Related papers: The simple emergence of complex molecular function

Many mechanisms, functions and structures of life have been unraveled. However, the fundamental driving force that propelled chemical evolution and led to life has remained obscure. The 2nd law of thermodynamics, written as an equation of…

Natural evolution gives the impression of leading to an open-ended process of increasing diversity and complexity. If our goal is to produce such open-endedness artificially, this suggests an approach driven by evolutionary metaphor. On the…

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…

Darwin's hypothesis that all extant life forms are descendants of a last common ancestor cell and diversification of life forms results from gradual mutation plus natural selection represents a mainstream view that has influenced biology…

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…

Inside every living cell is the cytoplasm: a fluid mixture of thousands of different macromolecules, predominantly proteins. This mixture is where most of the biochemistry occurs that enables living cells to function, and it is perhaps the…

Most real life systems have a random component: the multitude of endogenous and exogenous factors influencing them result in stochastic fluctuations of the parameters determining their dynamics. These empirical systems are in many cases…

The evolution processes of complex systems carry key information in the systems' functional properties. Applying machine learning algorithms, we demonstrate that the historical formation process of various networked complex systems can be…

We apply the theory of learning to physically renormalizable systems in an attempt to develop a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution…

The emergence of collective cooperation in competitive environments is a well-known phenomenon in biology, economics, and social systems. While most evolutionary game models focus on the evolution of strategies for a fixed game, how…

Evolution of life on earth was governed, primarily, by natural selection, with major contribution of other evolutionary processes, such as neutral variation, exaptation, and gene duplication. However, for biological evolution to take off, a…

Biological systems, unlike physical or chemical systems, are characterized by the very inhomogeneous distribution of their components. The immune system, in particular, is notable for self-organizing its structure. Classically, the dynamics…

The function of proteins arises from cooperative interactions and rearrangements of their amino acids, which exhibit large-scale dynamical modes. Long-range correlations have also been revealed in protein sequences, and this has motivated…

How do complex adaptive systems, such as life, emerge from simple constituent parts? In the 1990s Walter Fontana and Leo Buss proposed a novel modeling approach to this question, based on a formal model of computation known as $\lambda$…

The claim that life is an emergent phenomenon exhibiting novel properties and principles is often criticized for being in conflict with causal closure at the microscopic level. I argue that advances in cosmological theory suggesting an…

Scientific progress has long been understood as recombinant, with breakthroughs arising when existing ideas are joined in new ways. Empirical work in this tradition has focused on the inputs to discovery, asking whether a paper draws…

Many systems of interest exhibit nested emergent layers with their own rules and regularities, and our knowledge about them seems naturally organised around these levels. This paper proposes that this type of hierarchical emergence arises…

Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…

One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…

Evolution by natural selection can be seen an algorithm for generating creative solutions to difficult problems. More precisely, evolution by natural selection is a class of algorithms that share a set of properties. The question we address…