Related papers: General Mechanism of Evolution Shared by Proteins …

The origin of life is often framed primarily as a chemical problem, yet life's defining feature is evolution. Advances in geochemistry, prebiotic chemistry, and molecular biology have produced diverse scenarios for the emergence of genomes,…

Much recent work has explored molecular and population-genetic constraints on the rate of protein sequence evolution. The best predictor of evolutionary rate is expression level, for reasons which have remained unexplained. Here, we…

Neural codes appear efficient. Naturally, neuroscientists contend that an efficient process is responsible for generating efficient codes. They argue that natural selection is the efficient process that generates those codes. Although…

Evolution consists of distinct stages: cosmological, biological, linguistic. Since biology verges on natural sciences and linguistics, we expect that it shares structures and features from both forms of knowledge. Indeed, in DNA we…

Molecular biology is a nanotechnology that works--it has worked for billions of years and in an amazing variety of circumstances. At its core is a system for acquiring, processing and communicating information that is universal, from…

The molecular biology revolution of the last seventy five years has transformed our view of living systems. Scientific explanations of biological phenomena are now synonymous with the identification of the genes, proteins, and signaling…

We propose a mathematical framework for natural selection in finite populations. Traditionally, many of the selection-based processes used to describe cultural and genetic evolution (such as imitation and birth-death models) have been…

Human language is one of the most expressive tools for conveying intent, yet most artificial or biological systems lack mechanisms to interpret or respond meaningfully to it. Bridging this gap could enable more natural forms of control over…

Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…

Concomitant with the evolution of biological diversity must have been the evolution of mechanisms that facilitate evolution, due to the essentially infinite complexity of protein sequence space. We describe how evolvability can be an object…

Recent advances in neural network-based generative modeling have reignited the hopes in having computer systems capable of seamlessly conversing with humans and able to understand natural language. Neural architectures have been employed to…

Color naming in natural languages is not arbitrary: it reflects efficient partitions of perceptual color space modulated by the relative needs to communicate about different colors. These psychophysical and communicative constraints help…

We aim to provide an explanation for how the human brain might connect words for sentence formation. A novel approach to modeling syntactic representation is introduced, potentially showing the existence of universal syntactic structures…

We investigate mechanisms for language change within a framework where an unconventional signal for a meaning is first innovated, and then subsequently propagated through a speech community to replace the existing convention. We appeal to…

Human beings are talkative. What advantage did their ancestors find in communicating so much? Numerous authors consider this advantage to be "obvious" and "enormous". If so, the problem of the evolutionary emergence of language amounts to…

Many examples of cooperation exist in biology. In chemical systems however, which can sometimes be quite complex, we do not appear to observe intricate cooperative interactions. A key question for the origin of life, is then how can…

Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM…

The Categorical Compositional Distributional (DisCoCat) Model is a powerful mathematical model for composing the meaning of sentences in natural languages. Since we can think of biological sequences as the "language of life", it is…

We develop a ``unified'' model that describes both ``micro'' and ``macro'' evolutions within a single theoretical framework. The eco-system is described as a dynamic network; the population dynamics at each node of this network describes…

Grammatical features such as number and gender serve two central functions in human languages. While they encode salient semantic attributes like numerosity and animacy, they also offload sentence processing cost by predictably linking…