Biosystems最新文献

{"title":"Code Biology and abduction in the creative process","authors":"Camilla Robuschi","doi":"10.1016/j.biosystems.2025.105596","DOIUrl":"10.1016/j.biosystems.2025.105596","url":null,"abstract":"<div><div>In this paper, we investigate how abduction represents one of the fundamental stages within the broader process of creativity. We begin by revisiting the various definitions of abduction, starting with the one proposed by Peirce, who conceptualized it as a form of logical inference enabling a “jump to a conclusion” from given facts. Post-Peircean semiotics retains the central idea that abduction is a logical inference that allows for “best guessing” and, as such, can lead to both fallacious reasoning and highly innovative insights. Particularly relevant is Umberto Eco's classification of abduction into three types: overcoded, undercoded, and creative. Expanding the notion into an ecosystemic framework, we examine two significant definitions of abduction, namely those of Gregory Bateson and Victoria Alexander. Bateson argues that abduction is a fundamental process underpinning most of our perceptions and knowledge of the world, enhancing our capacity for abstraction. Alexander, on the other hand, introduces a concept closely related to abduction: stochastic resonance. We argue that the theoretical framework which best integrates and enriches these perspectives is found in the field of Code Biology, where abduction is conceived as a vital process that enables human beings to interpret their environment, where three processes are necessary for interpretation: coding, decoding and abduction. Finally, we present several theories of abduction developed within one of the most application-oriented domains of creativity studies: design.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105596"},"PeriodicalIF":1.9,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145114854","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":"Adaptive flexibility of cells through nonequilibrium entropy production","authors":"Yuika Ueda ,&nbsp;Shinji Deguchi","doi":"10.1016/j.biosystems.2025.105594","DOIUrl":"10.1016/j.biosystems.2025.105594","url":null,"abstract":"<div><div>Cellular adaptation to environmental changes relies on the dynamic remodeling of subcellular structures. Among these, periodic actomyosin assemblies are fundamental to the organization and function of the cytoskeletal architecture. In muscle-type cells, sarcomeres exhibit ordered structures of consistent lengths, optimized for stable force generation. By contrast, nonmuscle-type cells exhibit greater structural variability, with sarcomere-like periodic units of varying lengths that contribute not only to force generation but also to adaptive remodeling upon environmental cues. These structural differences have traditionally been attributed to the specific protein compositions unique to each cell type. However, the functional significance of such periodic unit variability remains poorly understood within a unified framework. Here, we propose a conceptual model grounded in nonequilibrium physics to provide a unified perspective on structural variability in cytoskeletal adaptation. Specifically, we demonstrate that the effective binding strength of these contractile units can be evaluated by quantifying structural randomness through Shannon entropy. The increased entropy associated with the inherent randomness of sarcomere-like assemblies in nonmuscle-type cells lowers the energy barrier for cytoskeletal remodeling, enabling flexible adaptation to environmental demands. In contrast, the ordered sarcomere arrangements in muscle-type cells correspond to higher binding energies, stabilizing cytoskeletal configurations for sustained force generation. While structural disorder is often regarded as a source of instability, our analysis reveals that it can serve as a driver of cytoskeletal remodeling and a foundation for adaptive cellular behavior. Thus, our study provides a unified theoretical foundation for understanding cytoskeletal adaptability across diverse cell types by integrating structural randomness into a nonequilibrium framework.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105594"},"PeriodicalIF":1.9,"publicationDate":"2025-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145071001","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":"Food codes as an AI-based framework to investigate bird foraging ecology and interspecific interactions","authors":"Almo Farina ,&nbsp;Luca Biancardi ,&nbsp;Giovanni Ancillotti","doi":"10.1016/j.biosystems.2025.105591","DOIUrl":"10.1016/j.biosystems.2025.105591","url":null,"abstract":"<div><div>Food codes activated by provisioning food through a garden bird feeder have proven to be an effective tool for investigating bird behavior and bird–human interactions. The experimental setup included a garden feeder with carefully controlled variables, such as its location and structure, the type of food provided, and its temporal distribution.</div><div>A total of 2.8 million image frames of birds at feeder were captured between November 2023 and May 2024 using a time-lapse camera system. Of these, 1,232,456 frames were classified through supervised image processing using the Squeezebrains SDK (<span><span>https://fabervision.com</span><svg><path></path></svg></span>), an AI-based image analysis tool specifically developed for wildlife monitoring. This approach enabled detailed insights into feeding preferences and interspecific interactions.