RNA forms on basalt lava glass in the presence of nucleoside triphosphates | Hacker News Reader

RNA forms on basalt lava glass in the presence of nucleoside triphosphates

liebertpub.com

323 pointssanketpatrikar71 comments

I believe submission title is inaccurate:

> This study shows that various mafic rock glasses almost certainly present on the surface of the Hadean Earth catalyze the formation of polyribonucleic acid in water starting from nucleoside triphosphates.

> Thus, the prebiotic relevance of this result very much depends on whether nucleoside triphosphates were present to Hadean impact fields.

In other words, RNA spontaneously forms on basalt lava glass in the presence of nucleoside triphosphates. These are compounds for which there is no known prebiologic formation process - we only know of nucleoside triphosphates as compounds created by living organisms.

Disclaimer: I am not an expert in this area, I just read the article.

>we only know of nucleoside triphosphates as compounds created by living organisms

That is your claim. But the article claims, and I'm not saying it's true, I also am not an expert… but it's an interesting claim:

"many proposals are emerging describing how triphosphates might have been made on the Hadean Earth"

Sure is an interesting claim. Key words include "proposals", "emerging", and "might" - sounds like we have not demonstrated any of those processes just yet, but the people who know what they are talking about think abiogenesis is possible.

In all scientific research someone comes up with a theory that proposes an idea as it emerges that might do something. It is science's job to the then test that theory to either prove or disprove it. The problem is that from my armchair quarterback role that these theories are getting submitted and then published in the media before any testing has been done. Which can be okay as maybe that will bring it to the attention of someone in a position to actually do the testing. However, it tends to come off sound like it is fact or widely accepted as true prematurely by some of the shoddy reporting

Triphosphates are like tiny "batteries". A lot of important reactions in a cell are just moving the third phosphate to another molecule to "move" the stored energy and do something useful later, or to move the third phosphate back to charge again the "battery".

So it's not expected to have a lot of charged batteries floating around. IIRC there are some non-biological process that produce triphosphates, but the amount is tiny^n. In a life-less world, is the production speed enough to make them accumulate until there the concentration is high enough for this reaction? Or they break before they can form RNA chains?

Also, IIRC there are some alternative proposal for the formation of the first RNA. All are horrible slow an inefficient. Is this new method slightly less slow and slightly more efficient?

Yes, that is exactly the problem.

It is an interesting result that there is spontaneous polymerization catalyzed by volcanic rock glasses, but this is an extremely simple reaction, which is expected to happen spontaneously in various conditions.

Making the monomers, i.e. the nucleoside triphosphates, requires a long chain of complex reactions, and also energy.

There is no doubt that RNA has first appeared accidentally, by spontaneous polymerization of nucleoside triphosphates, but those must have been produced by an already existing form of life, which had to use a continuous source of energy for complex molecule synthesis, e.g. dihydrogen, carbon monoxide and a ionic concentration gradient, which can be provided by submarine vents.

While the study does not offer any new information about the actual origin of life, the first accidental synthesis of RNA must have used some catalyst and that catalyst might have been a component of volcanic rocks, as shown in this study.

Only after some molecules of RNA with random composition already existed, due to spontaneous polymerization, it could happen for a RNA molecule to serve as a template for replication, during the polymerization of another RNA molecule. Therefore it is important to determine in which conditions the polymerization of RNA can happen, in the absence of specialized enzymes.

I trained as a biochemist and you nailed it. The submission title's claim is wildly more extraordinary than the actual result. It's like claiming "Lines of humans spontaneously appear on a hot tin roof" when what happened was "humans spontaneously link arms when placed upon a hot tin roof."

The original title is much less clickbaity ‘ Catalytic Synthesis of Polyribonucleic Acid on Prebiotic Rock Glasses’. Maybe one of the mods could change it since it’s not following the site rules anyways.

But is that original title going to properly convey significance to non-biologists/the lay audience?

Coming up with good titles that will survive the HN thoughtchamber is not easy.

