Biosystems最新文献

{"title":"Quantum information as the scientific basis for the explanation of human consciousness and its evolution","authors":"Thomas Görnitz","doi":"10.1016/j.biosystems.2025.105467","DOIUrl":"10.1016/j.biosystems.2025.105467","url":null,"abstract":"<div><div>A scientific explanation of consciousness and its evolution has become possible by a generalized quantum information concept. Crucial to this is a new understanding of matter and energy.</div><div>Our consciousness, being an information structure, processes the information that we absorb from our bodies and our environment. This information reaches us as properties of material objects and the massless quanta of light, the photons.</div><div>One of the properties of matter is motion – physically, kinetic energy. Einstein's E = mc² shows that motion can be converted into matter. Matter is thus equivalent to one of its properties.</div><div>The mathematical-physical structure of quantum theory has opened up a comprehensive view of the construction of complex systems from simple structures. Such a construction can and should begin with the simplest quantum structure, a quantum bit. Matter and also photons can thereby ultimately be understood as manifestations of abstract quantum information.</div><div>Abstract, i.e. still meaning-free, and absolute, i.e. cosmically based, bits of quantum information, AQIs, provide the common basis for consciousness, energy and matter. This explains the mutual influences between matter, energy and the information that is meaningful for a living being.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105467"},"PeriodicalIF":2.0,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143937268","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":"Holistic system analysis of the energetic power and efficiency of animal production","authors":"Douglas S. Glazier","doi":"10.1016/j.biosystems.2025.105470","DOIUrl":"10.1016/j.biosystems.2025.105470","url":null,"abstract":"<div><div>Major features of living systems are the rates (power) and ratios (efficiency) of their energy uptake and use, whose relationships are not entirely predictable from those seen in nonliving physical systems. Although the energetic power and efficiency of production (growth and reproduction) are known to respond to differences in ration level, diet, and other intrinsic and extrinsic factors, why these responses vary considerably among animals is little understood and often ignored in theoretical models. In this exploratory study I show that a holistic analysis of how the different responses of the efficiencies of resource uptake and use systems to variation in food levels and associated rates of energy flow (power) helps one predict the ration-dependent efficiency of conversion of ingested energy into growth and reproduction. When the relative influence of the efficiency of assimilation (resource supply) predominates (as in many herbivores), the efficiency of converting ingested energy into production tends to vary negatively with ration level and production power, whereas when the relative influence of the efficiency of converting assimilated energy into biological tissues (resource use) predominates (as in carnivores), the ingestive production efficiency tends to vary positively with ration level and production power. I also extend this analysis by showing how studies at multiple hierarchical levels of biological organization, from cells to ecosystems, may improve our understanding of the covariation of production efficiency with ration level or overall rate of energy flow (power). A new comprehensive theory of the power and efficiency of living systems is advocated.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105470"},"PeriodicalIF":2.0,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143873636","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":"","authors":"Richard Gordon","doi":"10.1016/j.biosystems.2025.105466","DOIUrl":"10.1016/j.biosystems.2025.105466","url":null,"abstract":"","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105466"},"PeriodicalIF":2.0,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143878516","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":"Field guide to Nath's research work on ATP synthesis and hydrolysis","authors":"Victor Wray","doi":"10.1016/j.biosystems.2025.105461","DOIUrl":"10.1016/j.biosystems.2025.105461","url":null,"abstract":"<div><div>Adenosine triphosphate (ATP) is the universal biological energy source that participates in the most prevalent chemical reactions in all cell life through the vital processes of oxidative phosphorylation (OXPHOS) and photosynthesis. Its synthesis and utilisation is an area of basic research that has seen significant progress over the last three decades. A series of Nath's publications in the 1990s culminated in a detailed description of the molecular mechanism of ATP synthesis in the F_O and F₁ portions of F_OF₁-ATP synthase in which energy from transmembrane ion gradients in F_O are converted into chemical energy of ATP in F₁. Subsequent papers provided a thorough theoretical basis and exploration of the validity of the new theory—named by other authors as Nath's torsional mechanism of energy transduction and ATP synthesis and Nath's two-ion theory of energy coupling. Violation of several physical laws by previous theories have been dealt with in considerable detail. In particular he has reevaluated the extensive literature on ATP hydrolysis and provides a rigorously argued tri-site molecular mechanism involving the three filled β-catalytic sites during hydrolysis by F_O F₁/F₁-ATPase. Numerous applications have been proposed throughout his work that has resulted in four substantial publications dealing with re-interpretation of the Warburg Effect in cancer cells and a trilogy of papers dealing with biological thermodynamics of ATP synthesis applied to problems in comparative physiology, biochemistry and ecology. Finally strict mathematical methods have opened up new approaches to validate mechanistic events in ATP synthesis/hydrolysis. Here we provide a field guide for easy access to the different aspects of this body of work.