Related papers: A note on retrodiction and machine evolution
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…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
The ribosome is one of the largest and most complex macromolecular machines in living cells. It polymerizes a protein in a step-by-step manner as directed by the corresponding nucleotide sequence on the template messenger RNA (mRNA) and…
Networks are widely used to represent interaction pattern among the components in complex systems. Structures of real networks from differ- ent domains may vary quite significantly. Since there is an interplay be- tween network architecture…
The biological world, especially its majority microbial component, is strongly interacting and may be dominated by collective effects. In this review, we provide a brief introduction for statistical physicists of the way in which living…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate, real-time data about their environmental conditions, but the biochemical reaction…
Recently, computational modelling became a very important research tool that enables us to study problems that for decades evaded scientific analysis. Evolutionary systems are certainly examples of such problems: they are composed of many…
The paradigm of large language models in natural language processing (NLP) has also shown promise in modeling biological languages, including proteins, RNA, and DNA. Both the auto-regressive generation paradigm and evaluation metrics have…
One can study communications by using Shannon's (1948) mathematical theory of communication. In social communications, however, the channels are not "fixed", but themselves subject to change. Communication systems change by communicating…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
Molecular communication promises to enable communication between nanomachines with a view to increasing their functionalities and open up new possible applications. Due to some of the biological properties, bacteria have been proposed as a…
The architecture of biological networks has been reported to exhibit high level of modularity, and to some extent, topological modules of networks overlap with known functional modules. However, how the modular topology of the molecular…
Currently, biological signaling is envisaged as a combination of activation and movement, triggered by local molecular interactions and molecular diffusion, respectively. However, we here suggest, that other fundamental physical mechanisms…
Proteins play crucial roles in every cellular process by interacting with each other, with nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental…
In current molecular communication (MC) systems, performing computational operations at the nanoscale remains challenging, restricting their applicability in complex scenarios such as adaptive biochemical control and advanced nanoscale…
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…
Identifying and understanding the large-scale biodiversity patterns in time and space is vital for conservation and addressing fundamental ecological and evolutionary questions. Network-based methods have proven useful for simplifying and…
Human language emerged abruptly. Diverse body forms evolved suddenly. Seed-bearing plants spread rapidly. How do complex evolutionary innovations arise so quickly? Resolving alternative claims remains difficult. The great events of the past…
Molecular communication is an expanding body of research. Recent advances in biology have encouraged using genetically engineered bacteria as the main component in the molecular communication. This has stimulated a new line of research that…