Posts Tagged ‘abiogenesis’
abiogenesis is heavy, man
So, once more into the breach, let’s try and have fun with abiogenesis. It supposedly starts with organic compounds, generally considered as carbon-based, though I’ve heard tell of the possibility of silicon-based life – presumably you want to start with an element that combines readily with others, and those elements, but carbon in particular, fit the bill. Hydrocarbons, the simplest of which is methane (CH4), are an obvious example. However, as far as I’m aware, we haven’t been able to bridge the gap between non-life and life, inanimate and animate, chemistry and biology, in any clear-cut way in our laboratories and experiments. Membranes, self-replications, chains, autocatalysis are all more or less required, but nobody seems to have any clear idea of how and when it all started here. There may have been a few starts that then ended, until one didn’t. Here’s a bit from Wikipedia:
Life functions through the chemistry of carbon and water, and builds on four chemical families: lipids for cell membranes, carbohydrates for chemical energy storage and structural composition, amino acids for protein metabolism, and the nucleic acids DNA and RNA for heredity. A theory of abiogenesis must explain the origins and interactions of these classes of molecules.
Sounds like hard work, especially the genetic stuff. So I’ll start with amino acids, since I don’t have a clue… We get them from food, essentially, but what is food but living stuff, organic stuff, and so goes the circle. But let’s keep going. They were first discovered/identified in the early 1800s, the first being asparagine, from asparagus, in 1806. Apparently our bodies need twenty types of these carbon-based molecules, strings of which, or chains of which, form proteins. Of those twenty, eleven can be made by our bodies, and are labeled non-essential, while the other nine, the essential ones, must be obtained by food. All in all they’re important for brain chemistry, hormone production, and for maintenance and repair of muscle, skin and organ tissues.
But how did amino acids come to be? And what’s the difference between L and D types of amino acids? Apparently they’re like the mirror image of each other which makes me think of chirality which I barely understand. Britannica starts one of its articles with this:
The question of why organisms on Earth consist of L-amino acids instead of D-amino acids is still an unresolved riddle. Some scientists have long suggested that a substantial fraction of the organic compounds that were the precursors to amino acids—and perhaps some amino acids themselves—on early Earth may have been derived from comet and meteorite impacts. One such organic-rich meteorite impact occurred on September 28, 1969, over Murchison, Victoria, Australia.
… which is interesting but doesn’t help much, though it’s certainly a cause for wonder. Anyway, the video referenced below tells me that of the 20 amino acids that build proteins in our body, 19 are chiral. Then one particular amino acid, alanine, is focussed on, as it’s one of the simplest enantiomers – pairs of molecules that are mirror images of each other, and so un-super-imposable.
So this molecular biology is about life-sustaining molecules but not quite organisms, and nobody knows precisely how complex molecules become organisms – otherwise we’d be having fun creating new life forms, and only gods are allowed to have that kind of fun.
So we haven’t made life yet, but we’re getting there?
I’ve heard of course of an RNA world that might have preceded the DNA one, so let’s go there for a while. Nucleotides, nucleic acids, nucleosides, nucleobases and such all have to be understood and connected together to make sense of it all. So from here on in it will be attempted definition after attempted definition, with further attempts to connect them all together.
So what about prebiotic synthesis? Or, to quote another video referenced below, ‘location… where can we find the satisfactory chemistry required to make bioactive molecules? And what were these first biomolecules? We must surely need water and carbon – that’s what life as we know it requires, at a minimum. Then there’s nitrogen, key to building proteins (amino acids being nitrogen-based), and RNA and DNA for ‘information’. And phosphorous, essential for building many biomolecules, ATP for cellular energy, and phospholipids for cell membranes. Also referenced are amphiphiles (never heard of them) for forming primitive cells. They’re made from phospholipids so I’m not sure of the difference, just as I’m not sure of the difference between lipids and fatty acids – and did somebody mention tryptophan…? You need largely to be there in the labs being educated by the experts, and observing and experimenting.
The discovery in quite recent times of hydrothermal deep ocean vents and the chemo-synthesised, sunlight-free ecosystems they support, has added fuel, such as hydrogen sulphide, to the quest for the earliest life forms. But, to quote Phy the Neutrophil:
In an alkaline vent environment, the conditions for chemistry heavily disfavour the formation of cells. While hydrothermal vents do have the chemistry to make long-chain fatty acids, the harsh salty environment of the ocean is going to make it very difficult for these proto-membranes to form.
