teacher I know what a synonym is, obviously. My guess is that a synonymous SNP is associated with, ‘synonymous’ with, some kind of malfunction or defect, or maybe different function or effect. A ‘missence’, as the diagram suggests.
Jacinta: No, it’s the non-synonymous SNPs that cause the problems, because coding DNA generally leads to effective function, that’s what it’s all about. If the SNP is synonymous then it works toward proper functioning, perhaps by a different pathway, or it just doesn’t affect the pathway.
Canto: What I’m learning about genetics/genomics is that the more I delve into the subject, the more there is to learn, and yet I don’t really want to specialise, I want to know a bit of everything. I’ve just learned, for example, that it’s not just a divide between coding and non-coding DNA, because a mutation near a coding region can have effects, deleterious or otherwise, I think.
Jacinta: I don’t know about that, but I’m learning some interesting random facts, for example that there appears to be more C-G base pairings in coding DNA than T-A. Just to get it in our heads, cytosine (a pyrimidine) always pairs with guanine (a purine), and the other pyrimidine, thymine, always pairs with adenine. Always purines with pyrimidines, and purines are the larger molecules, with a two-ring structure, rather than one for pyrimidines. Note the structure of thymine, above. Anyway, back to SNPs, which we’re interested in mainly for what they might tell us about earlier populations. I’ve just glanced through a 2020 research article – generally way to technical for lay persons or dilettantes like us, titled ‘Genome-wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains’. I did get some useful info from it though. The researchers compared the SNP method with ‘single base extension (SBE) typing’, and what they found was interesting enough:
The DNA samples were extracted from the skeletal remains of 59 human individuals dating back to the Late Bronze Age. The 3,000 years old bones had been discovered in the Lichtenstein Cave in Lower Saxony, Germany.
It seems that this was a kind of proof-of-concept piece of research, and they were able to obtain good to excellent results from two thirds of the skeletal samples:
With the applied technique, it was for the first time possible to get information about major phenotypic traits—eye and hair color—of an entire prehistoric population. The range of traits, varying from blonde to brown hair and blue to green-hazel eye colors for the majority of individuals is a plausible result for a Central European population.
Canto: Yes, that’s the exciting stuff – true it’s only going back 3000 years, and you could say that there were no surprises in the findings – but it brings the past back to life in such a vivid way… what can I say?
Jacinta: So you don’t want to know about haplotypes, and homozygous and heterozygous alleles? What’s wrong with you?
Canto: Okay, a haplotype – haven’t we gone through this? – a haplotype is a set of variants, or polymorphisms, along a single chromosome, involving one or more genes, that tend to stick together, inheritance-wise. We know that homozygous inheritance means inheritance from both parents whereas heterozygous means that you have a different genetic marker from each parent. A genetic marker is any ‘DNA sequence with a known location on a chromosome’. They may offer clues to inherited traits, such as diseases. All of this comes from the USA’s National Human Genome Research Institute, and I think I mostly understand it.
Jacinta: So SNPs can have all sorts of uses, regarding the present and the past, and tracing the present into the past, as with disease gene mapping. Their abundance within the genome has made them the go-to marker in bioinformatics. My guess, though, is we’ll never get to fully understand them without actually working with them. I mean, we can go through ScienceDirect, and jump from underlined term to underlined term (e.g. linkage disequilibrium, QTL mapping, PCR assays, point mutations and the like), but we’ll start to forget it all from the moment we have aha moments, because for us dilettantes, locked out of labs due to dumbness, shyness, laziness, poverty-ness etc, it’s all just book-larnin, sans even books. I suppose we just have to be grateful that we’ve, or they’ve, developed the technology to collect and analyse SNPs, to create libraries of them…
Canto: It seems like, as with so many fields, we’re at what Deutsch called ‘the beginning of infinity’ – but then didn’t they think that at the advent of string theory?
Jacinta: But we know this isn’t theory, this is about results. Tools producing results. Tools within the body, or rather natural phenomena made into tools by human ingenuity, like circles made into wheels, cubes into containers, triangles into struts. And we’re likely to get more and more out of DNA in the future. I recently learned about the petrous bone, though of course researchers have known about it for some years – it’s about the hardest part of the skull, down somewhere near the foramen magnum I think, and its density has, it seems, been a preservative for DNA – generally better than teeth. So that means more analysis of fossil collections. As David Reich puts it, technologies for analysing ancient DNA have created an explosion of information to rival the invention of the microscope/telescope a few hundred years ago.