</div><div>Nine bird species were identified: Great tit (<em>Parus major</em>) (65.59 % of all visits), blue tit (<em>Cyanistes caeruleus</em>) (13.62 %), house sparrow (<em>Passer domesticus</em>) (8.28 %), red-billed leiothrix (<em>Leiothrix lutea</em>) (5.90 %), siskin (<em>Carduelis spinus</em>) (2.84 %), chaffinch (<em>Fringilla coelebs</em>) (1.69 %), dunnock (<em>Prunella modularis</em>) (1.00 %), European robin (<em>Erithacus rubecula</em>) (0.59 %), and common blackbird (<em>Turdus merula</em>) (0.45 %). These species, belonging to different genera, visit the feeder at different times. The cluster analysis has categorized the bird species into three distinct groups based on their temporal preferences, leaving the chaffinch as an unclustered species: Group 1 (Blue tit, great tit, house sparrow, red-billed leiothrix), group 2 (Dunnock, siskin), group 3 (Common blackbird, European robin).</div><div>The potential interspecific competition, estimated by the number of frames shared concurrently by two species, was highest for the blue tit, great tit, and red-billed leiothrix, respectively. The chaffinch, siskin, common blackbird, European robin, and dunnock exhibited the highest scores for intraspecific, non-shared frames. Severe weather conditions appear to increase the number of visits to feeders.</div><div>Overall, food codes represent a robust approach, providing valuable insights into bird community dynamics while offering perspectives relevant to ecological management.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105591"},"PeriodicalIF":1.9,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145066597","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":"From life to evolution: the differentiation between storage and interface in natural and cultural systems","authors":"Kirill Postoutenko","doi":"10.1016/j.biosystems.2025.105590","DOIUrl":"10.1016/j.biosystems.2025.105590","url":null,"abstract":"<div><div>It has been long acknowledged that the functional differentiation between storage and interface, proposed by John von Neumann, is the essential condition for the self-reproduction of living beings: enabling evolution, the fundamental separation of memory from interaction increases the chances of open systems to withstand the all-devouring entropic pressure of the surrounding universe. However, the interest in the distinction has been very unevenly spread between natural and social sciences. This preliminary study is an attempt to fill the gap, at least in part.</div><div>Admittedly, the DNA code shares with human language a considerable number of features facilitating preservation and exchange of information. Those include invariance to environment, universality, stability, redundancy, ability to code elementary (1-bit) information and express it in partially ordered messages, rich grammar and hierarchically ordered semantics.</div><div>To be sure, in the biological world the domination of interface by storage has never been as complete as in the self-reproducing automata envisioned by John von Neumann: the standard direction of information flow (from nucleic acids to proteins) does not – and cannot - exclude the feedback from RNA to DNA. The same reflexivity is even more apparent in culture: while writing and print are usually more conservative and durable then spoken word and hence lend themselves naturally to conservation of canonical information, there is no mandatory and uniform subordination of speech to writing or print in social life. Therefore, it could be argued that culture, unlike nature, relies heavily on second-order practices upholding the differentiation between storage and interface for the purposes of cultural evolution. The whole class of canonical monotheist texts such as Bible or Quran is a poster example of this dynamics, and the final part of this paper seeks to uncover the storage-interface dualism in the monotheist religious communication of the last two millennia.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105590"},"PeriodicalIF":1.9,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145066572","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":"Opportunities in multiscale modeling of mosquito-borne flaviviruses","authors":"Carolin Zitzmann ,&nbsp;Neil Alvin B. Adia ,&nbsp;Priya S. Shah ,&nbsp;Carrie Manore","doi":"10.1016/j.biosystems.2025.105593","DOIUrl":"10.1016/j.biosystems.2025.105593","url":null,"abstract":"<div><div>Mosquito-borne flaviviruses, such as Zika, dengue, West Nile, and yellow fever virus, represent a growing public health concern due to their widespread distribution and the severe diseases they cause. These viruses are difficult to control as climate change and urbanization help mosquitoes expand into new areas, increasing the risk of outbreaks. Mathematical models play a key role in understanding their spread, providing insights at every level—from how the virus multiplies inside cells to how it circulates through entire populations. This review examines various approaches used in modeling arboviruses, including microscale models that focus on cellular and molecular dynamics, mesoscale models that address within-host processes, and macroscale models that capture population-level transmission. We briefly summarize the methodology used for models at each scale, which primarily consists of sets of differential equations with parameters that represent physical rates of change for different subprocesses. We particularly highlight how temperature affects virus transmission, which is key to understanding the impact of climate change. We also show how multiscale models can connect viral replication, immune response, and the spread of infection at a larger scale. This is essential for developing better vaccines and treatments, evaluating disease control measures, predicting the impact of climate change, and improving public health responses to outbreaks.