Mr Phy likes the Darwinian idea of a warm little pond, but also recognises that this too has its problems. In any case, some kind of cell or capsule formation, however or wherever it may have evolved, would be a major advance. Creating an enclosed micro-environment is likely to speed up the process of effective chemical development, and Mr Phy goes into much detail on this, and its alternatives, but of course I’m not strong on biochemistry, so proton gradients haven’t triggered my neurons.
But I must soldier on. AI has this to say on proton energetics:
All life uses proton gradients across membranes to drive energy production via ATP synthase. Because building proton pumps requires pre-existing energy, scientists propose that life began in alkaline hydrothermal vents, where natural geological pH gradients across inorganic pores provided the first proton-motive force before biological pumps evolved.
Adenosine triphosphate (ATP) , which I know is associated with mitochondria in humans, and is always called the ‘energy molecule’, or the energy storage molecule, as Wikipedia puts it, relies on this ATP synthase enzyme, which catalyses ATP using ADP (adenosine diphosphate) and inorganic phosphate. It gets very complicated with protons being pushed along an electrochemical gradient so that ATP can be stored by cells for future use.
Of course the evolution of ATP synthase, like so much in the make-up of the earliest life forms, is obscurely ancient, but well worth exploring as it appears to be central to all life. Wikipedia goes into hellish detail about it all, which is impressive and exhausting. I’m not sure if I can go on…
References
https://en.wikipedia.org/wiki/D-Amino_acid
https://www.britannica.com/science/amino-acid/Amino-acids-and-the-origin-of-life-on-Earth
introducing myself to abiogenesis, sort of
Yes, watch out for the creationists and their ultra ultra ultra male god…
So, more sciencey stuff by a non-scientist, this time on how life came about from non-life, and where exactly the boundary lies. I seem to recall, years ago, that Craig Venter, something of a maverick biochemist, or whatever, was competing with the ‘official’, i.e government-funded, program, to map the human genome, and it might’ve come out as a tie, but don’t quote me. And then Venter and Co went on to work on abiogenesis, and then I lost touch…
I was reminded of all this when I watched a video featuring a Christian fundamentalist and biochemist, James Tour (I keep thinking James Tool) and his fight with mainstream biochemists on the difficulty/impossibility of life coming from non-life, because, of course, God – or as Americans like to call him, Guard, because, as we know, Guard blesses America, and safeguards Him (because, as we know America is as fundamentally male as Guard) on an ongoing basis.
In googling Mr Tour, the first thing I came up with was ‘Is James Tour religious?’ The answer, of course, is another question – Do bears shit in the woods?
But let’s not get too lazy by mocking US silliness ad nauseam. In the video, Tour is shown violently lashing out at claims that there is any possible chemical pathway for something living – that’s to say self-sustaining – to have come from something purely chemical, no matter how complex. And yet, in spite of Tour’s noisy, over-the-top attacks on the whole abiogenesis program, presumably because it was ‘playing Guard’, in the end, when talking to a sympathetic and doubtless Christian interviewer, he admitted that we might one day work out the process that sparked life, in spite of its ‘infinite’ (or near-infinite) complexity, because, after all, Guard is infinite (or near-infinite?)….
I suspect he might regret that admission.
So, after all that, how are we going on the abiogenesis front? First, a little history. Spontaneous generation was once considered very much a thing, in the days before microscopes and such, and this is unsurprising, as I myself have seen maggots ‘suddenly’ infesting something rotting in a cupboard in my lazy house-sharing youth. Such situations caused considerable debate in earlier centuries, until better technologies and experiments, in particular the work of Louis Pasteur, finally disproved the concept. But this, of course, left a gap – if there was no spontaneous generation of life, and evolution by natural selection had nothing to say on the subject, then – maybe Guard? Or Guard of the Gap?
But enough of Guard, we already have complex collections of molecules, such as viruses, which seem to bridge the gap between life and non-life through their ability to replicate rapidly under particular conditions – but not independently. According to the RationalWiki on the subject:
Abiogenesis is not a single step event, but a process. Biological life has the properties or capabilities of organization, metabolism, homeostasis, growth, reproduction, response, and evolution.
So, it’s generally considered likely that abiogenesis cannot be sheeted home to one semi-miraculous event – more likely there were various combinatorial chemical developments that more or less succeeded in maintaining the above-mentioned properties. At some stage in this process, a stable life-form emerged that combined these ingredients effectively. This life-form has been dubbed the last universal common ancestor (LUCA).
Three elements appear to be essential – carbon, and hydrogen and oxygen in the form of water. The compounds focussed on by biochemists studying the subject are lipids, which can form membranes, carbohydrates, which can provide energy, amino acids, and nucleic acids (DNA and RNA) for reproduction.
