Biosystems最新文献

{"title":"Nature of Codes and Codes of Nature: A Short Excursion into the Past and the Future of the Biological Codes.","authors":"Barbora Jurková, Ľudmila Lacková Bennett","doi":"10.1016/j.biosystems.2026.105804","DOIUrl":"https://doi.org/10.1016/j.biosystems.2026.105804","url":null,"abstract":"<p><p>The scopes of this paper are threefold: Firstly, we attempt to illustrate the origins of the idea of digital codes inside of and beyond the field of biology, to better anchor the debate in the historical context. Secondly, we will try to answer the question: what is the explanatory power of the notion of code for today´s biological disciplines? Thirdly, we present a portfolio of possible alternatives to the concept of code and we conclude by proposing that the notion of code is still valid and important for today´s biology, but it cannot be reduced to the only explanatory mechanism nor to the only moving force for life. To bridge code and alternative approaches, we propose the Peirce's model of agapistic evolution.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105804"},"PeriodicalIF":1.9,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147845570","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":"Corrigendum to “Topology as biological code: information-driven evolution of neighborhood structures in self-organizing cellular systems” [Volume 263, May 2026, 105772]","authors":"Chaoran Chen","doi":"10.1016/j.biosystems.2026.105782","DOIUrl":"10.1016/j.biosystems.2026.105782","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"263 ","pages":"Article 105782"},"PeriodicalIF":1.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147624598","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":"Physical factors in origin of genetic code","authors":"Andrei Moldavanov","doi":"10.1016/j.biosystems.2026.105712","DOIUrl":"10.1016/j.biosystems.2026.105712","url":null,"abstract":"<div><div>A consistent physical approach underlying the origin of a genetic code (<em>GC</em>) based on the energy development in an open thermodynamic system (<em>OTS</em>) is considered. The main idea is to present the complex impact of physical environment to open system in the unified form of infinite number of random energy-based factors. Structurally, the suggested approach is divided into two parts. The initial, evolution-irrelevant, part deals with an appearance in <em>OTS</em>'s energy space of the triple-based energy structure due to the performance of the bifurcation points, given the quaternary flow of nucleotides contributing to the forming of <em>64</em> total/<em>20</em> unique codons. The second, evolutionary related part introduces the high-level three-step molecular machine to transform the incoming unique codon into one of <em>20</em> specific amino acids. Since formally the second part transformation is an equation of a dynamic energy balance, the suggested approach is aligned with the direction of evolutionary changes in <em>OTS</em>. Then, in general, the steps of <em>GC</em> evolution are (1) the forming of binary logic in considered energy space; (2) segregation of evolutionary energy space (<em>EES</em>); (3) splitting of <em>EES</em> into a few (2, 3, or 6 energy phases; (4) interaction of <em>4-</em>kinds flow of free nucleotides with the multi-phase <em>EES</em>; (5) the forming of original <em>GC</em>; (6) concurrence of the formed realizations of <em>GC</em> and arising of the master <em>4</em>^<em>3</em> version. The properties of the simulated <em>GC</em> are checked against the concrete observables. The used physical factors of an environment are the conserved quantities: energy, momentum, angular momentum, electric charge, and others.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"262 ","pages":"Article 105712"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146133676","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":"What kinds of empirical correlates for a general theory of living organization? Revisiting the (M, R)-system and its ‘replication’","authors":"Markus Mikael Weckström","doi":"10.1016/j.biosystems.2026.105720","DOIUrl":"10.1016/j.biosystems.2026.105720","url":null,"abstract":"<div><div>Robert Rosen proposed in the late 1950s the metabolism-repair or the (<strong><em>M, R</em></strong>)-system as a general model of living organization, or any “autonomous life form.” Since then, the model has persisted as a recurring subject of interest in certain areas of theoretical biology; however, beyond those specific circles, its influence on biological thought has remained minor. One likely reason for this is the difficulty of interpreting the conceptual insights of the model in concrete terms, which Rosen himself identified as the basically unresolved “realization problem.” In more recent literature, attempts to do so have focused relatively strictly on the cellular or even biochemical context, and suggested changes to the model's basic nomenclature: most notably, the technical term ‘replication’ appearing in the model has been interpreted as something quite unrelated to replication in the usual biological meaning of the term. The aim of the present paper is to argue, firstly, that this is likely to be a deviation from Rosen's original intentions, and secondly, that quite apart from those intentions, there is a practical way of applying the (<strong><em>M, R</em></strong>)-system for organizing standard empirical knowledge about any living organism, multicellulars included, and furthermore in such a way that formal ‘replication’ directly relates to biological replication. Without supposing this new practical scheme to be perfect or beyond further refinement, it is shown to exemplify an analytical point of view that is not covered by more familiar biological theories.