Scientists discover new “origins of life” chemical reactions
scripps.edu
scripps.edu
An analogy would be writing an article about the natural abundance of silicon on beaches and calling it "how computers are made."
We have a decent idea of how the first nucleic acids may have been synthesized, and we have a decent framework for how life evolved from protobiont to prokaryote to eukaryote to multicellular organisms. But there is an absolutely staggering gap between the synthesis of individual nucleotides and the synthesis of the first RNA replicase that we know nearly nothing about.
How is it not origins of life research to attack every step in the process?
If a student asked "how did life originate?" a response about about nucleic acid synthesis would be a bit disingenuous, because that covers only very, very tiny fraction of the surface area of the problem. The more honest answer would be that there are so many large gaps in our knowledge that we truly don't know.
To be clear, I'm not trying to cast skepticism on the whole of biology. There are other questions that we have much better answers to, like the evolutionary pathway from single cellular life to multicellular life. Or the evolutionary link between humans and great apes. But abiogenesis is not one of those questions.
Are the gaps really that large? We know that some configurations of nucleotids are enough to create a full metabolism, we know that they arrange at random, and we know how most of them appeared.
Except for the few nucleotides that we don't know how they existed, we do know that if you have enough of them on enough places, some kind of life will appear. So looks like the open question here is how those molecules appeared.
It's theorized that under the right conditions amino acids will bond to become proteins without needing the mediation of a ribosome. So it's certainly possible that with enough primordial soup you could get proteins. But that doesn't explain how the nucleotide string ends up getting treated as a reusable blueprint for proteins.
That seems like a pretty big gap.
Also, people have created RNA-only self replicating mechanisms that could quite well appear at random, with extremely low odds. Life probably comes from some structure with higher odds that we don't know about, but that's not a huge gap.
iirc the idea centered around the tRNA "code" having a pattern to it - one shaped by its binding affinity to part of the sequence that codes for the tRNA-aminoacyltransferase enzyme itself. I wish I remembered enough to find the reference.
edit: ah! think I remembered. the hypothesis was that the codon sequence had some sort of binding affinity to the amino acid it codes for. that there's a relationship between them, suggesting a world where codons attracted amino acids to bind to them without an enzyme linking them.
As the article title does not say or imply that the answer to this question has been found, let alone that it will be revealed in the article, this is at least beside the point.
In attempting to brush aside gliptic's pertinent question, you have switched to a general (and somewhat subjective) claim that does not seem to hold up in this specific case.
That, imo, is far more important.
We already had adding machines and the philosophy necessary for digital logic.
It may well be the case with the original system that initiated the process we call life. RNA (and by extension DNA) may have been a complete afterthought.
I'm always disappointed when I see this research outside of a systems context. Like, sure we can show these things happen, but show me a thermodynamic systems, in place,where this can happen.
In you metaphor about sand and beaches, this may be like taking some one to a dune field and saying 'see all this sand. That's where computers come from'.
Computers don’t arise randomly (without annoying semantic arguments).
If you believe the human brain's processes are computable, and you believe evolution is a random process, then you believe that computers arise randomly.
Is that what you mean by "annoying semantic arguments"?
Discussions of what constitutes a computer in this context or whether an nth order effect of a “random” process are just distracting.
You are right. They don't.
If you throw construction materials up 1 quadrillion times, how many times can they randomly fall in the form of a house?
My response is zero. Building a house is not a product of randomness, it's a product of intelligence and will.
Life also can't be a product of randomness. There's some intelligence and will going on in nature's laws to make life happen.
Or, perhaps you're arguing that the rules of the universe were designed in a way that guaranteed that life would arise?
Something else?
To me, Universal laws aren't random. If they were, I'd expect them to change from time to time.
These laws are immutable and inexorable. They respect, interact and cooperate perfectly with each other.
How did they come to exist and be that way if not by intelligence and will?
I have no idea how this works or came to exist, but it definitely doesn't look random to me.
And the universe also has a bunch of repeated structures, so why wouldn't a universe also be a repeated structure? A heart is a common one found in many different animals. They are each different in their own way, but it is a structure that is repeated. Same with atoms. They all follow the same basic structure, but it is repeated with just various configurations.
