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A DNA dialogue 2: the double helix

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

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

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

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

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

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

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

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

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

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

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

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

Jacinta: …….

Written by stewart henderson

January 16, 2020 at 5:13 pm

Posted in biochemistry, DNA, science

Tagged with , ,

A DNA dialogue 1: the human genome

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what genomics tells us

Canto: I’m often confused when I try to get my head around all the stuff about genes and DNA, and genomes and alleles and chromosomes, and XX and XY, and mitosis and meiosis, and dominant and recessive and so on. I’d like to get clear, if only I could.

Jacinta: That’s a big ask, and of course we’re both in the same boat. So let’s use the magical powers of the internet to find answers. For example, here’s something that confuses me. The Human Genome project, which ended around the year 2000, involved a mapping of the whole human genome, and that includes coding and non-coding genes, and I think it was found to contain 26,000 or so – what? Letters? Genes? Coding genes? Anyway there’s a number of questions there, but they’re not the questions that confuse me. I don’t get that we now, apparently, have worked out the genetic code for all humans, but each of us has different DNA. How, exactly, does our own individual DNA relate to the genome that determines the whole species? Presumably it’s some kind of subset?

Canto: Hmmm. This article from the Smithsonian tells us that the genetic difference between human individuals is very tiny, at around 0.1%. We humans differ from bonobos and chimps, two lineages of apes that separated much more recently, by about 1.2%….

Jacinta: Yes, yes, but how, with this tiny difference between us, are we able to use DNA forensically to identify individuals from a DNA sample?

Canto: Well, perhaps this Smithsonian article provides a clue. It says that the 1.2% difference between us and chimps reflects a particular way of counting. I won’t go into the details here but apparently another way of counting shows a 4-5% difference.

Jacinta: We probably do need to go into the details in the end, but clearly this tiny .1% difference between humans is enough for us to determine the DNA as coming from one individual rather than 7 to 8 billion others. Strangely enough, I can well believe that, given that we can detect gravitational waves and such – obviously using very different technology.

Canto: Yeah the magic of science. So the Human Genome Project was officially completed in April 2003. And here’s an interesting quote from Wikipedia:

The “genome” of any given individual is unique; mapping the “human genome” involved sequencing a small number of individuals and then assembling these together to get a complete sequence for each chromosome. Therefore, the finished human genome is a mosaic, not representing any one individual.

Of course it would have to be a mosaic, but how can it represent the whole human genome when it’s only drawn from a small number? And who were these individuals, how many, and where from?

Jacinta: The Wikipedia article does give more info on this. It tells us that the project isn’t really finished, as we’ve developed techniques and processes for faster and deeper analyses. As to your questions, when the ‘finished’ sequencing was announced, the mosaic was drawn from a small number of anonymous donors, all of European origin.

Canto: But we all originated from Africa anyway, so…

Jacinta: So maybe recent ‘origin’ isn’t so important. Anyway, that first sequencing is now known as the ‘reference genome’, but after that they did sequence the genomes of ‘multiple distinct ethnic groups’, so they’ve been busy. But here are some key findings, to finish off this first post. They found some 22,300 protein-coding genes, as well as a lot of what they used to call junk DNA – now known as non-coding DNA. That number is within the mammalian range for DNA, which no doubt surprised many. Another blow for human specialness? And they also found that there were many more segmental duplications than expected. That’s to say, sections of DNA that are almost identically repeated.We’ll have to explore the significance of this as we go along.

Canto: Yes, that’s enough for starters. Apparently our genome has over 3 billion nucleobase pairs, about which more later no doubt.

References

http://humanorigins.si.edu/evidence/genetics

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

Written by stewart henderson

January 13, 2020 at 11:48 pm

epigenetics and imprinting 4: the male-female thing

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Gametes are gametes because of epigenetic modifications in their pro-nuclei, but they have to lose these modifications, or transform them, when they come together to form zygotes. The male pro-nucleus DNA methylation is stripped away immediately after sperm penetrates egg. The egg pronucleus undergoes the same process, but more gradually. It’s like a wiping away of epigenetic memory, creating totipotency, which becomes a more limited pluripotency as the blastocyst, with its inner cell mass (ICM), forms. 

