It's been speculated for at least a decade now that geochemistry spawned biochemistry and life as we know it. This appears to be the latest instance of this pattern. One of the most notable examples is geothermal processes simply creating calm energy gradients that are stable for billions of years (e.g., underwater alkaline vents), which can then essentially "manufacture" organic compounds, which naturally assemble into more complex compounds like magnetic Lego blocks, which ...
I like to think of the Earth as a supercomputer running a vast self-interactive chemical computation of unfathomable scale for an unfathomably long amount of time. In this view, the Earth is roughly a ~10^38 ops/sec dissipative self-modifying search engine, of which life captures roughly ~10^35 ops/sec into metabolism, heredity, ecological competition, and evolutionary search. Once proper biological evolution kicked in, with some bumps along the road, it has had a general tendency to reallocate that immense compute capacity in a way that increases search adaptivity per joule by finding and stacking "search accelerators" (prebiotic geochemistry/biochemistry, replicators, cells, DNA/RNA/protein systems, mitochondria, sexual reproduction, multicellularity, nervous systems, intelligence / brains, language / culture, science / technology, ?).
AareyBaba 19 hours ago [-]
Yet, there is only one form of life on earth exhibiting cellular metabolism and DNA/RNA replication. That original life form formed as soon as the earth became suitable for life. In the 3+ billion years since, there has been no new life form created that we know of despite the ongoing unfathomable computations.
nilkn 15 hours ago [-]
That is not unexpected. There are three forms worth considering, actually: bacteria, archaea, and eukaryotes. The first two share DNA/RNA replication, but they operate in completely different ways. The third is dramatically more complex than either of the former two, yet emerged from them. Once the first two existed, they rapidly filled almost all possible niches available at that time, and there was no space for a third form to emerge (lest it be immediately consumed by the first two), unless that third form was exceptionally competitive (like eukaryotes were and are). The first two forms did emerge relatively early on. The third form, representing one of the most stunning advances in the history of life on Earth, took over two billion years of 10^35+ ops/second of continuous computation to emerge. In terms of total compute, that's about 10^25 greater than today's largest known frontier training run. After that point, evolutionary selection pressure began operating at higher levels of abstraction, selecting for complex multicellular morphological form and later on intelligence, culture, and beyond, over several additional billion years, while bactera and archaea continued to consume all available microscopic niches.
Beyond that, life itself modified the environment that produced the original process of abiogenesis. The early Earth featured a carbon-rich acidic ocean. After life emerged, metabolism began altering the planet’s redox chemistry, consuming available chemical free energy, transforming atmospheric and ocean composition, and eventually oxygenating the surface environment. In other words, the machinery that produced life was not left running in the same state. This is why I called it a self-modifying search engine -- search accelerants operate by changing the search landscape that the engine operates over.
v64 17 hours ago [-]
On 1 February 1871 Charles Darwin wrote about these publications to Joseph Hooker, and set out his own speculation that the original spark of life may have been in a "warm little pond, with all sorts of ammonia and phosphoric salts,—light, heat, electricity &c present, that a protein compound was chemically formed". Darwin explained that "at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed." [1]
"There's strikingly little agricultural innovation in this corner of France" they mused... as the ground shook from tanks and shrapnel bursts.
A glass of sea water seems so peaceful... with its turbulent combat hellscape of voracious protists and viral shrapnel, where you're lucky to make it through a day without being eaten or lysed.
hanjeanwat 7 hours ago [-]
Or, at least, our form of life outcompeted all others out there. We don’t actually know that life only started the one time.
4 hours ago [-]
nlitened 10 hours ago [-]
As I understand, earlier forms of life used RNAs as building blocks (instead of proteins encoded in DNA->RNA), so protein-based life _was_ a completely different form of life.
Some of the oldest replication machinery in our cells still uses the good old rusty RNA building blocks at its core (however nowadays they're propped up with proteins), and the newer machinery is almost entirely "high tech" proteins.
So you could say that in the billions of years, entirely new life forms were created, and they just completely displaced the older, less effecient ones. Probably pure-RNA life forms were not even the first ones, and they completely displaced even more primitive prior biotechnology when they appeared.
tardedmeme 9 hours ago [-]
This is, at this point in time, still a hypothesis.
jfarlow 19 hours ago [-]
Network effects + energetic fficiencies. On an energy landscape that includes integration over very short and very long lifetimes, the thalweg of utility/energy rests right about where the current codon optimizations are. And any schemes that deviate don't get to share in the others' bounty. Reusing your foods' effort saves a lot, metabolically.
ceejayoz 18 hours ago [-]
Well, yeah. Starting from absolute scratch is a lot harder than adapting something that already exists to new conditions.
17 hours ago [-]
IsTom 8 hours ago [-]
If there were more they could have been outcompeted early.
Shitty-kitty 14 hours ago [-]
Any "new life" has 0 chance in the crowded, highly competitive ecosystem.
13 hours ago [-]
fragmede 8 hours ago [-]
Is that still the case with the discovery extremophiles that exist on chemical vents deep under the ocean and far away from the sun? Or rather, how sure are we that they're the same form?
myrmidon 4 hours ago [-]
Yes. All known life shares an (assumed) last common universal ancestor (LUCA, presumed extinct), and there is significant evidence pointing that way.
We can infer properties and function by looking at genes shared between archea and bacteria that most likely came from such an ancestor; this paints a picture of a DNA-based anaerobic thermophile (think hydrothermal vents) with a membrane and simple anti-virus defenses (CAS).
customguy 19 hours ago [-]
Search for what though? On the face of it, life might also just be some eddies in the stream of energy flowing downhill, so to speak.
dtgriscom 17 hours ago [-]
> eddies in the stream of energy flowing downhill
"Ah... is he. Is he."
jpm_sd 9 hours ago [-]
there, behind that sofa!
17 hours ago [-]
flir 18 hours ago [-]
I don't know, but I'm pretty sure it's got something to do with laboratory mice.
s1artibartfast 11 hours ago [-]
Life isn't eddies, it is deepening the stream to paddle the boat.
We are entropy engines hastening the flow. For each bit of temporary order, we make two of disorder at the same time.
lioeters 11 hours ago [-]
> bit of temporary order
Isn't that what we call life? Or at least, life is part of that tendency toward anti-entropy which sounds strangely similar to creativity.
mrsvanwinkle 8 hours ago [-]
your name is all the most beautiful sounds in the world in a single word
AlienRobot 17 hours ago [-]
The answer to life, the universe and everything, I guess?
eks391 4 hours ago [-]
I almost agreed with your comment, but then I remembered there are countless planets with conditions unsuitable for life (as we know life). We have found a couple planets that are optimisticly closer to Earth conditions, but very few, and there is usually some characteristic that makes it a stretch still.
With that said, if Earth was compared to a super computer, the initial conditions and perturbations (weights and biases, or probabilistic inference) are very important, as most planets that are also performing ~10^38 ops/sec will never succesfully manufacture biochemistry/life.
nilkn 3 hours ago [-]
I've actually thought about this. My personal interpretation (which I admit is absolutely a bit playful, but I also find it very fulfilling) is that gravity acts like a resource allocator. It clumps matter together into stars, planets, etc., forcing it to interact, while keeping those objects far enough apart that they generally can run independently of each other for very long periods of time.