> The thermodynamic dissipation theory thus assgins an explicit thermodynamic function to life; the dissipative structuring, proliferation, and evolution of molecular pigments and their complexes from common precursor carbon based molecules under the impressed short wavelength solar photon potential to perform the explicit thermodynamic function of dissipating this light into long wavelength infrared light (heat). In a general sense, the origin of life is no different than the origin of other dissipative structuring processes like hurricanes and the water cycle, except that these latter processes deal with structuring involving hydrogen bonding while life deals with structuring involving covalent bonding. The external photon potential supplied continuously by the environment (our Sun), and its dissipation into heat by the assembly of dissipative structures, are, therefore, both integral components necessary for understanding life.
https://encyclopedia.pub/entry/6923
> The formula, based on established physics, indicates that when a group of atoms is driven by an external source of energy (like the sun or chemical fuel) and surrounded by a heat bath (like the ocean or atmosphere), it will often gradually restructure itself in order to dissipate increasingly more energy. This could mean that under certain conditions, matter inexorably acquires the key physical attribute associated with life.
https://www.quantamagazine.org/a-new-thermodynamics-theory-o...
Even if you claim there is a single god that created both of these things, backwards deriving the seed necessary to generate the current state, it still routes through this physical process which is describable with physics and could be extrapolated to other starting conditions or future scenarios that humans can utilize.
It makes no difference.
Some argue the origin is in the - supposedly random - combination of molecules.
Others think the answer is deeper and relates to more fundamental aspects of nature.
no, it's by backpropagation. error is propagated and minimized. simple equations lead to emergent complexity.
canyons form as water follows paths of least resistance, and incrementally erode rock. the water doesn't use its intelligence and will to construct a canal, even though the resulting river system looks like a max flow solution.
the intelligence and will emerges from the math. simple systems with enough feedback can become very sophisticated.
We're not discussing how things act intelligently, but rather why, what's the origin of the intelligence in the process.
Some argue there's no intelligence, it's just randomness. Others think this is not a rationally acceptable explanation for what nature is showing us.
If you arrange your biological soup a large number of times randomly, you will eventually land on a pattern that causes other nucleotides to arrange in a similar or improved pattern around it.
Not too dissimilar from thinking about the creation of specific atoms through various astronomical processes.
Even if you need to believe in god for some reason, it’s not incompatible with god defining the organic chemical reactions that enabled life to form via random interactions of nucleotides until they happened to land on god’s lucky number
It depends on what you call a house.
It will probably never fall in any given expected shape.
It may very well fall into multiple configurations that someone arriving at the scene after the fact, and without prior knowledge of what you expected when you run the experiment, would call a "house".
What it needs to form is any kind of a shelter that is better than not a shelter. A 4x8 sheet of plywood that happens to lean against a brick forming a roof is all that is required for a first house.
Life is a product of randomness. There is no intelligence or will going on in nature's laws. Neither of those things are required.
Would we conclude that everything in the Universe is alive?
I think that's a pretty interesting way of seeing things. And (to me, personally) it strengthens my view that there are intelligent processes going on in the Universe.
What is necessary for life to arise from a random stew of disorganized chemicals is far more than just a good arrangement of a few molecules that exhibit some characteristics of life. Since all life dies as part of the never-ending march toward entropy, you also need to be capable of some form of reproduction and able to carry out reproduction at a faster rate than death. What is the minimum complexity involved in such a thing? I'd argue that it's probably more complicated than any house in existence.
nucleotides spontaneously form, then start to bind to each other in chains. Those chains spontaneously fall apart and reform.
amino acids start to bind to the nucleotide chains and cause them to be more stable. Nucleotide chains bound to the amino acids have a longer life expectancy than those not bound to amino acids. The amino acids start to bind to each other (they naturally do). The RNA binding makes them slightly more energy efficient essentially catalyzing the reaction.
over millions or billions of years, random chaining of nucleotides leads to random chaining of proteins that are slightly more energy efficient. Those forms "outcompete" alternate forms.
Once a particular type of amino acid chain exists, it can influence other amino acid chains to follow the same structure. For example prions are extremely short but binding to normally folded versions of the protein causes the normal version to change patterns.
one of the interesting constraints is you don't have billions of years. Life appeared on Earth within 100 million years of the planet cooling down enough to have standing water, possibly even less, depending on your reading of the evidence that gets more disputed the farther back you go.
It took 2 billion years for prokaryotes to turn into eukaryotes, and it took another billion for eukaryotes to go multi-cellular, but somehow the initial development of a self-replicating cell with a code took less than a tenth of that.