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"262 ","pages":"Article 105720"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138118","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":"First evidence supporting the theory of the sensorimotor paradox on the origins of mind and language","authors":"Clémence Ortega Douville","doi":"10.1016/j.biosystems.2026.105691","DOIUrl":"10.1016/j.biosystems.2026.105691","url":null,"abstract":"<div><div>For now 15 years, I have been developing a hypothesis on the origins of mind and language during our evolution, called theory of the sensorimotor paradox. The core neuroimaging part of the hypothesis is that the switch in our relation to our hands, coming with bipedal stance, would have allowed us to disrupt the function of sensory prediction to resolve into motor action and sensory feedback: we can't take our hand as an object of interaction and have it grasp itself at the same time. This would later on be autonomised as mental representation. From there, non-resolution of prediction into motor action would prevent a system from liberating tension in order to be available again and collect feedback (meta-prediction). Using Schalk, G. et al.'s extensive dataset of EEG recordings on motor movement and imagery (2009), I am now able to support some of the theory's claims. Notably, meta-analysis of movement and imagery recordings tends to stress a higher variability of frequency activation amongst motor signals than imagery's. This would indicate a greater difficulty for a system to release tension in an effort to produce and maintain mental representation. Similar short oscillatory predictive change, but greater uncoupling of frontal and prefrontal regions suggests sensory suppression of efference-copy and greater instability toward the eventuality of collecting feedback when motor action is triggered, relying on somatosensory support. Event-related time-frequency analysis on proprioceptive areas shows delay of neural signal to mental representation compared to motor action, which could be a strong evidence of dissociation.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"262 ","pages":"Article 105691"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145985760","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":"Simulating tumor mitochondrial energetics through engineering-style energy metrics","authors":"Arturo Tozzi","doi":"10.1016/j.biosystems.2026.105719","DOIUrl":"10.1016/j.biosystems.2026.105719","url":null,"abstract":"<div><div>Cancer progression is linked to alterations in cellular energetics, where malignant cells reprogram their metabolism to sustain proliferation, resist stress and adapt to nutrient limitations. Recent work has shown that tumors actively remodel their microenvironment by acquiring functional mitochondria from surrounding stromal or immune cells. Mitochondrial transfer enhances tumor bioenergetics while simultaneously depleting immune cells of metabolic competence, thereby reinforcing both tumor growth and immune evasion. The energetic consequences in terms of throughput, efficiency and stored energy of these exchanges are not captured by conventional assays focused on oxygen consumption or glycolytic flux. We introduce a simulation-based framework for theoretical analysis of mitochondrial energetics that adapts engineering-style energy metrics to mitochondrial biology. Three theoretical, model-defined bioenergetic metrics are introduced: mitochondrial power density, expressing ATP production per unit mitochondrial volume; mitochondrial surface power density, relating ATP production to inner membrane area; and mitochondrial energy density, quantifying stored chemical free energy per unit volume. Using controlled in silico simulations of tumor and immune cell populations before and after modeled mitochondrial transfer, we examine how these descriptors vary under explicit simulation assumptions. Within our simulation framework, results indicate model-predicted differences between cell populations, with tumor-associated mitochondria occupying higher energetic throughput and immune-associated mitochondria exhibiting complementary reductions. Although exploratory and hypothesis-generating rather than validated biomarkers or clinical tools, our metrics provide a quantitative physical framework that may inform experimental studies of mitochondrial transfer and its energetic consequences, including efforts to disrupt pathogenic transfer and restore metabolic competence in immune cells.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"262 ","pages":"Article 105719"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146135628","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":"Why are the most lethal pathogens the simplest? Lack of D-amino acid usage, coherent fractal morphology, and Hz-level biological oscillations prevalent in beneficial pathogens","authors":"Monica M. Araujo","doi":"10.1016/j.biosystems.2026.105713","DOIUrl":"10.1016/j.biosystems.2026.105713","url":null,"abstract":"<div><div>This paper examines a biochemical paradox in microbial pathogenicity: the most lethal human pathogens (viruses, protozoa, prions) systematically lack D-amino acid usage, coherent fractal morphology, and Hz-level biological oscillations; these characteristics prevail in beneficial and treatable bacterial pathogens. Systematic analysis of 47 major human pathogens and quantitative fractal dimension analysis of 40 cryo-electron microscopy structures unveil refined hierarchical patterns within universally low structural complexity.</div><div>Bacterial pathogens employ D-amino acids in peptidoglycan synthesis and exhibit a broad structural repertoire spanning from 1.2610 to 1.9625 (mean 2D fractal dimension = 1.5502 ± 0.2543), overlapping the upper protozoal band (mean = 1.5865 ± 0.1322). Protozoa therefore show the highest central complexity, while bacteria display the widest variance and retain access to higher-order organization. Increasingly lethal pathogens systematically lack these features and occupy progressively reduced complexity bands (Fungi: 1.5074 ± 0.1600; Virus: 1.4388 ± 0.2575; Prion: 1.4060 ± 0.1727).</div><div>Among all structures analyzed, the HIV-1 capsid displayed the lowest complexity (D₂D = 1.1095), consistent with its historically high lethality and over 40 million cumulative deaths since the 1980s.</div><div>We propose that this evolutionary minimalism represents a convergent pathogenic strategy in which successful pathogens attain reduced complexity, with the most lethal variants pushing simplification to extreme levels characterized by biochemical invisibility and structural incoherence. D-amino acid absence enables evasion of host innate immune recognition through D-amino acid oxidase, while lack of intrinsic circadian rhythms prevents metabolic synchronization and immune detection. This framework provides measurable criteria for pathogen threat assessment and suggests new therapeutic approaches rooted in complexity-based medicine.