If you allow me to exercise some creative liberty with language, it's almost as if gravity is just launching countless trillions of parallel instances of the same computation, with nearly all possible initial starting conditions. Some of those initial conditions allow the local compute capacity to "descend" into finding more and more optimal ways to increase entropy and heat dissipation by exploiting local energy gradients (i.e., life).
In terms of the frequency of life, I'd expect basic microscopic life to be somewhat common, as it's "just" a way of exploiting geochemical energy gradients for local entropy maintenance. That doesn't necessarily even mean fully functioning cells, genetic codes, etc. It really just means molecular compounds or assemblies that exploit or create energy gradients. However, generally once that's kicked off, it's reasonable to consider that this generally would lead to the kinds of selection pressures that favor the development of what we'd know as basic cellular machinery and replication.
However, complex life I would expect to be almost vanishingly rare. The Earth only managed to figure it out a single time so far as we know (generating eukaryotes from bacteria/archaea) in billions of years. How many other planets feature roughly the same chemical computation which just never explored the right niche of chemical possibility to give rise to that complexity? This suggests to me the universe must expend unbelievably vast amounts of computation to overcome the threshold to complex life. I don't think it'd be unreasonable to assume that it requires thousands of separate "planetary computers", each with basic life, for only a single one to generate something like complex life (eukaryotes or equivalent), and that's to say nothing of the millions or billions of planets that don't generate any life at all.
philipallstar 8 hours ago [-]
> I like to think of the Earth as a supercomputer running a vast self-interactive chemical computation of unfathomable scale for an unfathomably long amount of time.
Or "I read the Hitch Hiker's Guide to the Galaxy".
4 hours ago [-]
4 hours ago [-]
rolisz 11 hours ago [-]
So Douglas Adams was right and the Earth is a computer created to calculate the ultimate question?
mncharity 16 hours ago [-]
> stacking "search accelerators" ([...])
On my long-term todo list, is making a didactic simplified tree-of-life, compressed reflecting highly conserved microRNA families (perhaps also Hox clusters and TF transcription factor families) as a regulatory complexity budget, expanding and refining. Traditional presentations obscure the stacking, for example making primates seem just another mammal, instead of a "WTF happened there".
bigbuppo 14 hours ago [-]
As Crime Pays But Botany Doesn't always says... botany is just applied geology, so it probably isn't a big stretch to extend that to the underlying chemistry.
matheusmoreira 18 hours ago [-]
I really like the way you think.
lazide 20 hours ago [-]
The Buddha nods.
buildsjets 1 days ago [-]
Reminds me of the Gamma Forest at Brookhaven National Labs. From 1961 thru 1978 they irradiated a section of the pine barrens forest with a cesium-137 source just to see what would happen. It sterilized the soil and hardly anything grows there, almost 50 years later.
That 1967 documentary highlights lichen and clumps of grass growing there. I imagine the soil ecology has been devastated and failed to regenerate which is why larger plants like trees haven't been able to return
HarHarVeryFunny 1 days ago [-]
That's a bit odd - why wouldn't wind blown non-sterile organic matter from the surrounding forest re-colonize the area?
buildsjets 23 hours ago [-]
That is probably why you can see some low scrubby undergrowth in the Google Earth view, but nothing that needs to put down deep roots has yet returned.
cyberax 22 hours ago [-]
There's nothing unusual there. Typically natural forests grow out in stages, with different generations of trees replacing each other.
Because they actually killed off everything, the "older" trees are not propagating there because they are not adapted for that. That's also why natural forests have clearings that can last for a while.
IAmBroom 31 minutes ago [-]
What's unusual (or "unnatural") is that it's not just the macro level that was annihilated, but even the subterranean fungal network. Fire won't do that (unless the soil is very thin). Drought won't.
What is happening is apparently the entire cycle of repopulation of a food source for the most fundamental of ecosystem anchors.
What surprising is that this should be the equivalent of planting a garden with fuly sterilized soil. As someone else noted, why aren't wind-borne spores and nematode corpses revitalizing the subterranean ecosystem?
jjk166 1 days ago [-]
If there's enough radioactive material and it is mobile enough (due to ground water or wind driven mixing) to stay near the surface it could sterilize any organic material that comes in faster than it can accumulate.
i_cannot_hack 24 hours ago [-]
"An area of oak-pine wood was selected East of Upton, and a tower was constructed that could raise and lower a canister from underground that contained radioactive source material, allowing for controlled dosage levels that emanated in a radius from the tower. The canister contained Cesium-137, which would emit ionizing gamma radiation without making the surrounding area radioactive itself."
tucnak 24 hours ago [-]
They said specifically that it were a cesium-137 source. I think the commentator is fair in pointing out that this finding is ultimately quite odd.
I'm guessing the distinct lack of Google Streetview on that circular bit of road nearby and the tracks implies a certain amount of resistance to access if you get off that dual carriageway to the west?
buildsjets 1 days ago [-]
That "circular bit of road" is the Relativistic Heavy Ion Collider, the second highest-powered particle accelerator on the planet.
Awesome! I had a good nose about the LHC when I was there a few years ago. I'm guessing that site isn't quite so enthusiastic about visitors?
The dump load for one of my wind turbines is a pair of 22Ω resistors recovered from one of CERN's "free for all" scrap piles :-)
scheme271 20 hours ago [-]
Brookhaven does classified research and access to the site is pretty restricted. The last time I visited there were guards with assault rifles at the gates. In comparison, Fermilab used to (and may still) let you walk onto the campus and wander about.
buildsjets 19 hours ago [-]
It's a Department of Energy facility. The primary purpose of the DOE is to further the development of nuclear weapons.
The present study challenges the traditional view that the *respiration of
organic carbon to CO2* is an exclusively intracellular process, revealing that
*organic compound respiration can occur spontaneously in an extracellular
context in soils*.
On the surface, it looks like they rediscovered that oxidation of organic / carbonaceous compounds occurs at low temperatures independently of presence of living organisms. The real contribution of the paper would be in elucidation of the specific mechanisms of oxidation of these organic compounds (e.g. via abiotic catalysis).
Coal oxidation at low temperatures is the major heat source responsible for
the self-heating and spontaneous combustion of coal and is an important source
of greenhouse gas emissions. This review focuses on the chemical reactions
occurring during low-temperature oxidation of coal. Current understanding
indicates that this process involves consumption of O2, formation of solid
oxygenated complexes, thermal decomposition of solid oxygenated complexes and
generation of gaseous oxidation products. Parameters, such as mass change,
heat release, oxygen consumption, and formation of oxidation products in the
gas or solid phase, have been used to qualitatively and quantitatively
describe the oxidation process. Reaction mechanisms have been proposed to
explain the characteristics of consumption of O2, and formation of oxidation
products in the gas and solid phases. Various kinetic models have also been
developed to describe the rate of oxygen consumption and the rates of
formation of gaseous oxidation products in terms of the rate parameters of the
relevant reactions, oxidation time, temperature, and initial concentration of
oxygen in the oxidising medium.
stymaar 23 hours ago [-]
Funnily enough, the title made me think about the PhD of a friend, and it turns out it's actually his lab that is featured here, and his name is even mentioned. What a star!
accrual 22 hours ago [-]
> They’re finding that the chemistry of life is not exclusive to life, he added. “It’s the chemistry of geology.”
This has me excited for missions to Europa and Enceladus. Vast quantities of tidal energy flexing unseen ocean floors for millennia is bound to produce some interesting chemistry, if not life.
This is like saying "wood burns, even when the tree is dead" but much, much slower.
