Evolution and Systems Biology

NECSI’s research into evolution clarifies basic issues in evolutionary dynamics such as how altruism arises, the origin and characterization of biodiversity, as well as the interplay of evolution with ecology.

Do we need to age? NECSI challenges the mathematical assumptions of traditional evolutionary theory and shows aging is programmed, and not an inherent biological breakdown.

Justin Werfel, Donald E. Ingber, and Yaneer Bar-Yam, Programed death is favored by natural selection in spatial systems, Physical Review Letters 114: 238103 (2015), doi: 10.1103/PhysRevLett.114.238103.

Justin Werfel, Donald E. Ingber, and Yaneer Bar-Yam, Theory and associated phenomenology for intrinsic mortality arising from natural selection, PLOS One (March 29, 2017).

Matthew Hardcastle and Yaneer Bar-Yam, Do we need to age? Extending the arc of life, NECSI (2015).

NECSI has weighed in on the altruism debate, showing that kin selection doesn't describe altruism in spatial and other cases.

Yaneer Bar-Yam, Brief discussion of the mathematics of kin and group selection, NECSI (January 22, 2019).

Michael J. Wade, David S. Wilson, Charles Goodnight, Doug Taylor, Yaneer Bar-Yam, Marcus A. M. de Aguiar, Blake Stacey, Justin Werfel, Guy A. Hoelzer, Edmund D. Brodie III, Peter Fields, Felix Breden, Timothy A. Linksvayer, Jeffrey A. Fletcher, Peter J. Richerson, James D. Bever, J. David Van Dyken, and Peter Zee, Multilevel and kin selection in a connected world, Nature 463: E8-E9 (2010).

Charles Goodnight, Erik Rauch, Hiroki Sayama, Marcus de Aguiar, Michel Baranger, and Yaneer Bar-Yam, Evolution in spatial predator-prey models and the "prudent predator:” The inadequacy of steady-state organism fitness and the concept of individual and group selection, Complexity 13: 23-44 (2008).

Justin K. Werfel and Yaneer Bar-Yam, The evolution of reproductive restraint through social communication, PNAS 101: 11019-11024 (2004).

NECSI discusses one of the most important questions in fundamental biology, how do new species form?

Elizabeth M. Baptestini, Marcus A.M. de Aguiar, and Yaneer Bar-Yam, Conditions for neutral speciation via isolation by distance, Journal of Theoretical Biology 335: 51–56 (2013).

Ayana B. Martins, Marcus A.M. de Aguiar, and Yaneer Bar-Yam, Evolution and stability of ring species, PNAS 201217034 (March 11, 2013).

Elizabeth M. Baptestini, Marcus A.M. de Aguiar, and Yaneer Bar-Yam, The role of sex separation in neutral speciation, Theoretical Ecology 6(2): 1-11 (2012).

Marcus A.M. de Aguiar and Yaneer Bar-Yam, The Moran model as a dynamical process on networks and its implications for neutral speciation, Physical Review E 84: 031901 (2011).

Marcus A.M. de Aguiar, Michel Baranger, Elizabeth M. Baptestini, Les Kaufman, and Yaneer Bar-Yam, Global patterns of speciation and diversity, Nature 460: 384-387 (2009).

Researchers at NECSI developed a formal model for the gene centered view of evolution, and demonstrated where it breaks down.

Yaneer Bar-Yam, Non-technical explanation of the breakdown of Neo-Darwinian — Gene Centered view, NECSI (February 29, 2016).

Hiroki Sayama, Les Kaufman, Marcus A.M. de Aguiar, Erik Rauch, Charles Goodnight, and Yaneer Bar-Yam, Breakdown of the gene-centered view: What is beyond Neo-Darwinian evolution?, in Unifying Themes in Complex Systems: Volume IV (Springer, 2002).

Yaneer Bar-Yam, Mean field theory and the gene centered view of evolution, NECSI.

Hiroki Sayama and Yaneer Bar-Yam, The gene centered view of evolution and symmetry breaking and pattern formation in spatially distributed evolutionary processes, in Nonlinear Dynamics in the Life and Social Sciences, W. Sulis and I. Trofimova, Eds. (NATO Science Series A/320, IOS Press, 2001), pp. 360-368.

Hiroki Sayama, Les Kaufman, and Yaneer Bar-Yam, Symmetry breaking and coarsening in spatially distributed evolutionary processes including sexual reproduction and disruptive selection, Physical Review E 62: 7065-7069 (2000).

Yaneer Bar-Yam, Formalizing the gene-centered view of evolution, Advances in Complex Systems 2, 277-281 (1999).

Yaneer Bar-Yam and Hiroki Sayama, Formalizing the gene-centered view of evolution, InterJournal, Brief Article 385.

NECSI researchers show that fitness depends on time scale across many generations.

Erik Rauch, Hiroki Sayama, and Yaneer Bar-Yam, Relationship between measures of fitness and time scale in evolution, Physical Review Letters 88: 228101 (2002).

Yosef E. Maruvka, Nadav M. Shnerb, Yaneer Bar-Yam, and John Wakeley, Recovering population parameters from a single gene genealogy: An unbiased estimator of the growth rate, Molecular Biology and Evolution 28(5): 1617–1631 (2010).

Erik M. Rauch, Hiroki Sayama, and Yaneer Bar-Yam, Dynamics and genealogy of strains in spatially extended host pathogen models, Journal of Theoretical Biology 221: 655-664 (2003).

NECSI models the dynamics of biodiversity, extinction events and the structure of populations.

David M. Schneider, Eduardo de Carmo, Yaneer Bar-Yam, and Marcus A.M. de Aguiar, Robustness against extinction by stochastic sex determination in small populations, Physical Review E 86: 041104 (October 2, 2012).