I’m fairly clueless, so I’ll start with amino acids. Wikipedia tells me they’re essential for ‘protein metabolism’, but apparently not all amino acids are involved in this process – far from it. Of the more than 500 amino acids that we know to exist, there are only 22 that are ‘incorporated into proteins’ and into the genetic code of all life. They’re called proteinogenic amino acids, or α-amino acids (alpha amino acids).
But what exactly is an amino acid? Obviously it’s an acid, which we tend to think is something negative that breaks down and destroys stuff. But then amino makes me think of animation, in a scrambled sort of way. I mean, life? They are described as organic molecules, or organic compounds after all. Why? Apparently, for many biochemists an organic compound is one containing carbon. The proteinogenic amino acids are the ‘raw material’ assembled by our ribosomes (by the ribosomes of all living cells?) into the multitudinous peptides and proteins that do so much mysterious work throughout our bodies. I’m getting most of this from Wikipedia, a fantastic resource that just keeps getting fantasticker. It’s article on abiogenesis is itself virtually book-length, and the links take you to dozens of other useful and lengthy articles.
So how did amino acids come into being? Before ribosomes, the amino acid-making machines in our cells, came into being, that is. Well, first we needed the elemental ingredients, and they existed billions of years ago, at the Earth’s formation, and even before the Sun had coalesced into the star we know today. In a PubMed article abstract, ‘The origin of the biologically coded amino acids’ (that’s to say the proteinogenic ones), the problem/solution is put this way:
The types of amino acids produced depend on the conditions which prevailed at the time of synthesis, which remain controversial. The selection of the biological set is likely due to chemical and early biological evolution acting on the environmentally available compounds based on their chemical properties. Once life arose, selection would have proceeded based on the functional utility of amino acids coupled with their accessibility by primitive metabolism and their compatibility with other biochemical processes.
So, before there was biological evolution there was chemical evolution, which also may have been a matter of fits and starts. For example, some have speculated that carbonaceous meteorites raining down on the early Earth may have provided a spark, or a boost. These speculations are forward-looking from the non-living, in a sense, while another approach is backward-looking from known candidates for LUCA. Here’s how Wikipedia puts it:
It appears there are 60 proteins common to all life and 355 prokaryotic genes that trace to LUCA; their functions imply that the LUCA was anaerobic with the Wood–Ljungdahl pathway, deriving energy by chemiosmosis, and maintaining its hereditary material with DNA, the genetic code, and ribosomes. Although the LUCA lived over 4 billion years ago (4 Gya), researchers believe it was far from the first form of life. Earlier cells might have had a leaky membrane and been powered by a naturally occurring proton gradient near a deep-sea white smoker hydrothermal vent.
I won’t pretend I understand all that, but prokaryotes are unicellular organisms, and anaerobic respiration utilises ‘electron transport chains’ other than – and less efficient than – oxygen. The Wood-Ljungdahl pathway is, inter alia, a proposed mechanism – still controversial – for the anaerobic prokaryotic life found at deep sea alkaline hydrothermal vents, in the late 1970s.
The key problem, it seems to me, is that of effective replication, way back in the day. DNA and RNA are both very complex molecules, and so they didn’t just spring into existence. The Wikipedia article articulates the problem in a sentence that’s easy to simply overlook:
Prebiotic synthesis creates a range of simple organic compounds, which are assembled into polymers such as proteins and RNA.
We’re still quite a way from understanding that ‘assembly’ stage, though we’ve managed a bit of prebiotic synthesis, but there’s no reason to assume that we can’t work it all out. Now if we could find simple, perhaps differently-organised life or proto-life on other planets or moons…
That’s astrobiology, apparently. And Wikipedia can explain it all better than me, so excuse my laziness.
The 2015 NASA strategy on the origin of life aimed to solve the puzzle by identifying interactions, intermediary structures and functions, energy sources, and environmental factors that contributed to the diversity, selection, and replication of evolvable macromolecular systems, and mapping the chemical landscape of potential primordial informational polymers. The advent of polymers that could replicate, store genetic information, and exhibit properties subject to selection was, it suggested, most likely a critical step in the emergence of prebiotic chemical evolution. Those polymers derived, in turn, from simple organic compounds such as nucleobases, amino acids, and sugars that could have been formed by reactions in the environment. A successful theory of the origin of life must explain how all these chemicals came into being.
Hoping to write about this more in the future, exploring any new developments, if any.
References
https://rationalwiki.org/wiki/Abiogenesis
https://en.wikipedia.org/wiki/Abiogenesis
more on abiogenesis – Greenland and other rocks, water everywhere, and the how question
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.