Canto: Yes, some of the developments he mentions are next-generation sequencing (which has vastly reduced sequencing costs), more efficient DNA extraction methods, improvements in separating human from microbial DNA, and again the use of the petrous bone for extraction – a bone which tends to remain intact longer than others.
Jacinta: Okay, so we might continue to blunder on in trying to make sense of this genomics stuff, or maybe not. Enough for now.
References
https://www.genome.gov/genetics-glossary/Nucleotide
https://medlineplus.gov/genetics/understanding/genomicresearch/snp/
https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/point-mutation
https://en.wikipedia.org/wiki/Coding_region
https://onlinelibrary.wiley.com/doi/full/10.1002/ajpa.23996
understanding genomics 1 – mitochondrial DNA
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.
References
https://www.genome.gov/genetics-glossary/Mitochondrial-DNA
https://en.wikipedia.org/wiki/Mitochondrial_Eve
https://en.wikipedia.org/wiki/Haplogroup
Did bonobos do it with chimps? Well, duh
bonobos or chimps? Or both? Or neither? What’s in a name…?
Canto: So we’ve been learning than we did it with Neanderthals, and that Neanderthals did it with Denisovans, and I remember hearing an anthropologist or palaeontologist saying that it’s likely that our split with our last common ancestor with chimps and bonobos – they call it the CHLCA (chimp-human last common ancestor, eliminating bonobos altogether, sigh) – wasn’t necessarily a clean break, which surely makes sense.
Jacinta: Well, yes, as we’ve read, the split was caused by the relatively sudden creation of the Congo River, but the word ‘relatively’, is, well, relative. So this raises the question of speciation in general. Think of those Galapagos finches that so intrigued Darwin. All about differently-shaped beaks, but it didn’t happen overnight.
Canto: Right, so here’s what a website with the rather all-encompassing title “Science” says about our topic:
Tens of thousands of years ago, modern humans slept around with Neandertals and swapped some genes. Now, it turns out one of our closest living relatives, chimpanzees, also dallied with another species. New research reveals that chimps mixed it up with bonobos at least twice during the 2 million years since these great apes started evolving their own identities. Although it’s not yet clear whether the acquired genes were ultimately beneficial or harmful, the finding strengthens the idea that such cross-species mating played an important role in the evolution of the great apes.
Jacinta: Interestingly this Congo River separation which led to a completely different species was repeated by other separations which led to four sub-species of chimps. Which leads me to wonder – what’s the difference between a new species and a sub-species? Why are bonobos ‘deserving’ of being called a different species?
Canto: Well the Science article has some fascinating further information. This was the work of Christina Hvilsom and colleagues, described as ‘conservation geneticists’. They were using any genetic differences they could find to work out where particular chimps were being caught or hunted. But, since the interbreeding of humans and Neanderthals, proven by DNA, had hit the headlines, Hvilsom wondered about the DNA of chimps. So, using the same methods that uncovered Neanderthal in humans –
she and her colleagues determined that 1% of the central chimpanzee’s genome is bonobo DNA. The genetic analysis indicates that this inbreeding happened during two time periods: 1.5 million years ago bonobo ancestors mixed with the ancestor of the eastern and central chimps. Then, just 200,000 years ago, central chimps got another boost of bonobo genes, the team reports today in Science. In contrast, the western chimp subspecies has no bonobo DNA, the researchers note, suggesting that only those chimps living close to the Congo River entertained bonobo consorts.
Jacinta: What this highlights, more than anything to me, is the importance and excitement of genetic and genomic analyses. Not that we’re experts on the topic, but it has clearly revolutionised the science of evolution, complicating it in quite exciting ways. Think again of those Galapogos finches. Separation, some interbreeding, more separation, less interbreeding, but with a few kinks along the way.
Canto: And we’re just beginning our play with genetics and genomics. There’s surely a lot more to come. Ah, to live forever…
Jacinta: So how did they know some inbreeding occurred? Can we understand the science of this without torturing ourselves?
