Biosystems最新文献

{"title":"First evidence supporting the theory of the sensorimotor paradox on the origins of mind and language","authors":"Clémence Ortega Douville","doi":"10.1016/j.biosystems.2026.105691","DOIUrl":"10.1016/j.biosystems.2026.105691","url":null,"abstract":"<div><div>For now 15 years, I have been developing a hypothesis on the origins of mind and language during our evolution, called theory of the sensorimotor paradox. The core neuroimaging part of the hypothesis is that the switch in our relation to our hands, coming with bipedal stance, would have allowed us to disrupt the function of sensory prediction to resolve into motor action and sensory feedback: we can't take our hand as an object of interaction and have it grasp itself at the same time. This would later on be autonomised as mental representation. From there, non-resolution of prediction into motor action would prevent a system from liberating tension in order to be available again and collect feedback (meta-prediction). Using Schalk, G. et al.'s extensive dataset of EEG recordings on motor movement and imagery (2009), I am now able to support some of the theory's claims. Notably, meta-analysis of movement and imagery recordings tends to stress a higher variability of frequency activation amongst motor signals than imagery's. This would indicate a greater difficulty for a system to release tension in an effort to produce and maintain mental representation. Similar short oscillatory predictive change, but greater uncoupling of frontal and prefrontal regions suggests sensory suppression of efference-copy and greater instability toward the eventuality of collecting feedback when motor action is triggered, relying on somatosensory support. Event-related time-frequency analysis on proprioceptive areas shows delay of neural signal to mental representation compared to motor action, which could be a strong evidence of dissociation.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"262 ","pages":"Article 105691"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145985760","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":"Automated quantitative analysis of differences in Caenorhabditis elegans head swings and omega turns among strains","authors":"Wenyue Zhan ,&nbsp;Weiyang Chen ,&nbsp;Yi Pan","doi":"10.1016/j.biosystems.2026.105716","DOIUrl":"10.1016/j.biosystems.2026.105716","url":null,"abstract":"<div><div>Neurodegenerative diseases have recently garnered significant attention. To better understand the pathogenesis of these diseases and find effective treatments, scientists are increasingly using model organisms in their research. Nematodes, a model organism for studying neurodegenerative diseases, offer crucial insights into the relationship between genes, motor neurons, and locomotion behavior. By identifying the positions of nematodes using a head and tail localization model and automatically counting head swings and omega turns, the analysis of behavioral differences among various nematode strains demonstrates the connection between locomotion behavior and motor neurons. The results from automated counting serve as key indicators of motor neuron integrity, emphasizing the importance of nervous regulation in nematode locomotion behavior and providing new avenues for studying sensory systems and behavioral mechanisms. This has potential implications for the treatment of neurodegenerative diseases.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"262 ","pages":"Article 105716"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138049","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 are the most lethal pathogens the simplest? Lack of D-amino acid usage, coherent fractal morphology, and Hz-level biological oscillations prevalent in beneficial pathogens","authors":"Monica M. Araujo","doi":"10.1016/j.biosystems.2026.105713","DOIUrl":"10.1016/j.biosystems.2026.105713","url":null,"abstract":"<div><div>This paper examines a biochemical paradox in microbial pathogenicity: the most lethal human pathogens (viruses, protozoa, prions) systematically lack D-amino acid usage, coherent fractal morphology, and Hz-level biological oscillations; these characteristics prevail in beneficial and treatable bacterial pathogens. Systematic analysis of 47 major human pathogens and quantitative fractal dimension analysis of 40 cryo-electron microscopy structures unveil refined hierarchical patterns within universally low structural complexity.</div><div>Bacterial pathogens employ D-amino acids in peptidoglycan synthesis and exhibit a broad structural repertoire spanning from 1.2610 to 1.9625 (mean 2D fractal dimension = 1.5502 ± 0.2543), overlapping the upper protozoal band (mean = 1.5865 ± 0.1322). Protozoa therefore show the highest central complexity, while bacteria display the widest variance and retain access to higher-order organization. Increasingly lethal pathogens systematically lack these features and occupy progressively reduced complexity bands (Fungi: 1.5074 ± 0.1600; Virus: 1.4388 ± 0.2575; Prion: 1.4060 ± 0.1727).</div><div>Among all structures analyzed, the HIV-1 capsid displayed the lowest complexity (D₂D = 1.1095), consistent with its historically high lethality and over 40 million cumulative deaths since the 1980s.