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105461"},"PeriodicalIF":2.0,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143883245","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":"Discrete Svelteness: Evaluating flow structures in generative constructal design","authors":"Matei C. Ignuta-Ciuncanu,&nbsp;Ricardo F. Martinez-Botas","doi":"10.1016/j.biosystems.2025.105459","DOIUrl":"10.1016/j.biosystems.2025.105459","url":null,"abstract":"<div><div>Constructal design theory posits that natural and engineered systems evolve toward improved flow efficiency, ensuring maximal access and adaptability. Generative design, in this context, functions as an evolutionary computational framework, leveraging algorithmic methods to simulate processes analogous to natural selection and self-organization. This approach enables the exploration and refinement of complex design spaces, fostering higher modeling resolution and morphological diversity beyond traditional parametric methods. In this study, we introduce Discrete Svelteness (DS), a spatially resolved metric that quantifies geometric efficiency at every point in a domain, addressing the limitations of traditional, global Svelteness measures.</div><div>We apply this framework to generative designs, specifically area-to-point (ATP), circle-to-point (CTP), and vascular flow (VF) configurations, demonstrating how DS reveals performance differences shaped by local adaptations to the environment and emergent patterns that conventional metrics overlook. Our analysis reveals that DS provides critical design insights aligned with the Constructal Law, which predicts that systems evolve to enhance flow efficiency through increased branching and spatial access. Furthermore, we examine the probability density functions (PDFs) of DS values, identifying distinct power-law and lighter-tailed right-skewed distributions (such as gamma or log-normal) that reflect the statistical signatures of self-organizing, evolutionary systems found in nature.</div><div>Additionally, we explore the trade-offs and optimization challenges in generative design, showing that increased degrees of freedom lead to more robust, diverse, and high-performing solutions. These dynamics parallel evolutionary processes in biological systems, where adaptability and efficiency emerge from complex interactions between structural constraints and environmental demands. Our findings position DS as a powerful tool for evaluating and guiding the evolution of flow architectures in both natural and engineered systems. By bridging global efficiency metrics with localized refinement, this work advances multi-scale evolutionary constructal design methodologies and offers new insights into the computational modeling of biological self-organization and evolutionary optimization.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"251 ","pages":"Article 105459"},"PeriodicalIF":2.0,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143835035","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":"Quantum information theoretic approach to the hard problem of consciousness","authors":"Danko D. Georgiev","doi":"10.1016/j.biosystems.2025.105458","DOIUrl":"10.1016/j.biosystems.2025.105458","url":null,"abstract":"<div><div>Functional theories of consciousness, based on emergence of conscious experiences from the execution of a particular function by an insentient brain, face the hard problem of consciousness of explaining why the insentient brain should produce any conscious experiences at all. This problem is exacerbated by the determinism characterizing the laws of classical physics, due to the resulting lack of causal potency of the emergent consciousness, which is not present already as a physical quantity in the deterministic equations of motion of the brain. Here, we present a quantum information theoretic approach to the hard problem of consciousness that avoids all of the drawbacks of emergence. This is achieved through reductive identification of first-person subjective conscious states with unobservable quantum state vectors in the brain, whereas the anatomically observable brain is viewed as a third-person objective construct created by classical bits of information obtained during the measurement of a subset of commuting quantum brain observables by the environment. Quantum resource theory further implies that the quantum features of consciousness granted by quantum no-go theorems cannot be replicated by any classical physical device.