Amino acids are common enough -- glycine has been found in comets and, controversially, even in the interstellar medium. Other amino acids have also been found in comets.
It's also presumed that cometary ice bombardment is the source of Earth's surface water, as ice or water present any earlier would have boiled off when the planet was young and hot.
It's not much of a stretch to imagine that comets brought amino acids, organic compounds, and minerals to Earth as they were bringing water ice. A lot of those aminos and organics would turn into tar, but some would be protected from UV radiation by that same tar. With a heat source, maybe some lightning strikes, a good location, and a lot of luck, you get RNA...
What we can't yet do is assign a probability or likelihood to this process. But the ingredients should be common enough.
About a half of the amino acids used in proteins, i.e. ten of them, can form easily in abiotic conditions and they are widespread in some celestial bodies.
They are easily distinguished from terrestrial contaminants, because they are a mixture of left-handed and right-handed isomers.
When analyzing the genetic code in order to determine which amino acids have already been used in the earlier versions of the genetic code and which have been added more recently, the same simpler amino acids that are easy to synthesize even in the absence of life are also those that appear to have been the only amino acids used earlier.
The article contains the phrase "Given the fact that the current scenario is that life on Earth started with RNA".
This is a fact that it is too often repeated like if it were true, when in reality one of the few things that can be said with certainty about the origin of life is that it has not started with RNA.
What must be true is only that RNA had existed a very long time before DNA and DNA has been an innovation that has been the result of a long evolution of already existing life forms, long before the last ancestor of all living beings that still exist now on Earth.
On the other hand, proteins, or more correctly said peptides, must have existed before any RNA. Moreover, ATP must have existed long before any RNA.
RNA has two main functions based on its information-storage property: the replication of RNA using a template of RNA (which was the single form of nucleic acid replication before the existence of DNA) and the synthesis of proteins using RNA as a template.
Both processes require complex molecular machines, so it is impossible for both of them to have appeared simultaneously. One process must have appeared before the other and there can be no doubt that the replication of RNA must have appeared before the synthesis of proteins.
Had synthesis of proteins appeared first, it would have been instantly lost at the death of the host living being, because the RNA able to be used as a template for proteins could not have been replicated, therefore it could not have been transmitted to descendants.
So in the beginning RNA must have been only a molecule with the ability of self replication. All its other functions have evolved in living beings where abundant RNA existed, being produced by self replication.
The RNA replication process requires energy and monomers, in the form of ATP together with the other 3 phosphorylated nucleotides. Therefore all 4 nucleotides and their phosphorylated forms like ATP must have existed before RNA.
ATP must have been used long before RNA, like today, as a means of extracting water from organic molecules, causing the condensations of monomers like amino acids into polymers like peptides.
The chemical reactions in the early living forms were certainly regulated much less well than in the present living beings, so many secondary undesirable reactions must have happened concurrently with the useful chemical reactions.
So the existence of abundant ATP and other phosphorylated nucleotides must have had as a consequence the initially undesirable polymerization and co-polymerization of the nucleotides, forming random RNA molecules, until by chance a self-replicating RNA molecule was produced.
Because the first self-replicating RNA molecule did not perform any useful function for the host life form, but it diverted useful nucleotides from its metabolism, this first self-replicating RNA molecule must be considered as the first virus. Only much later, after these early viruses have evolved the ability to synthesize proteins, some of them must have become integrated with their hosts, becoming their genome.
The catalytic functions that are now performed mostly by proteins, i.e. amino acid polymers that are synthesized using an RNA template, must have been performed earlier by peptides, i.e. typically shorter amino acid polymers that are synthesized without the use of RNA templates.
Even today, all living beings contain many non-ribosomal peptides, which are made without RNA, using processes that are much less understood than those that involve nucleic acids.
The difference between a living being that would be able to make only non-ribosomal peptides and one that makes proteins using RNA templates is pretty much the same difference as between a CPU with hard-wired control and a CPU with micro-programmed control, with the same advantages and disadvantages.
