Biosystems最新文献

Demographics of genetic admixture and expansion. 基因掺杂和扩展的人口统计学。

IF 2 4区生物学

Biosystems Pub Date : 2025-03-14 DOI: 10.1016/j.biosystems.2025.105455

Dalkhat M Ediev

引用次数: 0

Joint optimization of replicative rate and information storage set the letter size of primordial genetic alphabet

IF 2 4区生物学

Biosystems Pub Date : 2025-03-11 DOI: 10.1016/j.biosystems.2025.105442

Hemachander Subramanian

{"title":"Joint optimization of replicative rate and information storage set the letter size of primordial genetic alphabet","authors":"Hemachander Subramanian","doi":"10.1016/j.biosystems.2025.105442","DOIUrl":"10.1016/j.biosystems.2025.105442","url":null,"abstract":"<div><div>The simplest possible informational heteropolymer requires only a two-letter alphabet to be able to store information. The evolutionary choice of four monomers in the informational biomolecules RNA/DNA or their progenitors is intriguing, given the inherent difficulties in the simultaneous and localized prebiotic synthesis of all four monomers of progenitors of RNA/DNA from common precursors on early Earth. Excluding the scenario where a two-letter alphabet genome eventually expanded to include two more letters to code for more amino acids on teleological grounds, we show here that a replicatively superior heteropolymer sequence in an RNA-world-like scenario would have to be composed of at least four letters in order to predictably fold into a specific secondary structure, and hence must have out-competed the two-letter alphabet genomes. As a consequence of our earlier demonstration of the replicative rate advantage of maximal-nucleotide-skew sequences, in this follow-up article, we show that the competing constraints of maximum replicative rate and predictable secondary structure formation can be simultaneously satisfied only by maximally-skewed palindromic heteropolymer sequences composed of a minimum of four letters.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"251 ","pages":"Article 105442"},"PeriodicalIF":2.0,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143611314","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}

引用次数: 0

Human cognitive limitations and emotions: The emergence of social complexity

IF 2 4区生物学

Biosystems Pub Date : 2025-03-11 DOI: 10.1016/j.biosystems.2025.105454

Pedro C. Marijuán , Jorge Navarro

{"title":"Human cognitive limitations and emotions: The emergence of social complexity","authors":"Pedro C. Marijuán , Jorge Navarro","doi":"10.1016/j.biosystems.2025.105454","DOIUrl":"10.1016/j.biosystems.2025.105454","url":null,"abstract":"<div><div>An evolutionary approach to human cognition and social complexity, acknowledging the essential role of social emotions, is attempted. From the start, every kind of cognition, either artificial or natural, is limited. In living beings, it is the life cycle, life course, or life history what determines the extension, intensity, and limitations of the cognitive tools evolved to adapt to the own niche: from bacteria to multicellulars, animals, mammals, anthropoids, etc. Herein we will briefly survey some of those instances. In the human case, the essential niche becomes an extended social group with a rich diversity of cognitive links or ‘bonds’ in continuous interaction. Evolutionarily, the adaptation process to this social niche has involved a series of brain size increases, allowing, above all, the cognitive wonders inherent in language. But it has also involved a restructuring of the cognitive ‘shortcuts’ — essentially, emotions — that help individuals to navigate their own life in the natural environment and, especially, within the highly complex social milieu. Ultimately, this social adaptation process made possible the emergence of human ‘ultrasociality’ –the crux of Anthropogenesis-- and the most conspicuous behavioral traits still observable in contemporary societies, the effects of which also reverberate in the practice of science itself.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"251 ","pages":"Article 105454"},"PeriodicalIF":2.0,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143620218","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}

引用次数: 0

Physical limits of natural computation as the biological constraints of morphogenesis, evolution, and consciousness: On the 100th anniversary of Efim Liberman (1925–2011)

