Related papers: Degeneracy: a link between evolvability, robustnes…

This paper attempts to make feasible the evolutionary emergence of novelty in a supposedly deterministic world which behavior is associated with those of the mathematical dynamical systems. The work was motivated by the observation of…

Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…

A major challenge of interdisciplinary description of complex system behaviour is whether real systems of higher complexity levels can be understood with at least the same degree of objective, "scientific" rigour and universality as…

A quite general interaction process of a multi-component system is analysed by the extended effective potential method liberated from usual limitations of perturbation theory or integrable model. The obtained causally complete solution of…

Formal explainability guarantees the rigor of computed explanations, and so it is paramount in domains where rigor is critical, including those deemed high-risk. Unfortunately, since its inception formal explainability has been hampered by…

Evolution on neutral networks of genotypes has been found in models to concentrate on genotypes with high mutational robustness, to a degree determined by the topology of the network. Here analysis is generalized beyond neutral networks to…

The evolutionary biology of aging is fundamental to understanding the mechanisms of aging and how to develop anti-aging treatments. Thus far most evolutionary theory concerns the genetics of aging with limited physiological integration.…

With a view to connecting random mutation on the molecular level to punctuated equilibrium behavior on the phenotype level, we propose a new model for biological evolution, which incorporates random mutation and natural selection. In this…

A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex,…

Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…

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,…

Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…

We present a model that considers the maturation of the antibody population following primary antigen presentation as a global optimization problem. The trade-off that emerges from our model describes the balance between the safety of…

The evolutionary origins of ageing and age-associated diseases continue to pose a fundamental question in biology. This study is concerned with a recently proposed framework, which conceptualises development and ageing as a continuous…

Biological neural networks can perform complex computations to predict their environment, far above the limited predictive capabilities of individual neurons. While conventional approaches to understanding these computations often focus on…

Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…

Biological evolution continuously refines the design of species, resulting in highly optimised organisms over hundreds of millennia. Intuitively, we expect that random changes-evolution's primary mechanism-are more likely to be harmful than…

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…

Even when concepts similar to emergence have been used since antiquity, we lack an agreed definition. However, emergence has been identified as one of the main features of complex systems. Most would agree on the statement ``life is…

Robustness is key to engineering, automation, and science as a whole. However, the property of robustness is often underpinned by costly requirements such as over-provisioning, known uncertainty and predictive models, and known adversaries.…