The disequilibrium (sugars and free O₂) were produced by living organisms, and this is just the gradual drift back to a lower energy state. CO₂ is common in the universe, and not at all a sign of life. O₂ and sugars are rare.
conductr 3 hours ago [-]
This seems like the better explanation of my laybrain reading this and thinking; why would you start with soil? If it were a true geological phenomenon then shouldn’t they use a sterile jar of granite dust or something that only existed on earth prior to life? It seems like pointing at a jar of bio matter and saying we can’t stop it is not really a good methodology to base much upon. I barely ever even took a chemistry class in my life but something just feels wrong with this approach to me. I assume that’s what the other scientists who doubt the sterilization were thinking too.
LarsAlereon 17 hours ago [-]
This is honestly what I'm thinking. Carbohydrates and hydrocarbons will oxidize to CO2 and water in our atmosphere, and especially quickly at warm temperatures, in the presence of energy sources like sunlight, or in the presence of ozone or elevated oxygen levels. In general biological processes like aerobic decay are so much more effective that we ignore this, but it still happens.
greenbit 1 days ago [-]
This is great, if you have significant amounts of free oxygen to work with, which early earth evidently did not. Would be interesting to see if anaerobic metabolism could also occur without cellular confinement.
asdff 24 hours ago [-]
Biochemists have been doing just that for like 100 years. They'd take a bunch of yeast, grind the cells into a slurry releasing whatever is inside, separate the cell debris, and perform experiments measuring fermentation rate.
stymaar 23 hours ago [-]
It can, that's the reason why UHT milk has a relatively short shelf lifespan and degrades despite being devoid of living microorganisms. The enzymes keep doing their work long after the cell membrane is gone.
gamblor956 21 hours ago [-]
You might be thinking of something else. UHT has a very long shelf life compared to other forms of liquid milk.
stymaar 18 hours ago [-]
Compared to other forms forms of liquid milk indeed, but it has a rather short shelf life compared to most sterile food. (Imagine if canned meat or fish had the same shelf life than UHT milk…)
culi 20 hours ago [-]
The leading theories for the origins of chemical evolution (abiogenesis) actually focus on deep-sea hydrothermal, alkaline vents
JumpCrisscross 18 hours ago [-]
> leading theories for the origins of chemical evolution (abiogenesis) actually focus on deep-sea hydrothermal, alkaline vents
I thought the leading contenders were currently in tide pools?
That's a wild, out-there hypothesis. This is a factual observation that currently has no strong explanation hypotheses.
threwrfaway 16 hours ago [-]
[dead]
Shitty-kitty 12 hours ago [-]
AFIAK only Hydrofluorocarbons detection would be considered a unambiguous signal of life, and those require technology.
Life very much seems to be a natural process, largely un-distinguishable from other natural processes. Detection will come from Preponderance of evidence rather than a silver-bullet.
rbanffy 7 hours ago [-]
As anyone working in a large corporation can immediately tell you, "dead but breathing" is much more common than one might guess.
mparramon 17 hours ago [-]
That is not dead which can eternal lie,
And with strange aeons even death may die.
j16sdiz 1 days ago [-]
It feels next would be trying isolate the component that make CO2.
Try to use smaller sample. Put them under microscope, etc.
greenbit 24 hours ago [-]
Maybe it's the very molecules that the live cells were using, just doing their thing without the cells. Cells concentrate things by confining them in a small volume, but otoh, if you have damp particles, the thin water layer on the particles would be a kind of confining space, with the added advantage of surface area to exchange gases with.
andrewflnr 23 hours ago [-]
This is addressed later in the article. They think there's probably some of that activity but don't think those molecules could last long enough to produce the observed effect.
wagwang 1 days ago [-]
I might be dumb, but I figured they would just continuously subdivide the sample until they isolated it. Maybe CO2 sensors wont be sensitive enough?
BigTTYGothGF 18 hours ago [-]
I'm not going to track down the references to see if they did this, but surely protein mass spectrometry could show if they have enzymes that are still there.
trentnix 20 hours ago [-]
Genesis 2:7 (NIV)
Then the Lord God formed a man from the dust of the ground and breathed into his nostrils the breath of life, and the man became a living being.
emsign 1 days ago [-]
This is huge news if true for evaluating soil experiments on Mars. They could give false positives for life if they only look for metabolic products.
adrian_b 1 days ago [-]
In the second part of the article there is an explanation which for me is the most plausible, and which would not be applicable to Martian soil.
Even if they killed all living beings in the soil, after their death the enzymes that are the catalysts for metabolism would just become dispersed in the soil and they continue to catalyze reactions like those of the Krebs cycle.
After many years of storage the molecules of the enzymes will be degraded, i.e. they will break into fragments. That again does not mean much, because the catalytic action of the enzymes is typically caused by very small parts of the enzymes, which can remain intact even after fragmentation.
In general, the biggest part of an enzyme is just a scaffold that attaches the enzyme in precise places of a cell, usually on some intracellular membranes, so that a great number of enzymes can be assembled like a production line in a factory, to coordinate the metabolic reactions for maximum efficiency.
After death and enzyme fragmentation, even after many years, the catalytic fragments of the enzymes can still catalyze reactions like those of the Krebs cycle.
It is also possible that some of the observed chemical reactions are catalyzed by minerals present in the soil and not by remnants of the enzymes from the dead cells, but for now no evidence has been gathered about this.
Moreover, there are enzyme residues which are difficult to distinguish from abiotic minerals. Some of the enzymes involved here contain a catalytic part formed by a cluster of iron and sulfur atoms, which are attached to a protein molecule. That iron-sulfur cluster is pretty much identical with a very small fragment of an iron sulfide mineral.
cogman10 1 days ago [-]
Not as much as you might think.
We've found amino acids almost everywhere we look, including astroids [1].
It seems that the building blocks of life pretty naturally and readily form. Which is a pretty strong indicator that life is likely fairly common outside earth.
The amino acids that can be found everywhere include ten of the simpler amino-acids that are used in proteins (glycine, the 2 acids, the 3 branched, alanine, proline and the 2 alcohols).
The other 11 amino-acids from proteins have never been found where life does not exist. They are more complex and they seem to have been developed by living beings long after the appearance of life and the appearance of the genetic code (they seem to have substituted later the simpler amino-acids in certain locations of the map of the original genetic code, which encoded fewer amino-acids).
Moreover, while the simple amino-acids, including the ten that are used in proteins, can be found pretty much everywhere, wherever they were not produced by living beings they have been found in racemic mixtures, i.e. in equal amounts of left-handed and right-handed isomers, while in proteins only the left-handed isomers are used, so the living beings normally produce almost only left-handed isomers. Very small quantities of right-handed isomers are produced by some living beings, for other purposes than making proteins.
So it is relatively easy to distinguish amino-acids that have been produced by living beings from amino-acids that have been produced in abiotic conditions (i.e. the amino-acids produced in abiotic conditions are recognized by the absence of complex amino-acids and by the presence of great quantities of right-handed isomers).
asdff 23 hours ago [-]
I don't see the left handed aspect as necessary for life. To me this just suggests our common ancestor for life on earth made use of this chirality. Another group of organisms somewhere else could have evolved from an ancestor that makes use of right handed chirality. Or one that is hand-blind.
adrian_b 23 hours ago [-]
I agree.
It seems that the choice between left-handed and right-handed amino-acids was random.
