BiosystemsPub Date : 2025-08-26DOI: 10.1016/j.biosystems.2025.105575
Hirdesh Rohatgi
{"title":"The role of pure mathematics in resolving complex biological problems: Applications to F1-ATPase, achievements, and future directions","authors":"Hirdesh Rohatgi","doi":"10.1016/j.biosystems.2025.105575","DOIUrl":"10.1016/j.biosystems.2025.105575","url":null,"abstract":"<div><div>Mathematics should be a core component of biological research, not merely an auxiliary tool, to address intricate problems. Integration of pure mathematics into biological research offers a powerful avenue to address complex molecular-level problems whose complete elucidation has proven resistant to traditional experimental, theoretical, and computational approaches alone. This paper explores the application of mathematics in Nath's work on F<sub>1</sub>-ATPase, such as combinatorics, number theory, graph theory, and highlights its ability to elucidate molecular mechanisms, model biological systems, predict complex behaviors, validate models, and provide definitive conclusions. We quantify the economic toll of flawed research, and propose a mathematical framework to advance biological discovery, positioning mathematics as a transformative force to solve biological problems.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"257 ","pages":"Article 105575"},"PeriodicalIF":1.9,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144977424","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}
BiosystemsPub Date : 2025-08-24DOI: 10.1016/j.biosystems.2025.105568
Davor Juretić, Branka Bruvo Mađarić
{"title":"Scale-Invariant Dissipation Underlies Enzyme Catalytic Performance.","authors":"Davor Juretić, Branka Bruvo Mađarić","doi":"10.1016/j.biosystems.2025.105568","DOIUrl":"https://doi.org/10.1016/j.biosystems.2025.105568","url":null,"abstract":"<p><p>The role of energy dissipation in the evolution of living systems remains a subject of ongoing debate. Here, we quantify the dissipation associated with enzyme catalysis using minimalistic models of enzyme kinetics and a complete set of microscopic rate constants. We identify a power-law proportionality between total dissipated energy and key kinetic parameters- specifically, the catalytic constant and the specificity constant. These scale-invariant relationships hold across enzyme classes, biological domains, and natural or engineered enzymes. Consistent with Jensen's hypothesis, specialized enzymes display greater catalytic efficiency and higher dissipation. Yet, the wide range of observed efficiencies and dissipation values suggests that scale-independent organizational principles govern enzyme catalysis. Our findings indicate that biological evolution has not merely tolerated dissipation but has actively harnessed and regulated it within constraints imposed by functional and environmental demands. The scale-invariant perspective provides a unifying view of physical (dissipative) and biological (adaptive) evolutionary processes in the emergence of enzymatic function.</p>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":" ","pages":"105568"},"PeriodicalIF":1.9,"publicationDate":"2025-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144977437","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}
BiosystemsPub Date : 2025-08-23DOI: 10.1016/j.biosystems.2025.105570
Salvatore Chirumbolo , Antonio Vella
{"title":"Prigoginian informational dissipation (PID) as the cause of the emergence of a proto-self","authors":"Salvatore Chirumbolo , Antonio Vella","doi":"10.1016/j.biosystems.2025.105570","DOIUrl":"10.1016/j.biosystems.2025.105570","url":null,"abstract":"<div><div>This study introduces a theoretical framework where consciousness emerges as a consequence of Prigoginian Informational Dissipation (PID), a dynamic process through which information arises in far-from-equilibrium systems. By modelling particle interactions governed by dissipative feedback, the work demonstrates how structure, memory, and complexity evolve, culminating in a proto-self represented by the system centroid. This centroid transitions from a statistical average to an informational attractor, embodying recursive feedback and autopoietic coherence. The analysis incorporates entropy metrics, Lyapunov exponents, and nonlinear dynamics to trace the system trajectory from order to chaos. Results support the hypothesis that informational dissipation underlies the genesis of cognitive and self-organizing systems. Unlike prior models treating information as pre-existent, this approach frames it as emergent, situating cognition and consciousness within thermodynamic and information-theoretic processes. The findings advance an integrative view of life and mind, positing that consciousness arises not from structure alone, but from recursive stabilization of information in dissipative systems.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105570"},"PeriodicalIF":1.9,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144893591","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}
BiosystemsPub Date : 2025-08-23DOI: 10.1016/j.biosystems.2025.105569
Graham Scarr , Leonid Blyum , Stephen M. Levin , Susan Lowell de Solórzano
