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how evolution was proved to be true

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The origin of species is a natural phenomenon

Jean-Baptiste Lamarck

The origin of species is an object of inquiry

Charles Darwin

The origin of species is an object of experimental investigation

Hugo de Vries

(quoted in The Gene: an intimate history, by Siddhartha Mukherjee)

Gregor Mendel

I’ve recently read Siddhartha Mukherjee’s monumental book The Gene: an intimate history, a work of literature as well as science, and I don’t know quite where to start with its explorations and insights, but since, as a teacher to international students some of whom come from Arabic countries, I’m occasionally faced with disbelief regarding the Darwin-Wallace theory of natural selection from random variation (usually in some such form as ‘you don’t really believe we come from monkeys do you?’), I think it might be interesting, and useful for me, to trace the connections, in time and ideas, between that theory and the discovery of genes that the theory essentially led to.

One of the problems for Darwin’s theory, as first set down, was how variations could be fixed in subsequent generations. And of course another problem was – how could a variation occur in the first place? How were traits inherited, whether they varied from the parent or not? As Mukherjee points out, heredity needed to be both regular and irregular for the theory to work.

There were few clues in Darwin’s day about inheritance and mutation. Apart from realising that it must have something to do with reproduction, Darwin himself could only half-heartedly suggest an unoriginal notion of blending inheritance, while also leaning at times towards Lamarckian inheritance of acquired characteristics – which he at other times scoffed at.

Mukherjee argues here that Darwin’s weakness was impracticality: he was no experimenter, though a keen observer. The trouble was that no amount of observation, in Darwin’s day, would uncover genes. Even Mendel was unable to do that, at least not in the modern DNA sense. But in any case Darwin lacked Mendel’s experimental genius. Still, he did his best to develop a hypothesis of inheritance, knowing it was crucial to his overall theory. He called it pangenesis. It involved the idea of ‘gemmules’ inhabiting every cell of an organism’s body and somehow shaping the varieties of organs, tissues, bones and the like, and then specimens of these varied gemmules were collected into the germ cells to produce ‘mixed’ offspring, with gemmules from each partner. Darwin describes it rather vaguely in his book The Variation of Animals and Plants under Domestication, published in 1868:

They [the gemmules] are collected from all parts of the system to constitute the sexual elements, and their development in the next generation forms the new being; but they are likewise capable of transmission in a dormant state to future generations and may then be developed.

Darwin himself admitted his hypothesis to be ‘rash and crude’, and it was effectively demolished by a very smart Scotsman, Fleeming Jenkin, who pointed out that a trait would be diluted away by successive unions with those who didn’t have it (Jenkin gave as an example the trait of whiteness, i.e. having ‘white gemmules’, but a better example would be that of blue eyes). With an intermingling of sexual unions, specific traits would be blended over time into a kind of uniform grey, like paint pigments (think of Blue Mink’s hit song ‘Melting Pot’).

Darwin was aware of and much troubled by Jenkin’s critique, but he (and the scientific world) wasn’t aware that a paper published in 1866 had provided the solution – though he came tantalisingly close to that awareness. The paper, ‘Experiments in Plant Hybridisation’, by Gregor Mendel, reported carefully controlled experiments in the breeding of pea plants. First Mendel isolated ‘true-bred’ plants, noting seven true-bred traits, each of which had two variants (smooth or wrinkled seeds; yellow or green seeds; white or violet coloured flowers; flowers at the tip or at the branches; green or yellow pods; smooth or crumpled pods; tall or short plants). These variants of a particular trait are now known as alleles. 

Next, he began a whole series of painstaking experiments in cross-breeding. He wanted to know what would happen if, say, a green-podded plant was crossed with a yellow-podded one, or if a short plant was crossed with a tall one. Would they blend into an intermediate colour or height, or would one dominate? He was well aware that this was a key question for ‘the history of the evolution of organic forms’, as he put it.

He experimented in this way for some eight years, with thousands of crosses and crosses of crosses, and the more the crosses multiplied, the more clearly he found patterns emerging. The first pattern was clear – there was no blending. With each crossing of true-bred variants, only one variant appeared in the offspring – only tall plants, only round peas and so on. Mendel named them as dominant traits, and the non-appearing ones as recessive. This was already a monumental result, blowing away the blending hypothesis, but as always, the discovery raised as many questions as answers. What had happened to the recessive traits, and why were some traits recessive and others dominant?

Further experimentation revealed that disappeared traits could reappear in toto in further cross-breedings. Mendel had to carefully analyse the relations between different recessive and dominant traits as they were cross-bred in order to construct a mathematical model of the different ‘indivisible, independent particles of information’ and their interactions.

Although Mendel was alert to the importance of his work, he was spectacularly unsuccessful in alerting the biological community to this fact, due partly to his obscurity as a researcher, and partly to the underwhelming style of his landmark paper. Meanwhile others were aware of the centrality of inheritance to Darwin’s evolutionary theory. The German embryologist August Weismann added another nail to the coffin of the ‘gemmule’ hypothesis in 1883, a year after Darwin’s death, by showing that mice with surgically removed tails – thus having their ‘tail gemmules’ removed – never produced tail-less offspring. Weismann presented his own hypothesis, that hereditary information was always and only passed down vertically through the germ-line, that’s to say, through sperm and egg cells. But how could this be so? What was the nature of the information passed down, information that could contain stability and change at the same time?

The Dutch botanist Hugo de Vries, inspired by a meeting with Darwin himself not long before the latter’s death, was possessed by these questions and, though Mendel was completely unknown to him, he too looked for the answer through plant hybridisation, though less systematically and without the good fortune of hitting on true-breeding pea plants as his subjects. However, he gradually became aware of the particulate nature of hereditary information, with these particles (he called them ‘pangenes’, in deference to Darwin’s ‘pangenesis’), passing down information intact through the germ-line. Sperm and egg contributed equally, with no blending. He reported his findings in a paper entitled Hereditary monstrosities in 1897, and continued his work, hoping to develop a more detailed picture of the hereditary process. So imagine his surprise when in 1900 a colleague sent de Vries a paper he’d unearthed, written by ‘a certain Mendel’ from the 1860s, which displayed a clearer understanding of the hereditary process than anyone had so far managed. His response was to rush his own most recent work into press without mentioning Mendel. However, two other botanists, both as it happened working with pea hybrids, also stumbled on Mendel’s work at the same time. Thus, in a three-month period in 1900, three leading botanists wrote papers highly indebted to Mendel after more than three decades of profound silence.

