Pub Date : 2025-12-02DOI: 10.1016/j.biosystems.2025.105666
Bruno Gašperov, Branko Šter
Selection pressure, determining which individuals survive and reproduce, is traditionally regarded as an exogenous property of the environment. However, growing evidence from the Extended Evolutionary Synthesis (EES) suggests that the strength of selection can, to some extent, be modulated by the organisms themselves. In this paper, we propose a minimal game-theoretical model that formalizes the concept of endogenous selection pressure. In the model, individuals collectively determine the intensity of selection through their actions: each agent “votes” to either intensify or relax selection depending on its relative fitness rank. The aggregate outcome of these decisions defines the number of reproducers, , which is inversely related to the overall strength of selection. We analytically derive all pure strategy Nash equilibria of the game and examine their properties. By internalizing selection as a population-level emergent variable, the framework provides a tractable formalization of key principles from the EES and offers a foundation for exploring evolutionary dynamics that arise under the presence of endogenous selection pressure.
{"title":"Endogenous regulation of selection pressure: A minimal game-theoretical model","authors":"Bruno Gašperov, Branko Šter","doi":"10.1016/j.biosystems.2025.105666","DOIUrl":"10.1016/j.biosystems.2025.105666","url":null,"abstract":"<div><div>Selection pressure, determining which individuals survive and reproduce, is traditionally regarded as an exogenous property of the environment. However, growing evidence from the Extended Evolutionary Synthesis (EES) suggests that the strength of selection can, to some extent, be modulated by the organisms themselves. In this paper, we propose a minimal game-theoretical model that formalizes the concept of <em>endogenous selection pressure</em>. In the model, individuals collectively determine the intensity of selection through their actions: each agent “votes” to either intensify or relax selection depending on its relative fitness rank. The aggregate outcome of these decisions defines the number of reproducers, <span><math><mi>k</mi></math></span>, which is inversely related to the overall strength of selection. We analytically derive all pure strategy Nash equilibria of the game and examine their properties. By internalizing selection as a population-level emergent variable, the framework provides a tractable formalization of key principles from the EES and offers a foundation for exploring evolutionary dynamics that arise under the presence of endogenous selection pressure.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105666"},"PeriodicalIF":1.9,"publicationDate":"2025-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145679369","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}
Pub Date : 2025-12-01DOI: 10.1016/j.biosystems.2025.105665
Yifan Li , Denisa Vlasceanu , Ruby Kim
Tumor heterogeneity results from the continuous accumulation of mutations in cancer cells. High phenotypic diversity in cancer can reduce the efficacy of precisely targeted adaptive immune responses. To investigate the conditions under which tumor heterogeneity is sufficient for immune evasion, we developed an agent-based model at the level of individual cells. In this model, cancer phenotypes are represented as vectors, with mutation as a random walk on the corresponding phenotypic space. We evaluated various immune activation strategies by modulating the affinity threshold for activation and assessed their impact on tumor clearance rates. First, the model exhibited oscillatory behavior consistent with empirical observation, that we hypothesized was driven by negative frequency dependent selection. Further supporting this mechanism, the variance of cancer phenotypes consistently increases as the cancer population collapses. Finally, we identified conditions favoring either narrow or broad immune activation profiles, in accordance with theoretical predictions. These findings suggest potential strategies for optimizing immunotherapies, such as adoptive cell therapy, by tailoring the antigenic repertoire used to prime immune cells according to the adaptive dynamics of the target tumor population.