{"title":"Biotensegrity is the super-stability hypothesis for biology","authors":"Graham Scarr , Leonid Blyum , Stephen M. Levin , Susan Lowell de Solórzano","doi":"10.1016/j.biosystems.2025.105569","DOIUrl":"10.1016/j.biosystems.2025.105569","url":null,"abstract":"<div><div>Biotensegrity models living systems in ways that were inconceivable in the past but has taken some time to become widely accepted because of its challenges to generally accepted wisdom. Orthodox biomechanics is essentially based on mechanistic models from the seventeenth century and allowed over-simplified representations of anatomy and motion to persist to the present day, with the approximations and assumptions inherent within its methods routinely overlooked. Living organisms, however, are hugely complex, intrinsically indeterminate and exist in states that are far from equilibrium, and although their simplification within the machine model has enabled great progress in the mapping of structure to function — and benefitted our healthcare systems in remarkable ways — it has also obfuscated the foundational basis for stability, motion and life itself.</div><div>In contrast, biotensegrity is a conceptual framework that is founded on a fundamental set of self-organizing principles and includes all the complexities of life — at every heterarchical level from viruses to vertebrates and molecules to the whole organism — with stability and motion controlled from within the structure itself and the homeostatic algorithm of super-stability. Here, anatomy is no longer reduced to a set of discrete parts but becomes the physical representation of a hugely complex pattern of interacting force vectors, and which are themselves organized within a complex tensegrity configuration that enables each part of the system to adapt to its locally-changing environment in the most energy-efficient way — from embryo to adult — and remain intrinsically stable throughout.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105569"},"PeriodicalIF":1.9,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144902742","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}
BiosystemsPub Date : 2025-08-22DOI: 10.1016/j.biosystems.2025.105566
S.E. Shirmovsky , A.V. Chizhov
{"title":"The processes generating quantum entanglement in DNA","authors":"S.E. Shirmovsky , A.V. Chizhov","doi":"10.1016/j.biosystems.2025.105566","DOIUrl":"10.1016/j.biosystems.2025.105566","url":null,"abstract":"<div><div>The migration processes of a positive quasi-particle generating quantum entanglement in DNA are investigated. The study was performed on the short DNA strands. It has been shown that the entanglement migrates along the nitrogenous bases chain as a result of the tunnel effect. The entanglement processes have been studied on the DNA chains, for which the charge migration was experimentally confirmed, as well as on the Homo sapiens lipase A, lysosomal acid type gene (LIPA) short sequences. A high degree of nitrogenous bases entanglement was found reaching the values of 80%–90%. It was shown that the entanglement in DNA creates conditions for the energy and quantum states transfer in the genes not only through the chemical bonds, but also through a quantum channel using entanglement as well. The work concludes that the quantum entanglement can act as an additional communication channel between nitrogenous bases in DNA in the case of its partial destruction.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105566"},"PeriodicalIF":1.9,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144902739","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}
BiosystemsPub Date : 2025-08-13DOI: 10.1016/j.biosystems.2025.105565
Chika Edward Uzoigwe
{"title":"Negative membrane potentials potentiate multicellularity","authors":"Chika Edward Uzoigwe","doi":"10.1016/j.biosystems.2025.105565","DOIUrl":"10.1016/j.biosystems.2025.105565","url":null,"abstract":"<div><div>Why did evolution almost exclusively select negative membrane potentials? Why did natural selection not favour positive membrane potentials? Further, membrane constituents are also negatively charged, in the form phospholipids. Putative cis-charge repulsion represents an obstacle to the emergency of multicellularity. This is compounded by the fact that cells at the centre of nascent multicellular species are deprived of nutrients by diffusion and exposed to the highest levels metabolic detritus. Multicellularity appears <em>ab initio</em> maladaptive.</div><div>We present the hypothesis here that multicellularity may have been initiated, driven and potentiated by purely physical processes - one classical and one quantum. In water, negatively charged particles in the nano-to macro-molecular size-range, can aggregate, while positively charged repel one another. This counter-intuitive phenomenon has been consistently observed and recently attributed to the orientation of water molecules against the negatively charged surface and their re-orientation as negatively charged particles approach. This classical attraction works at long range, on a macromolecular scale. As two interfaces approximate closer, there is quantum attraction. Quantum nuclear effects of water hydrogen atoms are accentuated at interfacial layers compared to the bulk, due to the contraction of hydrogen bonds. This creates differences between the interfacial water and bulk in quantum free energy, which is only extinguished with the extrusion of intervening water. Quantum and classical attraction cooperate to initiate and stabilise multicellularity, while the whole process is possible because the membrane potential is negative and hydrogen is the dominant isotope rather than deuterium or tritium.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105565"},"PeriodicalIF":1.9,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859797","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}