Canto: David Reich’s book Who we are and how we got here tells the story of interbreeding between human populations, and how population genetics has revolutionised our understanding of the subject. With dread, I’ll try to explain the science behind it. First, the Science article quoted above mentions a split between bonobos and chimps 2 million years ago. Others I’ve noted go back only about a million years – for example a Cambridge University video referenced below. The inference, to me, is that there was a gradual separation over a fair amount of time, as aforementioned. I mean, how long does it take to create a major river? Now, I can’t get hold of the data on chimp-bonobo interbreeding in particular, so I’ll try to describe how geneticists detect interbreeding in general.
I’ll look at the human genome, and I’ll start at the beginning – a very good place to start. This largely comes from Who we are and how we got here, and the following quotes come from that book. The human genome consists of a double chain of 3 billion nucleobases, adenine, cytosine, guanine and thymine. That’s 6 billion bases (often called letters – A, C, G and T) in all. Genes are small sections of this base chain (called DNA), typically a thousand or so letters long. They’re templates or codes for building proteins of many and varied types for doing many different kinds of work, although there are segments in between made up of non-coding DNA.
Researchers have been able to ‘read’ these letters via machinery that creates chemical reactions to specific DNA sequences:
The reactions emit a different colour for each of the letters A, C, G and T, so that the sequence of letters can be scanned into a computer by a camera.
What anthropologists want to focus on are mutations – random errors in the copying process, which tend to occur at a rate of about one in every thousand letters. So, about 3 million differences, or mutations, per genome (3 billion genes, coding or non-coding). But genomes change over time due to these mutations and each individual’s genome is unique. The number of differences between two individuals’ genomes tells us something about their relatedness. The more differences, the less related. And there’s also a more or less constant rate of mutations:
So the density of differences provides a biological stopwatch, a record of how long it has been since key events occurred in the past.
As Reich recounts, it was the analysis of mitochondrial DNA, the tiny proportion of the genome that descends entirely down the maternal line, that became a corner-stone of the out-of-Africa understanding of human origins, which had been competing with the multi-regional hypothesis for decades. ‘Mitochondrial Eve’ – a rather ‘western’ moniker considering that the Adam and Eve myth is only one of a multitude of origin stories – lived in Botswana in Southern Africa about 160,000 to 200,000 years ago, given the variability of the genomic ‘clock’ – the mutation rate.
So, what does this have to do with chimps and bonobos? Well, The exact detail of how Hvilsom et al proved that their (slightly) more recent interbreeding events occurred is hidden behind a paywall, and you could say I’m a cheapskate but the reality is I’m quite poor, trying to bring up seven kids and a few dozen grandkids in a home not much bigger than a toilet, so… but truthfully I’m just getting by, and I just want to know in general the techniques used.
First, they have to find ancient specimens, I think. But, in a video referenced below, they raised the question – Can we ‘excavate’ ancient DNA from modern specimens? We’ve learned that many modern humans have a certain percentage of Neanderthal DNA, say around 2%, but each person’s 2% may be different. Aggregating those different segments can, if we analyse the genomes of enough humans, create a whole Neanderthal genome, though not one of any Neanderthal who ever lived! At least that’s how I’m reading it, in my dilettantish way. So what exactly does this tell us? I’m not at all sure – it’s a relatively new research area, and completely new to me.
The presenter of this video uses the heading, at least at the beginning of his talk, ‘A little Archaic introgression goes a long way’. So now I need to know what introgression means. A quick look-up tells me it’s:
‘the transfer of genetic information from one species to another as a result of hybridization between them and repeated backcrossing‘.
I’ve bolded two key words here. Hybridisation, in mammals, is ‘breeding between two distinct taxonomic units’. Note that the term species isn’t used, presumably because it has long been a questionable or loaded concept – life just seems too complex for such hard and fast divisions. Backcrossing seems self-explanatory. Without looking it up, I’d guess it’s just what we’ve been learning about. Canoodling after speciation should’ve ruled canoodling out.
But, looking it up – not so! It’s apparently not something happening in the real world, something like backsliding. But then… Here’s how Wikipedia puts it:
Backcrossing may be deliberately employed in animals to transfer a desirable trait in an animal of inferior genetic background to an animal of preferable genetic background.
This is unclear, to say the least. How could an animal, even a human, deliberately do this? We could do it to other animals, or try it, based on phenotypes. We’ve been doing that for centuries. What follows makes it more or less clear that this is about human experimentation with other animals, though.