</div><div>We propose that this evolutionary minimalism represents a convergent pathogenic strategy in which successful pathogens attain reduced complexity, with the most lethal variants pushing simplification to extreme levels characterized by biochemical invisibility and structural incoherence. D-amino acid absence enables evasion of host innate immune recognition through D-amino acid oxidase, while lack of intrinsic circadian rhythms prevents metabolic synchronization and immune detection. This framework provides measurable criteria for pathogen threat assessment and suggests new therapeutic approaches rooted in complexity-based medicine.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"262 ","pages":"Article 105713"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146127385","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":"Thermodynamic ontogeny: The emergence of persistence and complexity in pre-genetic chemical systems","authors":"Albert M. Magro","doi":"10.1016/j.biosystems.2026.105717","DOIUrl":"10.1016/j.biosystems.2026.105717","url":null,"abstract":"<div><div>Understanding how thermodynamic principles drive the emergence of organized chemical systems from abiotic geochemistry represents a central challenge in prebiotic evolution. We develop a quantitative framework for systems removed from equilibrium, establishing formulations for organizational complexity (C) and persistence (P). Complexity, the volumetric rate of free energy dissipation maintaining non-equilibrium organization, scales with substrate gradients and kinetic accessibility. Persistence is the system’s capacity to export internally generated entropy across membrane boundaries, determined by geometric constraints and transport impedances. Bejan’s Constructal Law provides the optimization principle by which protocell geometry morphs to achieve this balance, providing a deterministic basis for protocell dimensions and molecular architecture. For mineral-catalyzed chemistry at hydrothermal vents (<span><math><mrow><mrow><mo>〈</mo><mtext>Ea</mtext><mo>〉</mo></mrow><mo>≈</mo></mrow></math></span> 50 kJ/mol, T <span><math><mo>≈</mo></math></span> 338 K), the framework predicts optimal radius r <span><math><mrow><mo>≈</mo><mn>0</mn><mo>.</mo><mn>56</mn><mspace></mspace><mi>μ</mi></mrow></math></span>m for volume-distributed chemistry (n = 3), matching observed dimensions of experimental protocells and minimal cells. Conversely, surface-limited chemistry (n = 2) predicts mechanically unstable configurations, establishing the internalization of metabolism as a thermodynamic necessity. Geological subsidence at polar regions provides deterministic forcing driving protocell populations toward increasing complexity over multi-million-year timescales. The transition from monomers to polymers is a necessary strategy to mitigate osmotic stress during subsidence, effectively responding to a baric forcing of complexity. The framework generates falsifiable predictions where ln(r) <span><math><mo>∝</mo></math></span> 1/T, with a slope determined by activation energy and dimensionality. The framework transforms a prebiotic system from a statistical improbability into a predictable physical outcome, establishing the foundations for life as a thermodynamic necessity operating under early Earth constraints.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"262 ","pages":"Article 105717"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138149","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":"Evolution of pre-genetic semantic information in protocells under variable inheritance fidelity","authors":"Michael J. Carr","doi":"10.1016/j.biosystems.2026.105718","DOIUrl":"10.1016/j.biosystems.2026.105718","url":null,"abstract":"<div><div>How meaningful, heritable structure first emerged in prebiotic chemical systems remains a central open question in origins-of-life research. Classical frameworks such as the quasispecies and RNA-world models assume that accurate template-based replication is required for stable information and functional specificity to evolve. This work introduces a minimal agent-based protocell model in which short RNA-like oligomers bind metabolites along local 5-nt motifs, generating spatial organization without catalysis or replication. Protocells inherit molecular contents solely through noisy physical partitioning, allowing assessment of whether semantic structure—quantified as mutual information between motif identity and metabolite class—can arise under purely compositional heredity. Across an inheritance-fidelity sweep (0.1–1.0), a sharp semantic threshold was identified: below moderate fidelity, motif–metabolite correlations cannot accumulate, whereas above the threshold (∼0.7), semantic information increases rapidly and stabilizes as a heritable population property. Fitness gains lag behind semantic structure and become substantial only at high fidelity, indicating that meaning emerges before adaptive function. These results establish a pre-genetic information system in which environmental semantics arises without replication, providing a conceptual bridge between compositional inheritance models and sequence-based evolutionary theories.