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There are two main opposing schools of statistical reasoning, Frequentist and Bayesian approaches. Until recent days, the frequentist or classical approach has dominated the scientific research, but Bayesianism has reappeared with a strong…
Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. As a result, the key issues of how rapidly…
Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics…
Beginning with the Bell theorem, cyclic systems of dichotomous random variables have been the object of many foundational findings in quantum mechanics. Here, we ask the question: if one chooses a cyclic system "at random" (uniformly within…
While "complexity science" has achieved significant successes in several interdisciplinary fields such as economics and biology, it is only a very recent observation that legal systems -- from the way legal texts are drafted and connected…
This is an essay in what might be called ``mathematical metaphysics.'' There is a fundamental duality that run through mathematics and the natural sciences. The duality starts as the logical level; it is represented by the Boolean logic of…
Linguistic laws, the common statistical patterns of human language, have been investigated by quantitative linguists for nearly a century. Recently, biologists from a range of disciplines have started to explore the prevalence of these laws…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
The origins of life stands among the great open scientific questions of our time. While a number of proposals exist for possible starting points in the pathway from non-living to living matter, these have so far not achieved states of…
What do we do when cosmology raises questions it cannot answer? These include the existence of a multiverse and the universality of the laws of physics. We cannot settle any of these issues by experiment, and this is where philosophers…
A fundamental problem in science is how to make logical inferences from scientific data. Mere data does not suffice since additional information is necessary to select a domain of models or hypotheses and thus determine the likelihood of…
The molecular biology revolution of the last seventy five years has transformed our view of living systems. Scientific explanations of biological phenomena are now synonymous with the identification of the genes, proteins, and signaling…
Component systems - ensembles of realizations built from a shared repertoire of modular parts - are ubiquitous in biological, ecological, technological, and socio-cultural domains. From genomes to texts, cities, and software, these systems…
The discovery of general principles underlying the complexity and diversity of cellular and developmental systems is a central and long-standing aim of biology. Whilst new technologies collect data at an ever-accelerating rate, there is…
A vast array of transformative technologies developed over the past decade has enabled measurement and perturbation at ever increasing scale, yet our understanding of many systems remains limited by experimental capacity. Overcoming this…
A major challenge of interdisciplinary description of complex system behaviour is whether real systems of higher complexity levels can be understood with at least the same degree of objective, "scientific" rigour and universality as…
Modeling and simulation are recognized as important aspects of the scientific method for more than 70 years but its adoption in biology has been slow. Debates on its representativeness, usefulness, and whether the effort spent on such…
A new approach to complex systems aimed to resolve their paradoxes is proposed. Yet, the major inference is the prohibition of informational perpetuum mobile
In this review, we discuss the applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described.…
At its core, the physics paradigm adopts a reductionist approach, aiming to understand fundamental phenomena by decomposing them into simpler, elementary processes. While this strategy has been tremendously successful in physics, it has…