{"title":"Immune response precision customized to tumor adaptive kinetics","authors":"Yifan Li , Denisa Vlasceanu , Ruby Kim","doi":"10.1016/j.biosystems.2025.105665","DOIUrl":"10.1016/j.biosystems.2025.105665","url":null,"abstract":"<div><div>Tumor heterogeneity results from the continuous accumulation of mutations in cancer cells. High phenotypic diversity in cancer can reduce the efficacy of precisely targeted adaptive immune responses. To investigate the conditions under which tumor heterogeneity is sufficient for immune evasion, we developed an agent-based model at the level of individual cells. In this model, cancer phenotypes are represented as vectors, with mutation as a random walk on the corresponding phenotypic space. We evaluated various immune activation strategies by modulating the affinity threshold for activation and assessed their impact on tumor clearance rates. First, the model exhibited oscillatory behavior consistent with empirical observation, that we hypothesized was driven by negative frequency dependent selection. Further supporting this mechanism, the variance of cancer phenotypes consistently increases as the cancer population collapses. Finally, we identified conditions favoring either narrow or broad immune activation profiles, in accordance with theoretical predictions. These findings suggest potential strategies for optimizing immunotherapies, such as adoptive cell therapy, by tailoring the antigenic repertoire used to prime immune cells according to the adaptive dynamics of the target tumor population.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105665"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145670557","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}
Pub Date : 2025-12-01DOI: 10.1016/j.biosystems.2025.105647
Georgi Yordanov Georgiev
How and why do complex chemical and biological systems self-organize into ordered states far from thermodynamic equilibrium? Despite advances in thermodynamics, kinetics, and information theory, a unifying principle that links organization and efficiency across scales has remained elusive. If systems are open, the endpoints of the trajectories are restricted to the source and sink. We propose a stochastic-dissipative least-action triad framework in which (i) a path-ensemble weighting biases trajectories by their action cost, (ii) feedback processes sharpen this distribution, and (iii) the ensemble approaches a least-average-action attractor in steady state; otherwise it continues to decrease. We define a parametric cross-scale metric-Average Action Efficiency (AAE), the number of events over total action for them-and show that, under reinforcing feedback, identities derived from the exponential-family path measure imply decreasing average action and monotonically rising AAE. Our formulation could help bridge in its future extensions quantum, classical, and biological regimes while remaining computationally tractable because its empirical version relies on aggregate energetic and timing data rather than enumerating individual trajectories. At a non-equilibrium steady state, AAE reaches a local maximum consistent with the conditions and limitations of the current formulation. We connect AAE to thermodynamic and informational measures. A companion article (Part II) details empirical estimation strategies and applications.
{"title":"Stochastic-dissipative least-action framework for self-organizing biological systems, Part I: Variational rationale and Lyapunov-type behavior.","authors":"Georgi Yordanov Georgiev","doi":"10.1016/j.biosystems.2025.105647","DOIUrl":"https://doi.org/10.1016/j.biosystems.2025.105647","url":null,"abstract":"<p><p>How and why do complex chemical and biological systems self-organize into ordered states far from thermodynamic equilibrium? Despite advances in thermodynamics, kinetics, and information theory, a unifying principle that links organization and efficiency across scales has remained elusive. If systems are open, the endpoints of the trajectories are restricted to the source and sink. We propose a stochastic-dissipative least-action triad framework in which (i) a path-ensemble weighting biases trajectories by their action cost, (ii) feedback processes sharpen this distribution, and (iii) the ensemble approaches a least-average-action attractor in steady state; otherwise it continues to decrease. We define a parametric cross-scale metric-Average Action Efficiency (AAE), the number of events over total action for them-and show that, under reinforcing feedback, identities derived from the exponential-family path measure imply decreasing average action and monotonically rising AAE. Our formulation could help bridge in its future extensions quantum, classical, and biological regimes while remaining computationally tractable because its empirical version relies on aggregate energetic and timing data rather than enumerating individual trajectories. At a non-equilibrium steady state, AAE reaches a local maximum consistent with the conditions and limitations of the current formulation. We connect AAE to thermodynamic and informational measures. A companion article (Part II) details empirical estimation strategies and applications.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105647"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145670579","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}
Pub Date : 2025-11-29DOI: 10.1016/j.biosystems.2025.105663
Veysi Başhan
Marine Growth Prevention Systems (MGPS) are vital for maintaining vessel efficiency, reducing biofouling, and ensuring sustainable operation under variable marine conditions. However, their performance is often challenged by complex interdependencies among design, thermodynamic, and operational factors. In this study, a fuzzy DEMATEL (Decision Making Trial and Evaluation Laboratory) approach is employed to systematically evaluate and prioritize fifteen critical factors affecting MGPS effectiveness. The analysis integrates Constructal Law principles and bio-inspired design concepts to capture the dynamic interplay between entropy generation, copper ion distribution, electrode configuration, and structural adaptability. Expert evaluations from oceangoing chief engineers with academic and operational experience were used to construct the causal model. The results show that Structural Topology Efficiency (C13) and Evolutionary Robustness under Changing Conditions (C15) exhibited the highest causal influence (rᵢ – cⱼ > 0.35), whereas Biological Antifouling Analogy Consistency (C10) was found to be the most dependent factor (rᵢ – cⱼ < −0.28). Incorporating Constructal alignment principles reduced estimated entropy generation suggesting that thermodynamically optimized configurations can substantially enhance antifouling performance and energy efficiency. The cause–effect diagram highlights that adaptive topology and control responsiveness act as dominant design drivers, shaping electrochemical and flow-related outcomes. This study contributes to the literature by bridging fuzzy multi-criteria decision-making with thermodynamic and bio-organizational perspectives, offering both theoretical insights and practical design guidance. Furthermore, the findings open new research avenues toward integrating Constructal Law optimization with AI-based predictive control, CFD–multi-physics coupling, and self-healing MGPS architectures for next-generation sustainable marine systems.
