https://maps.app.goo.gl/pJYr6qiZnMdVwLJS6
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 :-)
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).
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-...
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.
They suggest that the soil can somehow catalyze metabolic reactions and break down complex carbohydrates without life but where would the complex carbohydrates come from?
I'm also curious how they could demonstrate that there isn't some sort of very constrained extremophile producing all their results that doesn't exactly colonize very well but will still function.
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, ?).
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.
Complete absence of anything like that is a pretty strong indicator by itself...
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.
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*.
Compare to this paper from 2003:
https://sci-hub.kvnp.top/10.1016/s0360-1285(03)00042-x
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.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?
that seems pretty major exaggeration
https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.0800...
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.
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.
Just about every molecule in every cell is already a maxwell's demon. They only fit together in specific ways.
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.
I thought the leading contenders were currently in tide pools?
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.
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.
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.
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".
Or "I read the Hitch Hiker's Guide to the Galaxy".
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.
> gravity is just launching countless trillions of parallel instances of the same computation, with nearly all possible initial starting conditions
Great take and conclusion, no issue with the playful language here. It makes sense that, entropy being a required output with time, and 'infinite' near isolated cases would find just about every way to create that entropy, to include the efficiency at creating it (life, as you said).
Lovely take. Earth is a supercomputer. And to play on sibling responses to your first comment, this supercomputer is solving the answer to life, the universe, and everything. The answer is entropy though, not 42
42
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 ...
But crucially, the speed of chemical reactions goes down by 2-3 times for every 10C. Ethane liquefies at -160C so most chemical reactions would be around 100000 times slower than at 0C. And many chemical reactions would not work at all because of the high activation energy.
It's possible that low-temperature life might utilize some highly unstable (at room temperature) compounds. But there are few low-energy pathways that can be used to _synthesize_ these compounds in the first place in nature.
These suggest that the life chemistry evolved in the proto solar cloud (and exploring the conditions in there would yield how that happened) and the life on Earth evolved from the already complex stuff that fell on it after the hadean phase.
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.
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.
But RNA alone is sufficient to template off itself and create new copies. It can fold into catalytic forms akin to folded proteins. It can even spontaneously generate into chains from the constituent monomers under certain assumed early earth conditions (1). There is a lot of literature behind this formation under various conditions. A lot of guestimates on what these conditions might translate to experimentally, but the general trend is that this seems to be possible under early earth conditions.
1. https://pubs.acs.org/doi/full/10.1021/acscentsci.5c00488
What is left is determining how the consitutent nucleotides might have formed. People have ideas on this though. This review is a bit old now but on topic at least: https://pmc.ncbi.nlm.nih.gov/articles/PMC6316623/#sec4-life-...
j16sdiz•1w ago
wagwang•1w ago
greenbit•1w ago
andrewflnr•1w ago