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Advances in biology have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. Theoretical biology used to primarily provide a basis to rationally examine the frameworks…
Ecological and evolutionary processes show various population dynamics depending on internal interactions and environmental changes. While crucial in predicting biological processes, discovering general relations for such nonlinear dynamics…
The origin of life on Earth via the spontaneous emergence of a protocell prior to Darwinian evolution remains a fundamental open question in physics and chemistry. Here, we develop a conceptual framework based on information theory and…
The question as to why most higher organisms reproduce sexually has remained open despite extensive research, and has been called "the queen of problems in evolutionary biology". Theories dating back to Weismann have suggested that the key…
The profound impact of Darwin's theory of evolution on biology has led to the acceptance of the theory in many complex systems that lie well beyond its original domain. Culture is one example that also exhibits key Darwinian evolutionary…
The long-term growth rate of populations in varying environments quantifies the evolutionary value of processing the information that biological individuals inherit from their ancestors and acquire from their environment. Previous models…
Darwinian evolution can be modeled in general terms as a flow in the space of fitness (i.e. reproductive rate) distributions. In the diffusion approximation, Tsimring et al. have showed that this flow admits "fitness wave" solutions:…
The possibility of physics in multiple time dimensions is investigated. Drawing on recent work by Walter Craig and myself, I show that, contrary to conventional wisdom, there is a well-posed initial value problem--deterministic, stable…
Darwinism conceives evolution as a consequence of random variation and natural selection, hence it is based on a materialistic, i.e. matter-based, view of science inspired by classical physics. But matter in itself is considered a very…
Open-ended evolutionary dynamics remains an elusive goal for artificial evolutionary systems. Many ideas exist in the biological literature beyond the basic Darwinian requirements of variation, differential reproduction and inheritance. I…
We apply the theory of learning to physically renormalizable systems in an attempt to develop a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution…
This paper introduces a variational formulation of natural selection, paying special attention to the nature of "things" and the way that different "kinds" of "things" are individuated from - and influence - each other. We use the Bayesian…
To learn about the past from a sample of genomic sequences, one needs to understand how evolutionary processes shape genetic diversity. Most population genetic inference is based on frameworks assuming adaptive evolution is rare. But if…
Observations on the past provide some hints about what will happen in the future, and this can be quantified using information theory. The ``predictive information'' defined in this way has connections to measures of complexity that have…
Darwin's book, Origin of the Species has been a source of public controversy for more than hundred and fifty years. Court cases and mountains of words have not dispelled this controversy. In this paper, a quantitative approach using simple…
The nature and source of evolutionary trends in complexity is difficult to assess from the fossil record, and the driven vs. passive nature of such trends has been debated for decades. There are also questions about how effectively…
This paper explores the idea that information is an essential and distinctive feature of living systems. Unlike non-living systems, living systems actively acquire, process, and use information about their environments to respond to…
Since its introduction in 2001, natural time analysis has been applied to diverse fields with remarkable results. Its validity has not been doubted by any publication to date. Here, we indicate that frequently asked questions on the…
The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. Yet, while evolution by natural selection requires new heritable traits to be produced and transmitted, it…
We study the performance of different methods for processing information, incorporating narrative selection within an evolutionary model. All agents update their beliefs according to Bayes' Rule, but some strategically choose the narrative…