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.
Programed death is favored by natural selection in spatial systems, J. Werfel, D.E. Ingber, Y. Bar-Yam (2015).
Theory and associated phenomenology for intrinsic mortality arising from natural selection, J. Werfel, D.E. Ingber, Y. Bar-Yam (2015).
Do we need to age? Extending the arc of life, M. Hardcastle, Y. Bar-Yam (2015).
NECSI has weighed in on the altruism debate, showing that kin selection doesn't describe altruism in spatial and other cases.
Brief discussion of the mathematics of kin and group selection, Y. Bar-Yam (January 22, 2019).
Multilevel and kin selection in a connected world, M.J. Wade, D.S. Wilson, C. Goodnight, D. Taylor, Y. Bar-Yam, M.A.M. de Aguiar, B. Stacey, J. Werfel, G.A. Hoelzer, E.D. Brodie III, P. Fields, F. Breden, T.A. Linksvayer, J.A. Fletcher, P.J. Richerson, J.D. Bever, J.D. Van Dyken, P. Zee (2010).
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, C. Goodnight, E. Rauch, H. Sayama, M. de Aguiar, M. Baranger, and Y. Bar-Yam (2008).
The evolution of reproductive restraint through social communication, J. K. Werfel, Y. Bar-Yam (2004).
NECSI discusses one of the most important questions in fundamental biology, how do new species form?
Conditions for neutral speciation via isolation by distance, E. M. Baptestini, M. A. M. de Aguiar, Yaneer Bar-Yam (2013).
Evolution and stability of ring species, A. B. Martins, M. A. M. de Aguiar, and Yaneer Bar-Yam (March 11, 2013).
The role of sex separation in neutral speciation, Elizabeth M. Baptestini, Marcus A.M. de Aguiar, Yaneer Bar-Yam (2012).
Global patterns of speciation and diversity, M.A.M. de Aguiar, M. Baranger, E.M. Baptestini, L. Kaufman, Y. Bar-Yam (2009).
The gene centered view
Researchers at NECSI developed a formal model for the gene centered view of evolution, and demonstrated where it breaks down.
Non-technical explanation of the breakdown of Neo-Darwinian — Gene Centered view, Y. Bar-Yam (February 29, 2016).
Breakdown of the gene-centered view: What is beyond Neo-Darwinian evolution?, in Unifying Themes in Complex Systems: Volume IV, H. Sayama, L. Kaufman, M. A. M. de Aguiar, E. Rauch, C. Goodnight, Y. Bar-Yam (2002).
Symmetry breaking and coarsening in spatially distributed evolutionary processes including sexual reproduction and disruptive selection, H. Sayama, L. Kaufman, Y. Bar-Yam (2000).
Formalizing the gene-centered view of evolution, Y. Bar-Yam (1999).
Formalizing the gene-centered view of evolution, Y. Bar-Yam, H. Sayama.
NECSI researchers show that fitness depends on time scale across many generations.
Relationship between measures of fitness and time scale in evolution, E. Rauch, H. Sayama, Y. Bar-Yam (2002).
Recovering population parameters from a single gene genealogy: An unbiased estimator of the growth rate, Y.E. Maruvka, N.M. Shnerb, Y. Bar-Yam, J. Wakeley (2010).
Dynamics and genealogy of strains in spatially extended host pathogen models, E. M. Rauch, H. Sayama, Y. Bar-Yam (2003).
NECSI models the dynamics of biodiversity, extinction events and the structure of populations.
Theory predicts uneven distribution of genetic diveristy within species, E. M. Rauch, Y. Bar-Yam (Sept. 23, 2004).
A new phylogenetic diversity measure generalizing the Shannon index and its application to Phyllostomid bats, B. Allen, M. Kon, Y. Bar-Yam (2009).
Robustness against extinction by stochastic sex determination in small populations, David M. Schneider, Eduardo de Carmo, Yaneer Bar-Yam, Marcus A.M. de Aguiar (October 2, 2012).
