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"If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous successive, slight modifications, my theory would absolutely break down". Can Darwinian random mutations and selection…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…
This paper makes a number of connections between life and various facets of genetic and evolutionary algorithms research. Specifically, it addresses the topics of adaptation, multiobjective optimization, decision making, deception, and…
``The purpose of life is to obtain knowledge, use it to live with as much satisfaction as possible, and pass it on with improvements and modifications to the next generation.'' This may sound philosophical, and the interpretation of words…
Chaitin's work, in its depth and breadth, encompasses many areas of scientific and philosophical interest. It helped establish the accepted mathematical concept of randomness, which in turn is the basis of tools that I have developed to…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
The rapidly increasing interest in the quantum properties of living matter stimulates a discussion of the fundamental properties of life as well as quantum mechanics. In this discussion often concepts are used that originate in philosophy…
This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the…
2019 marked the 75th anniversary of the publication of Erwin Schr\"{o}dinger's "What is Life?", a short book described by Roger Penrose in his preface to a reprint of this classic as "among the most influential scientific writings of the…
The mathematical formalisms used to model biological systems induce both latent and ambiguous assumptions that can limit or distort their representational capabilities. Developing formalisms that can represent systems more precisely is…
Modern life sciences research is increasingly relying on artificial intelligence approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying…
Niels Bohr's arguments indicating the non-applicability of quantum methodology to the study of the ultimate details of life given in his book "Atomic physics and human knowledge" conflict with the commonly held opposite view. The bases for…
Philosophy of science attempts to describe all parts of the scientific process in a general way in order to facilitate the description, execution and improvements of this process. So far, all proposed philosophies have only covered existing…
Reductionism has dominated science and philosophy for centuries. Complexity has recently shown that interactions---which reductionism neglects---are relevant for understanding phenomena. When interactions are considered, reductionism…
We present several philosophical ideas emerging from the studies of complex systems. We make a brief introduction to the basic concepts of complex systems, for then defining "abstraction levels". These are useful for representing…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
Over the past 50 years, the use of mathematical models, derived from physical reasoning, to describe molecular and cellular systems has evolved from an art of the few to a cornerstone of biological inquiry. George Oster stood out as a…
We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by…
In this paper, we develop a natural (empirical) relational theory for describing and modeling complex biological phenomena. We have as stepping stone the assertion: function implies structure. The theory is built upon a graph's theory…