Biosystems最新文献

{"title":"The Computational Genesis of a Self: Representational Time and Self-Modeling in Living Systems.","authors":"Poria Azadi","doi":"10.1016/j.biosystems.2026.105990","DOIUrl":"https://doi.org/10.1016/j.biosystems.2026.105990","url":null,"abstract":"<p><p>The transition from inanimate physicochemical dynamics to autonomous agency represents a fundamental challenge across theoretical biology and cognitive science. While traditional accounts have approached this transition through descriptive frameworks of autopoiesis, anticipatory systems, or the free energy principle, a formal deductive derivation linking computational irreducibility to functional agency has remained elusive. Here, a deductive framework demonstrates that core attributes of biological agency, specifically representational time, forward predictive processing, and self-modeling, emerge as operational necessities for an autonomous agent persisting within a computationally irreducible environment under a defined operational regime of delayed hazards and counterfactual pre-commitment. Grounded in organizational closure and viability theory, this framework establishes three principal deductive results. First, it is demonstrated that purely reactive behavioral strategies fail under observationally aliased environmental states requiring mutually incompatible viability-preserving actions; persisting under delayed viability hazards without lethal trial-and-error mandates the internal synthesis of a tripartite representational time. Second, this representational time is shown to share the operational organization of counterfactual forward prediction. Third, drawing upon closed-loop regulator theory, the Conant-Ashby theorem, and the internal model principle, it is established that evaluating candidate interventions over extended horizons (H > 1) in a coupled system requires internalizing the agent's own generative action dynamics, yielding a functional self-model distinct from simple state-dependent regulation. These formal derivations are subsequently grounded in concrete molecular and cellular phenomena, including cyanobacterial KaiABC timekeeping, synthetic protocellular clocks, microbial adaptive regulation, and bacterial chemotaxis, explicitly demarcating experimentally demonstrated substrates from theoretical extrapolations. Finally, the framework develops a theoretical bridge connecting computational irreducibility to the semiotic hypothesis of organic codes as physical adaptors bridging decoupled biological domains, incorporating the code-mediator-artifact distinction. The analysis concludes that within the specified operational regime, functional self-representation emerges as an inevitable computational consequence of autonomous persistence.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105990"},"PeriodicalIF":2.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149225257","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":"REDISCOVERING PEDRO ORTIZ CABANILLAS (1933-2011): PERUVIAN CYBERNETIC AND THE SOCIOBIOLOGICAL INFORMATIONAL THEORY.","authors":"Hans Contreras Pulache","doi":"10.1016/j.biosystems.2026.105989","DOIUrl":"https://doi.org/10.1016/j.biosystems.2026.105989","url":null,"abstract":"<p><p>Pedro Ortiz Cabanillas (1933-2011), a Peruvian neurologist and professor at Universidad Nacional Mayor de San Marcos, spent five decades building an Sociobiological Informational Theory: a systematic account of the universe, life, and organized society built around a single, redefined concept -information- understood as a material structure exclusive to living systems. Two works anchor his legacy: El Sistema de la Personalidad (1994), which gives the theory its first systematic exposition, and the Cuadernos de Psicobiología Social (2017), its most complete formulation. Ortiz proposed a five-level architecture of life (genetic, tissue, neural, psychic, and social information) governed by upward and downward determinations and by the primacy of negentropy over entropy. Working in a Lima hospital without internet access, without sustained contact with international science, and publishing almost exclusively in Spanish, Ortiz's theory remained completely unknown outside Peru. This article situates Ortiz's trajectory and theory historically, summarizes its core architecture -a body of thought that survived, barely, at the edge of disappearance- and argues for its relevance to contemporary debates on information in biology and consciousness.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105989"},"PeriodicalIF":2.1,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149197616","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":"Viability-localized autopoiesis II: Context-indexed repair transport and empirical diagnostics.","authors":"J J Segura","doi":"10.1016/j.biosystems.2026.105978","DOIUrl":"https://doi.org/10.1016/j.biosystems.2026.105978","url":null,"abstract":"<p><p>AP1-AP4 define viability-localized production closure, produced boundaries, admissibility-respecting realization, and existence of a globally coherent viable regime. They do not determine whether a repair relation calibrated in one biological context remains adequate after the context changes. This study develops that second-stage question without introducing a new definition of life or a canonical list of categorical operators. The central construction is a context-indexed family of adequate repair surrogates that separates three claims: local surrogate adequacy in each context, reuse of one selected reference relation across contexts, and existence of any shared context-blind relation over the tested context family. A standard overlap-gluing criterion is specialized to make the strongest incompatibility claim explicit. Two quantitative realizations are analyzed. In an Escherichia coli core flux-balance model, three environmental or reaction constraints remain globally feasible while their growth-capacity readouts differ strongly. In a literature-based repressilator model, all 17 tested contexts remain locally reconstructable with high held-out skill, whereas the relation calibrated at the reference condition has a finite threshold-dependent reuse region. The analysis uses strictly disjoint temporal training and evaluation windows, blocked model selection, persistence and state-support controls, and ten-seed sensitivity analysis. A separately fitted state-only relation remains accurate across the complete tested context family, demonstrating that failure of the selected relation does not imply absence of a shared relation. These calculations provide empirical diagnostics of context dependence while deliberately stopping short of claiming full AP1-AP4 validation or a boundary-specific early-warning law.