Biosystems最新文献

{"title":"Obesity, body heat loss, and efficiency in movement","authors":"Adrian Bejan","doi":"10.1016/j.biosystems.2025.105673","DOIUrl":"10.1016/j.biosystems.2025.105673","url":null,"abstract":"<div><div>This article makes an unexpected, counterintuitive theoretical step. Excessive inactive body mass (fat, carried load) has a negative impact on the efficiency of life movement to distances. Also negative is the impact of loss of body heat to the cold ambient. Surprisingly, the two negative impacts evolve naturally to a tradeoff such that the living body benefits from maximal efficiency in movement and access on the globe. The tradeoff reveals the amount of inactive mass (e.g., thickness of fat layer) most beneficial for movement. Tradeoffs between negative impacts govern the evolution (the morphing) of all moving <em>design</em> (animal, vehicle, river, etc.). For example, fat tends to be stored primarily at the interface between the warm inner body and the cold ambient. That's design in nature, configuration evolution. Furthermore, the perception of cold is physical and measurable in terms of physical outcomes: design for greater efficiency in movement on the globe, greater power, easier access, farther reach, economy and longer lifespan. Traditionally, perceptions are thought of as intangibles, opinions, beyond the predictive reach of physics. The physics underpinnings of perceptions, reaffirmed in this article, are essential to the future of robotics and AI, if such technologies are ever to compete with naked animal thought and action.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"259 ","pages":"Article 105673"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145726679","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":"How many and which types of primary cells (domains of life) emerged from LUCA, identified employing different genetic codes","authors":"Massimo Di Giulio","doi":"10.1016/j.biosystems.2025.105636","DOIUrl":"10.1016/j.biosystems.2025.105636","url":null,"abstract":"<div><div>The progenote- &gt; cell transition defines the evolutionary stage of the formation of a domain of life. Indeed, the progenote evolutionary stage cannot be or have a domain of life, because the progenote stage does not, by definition, contain cells, being an evolutionary stage with a genotype-phenotype relationship still in formation. Therefore, the progenote stage is certainly cell-free and therefore cannot be a domain of life, which is instead made up of cells. Consequently, it is at the moment in which a cell emerged from the progenote stage that the first domain of life was defined. In fact, this would be the first appearance of a cell in the history of life, since the progenote stage is cell-free. All of this would define the birth of a domain of life because it would represent the first and precise evolutionary point at which the first cell would be born, after the progenote stage. Furthermore, the progenote- &gt; cell transition is completely reflected in the transition from evolving genetic code to frozen genetic code. That is to say, a genetic code in evolution, i.e. still originating, would precisely reflect the definition of progenote because a code that is still originating should have a genotype-phenotype relationship yet to be defined and would identify, by definition, the stage of the progenote. A frozen genetic code, a fully formed, modern genetic code, would imply the cell stage, that is, the abandonment of the progenote stage. Indeed, nothing more than a modern genetic code might indicate the achievement of the cell stage because a fully developed genetic code would imply modern proteins, which in turn would imply that all the structures of that particular evolutionary stage would certainly belong to a cell stage, precisely because they are structures to be considered, in some sense, complete and definitive. In conclusion, the simple observation of specific variants of the genetic code would provide the opportunity to easily identify the domains of life because a genetic code possessed only by a certain type of organism would witness the transition from evolving genetic code to frozen genetic code and consequently the transition from progenote to cell, and would therefore identify a domain of life. In this way, that is to say, by using some variants of the genetic code, the following domains of life have been identified: Bacteria, Methanogens, and Non-Methanogenic Archaea. Eukaryotes, having the same genetic code as non-methanogenic archaea, would belong to the same domain as the latter. The discussion focuses on these three domains of life and their relationship with the domains of life suggested by other hypotheses, and on properties of the variants of the genetic code used to identify these domains.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105636"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145418440","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":"Value saturation: Architecture of subjective necessity","authors":"Joseph J. Trukovich","doi":"10.1016/j.biosystems.2025.105642","DOIUrl":"10.1016/j.biosystems.2025.105642","url":null,"abstract":"<div><div>Consciousness requires explanation for how biological architectures reliably generate it. This paper introduces Value Saturation, advancing an identity claim: phenomenal consciousness IS explicit recursive self-modeling saturated by homeostatic significance under perspectival entrapment. Building on the Reaction to Reflection framework, the theory distinguishes sentience (implicit recursion under survival stakes, Level 2) from subjective consciousness (explicit recursion where self-models become manipulable, Levels 4–5). Three integrated components prove necessary: interoceptive binding, homeostatic saturation, and perspectival entrapment. Testable predictions include developmental progression from birth sentience to subjective consciousness around ages 3–5, awareness-manipulation asymmetry, and clinical dissociations producing aberrant rather than absent phenomenology. Converging evidence from prediction error processing, homeostatic feelings, metacognitive hierarchies, and biological computing's thermodynamic advantages supports these requirements. The framework specifies falsification criteria and transforms consciousness into an empirically tractable investigation of organizational transitions in biological systems under thermodynamic constraints.