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Darwin claims in the {\em Origin} that similarity is evidence for common ancestry, but that adaptive similarities are "almost valueless" as evidence. This claim seems reasonable for some adaptive similarities but not for others. Here we…
Darwin's theory of evolution by natural selection does not predict long-term progress or advancement, nor does it provide a useful way to define or understand these concepts. Nevertheless, the history of life is marked by major trends that…
Life forms exhibit such a degree of exquisite organization that it seems impossible that they could have developed out of a process of trial and error, as intimated by the theory of Darwinian evolution. In this general public paper I…
We present a Hamiltonian approach for the wellknown Eigen model of the Darwin selection dynamics. Hamiltonization is carried out by means of the embedding of the population variable space, describing behavior of the system, into the space…
Bayesian methods since the time of Laplace have been understood by their practitioners as closely aligned to the scientific method. Indeed a recent champion of Bayesian methods, E. T. Jaynes, titled his textbook on the subject Probability…
Many complex adaptive systems contain a large diversity of specialized components. The specialization at the level of the microscopic degrees of freedom, and diversity at the level of the system as a whole are phenomena that appear during…
Darwinian dynamics is manifestly stochastic and nonconservative, but has a profound connection to conservative dynamics in physics. In the present paper the main ideas and logical steps leading to thermodynamics from Darwinian dynamics are…
Individual success in group-structured populations has two components. First, an individual gains by outcompeting its neighbors for local resources. Second, an individual's share of group success must be weighted by the total productivity…
It has been hypothesized that in the era just before the last universal common ancestor emerged, life on earth was fundamentally collective. Ancient life forms shared their genetic material freely through massive horizontal gene transfer…
Cooperation among unrelated individuals is frequently observed in social groups when their members combine efforts and resources to obtain a shared benefit that is unachievable by an individual alone. However, understanding why cooperation…
We present a simple model for describing the dynamics of the interaction between a homogeneous population or society, and the natural resources and reserves that the society needs for its survival. The model is formulated in terms of…
The ways in which natural selection can allow the proliferation of cooperative behavior have long been seen as a central problem in evolutionary biology. Most of the literature has focused on interactions between pairs of individuals and on…
The functioning of animal as well as human societies fundamentally relies on cooperation. Yet, defection is often favorable for the selfish individual, and social dilemmas arise. Selection by individuals' fitness, usually the basic driving…
Background: Speciation corresponds to the progressive establishment of reproductive barriers between groups of individuals derived from an ancestral stock. Since Darwin did not believe that reproductive barriers could be selected for, he…
Natural selection favors the more successful individuals. This is the elementary premise that pervades common models of evolution. Under extreme conditions, however, the process may no longer be probabilistic. Those that meet certain…
The evolution of complexity has been a central theme for Biology [2] and Artificial Life research [1]. It is generally agreed that complexity has increased in our universe, giving way to life, multi-cellularity, societies, and systems of…
Darwin's hypothesis that all extant life forms are descendants of a last common ancestor cell and diversification of life forms results from gradual mutation plus natural selection represents a mainstream view that has influenced biology…
The fact that humans cooperate with non-kin in large groups, or with people they will never meet again, is a long-standing evolutionary puzzle with profound implications. Cooperation is linked to altruism, the capacity to perform costly…
Because human cognition is creative and socially situated, knowledge accumulates, diffuses, and gets applied in new contexts, generating cultural analogs of phenomena observed in population genetics such as adaptation and drift. It is…
The theory of interaction-based evolution argues that, at the most basic level of analysis, there is a third alternative for how adaptive evolution works besides a) accidental mutation and natural selection and b) Lamarckism, namely, c)…