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This short text summarizes the work in biology proposed in our book, Perspectives on Organisms, where we analyse the unity proper to organisms by looking at it from different viewpoints. We discuss the theoretical roles of biological time,…
Development of several alternative mathematical models for the biological system in question and discrimination between such models using experimental data is the best way to robust conclusions. Models which challenge existing theories are…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
Quantum science and biology now intersect in three complementary directions: quantum in biology, quantum for biology, and biology for quantum. This review provides a structured narrative evidence map of that interface rather than an…
At present, there is a great deal of confusion regarding complexity and its measures (reviews on complexity measures are found in, e.g. Lloyd, 2001 and Shalizi, 2006 and more references therein). Moreover, there is also confusion regarding…
Biological evolution is realised through the same mechanisms of birth and death that underlie change in population density. The deep interdependence between ecology and evolution is well-established, and recent models focus on integrating…
Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode…
This paper gives a thorough critique of the foundations of quantum physics in its mainstream interpretation (i.e., treating pure states as primitives, without reference to hidden variables, and without modifications of the quantum laws).…
Though it goes without saying that linear algebra is fundamental to mathematical biology, polynomial algebra is less visible. In this article, we will give a brief tour of four diverse biological problems where multivariate polynomials play…
Examining individual components of cellular systems has been successful in uncovering molecular reactions and interactions. However, the challenge lies in integrating these components into a comprehensive system-scale map. This difficulty…
In this paper, we make a review on the concepts of rationality across several different fields, namely in economics, psychology and evolutionary biology and behavioural ecology. We review how processes like natural selection can help us…
Complex systems throughout Nature display structures and functions that are built and maintained, at least in part, by optimal energies flowing through them--not specific, ideal values, rather ranges in energy rate density below which…
Statistical classical mechanics and quantum mechanics are developed and well-known theories that represent a basis for modern physics. The two described theories are well known and have been well studied. As these theories contain numerous…
Finding general principles underlying brain function has been appealing to scientists. Indeed, in some branches of science like physics and chemistry (and to some degree biology) a general theory often can capture the essence of a wide…
Although conventional logical systems based on logical calculi have been successfully used in mathematics and beyond, they have definite limitations that restrict their application in many cases. For instance, the principal condition for…
Advances in science are being sought in newly available opportunities to collect massive quantities of data about complex systems. While key advances are being made in detailed mapping of systems, how to relate this data to solving many of…
Many questions in experimental mathematics are fundamentally inductive in nature. Here we demonstrate how Bayesian inference --the logic of partial beliefs-- can be used to quantify the evidence that finite data provide in favor of a…
Stochastic models, based on random processes, may lead to power law distributions, which provide long range correlations. The observation of power law behavior and the presence of long range correlations in biological systems has been…
Whether or not biodiversity dynamics tend toward stable equilibria remains an unsolved question in ecology and evolution with important implications for our understanding of diversity and its conservation. Phylo/population genetic models…
This paper presents a plausible reasoning system to illustrate some broad issues in knowledge representation: dualities between different reasoning forms, the difficulty of unifying complementary reasoning styles, and the approximate nature…