海洋防生长系统（MGPS）对于维持船舶效率、减少生物污染和确保在多变的海洋条件下可持续运行至关重要。然而，它们的性能经常受到设计、热力学和操作因素之间复杂的相互依赖关系的挑战。本研究采用模糊DEMATEL （Decision Making Trial and Evaluation Laboratory）方法，对影响MGPS有效性的15个关键因素进行系统评价和排序。该分析整合了构造法原理和仿生设计概念，以捕捉熵产生、铜离子分布、电极配置和结构适应性之间的动态相互作用。利用具有学术和操作经验的远洋总工程师的专家评价，构建了因果模型。结果表明，结构拓扑效率（C13）和变化条件下的进化稳健性（C15）的因果影响最大（r′′- cⱼ> 0.35），而生物防垢类比一致性（C10）是最相关的因素（r′′- cⱼ< -0.28）。结合结构对齐原则减少了估计的熵产生，这表明热力学优化的配置可以大大提高防污性能和能源效率。因果关系图强调，自适应拓扑和控制响应性是主要的设计驱动因素，形成电化学和流动相关的结果。本研究通过将模糊多准则决策与热力学和生物组织的观点联系起来，为文献做出了贡献，提供了理论见解和实际设计指导。此外，研究结果为将结构化优化与基于人工智能的预测控制、cfd -多物理场耦合和自修复MGPS体系结构集成到下一代可持续海洋系统开辟了新的研究途径。
{"title":"Integrating fuzzy DEMATEL and Constructal Law for biofouling dynamics in Marine Growth Prevention Systems","authors":"Veysi Başhan","doi":"10.1016/j.biosystems.2025.105663","DOIUrl":"10.1016/j.biosystems.2025.105663","url":null,"abstract":"<div><div>Marine Growth Prevention Systems (MGPS) are vital for maintaining vessel efficiency, reducing biofouling, and ensuring sustainable operation under variable marine conditions. However, their performance is often challenged by complex interdependencies among design, thermodynamic, and operational factors. In this study, a fuzzy DEMATEL (Decision Making Trial and Evaluation Laboratory) approach is employed to systematically evaluate and prioritize fifteen critical factors affecting MGPS effectiveness. The analysis integrates Constructal Law principles and bio-inspired design concepts to capture the dynamic interplay between entropy generation, copper ion distribution, electrode configuration, and structural adaptability. Expert evaluations from oceangoing chief engineers with academic and operational experience were used to construct the causal model. The results show that Structural Topology Efficiency (C13) and Evolutionary Robustness under Changing Conditions (C15) exhibited the highest causal influence (rᵢ – cⱼ > 0.35), whereas Biological Antifouling Analogy Consistency (C10) was found to be the most dependent factor (rᵢ – cⱼ < −0.28). Incorporating Constructal alignment principles reduced estimated entropy generation suggesting that thermodynamically optimized configurations can substantially enhance antifouling performance and energy efficiency. The cause–effect diagram highlights that adaptive topology and control responsiveness act as dominant design drivers, shaping electrochemical and flow-related outcomes. This study contributes to the literature by bridging fuzzy multi-criteria decision-making with thermodynamic and bio-organizational perspectives, offering both theoretical insights and practical design guidance. Furthermore, the findings open new research avenues toward integrating Constructal Law optimization with AI-based predictive control, CFD–multi-physics coupling, and self-healing MGPS architectures for next-generation sustainable marine systems.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105663"},"PeriodicalIF":1.9,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145650101","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}
Pub Date : 2025-11-28DOI: 10.1016/j.biosystems.2025.105664
Nicola Zengiaro
This article interrogates the ontological status of the virus, an entity that lacks cellular autonomy yet exhibits core evolutionary dynamics, to expose the limitations of classical definitions of life. The analysis moves beyond this classificatory impasse by integrating the paradigm of reticulate evolution, which repositions viruses as central agents in life's network history, with a materialist biosemiotics. This synthesis supports the paper's central thesis: that life is not an intrinsic property but an emergent condition defined by semiotic processes. To formalize this, we introduce the concept of semiotic resonance, a theoretical model defining life as the emergence of recursive interpretive coupling between material systems. This mechanism provides a physical and semiotic basis for biological organization, bridging the arbitrariness of codes with their material enactment. Ultimately, by reframing the virus as a paradigmatic case of resonance-dependent existence, this work proposes a shift in the study of life itself: away from classifying entities and toward an analysis of the relational thresholds where matter, meaning, and evolution converge.