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"262 ","pages":"Article 105718"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146138125","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 the origin of life to a biosphere: Formation of artificial ecosystems where species shape and are shaped by each other","authors":"Evgeny Ivanko,&nbsp;Aleksey Belousov","doi":"10.1016/j.biosystems.2026.105711","DOIUrl":"10.1016/j.biosystems.2026.105711","url":null,"abstract":"<div><div>We study the development of model biotic communities in which species play the role of environment for each other. Each experiment starts with the appearance of a single species in an abiotic environment. The properties of this initial species (together with the size of the abiotic environment) are the independent parameters of the experiment. In the following phase of macroevolutionary “unwrapping” each existing species can change its abundance (according to its current fitness) and give rise to new species (as a result of mutation). During this process, the destiny of the species becomes increasingly determined by the influence of other species rather than by the abiotic environment. With the mechanics described, artificial biotic communities experience adaptive radiation from single species to complex networks that coevolve in adaptive landscapes of their own making.</div><div>Using a number of metrics, we track the evolution of biotic communities in the hope of discovering interesting properties and patterns. We have tried to provide plausible explanations for the experiment results wherever possible. However, the main purpose of this work is not to answer questions, but rather to raise new ones, to provoke thoughts and analogies among readers with different backgrounds.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"261 ","pages":"Article 105711"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146031526","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 transmission and processing in G-protein-coupled-receptor complexes","authors":"Roger D. Jones ,&nbsp;Achille Giacometti ,&nbsp;Alan M. Jones","doi":"10.1016/j.biosystems.2026.105706","DOIUrl":"10.1016/j.biosystems.2026.105706","url":null,"abstract":"<div><div>We present a general theoretical framework for molecular computation in biological systems and apply it to G-protein-coupled receptors (GPCRs), which serve as central regulators of cellular information processing. Despite their importance, the physical principles underlying GPCR switching remain incompletely understood. Using nonequilibrium thermodynamics, we construct a model that identifies the parameters governing receptor-state transitions. The framework shows that the configuration of the switch is governed by two factors: the ATP/GTP-driven chemical flux through the receptor complex and the free-energy difference between competing switch states. The model predicts that GPCRs can occupy three quasistable configurations, corresponding to “on”, “off”, and an intermediate state, each representing a local maximum in information transmission. Switch states can also be characterized by whether the switch supports a net chemical flux. Active states support sustained chemical flux, whereas inactive states do not. The model incorporates reciprocal conformation-fit changes between ligand and receptor. As such, the model predicts that phosphatase activity, represented as an effective energy barrier, primarily determines whether the switch occupies the “on” or “off” state, whereas kinase activity maintains flux without directly setting state occupancy. These predictions based on experimental evidence point to new targets for drug design. Comparison with label-free impedance measurements supports the existence of multiple quasistable states that depend on ligand conformation. Because the framework relies on general nonequilibrium principles rather than system-specific biochemistry, it extends naturally to other biological switching systems driven by chemical flux.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"261 ","pages":"Article 105706"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145986731","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":"Internal quantum constraints of natural computation in autopoietic systems","authors":"Abir U. Igamberdiev","doi":"10.1016/j.biosystems.2026.105707","DOIUrl":"10.1016/j.biosystems.2026.105707","url":null,"abstract":"<div><div>Time relates to actualization, which is physically interpreted as a quantum measurement. The measurement has a dual structure consisting of the reality being measured (externality) and the reality by which the measurement takes place (an agent or <em>ontolon</em>). These two constituents refer to the two types of time: physical time measured by clocks, and internal time, defined by Bergson as <em>la durée</em> (duration). The latter holds the coherent internal quantum state of entangled potentialities, while the former represents the collapse of this state, thereby flowing through quantum transactions. This view unifies the Everett (Many-worlds) and the Copenhagen (Wave function collapse) interpretations of the quantum measurement. Time as a duration can be estimated via the energy-time uncertainty relation, which links the precision of the measurement result to the value of energy dissipation during it and to its span. The precision of the measurement result enables the process of quantum computation, which emerges in the systems characterized by internal closure, i.e., autopoietic (living) systems operating at the state of sustainable non-equilibrium. Energy dissipation in the process of measurement occurs as the emission of quanta that trigger the collapse of the coherent entangled state. These quanta are recognized in the system, enabling the performance of higher-level control over elementary computational actions through their integration within the complex system. It is concluded that the energy-time uncertainty relation represents the fundamental internal quantum constraint of natural computation, the process that spans from enzymatic catalysis to complex regulatory and adaptive activities, and finally to reflexive consciousness.