Chemical Filtering of Thymine over Uracil in Prebiotic Hydrothermal Systems: A Mass-Consistent Stochastic Model with Complementary Insights from UV Photodamage Pathways

The transition from RNA to DNA is one of the most consequential events in the history of life. RNA can self-replicate and catalyze, yet its 2′-OH group renders it labile under physiological conditions. DNA, by contrast, is chemically stable and stores information. The selective pressure that drove this transition must have been present in the prebiotic environment.Hydrothermal vents have long been proposed as natural reactors (Corliss et al., 1981; Miller & Bada, 1988). At temperatures 70–100 °C and alkaline pH, ribonucleotides are selectively hydrolyzed while deoxyribonucleotides persist. However, quantitative models that simultaneously track mass conservation, stochastic hydrolysis, UV damage, lipid compartmentalization, and pool drift are rare.This paper presents the complete implementation of UPDSF v6.1.1 (Unifying Prebiotic DNA Selection Framework), a fully reproducible, provenance-tracked, stochastic simulation framework. We demonstrate that a chemical filtering mechanism — not Darwinian evolution — can generate a thymine-over-uracil enrichment of 6.019× over 2400 hours, fully consistent with the two-environmental-channel definition of CSI.We further integrate insights from the complementary PNAS study of Khosh Abady, Karpourazar & Rentzepis (2026), which identifies UV photodamage pathways as the dominant selective pressure once life migrated to UV-exposed surface environments. This comparison reveals a complete two-stage prebiotic pathway.