Related papers: Open Questions about Time and Self-reference in Li…
One of the characteristic features of categorical systems theory is that the behavior of systems can be characterized by certain morphisms into them. In other words, behaviors form a representable covariant functor to Set. And more…
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…
Human beings possess the most sophisticated computational machinery in the known universe. We can understand language of rich descriptive power, and communicate in the same environment with astonishing clarity. Two of the many contributors…
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…
Noise is often used in the study of open systems, such as in classical Brownian motion and in Quantum Dynamics, to model the influence of the environment. However generalising results from G\"{o}del and Chaitin in mathematics suggests that…
Learning meaningful causal representations from observations has emerged as a crucial task for facilitating machine learning applications and driving scientific discoveries in fields such as climate science, biology, and physics. This…
Representations are internal models of the environment that can provide guidance to a behaving agent, even in the absence of sensory information. It is not clear how representations are developed and whether or not they are necessary or…
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…
We briefly review two concepts of time - the usual time associated with "being" and more recent ideas, answering to the description of "becoming". The approximation involved in the former is examined. Finally we argue that it is…
We suggest that ensembles of self-replicating entities such as biological systems naturally evolve into a self-organized critical state in which fluctuations, as well as waiting-times between phase transitions are distributed according to a…
Free will is an old philosophical enigma that has been recently revived by neuropsychology. We restrict ourselves to the problem that determinism seems to allow only an illusion of freedom but random decissions do not contain any freedom…
Causal representation learning promises to extend causal models to hidden causal variables from raw entangled measurements. However, most progress has focused on proving identifiability results in different settings, and we are not aware of…
The goal of this paper is to advance an extensible theory of living systems using an approach to biomathematics and biocomputation that suitably addresses self-organized, self-referential and anticipatory systems with multi-temporal…
A celebrated and controversial hypothesis conjectures that some biological systems --parts, aspects, or groups of them-- may extract important functional benefits from operating at the edge of instability, halfway between order and…
Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously…
The chapter presents some new approaches to describing the collective behavior of complex systems of mathematical biology based on the evolution equations of observables such as open systems. This representation of kinetic evolution has…
Life is a complex biological phenomenon represented by numerous chemical, physical and biological processes performed by a biothermodynamic system/cell/organism. Both living organisms and inanimate objects are subject to aging, a biological…
Probabilistic mental simulation is thought to play a key role in human reasoning, planning, and prediction, yet the demands of simulation in complex environments exceed realistic human capacity limits. A theory with growing evidence is that…
Biological and artificial information processing systems form representations of the world that they can use to categorize, reason, plan, navigate, and make decisions. How can we measure the similarity between the representations formed by…
This paper is an opinion paper that looks at the future of computing in the age of Generative \& Agentic AI. Current software systems are static and inflexible, leading to significant challenges in translating human goals into computational…