Anyway, I’m going well off-topic here. What I wanted to do is try to understand the proof of, or evidence for, bonobo-chimp interbreeding. I accept that it happened, well after the split between these two very similar-looking species. What could be less surprising? Along the way I’ve been reminded inter alia, of homozygous and heterozygous alleles, but I’ve been frustrated that straightforward information isn’t being made available to the general public, aka myself. I’ll pursue this further in later posts.
Jacinta: What a mess. Phenotype isn’t everything my friend. To a bonobo, a chimp probably looks like a neanderthal – a real bonehead… They probably only had sex with them out of pity. ‘Boys, we’ll show you a good time – like you’ve never had before.’
References
https://www.science.org/content/article/chimps-and-bonobos-had-flings-and-swapped-genes-past
David Reich, Who we are and how we got here, 2018
https://www.newscientist.com/article/2110682-chimps-and-bonobos-interbred-and-exchanged-genes/
exploring meiosis
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
reading matters 7
She has her mother’s laugh, by Carl Zimmer , science author and journalist, blogger, New York Times columnist, etc etc
content hints – inheritance and heredity, genetics and epigenetics, Darwin and Galton, the Hapsburg jaw, eugenics, Hugo de Vries, Theodor Boveri, Luther Burbank, Pearl and Carol Buck, Henry Goddard, The Kallikak Family, Hitler’s racial hygiene laws, morons, the five races etc, Frederick Douglass, Thomas Hunt Morgan, Emma Wolverton, PKU, chromosomal shuffling, meiosis, cultural inheritance, mitochondrial DNA, Mendel’s Law, August Weismann, germ and soma, twin studies, genetic predispositions, mongrels, Neanderthals, chimeras, exosomes, the Yandruwandha people, IVF, genomic engineering, Jennifer Doudna, CRISPR, ooplasm transfers, rogue experiments, gene drives, pluripotency, ethical battlegrounds.
Pinning down meiosis: sperm, mainly
Canto: Not very long ago I was reading Carl Zimmer’s book She has her mother’s laugh, and he was explaining meiosis. It was exciting, because I think I understood it. Being a regular science reader I’d read about meiosis and mitosis before but I could never remember, or perhaps I never clearly knew, the difference. But this time was different, and I thought ‘Yes!’, or maybe ‘Eureka!’ sounds better, because not only did I get it, or thought I did, but I thought ‘this is a new weapon against those who say they don’t believe in evolution’. There’s a fellow-teacher at my college who actually says this, but I’ve never really confronted her on it, apart from some mutterings.
Jacinta: So please explain yourself. Meiosis and mitosis are about cell division aren’t they?
Canto: Well I can’t explain myself, but at the time I thought ‘here’a new one-word response to those who say they don’t believe in evolution’. The other one-word responses being ‘genes’, ‘genetics’, ‘genomics’ and other variants. Well okay, I can give a partial explanation. Most everyone believes in evolution, that’s why they use smart phones rather than the earlier types of mobile phones or landlines or whatever. That’s why they use dishwashers and modern washing machines and modern computers, and drive modern cars instead of a horse-and-carriage, because evolution just means progressive development. What my fellow-teacher really should be saying is she doesn’t believe in the Darwin-Wallace theory of natural selection from random variation, but she doesn’t say that because I strongly suspect she doesn’t have a clue what that means.
Jacinta: Right, so she doesn’t believe in the particular theory…
Canto: Which is proven by genes, the essential mechanism of random variation, which of course Darwin was completely unaware of. And by meiosis, another essential source of variety.
Jacinta: So, meiosis. It’s quite complex. Zimmer gives a brief explanation as you say, and there’s also a number of videos, from Khan Academy, Crash Course Biology and others, so let’s try to describe it for ourselves, with emphasis on variety or variation, which is the essential thing.
Canto: Mitosis, and hopefully I now will never forget this, is the cell division and replication that goes on in our bodies at every moment, and which enables us to grow from a foetus to a strapping lad or lassie, to heal wounds and even to have multiple times more neurons than old fatty Frump, maybe. It occurs among the somatic cells, and it essentially does it by replicating cells exactly, like replacing or adding to like.
