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Updated: Oct 24, 2025

Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
Published on: May 2, 2025
Nothing in evolution makes sense except in the light of parasitism: evolution of complex replication strategies
Simon J Hickinbotham1, Susan Stepney2, Paulien Hogeweg3
1Department of Electronic Engineering, University of York, York, UK.
Abstract:
Parasitism emerges readily in models and laboratory experiments of RNA world and would lead to extinction unless prevented by compartmentalization or spatial patterning. Modelling replication as an active computational process opens up many degrees of freedom that are exploited to meet environmental challenges, and to modify the evolutionary process itself. Here, we use automata chemistry models and spatial RNA-world models to study the emergence of parasitism and the complexity that evolves in response. The system is initialized with a hand-designed replicator that copies other replicators with a small chance of point mutation. Almost immediately, short parasites arise; these are copied more quickly, and so have an evolutionary advantage. The replicators also become shorter, and so are replicated faster; they evolve a mechanism to slow down replication, which reduces the difference of replication rate of replicators and parasites. They also evolve explicit mechanisms to discriminate copies of self from parasites; these mechanisms become increasingly complex. New parasite species continually arise from mutated replicators, rather than from evolving parasite lineages. Evolution itself evolves, e.g. by effectively increasing point mutation rates, and by generating novel emergent mutational operators. Thus, parasitism drives the evolution of complex replicators and complex ecosystems.
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