Related papers: Emergence biases in molecular evolution

Gene expression is a biochemical process, where stochastic binding and un-binding events naturally generate fluctuations and cell-to-cell variability in gene dynamics. These fluctuations typically have destructive consequences for proper…

Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. As a result, the key issues of how rapidly…

Irreversibility, in which a transient perturbation leaves a system in a new state, is an emergent property in systems of interacting entities. This property has well-established implications in statistical physics but remains underexplored…

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…

Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…

Diversity is an important factor in evolutionary algorithms to prevent premature convergence towards a single local optimum. In order to maintain diversity throughout the process of evolution, various means exist in literature. We analyze…

Large Language Models (LLMs) are leading a new technological revolution as one of the most promising research streams toward artificial general intelligence. The scaling of these models, accomplished by increasing the number of parameters…

A common theme among the proposed models for network epidemics is the assumption that the propagating object, i.e., a virus or a piece of information, is transferred across the nodes without going through any modification or evolution.…

Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside of the range of conditions to…

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…

Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…

Microbial ecosystems exhibit a surprising amount of functionally relevant diversity at all levels of taxonomic resolution, presenting a significant challenge for most modeling frameworks. A long-standing hope of theoretical ecology is that…

Biological genotypes do not code directly for phenotypes; developmental physiology is the control layer that separates genomes from capacities ascertained by selection. A key aspect is competency, as cells are not a passive material but…

Motivated by present activities in (statistical) physics directed towards biological evolution, we review the interplay of three evolutionary forces: mutation, selection, and genetic drift. The review addresses itself to physicists and…

Emergent communication protocols among humans and artificial neural network agents do not yet share the same properties and show some critical mismatches in results. We describe three important phenomena with respect to the emergence and…

While noise is generally associated with uncertainties and often has a negative connotation in engineering, living organisms have evolved to adapt to (and even exploit) such uncertainty to ensure the survival of a species or implement…

Exposure bias refers to the train-test discrepancy that seemingly arises when an autoregressive generative model uses only ground-truth contexts at training time but generated ones at test time. We separate the contributions of the model…

Cancer progression involves the sequential accumulation of genetic alterations that cumulatively shape the tumour phenotype. In prostate cancer, tumours can follow divergent evolutionary trajectories that lead to distinct subtypes, but the…

Evolutionary Computation is a group of biologically inspired algorithms used to solve complex optimisation problems. It can be split into Evolutionary Algorithms, which take inspiration from genetic inheritance, and Swarm Intelligence…

Molecular traits, such as gene expression levels or protein binding affinities, are increasingly accessible to quantitative measurement by modern high-throughput techniques. Such traits measure molecular functions and, from an evolutionary…