Hugo de Vries

The next step of course, was to move beyond Mendel. De Vries, who soon corrected his unfair treatment of his predecessor, sought to answer the question ‘How do variants arise in the first place?’ He soon found the answer, and another solid proof of Darwin’s natural selection. The ‘random variation’ from which nature selected, according to the theory, could be replaced by a term of de Vries’ coinage, ‘mutation’. The Dutchman had collected many thousands of seeds from a wild primrose patch during his country rambles, which he planted in his garden. He identified some some 800 new variants, many of them strikingly original. These random ‘spontaneous mutants’, he realised, could be combined with natural selection to create the engine of evolution, the variety of all living things. And key to this variety wasn’t the living organisms themselves but their units of inheritance, units which either benefitted or handicapped their offspring under particular conditions of nature.

The era of genetics had begun. The tough-minded English biologist William Bateson became transfixed on reading a later paper of de Vries, citing Mendel, and henceforth became ‘Mendel’s bulldog’. In 1905 he coined the word ‘genetics’ for the study of heredity and variation, and successfully promoted that study at his home base, Cambridge. And just as Darwin’s idea of random variation sparked a search for the source of that variation, the idea of genetics and those particles of information known as ‘genes’ led to a worldwide explosion of research and inquiry into the nature of genes and how they worked – chromosomes, haploid and diploid cells, DNA, RNA, gene expression, genomics, the whole damn thing. We now see natural selection operating everywhere we’re prepared to look, as well as the principles of ‘artificial’ or human selection, in almost all the food we eat, the pets we fondle, and the superbugs we try so desperately to contain or eradicate. But of course there’s so much more to learn….

William Bateson

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Written by stewart henderson

June 14, 2017 at 5:42 pm

bonobo society, sex and females

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sexual dimorphism - a difference on average, but massive individual variation

sexual dimorphism – a difference on average, but massive individual variation

Men are bigger than women, slightly. That’s how things evolved. It’s called sexual dimorphism. It happens with many species, the genders are different in size, shape, coloration, whatever. With humans there’s a size difference, and something of a shape difference, in breasts and hips, but really these aren’t significant. Compare, say, the deep-water triplewort seadevil, a type of anglerfish, in which the female is around 30 cms long, and the male a little over a centimetre. The difference in mass would be too embarrassing to relate.

Among our primate cousins the greatest sexual dimorphism, in size as well as other features, is found in the mandrills, with the male being two to three times the size of the females. In some gorillas there’s a substantial size difference too in favour of the males, and in fact in all of the primate species the male has a size advantage. But size isn’t everything, and the bigger doesn’t have to always dominate.

Female bonobos are smaller than the males, even more so than in humans, yet they enjoy a higher social status than in any other primate society, probably including humans, though it’s hard to compare, since humanity’s many societies vary considerably on the roles and status of women. So how have females attained this exalted status within one of the most highly socialised primate species?

Bonobos and chimpanzees are equally our closest living relatives. It isn’t clear when exactly they separated from each other, but some experts claim it may have been less than a million years ago. Enough time for them to become quite distinct physically, according to the ethologist Franz De Waal. Bonobos are more gracile with longer limbs and a smaller head, and they have a distinctive hairstyle, with a neat parting down the middle. They’re also more easily individuated by their facial features, being in this sense more like humans. And there are also major differences in their social behaviour. Male chimps are dominant in the troupe, often brutally so, whereas bonobo society is less clearly hierarchical, and considerably less violent overall. De Waal, one of the world’s foremost experts on both primates, became interested in bonobos primarily through studies on aggression. He noted that sometimes, after a violent clash, two chimps would come together to hug and kiss. Being interested in such apparent reconciliations and their implications, he decided to look at reconciling behaviours in other primates. What he discovered in bonobos (at San Diego Zoo, which in 1983 housed the world’s largest captive colony) was rather ‘shocking’; their social life was profoundly mediated by sex. Not that he was the first to discover this; other primatologists had written about it, noting also that bonobo sex was far more human-like than chimp sex, but their observations were obscurely worded and not well disseminated. There are other aspects of the physical nature of sexual relations in bonobos that favour females, such as female sexual receptivity, indicated by swelling and a reddening of the genital area, which pertains for a much longer period than in chimps. Female bonobos, like humans and unlike other primates, are sexually receptive more or less all the time.

This isn’t to say that bonobos are oversexed, whatever that may mean. Sexual relations are far from constant, they are casual, sporadic and quickly done with. Often they’re associated with finding food, and it seems likely that sexual relations are used to reconcile tensions related to food availability and other potential causes of conflict.

So how does this use of sex relate to the status of females in bonobo society. I’ll explore this further in the next post.

bonobo relations - more than just sex

bonobo relations – more than just sex

Written by stewart henderson

September 4, 2016 at 1:32 pm

Abiogenesis – LUCA, gradients, amino acids, chemical evolution, ATP and the RNA world

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chemical-evolution-1

Jacinta: So now we’re thinking of the Earth 4 billion years BP, with an atmosphere we’re not quite sure of, and we want to explore the what and when of the first life forms. Haven’t we talked about this before?

Canto: Yeah we talked about the RNA world and viroids and abiogenesis, the gap between chemistry and biology, inter alia. This time we’re going to look more closely at the hunt for the earliest living things, and the environments they might’ve lived in.

Jacinta: And it started with one, it must have. LUA, or LUCA, the last universal common ancestor. Or the first, after a number of not-quite LUCAs, failed or only partially successful attempts. And finding LUCA would be much tougher than finding a viroid in a haystack, because you’re searching through an immensity of space and time.

Canto: But we’re much closer to finding it than in the past because we know so much more about what is common to all life forms.

Jacinta: Yes so are we looking definitely at the first DNA-based life form or are we probing the RNA world again?

