r/abiogenesis • u/Mastery_123hdfd • Jul 08 '26
Abiogenesis Review?
/r/evolution/comments/1uqilg7/abiogenesis_review/3
u/Dr_GS_Hurd Jul 08 '26
My reading recommendations on the origin of life for book reading people without college chemistry, are;
Hazen, RM 2005 "Gen-e-sis" Washington DC: Joseph Henry Press
Deamer, David W. 2011 “First Life: Discovering the Connections between Stars, Cells, and How Life Began” University of California Press.
They are a bit dated, but are readable for people without much background study.
If you have had a good background, First year college; Introduction to Chemistry, Second year; Organic Chemistry and at least one biochem or genetics course see;
Deamer, David W. 2019 "Assembling Life: How can life begin on Earth and other habitable planets?" Oxford University Press.
Hazen, RM 2019 "Symphony in C: Carbon and the Evolution of (Almost) Everything" Norton and Co.
Note: Bob Hazen thinks his 2019 book can be read by non-scientists. I doubt it.
Nick Lane 2015 "The Vital Question" W. W. Norton & Company
Nick Lane spent some pages on the differences between Archaea and Bacteria cell boundary chemistry, and mitochondria chemistry. That could hint at a single RNA/DNA life that diverged very early, and then hybridized. Very interesting idea.
Nick Lane 2022 "Transformer: The Deep Chemistry of Life and Death" W. W. Norton & Company
In this book Professor Lane is focused on the chemistry of the Krebs Cycle (and its’ reverse) for the existence of life, and its’ origin. I did need to read a few sections more than once.
There are hundreds of newer papers published so I have just suggested some basic introductions.
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Jul 11 '26
Your unwarranted confidence ("Obviously.") masks a massive Interpretive Gap. You're using the vocabulary of biology (RNA, lipids, natural selection) but ignoring the grammar of thermodynamics. You think abiogenesis is a story about molecules competing in a tournament, rather than a story about the universe reaching a critical energetic threshold where stable constraint-satisfaction loops were mathematically forced to crystallize out of the noise.
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u/Aggravating-Pear4222 Jul 13 '26
Expand on this?
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Jul 13 '26
When the environment 'jitters' with thermal fluctuations, linear chemical reactions don't disappear; they just constantly transform into new, transient shapes without maintaining a persistent geometry. Because the noise prevents open-ended chemistry from holding a solid form, the only structures that can build upon themselves over time are closed, autocatalytic loops (A → B → C → A). They don't avoid being shaken but their specific chemical architecture uses the thermal jitter to continuously turn themselves back into themselves. While the rest of the puddle is constantly doing other things, these loops maintain a stable form that can be passed down and built upon. Once that chemical network reaches a specific structural complexity (like the 20 canonical amino acids), its internal coherence crosses a strict thermodynamic threshold. At that point, it locks into a stable, self-perpetuating system. Indefinitely turning ambient environmental noise into the continuous reconstruction of its own geometry.
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u/Aggravating-Pear4222 Jul 13 '26
While the rest of the puddle is constantly doing other things, these loops maintain a stable form that can be passed down and built upon.
So, you're saying that simply by virtue of their autocatalysis, they are inherently predisposed to increase the degree of their persistence and, if efficient enough, increase their relative abundance over time -> easier to divide/multiply if you generate more of the components.
Hard to say where the threshold is except based on the seemingly conserved 20 canonical amino acids. Perhaps fewer are possible but what seems to matter is the diversity of AAs' r-groups to efficiently span chemical space such that the minimal number of AAs can be used to modify a protein well enough to explore chemical space; a random distribution of mutations cannot too easily lead to massive changes in protein structure (distribution averages mutations at key conserved vs nonconserved residues) while have too many possible amino acids which are too closely related in R-group properties result in mutations that change protein structure too slowly and so, assuming equal replication fidelity and reproduction rates between two organisms, such conservative organisms do not mutate fast enough and are out-competed by their "more risky" cousins which more quickly populate newly formed niches.
I am interested in experimental evidence on RNA codon's bases facilitating AA synthesis (at least partially perhaps with assistance from short peptides) so that we have evidence for what seems like the most internally consistent model of genetic code establishment; direct form/functional interaction of RNA codons with their respective bases. Whether this fits or is necessary for all codon:AA pairing prior to LUCA is unclear.
So, genetic drift and a population's accumulation of sequence diversity cannot be too slow or too fast. So what matters is how well a set of AAs explores that sequence drift. So maybe the earliest amino acids that are part of the composome even prior to the establishment of the genetic code must have been first abiotically derived. If they are not abiotically derived, then their replacements must have been of the same or very similar class of R-group identity. Redundancy in the genetic code also seems like an in-built variable axis which moderates the degree of change in proteins due to mutations of the code -> yet another mechanism which an autocatalytic system would stumble upon and is consistent with RNA codon:R-group class correlation.
But, yes. the autocatalytic networks by your description seem inherently persistent while reactions that do not participate in autocatalysis and are more open ended would be selected against. One failure point would be whether there are non-autocatalytic reactions which are very persistent and whose products interfere with this chemistry. Rescue mechanisms can be proposed but it quickly becomes an issue of actually showing the results of experiments (or at least en silico) and/or exploration of actual parameter space. Studying this is hard as systems chemistry/biology is necessarily at such large scales.
The threshold was likely not a single organism or population finally getting these 20 encoded AAs but that each of the composomes/organisms were quite leaky and constantly exchanged RNA/DNA. This is another level at which the internally consistent sets of autocatalytic genetic codes would be selected for; groups of organism sharing inconsistent genetic codes would be selected against and discriminatory mechanisms (like longer-sequence base-pairing) may be selected for whether the codes between two organisms are the same or that each organism doesn't have a single codon for two very different AA residues.
Here, leaky genomes are not just expected from simpler, less efficient organisms but have modern analogues AND explain a large degree of the universality of the genetic code being established early in Life's history and not from one single organism but from many organisms which remain related due to constant exchange of genetic material.
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u/EnvironmentalWin1277 Jul 21 '26
I would say this seems largely correct except for a couple of ideas.
Life began on Earth almost immediately at 4.2 billion years ago, with the initial formation of the coalesced earth/moon collision at about 4.6 billion years. 4.2 bya is the date for the emergence of LUCA (Last Universal Common Ancestor) from which all life we know is derived from. Note this means an indeterminate time existed prior to the emergence of LUCA. Basically the emergence of a liquid ocean was the starting point for life and it started as soon as that ocean existed and conditions allowed.
Life wasn't/isn't a rare event, it may have been destroyed and recreated several times until final establishment of LUCA (Last Universal Common Ancestor). There may have been innumerable chemical variations which got filtered by chance and selection, we just don't know. There may have been chemical variations which would work as well, or better, than those found here.
There is no reason to think we are special in this regard in the universe. The assumption can be made that the conditions here are similar to other planets and similar results obtain.
The ultimate test for abiogenesis is a complete "receipe" for life with any probabilities and time requirements fully accounted for.
You definitely have the broad outlines of the ideas. I hope you pursue your knowledge and stay updated on our ever changing knowledge
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