The existing, clickbaity title claims a significance that doesn't exist.

Seems more reasonable a claim than life was breathed into clay to form man.

I mean, if you imagine life on earth originated as a petri dish experiment by some advanced species the whole "breathed life into clay" might not be so far fetched, given some allowance for numerous translation context changes.

You're saying scientific processes (petri dish experiment) may have created life because we can't yet explain what scientific processes may have created life? And ancient, unscientific mythological fairy tales may somehow have encoded this event, despite having always been taken at face-value up until they were scientifically and rationally disproven?

Surely it goes without saying that the process only happens in the presence of the right precursors?

Consider the difference between

"Spontaneous appearance of human life in sealed room" and "Spontaneous appearance of human life in a sealed room containing two humans."

You're purposely making it extra misleading with this analogy by adding "in a sealed room", and also by using an example of a process that's already well understood

Still pretty cool. It’s helpful to know the conditions (and therefore planetary eras, etc) that catalyzed the development of more advanced lifeforms, to the extent that it dials in a more robust understanding of how our present ecology came to be

Also not expert.. I was looking around for the precursors and found that Ribose has been detected in meteorites[1]. That seems to leave finding prebiotic sources of the nucleobases, purine and pyrimidine.[2] Seems this is known, tho haven't seen a natural catalytic pathway to combine them into a nucleoside.

Purine can be synthesized from Formamide via simple heating[3], and Formamide is common enough that it's hypothesized as an alternative to water, for a universal solvent in exobiology.[4,5]

So, easy enough! ;)

As remarked in sibling, it seems the harder step is the energetic bump up to a triphosphate.

[1] https://en.wikipedia.org/wiki/Ribose [2] https://en.wikipedia.org/wiki/Nucleobase [3] https://en.wikipedia.org/wiki/Purine#Laboratory%20synthesis [4,5] https://en.wikipedia.org/wiki/Formamide https://en.wikipedia.org/wiki/Hypothetical_types_of_biochemi...

Ok, we've used your phrasing to replace the submitted title ("RNA spontaneously forms on basalt lava glass (abundant on Earth 4.35B years ago)"). Thanks!

I think the whole RNA thing is a bit over hyped. People like RNA because it looks somewhat like computer code, and our technology is just smitten with computers, these recent decades. And right along with that, it makes for such a painfully obvious way to implement inheritance and natural selection, a way to make genes.

But I think our focus is too narrow, we should think bigger than just obvious solutions. Now, it's great if the early oceans were awash with RNA, but does RNA exploit energy gradients on its own? The idea of all this random RNA just sloshing around, using nothing more than entropy, behaving as genes and inventing all the rest of it, just seems a little cart-before-the-horse.

What about metabolism-first? Is fire alive? It has many properties of life but, critically, lacks self regulation and heritability. Burns everything and goes out. Imagine though, a system of enzymes that can assimilate various specific kinds of molecules, and sustain production of those enzymes. Imagine this contained, compartmentalized in some way. Dynamically not much more complicated than simple fire, but crucially, the enzymes can be said to be inherited. These are not 'genes' as such, these are the actual machinery. It should be possible for natural selection to act on 'life' no more complicated than that. And that kind of system could then take find uses for RNA.

(And yes, the enzymes I refer to could be realized as RNA, but acting as the enzymes directly, not merely describing them, and this would confer some major benefits)

It's not quite a random soup though, RNA folding usually tries to minimize the energy exerted during the folding and binding process, no? Isn't this similar with fire, and enzymes, and other unconscious actors that appear to exhibit complex behavoirs but are just minimising some energy gradient?

I'm just painting broad strokes, trying to avoid the TL;DR threshold.

