arXiv subjects

John F. Malloy

Publications and source records attributed to John F. Malloy.

2 recordsLinked to original sources

arXiv2026

Elemental Stoichiometry as an Ecological Biosignature with Applications to Life Detection

The vast chemical space of possible small molecules, estimated at 10^60 compounds for molecules composed of just C, N, O, and S, is only sparsely occupied by biology. We propose that where life selects molecules within this space constitutes a detectable ecological signature: a fingerprint not of specific compounds, but of the statistical structure of elemental composition across molecules sam-pled from ecological systems. Here we introduce a framework combining Van Krevelen diagrams and element scaling laws to characterize the elemental composition of regions of chemical space occupied by biological systems and contrast them with other chemical systems. Applying this framework to 11,834 microbial metagenomic samples, we show that microbial metabolisms occupy a region of chemical space, which is enriched in heteroatoms such as P, S, N, and O relative to C, shifted toward higher O:C and H:C ratios. We observe sublinear element scaling with system size, yielding insights into how elemental constraints dictate how biological systems occupy chemical space. These patterns are distinct from a sample of 18,000 compounds from the comprehensive Reaxys synthetic chemical database. Critically, datasets from molecules detected in planetary science mission data occupy statistically distinct regions from both terrestrial biological and Reaxys distributions, demonstrating that with standardized methods for data collection, the approach could be developed to discriminate biotic from abiotic chemical signatures in small molecule data from planetary science missions. Our work shows how a combination of Van Krevelen fingerprinting and elemental scaling laws can provide a new class of ecological biosignatures for life detection leveraging mass spectrometric data from planetary missions, which could generalize beyond Earth's specific biochemistry.

q-bio.BM↗

arXiv2025

The Emergence of Chirality from Metabolism

Molecular chirality is critical to biochemical function, but it is unknown when chiral selectivity first became important in the evolutionary transition from geochemistry to biochemistry during the emergence of life. Here, we identify key transitions in the selection of chiral molecules in metabolic evolution, showing how achiral molecules (lacking chiral centers) may have given rise to specific and abundant chiral molecules in the elaboration of metabolic networks from geochemically available precursor molecules. Simulated expansions of biosphere-scale metabolism suggest new hypotheses about the evolution of chiral molecules within biochemistry, including a prominent role for both achiral and chiral compounds as nucleation sites of early metabolic network growth, an increasing enrichment of molecules with more chiral centers as these networks expand, and conservation of broken chiral symmetries along reaction pathways as a general organizing principle. We also find an unexpected enrichment in large, non-polymeric achiral molecules. Leveraging metabolic data of 40,023 genomes and metagenomes, we analyzed the statistics of chiral and achiral molecules in the large-scale organization of metabolism, revealing a chiral-enriched phase of network organization evidenced by system-size dependent chiral scaling laws that differ for individuals and ecosystems. By uncovering how metabolic networks could lead to chiral selection, our findings open new avenues for bridging metabolism and genetics-first approaches to the origin of chirality, allowing tools for better timing of major transitions in molecular organization during the emergence of life, understanding the role of chirality in extant and synthetic metabolisms, and informing targets for chirality-based biosignatures.

q-bio.MN↗