Biosystems最新文献

{"title":"Names, classification, structure and function and their inter-relationship to the Q cycle, photosynthesis and ATP synthesis","authors":"Brian J. Tindall","doi":"10.1016/j.biosystems.2025.105607","DOIUrl":"10.1016/j.biosystems.2025.105607","url":null,"abstract":"<div><div>At first sight prokaryote nomenclature the Q cycle, photosynthesis and the synthesis of ATP may appear to be poles apart. However, biology has set us a difficult task in taking chemistry and physics, wrapping it up in cloak of proteins, polysaccharides, lipids and nucleic acids and setting science the task of making sense of it all. It is in unravelling that cloak that we find that organisms have developed an amazing array of solutions to surviving on the planet Earth, none more diverse than the Bacteria and Archaea (descriptively “prokaryotes”). Taking a model organism may allow us to solve a particular question by looking at in depth. As we investigate them in more depth it is clear that while a chemical reaction may occur in a diversity of organism, there may be essential differences between very different organisms. In order to communicate what we find there is a need to have a set of standardised terms, like names of chemical compounds, enzymes, parts of organisms or organisms themselves. It is the task of the present paper to link the elements of names, classification, structure and function, the Q cycle, photosynthesis and ATP synthesis.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105607"},"PeriodicalIF":1.9,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145278063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reinterpretation of Jagendorf's classic experiment on photophosphorylation","authors":"Gabi Drochioiu","doi":"10.1016/j.biosystems.2025.105614","DOIUrl":"10.1016/j.biosystems.2025.105614","url":null,"abstract":"<div><div>Photophosphorylation is an anoxygenic process of ATP production, and here we provide relevant insights from recent literature with respect to multiple observations from classical experiments with chloroplasts, archaeal cells, or reconstituted vesicles. Since new and significant information on photophosphorylation has been accumulated, there is a strong necessity to reevaluate the experimental data obtained by Jagendorf, Racker, and other researchers, which were interpreted exclusively in light of the chemiosmotic hypothesis developed by Peter Mitchell. Although unsupported experimentally, the chemiosmotic hypothesis had the merit of proposing a molecular mechanism for the production of ATP molecules in mitochondria, which stimulated further biochemical research. Meanwhile, improved alternatives to the chemiosmotic concept have been advanced, as well as new theories based on recent experimental data. Therefore, it is desirable to carefully evaluate the advantages and drawbacks of these approaches.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105614"},"PeriodicalIF":1.9,"publicationDate":"2025-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145259943","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Neurons and neural networks to model proteins and protein networks.","authors":"Sandhya Samarasinghe, Tran Minh-Thai, Komal Sorthiya, Don Kulasiri","doi":"10.1016/j.biosystems.2025.105613","DOIUrl":"https://doi.org/10.1016/j.biosystems.2025.105613","url":null,"abstract":"<p><p>This study demonstrates the success of Auto-associative neural networks (ANNN) to represent protein networks, where each neuron maps to a protein and each neuron interaction to a specific protein interaction. Core mammalian cell cycle system with 12 proteins was used to train AANN with data generated from an ODE and Boolean models. When tested if AANN can find unknown system interactions, trained AANN with nonlinear (sigmoid) neurons captured accurate system dynamics but failed to capture the correct protein interactions. With correct protein interactions, AANN with linear neurons captured 50% of protein behaviour and sigmoid AANN captured all protein dynamics correctly. This allowed hybrid-AANN with linear and nonlinear neurons. Self-learning ability of AANN was tested but it was not evident in the current model architecture. When tested for their ability to hold past memory by training AANN as a recurrent network, system dynamics revealed near perfect accuracy, with the network heavily relying on the past state to produce the current state. We also tested if neurons can be trained separately and assembled into AANN. Linear, nonlinear and binary (for representing Boolean) neurons were trained. Linear neurons modelled most proteins (70%), and sigmoid neurons modelled all proteins correctly. Binary (perceptron) models successfully replicated Boolean rules of proteins. From these, a number of AANN models were assembled: sigmoid AANN accurately predicted the system; binary AANN revealed correct protein activation with temporal realism; two hybrid-AANN models, one with linear/sigmoid neuron models and another with binary/sigmoid neuron models, were successfully assembled to further simplify models.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105613"},"PeriodicalIF":1.9,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145276578","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The evolution and biophysical economics of energy currencies: from prebiotic electrochemistry to modern digital money","authors":"Anton V. Sukhoverkhov ,&nbsp;Alexey V. Melkikh","doi":"10.1016/j.biosystems.2025.105611","DOIUrl":"10.1016/j.biosystems.2025.105611","url":null,"abstract":"<div><div>The research analyses the evolution of ‘energy currencies’ from proto-metabolic electrochemistry to modern digital economies, theorising future prospects for their development. It examines electrons, hydrogen species (H₂, H⁻, H⁺), acetyl phosphate (AcP), and adenosine triphosphate (ATP) as universal <em>biological energy carriers/currencies</em>. The analysis highlights the <em>fundamental role</em> of electric charge (electricity) across biological and social systems, arguing that electrons (e⁻), protons (H⁺), and ions (Na⁺, K⁺, Ca²⁺, etc.) serve as critical mediators in the transduction of (electric) energy and information. The study augments the theoretical framework of <em>biophysical economics</em> by examining bioenergetics and the evolution of living organisms through the lens of an ‘energy economy’ and its ‘energy currencies’. The human biophysical economy is conceptualised here as an extension of the bioeconomy inherent to living systems, which co-opts analogous natural energy currencies (e.g., electricity). The novelty of the research resides in the development of unified theory of energy currencies that spans three distinct fields: <em>biological approaches</em> that metaphorically refer to certain forms of energy or energy processes as a ‘currency’; <em>social approaches</em> that construe money as a form or analogy of energy (‘virtual energy’), and <em>economic concepts</em> that propose to deploy energy as universal commodity money in trade. It is emphasized that the advent of modern digital currencies has become a critical juncture in the evolution of energy-based currencies, wherein ‘virtual energy’ reverts to an ‘electric flow’, merging energy and currency with ‘information flow’.