However, it is unlikely that other kinds of life forms could use both kinds indiscriminately, because mixing them creates difficulties in the assembling of polymers. So it is likely that amino-acids produced by some extra-terrestrial life form would also be predominantly of only one orientation, but it could happen to be the right-handed variant.
Moreover, extra-terrestrial life forms could use very different complex amino-acids, because there are much more of those than the 11 that have been added to the simple amino-acids in the terrestrial proteins.
asdff 23 hours ago [-]
That makes sense that the chirality can affect downstream polymer assembly or even folding in the higher order structures.
Likely we are all left handed on earth because our left handed ancestor outcompeted the right handed organisms in the primordial soup. Or the right handed organisms just didn't evolve in the first place here on earth and there was nothing to outcompete. There might still be some higher order advantages to shifting chirality one way or another. Certain molecules, such as methamphetamine, have differing bioactivity based on chirality. Maybe this can be regulated in some way such as to control the rate of some other downstream process. In an abstracted sense, chemists here on earth are already this organism as they refine reactions to produce desired chirality and reduce expenditure on undesired chirality.
ET could be using different amino acids, or more or fewer. I would hazard to guess there is immense selection to reduce the amino acid set to its most necessary components. This pressure has gotten to the point here on earth where even these necessary components might not all be produced endogenously by the organism who needs them, but consumed from the environment saving energy spent on synthesis. But this requires your neighbor to be producing these AAs, such that you consume them, and you having sufficient feedback mechanisms to not immediately consume all of your neighbor's species and put your own insufficient lineage to extinction.
adrian_b 21 hours ago [-]
The living beings use much more amino acids than those that compose proteins.
The relatively low number of amino acids that are used in proteins appears to be caused by the difficulty of modifying the genetic code by adding not yet encoded amino acids to the set of encoded amino acids.
Variations of the genetic code are known at various living beings, but nonetheless they are very rare, because a change in the genetic code requires a lot of other coordinated changes. A new kind of transfer RNA must be encoded in the genome (the only likely origin of such a new tRNA is a mutation in one of the existing) and that RNA molecule must be able to bind preferentially to the codons that are repurposed to encode a new amino acid, and also to molecules of that amino acid, which requires a lot of favorable change is the molecular structure of that RNA.
It seems that in the earliest form of genetic code, there were only 4 distinct symbols, i.e. of the 3 nucleobases of a codon only the central one was meaningful and the 2 peripheral nucleobases did not encode information.
The 4 original symbols selected between 4 major kinds of amino acids: the special amino acid glycine, an acid amino acid, a hydrophobic amino acid and an amino acid with intermediate behavior, like alanine or proline.
These variations would have been enough to build proteins with specific conformations.
The fact that a codon had 3 nucleobases, presumably to ensure the binding to transfer RNA molecules, even if only one of them encoded information, appears to have been a great luck, because this allowed later the expansion of the genetic code, because 3 bases give 64 combinations allowing the encoding of up to 64 symbols.
Most of the possible codons have remained ambiguous until today, but the number of encoded amino acids has increased slowly in time, up to 21, the most recent additions to the encoded set being those of the sulfur-containing amino acids, aromatic amino acids and selenium-containing amino acids.
As you say, there are disadvantages in using many kinds of amino acids, but there are also advantages, by allowing the creation of proteins with properties that are not achievable with a smaller set of amino acids.
The balance between advantages and disadvantages appears to have slowed down continuously the rate of adding new amino acids to the set encoded in the genetic code, so that the majority of the living beings of today have not added any new amino acid since several billion years ago.
Most of the expansions of the genetic code happened before the last common ancestor of all living beings of today, so that today there are very few living beings with more recent modifications in the genetic code.
cyberax 22 hours ago [-]
Life can even use something other than amino acids. They are really inconvenient when you think about it. Fixed nitrogen is extremely rare, and there are no nitrogen-containing minerals other than some exotic exceptions.
Amino acids are useful because they can be easily joined together and split apart (via the C-N bond). But there are other types of "molecular glues" that are viable, like sulfur or phosphorus.
adrian_b 21 hours ago [-]
Amino acids are much more likely to be involved in the appearance of life anywhere than other molecules.
For instance it would be much less surprising if an alien life form used another kind of polymer to store information, instead of nucleic acids, than if it would not use amino acids. The fact that on Earth the living beings eventually used ATP and RNA appears to have been determined in great part by chance, while the use of amino acids seems to have been much more deterministic.
Some of the simple amino acids are very easy to be synthesized in abiotic conditions, which is why they are ubiquitous in many celestial bodies.
The advantage of amino acids is that they do not contain only one end that can be attached to other molecules, but that they contain two such ends. A molecule with only one connector would attach to another, forming a dimer, after which no further reaction is possible.
A molecule with two connectors, like an amino acid that has both a carboxyl end and an amine end, can be daisy chained into a polymer of arbitrary length. This allows building complex structures.
There are other molecules with two connectors, but they are much more unlikely to appear in abiotic conditions.
Thioesters, i.e. a kind of organic molecules that are bound by a sulfur bridge, like you mention, appear to have been much more important when life has appeared on Earth than today, but such molecules were important as intermediates in metabolic reactions, not as structural blocks, like amino acids, and there are no known naturally-produced molecules with sulfur that could be used as easily as amino acids to make molecules with arbitrary complex shapes.
cyberax 19 hours ago [-]
> The fact that on Earth the living beings eventually used ATP and RNA appears to have been determined in great part by chance, while the use of amino acids seems to have been much more deterministic.
It looks like on Earth the RNA was the initial replicant. RNA can be folded into complex shapes and can have catalytic properties in itself. Ribosomes that assemble proteins have RNA at the active site with proteins only providing structural framework.
That's why amino acids might not end up being so universal.
don_esteban 13 hours ago [-]
There is no contradiction: simple amino acids as a basic building block being coopted by replicating RNA to build more sophisticated structures.
You can conceive other than nuclear-acids based replicant, using the same ubiquitous amino-acids to build a protein life not using RNA/DNA but some other encoding structure.
The question is what is the chemically most likely 'other'?
Also, what could be alternatives for ATP/sugars?
cyberax 10 hours ago [-]
Sugars are just chains of hydrocarbons with alcohol groups, they are probably going to be ubiquitous. ATP is useful because the phosphate groups make a stable bond that nevertheless can be hydrolyzed, releasing a lot of energy.
But the adenosine "backbone" of the ATP is more-or-less arbitrary. Other forms of life can use something different. Or they might use the phosphorus bonds themselves where terrestrial life uses peptide bonds.
Disulfide bonds exhibit similar properties, and terrestrial life also uses them to give additional "rigity" to certain proteins. It's also likely a late addition to the genetic code, cysteine is nestled between two stop codons (it clearly used up the initially reserved block of the address space tagged for future expansion).
And if you look at meteorites, sulfur compounds are _much_ more common. Sulfur chemistry also doesn't require scarce fixed nitrogen that could only be replenished by lightning before nitrogen-fixing enzymes first evolved.
So I don't believe at all that exactly our RNA/amino acids are going to be universal.
adrian_b 9 hours ago [-]
I also do not believe that our RNA and complex amino acids are likely to be universal.
On the other hand, the simple amino acids are known to be universal, both from chemical analyses of celestial bodies and from abiotic syntheses in laboratories.
In theory, sugars can be produced abiotically by the polymerization of formaldehyde. However, sugars are not very stable chemically and suitable catalysts for formaldehyde polymerization seem to be rare, because sugars are much less ubiquitous than amino acids in lifeless environments.
