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We discuss views about whether the universe can be rationally comprehended, starting with Plato, then Leibniz, and then the views of some distinguished scientists of the previous century. Based on this, we defend the thesis that…
This work focuses on the problem of exact model reduction of positive linear systems, by leveraging minimal realization theory. While determining the existence of a positive reachable realization remains in general an open problem, we are…
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex…
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…
Physicists study a wide variety of phenomena creating new interdisciplinary research fields by applying theories and methods originally developed in physics in order to solve problems in economics, social science, biology, medicine,…
Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several…
Abstraction is a powerful idea widely used in science, to model, reason and explain the behavior of systems in a more tractable search space, by omitting irrelevant details. While notions of abstraction have matured for deterministic…
This is a very basic introduction to some notions related to logic and complexity.
This work is an attempt for a state-of-the-art survey of natural and life sciences with the goal to define the scope and address the central questions of an original research program. It is focused on the phenomena of emergence, adaptive…
This is my attempt to answer Schr\"odinger's question: "What is Life?". In living cell the local combination of atoms is reproduced with incredible accuracy. In the case of protein biosynthesis the notion of the physical aspect of the…
There is a problem with the foundations of classical mathematics, and potentially even with the foundations of computer science, that mathematicians have by-and-large ignored. This essay is a call for practicing mathematicians who have been…
Classical thermodynamics and statistical mechanics describe systems in which nothing interacts with nothing. Even the highly refined theory of simple fluids does not deal very well with electrical interactions, boundary conditions, or…
Standard techniques for studying biological systems largely focus on their dynamical, or, more recently, their informational properties, usually taking either a reductionist or holistic perspective. Yet, studying only individual system…
Although living organisms are affected by many interrelated and unidentified variables, this complexity does not automatically impose a fundamental limitation on statistical inference. Nor need one invoke such complexity as an explanation…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
The vision of Organic Computing addresses challenges that arise in the design of future information systems that are comprised of numerous, heterogeneous, resource-constrained and error-prone components or devices. Here, the notion organic…
This article discusses the relationship between emergence and reductionism from the perspective of a condensed matter physicist. Reductionism and emergence play an intertwined role in the everyday life of the physicist, yet we rarely stop…
The aim of this essay is to propose a conception of mathematics that is fully consonant with naturalism. By that I mean the hypothesis that everything that exists is part of the natural world, which makes up a unitary whole.
Life continuously changes its own components and states at each moment through interaction with the external world, while maintaining its own individuality in a cyclical manner. Such a property, known as "autonomy," has been formulated…
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…