The Genomic Limit, Collapse, and Reorganization: A Physical Resolution to the C-value Paradox and the Trigger for the Cambrian Explosion

The C-value paradox and the Cambrian explosion remain two of the most profound enigmas in evolutionary biology. Here, we propose a unifying theoretical framework that resolves both phenomena as inevitable consequences of a thermodynamic and physical limit on 1D genome expansion, estimated near 1012 bp. To circumvent this packaging limit, complex lineages reorganized their genomes via strict "pruning" (removal of non-coding DNA), transitioning to a 3D topological strategy driven by liquid-liquid phase separation (LLPS). We contrast the adaptive radiation of mammals and teleosts—where pruning enables dense enhancer clustering and massive R6 topological complexity within LLPS droplets—with the evolutionary stasis of lungfish, where genomic bloating dilutes enhancers below the thermodynamic threshold required for phase separation. Furthermore, we demonstrate that the genomic capacity ratio between the theoretical maximum (1012 bp) and the minimum functional multicellular unit (5×106 bp) yields 2×105, corresponding to 17∼18 informational degrees of freedom. Modeled as a logistic potential transition P=1/(1+e-k), these 17∼18 highly unstable nodes underwent spontaneous symmetry breaking triggered by asymmetric cell division. This fundamental physical stabilization directly generated 34∼36 stable attractors, corresponding precisely to the number of fundamental animal body plans (phyla) established during the Cambrian explosion. This model provides a cohesive physical theory linking genomic capacity, topological phase transitions, and the mathematical constraints of macroevolution.