The role of phosphorus in biology is determined entirely by the property of the phosphate anions that they can eliminate water and condense into polyphosphates, then the polyphosphates can extract water from other molecules, forcing condensation reactions, which can be used for various purposes, e.g. for building polymers.
The nucleoside parts of ATP and related substances play only the role of a "handle", which can be used to control the location of the polyphosphate parts, so that they will perform their function where intended.
Thus for controlling the polyphosphates other molecules may also be suitable.
Disulfide bonds, which already exist in the pyrite mineral, must have had a crucial role in the origin of life. But their role is very different from that of polyphosphates, because they extract hydrogen, instead of extracting water, so they perform redox reactions, not condensation/hydrolysis reactions.
Thioesters are the sulfur compounds that can play the same role as ATP, by taking part in condensation/hydrolysis reactions.
There is no doubt that all the 5 elements H, C, N, O and S, which happen to be the most abundant electronegative elements in the entire Universe, must be used by any living being, since the origin of life. Whether phosphorus has also been used since the beginning, or it is a later addition, is uncertain, because thioesters could have been used originally for performing all the functions now done with phosphates like ATP.
Both nitrogen and phosphorus are affected by similar availability problems. While nitrogen is too volatile and most of it would always have been stored in dinitrogen gas, which is inert, instead of being stored in easy to use ammonia or hydrogen cyanide molecules (while hydrogen cyanide and carbon monoxide are now toxic for most living beings, it is likely that they both are very important for the appearance of life), for phosphorus the problem is that most of it is stored in insoluble phosphate minerals. This must have been alleviated around the origin of life by the fact that the early oceans were much more acidic than today, so much more phosphate ions would have remained dissolved in sea water, than today.
Unlike for phosphorus, there is no substitute for nitrogen in biology. The role of nitrogen in organic molecules is the same as the role of dopants in semiconductor devices. When nitrogen substitutes carbon in an organic molecule, that position in the molecule becomes positively charged, instead of being electrically neutral. These electric charges play very important roles in many chemical reactions.
The poor availability of nitrogen must have been the main constraint in the growth of the early forms of life, until the development of the nitrogenase catalysts that allow the use of dinitrogen from the atmosphere.
Similarly, it is likely that the earliest forms of life used carbon from carbon monoxide, whose lower availability limited growth until the development of a catalyst that reduces carbon dioxide to formic acid, which allowed the use of the more abundant carbon dioxide. Both catalysts, which are used to capture carbon dioxide and dinitrogen, appear to have used in their earliest variants molybdenum, or possibly the related tungsten. While molybdenum seems to be a later addition to the set of chemical elements used for life, iron, cobalt and nickel are all necessary for the appearance of life as catalysts, while potassium is also necessary since the beginning for maintaining the electrical neutrality of a water solution without producing solid precipitates that would cause death.
The abilities to use directly carbon dioxide and dinitrogen, which are the main constituents of most planetary atmospheres, and which were also the main constituents of the early atmosphere of the Earth, must have greatly expanded the environments suitable for life, which previously must have been restricted to small neighborhoods of hydrothermal vents or sources of volcanic gases.
don_esteban 45 minutes ago [-]
Great post! Thank you.
Is it conceivable that instead of water, some other solvent can be used? Those ethane/methane lakes on Titan ...
adrian_b 11 hours ago [-]
RNA was indeed the initial replicant, i.e. the first molecule that contained an arbitrary sequence of blocks and which could be used as a template to generate copies at itself.
However, such a replicant could appear only after a life form with metabolism already existed.
For replicating RNA, there must exist a complex system that extracts energy from the environment and uses that energy to synthesize nucleotides like ATP and then it uses additional energy to polymerize the nucleotides into RNA.
RNA itself or any other molecule capable of replication could not have had any role in that living system, because before the existence of replication, any molecule of RNA that would have appeared accidentally would have disappeared eventually, without descendants. Therefore the first molecule of RNA that has survived must have been self-replicating and it could not have other functions.
The first self-replicating RNA molecules have diverted resources from a pre-existing living being, by consuming nucleotides like ATP, which must have already been used long before the appearance of RNA, for implementing condensation reactions.
In other worrds, the first RNA molecule, i.e. the first nucleic acid molecule was a virus. Some of the present viruses might have had their origin as detached parts from some nuclei of cellular beings, but it is likely that most viruses descend from the primordial viruses and they have never been cellular life forms.
The cellular life forms must have appeared by symbiosis between a virus and a life form without nucleic acids.
It is a frequently believed myth that life requires a memory molecule, like a nucleic acid. This is a mistake perpetuated by people unfamiliar with engineering.
It is perfectly possible to have a chemical system that growths and replicates itself, without containing any molecule able to store arbitrary information, like a nucleic acid. The difference between such a chemical system and the cellular life forms of today has the same nature as the difference between a hard-wired processor and a microprogrammed processor, i.e. the nucleic acids play the role of the microprogram memory that controls the execution units of the processor, allowing the implementation of an arbitrary behavior by changing the sequence of microinstructions, while the hard-wired processor has a fixed behavior, which can be changed only by a redesign of its structure.
Information-storage molecules like the nucleic acids are without doubt necessary for the evolution of complex living beings, because they allow the random generation of a huge number of variants that can explore the solution space, from which survival will select optimized variants. The nucleic acids have brought to living beings the same kind of flexibility that programmable embedded computers have brought to various appliances, whose properties can now be changed by a software update, instead of a costly recall and hardware redesign.
In a "hard-wired" living being, evolution must be extremely improbable, because any change in some of its component molecules is likely to break the cycle of self-replication, leading to death without descendants.
In a self-replicating chemical system, there must be a long chain of chemical reactions, each using as input reactants the products of the previous reaction, while the first reaction in the chain must use the products of the last reaction, closing the cycle.
It is very likely that in such a self-replicating chemical system, peptides, i.e. relatively short chains of amino-acids, had a very important role in providing a scaffold that organized the chain of reactions.
Even today, most if not all living beings still produce so-called non-ribosomal peptides, which, unlike the proteins, are not produced by templates of RNA.
Unlike with the mechanism of protein synthesis by ribosomes, for now the mechanisms that establish the sequence of amino acids in non-ribosomal peptides are very poorly understood.
It is likely that at least some of the mechanisms of synthesis of non-ribosomal peptides are a remnant of the synthesis mechanisms used before the appearance of RNA.
pocksuppet 10 hours ago [-]
It could also be that other forms of life produce both forms, but selectively use one.
stevenwoo 1 days ago [-]
Tangentially related, this is a bit trying to sell upcoming book, but the discussion of origins of life was interesting to me. https://www.newscientist.com/article/2526959-how-a-radical-n...
YMMV but It’s free via my local library and Libby if you are stopped by the subscription nag.
contingencies 23 hours ago [-]
Soil's amazing. So is fungal diversity. Fungal insect interactions. Bryophytes. Slime molds. Ferns. If you have a lawn, do the world a favor and remove it. No need to mow and you'll be amazed at the world that emerges. Especially with a microscope.
Well, as far as I understand it's pretty much a given that it happened underwater or underground, to protect against cosmic radiation and other harsh conditions averse to lifeg so that's not really a "what if" unless you meant something else than I think you did.
Mind you, "soil" as we know it did not exist before life was there to create it. Geology as it exists on Earth does not exist on lifeless planets.