But re energy gradients, I'm talking about the difference between being able to tap into potential energy in the environment, vs just seeking some kind of equilibrium. Sure, a freshly crafted sequence of amino acids will find a shape to minimize the internal energy, and so you can say there's a gradient there, but that's different from taking in H2S and CO2 (or what have you) from the environment and reacting them to liberate non-thermal energy that can be used to get things done.

greenbit so in your mind what is a viroid? We have examples that are extant of RNA doing this. Sure its exploiting an established RNA system, but the point still stands as there's absolutely no reason you couldn't have viroids dealing with other catalytic networks making RNA. That's sort of the point, at some point everything was wandering viroids among autocatalytic networks with varying survival rates. That gets you selective pressure. Thats the transition you're talking about, from autocatalytic localised chemistry into RNA. The initial fitness benefit of RNA is that for one class of molecule you can have a lot of complex catalytic chemistry AND they have the ability through base pairing to catalyse their own exact replication.

Some afterthoughts:

In seeking abiogenesis what we're really looking for is the first replicators. Certainly RNA strands can self replicate, but how is a particular sequence alive? About as alive as a virus, perhaps. Ok, posit a whole world of naked RNA, with multitudes of different sequences. Has life arrived on such a world? I'd say the interesting event would still be downstream from there, when by chance some of those different sequences happened to cooperate to mutual advantage. But that's like viruses inventing the cell.

Whereas, if you allow for the spontaneous collaboration of mere enzymes to create self sustaining metabolism, you can get a system that should exhibit natural selection, even without genes.

I guess what I'm railing on about is this notion that we have one class of molecules that do the work, and another that merely describes other molecules. We create categories and labels for what we see, and then get stuck within those constructs. Truth is often more subtle.

RNA does all of those functions, thats why people think it was prevalent before DNA. There are very few DNA enzymes compared to RNA. RNA provides structure in complex with other molecules which is indirectly catalytic to their activity, as well as being catalytic directly from its own folded structure, then you also have coded information representing its own structure but later those of proteins with the establishment of the genetic code. But you have to remember ribosomes have to exist for the genetic code to mean anything, or at least whatever ribosomes looked like at the start, which is very likely just RNA and a couple of peptides.

Saw a video on YT that I think was saying what you just described might eventually build up a living cell. That would be pretty huge.

Life is not a binary. Life is a gradient of complexity.

You know RNA can work as enzymes right?

You’re basically saying ‘let’s create some other form that was doing the work’ - which could be true - weird small crevices with certain molecular properties and different metals exposed to heat gradients where ‘the soup’ tidally comes and goes and catalyses reactions - and maybe that was an important step, but you’re also overly easily dismissing something that not only can act as that first step (maybe with some help from some unknown catalyst as a bootstrap) with the added benefit of actual inheritance

>with the added benefit of actual inheritance

Has this inheritance actually been experimentally demonstrated? Yes, random assembly of inherently unstable RNA molecules in a nucleotide soup is possible. And agreed, some of these randomly assembled RNA molecules might have limited catalytic properties (nothing like peptides). But - we need a mechanism of genetic continuity - before we get to inheritance.

It’s often hard to tell between a genius who’s so far out away from others that what they say doesn’t make any sense or someone who has no clue what’s actually known about something. I’ll give that benefit of doubt to you but suffice to say I have no idea what you’re talking about.

The rna hypothesis is not overhyped. The fact of the matter is rna looks like a likely candidate that can form in the conditions of early earth, and it’s a perfect candidate for a single molecule that can become self replicating. We don’t know the math of the probability that this thing happened and how big an experiment volume we had in terms of environment size and time span, so hard to tell if this happened this way or not. Suffice to say I see no other plausible hypothesis proposed that is as believable as the RNA world. At least something I can understand anyway.

FWIW I do believe in the RNA world hypothesis only I don’t think it happened in earth, but some other planet at some point in past. I just think that space is filled with floating frozen microbial spores that can instantly (geologically speaking) inoculate any planet with the right conditions.