Canto: I think we’ll set aside the world of viroids and viruses for now, because we want to look at the ancestor of all independently-existing life forms, and they’re all DNA-based. And we also know that LUCA used ATP. So now I’m going to quote from an essay by Michael Le Page in the volume of the New Scientist Collection called ‘Origin, Evolution, Extinction’:

How did LUCA make its ATP? Anyone designing life from scratch would probably make ATP using chemical reactions inside the cell. But that’s not how it is done. Instead energy from food or sunlight is used to power a protein ‘pump’ that shunts hydrogen ions – protons – out of the cell. This creates a difference in proton concentration, or a gradient, across the cell membrane. Protons then flow back into the cell through another protein embedded in the membrane, which uses the energy to produce ATP.

Jacinta: You understand that?

Canto: Sort of.

Jacinta: ‘Energy from food or sunlight is used..’ that’s a bit of a leap. What food? The food we eat is organic, made from living or formerly living stuff, but LUCA is the first living thing, its food must be purely chemical, not biological.

Canto: Of course, not a problem. I believe the microbes at hydrothermal vents live largely on hydrogen sulphide, and of course sunlight is energy for photosynthesising oganisms such as cyanobacteria.

Jacinta: Okay, so your simplest living organisms, or the simplest ones we know, get their energy by chemosynthesis, or photosynthesis. Its energy, or fuel, not food.

Canto: Semantics.

Jacinta: But there are other problems with this quote re abiogenesis. For example, it’s talking about pre-existent cells and cell membranes. So assuming that cells had to precede ATP.

Canto: No, he’s telling us how cells make ATP today. So we have to find, or synthesise, all the essential ingredients that make up the most basic life forms that we know cell membranes, proteins, ATP and the like. And people are working towards this.

Jacinta: Yes and first of all they created these ‘building blocks of life’, as they always like to call them, amino acids, in the Miller-Urey experiments, since replicated many times over, but what exactly are nucleic acids? Are they the same things as nucleic acids?

Canto: Amino acids are about the simplest forms of organic compounds. It’s probably better to call them the building blocks of proteins. There are many different kinds, but generally each contain amine and carboxyl groups, that’s -NH2 and -COOH, together with a side chain, called an R group, which determines the type of amino acid. There’s a whole complicated lot of them and you could easily spend a whole lifetime fruitfully studying them. They’re important in cell structure and transport, all sorts of things. We’ve not only been able to create amino acids, but to combine them together into longer peptide chains. And we’ve also found large quantities of amino acids in meteorites such as the Murchison – as well as simple sugars and nitrogenous bases. In fact I think we’re gradually firming up the life-came from-space hypothesis.

Jacinta: But amino acids and proteins aren’t living entities, no matter how significant they are to living entities. We’ve never found living entities in space or beyond Earth. Your quote above suggests some of what we need. A boundary between outside and inside, a lipid or phospho-lipid boundary as I’ve heard it called, which must be semi-permeable to allow chemicals in on a very selective basis, as food or fuel.

Canto: I believe fatty acids formed the first membranes, not phospho-lipids. That’s important because we’ve found that fatty acids, which are made up of carbon, hydrogen and oxygen atoms joined together in a regular way, aren’t just built inside cells. There’s a very interesting video called What is Chemical Evolution?, produced by the Center for Chemical Evolution in the USA, that tells about this. Experimenters have heated up carbon monoxide and hydrogen along with many minerals common in the Earth’s crust and produced various carbon compounds including fatty acids. Obviously this could have and can still happen naturally on Earth, for example in the hot regions maybe below or certainly within the crust. It’s been found that large concentrations of fatty acids aggregate in warm water, creating a stable, ball-like configuration. This has to do with the attraction between the oxygen-carrying heads of fatty acids and the water molecules, and the repulsion of the carbon-carrying tails. The tails are forced together into a ball due to this repulsion, as the video shows.

fatty acids, with hydrophobic and hydrophilic ends, aggregating in solution

Jacinta: Yes it’s an intriguing video, and I’m almost feeling converted, especially as it goes further than aggregation due to these essentially electrical forces, but tries to find ways in which chemical structures evolve, so it tries to create a bridge between one type of evolution and another – the natural-selection type of evolution that operates upon reproducing organisms via mutation and selection, and the type of evolution that builds more complex and varied chemical structures from simpler compounds.

Canto: Yes but it’s not just the video that’s doing it, it’s the whole discipline or sub-branch of science called chemical evolution.

Jacinta: That’s right, it’s opening a window into that grey area between life and non-life and showing there’s a kind of space in our knowledge there that it would be exciting to try and fill, through observation and experimentation and testable hypotheses and the like. So the video, or the discipline, suggests that in chemical evolution, the highly complex process of reproduction through mitosis in eukaryotic cells or binary fission in prokaryotes is replaced by repetitive production, a simpler process that only takes place under certain limited conditions.

Canto: So under the right conditions the balls of fatty acids grow in number and themselves accumulate to form skins, and further forces – I think they’re hydrostatic forces – can cause the edges of these skins to fuse together to create ‘containers’, like vesicles inside cells.

Jacinta: So we’re talking about the creation of membranes, impermeable or semi-permeable, that can provide a safe haven for, whatever…

Canto: Yes, and at the end of the video, other self-assembling systems, such as proto-RNA, are intriguingly mentioned, so we might want to find out what’s known about that.

Jacinta: I think we’ll be doing a lot of reading and posting on this subject. I find it really fascinating. These limited conditions I mentioned – limited on today’s Earth surface, but not so much four billion years ago, include a reducing atmosphere lacking in free oxygen, and high temperatures, as well as a gradient – both a temperature gradient and a sort of molecular or chemical gradient, from more reducing to more oxidising you might say. These conditions exist today at hydrothermal vents, where archaebacteria are found, so researchers are naturally very interested in such environments, and in trying to replicate or simulate them.

Canto: And they’re interested in the boundary between chemical and biological evolution, and reproduction. There are so many interesting lines of inquiry, with RNA, with cell membranes….