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105642"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145453840","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":"Spectral bounds for Sombor and Sombor energy indices: A graph-theoretic study of neurotransmitter molecular networks","authors":"Nalini Devi K. ,&nbsp;Srinivasa G.","doi":"10.1016/j.biosystems.2025.105620","DOIUrl":"10.1016/j.biosystems.2025.105620","url":null,"abstract":"<div><div>This paper applies the recently introduced Sombor index and its spectral extension, the Sombor energy, to model and analyze the structural complexity of neurotransmitter molecular graphs. Let <span><math><mi>G</mi></math></span> denote a molecular graph whose vertices and edges correspond to atoms and covalent bonds, respectively. For each <span><math><mi>G</mi></math></span>, we compute <span><math><mrow><mi>S</mi><mi>O</mi><mrow><mo>(</mo><mi>G</mi><mo>)</mo></mrow></mrow></math></span> and <span><math><mrow><mi>S</mi><mi>O</mi><mi>E</mi><mrow><mo>(</mo><mi>G</mi><mo>)</mo></mrow></mrow></math></span>, and derive degree-based, spectral-radius, and Frobenius-norm bounds to quantify molecular irregularity. Unlike traditional indices such as Zagreb or Wiener, Sombor descriptors incorporate both degree heterogeneity and geometric weighting, offering refined sensitivity to branching and aromaticity. Comparative analysis across inhibitory (glycine, GABA) and excitatory or modulatory (dopamine, serotonin, norepinephrine) neurotransmitters reveals that higher Sombor measures correspond to greater structural and functional complexity. These results confirm that Sombor-based descriptors capture biologically interpretable differences in molecular organization. The study thereby extends spectral graph theory to neurochemical systems, providing a quantitative framework for cheminformatics, drug design, and functional classification of neurotransmitters.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105620"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145318828","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 ,&nbsp;Tran Nguyen Minh-Thai ,&nbsp;Komal Sorthiya ,&nbsp;Don Kulasiri","doi":"10.1016/j.biosystems.2025.105613","DOIUrl":"10.1016/j.biosystems.2025.105613","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105613"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","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":"Cultural accumulation or stasis? The impact of imitation and early teaching on hominin cultural evolution","authors":"Laureano Castro ,&nbsp;Daniel Castro-Cañadilla ,&nbsp;Miguel Ángel Castro-Nogueira ,&nbsp;Miguel Ángel Toro","doi":"10.1016/j.biosystems.2025.105641","DOIUrl":"10.1016/j.biosystems.2025.105641","url":null,"abstract":"<div><div>One way to investigate the origins of cumulative culture is by examining the increasing complexity of lithic technologies in the hominin lineage. This study presents a simplified model of cultural transmission in <em>Homo erectus</em> and <em>Homo heidelbergensis</em>, focusing on the emergence of cumulative culture in relation to Oldowan, Acheulean, and the transition to Mode 3 technologies. Acheulean toolmaking likely required high-fidelity transmission, possibly supported by early forms of teaching. However, the remarkable technological conservatism of the Acheulean record contrasts with the rapid accumulation of innovations in modern humans. Our model aims to shed light on this circumstance by analysing the roles played by imitation and early forms of teaching. Each lithic technology is classified into three behavioural levels (0–2), representing increasing complexity and adaptive value, which can be acquired through individual learning or social transmission. We introduce two genotypes: the <em>Imitator</em>, which enables basic social learning, and the <em>Assessor</em>, which adds evaluative teaching between parents and offspring. We analyse the cultural dynamics generated by each genotype in pure populations. Our results suggest that incremental cumulative culture depends critically on offspring reliably replicating the most complex behaviours of their parents. This dynamic favours the evolution of the Assessor genotype, as it enhances parent-offspring behavioural resemblance. Nonetheless, when replication fidelity falls short of establishing the highest level of complexity behaviours (Level 2) predominant, the Assessor genotype may inadvertently reinforce cultural stasis instead of driving cumulative cultural evolution, ultimately hindering the transition from Level 1 to Level 2 behaviours via individual learning.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105641"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145483723","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":"When Maxwell’s Demon leaves the room","authors":"P.G. Tello ,&nbsp;S. Kauffman","doi":"10.1016/j.biosystems.2025.105618","DOIUrl":"10.1016/j.biosystems.2025.105618","url":null,"abstract":"<div><div>This work revisits the Maxwell Demon paradigm to explore its implications for evolutionary dynamics from an information-theoretic perspective. By removing the Demon as an intentional agent, we reinterpret the emergence of order as a natural outcome of physical laws combined with stochastic processes. Using models inspired by information theory, such as binary and Z-channels, we show how random fluctuations (e.g., stochastic resonance) can decrease entropy, generate mutual information, and induce non-ergodicity. These dynamics highlight the role of memory and correlation as emergent features of purely physical interactions without recourse to purposeful agency. In this framework, evolutionary exaptations, rather than sole adaptations, emerge as key drivers of biological evolution. Finally, we connect our analysis with recent contributions on agency and memory, underscoring the relevance of informational concepts for understanding the purposeless yet structured dynamics of evolutionary processes.