Related papers: An applied mathematician's perspective on Rosennea…
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…
The famous biologist Robert Rosen argued for an intrinsic difference between biological and artificial life, supporting the claim that `living systems are not mechanisms'. This result, understood as the claim that life-like mechanisms are…
Various research initiatives try to utilize the operational principles of organisms and brains to develop alternative, biologically inspired computing paradigms and artificial cognitive systems. This paper reviews key features of the…
Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the…
The question of "what is life?" has challenged scientists and philosophers for centuries, producing an array of definitions that reflect both the mystery of its emergence and the diversity of disciplinary perspectives brought to bear on the…
All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support…
Biologists and physicists have a rich tradition of modeling living systems with simple models composed of a few interacting components. Despite the remarkable success of this approach, it remains unclear how to use such finely tuned models…
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…
Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive…
The aim of this essay is to analyze the role of quantum mechanics as an inherent characteristic of life. During the last ten years the problem of the origin of life has become an innovative research subject approached by many authors. The…
Basic problems in complex systems are surveyed in connection with Life. As a key issue for complex systems, complementarity between syntax/rule/parts and semantics/behavior/whole is stressed. To address the issue, a constructive approach…
Living systems exhibit a range of fundamental characteristics: they are active, self-referential, self-modifying systems. This paper explores how these characteristics create challenges for conventional scientific approaches and why they…
The science of complexity is based on a new way of thinking that stands in sharp contrast to the philosophy underlying Newtonian science, which is based on reductionism, determinism, and objective knowledge. This paper reviews the…
Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a…
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
We provide a critique of mathematical biology in light of rapid developments in modern machine learning. We argue that out of the three modelling activities -- (1) formulating models; (2) analysing models; and (3) fitting or comparing…
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…
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…
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…
The search for what differentiates inanimate matter from living things began in antiquity as a search for a "fundamental life force" embedded deep within living things - a special material unit owned only by life - later transforming to…