Not the GP but maybe I can help elucidate the position they're representing. The GP advocates for what is known as the "metabolism-first" hypothesis in origins of life theory. The motivation of this theory that some chemists and biologists find it implausible that a self-catalyzing RNA based biological machinery would have formed spontaneously from a collection of basic precursor chemicals, even given very long spans of time and large volumes of precursors. They believe this because nucleic acids are very complex structures and themselves require very complex biologic machinery to assemble, and their understanding of the likelihood of chemical reactions suggests its unreasonable to expect them to form in geological time spans. They posit that instead its more likely that nucleic acid based systems were themselves preceded by system(s) composed of sets of simpler chemicals (ones which are likely to form spontaneously) which together catalyze each other's formation (a so-called "auto-catalytic set"), and that this era of simple metabolisms eventually produced a nucleic acid based system which completely overtook and replaced/assimilated the more primitive auto-catalytic set world.

Here's a primer on the metabolism-first hypothesis: https://www.statedclearly.com/videos/what-is-the-metabolism-...

RNA first is about stored heritable genetic information? At least I've not met anyone who's in some hardline way RNA miraculously appears and starts creating the auto catalytic networks second. How does the RNA appear? Slowly at random from nothing? Why would anyone think this, it doesn't pass thought experiment level parsimony. The reason to highlight RNA first is because if you just looked at whats alive now you might assume DNA is the older molecule in use as its the primary store of genetic information for most things alive right now. The big idea is that it wasn't. That doesn't mean everyone means its the first molecule to exist in the history of molecular life...

because RNA is used in more old clade of tree of life. DNA is a younger character in history

Thanks for the reference. As the other commenter mentioned, this is great research but I don’t see it as with odds with a molecule of RNA being the first living thing ever. We didn’t discuss before what powered these RNA molecules, but clearly this research is showing us one aspect of it (preexisting metabolic pathway like reactions). These systems might be considered as evolving the same way the sun is evolving I suppose? In the end I would classify life as something that has encoded information on how to create itself and the machinery to do it (or at least the means to recruit the machinery and raw materials) and actually propagate itself perpetually in the right conditions. RNA is still the only viable candidate for that.

what I'm saying is,

RNA, great, that's a Thing. I just don't think that finding a mechanism for RNA to arise is the big step. I think the Big Step is going to be discovery of a set of molecules that use what's available to make more of that set.

Could the molecules in that set be RNA? Sure! Do they have to be RNA? I have no idea. How small can that set be? Can it be a single molecular species? That would be fascinating! I'd think it would probably take more than one, though.

I'm not trying to rain on anyone's parade, just trying to stir the pot of ideas.

So wait, you think there could be a potentially simpler system than a SINGLE MOLECULE OF RNA that is self replicating (I.e. if all you provide is a chemical solution with the raw base ingredients it can build more of itself with no other help)? That’s awesome. Please share, no hyperbole intended, what your hypothesis is.

But that doesn’t change the fact that RNA world fits the most amount of our observations. I already described proving it’s plausibility in our experiments. On top of that please don’t forget that ribosomes, the complexes that produce proteins in our body, are mostly RNA, and the rna part is the primary enzymatic system in it. That is, we actually have a vestige of a system where rna ruled the world.

I’m not even asking you for proof, I’m asking you to even put forward an actual molecular system that you think is better suited to explain this than rna.

You seem to already know this, but "Metabolism First" is the name used for the theory in biology that you just described[0]

The idea is that some self-catalyzing cycle(s) of reactions among chemicals structurally much simpler than nucleotides or even protein enzymes preceded the era of nucleic acid based biology, until being completely (or replaced) by said RNA/DNA based systems.

[0] Metabolism First primer: https://www.statedclearly.com/videos/what-is-the-metabolism-...

The RNA thing is more about what was the first storage of genetic heritable information, I don't know anyone in academia who imagines some kind of RNA world where auto catalytic networks weren't established first or alongside... So yes? You're creating a weird straw man argument for yourself. No one doesn't agree with you. That doesn't take away from the idea of stored information being in RNA before say DNA as it is today. Some of the more fun theories I've seen also focus around the ribosome as the original primary replicator rather than cells. With cells being the evolutionary consequence of ribosomes improving their efficiency.