{"title":"Viral thresholds and semiotic resonance: Rethinking the continuum between life and non-life","authors":"Nicola Zengiaro","doi":"10.1016/j.biosystems.2025.105664","DOIUrl":"10.1016/j.biosystems.2025.105664","url":null,"abstract":"<div><div>This article interrogates the ontological status of the virus, an entity that lacks cellular autonomy yet exhibits core evolutionary dynamics, to expose the limitations of classical definitions of life. The analysis moves beyond this classificatory impasse by integrating the paradigm of reticulate evolution, which repositions viruses as central agents in life's network history, with a materialist biosemiotics. This synthesis supports the paper's central thesis: that life is not an intrinsic property but an emergent condition defined by semiotic processes. To formalize this, we introduce the concept of semiotic resonance, a theoretical model defining life as the emergence of recursive interpretive coupling between material systems. This mechanism provides a physical and semiotic basis for biological organization, bridging the arbitrariness of codes with their material enactment. Ultimately, by reframing the virus as a paradigmatic case of resonance-dependent existence, this work proposes a shift in the study of life itself: away from classifying entities and toward an analysis of the relational thresholds where matter, meaning, and evolution converge.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105664"},"PeriodicalIF":1.9,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145650044","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}
Pub Date : 2025-11-26DOI: 10.1016/j.biosystems.2025.105661
Giuseppe Iurato
From a biological standpoint, the consciousness of a living organism equipped with a complex nervous system may be considered the result of the complex structure and functioning of its brain. Subsequently, the neurobiological bases of consciousness should be traced back to the systemic nature of the macroscale neural circuitries of the brain, which are, in turn, the basic outcomes of certain fundamental microscale neuronal processes whose spatiotemporal action gives rise to a much more complex systemic process called neural plasticity. It is closely related to brain evolution from both phylogenetic and ontogenetic perspectives. It is the primary neurobiological process that links the brain with internal and external environments and the related experiences. Since consciousness is a theoretical construct introduced mainly to account for the (ontogenetically evolving) integrative subject-object intermediation, it might be possible hypothesize the existence of a relationship between consciousness and neural plasticity, at least from a biological standpoint. In these terms, the phylogenetic development of human consciousness, when human lineage started after the split from that of nonhuman primates, might be partially inferred by comparing the (ontogenetic) development of human and nonhuman primate brains, using an extended meaning of the concept of neural plasticity as the main neurobiological process of reference. What seems to emerge from this comparison is the evolutionary occurrence, during anthropogenesis, of distinguishing (transcriptional) heterochronic phenomena concerning neurodevelopmental processes.
