Attractors of a Random Networked Dynamical System Have Something to Say about Life

Foundational Papers in Complexity Science pp. 1007–1051
DOI: 10.37911/9781947864535.33

Attractors of a Random Networked Dynamical System Have Something to Say about Life

Author: Sanjay Jain, University of Delhi and Santa Fe Institute

 

Excerpt

Stuart Kauffman’s work extends a hallowed tradition in statistical physics to a new domain: the system that governs the switching on and off of an organism’s genes. The fundamental postulate of statistical mechanics, originating in the work of Ludwig Boltzmann and Josiah Willard Gibbs, is an acknowledgement and celebration of ignorance. It asserts that for an isolated thermodynamic system at equilibrium all microstates of the system that are compatible with the macroscopic constraints of isolation (e.g., having the same fixed total energy E, volume V, and number of particles N) are equally probable. The statement of “equal probability” is an acknowledgment of complete ignorance or the maximization of entropy. However, this assertion of ignorance, circumscribed by what we do know about the system, is a source of great power. It defines a statistical ensemble, or a probability distribution over microstates, parameterized by E, V, and N, from which one can compute the average of any desired function of the microstates. Amazingly, averages computed from the theory agree with observations.

In the 1950s, Eugene Wigner introduced a statistical ensemble of matrices of a high-dimension N to describe the spacing of energy levels observed in individual atomic nuclei. Wigner’s hypothesis was tantamount to saying that certain properties of a complex-enough quantum mechanical system (like an atomic nucleus) are identical to the averages of a suitably chosen random ensemble of systems. These properties, too difficult to derive theoretically for any particular system, could be easily calculated from the ensemble and agreed with experiments. Random matrices have since been applied as a powerful tool in many different areas, including condensed matter physics, biology, and finance.

Bibliography

Abou-Jaoudé, W., P. Traynard, P. T. Monteiro, J. Saez-Rodriguez, T. Helikar, D. Thieffry, and C. Chaouiya. 2016. “Logical Modeling and Dynamical Analysis of Cellular Networks.” Frontiers in Genetics 7. https://doi.org/10.3389/fgene.2016.00094.

Bornholdt, S., and S. Kauffman. 2019. “Ensembles, Dynamics, and Cell Types: Revisiting the Statistical Mechanics Perspective on Cellular Regulation.” Journal of Theoretical Biology 467:15–22. https://doi.org/10.1016/j.jtbi.2019.01.036.

Daniels, B. C., H. Kim, D. Moore, S. Zhou, H. B. Smith, B. Karas, S. A. Kauffman, and S. I. Walker. 2018. “Criticality Distinguishes the Ensemble of Biological Regulatory Networks.” Physical Review Letters 121 (13): 138102. https://doi.org/10.1103/PhysRevLett.121.138102.

Delbruck, M. 1949. Unités Biologiques Douées de Continuité Génétique. Paris, France: Publications du Centre National de la Recherche Scientifique.

Derrida, B., and Y. Pomeau. 1986. “Random Networks of Automata: A Simple Annealed Approximation.” Europhysics Letters 1 (2): 45. https://doi.org/10.1209/0295-5075/1/2/001.

Farmer, J. D., S. A. Kauffman, and N. H. Packard. 1986. “Autocatalytic Replication of Polymers.” Physica D: Nonlinear Phenomena 22 (1): 50–67. https://doi.org/10.1016/0167-2789(86)90233-2.

Greil, F., and B. Drossel. 2005. “Dynamics of Critical Kauffman Networks under Asynchronous Stochastic Update.” Physical Review Letters 95 (4): 048701. https://doi.org/10.1103/PhysRevLett.95.048701.

Helikar, T., B. Kowal, S. McClenathan, M. Bruckner, T. Rowley, A. Madrahimov, B. Wicks, M. Shrestha, K. Limbu, and J. A. Rogers. 2012. “The Cell Collective: Toward an Open and Collaborative Approach to Systems Biology.” See also https://cellcollective.org. BMC Systems Biology 6:96. https://doi.org/10.1186/1752-0509-6-96.

Hopfield, J. J. 1982. “Neural Networks and Physical Systems with Emergent Collective Computational Abilities.” Proceedings of the National Academy of Sciences 79 (8): 2554–2558. https://doi.org/10.1073/pnas.79.8.2554.

Jain, S., and S. Krishna. 1998. “Autocatalytic Sets and the Growth of Complexity in an Evolutionary Model.” Physical Review Letters 81 (25): 5684–5687. https://doi.org/10.1103/PhysRevLett.81.5684.

