RNA world Archives

a) Biological evolution as stochastic optimization: Initially, wild-type cells x grow up a population. A mutant y grows up a population. The populations x and y compete. The winner (greater population) then fetches more resources. Fitness landscapes at the bottom show how the mutant is an experiment, where the winner decides the next step direction. b) Evolution annotated in terms of the Central Dogma: (Left, green) Wildtype starting point, NA encodes PR, which gives fitness F. (Top, red), Mutation in the blueprint NA, becoming NA’. (Red, green) both NA sequences grow up into populations. (Next) The populations compete for fitness. The winner, Fx now carries with it the winning sequence NAx and protein P Rx. -- [biorxiv.org]

RNA And Proteins Joined Up At The Origins Of Life: Persistence Is The Point

by Keith CowingJuly 21, 2026July 21, 2026

[biorxiv.org] What drove nucleic acids (NA) to associate with proteins (PR) at the Origins of Life? We reason from polymer physics and the Central Dogma (CD) that the fitness value […]

An RNA library containing a partially randomized sequence having an estimated complexity of ~1014 sequences

Origin & Evolution of Life

How Early RNA-based Life May Have Repaired Its Genome

by Keith CowingJuly 14, 2026July 14, 2026

[University of Notre Dame] In most modern cells, DNA stores the genetic blueprint, and relies on proteins to replicate, repair and build from those blueprints. At the same time, proteins […]

The contentious role of RNA in early evolution. The arrow represents the evolutionary trajectory from protobiology to the biological cell, with Protogenetics and the RNA-World as critical intermediary stages. The RNA-First paradigm implicitly assumes not only that RNA was fundamental to the emergence of genetic material but that the protobiological stage itself was already dominated by RNA chemistry, which this essay argues is incompatible with the combinatorial vastness of abiotic environments. -- Life

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

The RNA-First Fallacy: Conflating Evolutionary Ancestry with Prebiotic Primacy

by Keith CowingJune 11, 2026June 11, 2026

The RNA-World hypothesis remains the most widely accepted framework in origins-of-life research, anchored in compelling biochemical evidence for RNA’s deep evolutionary ancestry. However, this viewpoint routinely extends beyond that and […]

A very early stage in the origin of life on Earth -- Grok via Astrobiology.com

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life, Status Report

Membrane Information Organization At The Origin Of Life: From Interfaces To Informational Bodies

by Keith CowingMay 27, 2026May 27, 2026

Membranes are usually treated as passive containers in origin-of-life models, confining prebiotic chemistry, buffering diffusion, and sustaining gradients.

Evidence for ribozyme mass extinction. (A) Abundance distribution across all ten known small self-cleaving ribozyme families, showing the hammerhead's 91% dominance, a pattern characteristic of disaster taxa following mass extinction events. (B) Circular phylogeny of 80,548 unique hammerhead sequences colored by host taxonomic group. The star-like topology is consistent with post-bottleneck radiation, and the interspersion of distantly related host phyla around the tree reflects repeated independent colonization events rather than co-speciation, consistent with horizontal transfer of a single dominant survivor lineage. (C) Null distribution tests for Tajima's D (left) and Fu's Fs (right), each based on 10,000 coalescent replicates (n = 200, S = 40). Blue and orange histograms show the null distributions under neutral expectations; red dashed lines indicate the observed values (D = +2.28, upper-tail p = 0.013; Fs = −618.0, p < 0.0001). Observed D falls in the extreme upper tail (98.7% of null replicates below observed), indicating deep hierarchical structure; observed Fs falls far below any null replicate, indicating massive haplotype excess. The discordance between positive D and extremely negative Fs is diagnostic of ancient divergence preserved through a bottleneck followed by rapid within-lineage expansion. Full-sample values (n = 5,036) are D = +3.79, Fs = −690.8. -- biorxiv.org

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

A Ribozyme Mass Extinction At The RNA-cellular Boundary And Its Potential Imprint On The Genetic Code

by Keith CowingApril 13, 2026April 13, 2026

The transition from the RNA world to cellular life remains one of the least understood events in the history of biology.

HCN rainout rate over the conjoint parameter space of stellar effective temperature (Teff ) and effective solar flux in current Earth values (Seff ) and C/O ratio. a) Baseline Archean Earth C/O ratio of 0.514 with the black box on the plot and gray horizontal line on the colourbar representing the Archean Earth model and estimated maximum HCN delivery rate by meteorites, respectively; b) Histogram of all simulated HCN rainout rates with gray, black, and pink vertical dashed lines representing the estimated maximum exogenous HCN delivery rate, the Archean Earth model, and the median HCN rainout rate, respectively. -- astro-ph.EP

Astrochemistry, Atmospheres, Climate, Weather, Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Exoplanets, -moons, -comets, Genomics, Proteomics, Bioinformatics, Habitable Zones, Impact events, Meteorites & Asteroids, Origin & Evolution of Life, Status Report

Atmospheric Supply Of HCN Is Not The Rate Limiting Step For Prebiotic Chemistry Across Rocky Exoplanets

by Keith CowingMarch 22, 2026March 22, 2026

Hydrogen cyanide (HCN) is crucial for the RNA World hypothesis, forming biomolecules essential for early life.

Ribozymes are relics of molecular life forms

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life, Status Report

Modularity, Ecology, And Theoretical Evolution Of The Ribozyme Body Plan

by Keith CowingMarch 12, 2026March 12, 2026

Ribozymes are relics of molecular life forms from the primitive earth that are embedded within modern genomes across all kingdoms of life. Despite significant knowledge from decades of bioinformatic and […]

Kinetic processes of the strand-based RNA reactor model [12,13,15] and their projection onto motif kinetics. We consider heteropolymer strands consisting of the two complementary nucleotides X and Y, which could represent RNA or DNA nucleotides. (a) Schematic of the reactions within the strand reactor, including hybridization, dehybridization, templated ligation, and cleavage of oligonucleotide strands. Strands that are not covalently linked are separated by small gaps; four-nucleotide motifs, including 3′ or 5′ ends, are highlighted in green. In templated ligation, a 3′- and a 5′-end motif build a six-nucleotide motif that contains three overlapping four-nucleotide motifs. (b) At the level of sequence motifs, the kinetics are based on motif production and motif breakage reactions. In four-nucleotide motifs, strand ends are marked with 3′ or 5′, respectively. Templated ligation generates longer strands containing additional motifs, thereby contributing to motif production, while strand cleavage leads to to motif breakage. Hybridization is not explicitly represented in the motif-level description; instead, it is implicitly incorporated into the rate constants for motif production and breakage by assuming a hybridization-dehybridization equilibrium and deducing the corresponding dissociation constants. -- Physical Review E

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Sequence Motif Dynamics In RNA Pools

by Keith CowingMarch 6, 2026March 6, 2026

In RNA world scenarios, pools of RNA oligomers form strongly interacting, dynamic systems, which enable molecular evolution.

Unity of biopolymer biosynthesis, assembly and recalcitrance is predicted by chemical evolution.

Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Origins Of Life: Chemistry And Evolution

by Keith CowingJanuary 23, 2026January 23, 2026

Direct chemical synthesis and chemical evolution are conceptually different models for the prebiotic origin of RNA and other biopolymers. These models generate distinct predictions and motivate different experimental approaches.