Jacinta: But not exactly, otherwise we’d just be a growing blob of undifferentiated body cells, not liver, brain, blood, skin and other cells. That takes epigenetics, as I recall. Mitotically-created cells are identical as to chromosomes, but not as to expression. But anyway, meiosis. That’s how our germ cells are replicated.
Canto: Egg and sperm cells, together known as gametes. Khan Academy begins its article on meiosis with this:
… meiosis in humans is a division process that takes us from a diploid cell—one with two sets of chromosomes—to haploid cells—ones with a single set of chromosomes. In humans, the haploid cells made in meiosis are sperm and eggs. When a sperm and an egg join in fertilization, the two haploid sets of chromosomes form a complete diploid set: a new genome.
All fine, though this division process is damn complicated as we’ll discover. But what interested me in Zimmer’s account was this, and I’ll quote it at length, because it’s what got me excited about variation:
In men, meiosis takes place within a labyrinth of tubes coiled within the testicles. The tube walls are lined with sperm precursor cells, each carrying two copies of each chromosome, one from the man’s mother, the other from his father. When these cells divide, they copy all their DNA, so that now they have four copies of each chromosome. Rather than drawing apart from each other, however, the chromosomes stay together. A maternal and paternal copy of each chromosome line up alongside each other. Proteins descend on them and slice the chromosomes, making cuts at precisely the same spots.
As the cells repair these self inflicted wounds, a remarkable exchange can take place. A piece of DNA from one chromosome may get moved to the same position in the other, its own place taken by its counterpart. This molecular surgery cannot be rushed. All told, a cell may need three weeks to finish meiosis. Once it’s done, its chromosomes pull away from each other. The cell then divides twice, to make four new sperm cells. Each of the four cells inherits a single copy of all 23 chromosomes. But each sperm cell contains a different assembly of DNA.
Think of this last line – each sperm cell contains a different assembly of DNA.
Jacinta: Yes, and there can be up to a billion sperm cells released in each ejaculate, but who’s counting? And are they all different?
Canto: Apparently so. Even the Daily Mail says so, so it must be true. And when you think of it, if there weren’t differences, each offspring born from that man’s sperm would be a clone…
Jacinta: Not necessarily – what about the egg cells?
Canto: Yes, I believe it’s the same meiosis process with them, though not quite. Anyway, there’s the same mixing of chromosomes, so the chances of any two egg cells, or I should say their chromosomal complement, being identical is extremely small.
Jacinta: So, meiosis – I’ve been trying to pin it all down, but I don’t feel I’ve succeeded. Here goes, anyway. Meiosis is a special type of reproduction, confined only to our germ cells, the sperm and egg cells. The gametes. The haploid cells. As opposed to the diploid cells which make up all the somatic or body cells we have. That’s to say, those cells reproduce differently from diploid, somatic cells. But before I try to explain the complex process of their reproduction, what about their production? Where do these haploid cells come from? Now I might answer glibly that the egg cells, also called oocytes, come from the ovaries, and the spermatozoa come from the testes, but that’s not really my question.
Canto: In fact I’m not even sure if you’ve got it right so far. The egg cell is called an ovum. An oocyte is a precursor egg cell I think. I’m not sure if it matters much, but we’re looking at the production of these gametes. Presumably the kinds of gametes we produce depends on our gender, which is determined at conception? Of course, in these gender-bending days, who knows.
Jacinta: Oh dear. Let’s try not to get confused. Assume an embryo or foetus is straightforwardly male or female, or potentially so. I seem to recall that males only start producing sperm at puberty, whereas females produce all their egg cells before that, and only have a fixed number, and egg cells are quite huge in comparison to sperm, and even compared to your average somatic cells – though some neurons have super-long axons. When females reach the stage of menstruation, that’s when they start releasing eggs.
Canto: Okay in the above quote from Zimmer, sperm precursor cells are mentioned. They’re also called spermatocytes, and the labyrinth of coiled tubes he also mentions are the seminiferous tubules. This is where the meiosis happens, in males. There are two types of spermatocyte, primary and secondary. The primary spermatocytes are diploid, and the secondary, formed after the first meiosis process (meiosis 1), are haploid.
Jacinta: To possibly confuse matters further, there’s a multi-stage process happening in those seminiferous tubules, a process called spermatogenesis. It starts with the spermatogonia (and maybe we’ll leave the spermatogonium’s existence for another post), which are processed into primary spermatocytes, then into secondary spermatocytes, then into spermatids, then to sperm.