JackFr 1 days ago [-]
Obligatory Asimov: 'The most exciting phrase to hear in science, the one that heralds the most discoveries, is not "Eureka!" but 'That's funny...”'
roughly 21 hours ago [-]
Yep. The most interesting places in science are where the model breaks down.
nelox 14 hours ago [-]
The climate change deniers are gonna love this. CO2 from soil.
metalman 18 hours ago [-]
soil is a biological construct and only occurs on Earth, the regolith on other planets will not support life without major amendments and modifications.
there are orders of magnitude more types of minerals on earth that found in any sample from an extra terestrial source, and while not proven conclusivly there is strong evidence that the bulk of earthly minerals, have biological origins in there creation.
what is not disputed is that the entire top 10km or so of our planet has biological components and biological modifications, 3 billion years will do.that to a world,
the point bieng, is that extraterestrial regolith would be the substance to use in substantiating the premise under consideration, but was not.
tardedmeme 4 hours ago [-]
Supporting life is different from already having life. There are lifeforms that only rely upon soil for structural support and not for nutrients - they could probably grow on regolith as long as it's not too toxic. We could also spray it with needed nutrients.
pslab 11 hours ago [-]
[flagged]
bitwize 24 hours ago [-]
Life uh, finds a way.
Rendered at 17:47:10 GMT+0000 (Coordinated Universal Time) with Vercel.
I like to think of the Earth as a supercomputer running a vast self-interactive chemical computation of unfathomable scale for an unfathomably long amount of time. In this view, the Earth is roughly a ~10^38 ops/sec dissipative self-modifying search engine, of which life captures roughly ~10^35 ops/sec into metabolism, heredity, ecological competition, and evolutionary search. Once proper biological evolution kicked in, with some bumps along the road, it has had a general tendency to reallocate that immense compute capacity in a way that increases search adaptivity per joule by finding and stacking "search accelerators" (prebiotic geochemistry/biochemistry, replicators, cells, DNA/RNA/protein systems, mitochondria, sexual reproduction, multicellularity, nervous systems, intelligence / brains, language / culture, science / technology, ?).
Beyond that, life itself modified the environment that produced the original process of abiogenesis. The early Earth featured a carbon-rich acidic ocean. After life emerged, metabolism began altering the planet’s redox chemistry, consuming available chemical free energy, transforming atmospheric and ocean composition, and eventually oxygenating the surface environment. In other words, the machinery that produced life was not left running in the same state. This is why I called it a self-modifying search engine -- search accelerants operate by changing the search landscape that the engine operates over.
[1] https://en.wikipedia.org/wiki/Warm_little_pond
A glass of sea water seems so peaceful... with its turbulent combat hellscape of voracious protists and viral shrapnel, where you're lucky to make it through a day without being eaten or lysed.
Some of the oldest replication machinery in our cells still uses the good old rusty RNA building blocks at its core (however nowadays they're propped up with proteins), and the newer machinery is almost entirely "high tech" proteins.
So you could say that in the billions of years, entirely new life forms were created, and they just completely displaced the older, less effecient ones. Probably pure-RNA life forms were not even the first ones, and they completely displaced even more primitive prior biotechnology when they appeared.
We can infer properties and function by looking at genes shared between archea and bacteria that most likely came from such an ancestor; this paints a picture of a DNA-based anaerobic thermophile (think hydrothermal vents) with a membrane and simple anti-virus defenses (CAS).
"Ah... is he. Is he."
We are entropy engines hastening the flow. For each bit of temporary order, we make two of disorder at the same time.
Isn't that what we call life? Or at least, life is part of that tendency toward anti-entropy which sounds strangely similar to creativity.
With that said, if Earth was compared to a super computer, the initial conditions and perturbations (weights and biases, or probabilistic inference) are very important, as most planets that are also performing ~10^38 ops/sec will never succesfully manufacture biochemistry/life.
If you allow me to exercise some creative liberty with language, it's almost as if gravity is just launching countless trillions of parallel instances of the same computation, with nearly all possible initial starting conditions. Some of those initial conditions allow the local compute capacity to "descend" into finding more and more optimal ways to increase entropy and heat dissipation by exploiting local energy gradients (i.e., life).
In terms of the frequency of life, I'd expect basic microscopic life to be somewhat common, as it's "just" a way of exploiting geochemical energy gradients for local entropy maintenance. That doesn't necessarily even mean fully functioning cells, genetic codes, etc. It really just means molecular compounds or assemblies that exploit or create energy gradients. However, generally once that's kicked off, it's reasonable to consider that this generally would lead to the kinds of selection pressures that favor the development of what we'd know as basic cellular machinery and replication.
However, complex life I would expect to be almost vanishingly rare. The Earth only managed to figure it out a single time so far as we know (generating eukaryotes from bacteria/archaea) in billions of years. How many other planets feature roughly the same chemical computation which just never explored the right niche of chemical possibility to give rise to that complexity? This suggests to me the universe must expend unbelievably vast amounts of computation to overcome the threshold to complex life. I don't think it'd be unreasonable to assume that it requires thousands of separate "planetary computers", each with basic life, for only a single one to generate something like complex life (eukaryotes or equivalent), and that's to say nothing of the millions or billions of planets that don't generate any life at all.
Or "I read the Hitch Hiker's Guide to the Galaxy".
On my long-term todo list, is making a didactic simplified tree-of-life, compressed reflecting highly conserved microRNA families (perhaps also Hox clusters and TF transcription factor families) as a regulatory complexity budget, expanding and refining. Traditional presentations obscure the stacking, for example making primates seem just another mammal, instead of a "WTF happened there".
https://maps.app.goo.gl/pJYr6qiZnMdVwLJS6
https://www.atlasobscura.com/places/brookhaven-gamma-forest
https://www.youtube.com/watch?v=GsuiLxcDuHY&t=925s
that seems pretty major exaggeration
https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.0800...
Because they actually killed off everything, the "older" trees are not propagating there because they are not adapted for that. That's also why natural forests have clearings that can last for a while.
What is happening is apparently the entire cycle of repopulation of a food source for the most fundamental of ecosystem anchors.
What surprising is that this should be the equivalent of planting a garden with fuly sterilized soil. As someone else noted, why aren't wind-borne spores and nematode corpses revitalizing the subterranean ecosystem?
https://en.wikipedia.org/wiki/Relativistic_Heavy_Ion_Collide...
The dump load for one of my wind turbines is a pair of 22Ω resistors recovered from one of CERN's "free for all" scrap piles :-)
Compare to this paper from 2003:
https://sci-hub.kvnp.top/10.1016/s0360-1285(03)00042-x
This has me excited for missions to Europa and Enceladus. Vast quantities of tidal energy flexing unseen ocean floors for millennia is bound to produce some interesting chemistry, if not life.
The disequilibrium (sugars and free O₂) were produced by living organisms, and this is just the gradual drift back to a lower energy state. CO₂ is common in the universe, and not at all a sign of life. O₂ and sugars are rare.
I thought the leading contenders were currently in tide pools?
Then the Lord God formed a man from the dust of the ground and breathed into his nostrils the breath of life, and the man became a living being.
Even if they killed all living beings in the soil, after their death the enzymes that are the catalysts for metabolism would just become dispersed in the soil and they continue to catalyze reactions like those of the Krebs cycle.
After many years of storage the molecules of the enzymes will be degraded, i.e. they will break into fragments. That again does not mean much, because the catalytic action of the enzymes is typically caused by very small parts of the enzymes, which can remain intact even after fragmentation.
