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Posts Tagged ‘RNA

more on abiogenesis – Greenland and other rocks, water everywhere, and the how question

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rock formations that may or may not display signs of life

Jacinta: So I recently watched a Nova video on Youtube, which celebrates, through the geologist and mineralogist Robert Hazen, the relationship between rocks and life, or two worlds we tend to keep divided, the animate and the inanimate, and how they feed off each other. It was fascinating, and I’d like to talk about the effect of photosynthesis on the production of iron in the ocean, but first we should talk about those 3.8 billion-year-old Greenland rocks that we talked about way back when.

Canto: Ah, well, have you heard the latest? It comes from Quebec. Haematite tubes, similar to those produced by microbes around undersea hydrothermal vents, which could be up to 4.28 billion years old…

Jacinta: Yeah, couldabeen, wouldabeen, but I must say the video did argue for a watery planet much earlier than might have been expected, but no clue as yet as to where all that water came from.

Canto: You don’t buy the ‘it came from outer space’ meteor scenario?

Jacinta: I’m no expert but it sounds desperate.

Canto: We’ve found icy oceans on Europa and Enceladus, with probable hydrothermal vents, which we’re keen to explore, so maybe it’s not so weird after all.

Jacinta: Oceans of water?

Canto: Yes, and the Hubble Space Telescope recently observed what’s believed to be plumes of water vapour gushing out from Europa’s surface.

Jacinta: Interesting, but what’s most interesting is the diversity of these early signs of life. They’ve found chemical signatures in ancient microscopic zircon crystals, and ancient microbial mats as far apart as Australia and Greenland, and now, possibly, these very old haematite tubes, all very different from each other, and all very unlikely given what we think we know of the Earth’s early environment.

Canto: And they’re all connected with water, aren’t they? This is one of the mysteries to me, where did all the water come from – on Earth, Enceladus, Europa, Titan…?

Jacinta: Search me. It’s certainly exciting and promising though, NASA scientists say that water, chemistry and energy are the three essential requirements for life, and they reckon those moons have all the requirements. They’re hoping to send back probes to search for that life. But, you mentioned Titan. There’s an environment worth exploring, because, as the  NASA boffins tell us, it has rivers, lakes and rain, but it’s not water. So, to steal a phrase, there could be life there, but not as we know it Jim. And if we were able to find a diversity of life in our own solar system, what’s the likelihood of an almost infinitely greater diversity of life amongst the billions of other solar systems we now know to be out there?

Canto: I want to live forever! I want to have infinite time to explore these possibilities! I wanna be a time lord!

Jacinta: Yes but getting back down to Earth. We’re trying to pin down the first appearance of life here but it’s really difficult, and proving to be controversial, unsurprisingly. What isn’t controversial is that there is a window of about 1 billion years between the Earth’s formation and about 3.5 billion years ago when life must have started here.

Canto: Yes and you’re talking about the when, but the where and the how are likely just as controversial and certainly more important. You’ve mentioned Greenland, and I’ve mentioned the remote north of Quebec, and we’re talking about rocky regions that are difficult to get to and explore, and which have undergone great changes over the eons. So there’s plenty of geological argument about them as well. There’s no doubt these regions contain some of the oldest rocks yet discovered, but there’s a fair amount of doubt about their precise age.

Jacinta: Yes they’ve been much deformed over time, but geologists are finding evidence that they formed under the ocean, and that they show distinct signs of hydrothermal vent activity. As you know, hydrothermal vents have come to be associated with the earliest life forms.

Canto: Yes, the evidence appears to be indirect, and based on analogy at this point. Also, some geologists are tentatively putting the date of these rocks as far back as 4.3 billion years, and that’s very early in Earth’s history. I’m talking here about the Quebec material – what’s being said about the Greenland stuff, has it been verified as actual evidence of life?

Jacinta: Well all the reporting on that came out in August-September last year, all based on a paper in Nature, and I’ve not found anything more recent. The claim was that they’d found evidence of stromatolites, that’s the same features we’ve seen in rather a lot of docos recently, growing in shallow waters in Western Australia’s Shark Bay. They’re microbial mats that build up over time to create these mounds. Fossil evidence of stromatolites found in the Pilbara, also in Western Australia, are reliably dated to 3.5 billion years ago, and that’s the current record for earliest life forms, but the contested evidence of stromatolite fossils in Greenland, if validated, would take the record back another 200 million years, at least.

Canto: And these stromatolites evolved in shallow waters, right? Darwin’s warm, energetic little pond. Not like the microbes supposedly found in northern Quebec. Apparently there’s a tension between the fossil evidence, which generally supports the warm pond thesis, and the genetic and biochemical evidence which takes us more towards hydrothermal vents.

Jacinta: Yes, interesting, and anyway water.

Canto: Well we’re not going to be able to solve the water mystery here. Or answer the when question of first life. I’d like to change tack and think on the how question, surely the most interesting one.

Jacinta: Okay so this is where we turn to variations on, or more sophisticated elaborations of, the Miller-Urey-type experiments.

Canto: Yes – finding the recipe, as is emphasised in this documentary on life’s origins. In one part of the documentary, the story’s told about how John Sutherland and colleagues, workers in the field of prebiotic chemistry (a good term for googlers) have created a ribonucleotide, a building block of RNA, through manipulating plausible early-Earth conditions. This was certainly an exciting development, but progress in this field has been frustratingly slow. Sutherland’s work, and critiques of it, are given in more detail here.

Jacinta: Okay so I’ve googled ‘prebiotic chemistry’ as you suggested, and it’s led me to this article in Nature Chemistry which provides a good relatively untechnical intro to the field. Well okay, a bit technical here and there.

Canto: Yeah and it seems quite a small field considering the importance of the question ‘How did life get started?’

Jacinta: Sounds like they’re having trouble with funding. No pay-offs to the research, and it’s not as sexy as fundamental physics or astronomy. No techno-wizardry like LIGO or the LHC.

Canto: Yes, and you’ll only get really incremental advances. A lab-created nucleotide or two seems a bit of a distance from the beating heart of life to most people. And of course it’s impossible to know, when you do manage to create some building-block towards life from simpler chemicals, if that was how it happened here on Earth (if indeed life actually did start here rather than being transported from elsewhere).

Jacinta: A good last point. If all that water came down in a bunch of early meteor showers, that would seem to make life from meteors much more plausible.

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Written by stewart henderson

May 7, 2017 at 11:21 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