Life forms able to reproduce themselves must have existed before the appearance of the nucleic acids, but they must have been incapable of significant evolution, because any random change in the structure of the molecules that composed them would have been very likely to result in a defective organism that would have died without descendants. This is similar with a hard-wired control, where small random changes in the circuits are unlikely to result in a functional device.
On the other hand, once the structure of the enzymes was written in molecules of nucleic acids, the random copying errors could result in structures very different from the original structures, which could not have been obtained by gradual changes in the original structures without passing through non functional structures that could not have been inherited.
So the use of molecules that can store the structural information of a living being has enabled the evolution towards much more complex life forms, but it cannot have had any role in the apparition of the first life forms, because the replication of any such molecule requires energy that can be provided only by an already existing life form.
>On the other hand, proteins, or more correctly said peptides, must have existed before any RNA
How come? It seems you can have reproducing RNA without protein needed. Here's Gerald Joyce talking briefly about making those https://youtu.be/aBrYsFeeVzE?t=171
Awesome post and thanks for writing this out - probably the most insightful piece I’ve read on plausible origin of life through pre-RNA autocatalytic peptides. Would you be willing to share a contact email / online profile? (could edit afterward to delete if you are worried about spam from crawlers)
sorry if I missed it, but it sounds like you've just pushed the mystery one step back but still ended up with the same mystery - where did the original Titan species come from? is there any evidence for their existence other than your belief that an RNA replicator would have needed a host cell? would this host cell have been built out of lipid bilayers? what would its inside mechanisms be made of - if not protein or RNA?
> RNA has two main functions based on its information-storage property: the replication of RNA using a template of RNA (which was the single form of nucleic acid replication before the existence of DNA) and the synthesis of proteins using RNA as a template.
This heavily simplifies what RNA is capable of doing. When we talk about the ribosome templating rna to make protein, that is true, but the ribosome itself is made out of structural rRNA and some rna bound protein. RNAs have been found to have enzyme activity alone. When people talk about the RNA world hypothesis they mean that RNA is sufficient to be the information and catalytic unit of early life, as a sort of occams razor what is the most simple step with the fewest parts involved before taking more complicated steps with more separate pieces sort of way.
“ the majority of known ribozymes carry out mostly phosphoryl transfer reactions”
Now that sure seems like a potential smoking gun for an early phosphorylation based energy cycle.
Been a while since I interacted with this science, but I think the assumption about the magma ocean “boiling off” the water was an early idea that doesn’t hold up? The mantle holds an impressive amount of water dissolved inside it, as it turns out.
Not if it's hot enough that the water molecules reach escape velocity in the exosphere! (As happens with helium today, helium atoms being lighter move faster at a given temperature than water molecules)
It's not clear what the probability is over the ~hundreds of millions of years that it took on Earth. Could be that, under the conditions and on that timescale, we're an average or statistically unremarkable case.
I never like the emphasis on genetics and information in a lot of origin of life stuff. IMO it is too extensional; what is needed is good intensional reasoning.
At the heart of chemical life is https://en.wikipedia.org/wiki/Autocatalysis, this is a great intensional definition of the reproductive side. That just leaves the evolutionary side.
What do "genetics" achieve for reproduction. From the autocatalysis point of view, they create a family of "nearby" autocatalytic sets: because different nucleic acid sequences reproduce in much the same way, the conditions needed to propagate one should also propogate another. This in turn makes safer mutations and....Lamarckian inheritance! If you, a microrganism get a good mutation which makes you fit, and then you split, you pass that mutation on.
Genetics are sufficient for the above properties, but are they necessary? Probably not! We can probably find other things which have such a "dense/smooth mutation space" with fewer local maxima traps. Perhaps it is fine to say such things definitionally encode information, but IMO information still comes second, philosophically.
The meanings of both life and intelligence have been obscured by human conceit. We simply cannot accept that we came from what is essentially a random process over eons (which makes it no less extraordinary, but imo far more understandable). The science and math of LLMs and GPTs has been around for a while, but it took time and effort (people putting stuff online plus GPUs) to finally make it usable.