BiosystemsPub Date : 2025-08-12DOI: 10.1016/j.biosystems.2025.105564
Mariusz Pietruszka
{"title":"Field-induced coherence and Fröhlich condensation in hydrated DNA","authors":"Mariusz Pietruszka","doi":"10.1016/j.biosystems.2025.105564","DOIUrl":"10.1016/j.biosystems.2025.105564","url":null,"abstract":"<div><div>Hydrated DNA confined in quasi-two-dimensional water layers exhibits macroscopic quantum coherence at ambient conditions under moderate magnetic fields. At 6 °C and low DNA concentration (100 ng/μL), we observe a sharp transverse voltage jump (∼37 mV) near 100 mT, followed by five regular oscillations (>20 mV), indicating an earlier onset of coherence compared to room-temperature transitions (∼0.5 T) at higher DNA concentrations (1000 ng/μL). These features suggest the formation of a Fröhlich-like condensate stabilized by field-induced energy localization. The system's response unfolds as geometric 'Riemann slices,' coherence domains activated sequentially by the magnetic field. The nearly flat longitudinal voltage confirms a selective transverse transport regime. Fourier analysis reveals distinct low-frequency peaks, reflecting regular internal modulation within the coherent state. Together with earlier findings of Landau quantization and ultra-weak photon emission, our results support a hierarchical model of vibrational condensation and geometric coherence in DNA–water systems, with potential implications for bioenergetics and magnetosensitivity.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105564"},"PeriodicalIF":1.9,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144852282","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}
BiosystemsPub Date : 2025-08-11DOI: 10.1016/j.biosystems.2025.105553
William B. Miller Jr. , Jaime F. Cárdenas-García , František Baluška , Arthur S. Reber , Predrag Slijepčević , John C. Little
{"title":"A biogenic principle within the constructal law: The flow of information in biological systems","authors":"William B. Miller Jr. , Jaime F. Cárdenas-García , František Baluška , Arthur S. Reber , Predrag Slijepčević , John C. Little","doi":"10.1016/j.biosystems.2025.105553","DOIUrl":"10.1016/j.biosystems.2025.105553","url":null,"abstract":"<div><div>The Constructal Law states that ‘for a finite-size flow system to persist in time (to live) it must evolve such that it provides greater and greater access to the currents that flow through it.’ Arising from thermodynamics, this illuminating principle explains the properties and design features of many physical systems. It is now proposed that the definition of ‘currents that flow’ within the Constructal Law should be recognized to include the flow of information in living systems as a biogenic corollary. As the foundation of our biological system, cells seek to maximize their effective information about their external and internal environment. As their constructs, multicellular organisms reflect this requirement, accounting for living forms and their anatomic features. The cellular senome represents the crucial element of this flow, acting as the bioactive interface between environmental syntactic information and the internally-generated cellular semantic information upon which cellular actions depend. A Biogenic Principle as a corollary of the Constructal Law is presented, stating that for any finite-size living system to persist in time (to live), it must evolve to provide greater and greater access to the flow of information between itself and its environment, balanced against the constraining flow dynamics of natural physical systems. Within this biogenic principle, a Central Axiom of Biological Information can be identified: there is no unilateral flow of information in living systems.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105553"},"PeriodicalIF":1.9,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144849502","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}
BiosystemsPub Date : 2025-08-11DOI: 10.1016/j.biosystems.2025.105563
Poria Azadi
{"title":"Computational irreducibility as the foundation of agency: A formal model connecting undecidability to autonomous behavior in complex systems","authors":"Poria Azadi","doi":"10.1016/j.biosystems.2025.105563","DOIUrl":"10.1016/j.biosystems.2025.105563","url":null,"abstract":"<div><div>This article presents a formal model demonstrating that genuine autonomy, the ability of a system to self-regulate and pursue objectives, fundamentally implies computational unpredictability from an external perspective. I establish precise mathematical connections, proving that for any truly autonomous system, questions about its future behavior are fundamentally undecidable. This formal undecidability, rather than mere complexity, grounds a principled distinction between autonomous and non-autonomous systems. My framework integrates insights from computational theory and biology, particularly regarding emergent agency and computational irreducibility, to explain how novel information and purpose can arise within a physical universe. The findings have significant implications for artificial intelligence, biological modeling, and philosophical concepts like free will.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"256 ","pages":"Article 105563"},"PeriodicalIF":1.9,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144849505","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}