Pub Date : 2024-11-05DOI: 10.1016/j.biosystems.2024.105362
Shounan Lu , Yang Wang
Understanding and explaining cooperative behavior in human society has become an open question. In this paper, we propose a dynamic adjustment of pair relationships in a spatial prisoner's dilemma game. Unlike previous studies that individuals dynamically adjust the intensity of interaction with their opponents at each step, this work consider tolerance, in which the intensity of interaction is adjusted when the time of successive defections by an individual exceeds a tolerance threshold T. We find that although the proposed mechanism can significantly improve cooperation compared to traditional versions, a higher tolerance for continuous defection behavior is not conducive to the evolution of cooperation. Furthermore, an environmental adaptor that dynamically adjusts the paired relationship with the opponent at all times is beneficial for the evolution of cooperation. And the higher the degree of adjustment in the paired relationship, the lower the probability of continuous exploitation by defector. We hope that our work can provide some insights into explaining the existence and maintenance of cooperation.
理解和解释人类社会中的合作行为已成为一个悬而未决的问题。在本文中，我们提出了一种在空间囚徒困境博弈中动态调整配对关系的方法。与以往研究中个体在每一步都动态调整与对手互动强度不同，这项工作考虑了容忍度，即当个体连续叛逃的时间超过容忍阈值 T 时，互动强度就会被调整。我们发现，虽然与传统版本相比，所提出的机制能显著提高合作性，但对连续叛逃行为的更高容忍度并不利于合作的演化。此外，随时动态调整与对手配对关系的环境适应器也有利于合作的进化。而且，配对关系的调整程度越高，叛逃者持续利用的概率就越低。我们希望我们的研究能为解释合作的存在和维持提供一些启示。
{"title":"Adjustment of link weights based on tolerance promotes cooperation in spatial prisoner's dilemma game","authors":"Shounan Lu , Yang Wang","doi":"10.1016/j.biosystems.2024.105362","DOIUrl":"10.1016/j.biosystems.2024.105362","url":null,"abstract":"<div><div>Understanding and explaining cooperative behavior in human society has become an open question. In this paper, we propose a dynamic adjustment of pair relationships in a spatial prisoner's dilemma game. Unlike previous studies that individuals dynamically adjust the intensity of interaction with their opponents at each step, this work consider tolerance, in which the intensity of interaction is adjusted when the time of successive defections by an individual exceeds a tolerance threshold <em>T</em>. We find that although the proposed mechanism can significantly improve cooperation compared to traditional versions, a higher tolerance for continuous defection behavior is not conducive to the evolution of cooperation. Furthermore, an environmental adaptor that dynamically adjusts the paired relationship with the opponent at all times is beneficial for the evolution of cooperation. And the higher the degree of adjustment in the paired relationship, the lower the probability of continuous exploitation by defector. We hope that our work can provide some insights into explaining the existence and maintenance of cooperation.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105362"},"PeriodicalIF":2.0,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606475","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}
Pub Date : 2024-10-30DOI: 10.1016/j.biosystems.2024.105359
Abir U. Igamberdiev
The concept of centers of origin of cultivated plants (crop biodiversity hotspots) developed by Nikolai Vavilov (1887–1943) is essential for understanding the origin and evolution of human civilization. Vavilov formulated the principles of the Neolithic agricultural revolution and substantiated the basic patterns for the emergence of agricultural civilizations. He established that the center of speciation of the plants that have a potential for cultivation determines the origin of primary civilization. Humans actively performed the selection of plants with valuable properties, which led to the formation of new cultivated species and varieties, while the starting point for such unconsciously human-directed evolution was the presence of potentially useful traits due to the increased genetic diversity in the center of origin. The spreading of agriculturally important cultivars from the center of their origin led to the propagation of beneficial farming technologies over large areas. The establishment of human civilization resulted from the dynamic quasi-symbiotic relationship between humans and domesticated plants and animals, which human-driven evolution became an essential factor for the transformation and dynamics of human societies. In the addendum, we present archive materials on the cooperation of Nikolai Vavilov with the historians and ethnologists from the editorial board of the journal “Novy Vostok” (“Nouvel Orient”). These materials include his letters to Professor Ilya Borozdin.