Canto: Yes, so the first step you mention is mitotic, with diploid cells creating diploid cells, the primary spermatocytes…
Jacinta: And mitosis has those four steps or phases – PMAT, as students recall it; prophase, metaphase, anaphase and telophase, while meiosis has the same but in two parts, PMAT for meiosis 1 and PMAT for meiosis 2. So as we’ve already pointed out, this double-doubling process has a final result of four new cells. Now, before meiosis 1, the cells go through interphase, but I won’t detail that here. In prophase 1, chromosomes are brought together in pairs, called homologues. Their alleles are aligned together, but then this more or less random ‘crossing over’ occurs, presumably with the aid of some busy little proteins, which mixes the chromosomes up. Each homologue pair can have many of these crossovers. More mixing happens during metaphase 1, when homologue pairs, with their crossings-over, line up randomly at the metaphase plate. I’m not pretending to fully understand all this, but the main point is that the variety we find in the final product, the sperm cells, is brought about essentially during prophase and metaphase in meiosis 1 of the double cycle.
Canto: It does get me more interested in understanding meiosis more fundamentally though, as well as mitosis. The phases and the processes that bring them about, the proteins, the chromatin, the centromeres, the metaphase plate, and of course oogenesis, polar bodies and much much more.
Jacinta: Yes – I think meiosis does point to a lot of the variation in the world of organisms, but it would be hard to get those who ‘don’t believe in evolution’ to think about this and its relevance. They tend not to listen to explanations or to want to make connections.
Canto: You can give up on them or keep plugging away with the ‘what about this?’ or ‘can you explain that?’ Or demonstrate to them directly or indirectly, the results of those powerful explanations, in medicine, in astronomy, in our technology, and in our human relations.
References
She has her mother’s laugh: the powers, perversions and potential of heredity, by Carl Zimmer, 2018
https://en.wikipedia.org/wiki/Meiosis
https://www.khanacademy.org/science/biology/cellular-molecular-biology/meiosis/a/phases-of-meiosis
a DNA dialogue 6: Okazaki fragments, as promised
Canto: Okay, so first off, why are Okazaki fragments so called?
Jacinta: Well as anyone would guess, they’re named after someone Japanese, in this case two, the husband and wife team Reiji and Tsuneko Okazaki, who discovered these short, discontinuously synthesised stretches of DNA nucleotides in the 1960s.
Canto: Yes their story is intriguing – tragic but also inspiring. Reiji, the husband, was born in Hiroshima and died in 1975 from leukaemia, related to the 1945 A-bomb. He was only 44. Tsuneko Okazaki continued their research and went on to make many other contributions to genetics and molecular biology, as a professor, teacher, mentor and director of scientific institutes. Her achievements would surely make her a Nobel candidate, and she’s still alive, so maybe…
Jacinta: Now the key to Okazaki fragments is this lagging strand. Its directionality means that the DNA primase, followed by the DNA polymerase, must work ‘backwards’, away from the replication fork, to add nucleotides. This means that that they have to have periodic breaks – but I’m not sure exactly why – in creating this lagging strand. So the entire replication process is described as semi-discontinuous because of this fundamental difference between the continuously created leading strand and the stop-start ‘fragmentary’ (at least briefly) lagging strand.
Canto: But we need to know why this ‘backward’ movement has to be stop-start, and I’d also like to know more about this primase and polymerase, thank you.
Jacinta: Well the Okazakis and their team discovered this semi-discontinuous replication process in studying the replication of good old Escherichia coli, the go-to research bacterium, and it was a surprise at the time. Now, I’m looking at the explanation for this necessarily discontinuous process in Wikipedia, and I confess I don’t really understand it, but I’ll give it a go. Apparently the Okazakis ‘suggested that there is no found mechanism that showed continuous replication in the 3′ to 5′ direction, only 5′ to 3′ using DNA polymerase, a replication enzyme’, to quote from Wikipedia. So they were rather cleverly hypothesising that there must be another mechanism for the 3′ to 5′ lagging strand, which must be discontinuous.
Canto: And another way of saying that, is that the process must be fragmentary. And they used experiments to test this hypothesis?
