Posts Tagged ‘amino acids’
abiogenesis – some amateur explorations
woteva
One of the greatest mysteries and challenges we face, as living beings – if we’re interested – is how living beings came to be. And we’re the only form of living beings, that we know of, asking this question. Hans Castorp, the central character of Thomas Mann’s The Magic Mountain, pondered the matter in his loggia while taking the cure in an alpine sanatorium. He even went further than the What is life question, asking What is matter? Why is there something rather than nothing?
It was a novel that changed my life. From that reading experience I turned, quite abruptly, to science. I bought Scientific American every month, until I switched to New Scientist, and started reading books by Richard Dawkins, Peter Atkins et al. Of course I’ve never undertaken any formal studies in science, and I’ve always preferred the informal to the formal, and not being subject to authorities telling me what to learn or know. That’s why Hans Castorp, reading and musing in his loggia, so appealed to me.
So what do we know on this subject? When did life begin on Earth, and how? It could have been close to 4 billion years ago, only half a billion years(!) after our planet was fully formed. We don’t have solid evidence, though. The earliest accepted evidence goes back 3.5 billion years, of ‘bacteria-like organisms’. That sounds pretty complex already, and presumably the ‘ingredients’, the intracellular material that sustained and motivated these beings, were around long before. Complexifying chains of molecules, formed out of the ‘primordial soup’, to use an unhelpful term. We think RNA and DNA of course, or at least nucleic acid chains. But what are nucleic acids, and what are the parts thereof? Other essential components include proteins and lipids, with the latter being essential to create more or less permeable boundaries between the organic and the inorganic (or proto-organic?). Lipid molecules, as the Arvin Ash video referenced below tells us, consist of a hydrophilic body, of sorts, and a hydrophobic tail. These molecules tend to come together to form spheres, with the outer, bulkier, hydrophilic ends joining together to protect or insulate the hydrophobic tails from the watery outer environment.
So there’s always a ‘what came before’ question. Where did these lipid molecules spring from, not to mention the other bits and bobs of life? Well, on lipids, I’m relying, for now, on the same video. Carbon monoxide (CO), hydrogen and minerals found in the Earth’s crust can combine to form lipids. All of these components can be found in the hydrothermal vents so recently found in the Pacific depths. But lipid structures break down in the presence of salt or magnesium ions, and these ions are essential for cellular and RNA development. Big problem, as the primeval oceans are believed to be more salty than those of today – though apparently we’re far from being certain about this. In any case, a 2019 paper from the University of Washington showed that lipid spheres remained intact in the presence of amino acids, the building blocks of protein molecules. To quote from the video,
The enclosing of amino acids within cell walls allows them to concentrate within those walls and interact with each other to form proteins, which are part of the ‘trinity’, one of the essential components of life.
So lipid cell walls and proteins, both of course non-living, require each other to survive in salty or iron-rich water. But what about the nucleic acids, DNA and RNA? These are the self-replicating molecules, the genetic material, or precursor genetic material. Today we know that RNA is created from DNA to build proteins according to DNA’s code, but the fact that RNA is the simpler of the two genetic materials suggests to most analysts that it came first. So there’s a hypothesis called the ‘RNA world’, which is generally well accepted by those in the field, but unfortunately we’ve made little progress in working out how RNA came to be formed.
RNA is made up of three chemical components – ribose (a sugar), the nucleobases, and phosphate. A ribose-base-phosphate unit links with other such units to form RNA polymer. But it’s not well understood how these links were formed, and they haven’t been successfully replicated in human experiments. The ribose-base link has proved particularly problematic. As Arvin Ash describes it, ‘this is because cells in your body require complex enzymes to bring RNA building blocks together before they combine to form polymers’. He describes one study, however, which found that today’s RNA could have formed on the surface of clays ‘which act like a catalyst to bring RNA bases together’. A later study showed that the building blocks of RNA could have polymerised in the early Earth, using organic molecules from meteorites and interplanetary dust in shallow ponds, where wet/dry cycles would have been conducive to such polymerisation. They considered that these polymers were probably present on Earth shortly after its formation.