IF 2 4区生物学

Biosystems Pub Date : 2025-03-08 DOI: 10.1016/j.biosystems.2025.105451

Abir U. Igamberdiev , Nikita E. Shklovskiy-Kordi

{"title":"Physical limits of natural computation as the biological constraints of morphogenesis, evolution, and consciousness: On the 100th anniversary of Efim Liberman (1925–2011)","authors":"Abir U. Igamberdiev , Nikita E. Shklovskiy-Kordi","doi":"10.1016/j.biosystems.2025.105451","DOIUrl":"10.1016/j.biosystems.2025.105451","url":null,"abstract":"<div><div>Efim Liberman (1925–2011) introduced in 1972 the idea of natural computation realized internally by living systems. He considered the physical principles employed by living systems as essential constraints that limit the computational process occurring in the course of adaptation, morphogenesis, and neural activity. The most general limits determined by the physical fundamental constants are universal for all nature. However, the more specific constraints are intrinsic to each biological system and can be overcome in the course of the evolutionary process. We discuss the roles of biological macromolecules, particularly the cytoskeleton, in shaping the actualization patterns formed in the internal measurement process occurring in living systems. Cytoskeletal rearrangements determine cellular, morphogenetic, and perceptive transformations in living systems and participate in the combinatorial genetic events that lead to evolutionary transformations. The operation of neurons is based on the transmission of signals via the cytoskeleton, where the digital output is generated that can be decoded through a reflexive action of the perceiving agent. It is concluded that the principles of natural computation formulated by Liberman represent the most fundamental feature of living beings and form the basis for the general theory of biological systems, with essential consequences for understanding metabolic closure, morphogenesis, evolution, and consciousness.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"251 ","pages":"Article 105451"},"PeriodicalIF":2.0,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143587898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Progressive evolution of plants: A critical review

IF 2 4区生物学

Biosystems Pub Date : 2025-03-05 DOI: 10.1016/j.biosystems.2025.105444

A.V. Melkikh

引用次数: 0

From memory disorders to the development of depression: A system approach

IF 2 4区生物学

Biosystems Pub Date : 2025-03-04 DOI: 10.1016/j.biosystems.2025.105440

Grigory A. Grigoryan

{"title":"From memory disorders to the development of depression: A system approach","authors":"Grigory A. Grigoryan","doi":"10.1016/j.biosystems.2025.105440","DOIUrl":"10.1016/j.biosystems.2025.105440","url":null,"abstract":"<div><div>In this review, a hypothesis explaining the origin and genesis of depression development from the perspective of a holistic functional system of behavioral control is proposed. The core of the functional system is the memory apparatus, on which all other key components of the behavioral control system (sensory information, motivation, reinforcement, and motor activity) are interlocked. In the organization of memory traces (engrams) there are two inputs, sensory and motivational, through which the stimulus-stimulus (S-S) and stimulus-motor (S-R) engrams are formed. These engrams are organized and actualized by means of forward and backward conditional connections between cortical representations of sensory information and motivational structures of the brain. Through feedback connections from reinforcing (emotional) input to the memory apparatus, the S-S and S-R engrams are consolidated or weakened depending on the strength of reward or negative events. Depression begins with a breakdown in memory mechanisms. These breakdowns are related to problems with the three mentioned memory inputs: sensory, motivational, and reinforcing (emotional). Disruptions in sensory and motivational input lead to an inability to form new memory engrams, their actualization and retrieval. This creates difficulty in solving current and past unresolved problems, eliciting more accumulation and increasing difficulties in their solving. Unresolved tasks lead to weakening of the reinforcing input, and further impairment of consolidation of the acting engrams. Another reason for the weakening of reinforcing input is excessive action of directly harmful events or constant chronic stress. The review presents the current literature and some data from our laboratory in favor of each memory input's contribution and their impact on the development of depression, when they are problematic.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"251 ","pages":"Article 105440"},"PeriodicalIF":2.0,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574552","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}

引用次数: 0

Corrigendum to “Metabolic ecology in aquatic ecosystems: Viewed from trophic compartments and communities in food webs” [BioSystems 249(2025) 105401] 水生生态系统的代谢生态学：生物系统 249(2025) 105401]。