I have a layman theory on protocell organization. It can't explain replication, but hear me out. So one of the most likely candidate locations for abiogenesis, purportedly, are hydrothermal vents. Now, consider Cymatics (https://en.wikipedia.org/wiki/Cymatics). Maybe you can draw the same conclusion I did.
Wave formations are a source of order amidst the chaos (pressure waves in this case). This may be testable, even. If it did hold any truth, then the popular, common mythos' of "the Word" or "speaking things into existence", or creation via music etc... maybe was more intuitive than we realized :)
Well, my comment is going to end up hidden. I guess this just isn't that interesting, and I assume the video I am linking here will be seen as meaningless with no possible historical bearing on physics or chemistry.
Is there a good reason this is not being considered? Like, these abiogensis articles never say anything new, and have no interesting propositions. They say it's a mystery, then propose a vague implausibility that can only be explained by another mystery. Like, I would appreciate at least some creative thinking here.
Hmm, is there anything you can think of, barring an individual's death or mutation etc.., that we'd consider alive but can't reproduce or evolve? I hadn't thought of it previously, but that does seem like a fundamental difference between being inert and alive.
Amino acids are common enough -- glycine has been found in comets and, controversially, even in the interstellar medium. Other amino acids have also been found in comets.
Comet organics, under pressure, can turn into amino acids in situ: https://www.llnl.gov/article/36016/amino-acids-could-be-prod...
It's also presumed that cometary ice bombardment is the source of Earth's surface water, as ice or water present any earlier would have boiled off when the planet was young and hot.
It's not much of a stretch to imagine that comets brought amino acids, organic compounds, and minerals to Earth as they were bringing water ice. A lot of those aminos and organics would turn into tar, but some would be protected from UV radiation by that same tar. With a heat source, maybe some lightning strikes, a good location, and a lot of luck, you get RNA...
What we can't yet do is assign a probability or likelihood to this process. But the ingredients should be common enough.
About a half of the amino acids used in proteins, i.e. ten of them, can form easily in abiotic conditions and they are widespread in some celestial bodies.
They are easily distinguished from terrestrial contaminants, because they are a mixture of left-handed and right-handed isomers.
When analyzing the genetic code in order to determine which amino acids have already been used in the earlier versions of the genetic code and which have been added more recently, the same simpler amino acids that are easy to synthesize even in the absence of life are also those that appear to have been the only amino acids used earlier.
The article contains the phrase "Given the fact that the current scenario is that life on Earth started with RNA".
This is a fact that it is too often repeated like if it were true, when in reality one of the few things that can be said with certainty about the origin of life is that it has not started with RNA.
What must be true is only that RNA had existed a very long time before DNA and DNA has been an innovation that has been the result of a long evolution of already existing life forms, long before the last ancestor of all living beings that still exist now on Earth.
On the other hand, proteins, or more correctly said peptides, must have existed before any RNA. Moreover, ATP must have existed long before any RNA.
RNA has two main functions based on its information-storage property: the replication of RNA using a template of RNA (which was the single form of nucleic acid replication before the existence of DNA) and the synthesis of proteins using RNA as a template.
Both processes require complex molecular machines, so it is impossible for both of them to have appeared simultaneously. One process must have appeared before the other and there can be no doubt that the replication of RNA must have appeared before the synthesis of proteins.
Had synthesis of proteins appeared first, it would have been instantly lost at the death of the host living being, because the RNA able to be used as a template for proteins could not have been replicated, therefore it could not have been transmitted to descendants.
So in the beginning RNA must have been only a molecule with the ability of self replication. All its other functions have evolved in living beings where abundant RNA existed, being produced by self replication.
The RNA replication process requires energy and monomers, in the form of ATP together with the other 3 phosphorylated nucleotides. Therefore all 4 nucleotides and their phosphorylated forms like ATP must have existed before RNA.
ATP must have been used long before RNA, like today, as a means of extracting water from organic molecules, causing the condensations of monomers like amino acids into polymers like peptides.
