Related papers: The Dynamic Replicon: adapting to a changing cellu…
Even the simplest organisms are too complex to have spontaneously arisen fully-formed, yet precursors to first life must have emerged ab initio from their environment. A watershed event was the appearance of the first entity capable of…
Search for possible relationships between phylogeny and ontogeny is one of the most important issues in the field of evolutionary developmental biology. By representing developmental dynamics of spatially located cells with gene expression…
Motivation: Alternative splicing is an important mechanism in which the regions of pre-mRNAs are differentially joined in order to form different transcript isoforms. Alternative splicing is involved in the regulation of normal…
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…
A model of an organism as an autonomous intelligent system has been proposed. This model was used to analyze learning of an organism in various environmental conditions. Processes of learning were divided into two types: strong and weak…
Cell fate decisions in multicellular organisms are precisely coordinated, leading to highly reproducible macroscopic outcomes of developmental processes. The origins of this reproducibility can be found at the molecular level during the…
Artificial organisms are computer programs that self-replicate, mutate, compete and evolve. How do these lifelike information-processing behaviours could arise in diverse far-from-equilibrium physical systems remains an open question. Here,…
In this work, a neural network is trained to replicate the code that trains it using only its own output as input. A paradigm for evolutionary self-replication in neural programs is introduced, where program parameters are mutated, and the…
Can reproduction alone in the context of survival produce intelligence in our machines? In this work, self-replication is explored as a mechanism for the emergence of intelligent behavior in modern learning environments. By focusing purely…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
A big challenge in current biology is to understand the exact self-organization mechanism underlying complex multi-physics coupling developmental processes. With multiscale computations of from subcellular gene expressions to cell…
To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the…
Evolving genomes increase a number of their genes by gene duplications. To escape degradation in a functionless pseudogene, any gene duplicate needs to be guarded by negative (purifying) selection from otherwise inevitable fixation of…
We consider the influence of a terahertz field on the breathing dynamics of double-stranded DNA. We model the spontaneous formation of spatially localized openings of a damped and driven DNA chain, and find that linear instabilities lead to…
The origin and early evolution of eukaryotes are one of the major transitions in the evolution of life on earth. One of its most interesting aspects is the emergence of cellular organelles, their dynamics, their functions, and their…
Behavioral changes in animals and humans, as a consequence of an error or a verbal instruction, can be extremely rapid. Improvement in behavioral performances are usually associated in machine learning and reinforcement learning to synaptic…
Elucidating the architecture and dynamics of large scale genetic regulatory networks of cells is an important goal in systems biology. We study the system level dynamical properties of the genetic network of Escherichia coli that regulates…
We consider an unsupervised classifying agent that evolves by enforcing self-consistency of its labels under continual exposure to a data-generating environment. Because the agent's predictions feed back into its own regularized updates,…
We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state…