Related papers: A framework for parsing heritable information
This chapter reviews the mechanisms by which sensors gather information from the physical world and transform it into the electronic signals that are used in today's information and control systems. It introduces a new methodology for…
Dynamical systems in the life sciences are often composed of complex mixtures of overlapping behavioral regimes. Cellular subpopulations may shift from cycling to equilibrium dynamics or branch towards different developmental fates. The…
Sensor-driven systems are increasingly ubiquitous: they provide both data and information that can facilitate real-time decision-making and autonomous actuation, as well as enabling informed policy choices by service providers and…
The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. Yet, while evolution by natural selection requires new heritable traits to be produced and transmitted, it…
Cognition is the process of knowing. As carried out by a dynamical system, it is the process by which the system absorbs information into its state. A complex network of agents cognizes knowledge about its environment, internal dynamics and…
Humans perceive and interact with hundreds of objects every day. In doing so, they need to employ mental models of these objects and often exploit symmetries in the object's shape and appearance in order to learn generalizable and…
Phenotype-based screening has attracted much attention for identifying cell-active compounds. Transcriptional and proteomic profiles of cell population or single cells are informative phenotypic measures of cellular responses to…
This work illustrates potentials for recognition within {\em ad hoc} sensor networks if their nodes possess individual inter-related biologically inspired genetic codes. The work takes ideas from natural immune systems protecting organisms…
This research project investigates Lenia, an artificial life platform that simulates ecosystems of digital creatures. Lenia's ecosystem consists of simple, artificial organisms that can move, consume, grow, and reproduce. The platform is…
We study the problem of how a ``living'' system complex in structure can respond perfectly to local changes in the environment. Such a system is assumed to consist of a distributed ``living'' medium and a hierarchical ``supplying'' network…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
Understanding and predicting the evolution of across complex systems remains a fundamental challenge due to the absence of unified and computationally testable frameworks. Here we propose the Recursive Hierarchical Network(RHN),…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
There is an imperative need to provide quality of life to a growing population of older adults living independently. Personalised solutions that focus on the person and take into consideration their preferences and context are key. In this…
Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…
We present a systematic evaluation framework - thirty-seven analyses, 153 statistical tests, four cell types, two perturbation modalities - for assessing mechanistic interpretability in single-cell foundation models. Applying this framework…
We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…
Assembly theory predicts that a distinguishing signature of life is its ability to produce complex molecules in abundance, opening new possibilities for life detection. Experimental validation of this approach has so far relied on abiotic…
This paper considers neural representation through the lens of active inference, a normative framework for understanding brain function. It delves into how living organisms employ generative models to minimize the discrepancy between…
Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…