Acta Biotheoretica最新文献

{"title":"On a Physical Theory of Causation in Multiscale Analysis of Biological Systems","authors":"Sergey B. Yurchenko","doi":"10.1007/s10441-025-09511-6","DOIUrl":"10.1007/s10441-025-09511-6","url":null,"abstract":"<div><p>Causal analysis of multiscale systems is crucial for understanding how biological networks are organized and function across scales, including the origin of life itself. This article introduces an axiomatic theory of causation based on the physical concept of cause. Its rigorous derivation from first principles allows us to formulate the law of conservation of causation, expressed in terms of the continuity equation in fluid dynamics. This law states that the flow of causation in dynamical, endogenously coarse-grained systems is conserved across scales. This means that these systems are causally renormalizable across scales; both upward and downward causation are forbidden. The theory also introduces a tool for calculating (i) the minimal linear chain necessary for a biological system to causally connect its two components at a distance, and (ii) the spatial span of the system, defined not as a metric volume of space occupied by the system but as the number of scales causally spanned by its dynamics. Finally, it raises age-old questions about reductionism and emergence, determinism and agency in living systems.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"74 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595226","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 Curse of Darwinism","authors":"Rob Hengeveld","doi":"10.1007/s10441-025-09508-1","DOIUrl":"10.1007/s10441-025-09508-1","url":null,"abstract":"","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"74 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595227","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":"A Note on Quantifying the Contributions of Incidence Functions in Spatio-Temporal Epidemic Models","authors":"Mohamed Mehdaoui,&nbsp;Mouhcine Tilioua","doi":"10.1007/s10441-025-09512-5","DOIUrl":"10.1007/s10441-025-09512-5","url":null,"abstract":"<div><p>Reaction–diffusion epidemic models play a central role in understanding how infectious diseases propagate through space and time, offering valuable insight for public health analysis. A key element of such models is the incidence function, which governs the nonlinear interaction between susceptible and infected populations. Despite extensive studies on various incidence formulations, the systematic identification of a suitable one for a given setting remains an open question. This work introduces a theoretical framework that interprets the selection of an incidence function as quantifying the contribution of several plausible formulations to the overall transmission dynamics, inferred from observational data. The resulting problem takes the form of a PDE-constrained optimization, where the objective is to determine the optimal weights in a convex combination of incidence functions that best fit the observed epidemic patterns. The analysis establishes the Fréchet differentiability of the parameter-to-state operator and derives first-order optimality conditions via an adjoint system. A numerical illustration, based on the Landweber iteration method, highlights the framework’s potential as a mathematical tool to enhance modeling accuracy and support strategies aimed at disease prevention.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"74 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145595225","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":"Isomorphisms of Maximal Self-complementary (C^3)-codes","authors":"Christoph Begall,&nbsp;Lutz Strüngmann,&nbsp;Martin Starman,&nbsp;Ariane G. Tallee K.","doi":"10.1007/s10441-025-09510-7","DOIUrl":"10.1007/s10441-025-09510-7","url":null,"abstract":"<div><p>In this work, we investigate isomorphisms of graphs associated with the 216 maximal self-complementary <span>(C^3)</span>-codes over the genetic alphabet <span>({A,C,G,T})</span>. Such codes play an important role in maintaining the correct reading frame during the translational process in the ribosome and have been classified into 27 equivalence classes under the action of the dihedral group <span>(D_4)</span>. Naturally, this group action induces graph isomorphisms between the graphs associated with maximal self-complementary <span>(C^3)</span>-codes, as shown in Fimmel et al. (2016). However, we demonstrate here that these induced isomorphisms of the associated graphs are not the only graph isomorphisms between such codes. Specifically, we calculate the largely non-trivial automorphism groups of all the 216 graphs associated to maximal self-complementary <span>(C^3)</span>-codes and we show that no isomorphism exists between maximal self-complementary <span>(C^3)</span>-codes belonging to different equivalence classes. Finally, we provide examples illustrating that the assumptions of maximality, self-complementarity, or the <span>(C^3)</span>-property can not be omitted.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"73 4","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145538374","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":"Computational Model of Bone Remodeling Integrating Osteocyte Mechanotransduction and Microdamage-Driven Self-Repair","authors":"Diego A. Garzón-Alvarado,&nbsp;Carlos A. Duque-Daza,&nbsp;Juan Jairo Vaca-González,&nbsp;Estevam Barbosa Las Casas,&nbsp;Dorian L. Linero,&nbsp;Gregory de Boer,&nbsp;Raj Das,&nbsp;Salah Ramtani","doi":"10.1007/s10441-025-09505-4","DOIUrl":"10.1007/s10441-025-09505-4","url":null,"abstract":"<div><p>Bone remodeling is a fundamental physiological process that maintains skeletal integrity through a tightly regulated balance between bone resorption and formation. Mathematical modeling provides a powerful framework for understanding the complex regulatory mechanisms underlying this process, particularly the interplay between biomechanical stimuli and cellular