So Ash describes a trinity – RNA, lipids and proteins. What about the proteins? We can go back to the Miller-Urey experiments of the 1950s, which showed that amino acids, the essential components of proteins, as well as other organic compounds, could be produced under particular atmospheric conditions, which they were able to replicate in the laboratory.
So, all these precursors might be explained, but they still need to combine for life as we know it, however basic. This is the big question that still needs to be answered. We haven’t discovered any precise mechanism, but oodles of time, and incremental steps are probably required, and there is surely a possibility of this in the first billions of our planet’s existence, wherein trillions of molecular interactions may have taken place. It’s something of a numbers game, something that many earlier theorists, and today’s creationists, have not taken sufficient account of. It’s also probable that the earliest life forms, those sparks, were so basic that they were quickly improved upon and rendered obsolete by – evolution. But that’s another story…
Needless to say, this piece was more or less wholly reliant on Arvin Ash’s excellent video, which I highly recommend.
References
Why is the Ocean So Salty?
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 oxytocin fantasies: an interminable conversation 3
not sure if this measures a significant difference
Canto: So, as it turns out, the bonobo-oxytocin connection is all the rage on the internet. I mean, there are at least two articles on it. Here’s a quote from a PubMed article called ‘Divergent effects of oxytocin on eye contact in bonobos and chimpanzees’:
Previous studies have shown that bonobos and chimpanzees, humans’ two closest relatives, demonstrate considerable behavioral differences, including that bonobos look more at others’ eyes than chimpanzees. Oxytocin is known to increase attention to another’s eyes in many mammalian species (e.g. dogs, monkeys, and humans), yet this effect has not been tested in any nonhuman great ape species.
Jacinta: Hmm, so how do they know this? Presumably they’ve dosed subjects with oxytocin and measured their eye contact against controls?
Canto: No no, they know that bonobos have more eye contact than chimps, simply from observation. So they might infer from this that bonobos produce more oxytocin naturally than chimps…
Jacinta: So do women produce more oxytocin than men I wonder? I presume women make more eye contact than men.
Canto: Well in this study they dosed both bonobos and chimps with oxytocin, and the effect – more eye contact – was greater in bonobos than chimps. In fact, chimps even tended to avoid eye contact when shown images of conspecifics.
Jacinta: So, it’s a matter of interplay between this hormone/neurotransmitter and social conditioning?
Canto: Maybe, but you’d think that an increase in this supposedly touchy-feely hormone would act against social conditioning. Isn’t this the point of that drug, ecstacy? That it reduces social inhibitions… But presumably nothing is ever so simple. Being poor, I only have access to the abstract of this paper, but another abstract, which looks at the effects of oxytocin and vasopressin on chimps, describes them as neuropeptides, just to confuse matters. The abstract also refers to about a dozen brain regions, as well as specific oxytocin and vasopressin receptors, so it gets pretty complicated.
Jacinta: Okay, vasopressin… from Wikipedia:
Human vasopressin, also called antidiuretic hormone (ADH), arginine vasopressin (AVP), or argipressin, is a hormone synthesised from the AVP gene as a peptide prohormone in neurons in the hypothalamus, and is converted to AVP. It then travels down the axon terminating in the posterior pituitary, and is released from vesicles into the circulation in response to extracellular hypertonicity (hyperosmolality). AVP has two major functions… etc etc
Canto: Okay thanks for that, let’s stick with oxytocin for now. It’s produced in the hypothalamus, a smallish region buried deep within the brain, just below the larger thalamus and above the even smaller amygdala. It releases and manages a variety of hormones. Brain signals are sent to the hypothalamus, exciting it to release oxytocin and other hormones, which are secreted into the bloodstream by the posterior pituitary gland….