{"title":"Human-driven evolution of cultivated plants and the origin of early civilizations: The concept of Neolithic revolution in the works of Nikolai Vavilov","authors":"Abir U. Igamberdiev","doi":"10.1016/j.biosystems.2024.105359","DOIUrl":"10.1016/j.biosystems.2024.105359","url":null,"abstract":"<div><div>The concept of centers of origin of cultivated plants (crop biodiversity hotspots) developed by Nikolai Vavilov (1887–1943) is essential for understanding the origin and evolution of human civilization. Vavilov formulated the principles of the Neolithic agricultural revolution and substantiated the basic patterns for the emergence of agricultural civilizations. He established that the center of speciation of the plants that have a potential for cultivation determines the origin of primary civilization. Humans actively performed the selection of plants with valuable properties, which led to the formation of new cultivated species and varieties, while the starting point for such unconsciously human-directed evolution was the presence of potentially useful traits due to the increased genetic diversity in the center of origin. The spreading of agriculturally important cultivars from the center of their origin led to the propagation of beneficial farming technologies over large areas. The establishment of human civilization resulted from the dynamic quasi-symbiotic relationship between humans and domesticated plants and animals, which human-driven evolution became an essential factor for the transformation and dynamics of human societies. In the addendum, we present archive materials on the cooperation of Nikolai Vavilov with the historians and ethnologists from the editorial board of the journal “Novy Vostok” (“Nouvel Orient”). These materials include his letters to Professor Ilya Borozdin.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"247 ","pages":"Article 105359"},"PeriodicalIF":2.0,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142565068","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}
Pub Date : 2024-10-22DOI: 10.1016/j.biosystems.2024.105358
Guodong Huang, Shu Zhou, Rui Zhu, Yunhai Wang, Yuan Chai
Chaotic sequences are widely used in secure communication due to their high randomness. Chaotic resonance (CR) refers to the resonant response of a system to weak signals induced by chaotic activity, but its practical application remains limited. This study designs a simplified FitzHugh-Nagumo (FHN) auditory neuron model by simulating the physiological activities of auditory neurons and considering the combined stimulation of chaotic activity and sound signals. It is found that the neuron dynamics depend on both external sound stimuli and chaotic current intensity. Chaotic currents induce spikes in the neuron output sequence through CR, and the spikes become more frequent with increasing current intensity, eventually leading to a chaotic state regardless of the initial state. However, the sensitivity of the initial value of this chaotic sequence shifts to the chaotic current excitation system. The injection of chaotic currents can reduce the system's average Hamiltonian energy under certain conditions. By measuring the complexity of the generated sequences, we find that the addition of chaotic currents can enhance the complexity of the original sequences, and the enhancement ability increases with the intensity. This provides a new approach to enhance the complexity of original chaotic sequences. Moreover, different chaotic currents can induce different chaotic sequences with varying abilities to enhance the complexity of the original sequences. We hope our work can contribute to secure communication.