In general, the biggest part of an enzyme is just a scaffold that attaches the enzyme in precise places of a cell, usually on some intracellular membranes, so that a great number of enzymes can be assembled like a production line in a factory, to coordinate the metabolic reactions for maximum efficiency.
After death and enzyme fragmentation, even after many years, the catalytic fragments of the enzymes can still catalyze reactions like those of the Krebs cycle.
It is also possible that some of the observed chemical reactions are catalyzed by minerals present in the soil and not by remnants of the enzymes from the dead cells, but for now no evidence has been gathered about this.
Moreover, there are enzyme residues which are difficult to distinguish from abiotic minerals. Some of the enzymes involved here contain a catalytic part formed by a cluster of iron and sulfur atoms, which are attached to a protein molecule. That iron-sulfur cluster is pretty much identical with a very small fragment of an iron sulfide mineral.
We've found amino acids almost everywhere we look, including astroids [1].
It seems that the building blocks of life pretty naturally and readily form. Which is a pretty strong indicator that life is likely fairly common outside earth.
[1] https://www.nasa.gov/news-release/nasas-asteroid-bennu-sampl...
The other 11 amino-acids from proteins have never been found where life does not exist. They are more complex and they seem to have been developed by living beings long after the appearance of life and the appearance of the genetic code (they seem to have substituted later the simpler amino-acids in certain locations of the map of the original genetic code, which encoded fewer amino-acids).
Moreover, while the simple amino-acids, including the ten that are used in proteins, can be found pretty much everywhere, wherever they were not produced by living beings they have been found in racemic mixtures, i.e. in equal amounts of left-handed and right-handed isomers, while in proteins only the left-handed isomers are used, so the living beings normally produce almost only left-handed isomers. Very small quantities of right-handed isomers are produced by some living beings, for other purposes than making proteins.
So it is relatively easy to distinguish amino-acids that have been produced by living beings from amino-acids that have been produced in abiotic conditions (i.e. the amino-acids produced in abiotic conditions are recognized by the absence of complex amino-acids and by the presence of great quantities of right-handed isomers).
It seems that the choice between left-handed and right-handed amino-acids was random.
However, it is unlikely that other kinds of life forms could use both kinds indiscriminately, because mixing them creates difficulties in the assembling of polymers. So it is likely that amino-acids produced by some extra-terrestrial life form would also be predominantly of only one orientation, but it could happen to be the right-handed variant.
Moreover, extra-terrestrial life forms could use very different complex amino-acids, because there are much more of those than the 11 that have been added to the simple amino-acids in the terrestrial proteins.
Likely we are all left handed on earth because our left handed ancestor outcompeted the right handed organisms in the primordial soup. Or the right handed organisms just didn't evolve in the first place here on earth and there was nothing to outcompete. There might still be some higher order advantages to shifting chirality one way or another. Certain molecules, such as methamphetamine, have differing bioactivity based on chirality. Maybe this can be regulated in some way such as to control the rate of some other downstream process. In an abstracted sense, chemists here on earth are already this organism as they refine reactions to produce desired chirality and reduce expenditure on undesired chirality.
ET could be using different amino acids, or more or fewer. I would hazard to guess there is immense selection to reduce the amino acid set to its most necessary components. This pressure has gotten to the point here on earth where even these necessary components might not all be produced endogenously by the organism who needs them, but consumed from the environment saving energy spent on synthesis. But this requires your neighbor to be producing these AAs, such that you consume them, and you having sufficient feedback mechanisms to not immediately consume all of your neighbor's species and put your own insufficient lineage to extinction.
The relatively low number of amino acids that are used in proteins appears to be caused by the difficulty of modifying the genetic code by adding not yet encoded amino acids to the set of encoded amino acids.
Variations of the genetic code are known at various living beings, but nonetheless they are very rare, because a change in the genetic code requires a lot of other coordinated changes. A new kind of transfer RNA must be encoded in the genome (the only likely origin of such a new tRNA is a mutation in one of the existing) and that RNA molecule must be able to bind preferentially to the codons that are repurposed to encode a new amino acid, and also to molecules of that amino acid, which requires a lot of favorable change is the molecular structure of that RNA.
It seems that in the earliest form of genetic code, there were only 4 distinct symbols, i.e. of the 3 nucleobases of a codon only the central one was meaningful and the 2 peripheral nucleobases did not encode information.
The 4 original symbols selected between 4 major kinds of amino acids: the special amino acid glycine, an acid amino acid, a hydrophobic amino acid and an amino acid with intermediate behavior, like alanine or proline.
These variations would have been enough to build proteins with specific conformations.
The fact that a codon had 3 nucleobases, presumably to ensure the binding to transfer RNA molecules, even if only one of them encoded information, appears to have been a great luck, because this allowed later the expansion of the genetic code, because 3 bases give 64 combinations allowing the encoding of up to 64 symbols.
Most of the possible codons have remained ambiguous until today, but the number of encoded amino acids has increased slowly in time, up to 21, the most recent additions to the encoded set being those of the sulfur-containing amino acids, aromatic amino acids and selenium-containing amino acids.
As you say, there are disadvantages in using many kinds of amino acids, but there are also advantages, by allowing the creation of proteins with properties that are not achievable with a smaller set of amino acids.
The balance between advantages and disadvantages appears to have slowed down continuously the rate of adding new amino acids to the set encoded in the genetic code, so that the majority of the living beings of today have not added any new amino acid since several billion years ago.
Most of the expansions of the genetic code happened before the last common ancestor of all living beings of today, so that today there are very few living beings with more recent modifications in the genetic code.
Amino acids are useful because they can be easily joined together and split apart (via the C-N bond). But there are other types of "molecular glues" that are viable, like sulfur or phosphorus.
For instance it would be much less surprising if an alien life form used another kind of polymer to store information, instead of nucleic acids, than if it would not use amino acids. The fact that on Earth the living beings eventually used ATP and RNA appears to have been determined in great part by chance, while the use of amino acids seems to have been much more deterministic.
Some of the simple amino acids are very easy to be synthesized in abiotic conditions, which is why they are ubiquitous in many celestial bodies.
The advantage of amino acids is that they do not contain only one end that can be attached to other molecules, but that they contain two such ends. A molecule with only one connector would attach to another, forming a dimer, after which no further reaction is possible.
A molecule with two connectors, like an amino acid that has both a carboxyl end and an amine end, can be daisy chained into a polymer of arbitrary length. This allows building complex structures.
There are other molecules with two connectors, but they are much more unlikely to appear in abiotic conditions.
Thioesters, i.e. a kind of organic molecules that are bound by a sulfur bridge, like you mention, appear to have been much more important when life has appeared on Earth than today, but such molecules were important as intermediates in metabolic reactions, not as structural blocks, like amino acids, and there are no known naturally-produced molecules with sulfur that could be used as easily as amino acids to make molecules with arbitrary complex shapes.
It looks like on Earth the RNA was the initial replicant. RNA can be folded into complex shapes and can have catalytic properties in itself. Ribosomes that assemble proteins have RNA at the active site with proteins only providing structural framework.
That's why amino acids might not end up being so universal.
You can conceive other than nuclear-acids based replicant, using the same ubiquitous amino-acids to build a protein life not using RNA/DNA but some other encoding structure.
The question is what is the chemically most likely 'other'? Also, what could be alternatives for ATP/sugars?
