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Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…
A biological circuit is a neural or biochemical cascade, taking inputs and producing outputs. How have biological circuits learned to solve environmental challenges over the history of life? The answer certainly follows Dobzhansky's famous…
The physiological tradition of biological research analyzes biological systems using reduced descriptions much as an engineer uses a 'black box' description of an amplifier. Simple models have been used by physiologists for a very long…
Much of biology (and, indeed, all of science) is becoming increasingly computational. We tend to think of this in regards to algorithmic approaches and software tools, as well as increased computing power. There has also been a shift…
Our binary intuitive understanding of life and lifelikeness is good enough for daily life, but not for research in the natural sciences. Here we propose an operational definition of lifeness of a particular entity as a scalar, product of…
This thesis is about the study of complex systems through simple models. Our work evidences the relevance of this kind of modeling in science, which provides us with a better understanding of nature at minimum cost. The fundamentals tools…
Biological systems reach hierarchical complexity that has no counterpart outside the realm of biology. Undoubtedly, biological entities obey the fundamental physical laws. Can today's physics provide an explanatory framework for…
We propose a theoretical model for species that is focused on intrinsic organization and processes. Specifically, we regard species to be networks of organisms integrated by reproductive mechanisms (e.g., conjugation, meiosis, syngamy)…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
There are innumerable 'biological complexity measure's. While some patterns emerge from these attempts to represent biological complexity, a single measure to encompass the seemingly countless features of biological systems, still eludes…
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…
Many biological functions are executed by molecular machines, which consume energy and convert it into mechanical work. Biological machines have evolved to transport cargo, facilitate folding of proteins and RNA, remodel chromatin and…
An introduction to some basic ideas of the author's "quantum cybernetics" is given, which depicts waves and "particles" as mutually dependent system components, thus defining "organizationally closed systems" characterized by a fundamental…
We discuss the role and merits of symmetry methods for the analysis of biological systems. In particular, we consider systems of first order ordinary differential equations and provide a comprehensive review of the geometrical foundations…
Most Relevant Explanation (MRE) is a method for finding multivariate explanations for given evidence in Bayesian networks [12]. This paper studies the theoretical properties of MRE and develops an algorithm for finding multiple top MRE…
Nonlinear constrained optimization problems are encountered in many scientific fields. To utilize the huge calculation power of current computers, many mathematic models are also rebuilt as optimization problems. Most of them have…
The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them.…
This paper is about how we study statistical methods. As an example, it uses the random regressions model, in which the intercept and slope of cluster-specific regression lines are modeled as a bivariate random effect. Maximizing this…
At the heart of many contemporary theories of life is the concept of biological self-organisation: organisms have to continuously produce and maintain the conditions of their own existence in order to stay alive. The way in which these…