Stability and instability of polymorphic populations and the role of multiple breeding seasons in phase III of Wright's shifting balance theory, M. A.M. de Aguiar, H. Sayama, E. Rauch, Y. Bar-Yam, M. Baranger (2002).
Predator-Prey and Host-Pathogen Models
NECSI research looks at predator-prey and host-pathogen dynamics, including in human health.
Long-range interactions and evolutionary stability in a predator-prey system, E. M. Rauch, Y. Bar-Yam (2006).
Invasion and extinction in the mean field approximation for a spatial host-pathogen model, M. A. M. de Aguiar, E. M. Rauch, Y. Bar-Yam (2004).
Mean field approximation to a spatial host-pathogen model, E. M. Rauch, M. A. M. de Aguiar, Y. Bar-Yam (2003).
Somatic evolution in the immune system: the need for germinal centers for efficient affinity maturation, Pierre D. M., D. Goldman, Y. Bar-Yam & A. S. Perelson (1997).
Evolutionary Cellular Automata
NECSI has developed cellular automata models of evolutionary self-replication.
Self-Replicating Worms That Increase Structural Complexity Through Gene Transmission, in Artificial Life, H. Sayama (2000).
A new structurally dissolvable self-reproducing loop evolving in a simple cellular automata space, in Artificial Life, H. Sayama (1999).
Biodiversity, Ecology and Evolution
The effects of ecology on evolution are studied at NECSI.
Estimating the total genetic diversity of a spatial field population from a sample and implications of its dependence on habitat areas, E. M. Rauch, Y. Bar-Yam (July 12, 2005).
The Moran model as a dynamical process on networks and its implications for neutral speciation, Marcus A.M. de Aguiar, Yaneer Bar-Yam, (2011).
Beyond the mean field in host-pathogen spatial ecology, Blake C. Stacey, Andreas Gros, Yaneer Bar-Yam (October 5, 2011).
Spontaneous Pattern Formation
Biological patterns, including Turing patterns, can spontaneously form during individual development and across populations.
Spontaneous pattern formation and genetic diversity in habitats with irregular geographical features, H. Sayama, L. Kaufman, Y. Bar-Yam (2003).
Spontaneous pattern formation and genetic invasion in locally mating and competing populations, H. Sayama, M.A.M. de Aguiar, Y. Bar-Yam, M. Baranger (2002).
The role of spontaneous pattern formation in the creation and maintenance of biological diversity, H. Sayama, L. Kaufman, Y. Bar-Yam.
Robustness of spontaneous pattern formation in spatially distributed genetic populations, M. A. M. de Aguiar, M. Baranger, Y. Bar-Yam, H. Sayama (2003).
Spontaneous pattern formation and diversity in spatially structured evolutionary ecology, H. Sayama, L. Kaufman, and Y. Bar-Yam (2006).
Interplay between Turing pattern formation and domain coarsening in spatially extended population models, H. Sayama, M. A. M. de Aguiar, Y. Bar-Yam, M. Baranger (2003).
Researchers at NECSI study the dynamics within and between cells.
How changes in extracellular matrix mechanics and gene expression variability might combine to drive cancer progression, J. Werfel, S. Krause, A. G. Bischof, R. J. Mannix, H. Tobin, et al (2013).
Attractors and democratic dynamics, Y. Bar-Yam, D. Harmon, B. L. de Bivort (2009).
Empirical multiscale networks of cellular regulation, B. de Bivort, S. Huang, Y. Bar-Yam (2007).
Metabolic implications for the mechanism of mitochondrial endosymbiosis and human hereditary disorders, B. L. de Bivort, C.-C. Chen, F. Perretti, G. Negrob, T. M. Philip, Y. Bar-Yam (2007).
Cell fates as high-dimensional attractor states of a complex gene-regulatory network, S. Huang, G. Eichler, Y. Bar-Yam, D. E. Ingber (2005).
Dynamics of cellular-level function and regulation derived from Murine expression array data, B. de Bivort, S. Huang, Y. Bar-Yam (2004).