Notes: Chapter 4c: The Physics of Persistence

Chapter notes for “Chapter 4c: The Physics of Persistence”

Notes

³ Eric J. Chaisson, Cosmic Evolution: The Rise of Complexity in Nature (2001). Energy rate density (φm) provides a single metric for complexity from galaxies to civilizations.

⁸ Per Bak, How Nature Works: The Science of Self-Organized Criticality (1996). Bak’s sandpile model demonstrated how complex systems naturally evolve to critical states where events of all sizes occur according to power law distributions.

^8a Couzin, I.D. et al., “Effective leadership and decision-making in animal groups on the move,” Nature 433 (2005): 513–516. See also Rosenthal, S.B. et al., “Revealing the hidden networks of interaction in mobile animal groups allows prediction of complex behavioral contagion,” PNAS 112 (2015): 4690–4695, which measured information wave speeds in golden shiner schools. Couzin is director of the Department of Collective Behavior at the Max Planck Institute of Animal Behavior and a full professor at the University of Konstanz.

^8b Sosna, M.M.G. et al., “Individual and collective encoding of risk in animal groups,” PNAS 116 (2019): 20556–20561. The study demonstrated that fish under chemical alarm cues restructure their social network topology toward the critical point, optimizing the tradeoff between robustness and sensitivity — consistent with the prediction that natural selection tunes collective systems near phase transitions.

^8c Bazazi, S. et al., “Collective motion and cannibalism in locust migratory bands,” Current Biology 18 (2008): 735–739. Couzin and colleagues showed that locust marching bands are driven by cannibalistic interactions (following to consume, fleeing to avoid being consumed) rather than by the information-transfer mechanisms that govern fish schools and bird flocks. During plague years, locusts invade more than one-fifth of the world’s land cover and affect the livelihood of one in ten people.

²⁰ Albert-László Barabási and Réka Albert, “Emergence of Scaling in Random Networks,” Science 286 (1999): 509-512. This paper introduced the preferential attachment mechanism and showed how it produces scale-free networks.

²² Paul A. David, “Clio and the Economics of QWERTY,” American Economic Review 75:2 (1985): 332-337. See also W. Brian Arthur, Increasing Returns and Path Dependence in the Economy (Ann Arbor: University of Michigan Press, 1994).

³⁴ Grassé, Pierre-Paul, “La reconstruction du nid et les coordinations interindividuelles chez Bellicositermes natalensis,” Insectes Sociaux 6 (1959): 41-80. Grassé coined the term stigmergy to describe how termites coordinate nest-building through environmental modification rather than direct communication.

^34a Legris, M. et al., “Perception of light direction by plant phototropism requires intercellular air spaces,” Science 383 (2024): 164–170. The abcg5 mutation that floods intercellular air spaces eliminates phototropic bending while leaving light-sensing photoreceptors intact — demonstrating that the physical scattering of light, rather than a molecular mechanism alone, is required for directional sensing. The finding resolves a question first posed by Charles and Francis Darwin in The Power of Movement in Plants (1880). Research conducted at the University of Lausanne.

³⁶ Beggs, John M. and Dietmar Plenz, “Neuronal avalanches in neocortical circuits,” Journal of Neuroscience 23 (2003): 11167-11177. Spontaneous cortical activity follows power-law distributions characteristic of systems poised at criticality.

³⁷ Lorenz, Edward N., “Deterministic Nonperiodic Flow,” Journal of the Atmospheric Sciences 20 (1963): 130-141. Lorenz’s foundational paper introduced the strange attractor that bears his name and launched the field of chaos theory.

⁴⁴ Simon, Herbert A., “The Architecture of Complexity,” Proceedings of the American Philosophical Society 106 (1962): 467-482. Simon argued that complex systems evolve far more rapidly when composed of stable, semi-independent subsystems (modules) than when monolithic.

^44a Lanfear, R., “Do plants have a segregated germline?” PLOS Biology 16 (2018): e2005439. Lanfear’s review challenges the conventional assumption that plants lack germlines, surveying evidence that apical meristem stem cells divide rarely enough to function as mutation-shielding tissue. Cell-tracking data: Burian, A. et al., “Patterns of stem cell divisions contribute to plant longevity,” Current Biology 26 (2016): 1385–1394. Říha telomere study: Watson, J.M. et al., “Germline replications and somatic mutation accumulation are independent of vegetative life span in Arabidopsis,” PNAS 113 (2016): 12226–12231. Strawberry runner germline evidence: Whittle, C.A. and Extavour, C.G., data from Hurst, L.D. et al., “Somatic mutation rates scale with generation time across plants,” PLOS Biology (2019). Oak mutation rate: Schmid-Siegert, E. et al., “Low number of fixed somatic mutations in a long-lived oak tree,” Nature Plants 3 (2017): 926–929. Sitka spruce: Hanlon, V.C.T. et al., “Somatic mutations substantially increase the per-generation mutation rate in the conifer Picea sitchensis,” Evolution Letters 3 (2019): 348–358.

^44b Briat, C., Gupta, A., and Khammash, M., “Antithetic Integral Feedback Ensures Robust Perfect Adaptation in Noisy Biomolecular Networks,” Cell Systems 2 (2016): 15–26 (the controller motif); Aoki, S.K., Lillacci, G., Gupta, A., Baumschlager, A., Schweingruber, D., and Khammash, M., “A universal biomolecular integral feedback controller for robust perfect adaptation,” Nature 570 (2019): 533–537 (experimental realization in E. coli). Uniqueness proof: Gupta, A. and Khammash, M., “Universal structural requirements for maximal robust perfect adaptation in biomolecular networks,” PNAS 119(43) (2022): e2207802119, DOI: 10.1073/pnas.2207802119. Lim, X., “Math Reveals the Secrets of Cells’ Feedback Circuitry,” Quanta Magazine (18 September 2019).

⁴ On resonance and particle physics: Brubaker, B., “How the Physics of Resonance Shapes Reality,” Quanta Magazine (January 26, 2022). The characterization of particles as resonant excitations of quantum fields — “localized, resonant excitations of these fields, vibrating like springs in an infinite mattress” — is standard quantum field theory. Short-lived particles observed only through their bump on a scattering amplitude curve are literally called “resonances” in the literature. See also Strassler, M. (Harvard), quoted therein: “As with the wineglass, you’re sweeping through a system that wants to resonate. You’ll make anything vibrate that can.”