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105611"},"PeriodicalIF":1.9,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145266323","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spiking neural P systems with structural plasticity and weights","authors":"Guimin Ning ,&nbsp;Shihan Huang ,&nbsp;Yang Deng ,&nbsp;Zhang Sun ,&nbsp;Xiaoxiao Song","doi":"10.1016/j.biosystems.2025.105612","DOIUrl":"10.1016/j.biosystems.2025.105612","url":null,"abstract":"<div><div>Spiking neural (SN) P systems are computational models inspired by the functional and structural attributes of biological neurons and nervous systems. Drawing on insights from biological research, these systems incorporate intriguing mechanisms that have been studied for their computational capabilities and universality. In our current research, we integrate structural plasticity and synaptic weights in synchronous mode, termed as <em>SN P systems with structural plasticity and weights</em> (SNP-SPW systems). These systems utilize plasticity spiking rules to modify their architecture and generate new spikes dynamically. The number of spikes received by post-synaptic neurons could be modulated by the synaptic weights. We have demonstrated that SNP-SPW systems can generate all recursively enumerable sets of numbers, thus establishing their computational universality. Furthermore, we present a small universal SNP-SPW system that requires only nine neurons to perform computing all Turing-computable functions.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105612"},"PeriodicalIF":1.9,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145259887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Beyond the genome: A multi-scale, agent-based taxonomy of biological codes and energetic constraints","authors":"Cris Micheli ,&nbsp;Robert Prinz ,&nbsp;Pier Luigi Gentili","doi":"10.1016/j.biosystems.2025.105604","DOIUrl":"10.1016/j.biosystems.2025.105604","url":null,"abstract":"<div><div>This work critically examines the organizational principles governing living systems and introduces emerging rules that pave the way for a computational approach to understanding life. It challenges the conventional assumption of the modern synthesis, which claims that the code of life resides solely in DNA, genetic networks, and epigenetics. Instead, we argue that the information essential for sustaining life is distributed across multiple scales. Drawing from diverse frameworks such as cybernetics and machine learning, we propose a fresh perspective on this fundamental question.</div><div>We begin by exploring the complexity of life and propose a thoughtfully constructed preliminary taxonomy of biological codes, while recognizing the potential for alternative frameworks. This interpretation integrates speculative ideas from concepts like constraint closure and agent-based modeling, framing the hierarchy of life as governed by a dynamic tension between stability and exploration. Building on this foundation, we analyze the compositional rules and properties of biological codes, uncovering their hierarchical and causal relationships across scales. We emphasize the cell's role as a fundamental cybernetic agent and discuss how this framework contributes to understanding natural phenomena such as cellular differentiation and collaboration.</div><div>The theoretical implications of this perspective highlight the importance of emergence and top-down interactions in fostering complexity. We argue that information distributed across multiple scales is necessary but not sufficient for sustaining life because living systems are open and dynamic, relying fundamentally on environmental interactions, subjected to entropy, mass, and energy exchanges. Additionally, any form of life functions as a physical information-processing system, further emphasizing the intricate interplay between structure and environment. We propose that available energy not only sustains autopoiesis in biological systems, but a fraction of it also drives their adaptation and evolution in an exploratory fashion.</div><div>Finally, we present a practical example and outline future directions for this approach. Specifically, we illustrate how our framework advances the understanding of protein folding agents, particularly in deciphering their regulatory dynamics and interactions with chaperones and organelles. By bridging theoretical concepts with practical examples, this work seeks to provide a framework for analyzing and manipulating complex biological systems, with potential implications for fields such as systems biology and Artificial Intelligence.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105604"},"PeriodicalIF":1.9,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145240159","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The origin and evolution of life as continuing expansion of viral hosts","authors":"Lev G. Nemchinov","doi":"10.1016/j.biosystems.2025.105609","DOIUrl":"10.1016/j.biosystems.2025.105609","url":null,"abstract":"<div><div>The emergence of life on Earth likely involved a complicated evolution of the primeval residues via basic intermediate forms capable of self-replication. These primordial replicators could have further evolved into archaic virus-like structures, which in turn became the precursors of the cellular life forms. If viruses were indeed the predecessors of the first cellular life forms as suggested by the ‘primordial virus world’ and ‘virus-first’ scenarios, could their hosts themselves emerged and evolved predominantly as factories and reservoirs for virus production and dissemination? In other words, is that hypothetically possible that viruses were not only the originators of cellular life forms and the selfish driving force behind their evolution, but the fundamental reason for both their existence and biological heterogeneity? A short note presented here deliberates on this not entirely unfeasible course of events.