dynamics. This study introduces a new mathematical model of bone remodeling designed to capture the temporal evolution of key bone cell populations and their response to mechanical stimuli within a simplified yet biologically informed architecture. We formulate a system of coupled nonlinear ordinary differential equations to describe the dynamics of osteoclasts, osteoblasts, and osteocytes within a single basic multicellular unit (BMU). The model incorporates feedback regulation via strain energy density, allowing mechanical input to influence cellular activity and bone surface transitions. Initial conditions are assigned to reflect the sequential activation of bone remodeling phases. Physiological parameters are adopted from well-established literature, while non-sourced parameters are tuned to ensure model stability and biological plausibility. The simulations reproduce the canonical sequence of bone remodeling: initiation, resorption, reversal, and formation. The model captures the coupling between mechanical loading and cellular activity, demonstrating how osteocyte signaling can modulate the recruitment of osteoclasts and osteoblasts. The results also highlight the system’s capacity to stabilize around a dynamic equilibrium, sensitive to both internal parameters and external mechanical inputs. This model offers a minimal yet comprehensive representation of bone remodeling dynamics within a single BMU, integrating mechanical and biological controls into a unified mathematical structure. It provides a foundation for future extensions toward spatially distributed models and applications in mechanobiological simulation and computational bone health assessment.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"73 4","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145406272","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":"Assessing the Impact of Routine and Campaign Vaccination on Measles Transmission: A Modeling Study","authors":"Kelly Joëlle Gatore Sinigirira,&nbsp;Olumuyiwa James Peter,&nbsp;Ghaniyyat Bolanle Balogun,&nbsp;Gbolahan Bolarin","doi":"10.1007/s10441-025-09507-2","DOIUrl":"10.1007/s10441-025-09507-2","url":null,"abstract":"<div><p>Measles remains a major global public health challenge despite available vaccines. To evaluate the combined impact of routine immunization and supplementary vaccination campaigns, we developed a compartmental mathematical model that incorporates declining immunity and breakthrough infections. We derived the control reproduction number using the next-generation matrix method, analyzed stability and bifurcation properties of the equilibria, and conducted sensitivity analysis to determine key drivers of transmission. The model was parameterized from the literature and calibrated to 2024 Nigerian measles case data using Markov Chain Monte Carlo sampling. The model revealed that the disease-free equilibrium is globally stable when the control reproduction number is less than one, but a backward bifurcation indicates that reducing the reproduction number below unity may not suffice for elimination. Sensitivity analysis identified the transmission rate among vaccinated individuals, breakthrough infections, and waning immunity as dominant drivers of transmission. Simulations demonstrated that while routine vaccination delays and reduces outbreak peaks, it does not interrupt transmission alone; annual campaigns outperform biennial strategies, preventing 40% more cases; and combined vaccination reduces the reproduction number below unity while preventing 65-80% of infections versus no vaccination. Critically, temporary disruptions in routine coverage significantly increase outbreak risk, and maintaining vaccine efficacy above 90% alongside hospitalization of at least 50% of infectious individuals is essential for containment. These results underscore that high-coverage routine vaccination must be integrated with periodic high-intensity campaigns and robust clinical care to close immunity gaps, mitigate waning protection, and accelerate measles elimination.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"73 4","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145290689","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":"Reciprocal Causation and Statistical Reciprocity","authors":"Tiago Rama","doi":"10.1007/s10441-025-09506-3","DOIUrl":"10.1007/s10441-025-09506-3","url":null,"abstract":"<div>\u0000 \u0000 <p>Ernst Mayr famously distinguished between proximate and ultimate causal explanations. His view was decisive in the fact that development was not included in the theory of evolution. Nevertheless, the explanatory role of developmental processes in evolution is a central theme of current theoretical biology, which has led to several revisions of Mayr’s distinction. One of the reasons for this is that the interactions between organisms and the environment influence evolution. This is a cornerstone of the Extended Evolutionary Synthesis. How are these reciprocal interactions integrated into evolutionary theory? I will argue that this question can sometimes be answered by adopting an interactivist view based on a <i>reinterpretation</i> of reciprocal causation: developmental processes (such as niche construction or developmental plasticity) interact reciprocally with natural selection to produce evolved traits. In the following, I will critically analyze Mayr’s critics to determine whether the integration of development and evolution based on the reinterpretation of reciprocal causation is an appropriate alternative. I will argue that this is not the case, since this interactivist framework raises several explanatory problems. Instead, I should reconsider Mayr’s distinction by adopting an alternative view of evolutionary causation, known as the statisticalist view of natural selection, which posits that the only level of causation is the individual level and that ultimate explanations are statistical in nature. I argue that this framework avoids the explanatory problems identified earlier. To explore the relationship between organisms–environment reciprocal causation and ultimate explanations, I introduce the concept of ‘statistical reciprocity’ to measure the statistical effects of reciprocal causation in population changes. I situate this proposal within a general framework I call ‘population ontogenetics’, which is seen as an attempt to unify development and evolution beyond interactivist positions.