Related papers: A framework for parsing heritable information
Life on earth is distinguished by long-lived correlations in time. The patterns of material organization that characterize living organisms today are contingent on events that occurred billions of years ago. This contingency is a necessary…
Living systems can be understood as organized entities that capture, transform, and reproduce information. Classical gene-centered models explain adaptation through frequency changes driven by differential fitness, yet they often overlook…
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…
What is information, physically, and why does it so reliably emerge in living, cultural, and technological systems? Existing theories quantify uncertainty, cost, or compressibility, but do not identify which physical structures count as…
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…
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…
Despite the obvious advantage of simple life forms capable of fast replication, different levels of cognitive complexity have been achieved by living systems in terms of their potential to cope with environmental uncertainty. Against the…
We consider a living organism as an observer of the evolution of its environment recording sensory information about the state space X of the environment in real time. Sensory information is sampled and then processed on two levels. On the…
Life occurs in concentrated `Ringer Solutions' derived from seawater that Lesser Blum studied for most of his life. As we worked together, Lesser and I realized that the questions asked of those solutions were quite different in biology…
Our binary intuitive understanding of life and lifelikeness is good enough for daily life, but not for research in the natural sciences. Here we propose an operational definition of lifeness of a particular entity as a scalar, product of…
Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…
Similarities between entities occur frequently in many real-world scenarios. For over a century, researchers in different fields have proposed a range of approaches to measure the similarity between entities. More recently, inspired by…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
This paper proposes a conceptual framework in which intelligence and consciousness emerge from relational structure rather than from prediction or domain-specific mechanisms. Intelligence is defined as the capacity to form and integrate…
Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown…
Long ago, life obtained nucleotides in the course of evolution and became a vehicle for them. Before assembly with nucleotides, in the pre-RNA era, what system dominated heredity? What was the subject of survival competition? Is it still a…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…
Previous models for learning the semantic vectors of items and their groups, such as words, sentences, nodes, and graphs, using distributed representation have been based on the assumption that the basic sense of an item corresponds to one…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
The idea of the inheritance of biological processes, such as the developmental process or the life cycle of an organism, has been discussed in the biology literature, but formal mathematical descriptions and plausible data analysis…