biorxiv.org Archives

Heterogeneous degree distributions. a) The Hot Jupiter chemical reaction network's degree distributions are represented by its complementary cumulative density function (CCDF) versus degree k. Homogeneous and heterogeneous fits corresponding to exponential and power-law degree distributions, respectively, work equally well. b) Same as a), but for the ORD chemical reaction network. A power-law degree distribution is a better fit. c) Power-law fit exponent 𝛂 versus average degree. Marker sizes describe the size of the network and marker shapes describe the most likely distribution. -- biorxiv.org

Biochemistry & Organic Chemistry, Biosignatures & Paleobiology, Exploration Gear & Tech, Imaging & Spectroscopy, Missions & Hardware, Status Report, Tricorders & Sensors

Tricorder Tech: Agnostic Tools for Life Detection: A Multiscale Approach to Biological and Chemical Reaction Networks

by Keith CowingSeptember 3, 2025September 3, 2025

Life manifests itself across a variety of different operative scales, ranging from molecular networks up to ecologies.

Spread of niche constructors across a metapopulation through diffusion This simulation introduces the diffusion of units across microenvironments.

Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Microbiology & Virology, Nanotechnology & SynBio, Origin & Evolution of Life, Status Report

A Niche Construction-based Perspective On Chemical Evolution Before Replication And Reproduction

by Keith CowingAugust 4, 2025August 4, 2025

Conceptual analysis has, in the past decades, established that evolution by natural selection (ENS) can occur without reproduction (1–6). This theoretical advancement has significant imports for research on the origins […]

Model depicting the importance of RNP condensate in mediating survival under Mars-like stress condition -- biorxiv.org

Atmospheres, Climate, Weather, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Mars, Origin & Evolution of Life, Status Report

Ribonucleoprotein (RNP) Condensates Modulate Survival In Response To Mars-like Stress Conditions

by Keith CowingJuly 15, 2025July 14, 2025

Scientific advances have emboldened human efforts toward exploring the potential of extinct, extant, or future life on Mars.

Microscopic images of DA:DOH (1:1) vesicles under different conditions. Vesicular flocculation can be observed upon addition of NaCl, as well as reduction in the number of visible particles upon addition of MgCl2. Staining with Rhodamine 6G. Scale bar: 5 µm; Red arrow - unilamellar vesicle; yellow arrow - possible multilamellar vesicle; blue arrow - punctate structure; green arrow - flocs. -- biorxiv.org

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

Peptides At Vesicle And Mineral Prebiotic Interfaces

by Keith CowingJuly 15, 2025July 14, 2025

The origin of life likely involved a complex interplay between organic molecules and mineral surfaces, yet the molecular details of these interactions remain poorly understood.

Normalized nosZ transcript abundance in metatranscriptomes of marine (red) and lacustrine (green) euxinia. Shown is the ratio of nosZ to rplF transcripts for comparison across 245 datasets with different sequencing depths. Estimates of sulfide concentrations in Proterozoic oceans are shown with dotted vertical lines, with recent estimates in pelagic regions around 2-5 µM (Ozaki et al., 2018). biorxiv.org

Beta Pictoris, Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biosignatures & Paleobiology, Gaia - Planetary Perspectives, Genomics, Proteomics, Bioinformatics, Habitable Zones, Microbiology & Virology, Origin & Evolution of Life, Status Report, Water/Hycean Worlds & Oceanography

Microbial N2O Reduction in Sulfidic Waters: Implications For Proterozoic Oceans

by Keith CowingJuly 14, 2025

Throughout Earth’s history, shifts in ocean redox influenced the bioavailability of trace metals, shaping the activity of microorganisms.

Multi-layered pipeline for identifying bacterium/archaeon pairs with similar genomic signatures. Layer 1: Five selected non-parametric clustering methods identify clusters of organisms with similar genomic signatures. The clusters containing both bacteria and archaea (green) generate a list of 78 candidate bacterium–archaeon pairs, grouped by these algorithms based on their similar genomic signatures. Layer 2-a:: The candidate pairs from Layer 1 undergo pairwise distance calculations between their FCGRs using four different distance metrics. Only 40 pairs, with the majority of distances below empirically determined thresholds, are retained. Layer 2-b: In parallel to FCGR comparison, a biological analysis is conducted on the output pairs from Layer 1. This includes checking environment labels and examining metadata about their living environments to select pairs isolated from similar types of extreme environments, resulting in 20 pairs. The final output is a list of 15 bacterium/archaeon pairs (comprising 16 unique genera and 20 unique species) that passed all filtering layers. These pairs can confidently be proposed as maximally divergent microbes that share similar genomic signatures associated with their living environments. -- biorxiv.org

AI - Data - Apps - Cybernetics, Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Extremeophiles and Extreme Environments, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Nomenclature, Systematics, Natural History, Status Report

Life At The Extremes: Maximally Divergent Microbes With Similar Genomic Signatures Linked To Extreme Environments

by Keith CowingJune 30, 2025June 28, 2025

Extreme environments impose strong mutation and selection pressures that drive distinctive, yet understudied, genomic adaptations in extremophiles.

