Related papers: Emergence biases in molecular evolution
Recent work claims that large language models display emergent abilities, abilities not present in smaller-scale models that are present in larger-scale models. What makes emergent abilities intriguing is two-fold: their sharpness,…
The term emergence is increasingly used across scientific disciplines to describe phenomena that arise from interactions among a system's components but cannot be readily inferred by examining those components in isolation. While often…
Phenotype of biological systems needs to be robust against mutation in order to sustain themselves between generations. On the other hand, phenotype of an individual also needs to be robust against fluctuations of both internal and external…
Antagonistic interactions in biological systems, which occur when one perturbation blunts the effect of another, are typically interpreted as evidence that the two perturbations impact the same cellular pathway or function. Yet, this…
Evolution is a dynamic process. The two classical forces of evolution are mutation and selection. Assuming small mutation rates, evolution can be predicted based solely on the fitness differences between phenotypes. Predicting an…
The Extended Evolutionary Synthesis (EES) is beginning to fulfill the whole promise of Darwinian insight through its extension of evolutionary understanding from the biological domain to include cultural information evolution. Several…
An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive…
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…
As large language models (LLMs) are adopted into frameworks that grant them the capacity to make real decisions, it is increasingly important to ensure that they are unbiased. In this paper, we argue that the predominant approach of simply…
Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…
A fundamental question for evolutionary biology is why rates of evolution vary dramatically between proteins. Perhaps surprisingly, it is controversial how much a protein's functional importance affects its rate of evolution. In most…
This paper thoroughly investigates a range of popular DE configurations to identify components responsible for the emergence of structural bias - recently identified tendency of the algorithm to prefer some regions of the search space for…
The Abstraction Refinement Model has been widely adopted since it was firstly proposed many decades ago. This powerful model of software evolution process brings important properties into the system under development, properties such as the…
Is evolution always gradual or can it make leaps? We examine a mathematical model of an evolutionary process on a fitness landscape and obtain analytic solutions for the probability of multi-mutation leaps, that is, several mutations…
Laboratory experiments with bacterial colonies, under well-controlled conditions often lead to evolutionary diversification, where at least two ecotypes emerge from an initially monomorphic population. Empirical evidence suggests that such…
Computational modelling with multi-agent systems is becoming an important technique of studying language evolution. We present a brief introduction into this rapidly developing field, as well as our own contributions that include an…
Robustness, the insensitivity of some of a biological system's functionalities to a set of distinct conditions, is intimately linked to fitness. Recent studies suggest that it may also play a vital role in enabling the evolution of species.…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…
The dynamic instability of the living systems and the "superposition" of different forms of randomness are viewed as a component of the contingently increasing organization of life along evolution. We briefly survey how classical and…
Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions (from molecules in gene regulatory…