Marcus A.M. de Aguiar, Hiroki Sayama, Erik Rauch, Yaneer Bar-Yam, and Michel Baranger, Stability and instability of polymorphic populations and the role of multiple breeding seasons in phase III of Wright's shifting balance theory, Physical Review E 65: 031909 (2002).

NECSI research looks at predator-prey and host-pathogen dynamics, including in human health.

Blake C. Stacey, Andreas Gros, and Yaneer Bar-Yam, Beyond the mean field in host-pathogen spatial ecology, arXiv:1110.3845 (October 18, 2011).

Erik M. Rauch and Yaneer Bar-Yam, Long-range interactions and evolutionary stability in a predator-prey system, Physical Review E 73: 020903 (2006).

Marcus A.M. de Aguiar, Erik M. Rauch, and Yaneer Bar-Yam, Invasion and extinction in the mean field approximation for a spatial host-pathogen model, Journal of Statistical Physics 114: 1417-1451 (2004).

Erik M. Rauch, Marcus A.M. de Aguiar, and Yaneer Bar-Yam, Mean field approximation to a spatial host-pathogen model, Physical Review E 67: 047102 (2003).

Darren M. Pierre, Daniel Goldman, Yaneer Bar-Yam, and Alan S. Perelson, Somatic evolution in the immune system: the need for germinal centers for efficient affinity maturation, Journal of Theoretical Biology 186: 159-171 (1997).

NECSI has developed cellular automata models of evolutionary self-replication.

Hiroki Sayama, Self-replicating worms that increase structural complexity through gene transmission, in Artificial Life, M.A. Bedau, J.S. McCaskill, N.H. Packard, S. Rasmussen, Eds. (MIT Press, 2000), pp. 21-30.

Hiroki Sayama, A new structurally dissolvable self-reproducing loop evolving in a simple cellular automata space, Artificial Life 5(4): 343-365 (1999).

Hiroki Sayama, Spontaneous evolution of self-reproducing loops on cellular automata, InterJournal, Brief Article 236.

The effects of ecology on evolution are studied at NECSI.

Benjamin Allen, Mark Kon, and Yaneer Bar-Yam, A new phylogenetic diversity measure generalizing the Shannon index and its application to Phyllostomid bats, 174(2) (2009).

Erik M. Rauch and Yaneer Bar-Yam, Theory predicts uneven distribution of genetic diveristy within species, Nature 431: 449-452 (September 23, 2004).

Erik M. Rauch and Yaneer Bar-Yam, Estimating the total genetic diversity of a spatial field population from a sample and implications of its dependence on habitat areas, Proceedings of the National Academy of Sciences 102: 9826-9829 (2005).

Biological patterns, including Turing patterns, can spontaneously form during individual development and across populations.

Hiroki Sayama, Les Kaufman, and Yaneer Bar-Yam, Spontaneous pattern formation and diversity in spatially structured evolutionary ecology, Journal of Conservation Biology 17: 893 (2003)

Hiroki Sayama, Les Kaufman, and Yaneer Bar-Yam, Spontaneous pattern formation and genetic diversity in habitats with irregular geographical features, Conservation Biology 17(3): 893-900 (2003).

Hiroki Sayama, Marcus A.M. de Aguiar, Yaneer Bar-Yam, and Michel Baranger, Spontaneous pattern formation and genetic invasion in locally mating and competing populations, Physical Review E 65: 051919 (2002).

Hiroki Sayama, Les Kaufman, and Yaneer Bar-Yam, The role of spontaneous pattern formation in the creation and maintenance of biological diversity, InterJournal, Brief Article 417.

Yaneer Bar-Yam, Making Things Work, Chapter 6 and 7 (Knowledge Press, 2004).

Marcus A.M. de Aguiar, Michel Baranger, Yaneer Bar-Yam, and Hiroki Sayama, Robustness of spontaneous pattern formation in spatially distributed genetic populations, Brazilian Journal of Physics 33: 514 (2003).

Hiroki Sayama, Marcus A.M. de Aguiar, Yaneer Bar-Yam, and Michel Baranger, Interplay between Turing pattern formation and domain coarsening in spatially extended population models, FORMA 18 (2003).

Researchers at NECSI study the dynamics within and between cells.

Justin Werfel, Silva Krause, Ashley G. Bischof, Robert J. Mannix, Heather Tobin, Yaneer BarYam, Robert M. Bellin, and Donald E. Ingber, How changes in extracellular matrix mechanics and gene expression variability might combine to drive cancer progression, PLoS ONE 8: e76122 (2013).

Yaneer Bar-Yam, Dion Harmon, and Benjamin de Bivort, Attractors and democratic dynamics, Science 323(5917): 1016-1017 (2009).

Benjamin de Bivort, Sui Huang, and Yaneer Bar-Yam, Empirical multiscale networks of cellular regulation, PLoS Computational Biology 3: e207 (2007).

Benjamin Lovegren de Bivort, Chun-Chung Chen, Fabrizio Perretti, Giacomo Negro, Thomas M. Philip, and Yaneer Bar-Yam, Metabolic implications for the mechanism of mitochondrial endosymbiosis and human hereditary disorders, Journal of Theoretical Biology (2007).

Sui Huang, Gabriel Eichler, Yaneer Bar-Yam, and Donald E. Ingber, Cell fates as high-dimensional attractor states of a complex gene-regulatory network, Physical Review Letters 94: 128701 (2005).

Benjamin de Bivort, Sui Huang, and Yaneer Bar-Yam, Dynamics of cellular-level function and regulation derived from Murine expression array data, PNAS 101: 17687-17692 (2004).

Evolution and Sports

What can team sports tell us about evolution?

Yaneer Bar-Yam, Complex systems and sports: Complex systems insights to building effective teams, NECSI (2003).