Jacinta: Researchers are particularly interested in alkaline thermal vents, where alkaline fluids well up from beneath  the sea floor at high temperatures. When this fluid hits the ocean water, minerals precipitate out and gradually create porous chimneys up to 60 metres high. They would’ve been rich in iron and sulphide, good for catalysing complex organic reactions, according to Le Page. The temperature gradients created would’ve favoured organic compounds and would’ve likely encouraged the building of complexity, so they may have been the sites in which the RNA world began, if it ever did.

a hydrothermal vent off the coast of New Zealand. Image from NOAA

a hydrothermal vent off the coast of New Zealand. Image from NOAA

Canto: So I think we should pursue this further. There are a lot of researchers homing in on this area, so I suspect further progress will be made soon.

Jacinta: Yes, we need to explore the exploitation of proton gradients, the development  of proton pumps and the production of ATP, leaky membranes and a whole lot of other fun stuff.

Canto: I think we need to get our heads around ATP and its production too, because that looks pretty damn complex.

Jacinta: Next time maybe.

 

Written by stewart henderson

July 29, 2016 at 8:51 am

clever Charlie Darwin

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A photo taken by me! King Charles seated in state in the Musuem of Natural History, London. It was a thrill to be granted an audience

A photo taken by me! King Charles seated in state in the Musuem of Natural History, London. It was a thrill to be granted an audience

I recently decided to reread Darwin’s Origin of Species, which was really reading it for the first time as my first reading was pretty cursory, and I could barely follow the wealth of particular knowledge he used for cumulative effect to adduce his theory. This time I’ve been doing a closer reading, and becoming increasingly impressed, and I’ve only read the first chapter, ‘Variation under Domestication’.

Darwin’s argument here of course is that domesticated horses, dogs, birds and plants have been artificially selected over long periods of time, and often unconsciously, to suit human needs and tastes. This might seem screamingly obvious today, and to a degree it was recognised in Darwin’s time, but because of an inability to take the long view, and also because of the then-prevalent paradigm of the fixity of species, breeders and nurserymen tended to under-estimate their own cumulative powers, and to claim, for example, that dogs and pigeons had always come in many varieties. Even Darwin was uncertain, and was willing to concede – writing of course before the advent of Mendelian genetics, never mind the revolution wrought by the identification and analysis of DNA as the molecule of inheritance – that in some cases the breeders might be right:

In the case of most of our anciently domesticated animals and plants, I do not think it is possible to come to any definite conclusion, whether they have descended from one or several species.

He was even prepared to concede that it was ‘highly probable that our domestic dogs have descended from several wild species’, while at the same time arguing that the breeding of dogs, in Egypt, other parts of Africa and Australia (where, in his Beagle travels, he observed dingoes, which he may have seen as semi-domesticated by the Aborigines) extended back far further in time than most people suspected. We now know that Darwin’s concession here was ‘premature’. The latest research strongly suggests that our domesticated dogs trace their ancestry to a group of European wolves dating from 19,000 to 32,000 years ago, and probably now extinct. That’s a time-frame Darwin would’ve baulked at, and it’s both funny and kind of tragic that this is something I’ve ‘discovered’ after 30 seconds of selective internet searching. There’s no doubt, though that Darwin’s bold but always informed speculations were heading in the right direction.

Particularly informed –  and bold – were his speculations about pigeons. This is hardly surprising as he spent several years studying and breeding them himself. Interestingly, he started doing so because he’d become convinced that all the fancy pigeons then on show were most likely derived from one common species, the rock pigeon or rock dove (Columba livia), a view already held by some naturalists but few breeders.  He devotes several pages in Chapter 1 to arguing his case, for example pointing out that the ‘several distinct species’ argued for by breeders can be crossed with complete success, that’s to say with no signs of sterility or more than usually defective offspring.

So, as with dogs, I decided to look up what the latest research was on the ancestry of English carriers, short-faced tumblers, runts, fantails, common tumblers, barbs, pouters, trumpeters and laughers, to name some of the pigeons Darwin mentions in the chapter, and was excited to find that a piece of research published as recently as 2013 has confirmed Darwin’s hypothesis. Cheaper and faster genome sequencing technologies have enabled researchers to sequence the genomes of many wild and domesticated birds, and they’ve found that all of the latter are clearly closer to C livia than to any other wild species. It only took just over 150 years for Darwin to be proven correct.

Close reading like this really does reap some fun rewards, and I’ll finish with two more examples. Darwin wrote of how in the world of breeding, quite a drastic change can be brought about in one breeding step, as in the case of the fuller’s teasel with its hooks. He goes on:

So it has probably been with the turnspit dog; and this is known to have been the case with the ancon sheep.

Not knowing wtf he was talking about, I irritatedly decided to look up these unknown creatures. The turnspit dog is a now-extinct breed, bred specifically from around the 16th century to provide the dogpower to turn meat on a spit, the only conceivable way of cooking large joints of meat in your average fancy household for a couple of centuries. The dog, or dogs, because the system worked better if you had two of them engaged in shift work, turned a wheel by running inside it, rat-like, until the meat was cooked. They were known to be long-bodied and short-legged, but details of how they were bred aren’t known, as they were apparently beneath scholarly consideration. They certainly weren’t seen as cuddly pets – if you treat creatures as slaves it heightens your contempt for then (cf Aristotle) – and they were even taken to church as foot-warmers. They’d disappeared entirely by the end of the 19th century.

It's a dog's life?

It’s a dog’s life?

The ancon sheep was a short-legged type, apparently bred from a single individual in the USA in the late nineteenth century, its short legs having the singular advantage, to some, of curtailing its hopes of freedom by jumping the fence. The term ‘ancon’ has since been used by breeding researchers to describe strains of creatures arising from an individual with the same phenotype.

Achondroplastic_sheep

Written by stewart henderson

June 4, 2016 at 11:00 am

What is a trisomy?

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img014

Canto: So I happened to watch an excellent video from the Royal Institute recently, a talk by the beautifully named and beautifully voiced Irish geneticist, Aoife Mclysaght…

Jacinta: How do you pronounce that?

Canto: It’s pronounced Aoife Mclysaght…

Jacinta: Oh right.

Canto: So the theme was that everything in biology makes sense only in the light of evolution, and she was illustrating this through her area of interest and research, gene duplication. And along the way she talked about trisomies, particularly trisomy 21, usually referred to as Down Syndome.

Jacinta: A trisomy involves having an extra copy of a chromosome, in this case chromosome 21.

Canto: Very good, and the extra copy is a perfectly good copy, but having that extra copy causes major problems, obviously.