</p>\u0000 </div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"73 4","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Why and How to Use Process Philosophy in Everyday Ecology and Biology?","authors":"Cédric Gaucherel","doi":"10.1007/s10441-025-09504-5","DOIUrl":"10.1007/s10441-025-09504-5","url":null,"abstract":"<div><p>Recent studies in biology and ecology show striking convergences with process philosophy (PP). Biologists today are debating the real nature of evolution and of life itself, which is increasingly considered as a set of interrelated processes rather than a set of tangible species and material lineages. This perspective of focusing on changes can also be found with ecologists and environmental ethicists, whose studies feed into as well as draw on PP principles. Despite such connections, the PP-based approach has not yet been adopted in ecology or biology, and appears to be rarely <i>used</i> in practice. We face a problem: How to transform PP from an epistemological pillar into a useful ontological pillar in ecology and further on in biology? To answer, we developed here simple qualitative, discrete-event ecosystem models based on a process network representation instead of on a more tangible interaction network. Comparing rigorous models developed with a traditional materialist view, like those commonly used in ecology, with models built here on a PP-based view, provides a first illustration of the way PP could be concretely applied in and could benefit to ecology and biology, by directly handling processes. Hence, <i>putting PP into practice</i> suggests handling processes first, and then only deducing objects lasting in time and composing the system under study. We also show with examples that following PP principles may sometimes lead to different conclusions, despite handling the same material components of the system under study. Additionally, PP sheds new light on the age-old pattern/process debate and on some others in biology and ecology.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"73 4","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028397","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":"Conformal Patterns in the Growth of Human Skulls","authors":"M. Y. Tufail,&nbsp;S. Gul","doi":"10.1007/s10441-025-09503-6","DOIUrl":"10.1007/s10441-025-09503-6","url":null,"abstract":"<div><p>In 1917, over a century ago, D’Arcy Wentworth Thompson published his groundbreaking book “On Growth and Form”, in which he proposed various mathematical transformations between the shapes of organisms. This paper explores one of the transformations he suggested the conformal pattern-specifically in the context of the ontogenetic growth of human skulls. We applied two alternative algorithms to construct conformal transformations and used them to investigate the growth of human skulls. Our findings indicate that the conformal transformation cannot be dismissed as a potential model for the growth of human skulls.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"73 3","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144887940","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":"Assessment of the Efficiency of Vaccination and Short-term Isolation in Lowering the Disease Load in Koalas Population","authors":"Parimita Roy,&nbsp;Sanjoli Jain,&nbsp;Ranjit Kumar Upadhyay,&nbsp;Ani Jain","doi":"10.1007/s10441-025-09501-8","DOIUrl":"10.1007/s10441-025-09501-8","url":null,"abstract":"<div><p>Koala populations in some regions of eastern Australia are in critical condition. Our research aims to develop effective conservation strategies for these declining koalas threatened by chlamydia infection, predation, and climate change. To achieve this, we developed a mathematical model that includes populations of dingoes and koalas categorized as susceptible, infected, and confined. We conducted a bifurcation analysis within the ordinary differential equations (ODE) model to explore the occurrence of a Hopf bifurcation. This analysis aimed to identify conditions under which the system undergoes qualitative changes in its dynamics, specifically transitions from stable equilibrium points to periodic oscillations. By examining how the system’s behavior shifts as parameters are varied, we could determine the thresholds at which these bifurcations occur, providing insights into the potential for oscillatory patterns in koala populations and disease dynamics. Additionally, we performed a global sensitivity analysis using the partial rank correlation coefficient (PRCC) method. This approach helped us evaluate the relative importance of different parameters on disease prevalence and koala mortality. Extensive numerical simulations allowed us to compare the outcomes of deterministic, stochastic, and diffusive models. Our research indicates that the survival of koala populations is significantly influenced by several key factors: the presence of dingoes, vaccination efforts, and temporary quarantining. Simulations of spatially explicit systems show that increased diffusion among dingoes leads to a more significant clustering of the infected koala population. Our study offers theoretical evidence that vaccination and temporary isolation strategies can significantly improve health outcomes for koalas infected with Chlamydia.</p></div>","PeriodicalId":7057,"journal":{"name":"Acta Biotheoretica","volume":"73 3","pages":""},"PeriodicalIF":1.5,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144832247","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}