Related papers: The simple emergence of complex molecular function

Molecular evolution is the process of simulating the natural evolution of molecules in chemical space to explore potential molecular structures and properties. The relationships between similar molecules are often described through…

A hallmark of intelligence is the ability to autonomously learn new flexible, cognitive behaviors - that is, behaviors where the appropriate action depends not just on immediate stimuli (as in simple reflexive stimulus-response…

The theory of evolution by natural selection cannot be used to evaluate the truth value of the following proposition: Through evolution, there exists at least one species that can adapt to any one given environment. To address this issue,…

A full accounting of biological robustness remains elusive; both in terms of the mechanisms by which robustness is achieved and the forces that have caused robustness to grow over evolutionary time. Although its importance to topics such as…

Active systems across scales, ranging from molecular machines to human crowds, are usually modeled as assemblies of self-propelled particles driven by internally generated forces. However, these models often assume memoryless dynamics and…

Emergent patterns in complex systems are related to many intriguing phenomena in modern science and philosophy. Several conceptions such as weak, strong and robust emergence have been proposed to emphasize different epistemological and…

Based on the oligomer-world hypothesis we propose an abstract model where the molecular recognition among oligomers is described in the shape space. The origin of life in the oligomer world is regarded as the establishment of a metabolic…

A qualitatively new, much more liberal and efficient organisation of science is proposed and justified, in connection with growing debate about further role and development of fundamental science. Although the key ideas can be explained…

Darwin's theory of evolution by natural selection does not predict long-term progress or advancement, nor does it provide a useful way to define or understand these concepts. Nevertheless, the history of life is marked by major trends that…

The origin of macroscopic complexity is traced in a wide range of systems (imunology, ecology, finance, marketing, etc) to the discrete and auto-catalytic (i.e. multiplicative) character of their elementary components. Even in the simplest…

The network concept is increasingly used for the description of complex systems. Here we summarize key aspects of the evolvability and robustness of the hierarchical network-set of macromolecules, cells, organisms, and ecosystems. Listing…

In the last years the debate on complexity has been developing and developing in transdisciplinary way to meet the need of explanation for highly organized collective behaviors and sophisticated hierarchical arrangements in physical,…

We explore how physical scale and population size shape the emergence of complex behaviors in open-ended ecological environments. In our setting, agents are unsupervised and have no explicit rewards or learning objectives but instead evolve…

We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of…

Attention is drawn to the possibility that self-organizing biological neural networks could spontaneously acquire the capability to carry out sophisticated computations. In particular it is shown that the effective action governing the…

We argue that protein native state structures reside in a novel "phase" of matter which confers on proteins their many amazing characteristics. This phase arises from the common features of all globular proteins and is characterized by a…

We consider emergence from the perspective of dynamics: states of a system evolving with time. We focus on the role of a decomposition of wholes into parts, and attempt to characterize relationships between levels without reference to…

This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…

Physical emergence - crystals, rocks, sandpiles, turbulent eddies, planets, stars - is fundamentally different from biological emergence - amoeba, cells, mice, humans - even though the latter is based in the former. This paper points out…

Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…