Maybe it's the sources I look at, which unfortunately tend to be journalistic rather than scientific. So I encounter something like 10x as many items about RNA/DNA for every one about abiogenesis that focuses on something else.

> (And yes, the enzymes I refer to could be realized as RNA, but acting as the enzymes directly, not merely describing them, and this would confer some major benefits)

Isn’t the standard model that chemical complexes of increasing sophistication formed around volcanic vents until the molecules involved looked like viroids or other ribozymes?

Then there’s an evolutionary fork, where the RNA moves towards DNA for storage and proteins for work, but the relationship remains mediated by RNA, eg in mitochondria.

> And yes, the enzymes I refer to could be realized as RNA, but acting as the enzymes directly, not merely describing them

RNA can act as an enzyme (https://en.wikipedia.org/wiki/Ribozyme). This fact is one of the arguments in favor of the RNA world hypothesis.

If you haven't read "The Vital Question" by Nick Lane yet, then you really should.

One of the book's suggestions is that an energy-first analysis of life and the origins of life, can be incredibly explanatory—particularly since Science (and Pop-Science) has been so focused on genetics for so long.

In terms of the origins of life, the idea is essentially that rather than try to imagine how RNA could "just appear", we should look for places where there were natural, persistent, energy fluxes (the "fires" as you say), and try to understand how these energy fluxes began to resemble cells. i.e., were constrained into cell-sizes and began replicating.

Incidentally, the theory that Nick Lane puts forward of which particular energy fluxes gave rise to life is sea-floor alkaline hydrothermal vents[1]—which is also discussed in the book.

[1] https://nick-lane.net/publications/origin-life-alkaline-hydr...

There is a podcast interview [1] with Nick Lane by Sean Carrol that goes into more detail along these lines - a very compelling argument!

[1]https://www.preposterousuniverse.com/podcast/2022/05/23/198-...

This is a very interesting result. Does anyone know how likely ribonucleoside triphosphates are to be formed in young earth conditions? What is the state of the research on this topic?

It seems like this is a pre-print but if it stands up to peer review this would appear to be a big step forward in our understanding of abiogenesis, and would seem to be good evidence for the RNA world hypothesis.

I always kind of hoped abiogenesis happened multiple times on multiple worlds, rather than once and then spread through panspermia. This result seems to indicate it could have happened here.

Wouldn't it be fascinating if it happened multiple times right here on earth, even.

Even if it were possible to happen repeatedly wouldn't the prior generation be immediately able to out compete (immediately consume) the nascently developed life?

Interesting work. One thing to keep in mind is that early environments were anoxic, as free oxygen only arose after the development of photosynthesis on a global scale. This should have made abiotic synthesis relatively easier as oxygen acts as kind of bleach (production of OH radical etc.), so it's likely early oceans were awash with a wide variety of organic molecules, as well as tons of dissolved iron and sulfur species, likely phosphorous as well.

People have also described a wide variety of catalytic activities with carbon dioxide and hydrogen catalyzed at hydrothermal vent environments by metals, such as the formation of small aldehydes and ketones (short-chain/branched carbon molecules with double bonds incorporating an oxygen atom) which can then go on to participate in other reactions with ammonia and hydrogen plausibly leading to amino acids. Another simple abiotic reaction is the formation of hydroxlamine (H2N-OH) which can feed into the synthesis of the simple ring structures of nitogenous bases (the components, plus five-carbon sugars, of the A,U,C,G's of RNA). See:

Unified prebiotically plausible synthesis of pyrimidine and purine RNA ribonucleotides (2019)

https://www.science.org/doi/10.1126/science.aax2747

Abiotic synthesis of amino acids in the recesses of the oceanic lithosphere (2018)

https://www.nature.com/articles/s41586-018-0684-z

Both those articles are on sci-hub.se for those interested.