Jacinta: The term ‘trisomy’ refers of course to three – having three rather than two sets of a particular chromosome. Humans normally have two sets of 23 chromosomes. I have a relative who has a rare and unnamed form of trisomy, or at least a rare form of chromosomal disorder, which, when looking into it, I decided must be a trisomy. But since then I’ve discovered that Williams syndrome – which I learned about from another person I know with that condition – isn’t a trisomy, but the result of genes missing from chromosome 7. So now I’ve gone from thinking that trisomies accounted for all or most sorts of genetic intellectual disabilities to… I don’t know.

Canto: To a position of deeper ignorance. So people with trisomies have 47 chromosomes, with Down syndrome being the most common. Others include Edward syndrome (trisomy 18) and Patau syndrome (trisomy 13). Interestingly, though, there’s another rarer form of Down syndrome that’s due to translocation – that’s when a part of a chromosome – in this case chromosome 21 – migrates to another chromosome, usually chromosome 14, during cell division

Jacinta: That complicates matters… So do we know what causes these trisomies, and these translocations? They seem to be very specific, occurring for only particular chromosomes, or bits of them.

Canto: Well you’re right in that trisomies 21, 18 and 13 are relatively common – I mean rare but more common than a trisomy 9 or 15 or 19, just to pick out any numbers less than 23. We do know that trisomies become more common with older egg cells. As you know, your egg cells are as old as you are, and they become a little decrepit with age like yourself.

Jacinta: We’re both slouching to oblivion.

Canto: It’s also the case that most trisomies don’t survive to term, in fact they mostly miscarry so early that the mother doesn’t even know she’s been pregnant. So presumably those trisomies I just picked at random, if they occur at all, have more fatal consequences. It seems in any case that a trisomy occurs when cells divide but one chromosome somehow sticks to its homologue and is carried with it into the new cell. So maybe some chromosomes are more ‘sticky’ than others?

Jacinta: I think we need to do a deeper dive, as one pundit likes to say, into meiosis and aneuploidy.

Canto: Aneuploidy?

Jacinta: That’s just when you have an abnormal number of chromosomes per cell: it could be less or more. Actually trisomy 16 is the most common form, but fatal in its full-blown version. It can exist in mosaic form – when not all the cells have it.

Canto: So can you explain meiosis for us?

Jacinta: A long story but fascinating of course. It’s the basis of sexual reproduction for all eukaryotes. So before eukaryotic germ cells or gametes divide they need to replicate their chromosomes so that the resulting pair of cells has an equal share. This period of replication is known as the S phase.

Canto: Wait a minute, does this mean that in the S phase humans have 92 chromosomes per cell instead of 46?

Jacinta: Don’t bog me down with clever questions. Taking another step back, we have this whole process called the cell cycle, which we divide into phases. We can start anywhere, since it’s a cycle, if you know what I mean, but if you need a beginning it’s the prophase. Anyway, the S phase comes after the G1 phase and before the G2 phase. S, by the way, stands for synthesis, and G here stands for gap. Together these three phases make up the interphase, at the end of which we have the prophase of a new cell cycle, though actually meiosis isn’t a cycle the way mitosis (non-sexual reproduction or cell division) is. To be accurate, the next phase is called prophase 1, which is followed by metaphase 1, anaphase 1 and telophase 1 before we have prophase 2….

Canto: Stop cycling I’m getting dizzy.

Jacinta: Well yes believe me it’s complicated, and I haven’t begun yet. But you did ask for it.

Canto: Can you give the simplified version?

Jacinta: Not really.

Canto: Okay, we’ll leave that for another day. Focusing in on the part of meiosis when these trisomies and other anomalies occur, it seems that the problem isn’t so much stickiness as non-stickiness. Think of gametes. In mammals such as humans there are two types, egg and sperm cells. They’re differentiated by their sex chromosomes, chromosome 23…

Jacinta: And also by the fact that the egg cell is like the sun and the sperm cell is like the earth.

Canto: Well, sort of, in terms of volume. Now, after meiosis – which occurs in phases, meiosis 1 and meiosis 2, creating two daughter cells then four grand-daughter cells, so to speak – each of these grand-daughter gametes should be haploid. That’s to say, they should contain only one of each of the 23 chromosomes. But nothing’s perfect and sometimes there are errors, and we’re not clear about why, though the chances of error rise with the age of the female as mentioned before. Mostly the problem is that the chromosomes didn’t properly separate, a state called chromosome nondisjunction. Something to do with the spindle apparatus not functioning properly due to a lack of cohesion of the chromosome. This occurs rather more frequently in female meiosis, or oogenesis, than in male meiosis, or spermatogenesis, they’re not sure exactly why.

chromosome_nondisjunction_meiosis

Jacinta: Well I must say that’s all very enlightening, and salutary, as it’s made me aware of how little I know about genetics in general. Now I know a teensy bit more. As to trisomies and other such chromosomal problems, what they know just makes me keen to know more about how we might detect them and possibly in the deep future rectify them at source. But the science is clearly a long way from that…

Canto: Well you never know. Genetics is a fast-moving field.

Jacinta: we must explore it more. It’s serious fun.

Written by stewart henderson

January 31, 2016 at 10:06 pm

this one’s for the birds

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clevercrow1

Canto: If anybody doesn’t appreciate the beauty and complexity and general magnificence of birds they should pee off and never darken this blog again.

Jacinta: Right. Now what brought that on, mate?

Canto: Oh just a general statement of position vis-à-vis other species. Charles Darwin, an old friend of mine, was pretty disdainful of human specialness in his correspondence, but he kept a low profile – on this and everything else – in public. I want to be a bit more overt about these things. And one of the things that really amazes me about birds, apart from their physical beauty, is how much goes on in those teeny noggins of theirs.

Jacinta: Yes, but what really brought this on? I haven’t heard you rhapsodising about birds before.

Canto: You haven’t been inside my vast noggin mate. Actually I’ve been taking photos – or trying to – of the bird life around here; magpies, magpie-larks, crows, rainbow lorikeets, honeyeaters, galahs, corellas, sulphur-crested cockies, as well as the pelicans, black swans, cormorants, moorhens, coots and mallard ducks by the river, not to mention the ubiquitous Australian white ibis and the masked lapwing.