{"title":"Complex dynamic behavioral transitions in auditory neurons induced by chaotic activity","authors":"Guodong Huang, Shu Zhou, Rui Zhu, Yunhai Wang, Yuan Chai","doi":"10.1016/j.biosystems.2024.105358","DOIUrl":"10.1016/j.biosystems.2024.105358","url":null,"abstract":"<div><div>Chaotic sequences are widely used in secure communication due to their high randomness. Chaotic resonance (CR) refers to the resonant response of a system to weak signals induced by chaotic activity, but its practical application remains limited. This study designs a simplified FitzHugh-Nagumo (FHN) auditory neuron model by simulating the physiological activities of auditory neurons and considering the combined stimulation of chaotic activity and sound signals. It is found that the neuron dynamics depend on both external sound stimuli and chaotic current intensity. Chaotic currents induce spikes in the neuron output sequence through CR, and the spikes become more frequent with increasing current intensity, eventually leading to a chaotic state regardless of the initial state. However, the sensitivity of the initial value of this chaotic sequence shifts to the chaotic current excitation system. The injection of chaotic currents can reduce the system's average Hamiltonian energy under certain conditions. By measuring the complexity of the generated sequences, we find that the addition of chaotic currents can enhance the complexity of the original sequences, and the enhancement ability increases with the intensity. This provides a new approach to enhance the complexity of original chaotic sequences. Moreover, different chaotic currents can induce different chaotic sequences with varying abilities to enhance the complexity of the original sequences. We hope our work can contribute to secure communication.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105358"},"PeriodicalIF":2.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142512370","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}
Pub Date : 2024-10-21DOI: 10.1016/j.biosystems.2024.105357
Nikita V. Dovidchenko , Mikhail Yu. Lobanov , Oxana V. Galzitskaya
It is well known that there is a codon usage bias in genomes, that is, some codons are observed more often than others. Codons implicated in the homo-repeats regions in human proteins are no exception. In this work, we analyzed the codon usage bias for all amino acid residues in homo-repeats larger than 4 in 3753 human proteins from 20447 protein sequences from the canonically reviewed human proteome. We have discovered that almost all homo-repeats in the human proteome, most of which encode Ala, Glu, Gly, Leu, Pro, and Ser (∼80% of all homo-repeats), have a codon usage bias, i.e. are mainly encoded by one codon. Moreover, there is a strong shift in homo-repeats in favor of the content of GC rich codons. Homo-repeats with Ala, Glu, Gly, Leu, Pro, and Ser predominate in the PDB, which has both ordered and disordered status. Examining the distribution of splicing sites, we found that about 15% of homo-repeats either contain or are located within 10 nucleotides of the splicing site, and Glu and Leu predominate in these homo-repeats. Our data is important for future study of the functions of homo-repeats, protein-protein interactions, and evolutionary fitness.
{"title":"Is there a bias in the codon frequency corresponding to homo-repeats found in human proteins?","authors":"Nikita V. Dovidchenko , Mikhail Yu. Lobanov , Oxana V. Galzitskaya","doi":"10.1016/j.biosystems.2024.105357","DOIUrl":"10.1016/j.biosystems.2024.105357","url":null,"abstract":"<div><div>It is well known that there is a codon usage bias in genomes, that is, some codons are observed more often than others. Codons implicated in the homo-repeats regions in human proteins are no exception. In this work, we analyzed the codon usage bias for all amino acid residues in homo-repeats larger than 4 in 3753 human proteins from 20447 protein sequences from the canonically reviewed human proteome. We have discovered that almost all homo-repeats in the human proteome, most of which encode Ala, Glu, Gly, Leu, Pro, and Ser (∼80% of all homo-repeats), have a codon usage bias, i.e. are mainly encoded by one codon. Moreover, there is a strong shift in homo-repeats in favor of the content of GC rich codons. Homo-repeats with Ala, Glu, Gly, Leu, Pro, and Ser predominate in the PDB, which has both ordered and disordered status. Examining the distribution of splicing sites, we found that about 15% of homo-repeats either contain or are located within 10 nucleotides of the splicing site, and Glu and Leu predominate in these homo-repeats. Our data is important for future study of the functions of homo-repeats, protein-protein interactions, and evolutionary fitness.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105357"},"PeriodicalIF":2.0,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142512371","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}
Pub Date : 2024-10-20DOI: 10.1016/j.biosystems.2024.105352
Cooper Doe, David Brown, Hanqing Li
Understanding the function of common motifs in gene regulatory networks is an important goal of systems biology. Feed forward loops (FFLs) are an example of such a motif. In FFLs, a gene (X) regulates another gene (Z) both directly and via an intermediary gene (Y). Previous theoretical studies have suggested several possible functions for FFLs, based on their transient responses to changes in input signals (using deterministic models) and their fluctuations around steady state (using stochastic models). In this paper we study stochastic models of the two most common FFLs, “coherent type 1” and “incoherent type 1”. We incorporate molecular noise by treating DNA binding, transcription, translation, and decay as stochastic processes. By comparing the dynamics of these loops with models of alternative networks (in which X does not regulate Y), we explore how FFLs act to process information in the presence of noise. This work highlights the importance of incorporating realistic molecular noise in studying both the transient and steady-state behavior of gene regulatory networks.