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105593"},"PeriodicalIF":1.9,"publicationDate":"2025-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145066619","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":"Studying organisational closure in biological systems with process-enablement graphs","authors":"Emmy Brown ,&nbsp;Sean T. Vittadello","doi":"10.1016/j.biosystems.2025.105567","DOIUrl":"10.1016/j.biosystems.2025.105567","url":null,"abstract":"<div><div>At the heart of many contemporary theories of life is the concept of biological self-organisation: organisms have to continuously produce and maintain the conditions of their own existence in order to stay alive. The way in which these varying accounts articulate this concept, however, differs quite significantly. As a result, it can be difficult to identify self-organising features within biological systems, and to compare different descriptions of such features. In this article, we develop a graph-theoretic formalism – process-enablement graphs – to study the organisational structure of living systems. A process-enablement graph is a directed graph where the vertices represent processes, the edges represent direct enablements, and a cycle within the graph captures a self-organising component of a physical system in a general and abstract way. We use our notion of a process-enablement graph to provide a concise definition of organisational closure in the language of graph theory. Further, we define a class of graph homomorphism which allows us to compare biological models as process-enablement graphs. These homomorphisms facilitate a comparison of descriptions of self-organisation in a consistent and precise manner. We apply our formalism to a range of classical theories of life including autopoiesis, <span><math><mrow><mo>(</mo><mi>F</mi><mo>,</mo><mi>A</mi><mo>)</mo></mrow></math></span>-systems, and autocatalytic sets. We demonstrate exactly how these models are similar, and where they differ, with respect to their organisational structure. While our current framework does not demarcate living systems from non-living ones, it does allow us to better study systems that lie in the grey area between life and non-life.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105567"},"PeriodicalIF":1.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145042085","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":"Spatial multi-omics technologies and applications in cancer","authors":"Lulin Ji","doi":"10.1016/j.biosystems.2025.105576","DOIUrl":"10.1016/j.biosystems.2025.105576","url":null,"abstract":"<div><div>Spatial multi-omics integrates individual genomics technologies with a single technology that simultaneously acquires data from multiple genomics, enabling parallel or even identical tissue sections for joint analysis of cells in tissues. It facilitates the analysis of cell-cell-interactions and provides a three-dimensional panoramic view of tissues. Thus, joint profiling of spatial multi-omics features may enable us to reconstruct key processes in tumorigenesis. Through spatial multi-omics technology, researchers have revealed spatial cellular interactions, TLS identification, changes in immune function, and established a spatial map of human tumors and a spatial gene database, which facilitates the development of personalized tumor therapy. In the future, there may be a need to further develop new spatial analysis techniques and tools, mainly in terms of spatial and temporal resolution, throughput, and sensitivity, to aid in cancer diagnosis and treatment and to decode novel mechanisms of tumorigenesis and development. In this review, we provide guidance for selecting appropriate spatial multi-omics techniques by elucidating the advantages and disadvantages of various spatial multi-omics and highlight advances in cancer field of spatial multi-omics technologies.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105576"},"PeriodicalIF":1.