The ICM cells begin differentiating through the regulation of some key genes. For example, a gene codes for a protein that switches on a set of genes, which code for proteins in a cascading effect. But it’s not quite a matter of switching genes on or off, it’s rather more complex. The process is called gene reprogramming, and it’s of course done effortlessly during every reproductive cycle. Artificial reprogramming of the kind carried out by Yamanaka and others, an essential part of cloning, hasn’t come close to this natural process that goes on in mammals and other species every day.

Clearly, though the epigenetic reprogramming for the female pronucleus is different from that carried out more swiftly in the male. As Carey puts it, ‘the pattern of epigenetic modifications in sperm is one that allows the male pronucleus to be reprogrammed relatively easily.’ Human researchers haven’t been particularly successful in reprogramming an adult nucleus by various methods, such as transferring it to a fertilised egg or treating it with the four genes isolated by Yamanaka. The natural process of gene reprogramming eliminates most of the epigenetic effects accumulated in the parent genes, but as the reprogramming is a different process in the male and female pro-nucleus, this shows that they aren’t functionally equivalent. There is a ‘parent-of-origin effect’. Experiments done on mice to explore this effect found that DNA methylation, an important form of chromatin modification (and the first one discovered), was passed on to offspring by the female parent. That’s to say, DNA from the female was more heavily methylated than that from the male. Carey describes the DNA as ‘bar-coded’ as coming from the male or the female. The common term for this is imprinting, and it’s entirely epigenetic.

Imprinting has been cast by Carey, and no doubt others, as an aspect of the ‘battle of the sexes’. This battle may well be imprinted in the pronuclei of the fertilised egg. Here’s how Carey puts the two opposing positions:

Male: This pregnant female is carrying my genes in the form of this foetus. I may never mate with her again. I want my foetus to get as big as possible so that it has the greatest chance of passing on my genes.

Female: I want this foetus to pass on my genes. But I don’t want it to be at the cost of draining me so much that I never reproduce again. I want more than this one chance to pass on my genes.

So there’s a kind of balance that has developed in we eutherian mammals, in a battle to ensure that neither sex gains the upper hand. Further experiments on mice in recent times have explored how this battle is played out epigenetically. I’ll look at them in the next post in this series.

Reference

The Epigenetics Revolution, by Nessa Carey, 2011

Written by stewart henderson

January 9, 2020 at 10:50 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

Einstein, science and the natural world: a rabid discourse

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Einstein around 1915

Einstein around 1915

Canto: Well, we’re celebrating this month what is surely the greatest achievement by a single person in the history of science, the general theory of relativity. I thought it might be a good time to reflect on that achievement, on science generally, and on the impetus that drives us to explore and understand as fully as possible the world around us.

Jacinta: The world that made us.

Canto: Précisément.

Jacinta: Well, first can I speak of Einstein as a political animal, because that has influenced me, or rather, his political views seem to chime with mine. He’s been described as a supra-nationalist, which to me is a kind of political humanism. We’re moving very gradually towards this supra-nationalism, with the European Union, the African Union, and various intergovernmental and international organisations whose goals are largely political. Einstein also saw the intellectual venture that is science as an international community venture, science as an international language, and an international community undertaking. And with the development of nuclear weapons, which clearly troubled him very deeply, he recognised more forcefully than ever the need for us to take international responsibility for our rapidly developing and potentially world-threatening technology. In his day it was nuclear weapons. Today, they’re still a threat – you’ll never get that genie back in the bottle – but there are so many other threats posed by a whole range of technologies, and we need to recognise them, inform ourselves about them, and co-operate to reduce the harm, and where possible find less destructive but still effective alternatives.

Canto: A great little speech Jas, suitable for the UN general assembly…

Jacinta: That great sinkhole of fine and fruitless speeches. So let’s get back to general relativity, what marks it off from special relativity?

Canto: Well I’m not a physicist, and I’m certainly no mathematician, but broadly speaking, general relativity is a theory of gravity. Basically, after developing special relativity, which dealt with the concepts of space and time, in 1905, he felt that he needed a more comprehensive relativistic theory incorporating gravity.

Jacinta: But hang on, was there really anything wrong with space and time before he got his hands on them? Why couldn’t he leave them alone?

Canto: OMG, you’re taking me right back to basics, aren’t you? If I had world enough, and time…

Jacinta: Actually the special theory was essentially an attempt – monumentally successful – to square Maxwell’s electromagnetism equations with the laws of Newton, a squaring up which involved enormous consequences for our understanding of space and time, which have ever since been connected in the concept – well, more than a concept, since it has been verified to the utmost – of the fourth, spacetime, dimension.