And how do you suppose the intelligence you refer to originated? You're not offering a solution, you're merely adding another layer of complexity that still needs an explanation along the same lines.
So in your example with the house here is how it might be:
Throwing 1 quadrillion times materials will they arrange in a fundation? Of course. Then throw again and will there be some kind of wall or pillar?
Then you now have foundation and pillars. Throw again a huge number of times, will there be materials that might form a wall?
Please also take into consideration that evolution is not only in a vertical progression (from materials to house) but also running horizontally (like creating multiple types of walls of all shapes before going for a roof).
But more importantly evolution will not create a house as long as there is not need for one.
On the other hand, as we are poaching the limits of science: how do you know that given a close to infinite number of arrangements those materials will not arrange into a house?
Darwinian evolution in the narrow sense is duplication of life plus random variation plus filtering (that may also be random, but which at a minimum contains some bias which is, if not consistent over time, at least usually changes very slowly compared to the rate of random of variation.)
Darwinian evolution in the broad sense is the same thing, but without the “of life” part.
But abiogenesis is not Darwinian evolution in the narrow sense, and may or may not significantly involve Darwinian evolution in the broad sense, so arguing about what evolution is or is not in the context of the initial creation of life as opposed to the explosion of diversity of life after its initial creation is, at best, skipping steps.
Intelligence fits into this in interesting ways. One way to consider it is as a guide to the assembly process from less complex from more complex.
As if, contrary to that, humans do/did.
To be fair, the probability gets closer to one if you expand your view to include the entire universe and assume that it is many, many orders of magnitude larger than the visible universe. But my take away, at least, is that we are not dealing with a situation where random assembly of RNA is so likely to generate self-replicating sequences that abiogenesis was effectively an inevitability. That was the narrative I was sold in grade school and undergrad, but it appears to be wrong.
There are a good number of free parameters in the journal article that I linked: The fraction of RNA sequences that are self-replicating, the fraction of planets that are habitable for life, the average decay rate of RNA on a habitable planet, etc.
You take can take issue with the empirical estimates for those parameters, but that points to missing pieces in the framework: Was there a chemical process on early earth that stabilized RNA oligomers that no longer exists? Are self-replicating RNA sequences more common than we believe? If so, why haven't we encountered more of them in nature? And so on. In my opinion, these are the truly interesting questions, not whether nucleotides and amino acids can form spontaneously.
[1] https://www.nature.com/articles/s41598-020-58060-0
[2] https://mathscholar.org/2020/05/the-origin-of-life-in-an-inf...
Is that meaningful? No matter how unlikely our existence is, here we are.
But it parallelizes extremely well - throughout the entire universe for billions of years.
And then of course there’s https://en.m.wikipedia.org/wiki/Panpsychism.
Almost certainly yes.
> If so, why haven't we encountered more of them in nature?
Because they can't compete with modern life. Nearly all of the biomass on earth is in use. A primitive replicator, even if it arose today, would have to compete for resources against all the existing life on earth. It wouldn't stand a chance. This is the reason there is only one universal common ancestor. It's not necessarily that abiogenesis only happened once, it's that only the descendants of one common ancestor survive today. All traces of all other abiogenesis events have been obliterated.
You have to compute the abiogenesis odds for an environment that, by definition, does not yet include life. Here is a rough back-of-the-envelope approximation: the biomass of earth is about 2^52kg. Avogadro's number is 2^76. So there is the potential for the early earth to have 2^120 nucleotide bases and amino acid molecules floating around. If the complexity of a simple replicator is around O(100) bits then the odds of finding one by chance when you are rolling that many dice in parallel approaches 1 in just a few million years. After that, evolution takes over.
Second, yes, today's world has an enormous amount of amino acids and nucleic acids, but that is after billions of years of enzyme-catalyzed synthesis inside trillions of living cells. The prevalence of amino acids/nucleic acids prior to abiogenesis would have been orders of magnitude lower in a world where those enzyme pathways didn't exist yet and biologic molecules with catalytic activity were still in the process of being bootstrapped.
Third, does your back of the envelope calculation account for the very short half life of RNA? That is really the biggest issue. If RNA didn't decay, then forget about hundred base sequences; the primordial earth might have been filled with million base sequences.
The figure I cited is the carbon biomass.
https://www.visualcapitalist.com/all-the-biomass-of-earth-in...
