Related papers: The simple emergence of complex molecular function
Nature features a plethora of extraordinary photonic architectures that have been optimized through natural evolution. While numerical optimization is increasingly and successfully used in photonics, it has yet to replicate any of these…
The theory of interaction-based evolution argues that, at the most basic level of analysis, there is a third alternative for how adaptive evolution works besides a) accidental mutation and natural selection and b) Lamarckism, namely, c)…
To analyze the evolutionary emergence of structural complexity in physical processes we introduce a general, but tractable, model of objects that interact to produce new objects. Since the objects--\emph{$epsilon$-machines}--have well…
A new class of functions is presented. The structure of the algorithm, particularly the selection criteria (branching), is used to define the fundamental property of the new class. The most interesting property of the new functions is that…
The evolution of complexity has been a central theme for Biology [2] and Artificial Life research [1]. It is generally agreed that complexity has increased in our universe, giving way to life, multi-cellularity, societies, and systems of…
We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
Biological networks have evolved to be highly functional within uncertain environments while remaining extremely adaptable. One of the main contributors to the robustness and evolvability of biological networks is believed to be their…
The rise of multicellularity in the early evolution of life represents a major challenge for evolutionary biology. Guidance for finding answers has emerged from disparate fields, from phylogenetics to modelling and synthetic biology, but…
The concept of evolutionary development of structures constituted a \emph{real} revolution in biology: it was possible to understand how the very complex structures of life can arise in an out-of-equilibrium system. The investigation of…
Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…
A phenomenological model of self-organization explaining the emergence of a complexity with features that apparently satisfy the specific criteria usually required for recognizing the appearance of life in laboratory is presented. The…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
One of the longest standing open problems in science is how life arises from non-living matter. If it is possible to measure this transition in the lab, then it might be possible to understand the physical mechanisms by which the emergence…
This work gives a mathematical study of tissue dynamics. We combine within-cell genome dynamics and diffusion between cells, where the synthesis of the two gives rise to the emergence of function. We introduce a concept of monotonicity and…
One of the basic questions of phylogenomics is how gene function evolves, whether among species or inside gene families. In this chapter, we provide a brief overview of the problems associated with defining gene function in a manner which…
The evolution of complexity has been a central theme for Biology and Artificial Life (Bonner, 1988; Bedau et al., 2000). Complexification has been interpreted in different ways: as a process of diversification between evolving units…
We study the probabilities of evolution based on random mutations and natural selection. We conclude that evolution to multicellular eukaryots, or even prokaryots, is unlikely to be the result of only random mutations. Complex organisms…
The functioning of machines typically requires a concerted action of their parts. This requirement also holds for molecular motors that drive vital cellular processes and imposes constraints on their conformational changes as well as the…
A common trait of complex systems is that they can be represented by means of a network of interacting parts. It is, in fact, the network organisation (more than the parts) what largely conditions most higher-level properties, which are not…