Kauffman, S. A. 1993. The Origins of Order: Self-Organization and Selection in Evolution. New York, NY: Oxford University Press.

Klemm, K., and S. Bornholdt. 2005. “Stable and Unstable Attractors in Boolean Networks.” Physical Review E 72 (5): 055101(R). https://doi.org/10.1103/PhysRevE.72.055101.

Langton, C. G. 1986. “Studying Artificial Life with Cellular Automata.” Physica D: Nonlinear Phenomena 22 (1–3): 120–149. https://doi.org/10.1016/0167-2789(86)90237-X.

May, R. 1972. “Will a Large Complex System be Stable?” Nature 238:413–414. https://doi.org/10.1038/238413a0.

Mihaljev, T., and B. Drossel. 2006. “Scaling in a General Class of Critical Random Boolean Networks.” Physical Review E 74 (4): 046101. https://doi.org/10.1103/PhysRevE.74.046101.

Monod, J., and F. Jacob. 1961. “General Conclusions: Teleonomic Mechanisms in Cellular Metabolism, Growth, and Differentiation.” Cold Spring Harbor Symposia Quantitative Biology 26:389–401. https://doi.org/10.1101/SQB.1961.026.01.048.

Mora, T., and W. Bialek. 2011. “Are Biological Systems Poised at Criticality?” Journal of Statistical Physics 144:268–302. https://doi.org/10.1007/s10955-011-0229-4.

Packard, N. H. 1988. “Adaptation toward the Edge of Chaos.” In Dynamic Patterns in Complex Systems: Proceedings of a Conference, Sponsored by Florida Atlantic University, Held in Honor of Hermann Haken on the Occasion of his 60th Birthday, edited by J. A. S. Kelso, A. J. Mandell, and M. F. Shlesinger, 293–301. Singapore: World Scientific.

Park, H. K., F. X. Costa, L. M. Rocha, R. Albert, and J. C. Rozum. 2023. “Models of Cell Processes are Far from the Edge of Chaos.” PRX Life 1 (023009). https://doi.org/10.1103/PRXLife.1.023009.

Roli, A., M. Villani, A. Filisetti, and R. Serra. 2018. “Dynamical Criticality: Overview and Open Questions.” Journal of Systems Science and Complexity 31:647–663. https://doi.org/10.1007/s11424-017-6117-5.

Rozum, J. C., J. G. T. Zañudo, X. Gan, D. Deritei, and R. Albert. 2021. “Parity and Time Reversal Elucidate Both Decision-Making in Empirical Models and Attractor Scaling in Critical Boolean Networks.” Science Advances 7 (29). https://doi.org/10.1126/sciadv.abf8124.

Samal, A., and S. Jain. 2008. “The Regulatory Network of E. Coli Metabolism as a Boolean Dynamical System Exhibits both Homeostasis and Flexibility of Response.” BMC Systems Biology 2 (21). https://doi.org/10.1186/1752-0509-2-21.

Samuelsson, B., and C. Troein. 2003. “Superpolynomial Growth in the Number of Attractors in Kauffman Networks.” Physical Review Letters 90 (9): 098701. https://doi.org/10.1103/PhysRevLett.90.098701.

Sugita, M. 1963. “Functional Analysis of Chemical Systems in Vivo Using a Logical Circuit Equivalent. II. The Idea of a Molecular Automaton.” Journal of Theoretical Biology 4 (2): 179–192. https://doi.org/10.1016/0022-5193(63)90027-4.

Thom, R. 1968. “Une Théorie Dynamique de la Morphogenèse.” In Towards a Theoretical Biology I, edited by C. H. Waddington. Reprinted in English translation in Thom (1983): Mathematical Models of Morphogenesis.

Thomas, R. 1973. “Boolean Formalization of Genetic Control Circuits.” Journal of Theoretical Biology 42 (3): 563–585. https://doi.org/10.1016/0022-5193(73)90247-6.

Waddington, C. H. 1940. Introduction to Modern Genetics. London, UK: George Allen and Unwin, Ltd. 1957. Strategy of the Genes. London, UK: Routledge. https://doi.org/10.4324/9781315765471.

Walker, C. C., and W. R. Ashby. 1966. “On Temporal Characteristics of Behavior in Certain Complex Systems.” Kybernetik 3:100–108. https://doi.org/10.1007/BF00299903.

Wigner, E. 1955. “Characteristic Vectors of Bordered Matrices with Infinite Dimensions.” Annals of Mathematics 62 (3): 548–564. https://doi.org/10.2307/1970079.

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