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145042091","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":"GATA TF Class Classifier: AI-based functional prediction and taxonomic profiling in angiosperm GATA transcription factors","authors":"Mangi Kim","doi":"10.1016/j.biosystems.2025.105589","DOIUrl":"10.1016/j.biosystems.2025.105589","url":null,"abstract":"<div><div>GATA transcription factors (TFs) are key regulators of diverse physiological and developmental processes in angiosperms. Although they are traditionally classified into four functional classes (A-D) based on phylogenetic relationships, large-scale classification across plant genomes remains limited by the labor-intensive nature of tree-based approaches. To overcome this limitation, this study presents the GATA TF Class Classifier, a scalable sequence-based tool for genome-wide functional classification of GATA TFs across angiosperm species. The model was trained on 700 curated full-length sequences from 23 species, encoded with ProtBERT, reduced via principal component analysis (PCA) with six additional features, and classified into functional classes using a support vector machine (SVM). The model achieved an average accuracy of 94.29 %, with balanced performance across all classes, as confirmed by repeated stratified 5-fold cross-validation. When applied to 4170 GATA TFs from 121 angiosperm genomes, the classifier showed that classes A and B were relatively abundant, whereas classes C and D were less represented, implying that each class may perform distinct biological functions. In addition, this study performed a taxonomic analysis of the predicted GATA TF classes to investigate their characteristics across major angiosperm lineages. Taken together, the classifier facilitates large-scale annotation and offers insights into the lineage-specific diversification and functional evolution of GATA TFs in angiosperms.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105589"},"PeriodicalIF":1.9,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145042082","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":"Influence of oxidative stress on women’s fertility: A model with a generational age Caputo’s fractional derivative","authors":"A.M. Portillo ,&nbsp;J.A. García-Velasco ,&nbsp;E. Varela","doi":"10.1016/j.biosystems.2025.105577","DOIUrl":"10.1016/j.biosystems.2025.105577","url":null,"abstract":"<div><div>Cellular aging associated with telomeric shortening plays an important role in female fertility. In addition to natural decline, due to the loss of telomeric repeats during cell division, other factors such oxidative stress (OS), accelerate telomere shortening by causing a dramatic loss of telomeric repeats. Thus, mathematical models to better understand the accelerated aging leading to infertility are lacking in the literature. An initial and boundary value problem (IBVP) with a diffusion-advection equation was considered to describe the evolution of a cell population undergoing a gradual decrease of the proliferation potential due to the end-replication problem (<span><span>Olovnikov, 1973</span></span>). In this paper we propose a continuum model that attempts to capture the random telomere shortening caused by OS, replacing the advection term with a Caputo’s fractional derivative of order <span><math><mi>β</mi></math></span>, <span><math><mrow><mn>0</mn><mo>&lt;</mo><mi>β</mi><mo>&lt;</mo><mn>1</mn></mrow></math></span>, with respect to the generational age. The distance between the order of the Caputo derivative and 1 was considered the oxidation parameter. The mathematical model was applied to the human follicular growth from preantral to pre-ovulatory follicle, in young and older women to study the influence of oxidation and low telomerase activity on the aging rate of the pre-ovulatory follicle. We observed that as OS increases, the generational age of granulosa cells (GCs) increases as well, suggesting that telomeres of these GCs will be aged. Although middle-aged women treated with antioxidants could reduce the negative effects of OS on telomeres, antioxidants in combination with good levels of telomerase activity yield the best results regarding the reduction of generational aging of GCs.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105577"},"PeriodicalIF":1.9,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145027121","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":"Viscous DNA and RNA: Quantum damped dynamical random systems","authors":"Hamze Mousavi,&nbsp;Samira Jalilvand","doi":"10.1016/j.biosystems.2025.105578","DOIUrl":"10.1016/j.biosystems.2025.105578","url":null,"abstract":"<div><div>From a physics perspective, DNA and RNA molecules are characterized as dynamic biological structures that exhibit vibrations across a range of time scales. To conduct a more accurate investigation of their dynamic properties, it is essential to consider the environmental conditions surrounding these molecules. A harmonic Hamiltonian that incorporates damping, along with the Green’s function method, has been utilized to analyze the vibrational responses of viscous DNA and RNA strands. The DNA molecule is represented using a fishbone model alongside two distinct double-strand configurations, while a half-ladder model is applied to the RNA molecule. The interconnections between sub-sites are represented by linear springs, with the stiffness of the vertical springs and the damping coefficients of the dashpots varying randomly throughout the length of the systems. Furthermore, each model is examined under three distinct configurations: infinite, finite, and cyclic. The results reveal that the fluctuations in the density of states curves exhibit a gradual decline, leading to a broadening of the sharp peaks as the damping coefficient increases. Additionally, the vibrational modes become progressively less distinct with an increase in system damping, a finding that aligns well with the principles of wave mechanics and vibrational motion.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105578"},"PeriodicalIF":1.9,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145027122","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}