Canto: Well done, and there were other vital implications too, as expressed in E = mc², equivalating mass and energy.

Jacinta: Is that a word?

Canto: It is now.

Jacinta: So when can we stop pretending that we understand any of this shite?

Canto: Not for a while yet. The relevance of relativity goes back to Galileo and Newton. It all has to do with frames of reference. At the turn of the century, when Einstein was starting to really focus on this stuff, there was a lot of controversy about whether ‘ether’ existed – a postulated quasi-magical invisible medium through which electromagnetic and light waves propagated. This ether was supposed to provide an absolute frame of reference, but it had some contradictory properties, and seemed designed to explain away some intractable problems of physics. In any case, some important experimental work effectively quashed the ether hypothesis, and Einstein sought to reconcile the problems by deriving special relativity from two essential postulates, constant light speed and a ‘principle of relativity’, under which physical laws are the same regardless of the inertial frame of reference.

the general theory - get it?

the general theory – get it?

Jacinta: What do you mean, ‘the initial frame of reference’?

Canto: No, I said ‘the inertial frame of reference’. That’s one that describes all parameters homogenously, in such a way that any such frame is in a constant motion with respect to other such frames. But I won’t go into the mathematics of it all here.

Jacinta: As if you could.

Canto: Okay. Okay. I won’t go any further in trying to elucidate Einstein’s work, to myself, you or anyone else. At the end of it all I wanted to celebrate the heart of Einstein’s genius, which I think represents the best and most exciting element in our civilisation.

Jacinta: Drumroll. Now, expose this heart to us.

Canto: Well we’ve barely touched on the general theory, but what Einstein’s work on gravity teaches us is that by not leaving things well alone, as you put it, we can make enormous strides. Of course it took insight, hard work, and a full and deep understanding of the issues at stake, and of the work that had already been done to resolve those issues. And I don’t think Einstein was intending to be a revolutionary. He was simply exercised by the problems posed in trying to understand, dare I say, the very nature of reality. And he rose to that challenge and transformed our understanding of reality more than any other person in human history. It’s unlikely that anything so transformative will ever come again – from the mind of a single human being.

Jacinta: Yes it’s an interesting point, and it takes a particular development of culture to allow that kind of transformative thinking. It took Europe centuries to emerge from a sort of hegemony of dogmatism and orthodoxy. During the so-called dark ages, when warfare was an everyday phenomenon, and later too, right through to the Thirty Years War and beyond, one thing that could never be disputed amongst all that disputation was that the Bible was the word of God. Nowadays, few people believe that, and that’s a positive development in the evolution of culture. It frees us to look at morality from a broader, richer, extra-Biblical perspective..

Canto: Yes we no longer have to even pretend that our morality comes from such sources.

Jacinta: Yes and I’m thinking of other parts of the world that are locked in to this submissive way of thinking. A teaching colleague, an otherwise very liberal Moslem, told me the other day that he didn’t believe in gay marriage, because the Qu-ran laid down the law on homosexuals, and the Qu-ran, because written by God, is perfect. Of course I had to call BS on that, which made me quite sad, because I get on very well with him, on a professional and personal basis. It just highlights to me the crushing nature of culture, how it blinds even the best people to the nature of reality.

Canto: Not being capable of questioning, not even being aware of that incapability, that seems to me the most horrible blight, and yet as you say, it wasn’t so long ago that our forebears weren’t capable of questioning the legitimacy of Christianity’s ‘sacred texts’, in spite of interpreting those remarkably fluid texts in myriad ways.

Jacinta: And yet out of that bound-in world, modern science had its birth. Some modern atheists might claim the likes of Galileo and Francis Bacon as one of their own, but none of our scientific pioneers were atheists in the modern sense. Yet the principles they laid down led inevitably to the questioning of sacred texts and the gods described in them.

Canto: Of course, and the phenomenal success of the tightened epistemology that has produced the scientific and technological revolution we’re enjoying now, with exoplanets abounding, and the revelations of Homo floresiensis, Homo naledi and the Denisovan hominin, and our unique microbiome, and recent work on the interoreceptive tract leading to to the anterior insular cortex, and so on and on and on, and the constant shaking up of old certainties and opening up of new pathways, all happening at a giddying accelerating rate, all of this leaves the ‘certainty of faith’ looking embarrassingly silly and feeble.