One interesting speculation is that RNA and protein developed more or less simultaneously, and that short protein chains were affiliated with short RNA chains from the very beginning. This could plausibly result in a proto-ribosomal entity capable of self-replication using the abiotic pool of nucleosides and and amino acids as raw material. This idea has been around for ~20 years, here's something recent on it:

A prebiotically plausible scenario of an RNA–peptide world (May 2022)

https://www.nature.com/articles/s41586-022-04676-3

These kinds of reactions would seem to be quite plausible on other worlds with a liquid ocean. Also, they had millions of years to develop, meaning low-probability events aren't ruled out. Life is probably widespread in our universe.

Critically, formed from ribonucleoside triphosphates. This is an important step, but there are others needed to give us the complete chain of generation.

Yes, but it does hint that spontaneous emergence of basic life building blocks is a more and more viable hypothesis.

And that, given similar conditions, other worlds could develop ecosystems analogue to ours.

Theorising that high carbon steel can form by mistake in some scenarios is no where even remotely close to the information management necessary to spontaneously create a tesla.

And even a Tesla is no where remotely close to the organic cell. The smallest known functional, and most importantly, stable biological unit.

Even if rna is formed, what will read it?

Those are good questions, but having questions doesn't decrease my interest, it just gives it context.

> Even if rna is formed, what will read it?

That's the interesting part of RNA. You don't need a reader!

RNA can act like an enzyme. They can fold and form strange shapes and have some "sticky" parts, so they can replace the activity of enzymes. Enzymes made of proteins are more efficient, so now most(all?) enzymes are made of proteins. But in the initial form of life perhaps enzymes were just a short RNA strip.

RNA can be copied. They can be in a single strain, and they can collect the parts [1] and make an inverse copy, and then separate. DNA is better with a lot of helper enzymes is much better, but in the initial form of life perhaps RNA is good enough.

None of these steps need a reader, so perhaps they can form an initial and very inefficient life(almost-life) form.

[1] the parts: https://en.wikipedia.org/wiki/Nucleoside_triphosphate

Thats fascinating and I appreciate knowing that.

About this:

> None of these steps need a reader, so perhaps they can form an initial and very inefficient life(almost-life) form.

May I ask, have you ever considered if any of these systems that you're researching or investigating are the product of deliberate engineering rather than random chance?

Makes me wonder how abundant basalt lava glass is on planets in the goldilocks zone.

>This polyribonucleic acid averages 100–300 nucleotides in length, with a substantial fraction of 3′,-5′-dinucleotide linkages

Notably they don't distinguish linear vs. branched RNAs, it's the linear ones which are likely to be more interesting for the development of life.

For those interested in the chemical origins of life, the Lex Fridman podcast has a fascinating interview with University of Glasgow chemist Dr. Lee Cronin who has done some of the fundamental research in this field. It's long but worth a listen.

https://lexfridman.com/lee-cronin/

So is the spike protein shedding real. I've learned in school that viruses directly exchange genetic information with each other. The possibility of wild RNA coming from the environment would be something new.

Isn‘t RNA on its own useless?

Doesn‘t it need the cells molecular machines to execute it?

This seems to be the computer equivalent to: Cosmic rays formed a hello world program on this memory chip in my drawer.

RNA molecules can act as catalysts. See https://en.wikipedia.org/wiki/Ribozyme

From the ashes we rise

Your comment made me think about what is the principal point of evolution:

New ideas/species/functions are not born from competition, they are formed by mixing up.

And filtering.

How this fits in the RNA world hypothesis?

It's in favor of the RNA word hypothesis, because it gives a possible explanation of how the first RNA was formed.

IIRC there are other proposed methods to produce RNA. IIUC this method assumes that there are many triphosphates floating around, that is possible but needs another explanation.

So IMHO it's just a tiny step in the right direction, but not a "breakthrough" like some press articles claim.

Thanks for the explanation!

I will read this later

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