IF 2 4区生物学

Biosystems Pub Date : 2025-03-04 DOI: 10.1016/j.biosystems.2025.105441

Ichiro Aoki

引用次数: 0

Reliability and energy function of an oscillator and map neuron

IF 2 4区生物学

Biosystems Pub Date : 2025-03-03 DOI: 10.1016/j.biosystems.2025.105443

Qun Guo , Guodong Ren , Chunni Wang , Zhigang Zhu

{"title":"Reliability and energy function of an oscillator and map neuron","authors":"Qun Guo , Guodong Ren , Chunni Wang , Zhigang Zhu","doi":"10.1016/j.biosystems.2025.105443","DOIUrl":"10.1016/j.biosystems.2025.105443","url":null,"abstract":"<div><div>External physical and chemical stimuli can be perceived and encoded in biological neurons, and then synaptic couplings guide neurons to present appropriate firing modes in electrical activities. Oscillator-like and map neurons can produce similar deriving-responses while the working mechanism is open before considering the effect of membrane properties and channels function. In this study, a theoretical neuron model is proposed by involving two capacitive variables and a memristive channel sensitive to external electric field, and the double-layer membrane property is relative to temperature. During circuit approach, two capacitors are connected via a thermistor, and a charge-dependent memristor (CDM) is connected into one branch circuit of the neural circuit. The temperature-dependent and memristive neuron model is described by a nonlinear oscillator containing four variables and energy function is defined from physical aspect. Furthermore, linear transformation is applied to the sampled time variables from the oscillator neuron, and an equivalent map neuron following covariance is obtained for dynamical analysis, energy definition and adaptive control, and similar coherence resonance is detected under noisy excitation. The results show how to obtain reliable map neurons with exact energy function, and adaptive control law under energy flow becomes reasonable.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"251 ","pages":"Article 105443"},"PeriodicalIF":2.0,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143562080","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}

引用次数: 0

Understanding nature’s selection of genetic languages

IF 2 4区生物学

Biosystems Pub Date : 2025-03-03 DOI: 10.1016/j.biosystems.2025.105428

Apoorva D. Patel

{"title":"Understanding nature’s selection of genetic languages","authors":"Apoorva D. Patel","doi":"10.1016/j.biosystems.2025.105428","DOIUrl":"10.1016/j.biosystems.2025.105428","url":null,"abstract":"<div><div>All living organisms use two universal genetic languages in their molecular biology machinery, one containing four nucleotide bases in its alphabet, and the other containing twenty amino acids in its alphabet. They can be understood as the optimal encodings of genetic information for the tasks they carry out, i.e. replication/transcription for DNA/RNA and translation for polypeptide chains. These tasks select needed letters of the alphabet by complementary nucleotide base-pairing, from a collection of molecules in the cell. The computer science paradigm for this process is database search; various algorithms for it can be constructed and compared according to number of attempts (or queries) they need to make to find the correct nucleotide base-pairing. Grover’s search algorithm based on oscillatory wave dynamics perfectly fits the number of queries needed to search the genetic alphabets, and it is more efficient than the best Boolean search algorithm (i.e. binary tree search) that needs a larger number of queries. This result strongly suggests that the universal genetic languages have been selected by evolution as the optimal alphabets for the tasks they carry out, and are not an accident of history. The outstanding challenge is to demonstrate how Grover’s search algorithm would be executed in vivo by the living organisms.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"250 ","pages":"Article 105428"},"PeriodicalIF":2.0,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143534427","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}

引用次数: 0

Codes of praxis: How recursivity constitutes human social practices

IF 2 4区生物学

Biosystems Pub Date : 2025-02-24 DOI: 10.1016/j.biosystems.2025.105429

Rasmus Gahrn-Andersen

{"title":"Codes of praxis: How recursivity constitutes human social practices","authors":"Rasmus Gahrn-Andersen","doi":"10.1016/j.biosystems.2025.105429","DOIUrl":"10.1016/j.biosystems.2025.105429","url":null,"abstract":"<div><div>The paper addresses a criticism raised by Kull (2020) against Code Biology. Kull's critique targets key ontological and epistemological assumptions within Code Biology and, if valid, could effectively subordinate it to Peircean Biosemiotics. After examining the core of Kull's argument, the paper counters a significant aspect of his claim: that cognition necessarily involves interpretation-driven decision-making, wherein an agent is always faced with at least two alternatives when acting upon the world. Drawing from radical cognitive science and general Code Biology, the paper argues that basic cognitive processes are devoid of mental content and, therefore, should not be described in mentalist terms such as ‘decision-making’ or ‘interpretation.’ In this connection, insights from phenomenological accounts of skill acquisition demonstrate that even sophisticated forms of human cognition can occur without explicit reasoning about alternatives. In such cases, the environment itself elicits skillful responses. Building on this, the paper introduces the concept of praxeological codes—understood as codified relations characteristic of human socio-practical activity—which can be used to explain what Maturana identifies as the ‘recursivity’ of practical doings. In this connection, the paper provides an account of core aspects of human socio-practical behavior.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"251 ","pages":"Article 105429"},"PeriodicalIF":2.0,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143517072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0