Jacinta: And you know why ‘I fucking love science’, to steal someone else’s great line? It’s not because of science itself, that’s only a means. It’s what it reveals about our world that’s amazing. It’s the world of stuff – animate and inanimate – that’s amazing. The fact that this solid table we’re sitting at is made of mostly empty space – a solidity consisting entirely of electrochemical bonds, if that’s the right term, between particles we can’t see but whose existence has been proven a zillion times over, and the fact that as we sit here on a still, springtime day, with a slight breeze tickling our faces, we’re completely oblivious of the fact that we hurtling around on the surface of this earth, making a full circle every 24 hours, at a speed of nearly 1700 kms per hour. And at the same time we’re revolving around the sun at a far greater speed, 100,000 kms per hour. And not only that, we’re in a solar system that’s spinning around in the outer regions of our galaxy at around 800,000 kilometres an hour. And not only that… well, we don’t feel an effing thing. It’s the counter-intuitive facts about the natural world that our current methods of investigation reveal – these are just mind-blowing. And if your mind doesn’t get blown by it, then you haven’t a mind worth blowing.

Canto: And we have two metres of DNA packed into each nucleus of the trillions of cells in our body. Who’d’ve thunkit?

whatever

whatever

Written by stewart henderson

November 23, 2015 at 11:33 pm

how did life begin?: part 2 – RNA, panspermia, viroids and reviving the blob

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1280px-Difference_DNA_RNA-EN

Jacinta: So you’re going to talk about RNA, I know that stands for ribonucleic acid, and DNA is deoxy-ribonucleic acid, so – RNA is DNA without the oxygen?

Canto: Uhhh, you mean DNA is RNA without the oxygen.

Jacinta: Whatever, they’re big complex molecules aren’t they, but RNA is simpler, and less stable I think.

Canto: Okay, I’ll take it from here. We haven’t really known for very long that DNA is the essential material for coding and replicating life, and it’s a very complex molecule made up of four chemical bases, adenine, guanine, thymine and cytosine, better known as A, G, T and C. They connect to form base pairs, A always pairing with T and C with G.

Jacinta: What the hell are chemical bases? Do you mean bases as opposed to acids?

Canto: Well, yes. These bases, also called nucleobases, accept hydrogen ions, which have a positive charge. It’s all about pair bonding. The nucleobases – A, G, C and T, as well as uracil, found in RNA – are nitrogen-containing compounds which are attached to sugars… but let’s not get bogged down too much. The point is that DNA and RNA are nucleic acids that code for life, and most of the researchers chasing down the origin of life believe that RNA is a precursor of DNA in the process of replication.

Jacinta: And presumably there are precursors to RNA and so on.

Canto: Well presumably, but let’s just look at RNA, because we have a fair amount of evidence that this molecule preceded DNA as a ‘life-engine’, so to speak, and really no solid evidence, that I know of, of anything before RNA.

Jacinta: Okay so what is this evidence, and why did DNA take over?

Canto: Right, now the subject we’re entering into here is abiogenesis, the process by which life emerged from the inanimate. RNA is probably well down the chain from this emergence, but better to start with it than to dive into speculation. Now as you probably know, RNA has a single helical structure, and today it’s heavily involved in the process whereby DNA ‘creates’ proteins. In fact, all current life forms involve the action and interaction of three types of macromolecule, DNA, RNA and proteins…

Jacinta: But of course these complex molecules didn’t spring from nowhere.

Canto: Well we don’t know how they were built up, and many pundits think they may have been seeded here from elsewhere during the late heavy bombardment, which came to an end about 3.8 billion years ago, around the time that those Greenland rocks, with their heavy load of organic carbon, have been dated to. It seems plausible considering how quickly life seems to have taken off here.

Jacinta: Okay so tell us about RNA, how does it relate to the other two macromolecules?

Canto: Well, RNA is able to store genetic information, like DNA, and in fact it’s the genetic material for some of our scariest viruses, such as ebola, SARS, hep C, polio – not to mention influenza.

Jacinta: Wow, I didn’t know that. But one thing I do know about viruses is that they can’t exist independently of a host, so is RNA the basis of any truly independent life forms?

Canto: Not currently, on our planet, as far as we know, but the evidence is fairly strong that RNA has been central to life here from the very beginning, as it is still key to the most basic components of cells such as ribosomes, ATP and other co-enzymes. This suggests that RNA was once even more central, but in some areas it’s been subordinated to, and harnessed to, the more complex and recent DNA molecule. But, yes, since we can’t look at RNA coding for independent life-forms, we need to wind the clock back still further to look at precursors and other constituents of life, such as amino acids and peptides.