{"title":"Neural plasticity, heterochrony, and the onto-phylogeny of consciousness","authors":"Giuseppe Iurato","doi":"10.1016/j.biosystems.2025.105661","DOIUrl":"10.1016/j.biosystems.2025.105661","url":null,"abstract":"<div><div>From a biological standpoint, the consciousness of a living organism equipped with a complex nervous system may be considered the result of the complex structure and functioning of its brain. Subsequently, the neurobiological bases of consciousness should be traced back to the systemic nature of the macroscale neural circuitries of the brain, which are, in turn, the basic outcomes of certain fundamental microscale neuronal processes whose spatiotemporal action gives rise to a much more complex systemic process called neural plasticity. It is closely related to brain evolution from both phylogenetic and ontogenetic perspectives. It is the primary neurobiological process that links the brain with internal and external environments and the related experiences. Since consciousness is a theoretical construct introduced mainly to account for the (ontogenetically evolving) integrative subject-object intermediation, it might be possible hypothesize the existence of a relationship between consciousness and neural plasticity, at least from a biological standpoint. In these terms, the phylogenetic development of human consciousness, when human lineage started after the split from that of nonhuman primates, might be partially inferred by comparing the (ontogenetic) development of human and nonhuman primate brains, using an extended meaning of the concept of neural plasticity as the main neurobiological process of reference. What seems to emerge from this comparison is the evolutionary occurrence, during anthropogenesis, of distinguishing (transcriptional) heterochronic phenomena concerning neurodevelopmental processes.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105661"},"PeriodicalIF":1.9,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145642315","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}
Pub Date : 2025-11-22DOI: 10.1016/j.biosystems.2025.105658
Rama Krishna K
This paper proposes a new kinematic linkage model for the actin–myosin contraction mechanism. For studying the mechanical movements, the structures of myosin and actin are first modeled using rigid links and kinematic pairs. A kinematic mechanism has been proposed taking into consideration the experimentally observed changes in the angles of the links. The model has been validated with the experimentally available stroke length of the actin during the power-stroke. The present work also revisits the classical swinging lever arm model (SLAM) and for the first time, proposes kinematic linkage model for SLAM. The prominent contribution of the paper is the development of a planar kinematic linkage model based on Nath’s Rotation-Twist-Tilt (RTT)/Rotation-Uncoiling-Tilt (RUT) model. The value of torsional spring stiffness of 534 pN-nm/rad has been estimated based on the RTT/RUT model for the first time. It is shown that the proposed kinematic model validates the experimentally measured, 5.3 nm stroke length of the actin filament, reported in literature.
{"title":"Kinematic linkage models of muscle contraction: A mechanical engineering perspective","authors":"Rama Krishna K","doi":"10.1016/j.biosystems.2025.105658","DOIUrl":"10.1016/j.biosystems.2025.105658","url":null,"abstract":"<div><div>This paper proposes a new kinematic linkage model for the actin–myosin contraction mechanism. For studying the mechanical movements, the structures of myosin and actin are first modeled using rigid links and kinematic pairs. A kinematic mechanism has been proposed taking into consideration the experimentally observed changes in the angles of the links. The model has been validated with the experimentally available stroke length of the actin during the power-stroke. The present work also revisits the classical swinging lever arm model (SLAM) and for the first time, proposes kinematic linkage model for SLAM. The prominent contribution of the paper is the development of a planar kinematic linkage model based on Nath’s Rotation-Twist-Tilt (RTT)/Rotation-Uncoiling-Tilt (RUT) model. The value of torsional spring stiffness of 534 pN-nm/rad has been estimated based on the RTT/RUT model for the first time. It is shown that the proposed kinematic model validates the experimentally measured, 5.3 nm stroke length of the actin filament, reported in literature.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105658"},"PeriodicalIF":1.9,"publicationDate":"2025-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145598163","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}
Pub Date : 2025-11-21DOI: 10.1016/j.biosystems.2025.105637
Sungchul Ji
The chemiosmotic model of oxidative phosphorylation (oxphos) proposed by Peter Mitchell in 1961 was revisited and its basic mechanistic assumptions that oxphos is driven by protonmotive force either across or within the mitochondrial inner membrane were re-evaluated in light of recent findings. Available evidence strongly suggests that non-chemiosmotic mechanisms such as the conformon or detailed conformational change-mediated mechanisms, such as Nath's torsional mechanism of energy transduction and ATP synthesis, are needed to explain the phenomenon of oxphos in enzymologically and quantum-mechanically realistic terms. An in-depth analysis of oxphos, taking into account recent findings reveal the logical errors or fallacies in dismissing conformational change-based models in favor of the chemiosmotic theory, and suggests the principal mechanistic events underlying chemomechanical coupling in bioenergetic processes in general.