But the adenosine "backbone" of the ATP is more-or-less arbitrary. Other forms of life can use something different. Or they might use the phosphorus bonds themselves where terrestrial life uses peptide bonds.
Disulfide bonds exhibit similar properties, and terrestrial life also uses them to give additional "rigity" to certain proteins. It's also likely a late addition to the genetic code, cysteine is nestled between two stop codons (it clearly used up the initially reserved block of the address space tagged for future expansion).
And if you look at meteorites, sulfur compounds are _much_ more common. Sulfur chemistry also doesn't require scarce fixed nitrogen that could only be replenished by lightning before nitrogen-fixing enzymes first evolved.
So I don't believe at all that exactly our RNA/amino acids are going to be universal.
On the other hand, the simple amino acids are known to be universal, both from chemical analyses of celestial bodies and from abiotic syntheses in laboratories.
In theory, sugars can be produced abiotically by the polymerization of formaldehyde. However, sugars are not very stable chemically and suitable catalysts for formaldehyde polymerization seem to be rare, because sugars are much less ubiquitous than amino acids in lifeless environments.
The role of phosphorus in biology is determined entirely by the property of the phosphate anions that they can eliminate water and condense into polyphosphates, then the polyphosphates can extract water from other molecules, forcing condensation reactions, which can be used for various purposes, e.g. for building polymers.
The nucleoside parts of ATP and related substances play only the role of a "handle", which can be used to control the location of the polyphosphate parts, so that they will perform their function where intended.
Thus for controlling the polyphosphates other molecules may also be suitable.
Disulfide bonds, which already exist in the pyrite mineral, must have had a crucial role in the origin of life. But their role is very different from that of polyphosphates, because they extract hydrogen, instead of extracting water, so they perform redox reactions, not condensation/hydrolysis reactions.
Thioesters are the sulfur compounds that can play the same role as ATP, by taking part in condensation/hydrolysis reactions.
There is no doubt that all the 5 elements H, C, N, O and S, which happen to be the most abundant electronegative elements in the entire Universe, must be used by any living being, since the origin of life. Whether phosphorus has also been used since the beginning, or it is a later addition, is uncertain, because thioesters could have been used originally for performing all the functions now done with phosphates like ATP.
Both nitrogen and phosphorus are affected by similar availability problems. While nitrogen is too volatile and most of it would always have been stored in dinitrogen gas, which is inert, instead of being stored in easy to use ammonia or hydrogen cyanide molecules (while hydrogen cyanide and carbon monoxide are now toxic for most living beings, it is likely that they both are very important for the appearance of life), for phosphorus the problem is that most of it is stored in insoluble phosphate minerals. This must have been alleviated around the origin of life by the fact that the early oceans were much more acidic than today, so much more phosphate ions would have remained dissolved in sea water, than today.
Unlike for phosphorus, there is no substitute for nitrogen in biology. The role of nitrogen in organic molecules is the same as the role of dopants in semiconductor devices. When nitrogen substitutes carbon in an organic molecule, that position in the molecule becomes positively charged, instead of being electrically neutral. These electric charges play very important roles in many chemical reactions.
The poor availability of nitrogen must have been the main constraint in the growth of the early forms of life, until the development of the nitrogenase catalysts that allow the use of dinitrogen from the atmosphere.
Similarly, it is likely that the earliest forms of life used carbon from carbon monoxide, whose lower availability limited growth until the development of a catalyst that reduces carbon dioxide to formic acid, which allowed the use of the more abundant carbon dioxide. Both catalysts, which are used to capture carbon dioxide and dinitrogen, appear to have used in their earliest variants molybdenum, or possibly the related tungsten. While molybdenum seems to be a later addition to the set of chemical elements used for life, iron, cobalt and nickel are all necessary for the appearance of life as catalysts, while potassium is also necessary since the beginning for maintaining the electrical neutrality of a water solution without producing solid precipitates that would cause death.
The abilities to use directly carbon dioxide and dinitrogen, which are the main constituents of most planetary atmospheres, and which were also the main constituents of the early atmosphere of the Earth, must have greatly expanded the environments suitable for life, which previously must have been restricted to small neighborhoods of hydrothermal vents or sources of volcanic gases.
Is it conceivable that instead of water, some other solvent can be used? Those ethane/methane lakes on Titan ...
However, such a replicant could appear only after a life form with metabolism already existed.
For replicating RNA, there must exist a complex system that extracts energy from the environment and uses that energy to synthesize nucleotides like ATP and then it uses additional energy to polymerize the nucleotides into RNA.
RNA itself or any other molecule capable of replication could not have had any role in that living system, because before the existence of replication, any molecule of RNA that would have appeared accidentally would have disappeared eventually, without descendants. Therefore the first molecule of RNA that has survived must have been self-replicating and it could not have other functions.
The first self-replicating RNA molecules have diverted resources from a pre-existing living being, by consuming nucleotides like ATP, which must have already been used long before the appearance of RNA, for implementing condensation reactions.
In other worrds, the first RNA molecule, i.e. the first nucleic acid molecule was a virus. Some of the present viruses might have had their origin as detached parts from some nuclei of cellular beings, but it is likely that most viruses descend from the primordial viruses and they have never been cellular life forms.
The cellular life forms must have appeared by symbiosis between a virus and a life form without nucleic acids.
It is a frequently believed myth that life requires a memory molecule, like a nucleic acid. This is a mistake perpetuated by people unfamiliar with engineering.
It is perfectly possible to have a chemical system that growths and replicates itself, without containing any molecule able to store arbitrary information, like a nucleic acid. The difference between such a chemical system and the cellular life forms of today has the same nature as the difference between a hard-wired processor and a microprogrammed processor, i.e. the nucleic acids play the role of the microprogram memory that controls the execution units of the processor, allowing the implementation of an arbitrary behavior by changing the sequence of microinstructions, while the hard-wired processor has a fixed behavior, which can be changed only by a redesign of its structure.
Information-storage molecules like the nucleic acids are without doubt necessary for the evolution of complex living beings, because they allow the random generation of a huge number of variants that can explore the solution space, from which survival will select optimized variants. The nucleic acids have brought to living beings the same kind of flexibility that programmable embedded computers have brought to various appliances, whose properties can now be changed by a software update, instead of a costly recall and hardware redesign.
In a "hard-wired" living being, evolution must be extremely improbable, because any change in some of its component molecules is likely to break the cycle of self-replication, leading to death without descendants.
In a self-replicating chemical system, there must be a long chain of chemical reactions, each using as input reactants the products of the previous reaction, while the first reaction in the chain must use the products of the last reaction, closing the cycle.
It is very likely that in such a self-replicating chemical system, peptides, i.e. relatively short chains of amino-acids, had a very important role in providing a scaffold that organized the chain of reactions.
Even today, most if not all living beings still produce so-called non-ribosomal peptides, which, unlike the proteins, are not produced by templates of RNA.
Unlike with the mechanism of protein synthesis by ribosomes, for now the mechanisms that establish the sequence of amino acids in non-ribosomal peptides are very poorly understood.
It is likely that at least some of the mechanisms of synthesis of non-ribosomal peptides are a remnant of the synthesis mechanisms used before the appearance of RNA.
Theory on the emergence of photosynthesis whereby chlorophyll-like structures first evolved from harvesting heat rather than light: https://www.inaturalist.org/journal/mjpapay/45240-the-first-...
Mind you, "soil" as we know it did not exist before life was there to create it. Geology as it exists on Earth does not exist on lifeless planets.