{"title":"Dynamics of two feed forward genetic motifs in the presence of molecular noise","authors":"Cooper Doe, David Brown, Hanqing Li","doi":"10.1016/j.biosystems.2024.105352","DOIUrl":"10.1016/j.biosystems.2024.105352","url":null,"abstract":"<div><div>Understanding the function of common motifs in gene regulatory networks is an important goal of systems biology. Feed forward loops (FFLs) are an example of such a motif. In FFLs, a gene (X) regulates another gene (Z) both directly and via an intermediary gene (Y). Previous theoretical studies have suggested several possible functions for FFLs, based on their transient responses to changes in input signals (using deterministic models) and their fluctuations around steady state (using stochastic models). In this paper we study stochastic models of the two most common FFLs, “coherent type 1” and “incoherent type 1”. We incorporate molecular noise by treating DNA binding, transcription, translation, and decay as stochastic processes. By comparing the dynamics of these loops with models of alternative networks (in which X does not regulate Y), we explore how FFLs act to process information in the presence of noise. This work highlights the importance of incorporating realistic molecular noise in studying both the transient and steady-state behavior of gene regulatory networks.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105352"},"PeriodicalIF":2.0,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479897","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}
Pub Date : 2024-10-20DOI: 10.1016/j.biosystems.2024.105351
Diego M. Bustos
New mathematical tools help understand cell functions, adaptability, and evolvability to discover hidden variables to predict phenotypes that could be tested in the future in wet labs. Different models have been successfully used to discover the properties of the protein-protein interaction networks or interactomes. I found that in the hyperbolic Popularity-Similarity model, cellular proteins with the highest contents of structural intrinsic disorder cluster together in many different eukaryotic interactomes and this is not the case for the prokaryotic E. coli, where proteins with high degree of intrinsic disorder are scarce. I also found that the normalized theta variable from the Popularity-Similarity model for orthologues proteins correlate to the complexity of the organisms in analysis.
{"title":"Intrinsic structural disorder on proteins is involved in the interactome evolution","authors":"Diego M. Bustos","doi":"10.1016/j.biosystems.2024.105351","DOIUrl":"10.1016/j.biosystems.2024.105351","url":null,"abstract":"<div><div>New mathematical tools help understand cell functions, adaptability, and evolvability to discover hidden variables to predict phenotypes that could be tested in the future in wet labs. Different models have been successfully used to discover the properties of the protein-protein interaction networks or interactomes. I found that in the hyperbolic Popularity-Similarity model, cellular proteins with the highest contents of structural intrinsic disorder cluster together in many different eukaryotic interactomes and this is not the case for the prokaryotic <em>E. coli,</em> where proteins with high degree of intrinsic disorder are scarce. I also found that the normalized theta variable from the Popularity-Similarity model for orthologues proteins correlate to the complexity of the organisms in analysis.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105351"},"PeriodicalIF":2.0,"publicationDate":"2024-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479898","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}
Pub Date : 2024-10-19DOI: 10.1016/j.biosystems.2024.105350
Clémence Ortega Douville
As a hypothesis on the origins of mind and language, the evolutionary theory of the sensorimotor paradox suggests that capacities for imagination, self-representation and abstraction would operate from a dissociation in what is known as the forward model. In some studies, sensory perception is understood as a system of prediction and confirmation (feedforward and feedback processes) that would share common yet distinct and overlapping neural networks with mental imagery. The latter would then mostly operate through internal feedback processes. The hypothesis of our theory is that dissociation and parallelism between those processes would make it less likely for imaginary prediction to match and simultaneously coincide with any sensory feedback, contradicting the stimulus/response pattern. The gap between the two and the effort required to maintain this gap, born from the development of bipedal stance and a radical change to our relation to our own hands, would be the very structural foundation to our capacity to elaborate abstract thoughts, by partially blocking and inhibiting motor action. Mental imagery would structurally be dissociated from perception, though maintaining an intricated relation of interdependence. Moreover, the content of the images would be subordinate to their function as emotional regulators, prioritising consistency with some global, conditional and socially learnt body-image. As a higher-level and proto-aesthetic function, we can speculate that the action and instrumentalisation of dissociating imagination from perception would become the actual prediction and their coordination, the expected feedback.