The chemical reactions in the early living forms were certainly regulated much less well than in the present living beings, so many secondary undesirable reactions must have happened concurrently with the useful chemical reactions.
So the existence of abundant ATP and other phosphorylated nucleotides must have had as a consequence the initially undesirable polymerization and co-polymerization of the nucleotides, forming random RNA molecules, until by chance a self-replicating RNA molecule was produced.
Because the first self-replicating RNA molecule did not perform any useful function for the host life form, but it diverted useful nucleotides from its metabolism, this first self-replicating RNA molecule must be considered as the first virus. Only much later, after these early viruses have evolved the ability to synthesize proteins, some of them must have become integrated with their hosts, becoming their genome.
The catalytic functions that are now performed mostly by proteins, i.e. amino acid polymers that are synthesized using an RNA template, must have been performed earlier by peptides, i.e. typically shorter amino acid polymers that are synthesized without the use of RNA templates.
Even today, all living beings contain many non-ribosomal peptides, which are made without RNA, using processes that are much less understood than those that involve nucleic acids.
The difference between a living being that would be able to make only non-ribosomal peptides and one that makes proteins using RNA templates is pretty much the same difference as between a CPU with hard-wired control and a CPU with micro-programmed control, with the same advantages and disadvantages.
Life forms able to reproduce themselves must have existed before the appearance of the nucleic acids, but they must have been incapable of significant evolution, because any random change in the structure of the molecules that composed them would have been very likely to result in a defective organism that would have died without descendants. This is similar with a hard-wired control, where small random changes in the circuits are unlikely to result in a functional device.
On the other hand, once the structure of the enzymes was written in molecules of nucleic acids, the random copying errors could result in structures very different from the original structures, which could not have been obtained by gradual changes in the original structures without passing through non functional structures that could not have been inherited.
So the use of molecules that can store the structural information of a living being has enabled the evolution towards much more complex life forms, but it cannot have had any role in the apparition of the first life forms, because the replication of any such molecule requires energy that can be provided only by an already existing life form.
>On the other hand, proteins, or more correctly said peptides, must have existed before any RNA
How come? It seems you can have reproducing RNA without protein needed. Here's Gerald Joyce talking briefly about making those https://youtu.be/aBrYsFeeVzE?t=171
2 replies →
Awesome post and thanks for writing this out - probably the most insightful piece I’ve read on plausible origin of life through pre-RNA autocatalytic peptides. Would you be willing to share a contact email / online profile? (could edit afterward to delete if you are worried about spam from crawlers)
1 reply →
Beautiful work! Do you have any thoughts on the relative size of complexity spaces explored by different forms of mutation?
sorry if I missed it, but it sounds like you've just pushed the mystery one step back but still ended up with the same mystery - where did the original Titan species come from? is there any evidence for their existence other than your belief that an RNA replicator would have needed a host cell? would this host cell have been built out of lipid bilayers? what would its inside mechanisms be made of - if not protein or RNA?
3 replies →
> RNA has two main functions based on its information-storage property: the replication of RNA using a template of RNA (which was the single form of nucleic acid replication before the existence of DNA) and the synthesis of proteins using RNA as a template.
This heavily simplifies what RNA is capable of doing. When we talk about the ribosome templating rna to make protein, that is true, but the ribosome itself is made out of structural rRNA and some rna bound protein. RNAs have been found to have enzyme activity alone. When people talk about the RNA world hypothesis they mean that RNA is sufficient to be the information and catalytic unit of early life, as a sort of occams razor what is the most simple step with the fewest parts involved before taking more complicated steps with more separate pieces sort of way.
“ the majority of known ribozymes carry out mostly phosphoryl transfer reactions”
Now that sure seems like a potential smoking gun for an early phosphorylation based energy cycle.
https://pmc.ncbi.nlm.nih.gov/articles/PMC10583251/
Thank you so much. Awesome post.
Thanks. People like you make HN an enjoyable place.