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"262 ","pages":"Article 105713"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146127385","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":"Thermodynamic ontogeny: The emergence of persistence and complexity in pre-genetic chemical systems","authors":"Albert M. Magro","doi":"10.1016/j.biosystems.2026.105717","DOIUrl":"10.1016/j.biosystems.2026.105717","url":null,"abstract":"<div><div>Understanding how thermodynamic principles drive the emergence of organized chemical systems from abiotic geochemistry represents a central challenge in prebiotic evolution. We develop a quantitative framework for systems removed from equilibrium, establishing formulations for organizational complexity (C) and persistence (P). Complexity, the volumetric rate of free energy dissipation maintaining non-equilibrium organization, scales with substrate gradients and kinetic accessibility. Persistence is the system’s capacity to export internally generated entropy across membrane boundaries, determined by geometric constraints and transport impedances. Bejan’s Constructal Law provides the optimization principle by which protocell geometry morphs to achieve this balance, providing a deterministic basis for protocell dimensions and molecular architecture. For mineral-catalyzed chemistry at hydrothermal vents (<span><math><mrow><mrow><mo>〈</mo><mtext>Ea</mtext><mo>〉</mo></mrow><mo>≈</mo></mrow></math></span> 50 kJ/mol, T <span><math><mo>≈</mo></math></span> 338 K), the framework predicts optimal radius r <span><math><mrow><mo>≈</mo><mn>0</mn><mo>.</mo><mn>56</mn><mspace></mspace><mi>μ</mi></mrow></math></span>m for volume-distributed chemistry (n = 3), matching observed dimensions of experimental protocells and minimal cells. Conversely, surface-limited chemistry (n = 2) predicts mechanically unstable configurations, establishing the internalization of metabolism as a thermodynamic necessity. Geological subsidence at polar regions provides deterministic forcing driving protocell populations toward increasing complexity over multi-million-year timescales. The transition from monomers to polymers is a necessary strategy to mitigate osmotic stress during subsidence, effectively responding to a baric forcing of complexity. The framework generates falsifiable predictions where ln(r) <span><math><mo>∝</mo></math></span> 1/T, with a slope determined by activation energy and dimensionality. The framework transforms a prebiotic system from a statistical improbability into a predictable physical outcome, establishing the foundations for life as a thermodynamic necessity operating under early Earth constraints.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"262 ","pages":"Article 105717"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138149","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":"Automated quantitative analysis of differences in Caenorhabditis elegans head swings and omega turns among strains","authors":"Wenyue Zhan ,&nbsp;Weiyang Chen ,&nbsp;Yi Pan","doi":"10.1016/j.biosystems.2026.105716","DOIUrl":"10.1016/j.biosystems.2026.105716","url":null,"abstract":"<div><div>Neurodegenerative diseases have recently garnered significant attention. To better understand the pathogenesis of these diseases and find effective treatments, scientists are increasingly using model organisms in their research. Nematodes, a model organism for studying neurodegenerative diseases, offer crucial insights into the relationship between genes, motor neurons, and locomotion behavior. By identifying the positions of nematodes using a head and tail localization model and automatically counting head swings and omega turns, the analysis of behavioral differences among various nematode strains demonstrates the connection between locomotion behavior and motor neurons. The results from automated counting serve as key indicators of motor neuron integrity, emphasizing the importance of nervous regulation in nematode locomotion behavior and providing new avenues for studying sensory systems and behavioral mechanisms. This has potential implications for the treatment of neurodegenerative diseases.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"262 ","pages":"Article 105716"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138049","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":"Evolution of pre-genetic semantic information in protocells under variable inheritance fidelity","authors":"Michael J. Carr","doi":"10.1016/j.biosystems.2026.105718","DOIUrl":"10.1016/j.biosystems.2026.105718","url":null,"abstract":"<div><div>How meaningful, heritable structure first emerged in prebiotic chemical systems remains a central open question in origins-of-life research. Classical frameworks such as the quasispecies and RNA-world models assume that accurate template-based replication is required for stable information and functional specificity to evolve. This work introduces a minimal agent-based protocell model in which short RNA-like oligomers bind metabolites along local 5-nt motifs, generating spatial organization without catalysis or replication. Protocells inherit molecular contents solely through noisy physical partitioning, allowing assessment of whether semantic structure—quantified as mutual information between motif identity and metabolite class—can arise under purely compositional heredity. Across an inheritance-fidelity sweep (0.1–1.0), a sharp semantic threshold was identified: below moderate fidelity, motif–metabolite correlations cannot accumulate, whereas above the threshold (∼0.7), semantic information increases rapidly and stabilizes as a heritable population property. Fitness gains lag behind semantic structure and become substantial only at high fidelity, indicating that meaning emerges before adaptive function. These results establish a pre-genetic information system in which environmental semantics arises without replication, providing a conceptual bridge between compositional inheritance models and sequence-based evolutionary theories.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"262 ","pages":"Article 105718"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138125","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}