Jacinta: Correct, and I won’t go into the process of testing, as if I could. It involved pulse-labelling. Don’t ask, but it has something to do with radioactivity. Anyway, the test was successful, and was supported by the discovery shortly afterwards of polynucleotide ligase, the enzyme that stitches these fragments together. Now, you want to know more about primase, polymerase, and now ligase no doubt. So here’s a bit of the low-down. DNA primase is, to confuse you, an RNA polymerase, which synthesises RNA from a DNA template. It’s a catalyst in the synthesis of a short RNA segment, known as a primer. It’s extremely important in DNA replication, because no polymerase (and you know how polymerase keeps getting associated with primase) can make anything happen without an RNA (or DNA) primer.
Canto: But why? This is getting so complicated.
Jacinta: I assure you, we’ve barely scratched the surface….
Canto: Well, Socrates was right – there’s an essential wisdom in being aware of how ignorant you are. We’ll battle on in our small way.
a DNA dialogue 5: a first look at DNA replication
Jacinta: So let’s scratch some more of the surface of the subject of DNA and genetics. A useful datum to remember, the human genome consists of more than 3 billion DNA bases. We were talking last time about pyrimidines and purines, and base pairs. Let’s talk now about how DNA unzips.
Canto: Well the base pairs are connected by hydrogen bonds, and the two DNA strands, the backbones of the molecule, run in opposite, or anti-parallel, directions, from the 5′ (five prime) end to the 3′ (three prime) end. So, while one strand runs from 5′ to 3′ (the sense strand), the other runs 3′ to 5′ (the antisense strand).
Jacinta: Right, so what we’re talking about here is DNA replication, which involves breaking those hydrogen bonds, among other things.
Canto: Yes, so that backbone, or double backbone whatever, where the strands run anti-parallel, is a phosphate-sugar construction, and the sugar is deoxyribose, a five-carbon sugar. This sugar is oriented in one strand from 5′ to 3′, that’s to say the 5′ carbon connects to a phosphate group at one end, while the 3′ carbon connects to a phosphate group at the other end, while in the other strand the sugar is oriented in the opposite direction.
Jacinta: Yes, and this is essential for replication. The protein called DNA polymerase should be introduced here, with thanks to Khan Academy. It adds nucleotides to the 3′ end to grow a DNA strand…
Canto: Yes, but I think that’s part of the zipping process rather than the unzipping… it’s all very complicated but we need to keep working on it…
Jacinta: Yes, according to Khan Academy, the first step in this replication is to unwind the tightly wound double helix, which occurs through the action of an enzyme called topoisomerase. We could probably do a heap of posts on each of these enzymes, and then some. Anyway, to over-simplify, topoisomerase acts on the DNA such that the hydrogen bonds between the nitrogenous bases can be broken by another enzyme called helicase.
Canto: And that’s when we get to add nucleotides. So we have the two split strands, one of which is a 3′ strand, now called the leading strand, the other a 5′ strand, called the lagging strand. Don’t ask.
Jacinta: The leading strand is the one you add nucleotides to, creating another strand going in the 5′ to 3′ direction. This apparently requires an RNA primer. Don’t ask. DNA primase provides this RNA primer, and once this has occurred, DNA polymerase can start adding nucleotides to the 3′ end, following the open zipper, so to speak.
Canto: The lagging strand is a bit more complex though, as you apparently can’t add nucleotides in that other direction, the 5′ direction, not with any polymerase no how. So, according to Khan, ‘biology’ adds primers (don’t ask) made up of several RNA nucleotides.
Jacinta: Again, according to Khan, the DNA primase, which works along the single strand, is responsible for adding these primers to the lagging strand so that the polymerase can work ‘backwards’ along that strand, adding nucleotides in the right, 3′, direction. So it’s called the lagging strand because it has to work through this more long, drawn-out process.
Canto: Yes, and apparently, this means that you have all these fragments of DNA, called Okazaki fragments. I’m not sure how that works…
Jacinta: Let’s devote our next post on this subject entirely to Okazaki fragments. That could clarify a lot. Or not.
Canto: Okay, let’s. Goody goody gumdrops. In any case, these fragments can be kind of sewn together using DNA ligase, presumably another miraculous enzyme. And the RNA becomes DNA. Don’t ask. I’m sure all will be revealed with further research and investigation.
References
Leading and lagging strands in DNA replication (Khan Academy video)