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105618"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145309894","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":"An energy landscape-based theoretical framework for understanding the self-organization of functions in a living system under the dynamical component interaction","authors":"Ryunosuke Suzuki ,&nbsp;Taiji Adachi","doi":"10.1016/j.biosystems.2025.105631","DOIUrl":"10.1016/j.biosystems.2025.105631","url":null,"abstract":"<div><div>In a living system composed of interacting components such as molecules, cells, and tissues, each component often changes its internal states in response to interactions with its surrounding components. For example, individual tissues exhibit component-level responsive behavior, such as growth and remodeling, in response to their mechanical interactions, resulting in the self-organization of functions of a multi-tissue system. Along with the responsive behavior of the components, their interactions exhibit dynamical changes, which strongly influence the self-organization of system functions. To understand how the self-organization of system functions occurs from such dynamical interactions due to component-level responsive behavior, this study proposes a theoretical framework that formulates the dynamics of interactions among components due to the component-level responsive behavior. For modeling the responsive internal state changes, we assign an energy landscape and its associated energy rate landscape for each component, leading to the generalized gradient flow model of responsive behavior. Then, we represent interaction dynamics based on temporal changes in these energy and energy rate landscapes by formulating temporal changes in the environmental states of each component due to the responsive behavior of individual components. Through case studies using simplified models of mechanically interacting tissues under morphological changes, our theoretical framework demonstrates that temporal changes in applied forces due to morphological changes of individual tissues determine the self-organization of system functions. These findings highlight that expressing interaction dynamics based on temporal changes in energy and energy rate landscapes offers a powerful theoretical framework for understanding how component-level responsive behavior organizes system functions.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105631"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145370392","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":"Information and the living tree of life: A theory of measurement grounded in biology","authors":"Kevin Hudnall","doi":"10.1016/j.biosystems.2025.105610","DOIUrl":"10.1016/j.biosystems.2025.105610","url":null,"abstract":"<div><div>We extend a formal framework that previously derived time from the multifractal structure of biological lineages (Hudnall and D’Souza, 2025). That work showed that time itself is multifractal – not a universal background dimension, but an observer-dependent geometry. Here we develop the corresponding theory of measurement: showing that a multifractal conception of time not only permend a formal framework that previously derived time from the multifractal structure of biological lineages (Hudnall and D’Souza, 2025). That work showed that time itself is multifractal – not a universal background dimension, but an observer-dependent geometry. Here we develop the corresponding theory of measurement: showing that a multifractal conception of time not only permits measurement, but grounds it more rigorously in the structure of biology. The tree of life is modeled as the outcome of stochastic, convex branching, and we show how information-theoretic and fractal measures render its multifractal geometry into measurable, observer-relative time intervals. At the core is a dilation equation that expresses relative time elapse between entities as dimensionless ratios. Operational standards such as the SI second remain valid, but our framework makes explicit their lineage-dependence. This framework unifies measurement theory with biological form, preserves full compatibility with established science, and provides a biologically grounded theory of observation. It enables comparative analyses of duration and kinematics across lineages, with predictions that are directly open to experimental validation.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105610"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145287622","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 limits of falsifiability: Dimensionality, measurement thresholds, and the sub-Landauer domain in biological systems","authors":"Ian Todd","doi":"10.1016/j.biosystems.2025.105608","DOIUrl":"10.1016/j.biosystems.2025.105608","url":null,"abstract":"<div><div>Karl Popper’s falsifiability criterion assumes that scientific hypotheses can be reduced to binary tests. We show this assumption is <em>scale-dependent</em> and can <em>saturate</em> in high-dimensional biological systems operating near physical measurement limits, especially near criticality. In neural networks, much relevant information exists as patterns below the Landauer threshold for irreversible bit recording—signals too weak for individual neurons to detect but detectable when pooled across populations. These sub-threshold patterns cannot be projected into binary outcomes without destroying their causal structure. We develop a framework connecting dimensionality, thermodynamic measurement limits, and biological epistemology, showing that Popperian logic represents a special case applicable only to low-dimensional systems with strong signals. Our analysis has implications for neuroscience, where aspects of conscious processing may in part depend on sub-threshold coherence patterns that resist binary measurement, motivating a shift from single-case hypothesis tests to multi-scale, ensemble-based inference. The framework extends to other complex biological systems including ecological networks, protein folding dynamics, and evolutionary processes where causal relationships exist as irreducible multi-dimensional structures operating below classical measurement thresholds.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"258 ","pages":"Article 105608"},"PeriodicalIF":1.9,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145287667","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}