Jacinta: Well I didn’t know you cared. Of course I agree with you on the beauty of these beasties. Better than any tattoo I’ve seen. So you’re becoming a twitcher?

Canto: I wouldn’t go that far, but I’ve been nurturing my fledgling interest with a book on the sensory world of birds, called, appropriately, Bird sense, by a British biologist and bird specialist, Tim Birkhead. It’s divided into sections on the senses of birds – a very diverse set of creatures, it needs to be said. So we have vision, hearing, smell, taste, touch, and that wonderful magnetic sense that so much has been made of recently.

Jacinta: So we can’t generalise about birds, but I know at least some of them have great eyesight, as in ‘eyes like an eagle’.

Canto: Well, as it happens, our own Aussie wedge-tailed eagle has the most acute sense of vision of any creature so far recorded.

Jacinta: Well actually it isn’t ours, it just happens to inhabit the same land-form as us.

Canto: How pedantic, but how true. But Birkhead points out that there are horses for courses. Different birds have vision adapted for particular lifestyles. The wedge-tail’s eyes are perfectly adapted to the clear blue skies and bright light of our hinterland, but think of owl eyes. Notice how they both face forward? They’re mostly nocturnal and so they need good night vision. They’ve done light-detection experiments with tawny owls, which show that on the whole they could detect lower light levels than humans. They also have much larger eyes, compared with other birds. In fact their eyes are much the same size as ours, but with larger pupils, letting in more light. They’ve worked out, I don’t know how, that the image on an owl’s retina is about twice as bright as on the average human’s.

Jacinta: So their light-sensitivity is excellent, but visual acuity – not half so good as the wedge-tailed eagle’s?

wedge-tailed eagle - world's acutest eyes

wedge-tailed eagle – world’s acutest eyes

Canto: Right – natural selection is about adaptation to particular survival strategies within particular environments, and visual acuity isn’t so useful in the dark, when there’s only so much light around, and that’s why barn owls, who have about 100 times the light-sensitivity of pigeons, also happen to have very good hearing – handy for hunting in the dark, as there’s only so much you can see on a moonless night, no matter how sensitive your eyes are. They also learn to become familiar with obstacles by keeping to the same territory throughout their lives.

face of a barn owl - 'one cannot help thinking of a sound-collecting device, quoth researcher Masakazu Konishi

face of a barn owl – ‘one cannot help thinking of a sound-collecting device’, quoth researcher Masakazu Konishi

Jacinta: So they don’t echo-locate, do they?

Canto: No, though researchers now know of a number of species, such as oilbirds, that do. Barn owls, though, have asymmetrical ear-holes, one being higher in the head than the other, which helps them to pinpoint sound. It was once thought that they had infra-red vision, because of their ability to catch mice in apparently total darkness, but subsequent experiments have shown that it’s all about their hearing, in combination with vision.

Jacinta: Well you were talking about those amazing little brains of birds in general, and I must say I’ve heard some tales about their smarts, including how crows use cars to crack nuts for them, which must be true because it was in a David Attenborough program.

Canto: Yes, and they know how to drop their nuts near pedestrian crossings and traffic lights, so they can retrieve their crushed nuts safely. The genus Corvus, including ravens, crows and rooks, has been a fun target for investigation, and there’s plenty of material about their impressive abilities online.

seeing is believing

seeing is believing

Jacinta: So what other tales do you have to tell, and can you shed any light on how all this cleverness comes in such small packages?

Canto: Well Birkhead has been studying guillemots for years. These are seabirds that congregate on cliff faces in the islands around Britain, and throughout northern Europe and Canada. They’re highly monogamous, and get very attached to each other, and thereby hangs another fascinating tale. They migrate south in the winter, and often get separated for lengthy periods, and it’s been noted that when they spot their partner returning, as a speck in the distance, they get highly excited and agitated, and the greeting ceremony when they get together is a joy to behold, apparently – though probably not as spectacular as that of gannets. Here’s the question, though – how the hell can they recognise their partner in the distance? Common guillemots breed in colonies, butt-to-butt, and certainly to us one guillemot looks pretty well identical to another. No creature could possibly have such acute vision, surely?

Jacinta: Is that a rhetorical question?

Canto: No no, but it has no answer, so far. It’s a mystery. It’s unlikely to be sight, or hearing, or smell, so what is it?

Jacinta: What about this magnetic sense? But that’s only about orientation for long flights, isn’t it?

Canto: Yes we might discuss that later, but though it’s obvious that birds are tuned into their own species much more than we are, the means by which they recognise individuals are unknown, though someone’s bound to devise an ingenious experiment that’ll further our knowledge.

Jacinta: Oh right, so something’s bound to turn up? Actually I wonder if the fact that people used to say that all Chinese look the same, which sounds absurd today, might one day be the case with birds – we’ll look back and think, how could we possibly have been so blind as to think all seagulls looked the same?

Canto: Hmmm, I think that would take a lot of evolving. Anyway, birds are not just monogamous (and anyway some species are way more monogamous than others, and they all like to have a bit on the side now and then) but they do, some of them, have distinctly sociable behaviours. Ever heard of allopreening?

Jacinta: No but I’ve heard the saying ‘birds of a feather flock together’ and that’s pretty sociable. Safety in numbers I suppose. But go on, enlighten me.

Canto: Well, allopreening just means mutual preening, and it usually occurs between mates – and I don’t mean in the Australian sense – but it’s also used for more general bonding within larger groups.

Jacinta: Like, checking each other out for fleas and such, like chimps?

Cant: Yeah, though this particular term is usually reserved for birds. Obviously it serves a hygienic purpose, but it also helps calm ruffled feathers when flocks of colonies live beak by jowl. And if you ever get close enough to see this, you’ll notice the preened bird goes all relaxed and has this eyes half-closed, blissed-out look on her face, but we can’t really say that coz it’s anthropomorphising, and who knows if they can experience real pleasure?

Jacinta: Yes, I very much doubt it – they can only experience fake pleasure, surely.

Canto: It’s only anecdotal evidence I suppose, but that ‘look’ of contentment when birds are snuggling together, the drooping air some adopt when they’ve lost a partner, as well as ‘bystander affiliation’, seen in members of the Corvus genus, all of these are highly suggestive of strong emotion.