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"251 ","pages":"Article 105458"},"PeriodicalIF":2.0,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143815045","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":"Cognitive control and consciousness in open biological systems","authors":"Andres Kriete","doi":"10.1016/j.biosystems.2025.105457","DOIUrl":"10.1016/j.biosystems.2025.105457","url":null,"abstract":"<div><div>Thermodynamically open biological systems not only sustain a life-supporting mutual relationship with their environment by exchanging matter and energy but also constantly seek information to navigate probabilistic changes in their surroundings. This work argues that cognition and conscious thought should not be viewed in isolation but rather as parts of an integral control of biological systems to identify and act upon meaningful, semantic information to sustain viability. Under this framework, the development of key cognitive control capacities in centralized nervous systems and the resulting behavior are categorized into distinct Markov decision processes: decision-making with partially observable sensory exteroceptive and interoceptive information, learning and memory, and symbolic communication. It is proposed that the state of conscious thought arises from a control mechanism for speech production resembling actuator control in engineered systems. Also known as the phonological loop, this feedback from the motor to the sensory cortex provides a third type of information flowing into the sensory cortex. The continuous, dissipative loop updates the fleeting working memory and provides humans with an advanced layer of control through a sense of self, agency and perception of flow in time. These capacities define distinct degrees of information fitness in the evolution of information-powered organisms.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"251 ","pages":"Article 105457"},"PeriodicalIF":2.0,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143796810","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":"Code poiesis: Life's fuel","authors":"Anna Aragno","doi":"10.1016/j.biosystems.2025.105460","DOIUrl":"10.1016/j.biosystems.2025.105460","url":null,"abstract":"<div><div>This paper highlights the coupling of copying <em>and</em> coding as central to the promulgation of life, leading to the concept of code-poiesis as the self-generating propulsion behind macro-evolutionary shifts. My goal is to better integrate body with mind and, following Freud, to find the archaic origins of human cognition through the universal unconscious phenomenon of the ‘dream.’ Uncovering this continuity is buttressed by the deep parallels Barbieri finds between the origins of life and the origins of mind. His three macroevolutionary transitions –from organic to neural to cultural – are examined identifying the reiteration of copy-and-code at each shift while contributing a singular psychoanalytic piece at the neural level via Freudian dream theory through which the leap from brain to <em>mind</em> is explained. The main underlying question is; if the two key Barbierian mechanisms, copy and code; 1) begin the promulgation of life, and; 2) propel semiotic progressions in micro-developmental steps into macro-evolutionary stages, then we ought to be able to find them reiterated in different ways, isomorphically, at ever higher, more complex levels of organization of the human nervous system. Here I demonstrate how, and in what ways, this is so. Finally, a fourth evolutionary stage already in progress is discussed: the externalization of mind in the <em>computational age</em> of the algorithm.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"252 ","pages":"Article 105460"},"PeriodicalIF":2.0,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789370","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":"CHTW(R)-system in Ca2+ transport modelling","authors":"Alexander Yu Chunikhin,&nbsp;Hanna V. Danylovych,&nbsp;Yurii V. Danylovych","doi":"10.1016/j.biosystems.2025.105456","DOIUrl":"10.1016/j.biosystems.2025.105456","url":null,"abstract":"<div><div>In (Chunikhin, 2023; Chunikhin, 2024) the concept of CHTW-systems as a multidimensional representation of Petri nets was proposed based on the assumption of multidimensional distribution of tokens (resources) in positions (branes) and, accordingly, multidimensional representation of transitions and arcs. We consider the case when the main parameters of CHTW-system (threshold functions and rate functions) change in accordance with the values of the mark-functions (multidimensional resource) of some container branes of the same CHTW-system. The modification of the basic CHTW-system was designated as a CHTW(R) system, in which (R) means a <strong>R</strong>esource control of the system parameters. This approach was used to analyze changes in Ca²⁺ concentration in mitochondria.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"251 ","pages":"Article 105456"},"PeriodicalIF":2.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143732852","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":"Demographics of genetic admixture and expansion","authors":"Dalkhat M. Ediev","doi":"10.1016/j.biosystems.2025.105455","DOIUrl":"10.1016/j.biosystems.2025.105455","url":null,"abstract":"<div><div>We explore the dynamics of genetic admixture and expansion, as well as language assimilation, through mathematical-demographic modeling. Our primary goal is to address the population-genetics 'paradox' wherein autosomes and allosomes present markedly different, if not contradictory, pictures of past migrations. We demonstrate that this paradox may find a purely demographic explanation, as single-sex and two-sex reproduction models exhibit markedly distinct dynamics. We illustrate that the three processes—allosomal expansion, autosomal admixture, and language assimilation—occur at significantly different modes, potentially explaining the varied outcomes of these processes upon the completion of ethnogenetic transitions. Our research offers valuable insights into the intricate interplay between demography, genetics, and social organization, providing implications for historical scenarios and enhancing our understanding of the long-term consequences of migration and social cohesion.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"251 ","pages":"Article 105455"},"PeriodicalIF":2.0,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143639654","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}