{"title":"Reality and imagination intertwined: A sensorimotor paradox interpretation","authors":"Clémence Ortega Douville","doi":"10.1016/j.biosystems.2024.105350","DOIUrl":"10.1016/j.biosystems.2024.105350","url":null,"abstract":"<div><div>As a hypothesis on the origins of mind and language, the evolutionary theory of the sensorimotor paradox suggests that capacities for imagination, self-representation and abstraction would operate from a dissociation in what is known as the forward model. In some studies, sensory perception is understood as a system of prediction and confirmation (feedforward and feedback processes) that would share common yet distinct and overlapping neural networks with mental imagery. The latter would then mostly operate through internal feedback processes. The hypothesis of our theory is that dissociation and parallelism between those processes would make it less likely for imaginary prediction to match and simultaneously coincide with any sensory feedback, contradicting the stimulus/response pattern. The gap between the two and the effort required to maintain this gap, born from the development of bipedal stance and a radical change to our relation to our own hands, would be the very structural foundation to our capacity to elaborate abstract thoughts, by partially blocking and inhibiting motor action. Mental imagery would structurally be dissociated from perception, though maintaining an intricated relation of interdependence. Moreover, the content of the images would be subordinate to their function as emotional regulators, prioritising consistency with some global, conditional and socially learnt body-image. As a higher-level and proto-aesthetic function, we can speculate that the action and instrumentalisation of dissociating imagination from perception would become the actual prediction and their coordination, the expected feedback.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105350"},"PeriodicalIF":2.0,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479900","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}
Pub Date : 2024-10-18DOI: 10.1016/j.biosystems.2024.105353
Ekaterina Yurova Axelsson, Andrei Khrennikov
The genetic code is a map which gives the correspondence between codons in DNA and amino acids. In the attractor dynamical model (ADM), genetic codes can be described as the sets of the cyclic attractors of discrete dynamical systems - the iterations of functions acting in the ring of 2-adic integers This ring arises from representation of nucleotides by binary vectors and hence codons by triples of binary vectors. We construct a Universal Function such that the dynamical functions for all known genetic codes can be obtained from by simple transformations on the set of codon cycles - the “Addition” and “Division” operations. ADM can be employed for study of phylogenetic dynamics of genetic codes. One can speculate that the “common ancestor genetic code” was caused by We remark that this function has 24 cyclic attractors which distribution coincides with the distribution for the hypothetical pre-LUCA code. This coupling of the Universal Function with the pre-LUCA code assigns the genetic codes evolution perspective to ADM. All genetic codes are generated from through the special chains of the “Addition” and “Division” operations. The challenging problem is to assign the biological meaning to these mathematical operations.