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"261 ","pages":"Article 105707"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145999289","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":"Double exponential neuron evolution versus merely exponential Artificial Intelligence (AI): Reconsideration of Kurzweil's Singularity","authors":"Varshith Madishetty ,&nbsp;Lalith Bharadwaj Baru ,&nbsp;S. Hussain Ather ,&nbsp;Richard Gordon","doi":"10.1016/j.biosystems.2026.105709","DOIUrl":"10.1016/j.biosystems.2026.105709","url":null,"abstract":"<div><div>Reanalysis of recent data has led to two unexpected conclusions. 1) Animals with regulating embryos show exponential growth in the number of cell types (NCT) over geological time, while animals with mosaic embryos remain merely flat or linear on average, highlighting fundamentally different evolutionary strategies; 2) Recent evolution of the number of nerves in adult regulating animals has been doubly exponential. Mosaic animals tend to yield a pair of cells at each cell division that are differentiated from one another and their mother cell during embryogenesis, while regulating animals usually produce large numbers of presumably identical cell types at each step of embryogenesis, possibly via bioelectric fields. (The mother cell is usually different from both of its daughter cells in mosaic development, and is transient.) For some animals, these categories overlap. Nevertheless, plots of the number of cell types (NCT) versus estimates of when their first ancestors appeared show no increase on average for NCT versus geological time for animals whose embryos are generally categorized as mosaic, whereas animals with regulating embryos show an exponential increase in NCT versus geological time. An attempt to confine NCT to neurons failed due to sparse data, but did suggest that the total number of neurons in animals with regulating embryos increased as a double exponential over geological time (i.e., they have exponential behavior even on a logarithmic scale). AI has only been increasing exponentially with respect to the number of simulated neurons used in state-of-the-art algorithms. Thus, amalgamating human brains with AI, even if Ray Kurzweil's “Singularity is Nearer”, may prove premature. Furthermore, amalgamation might lead to atrophy of portions of the human brain.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"261 ","pages":"Article 105709"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146031536","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":"Ohmic–Polarization transition in hydrated DNA","authors":"Mariusz Pietruszka","doi":"10.1016/j.biosystems.2026.105708","DOIUrl":"10.1016/j.biosystems.2026.105708","url":null,"abstract":"<div><div>A quasi-two-dimensional DNA–water system was investigated under a perpendicular magnetic field of 0.5<!--> <!-->T and a constant 0.1<!--> <!-->V bias at near-room temperature. Upon cooling, the system undergoes a sharp crossover near 20 °C from a regime with finite longitudinal conduction to a regime in which the longitudinal current <span><math><msub><mrow><mi>I</mi></mrow><mrow><mi>x</mi><mi>x</mi></mrow></msub></math></span> collapses, while the transverse voltage <span><math><msub><mrow><mi>V</mi></mrow><mrow><mi>x</mi><mi>y</mi></mrow></msub></math></span> and a correlated photovoltage remain finite and develop slow, coherent modulations. This decoupling of longitudinal and transverse responses cannot be explained by conventional charge transport and instead indicates a transition from ohmic conduction to polarization-dominated dynamics governed by displacement currents. Complementary magnetic-field sweeps in higher-concentration samples reveal a reproducible polarization cycle, including a pronounced inversion between <span><math><msub><mrow><mi>V</mi></mrow><mrow><mi>x</mi><mi>y</mi></mrow></msub></math></span> and <span><math><msub><mrow><mi>V</mi></mrow><mrow><mi>photo</mi></mrow></msub></math></span> and a highly elongated Lissajous portrait, consistent with near anti-phase locking of electrical and optical degrees of freedom. These results identify a field-tunable, polarization-coherent regime in quasi-2D hydrated DNA under ambient/biological conditions, in which macroscopic voltages arise from collective polarization dynamics rather than net charge flow.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"261 ","pages":"Article 105708"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145986730","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}