Jacinta: Which are chemical molecules, not biological ones. It seems to me we’re still a long way from working out the leap from chemistry to biology.

a peptide or amide bond - a covalent bond between two amino acid molecules

a peptide or amide bond – a covalent bond between two amino acid molecules

Canto: Yes, yes but we’re bridging various gaps. Peptides are created from amino acids, as you know. They are chains of amino acids linked by peptide bonds, and proteins are only distinguished from peptides in that they’re bigger versions of them, and bonded in a particular biologically useful way. You’ll notice when you read about this stuff that the terms ‘chemistry’ and ‘biology’ are used rather arbitrarily – a chemical compound can be referred to as a biological compound and vice versa. But various experiments have cast light on how increasingly ‘biological’ constituents are formed from simpler elements. For example, you may know that meteorites and comets, which bombarded the early earth in great numbers, contained plenty of amino acids – we’ve counted more than 70 different amino acids derived from meteorites, such as the Murchison meteorite that landed in Victoria in 1969. Another probable source of these amino acids, and even more complex and ‘biological’ molecules is comets, which also contain a lot of water in frozen form, but this has raised the question of how these molecules could have survived the impact of these colossal objects, which released enormous energy, some of them partially vaporising the earth’s crust. But an ingenious experiment, described in this video, and elsewhere, was able to simulate a comet’s impact, creating pressures many times greater than that experienced in our deepest oceans, to see what would happen to the amino acids. It was expected that they would barely survive the impact, but surprisingly they not only survived but forged bonds that created complex peptides.

a fragment of Murchison meteorite - of which there are many. This carbonaceous chondrite is still being analysed for organic compounds. Up to 70 amino acids identified so far

a fragment of Murchison meteorite – of which there are many. This carbonaceous chondrite is still being analysed for organic compounds. Up to 70 amino acids identified so far

Jacinta: Mmmm, that is interesting. So, the gap between peptides, or proteins, and RNA, what do we know about that?

Canto: Well, now you’re getting into highly speculative territory, but it’s certainly worth speculating about. Firstly, though, in trying to solve this origin of life problem, we have to note that the earth’s atmosphere was incredibly different from what it is now. In fact it was probably quite different from the way Haldane and Oparin and later Miller and Urey envisaged it. It was predominantly carbon dioxide, with hydrogen sulphide, methane and other unpleasant gases – unpleasant to us, that is. That, together with the continual bombardment from outer space has led some scientists to suggest that the place to find the earliest life forms isn’t the open surface but in hidden nooks and crannies or deep underground, in more protected environments.

Jacinta: Yeah the discoveries of so-called extremophiles has made that idea fashionable, no doubt, but presumably these extremophiles are all DNA-based, so I don’t see how investigating them will answer my question.

Canto: Okay, so it’s back to RNA. The thing is, I don’t want to go into the properties of RNA here, it’s just too complicated.

Jacinta: I believe it was Richard Feynman who said something like ‘to fully understand a thing you have to build it’. So there’s still this leap from polypeptides or proteins, which don’t code for anything, they’re just built by ribosomes – RNA structures – from DNA instructions, to sophisticated coded replicators. We have no idea how DNA or RNA came into being, and nobody has successfully created life apart from Doktor Frankenstein. So it’s all a bit disappointing.

Canto: You must surely be joking, or just playing devil’s advocate. You know very well that this is an incredibly difficult nut to crack, and we’ve made huge progress, new discoveries are being made all the time in this field.

Jacinta: Okay, impress me.

Canto: Well, only this year NASA scientists have reported that the nucleobases uracil, thymine and cytosine, essential ingredients of DNA and RNA, have been created in the laboratory, from ingredients found only in outer space – for example pyramidine, which they’ve hypothesised was first created in giant red stars – and they’ve found pyrimidine in meteors. So, another step towards creating life, and further evidence that life here may have been seeded from elsewhere. And if that doesn’t impress you, what about viroids?

Jacinta: Uhhh… what are they, viral androids? Which reminds me, what about the artificial intelligence route to creating life? Intelligent life, what’s more exciting.