Biochemical requirements and toxicities for oxygen, iron and sulfide restrict conditions for endosymbiosis: Iron, sulfide and oxygen readily react with one another, leading to reservoir fluctuations that characterize Paleoproterozoic marine chemistry. A narrower set of interactive conditions involving these three chemicals (dotted box) are circumscribed by the context of cellular homeostatic constraints, which differ among organisms. Iron is biphasic: it is essential at lower cellular concentrations but toxic at higher cellular concentrations. Iron and oxygen homeostatic constraints must have been operable within archaea and bacteria across the process of endosymbiosis, up to and including full endogenization of the mitochondrion into a eukaryotic organelle. -- biorxiv.org

Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Microbiology & Virology, Origin & Evolution of Life, Status Report

Did Iron Suppress Eukaryote Emergence and Early Radiation?

by Keith CowingJune 29, 2025June 28, 2025

The last eukaryotic common ancestor (LECA) is widely thought to have been an oxygen-respiring organism, arising through endosymbiosis when a free-living bacterium became the mitochondrion.

N-isotope fractionation values observed in this study compared to the sedimentary δ15N record a, and known ranges of extant microbial biomass b, The sedimentary database includes bulk rock δ15N (dark grey) and kerogen δ15N (light grey), from both marine and nonmarine rocks across a range of very low to moderate metamorphic grades22,39,40. The purple bar in a and b represents the average fractionation signature of all ancestors in this study and is largely coincident with the minimum d15N values seen in the rock record which are presumed to record nitrogen-fixation unaffected by subsequent nitrogen cycling. The partial range of bacterial and fractionation signatures are labeled as the modern range of N-isotopic values41 (see Figure S3 for extended range). -- biorxiv.org

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

Persistent Nitrogenase Isotope Signatures Over Two Billion Years Of Engineered Evolution

by Keith CowingJune 28, 2025

Nitrogen isotope fractionation (ε15N) in sedimentary rocks has provided evidence for biological nitrogen fixation, and thus primary productivity, on the early Earth.

Adapted from fig. 1.8 of [2]. Modern protein synthesis; the anticodon at one end of a tRNA molecule binds to its complementary codon in mRNA derived directly from the genome. Sequence-to-sequence translation is not highly parallel, in this model, and the process can be characterized in terms of the Shannon uncertainty in the transmission of information between codon machinery and amino acid machinery. -- biorxiv.org

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

Biochemical ‘Cambrian’ Explosion-implosions: The Generation And Pruning Of Genetic Codes

by Keith CowingJune 27, 2025June 27, 2025

Tlusty’s topological analysis of the genetic code suggests ecosystem changes in available metabolic free energy that predated the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and […]

AI - Data - Apps - Cybernetics, Astrochemistry, Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Space Life Science, Status Report

ChemOrigins: A Community Curated Database For Origins Of Life Chemistry

by Keith CowingJune 20, 2025June 20, 2025

The origin of life is one of the most compelling questions in science. While experimental prebiotic chemistry has produced a wide range of reactions and plausible pathways, the resulting data […]

biorxiv.org

Tricorder Tech: Agnostic Tools for Life Detection: A Multiscale Approach to Biological and Chemical Reaction Networks

A Niche Construction-based Perspective On Chemical Evolution Before Replication And Reproduction

Ribonucleoprotein (RNP) Condensates Modulate Survival In Response To Mars-like Stress Conditions

Peptides At Vesicle And Mineral Prebiotic Interfaces

Microbial N2O Reduction in Sulfidic Waters: Implications For Proterozoic Oceans

Life At The Extremes: Maximally Divergent Microbes With Similar Genomic Signatures Linked To Extreme Environments

Did Iron Suppress Eukaryote Emergence and Early Radiation?

Persistent Nitrogenase Isotope Signatures Over Two Billion Years Of Engineered Evolution

Biochemical ‘Cambrian’ Explosion-implosions: The Generation And Pruning Of Genetic Codes

ChemOrigins: A Community Curated Database For Origins Of Life Chemistry

NASA Planetary Protection Handbook

NASA Scientists Search For Clues About Mars’ Past In Scotland

A Temperate Sub-Neptune Transiting The M4 Dwarf TOI-210 Identified By NIRPS And TESS — Uncovering Hidden M-dwarf Planetary Systems In The Near-infrared

Nonequilibrium Formation of Pyridine (C5H5N) in Interstellar Ice Analogs: Implications for Biorelevant Nitrogen Heterocycles in Ryugu and Bennu

The Abundance And Emission Of PAHs From The Local To Early Universe