Notes: Chapter 4: The Coming Together of Things
Chapter notes for “Chapter 4: The Coming Together of Things”
Notes
1 Ilya Prigogine, Order Out of Chaos: Man’s New Dialogue with Nature (1984, with Isabelle Stengers). See also his technical work From Being to Becoming: Time and Complexity in the Physical Sciences (1980).
1a Schneider, E.D. and Kay, J.J., “Life as a Manifestation of the Second Law of Thermodynamics,” Mathematical and Computer Modelling 19(6-8): 25-48 (1994). The thermal measurements were taken at the H.J. Andrews Experimental Forest in Oregon. Kleidon, A., “Life, hierarchy, and the thermodynamic machinery of planet Earth,” Physics of Life Reviews 7(4): 424-460 (2010), extends the result to planetary scale.
2 Peter A. Corning, The Synergism Hypothesis: A Theory of Progressive Evolution (1983). Corning develops synergy as a thermodynamic concept grounding evolutionary innovation.
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.
4 Margulis, Lynn, “On the origin of mitosing cells,” Journal of Theoretical Biology 14 (1967): 225-274. Margulis’s endosymbiotic theory — that mitochondria and chloroplasts descended from free-living bacteria — was initially rejected by fifteen journals before publication. It is now the accepted account of eukaryotic origins.
5 Lane, Nick, Power, Sex, Suicide: Mitochondria and the Meaning of Life (2005). Oxford University Press. Lane provides a comprehensive account of mitochondrial biology, including the estimate of mitochondrial contribution to body mass.
5b Tschitschko, B., et al., “Symbiotic diazotrophic UCYN-A use a dedicated mechanism for nitrogen fixation within an early-branching diatom lineage,” Nature (2024). Two species, Tectiglobus diatomicola and T. profundi, were identified inside Haslea diatoms from multiple ocean basins. The global nitrogen fixation estimate is based on metagenome-assembled genome abundance across ocean sampling stations.
5c Coale, T.H., et al., “Nitrogen-fixing organelle in a marine alga,” Science 384 (2024): 217–222. The cyanobacterium UCYN-A, inside the algal host Braarudosphaera bigelowii, has crossed the threshold from symbiont to organelle, confirmed by coordinated division, genome reduction, and protein import.
5d Simon, Herbert A., “The Architecture of Complexity,” Proceedings of the American Philosophical Society 106(6) (1962): 467–482.
5a Inter-mitochondrial junctions and cristae alignment: Martin Picard et al., “Trans-mitochondrial coordination of cristae at regulated membrane junctions,” Nature Communications 6 (2015): 6259. doi: 10.1038/ncomms7259. The study found that adjacent mitochondria align their cristae across contact sites, implying a signaling mechanism, likely electromagnetic given the ~180 mV membrane potential across the inner membrane, that coordinates internal structure between organelles. Nanotunnels: Vincent, A.E. et al., “Mitochondrial nanotunnels,” Trends in Cell Biology 27 (2017): 787–799. Synchronized oscillations in salivary glands: Natalie Porat-Shliom et al., “In vivo tissue-wide synchronization of mitochondrial metabolic oscillations,” Cell Reports 9 (2014): 514–521. Cardiac arrhythmia from mitochondrial coupling: Brian O’Rourke et al., “Oscillations of membrane current and excitability driven by metabolic oscillations in heart cells,” Science 265 (1994): 962–966; Aon, M.A. et al., “Synchronized whole cell oscillations in mitochondrial metabolism triggered by a local release of reactive oxygen species in cardiac myocytes,” Journal of Biological Chemistry 278 (2003): 44735–44744. For the social-organelle framework: Picard and Sandi (2021); see Chapter 6, note 32a.
6 The “standard telling” draws on two foundational papers: Hamilton, W.D., “The Genetical Evolution of Social Behavior,” Journal of Theoretical Biology 7 (1964): 1-52, which introduced inclusive fitness and kin selection; and Trivers, R.L., “The Evolution of Reciprocal Altruism,” Quarterly Review of Biology 46 (1971): 35-57, which showed how cooperation can evolve among non-relatives through repeated interaction.
7 Aratani et al. (2023). See bibliography for full citation. The Saitama University team used transgenic Arabidopsis thaliana expressing a calcium-sensitive fluorescent reporter to visualize real-time plant volatile signaling.
8 Khait et al. (2023). See bibliography for full citation. The study demonstrated that tomato and tobacco plants emit airborne ultrasonic clicks distinguishable by stress type, detectable at distances of several meters.
9 Church, George, et al., “Confronting risks of mirror life,” Science 386 (2024): 1351-1358. A consortium of scientists warned that synthetic mirror-image microorganisms could pose catastrophic ecological risks because existing biological defenses evolved to interact with molecules of a specific chirality.
10 Hofstadter, Douglas R., Gödel, Escher, Bach: An Eternal Golden Braid (Basic Books, 1979), p. 322.
11 Ratcliff, W.C. et al., “Experimental evolution of multicellularity,” Proceedings of the National Academy of Sciences 109 (2012): 1595–1600. Within 60 days, all replicate populations evolved clumped growth through a single ACE2 mutation. Follow-up: Bozdag, G.O. et al., “De novo evolution of macroscopic multicellularity,” Nature 617 (2023): 747–754 — anaerobic snowflake yeast evolved macroscopic size (20,000× initial volume) over 600 days, with material toughness increasing 10,000-fold. See also Greenwood, V., “Single Cells Evolve Large Multicellular Forms in Just Two Years,” Quanta Magazine (22 September 2021).