Jacinta: Fuck it, let’s stop beating about the bush, of course they have emotions, it’s only human vested interest that says no, isn’t it? I mean it’s a lot easier to keep birds in tiny little cages for our convenience, and to burn their beaks off when they get stressed and aggressive with each other, than to admit they have feelings just a bit like our own, right? That might mean going to the awful effort of treating them with dignity.

Canto: Yyesss. Well on that note, we might make like the birds and flock off…

how the flock do they do that?

how the flock do they do that?

Written by stewart henderson

November 13, 2015 at 12:06 pm

HIT, mitochondria and health

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comparing-hit-with-other-exercise

 

and for a gentler form of exercise...

and for a gentler form of exercise…

Jacinta: Well now, I know you’re dying to explore the recently touted benefits of your favourite exercise, so let’s have it.

Canto: Yes, I’m very much a HIT man, that’s high intensity interval training, highly recommendable because it takes so little time and only requires an exercise bike. I was put onto it by one of Michael Mosley’s documentaries, though I’ve been a rather theoretical enthusiast in recent times, having trouble overcoming my laziness and my pain-avoidance tendencies, because though it’s short exercise it is a little painful.

Jacinta: So the recent Catalyst episode has brought your enthusiasm surging back?

Canto: Naturellement, especially as it brings with it some new research to focus on. Mitochondria – what do you know about them?

Jacinta: That they are organelles in our cells, believed to have originated as bacteria but to have united with our eukaryotic cells way back in time in a process known as endosymbiosis. They’re also responsible for producing ATP, the energy molecules… though I’ve no idea how, or what an energy molecule actually is.

Canto: That’s music to my ears.

Jacinta: The dulcet tones of ignorance?

Canto: In the country of the blind the one-eyed science pundit is king, and I’d rather be a king than a commoner, so hear ye, my subject.

Jacinta: I may be blind but I’m all ears, Your Majesty.

Canto: Well, as the Catalyst program tells us, mitochondria are about a billion times smaller than a grain of sand, but the world at nanoscales has really opened up to us in recent decades. Mitochondria are good for us, and the more the merrier. And the evidence is that HIT exercise can not only increase the production of mitochondria but increase their function.

Jacinta: So how do we produce mitochondria?

Canto: Are you going to keep interrupting me with questions? Okay, the production of mitochondria relies on our oxygen intake. The story goes that we fill our lungs with oxygen and it enters the bloodstream for a specific purpose…

Jacinta: Hang on, we fill our lungs with air, not just oxygen, so how does the oxygen get separated, and how does the blood take up the oxygen? Aren’t you skipping a few steps here?

Canto: Yes, go and research it yourself and you can report on it next time. The destination of this inhaled oxygen is the mitochondria. There are billions of these mitochondria in our musculature, though the more fit and trained up you are, the more you’re likely to have. Mitochondria apparently comprise some 10% of our body mass, which I’m sure will come as a surprise. Now oxygen, as you know, acts as a corrosive through the process known as oxidation, which involves the loss of electrons…

Jacinta: Hang on…

Canto: Please shut up. So oxygen can have a negative effect on proteins, enzymes and even our DNA, but mitochondria uses this corrosive electron-stripping power to break down nutrients and to create energy in the form of adenosine triphosphate (ATP). Don’t ask! Of course this doesn’t just happen in humans but in all other mammals and complex creatures, and in plants. And that brings us to physical fitness, and the VO2 Max, which is, essentially, the measure of the fitness of our mitochondria. The term stands for volume (V), oxygen (O2), and of course maximum, though generally those concerned with aerobic fitness don’t make the association with mitochondria, they’re just looking at increasing their maximum oxygen consumption levels. Now it’s not an easy thing for impoverished nonentities like us to find out what our VO2 Max is, but it’s probably pretty pathetic. It’s something that endurance athletes tend to obsess about as they try to improve their performance – I believe rowers in particular have some of the highest levels. I notice there’s at least one VO2 Max app on the market – going very cheap too – but I’d be very sceptical about its reliability. In the testing facility shown on Catalyst they measure it via a version of HIT. They get the subject to ride an exercise bike, building up speed till she’s going as fast as she can, and she can go no faster and starts slowing down. That peak represents her VO2 Max. She will be tested 16 weeks later, after a mere 6 minutes of HIT a week, and you can bet your rented house that her VO2 Max will have substantially improved.

Jacinta: So for us low-lifes – excuse my interruption – who can’t easily or cheaply measure improvements in our VO2 Max or, say, our fat to muscle ratio, we just have to feel the difference in aerobic fitness, mitochondrial health and the like…

Canto: Yeah, and your weight will go down too, if you’re carrying a bit extra, as we both are. And the exertion will make you feel better and healthier, I guarantee it. We all know that the placebo effect is real after all. But seriously, I’m sure if we keep to a regime of HIT – say 3 bursts of 20-second full-pelt pedalling interspersed with a minute or so of more relaxed pedalling, or even if we start with 10-second bursts and then 15-second bursts, maybe eventually getting up to 30-second bursts, we’ll feel it getting easier, and it won’t be purely subjective even if we have no way of objectively measuring it.

Jacinta: But shouldn’t we consult a doctor beforehand? I already feel a heart-attack coming on.

Canto: I know you’re joking, but certainly anyone who has any kind of heart condition, or are diabetic or pre-diabetic or have any other serious chronic condition should discuss it with their GP, but really, apart from your couch potato tendencies, there’s nothing wrong with you.

Jacinta: You’re right, and I’m looking forward to the challenge, even though I’m already a to-die-for, effortlessly slim, perpetually twenty-two year old intellectual beauty..

Canto: And I’m the ultimate metrosexual hipster of indeterminate age and shoe size, discreetly tattooed and tucked…

Jacinta: Ah, yuck, you stupid twat, tattoos are the most repugnant fashion development of all time. At least you’re not a spornosexual, yuk, stay away from the gym or I’ll never speak to you again .