Canto: Another time. Viroids are described as ‘sub viral pathogens’. We were talking about viruses before, as a kind of halfway house between the living and the lifeless, but really they’re much more on the side of the living. The smallest known pathogenic virus is over 2000 nucleobases long, and the biggest – well, a megavirus was famously identified just last year and revived after being frozen in Siberian permafrost for something like 35,000 years…

Jacinta: An ancient megavirus has been revived…? WTF? Who thought that was a great idea? Wait a minute, the Siberian permafrost, wasn’t that where Steve MacQueen and his mates dropped The Blob? Megadeath, not just a shite band! We’re doomed!

Canto: Well, strictly speaking it’s a virion, a virus without a host, which means it’s in a kind of dormant phase, like a seed. But I don’t want to talk about megaviruses, fascinating though they are – and very new discoveries. I want to talk about viroids, which are plant pathogens. They consist of short strands of RNA, only a few hundred nucleases long, without the protein coat that characterises viruses, and their existence tends to support the ‘RNA world hypothesis’. It was the discoverer and namer of viroids, Theodor Diener, who pointed out that they were vitally important macromolecules for explaining essential steps in the evolution of life from inanimate matter. That was back in 1989, but his remarks were ignored, and only rediscovered in 2014. So viroids are now a big focus in abiogenesis. They’ve even been called living relics of the pre-cellular RNA world.

Viroid

Jacinta: Okay, I’m more or less impressed. We’ll have to do more on abiogenesis in the future, it’s an intriguing topic, with more breakthroughs in the offing it seems. ..

 

 

Written by stewart henderson

September 28, 2015 at 11:23 pm

mitochondrial DNA, ancient civilisations and early writing

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linear A

linear A

It seems to me we’re living in a world of knowledge revolutions, such as a consciousness revolution, a DNA revolution, a cosmological revolution, a stem-cell revolution, in fact every area of science or technology you care to look at seems to be undergoing revolutionary change, with far more happening than you can ever get your head around, especially if you’re as slow, eternally baffled and wide-eyed as I am. Anyway, I find mucking around in the shallows a lot of fun.

The use of mitochondrial and nuclear DNA to trace the provenance of ancient civilizations is one heady development worth keeping tabs on. One such civilization is the Minoan, which flourished 4000 years ago on the island of Crete. More precisely, it’s believed to have lasted for 12 centuries before coming to a sudden end at around 1500 BCE, probably as a result of a volcanic eruption followed by a tsunami. Arthur Evans, the famed excavator of its palatial remains, named the civilization Minoan after the mythical Minos, king of Crete. He believed it to have been a product of refugees or travellers from Egypt, a view which has divided scholars since. A recent mitochondrial DNA analysis, however, has tended to support the view that the Minoan civilisation was indigenous and independently arrived at. However, mitochondrial DNA, which traces back strictly through the female line, has its limitations, and there are plans for further research using nuclear DNA. It’s unlikely that we’ll completely unravel the web of relations that led to the surge in complexity known as the Cretan bronze age in about 2700 BCE, but DNA analysis is certainly helping to clarify the picture.

When I read about ancient civilizations I’m always interested in how they fit into a wider picture. The Minoans seem to have possessed an open, largely peaceful trading culture, so the links would no doubt have been numerous. There’s plenty of evidence of cultural exchange with Egypt over the period. One of the interesting features of early Minoan civilization is its writing system and how it connects with others, particularly Egyptian writing. The earliest writing forms found on Crete, Cretan hieroglyphs and Linear A, are as yet undeciphered. They appear to be related, but have so far have not been traced to any other known language. Linear B, a later Mycenaean-influenced form, was deciphered in the fifties, and this created an expectation that Linear A, which showed superficial similarities to Linear B (both are described as linear because they are more line-based than Cretan hieroglyphs), would soon be cracked, but the logograms or graphemes of Linear A are largely unique. Cretan hieroglyphs bear some relation to Egyptian hieroglyphs but also to various early Mesopotamian writings, so it’s not certain whether it was independently developed. This form of writing, which goes back at least to 3000 BCE, seems to have disappeared by 1700 BCE.

So we seem to have had a relatively sudden evolution of writing around the Mediterranean and the Mesopotamian regions in the late fourth millenium BCE, though various proto-writing forms had existed for millenia beforehand. The big question here is whether the spark that created a more complex and useful type of writing occurred in only one place and was carried to other places by travellers and traders, or was it a matter of similar conditions fostering a set of sparks in the region, kind of coincidentally but not really. Maybe that’s something to explore further but I’m done for now.

Written by stewart henderson

May 18, 2013 at 11:16 pm

Posted in DNA, history, language

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