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105609"},"PeriodicalIF":1.9,"publicationDate":"2025-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145240128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The scientometric approach to Code Biology: What the title tells about the field.","authors":"Omar Paredes, Robert Prinz","doi":"10.1016/j.biosystems.2025.105552","DOIUrl":"10.1016/j.biosystems.2025.105552","url":null,"abstract":"<p><p>Code Biology has emerged as a conceptual framework for investigating how information is encoded, transmitted, and interpreted in living systems. Building on recent efforts to catalog biological codes across disciplines, we present the first comprehensive scientometric analysis of the field. Using a curated corpus of publications explicitly invoking the term code, we apply full-text natural language processing and unsupervised topic modeling to map the intellectual landscape of Code Biology. Our analysis reveals 24 distinct thematic clusters, ranging from molecular mechanisms and regulatory architectures to neural information processing and philosophical discourse on meaning and organization. This approach offers insights that conventional literature reviews often miss-uncovering latent patterns, inter-topic correlations, and conceptual blind spots. In doing so, we expose the field's current fragmentation into isolated knowledge niches and highlight the need for integrative models of how biological codes interact across scales. Temporal and geographical analyses reveal distinct phases in the development of Code Biology, shifting from gene-centric and mechanistic views to increasingly symbolic, cognitive, and systems-oriented paradigms. Collaboration network analysis further shows the emergence of modular scientific communities and identifies key interdisciplinary contributors shaping the field. Taken together, our results establish the foundation for a new branch of code biology, dedicated to the empirical and conceptual mapping of coding processes in biology based on literature. We propose key research directions, including the structural grammar of neural codes, the role of prebiotic and evolutionary codes in transitions of life, and the intersection between biological and artificial coding systems. This work provides not only a roadmap for future research but also a call to develop standardized frameworks capable of bridging molecular, neural, and symbolic dimensions of biological information processing.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105552"},"PeriodicalIF":1.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144812654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Teeth between the eyes: Extra-oral dentition in chimaeras as evidence for biological codes","authors":"João Carlos Major","doi":"10.1016/j.biosystems.2025.105605","DOIUrl":"10.1016/j.biosystems.2025.105605","url":null,"abstract":"<div><div>The recent discovery of functional dentition on the cranial tenaculum of male <em>Hydrolagus colliei</em> (spotted ratfish), published in a 2025 issue of the <em>Proceedings of the National Academy of Sciences</em>, provides a compelling empirical example for the theory of biological codes. Described as a reversal of the long-standing assumption that teeth are exclusively oral structures, this case demonstrates how codified developmental programs can be reused in novel anatomical and functional contexts.</div><div>This paper explores how the appearance of extra-oral teeth illustrates the triadic structure of code, mediator, and artifact as proposed by Code Biology. Drawing on Barbieri's framework and recent research bridging biological, neural, and symbolic systems, the study argues that biological meaning arises through arbitrary yet functional correspondences, activated and modulated by developmentally regulated mediators, leading to adaptive morphological innovations.</div><div>The framework presented is not merely metaphorical; it is empirically grounded, conceptually robust, and testable — offering a powerful explanation not only for evolutionary novelty but also for how structured meaning arises in living, cognitive, and cultural systems. By tracing how biological codes give rise to artifacts of both functional and formal relevance, this case contributes to a broader theoretical model that connects morphogenesis, neural semiosis, and archetypal patterns within a unified semiotic view of life.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105605"},"PeriodicalIF":1.9,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145214279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Are there grounded semantics in (model) organisms?","authors":"Claudio J. Rodríguez Higuera","doi":"10.1016/j.biosystems.2025.105606","DOIUrl":"10.1016/j.biosystems.2025.105606","url":null,"abstract":"<div><div>When trying to convene a sense of <em>meaning</em> as a biological property, we should probably want to figure out how exactly we are supposed to cash out the notion of <em>meaning</em> that we have in mind in the first place. Though certainly not the same, meaning and semantics ought to be seen as related, and satisfying a definition for each is a desirable theoretical step forward in trying to understand whether and how meaning is connected with explanations in biology.</div><div>On the one hand, a constrained definition of <em>semantics</em> is indicative of a linguistic intuition about meaning. On the other, this same notion can stifle a more proper understanding of meaning in simple and non-linguistic organisms. In this paper, I wish to propose a reduced view of <em>content</em> for handling meaning while retaining a guiding notion of semanticity that will influence how we look at experience in non-linguistic organisms. In order to achieve this, I will look at how biology conceptualizes model organisms and propose a philosophical model organism to make our abstract notions of meaning and meaning-making approachable.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105606"},"PeriodicalIF":1.9,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145214317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}