{"title":"Chemiosmotic vs conformational models of oxidative phosphorylation: Theory and mechanistic insights","authors":"Sungchul Ji","doi":"10.1016/j.biosystems.2025.105637","DOIUrl":"10.1016/j.biosystems.2025.105637","url":null,"abstract":"<div><div>The chemiosmotic model of oxidative phosphorylation (oxphos) proposed by Peter Mitchell in 1961 was revisited and its basic mechanistic assumptions that oxphos is driven by protonmotive force either across or within the mitochondrial inner membrane were re-evaluated in light of recent findings. Available evidence strongly suggests that non-chemiosmotic mechanisms such as the conformon or detailed conformational change-mediated mechanisms, such as Nath's torsional mechanism of energy transduction and ATP synthesis, are needed to explain the phenomenon of oxphos in enzymologically and quantum-mechanically realistic terms. An in-depth analysis of oxphos, taking into account recent findings reveal the logical errors or fallacies in dismissing conformational change-based models in favor of the chemiosmotic theory, and suggests the principal mechanistic events underlying chemomechanical coupling in bioenergetic processes in general.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105637"},"PeriodicalIF":1.9,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589847","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}
Pub Date : 2025-11-21DOI: 10.1016/j.biosystems.2025.105660
Serge Dolgikh
The emergence of biology from planetary chemistry remains one of the central open questions in planetary physics, chemistry and biochemistry. In this study, we address an important aspect of this problem: whether abiogenesis is a statistically regular process under broadly defined planetary conditions, or a unique, highly contingent event. To examine it, we introduce a conceptual framework of regularity-relevant classes of adaptive planetary physico-chemical systems: the adaptability ladder model, that formalizes the progression from chemically rich but unorganized environments to stable biochemical systems. The model provides a structured approach to the regularity question, examining potential constrains and bottlenecks in specific adaptive classes and formulate formal statements of the regularity hypothesis: specialized for individual classes and strong (or general) across the full adaptive spectrum. We then assess their differential detectability across observation channels: laboratory simulation, in situ exploration, and remote sensing. Our analysis reveals a strong complementarity between detection channels and the regularity classes, with fragile proto-biotic states accessible primarily through laboratory studies. We observe that under the regularity hypothesis, such early adaptive states should emerge reproducibly under appropriate simulated planetary conditions. This result establishes a direct and testable link between laboratory experimentation and the general question of the regularity of biological emergence, positioning lab-based studies as central to future progress. The framework extends conventional definitions of planetary habitability, traditionally focused on terrestrial-class physical and chemical conditions by incorporating informational aspects, specifically compositional and interactive diversity. This broader perspective informs the strategic prioritization of empirical search efforts, bridging theoretical insights with observable planetary conditions.
{"title":"On the transitional character and regularity of planetary abiogenesis","authors":"Serge Dolgikh","doi":"10.1016/j.biosystems.2025.105660","DOIUrl":"10.1016/j.biosystems.2025.105660","url":null,"abstract":"<div><div>The emergence of biology from planetary chemistry remains one of the central open questions in planetary physics, chemistry and biochemistry. In this study, we address an important aspect of this problem: whether abiogenesis is a statistically regular process under broadly defined planetary conditions, or a unique, highly contingent event. To examine it, we introduce a conceptual framework of regularity-relevant classes of adaptive planetary physico-chemical systems: the adaptability ladder model, that formalizes the progression from chemically rich but unorganized environments to stable biochemical systems. The model provides a structured approach to the regularity question, examining potential constrains and bottlenecks in specific adaptive classes and formulate formal statements of the regularity hypothesis: specialized for individual classes and strong (or general) across the full adaptive spectrum. We then assess their differential detectability across observation channels: laboratory simulation, in situ exploration, and remote sensing. Our analysis reveals a strong complementarity between detection channels and the regularity classes, with fragile proto-biotic states accessible primarily through laboratory studies. We observe that under the regularity hypothesis, such early adaptive states should emerge reproducibly under appropriate simulated planetary conditions. This result establishes a direct and testable link between laboratory experimentation and the general question of the regularity of biological emergence, positioning lab-based studies as central to future progress. The framework extends conventional definitions of planetary habitability, traditionally focused on terrestrial-class physical and chemical conditions by incorporating informational aspects, specifically compositional and interactive diversity. This broader perspective informs the strategic prioritization of empirical search efforts, bridging theoretical insights with observable planetary conditions.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105660"},"PeriodicalIF":1.9,"publicationDate":"2025-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145589795","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}
Pub Date : 2025-11-20DOI: 10.1016/j.biosystems.2025.105659
Hervé Zwirn
In this article, we propose to use the formalism of quantum mechanics to describe and explain the so-called "abnormal" behaviour of agents in certain decision or choice contexts. The basic idea is to postulate that the preferences of these agents are indeterminate (in the quantum sense of the term) before the choice is made or the decision is taken. An agent's state before the decision is represented by a superposition of potential preferences. The decision is assimilated to a measure of the agent's state and leads to a projection of the state onto one of the particular preferences. We therefore consider that uncertainty about preferences is not linked to incomplete information but to essential indeterminacy. We explore the consequences of these hypotheses on the usual concepts of decision theory and apply the formalism to the problem of the so-called "framing" effect.
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