Been a while since I interacted with this science, but I think the assumption about the magma ocean “boiling off” the water was an early idea that doesn’t hold up? The mantle holds an impressive amount of water dissolved inside it, as it turns out.
But boiling off would have still kept that water in the atmosphere right?
Not if it's hot enough that the water molecules reach escape velocity in the exosphere! (As happens with helium today, helium atoms being lighter move faster at a given temperature than water molecules)
You don't need that much luck when you have billions of years.
Probability is believed to be quite low based on nobody having reproduced the process in the lab.
It's not clear what the probability is over the ~hundreds of millions of years that it took on Earth. Could be that, under the conditions and on that timescale, we're an average or statistically unremarkable case.
2 replies →
Low probabilities become certainties with billions of tests per year over hundreds of millions of years.
14 replies →
I never like the emphasis on genetics and information in a lot of origin of life stuff. IMO it is too extensional; what is needed is good intensional reasoning.
At the heart of chemical life is https://en.wikipedia.org/wiki/Autocatalysis, this is a great intensional definition of the reproductive side. That just leaves the evolutionary side.
What do "genetics" achieve for reproduction. From the autocatalysis point of view, they create a family of "nearby" autocatalytic sets: because different nucleic acid sequences reproduce in much the same way, the conditions needed to propagate one should also propogate another. This in turn makes safer mutations and....Lamarckian inheritance! If you, a microrganism get a good mutation which makes you fit, and then you split, you pass that mutation on.
Genetics are sufficient for the above properties, but are they necessary? Probably not! We can probably find other things which have such a "dense/smooth mutation space" with fewer local maxima traps. Perhaps it is fine to say such things definitionally encode information, but IMO information still comes second, philosophically.
The meanings of both life and intelligence have been obscured by human conceit. We simply cannot accept that we came from what is essentially a random process over eons (which makes it no less extraordinary, but imo far more understandable). The science and math of LLMs and GPTs has been around for a while, but it took time and effort (people putting stuff online plus GPUs) to finally make it usable.
My book dives into the timeline of life's origins as well as summarizing how we know what we know about roughly when life started:
https://impacts.to/downloads/lowres/impacts.pdf#page=10
The little orange dot represents where the events happened along the timeline between the start of the universe and recent times.
https://archive.ph/585kK
I have a layman theory on protocell organization. It can't explain replication, but hear me out. So one of the most likely candidate locations for abiogenesis, purportedly, are hydrothermal vents. Now, consider Cymatics (https://en.wikipedia.org/wiki/Cymatics). Maybe you can draw the same conclusion I did.
Wave formations are a source of order amidst the chaos (pressure waves in this case). This may be testable, even. If it did hold any truth, then the popular, common mythos' of "the Word" or "speaking things into existence", or creation via music etc... maybe was more intuitive than we realized :)
https://www.youtube.com/watch?v=OWLtTP07FCw
Well, my comment is going to end up hidden. I guess this just isn't that interesting, and I assume the video I am linking here will be seen as meaningless with no possible historical bearing on physics or chemistry.
Is there a good reason this is not being considered? Like, these abiogensis articles never say anything new, and have no interesting propositions. They say it's a mystery, then propose a vague implausibility that can only be explained by another mystery. Like, I would appreciate at least some creative thinking here.
>it has to be able to reproduce and evolve by natural selection
Not sure why something has to be able to evolve by natural selection in order to be considered alive.
Hmm, is there anything you can think of, barring an individual's death or mutation etc.., that we'd consider alive but can't reproduce or evolve? I hadn't thought of it previously, but that does seem like a fundamental difference between being inert and alive.
Just think about it, a conscious being deciding what a life should be. There is certainly a bias towards how we were made.
I mean. It was God (whatever that means to you).
Well, you had a chance to have a Programmer joke here, as it was RANDOM.
However, the issue with Life is that God is only human made concept and not all human societies have that concept as well.
Oh, you mean "Programmer #1" using the original assembly language?
But where did Ready Programmer #1 come from? and we're back to square one :)
5 replies →