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, ?).
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".
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.
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.
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.
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 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.
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.
"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."
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.
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
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?
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.
> 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.
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!
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.
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.
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.
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.
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.
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…)
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.
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.
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.
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.
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).
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.
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.
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.
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.
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.
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.
> 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.
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.
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.
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.
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, ?).
> 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".
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.
> eddies in the stream of energy flowing downhill
"Ah... is he. Is he."
I don't know, but I'm pretty sure it's got something to do with laboratory mice.
The answer to life, the universe and everything, I guess?
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.
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]
[1] https://en.wikipedia.org/wiki/Warm_little_pond
"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.
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.
Well, yeah. Starting from absolute scratch is a lot harder than adapting something that already exists to new conditions.
I really like the way you think.
The Buddha nods.
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.
https://maps.app.goo.gl/pJYr6qiZnMdVwLJS6
https://www.atlasobscura.com/places/brookhaven-gamma-forest
https://www.youtube.com/watch?v=GsuiLxcDuHY&t=925s
> hardly anything grows there, almost 50 years later.
that seems pretty major exaggeration
https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.0800...
That's a bit odd - why wouldn't wind blown non-sterile organic matter from the surrounding forest re-colonize the area?
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.
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.
"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."
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.
https://en.wikipedia.org/wiki/Mycorrhiza
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.
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
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?
That "circular bit of road" is the Relativistic Heavy Ion Collider, the second highest-powered particle accelerator on the planet.
https://en.wikipedia.org/wiki/Relativistic_Heavy_Ion_Collide...
"Was" It shut down earlier this year.
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 :-)
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.
It's a Department of Energy facility. The primary purpose of the DOE is to further the development of nuclear weapons.
> 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.
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!
Reminds me of the abiogenic petroleum: https://en.wikipedia.org/wiki/Abiogenic_petroleum_origin
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.
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.
That is not dead which can eternal lie, And with strange aeons even death may die.
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.
The leading theories for the origins of chemical evolution (abiogenesis) actually focus on deep-sea hydrothermal, alkaline vents
> 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?
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.
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.
You might be thinking of something else. UHT has a very long shelf life compared to other forms of liquid milk.
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…)
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.
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.
It feels next would be trying isolate the component that make CO2. Try to use smaller sample. Put them under microscope, etc.
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.
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.
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?
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.
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.
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.
[1] https://www.nasa.gov/news-release/nasas-asteroid-bennu-sampl...
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).
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.
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.
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.
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.
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.
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.
> 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.
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.
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.
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-...
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.
Obligatory Asimov: 'The most exciting phrase to hear in science, the one that heralds the most discoveries, is not "Eureka!" but 'That's funny...”'
Yep. The most interesting places in science are where the model breaks down.
Life uh, finds a way.