Canto: Promise? Anyway, around 35 is the average VO2 Max, but that’s a bit meaningless for us low-lifes as you say. Top athletes have levels in the 60s and 70s, with the highest ever recorded being around 96 or 97 for humans, but some mammals – like racehorses and Siberian sled dogs – can reach much higher levels. But there’s also going to be a big improvement in your fat-to-muscle ratio with regular bouts of HIT. In the Catalyst episode, the reporter took a DEXA body composition scan to measure this ratio. It also measures bone density. DEXA stands for Dual Energy X-ray Absorptiometry, that means you’re subjected to 10 minutes of very low-dose x-radiation at two different energy levels. It measures the relative densities of the different tissues. You can get this scan done in Adelaide, for a baseline measure, but it’ll probably cost an arm and a leg.

Jacinta: One way to lose weight. Cheaper to just take it for granted that you’re getting more muscular with every HIT.

Canto: Spoken like a true scientist. But generally, inactivity itself is a health problem, and anything that raises your metabolism, as HIT most definitely does, will be good for you, if it doesn’t kill you. And of course one of the most exciting findings in recent times is that your VO2 Max can be raised, with all the associated health benefits, without spending crazy amounts of time and money at the gym.

Jacinta: So how did they make this discovery?

Canto: Well I suppose they were doing a lot of experimenting and testing around the health benefits of exercise, but one test, a Wingate test, involved 30 seconds of all-out pedalling on an exercise bike, repeated a few times between periods of rest, to make up to two or three minutes of full-on exercise per session.

Jacinta: And this was for already-athletic types, right?

Canto: Yes – not advisable for middle-aged or post-middle-aged couch potatoes to start on that regimen. I’m currently doing three fifteen-second bursts, building up to 20-second bursts, then up to 30 seconds and no more. So researchers found that endurance levels can be dramatically improved after just six minutes or so of this kind of exercise. A doubling of endurance capacity, no less. Compare this to the current recommendations of 150 minutes a week. Who ever does that, apart from gym junkies?

Jacinta: So, it’s like this incredible short-cut to health.

Canto: Well of course it isn’t the solution to all ills, but among other things such a quick turn-around is a great motivator towards a healthier lifestyle all round. And it doesn’t have to be an exercise bike – you can adapt it, for example you can get yourself outside and do interspersed 30-second sprints, but I hate running and I’ve got a gammy knee so I’ll stay on the bike.

Jacinta: So, have they looked more into the actual science of this? What’s happening here?

Canto: Well again it seems to be about sucking in oxygen and providing a drug hit to the mitochondria. They did this rather nasty experiment with mice, genetically modifying them so that their mitochondrial DNA wasn’t functioning properly – their mitochondria were getting worn out. They looked pretty sorry-looking compared to the control mice, prematurely ageing as evidenced in their fur, their neural activity, heart function and sensory abilities. Their life-span was about half that of normal mice, and no drugs improved the situation.  Then they set them on a treadmill regularly, 3 times a week, at a brisk pace, for 45 minutes each session, which you might think would’ve killed them off all the more quickly, but the result was a spectacular improvement in mitochondria production and overall health and energy levels.

Jacinta: And this was in genetically modified mice?

Canto: Apparently so. The program didn’t go into detail about that, except to say that the bad mitochondria were apparently being selected against. Now of course we’re talking about mice here, and this was looking at endurance fitness rather than HIT, but it’s been shown that HIT does all the right things, and in some areas performs better than endurance training. Reductions in blood pressure, improvements in insulin sensitivity, in muscle to fat ratio, in VO2 max all in a matter of weeks, but the really interesting finding was that with HIT, improvement in mitochondrial function was significant – which wasn’t the case after endurance training.

Jacinta: How do they know that?

Canto: They took muscle samples and measured the ability of the muscles to produce oxygen – basically a measure of mitochondrial function. After just four weeks of HIT, mitochondrial function improved by up to 30%, while endurance training over the same period showed little or no change.

Jacinta: Wow. Doesn’t say much for endurance training.

Canto: Well endurance training does improve your VO2 max and it’s hardly bad for you. But the thing with these quick sprints is the difference at the muscle level. Sports medicine distinguishes between fast-twitch, slow-twitch and intermediate muscle fibres. HIT uses a wider range of muscles and muscle types than endurance work, and that seems to be the key. Improvement in mitochondrial function confers a heap of benefits, so this kind of exercise wards off neurological and other conditions, including muscle weakness and epidermal deterioration, the tell-tale signs of ageing. In fact all exercise does this. Ever heard of the stratum corneum?

Jacinta: Mmmm, corneum, cornea, isn’t that part of the eye?

Canto: Excellent guess but wrong in this case. The stratum corneum is the top layer of the epidermis, the skin. It starts to thicken as you age, and the layer underneath gets thinner as your mitochondrial function reduces. You can slow down that process quite significantly with regular exercise. They did skin biopsies of sedentary people over 65 before and after endurance training. After just 3 months the skin showed great improvement – a 20 to 30 ‘youthening effect’, according to one researcher. The dead outer layer thinned, and the dermis, full of collagen fibres, thickened. So, clearly, you’re never too old to start.

Jacinta: Or never too young. So okay I’ll start.

Canto: Great, but let me describe one more impressive study, being done on menopausal women using HIT. Menopause is about a major decline in estrogen, which has serious vascular, heart and metabolic effects, as well as insulin resistance. You tend to produce a lot of bad visceral fat which negatively affects the liver, due to the over-production of cytokines – but that’s another story. Anyway, the women were given a sprint regime, of just a short period of fast peddling interspersed with more relaxing peddling, amounting to eight minutes of fast but not hard exercise all up. The results of this research haven’t been published yet, but the women’s self-reporting is all very positive, which isn’t surprising. The research is also based on previous research with obese young men, and the exercise proved very effective. Visceral fat is generally much easier to reduce than subcutaneous fat.

Jacinta: Okay, so we’re going to do this?

Canto: Absolutely. And finally, here are some links.

 

The Catalyst episode, http://www.abc.net.au/catalyst/stories/4319131.htm

http://www.tabataprotocol.com

https://newsroom.unsw.edu.au/news/health/sprint-fight-fat

High-Intensity Training and Changes in Muscle Fiber, [www.springerlink.com/content/1137px7x66667132]

Written by stewart henderson

October 16, 2015 at 8:34 am