> that is after billions of years of enzyme-catalyzed synthesis inside trillions of living cells
Doesn't matter. What matters is the size of the search space that could be explored by the chemistry, and if even a single replicator exists in that search space. The extent to which that first replicator resembles present-day life is irrelevant. The only reason to refer to that at all is to get some idea of what the information content of a minimal replicator is.
> Third, does your back of the envelope calculation account for the very short half life of RNA?
Again, it doesn't matter. As long as the half-life of the replicator is more than the time it takes it to produce >2 offspring, that's enough to get the ball rolling.
This may be the original article discussing this hypothesis:
"The ribosome as a missing link in the evolution of life" (2015) Root-Bernstein & Root-Bernstein, J. Theoretical Biology
https://sci-hub.se/10.1016/j.jtbi.2014.11.025
> "Evolvable entities existing between self-replicating polymers and fully functional cells would presumably have many, though not all, of the functions of a cell, yet be significantly simpler in composition and organization. These entities would be able to self-organize and replicate themselves; store information and replicate that information; translate the information into the components necessary to produce their functional structures; capture metabolic components and energy; and transform these into useful biochemical networks. Norris and his colleagues have called functional forms of organization midway between macromolecules and cells “hyperstructures” (Norris et al., 2007). Such hyperstructures had to be instantiated as evolvable entities, meaning that their components would be subject to variation, replication and natural selection."
Really? Nucleotides are already too complex to have been produced in any valid OoL experiment at more than vanishingly small concentrations. Experiments that demonstrate some chemical X can be produced, and then lead to another experiment where X is made available in pure form at high concentration (and then rinse and repeat down the synthesis chain), don't tell us anything interesting at all.
RNA-Peptide coevolution is the spontaneous immergence of 'replicating' matter. No one molecule in the system has all the requisites for life, but as a whole they do. (I.E.amino acids and nucleobases can transmit information, replicate, move and 'sense' about the world). Pushing this idea of self-replicating orgiins of life back may illuminate the issue. RNA generation doesn't have to be random, it can be selected for like any other evolutionary proceses.
Finally, Listen to what you are saying... The rhetoric was much different 10 years ago.
We have scientifically narrowed the limit of what we can't explain, and this very small gap in our knowledge is what's left. We are making progress in understandng the origins of life.
- free energy powers growth
- growth is thermodynamically favorable
- heredity is growth, doubling by exact copying
- growth combines carbon and energy metabolism
- growth is driven by environmental disequilibria
That doesn't explain away the mystery of the first RNA replicase, but I really like how it explains growth and doubling as a form a growth. That's copy-pasted from a newsletter draft I'm writing. It'll be posted next week on https://0123.substack.com
Paul Falkowski's Life's Engines is also quite good.
This is all well and good, interesting chemistry even.
However, α-keto acids are not the kinds of things just laying around. These are reactive species and so would interact in a variety of ways with environmental nuclophiles, oxidants, and other stuff.
The article doesn't link to the study in question, which is unfortunate and inexcusable. It does link to a study on a different system earlier this year.
Origins of life research has been plagued with efforts that front-load the problem in various ways. For example, how do we make proteins abiotically? How do we make sugars abiotically?
Load up a flask with all the amino acids you want. Zap it with whatever you want in terms of energy. At the end of it you won't have much but a mess.
There seem to be fundamental principles we're missing that go beyond reaction pathways. Not many people are working on that problem. It's extremely risky for both PIs and students, and almost impossible to fund.
https://www.nobelprize.org/prizes/medicine/2009/szostak/lect...
The discussion is really incredible. It really changed my naive perspective of life, and the universe.
R-C(=O)COO -- (CO2, "NH3", CN-, H2O) --> R-Hydantoin (?) --> aminated amino acid --> alfa-amino acids
where R = {H, CH3, CH2COO}.
(ps : Apologies to any chemists reading this...)
We don't even have a clear definition of tall—is a person 6' 4" tall? How about 6' 3"? Or 6' 2"? Or 6' 1"? And yet a building 6' 4" high would be tiny. What about a rock—is a rock high 6' 4" tall?
But, a good definition must come after understanding, not before. And, just because something doesn't have a precise definition or understanding doesn't mean that understanding can't be improved, or even branched, in the form of a discovery, to create some new label that better fits the concept.
Until then, we have to live with something fuzzy, with the understanding that it is somewhat incorrect (which anyone familiar with biology will happily tell you). Lack of definition, which is lack of understanding, doesn't impede discovery. Lack of definition and understanding are necessary requirements for discovery.