Jacinta: Can you tell me what oxytocin is actually made of? Its structure? The term ‘hormone’ is just a black box to me.
Canto: Okay, here’s a diagram of oxytocin to try and make sense of:
It’s a polypeptide. A peptide is basically an amino acid chain. FYI:
An amino acid is an organic molecule that is made up of a basic amino group (−NH2), an acidic carboxyl group (−COOH), and an organic R group (or side chain) that is unique to each amino acid. The term amino acid is short for α-amino [alpha-amino] carboxylic acid.
Jacinta: So these are coded for, ultimately, by genes?
Canto: Yes, we’re heading backwards here, but each amino acid is encoded by a sequence of three of the four base pairs in our DNA. Anyway oxytocin, among other things is sometimes given to women while in labour. It helps with the contractions apparently. I’ve also heard that the recreational drug ‘ecstasy’, or MDMA, works essentially by releasing oxytocin.
Jacinta: It just so happens I’ve found an interesting 2014 paper published in Neuropsychopharmacology, my new favourite journal, called ‘Effects of MDMA and Intranasal Oxytocin on Social and Emotional Processing’, and here’s a quote from the abstract:
Oxytocin produced small but significant increases in feelings of sociability and enhanced recognition of sad facial expressions. Additionally, responses to oxytocin were related to responses to MDMA with subjects on two subjective measures of sociability. Thus, MDMA increased euphoria and feelings of sociability, perhaps by reducing sensitivity to subtle signs of negative emotions in others. The present findings provide only limited support for the idea that oxytocin produces the prosocial effects of MDMA.
Canto: That is interesting. If that finding can be replicated, I’d say forget the MDMA, dose people with oxytocin. A small but significant increase in feelings of sociability might just be enough to transform our human world.
Jacinta: Hmmm. Small but significant – that sounds a mite contradictory.
Canto: Not the same as significantly small. That slightly significant dose, administered to Messrs Pudding and Pingpong and their enablers, might’ve saved the lives of many Ukrainians, Uyghurs and advocates of multiculturalism, democracy, feminism and other wild and woolly notions. And it doesn’t really transform characters, it just softens their edges.
Jacinta: Yes it’s a nice fantasy – more productive than butchering the butchers, a fantasy I occasionally indulge in. But not workable really.
Canto: Why not? We dosed petrol with lead, and look at how that worked out. It certainly had an effect. In Japan they still use radium baths (at very low levels) for health purposes, even claiming it as a cure for cancer. I’m not sure if oxytocin baths can ever be a thing, but if so I’m sure there will be early adopters.
Jacinta: Well, it’s good to think positively. Oxytocin is often thought of as a bonding hormone between mother and child. The key would be to ensure it facilitates a more general bonding: to cause Mr Pingpong, for example, to see Uyghur, Tibetan, Yi, Limi, and all the other non-Han ethnicities in China as his sisters – or lovers even, revolting as that would be to those peoples.
Canto: Better than being their oppressors and exterminators.
Jacinta: Slightly. But I wonder, quite seriously, if, assuming such a dose of bonding could be effectuated, we could still function as the sometimes rational, problem-solving, highly creative species we indubitably are. Would there be a price to pay for all that oxytocin? And how would this affect all those other hormones and neurotransmitters and all their myriad effects? Humans are notorious for causing extra problems with their solutions, e.g lead, DDT, etc etc.
Canto: Well, there’s no need to worry about the fallout from this solution as yet. I just googled Putin and oxytocin together and came up empty. Obviously we’re way ahead of the curve.
Jacinta: Haha, it’s not a curve these days, it’s a pivot. Get with the program!
References
https://pubmed.ncbi.nlm.nih.gov/33388536/
https://www.yourhormones.info/hormones/oxytocin/
https://www.acs.org/content/acs/en/molecule-of-the-week/archive/o/oxytocin.html
https://www.britannica.com/science/amino-acid
https://www.wsj.com/articles/BL-JRTB-11551