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105978"},"PeriodicalIF":2.1,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149185156","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":"Fluid-structure interactions in the xylem: A nonlinear reaction-diffusion model of hydraulic segmentation and pressure-actuated microvalves.","authors":"Luis Alberto Hernández-Hernández, Víctor Hugo Pérez-España, Arturo Hernández-Hernández, José Alfredo Pescador-Rojas, Anahí Alvarado-Sánchez, José de Jesús Pelayo Cárdenas, Francisco Javier Martínez-Farías","doi":"10.1016/j.biosystems.2026.105981","DOIUrl":"https://doi.org/10.1016/j.biosystems.2026.105981","url":null,"abstract":"&lt;p&gt;&lt;p&gt;While the Cohesion-Tension theory explains primary advective sap ascent, standard continuous models often neglect the mechanical regulatory role of bordered pits during secondary transport, such as capillary refilling. To address this, we model the conifer xylem as a network of pressure-actuated elastic microvalves governed by fluid-structure interactions. By coupling Darcy flow with state-dependent hydraulic capacitance and aquaporin-mediated transcellular refilling, we derive a macroscopic, asymmetric Fisher-Kolmogorov reaction-diffusion equation. Analytically, unimpeded fluid recovery propagates as coherent saturation wavefronts bounded by a Kolmogorov-Petrovsky-Piskunov critical velocity, which places the threshold on the same scale as overnight hydraulic recovery, although a front velocity for conifer stems is not at present well constrained empirically. If macroscopic diffusivity or elastic buffering rates drop below this structurally invariant limit, the wavefront collapses, providing a theoretical analog for catastrophic hydraulic failure. Conversely, once a refilling front separates a continuous liquid column from an embolized compartment held near atmospheric pressure by its gas phase, the membrane between them sustains the full head of that column-as tension developed at the column's own top, not as a weight resting upon it-and the microvalves actuate when this differential exceeds the elastic restitution limit of the margo. Crucially, our framework evaluates this topological shift via a piecewise integral: valve closures generate structural septa that physically isolate the lower fluid column and mathematically reset the pressure field for subsequent ascent. This provides a formal mathematical demonstration of hydraulic segmentation-the iterative stacking of mechanically decoupled fluid reservoirs, each of which need only sustain the tension generated over its own height rather than over the whole tree. Furthermore, by deducing a state-dependent capacitance factor to enforce absolute fluid-volume conservation, the closed-valve asymptotic limit yields an exact localized profile that functions as a threshold rather than an attractor: it sets a minimum sequestered volume, 4D/γ, below which an isolated reserve is reabsorbed by the surrounding living tissue. These profiles represent hydraulically sequestered capacitive buffers, mathematically mirroring how trees sequence drought responses to prioritize stem elastic water storage. Because the hydrostatic multiplier is fixed by the specific weight of water and the margo threshold has been measured directly, the predicted spacing of these septa follows with no adjustable parameter, and places segmentation in the range 33-97 m for the Pinaceae, its onset governed by the weakest pits of the population-within the range of heights attained by the tallest conifers. We emphasise that this remains a mechanism permitted by the physics and compatible with the known biology rather than one yet de","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105981"},"PeriodicalIF":2.1,"publicationDate":"2026-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149185176","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":"Mathematical modeling and intelligent methods in systems biology and medicine applied to complex diseases: An overview.","authors":"Matías Alvarado-Mentado, Moises Omar León-Pineda, Farid García-Lamont","doi":"10.1016/j.biosystems.2026.105969","DOIUrl":"https://doi.org/10.1016/j.biosystems.2026.105969","url":null,"abstract":"<p><p>This article presents a comprehensive analysis of the intersection between mathematical models, classic algorithmic simulations as well as with machine learnig, alongside their applications, in biology, medicine and bioinformatics. From the first models on population growth and competition, we review the evolution of formalizations to present modeling of complex diseases such as diabetes, cancer, aging, and neurodegenerative disorders. Mathematical models are introduced and categorized, alongside the algorithms and computational methods from deterministic models on exponential and logistic growth, predator-prey dynamics, SIR framework, and cellular automata. The stochastic models on reaction-diffusion, Monte Carlo methods, Markov chains, and Bayesian networks. Thermodynamics-based models on phase transitions and cancer growth; as well the close related Ising Hamiltonian-based models on cancer immunoediting, joint to aspects on genetic and phenotype immune response. The role of classic and deep machine learning -hybrid- models for integrating multi-omic data in challenging scenario prediction. It is highlighted through relevant applications on systems and precision medicine.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105969"},"PeriodicalIF":2.1,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149118084","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":"Formalizing autopoiesis: Toward a Categorical-Thermodynamic Calculus of Closure.","authors":"Rodrigo Ramírez-Tagle","doi":"10.1016/j.biosystems.2026.105918","DOIUrl":"10.1016/j.biosystems.2026.105918","url":null,"abstract":"<p><p>The concept of autopoiesis, introduced by Varela and Maturana (1974) to characterize the organizational closure shared by all living systems, has remained an open challenge for rigorous mathematical treatment. This paper traces Varela's formalization program from Spencer-Brown's calculus of distinctions through the Arithmetic of Closure and Form Dynamics, to the emergence of the Eigenform as a fixed-point model of biological identity. We analyze the methodological gap between this deterministic algebraic framework and the stochastic dynamics characteristic of living systems, and identify it as the central open problem motivating contemporary post-Varelian research. As a programmatic proposal rather than a completed formal system, we outline a Categorical-Thermodynamic Calculus of Closure that would integrate lambda-calculus fixed-point operators, topological category theory, and variational free energy minimization into a common setting for autopoietic systems under thermodynamic noise. We position this proposal within the contemporary cartography of autopoiesis, restrict its scope to autopoiesis in its strict organizational sense, and maintain a clear distinction between autopoietic organization and its formal representation. Rather than claiming a finished formalization, we identify the primitives, open problems, and evaluation criteria that such a formalization would require, and discuss the direction this sets for theoretical biology, cognitive science, and the foundations of autonomous systems.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105918"},"PeriodicalIF":2.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148708449","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":"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}