遗传密码是 DNA 密码子与氨基酸之间的对应关系图。在吸引子动力学模型（ADM）中，遗传密码可以描述为离散动力系统的循环吸引子集--作用于二元整数环 Z2 的函数迭代。二进制向量表示核苷酸，二进制向量的三元组表示密码子，从而产生了这个环。我们构建了一个通用函数 B，通过对密码子循环集的简单变换--"加法 "和 "除法 "运算--可以从 B 得到所有已知遗传密码的动力学函数。ADM 可用于研究遗传密码的系统发育动力学。我们可以推测，"共同祖先遗传密码 "是由 B 引起的。我们注意到，该函数有 24 个循环吸引子，其分布与假定的前 LUCA 密码的分布相吻合。通用函数与前 LUCA 代码的这种耦合将遗传密码进化的视角赋予了 ADM。所有遗传密码都是通过 "加法 "和 "除法 "运算的特殊链从 B 生成的。如何为这些数学运算赋予生物学意义是一个具有挑战性的问题。
{"title":"Universal dynamical function behind all genetic codes: P-adic attractor dynamical model","authors":"Ekaterina Yurova Axelsson, Andrei Khrennikov","doi":"10.1016/j.biosystems.2024.105353","DOIUrl":"10.1016/j.biosystems.2024.105353","url":null,"abstract":"<div><div>The genetic code is a map which gives the correspondence between codons in DNA and amino acids. In the attractor dynamical model (ADM), genetic codes can be described as the sets of the cyclic attractors of discrete dynamical systems - the iterations of functions acting in the ring of 2-adic integers <span><math><mrow><msub><mrow><mi>Z</mi></mrow><mrow><mn>2</mn></mrow></msub><mo>.</mo></mrow></math></span> This ring arises from representation of nucleotides by binary vectors and hence codons by triples of binary vectors. We construct a Universal Function <span><math><mi>B</mi></math></span> such that the dynamical functions for all known genetic codes can be obtained from <span><math><mi>B</mi></math></span> by simple transformations on the set of codon cycles - the “Addition” and “Division” operations. ADM can be employed for study of phylogenetic dynamics of genetic codes. One can speculate that the “common ancestor genetic code” was caused by <span><math><mrow><mi>B</mi><mo>.</mo></mrow></math></span> We remark that this function has 24 cyclic attractors which distribution coincides with the distribution for the hypothetical pre-LUCA code. This coupling of the Universal Function with the pre-LUCA code assigns the genetic codes evolution perspective to ADM. All genetic codes are generated from <span><math><mi>B</mi></math></span> through the special chains of the “Addition” and “Division” operations. The challenging problem is to assign the biological meaning to these mathematical operations.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105353"},"PeriodicalIF":2.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479902","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}
Pub Date : 2024-10-18DOI: 10.1016/j.biosystems.2024.105356
Breno B. Just , Sávio Torres de Farias
There is no consensus about what cognition is. Different perspectives conceptualize it in different ways. In the same vein, there is no agreement about which systems are truly cognitive. This begs the question, what makes a process or a system cognitive? One of the most conspicuous features of cognition is that it is a set of processes. Cognition, in the end, is a collection of processes such as perception, memory, learning, decision-making, problem-solving, goal-directedness, attention, anticipation, communication, and maybe emotion. There is a debate about what they mean, and which systems possess these processes. One aspect of this problem concerns the level at which cognition and the single processes are conceptualized. To make this scenario clear, evolutionary and self-maintenance arguments are taken. Given the evolutive landscape, one sees processes shared by all organisms and their derivations in specific taxa. No matter which side of the complexity spectrum one favors, the similarities of the simple processes with the complex ones cannot be ignored, and the differences of some complex processes with their simple versions cannot be blurred. A final cognitive framework must make sense of both sides of the spectrum, their differences and similarities. Here, we discuss from an evolutionary perspective the basic elements shared by all living beings and whether these may be necessary and sufficient for understanding the cognitive process. Following these considerations, cognition can be expanded to every living being. Cognition is the set of informational and dynamic processes an organism must interact with and grasp aspects of its world. Understood at their most basic level, perception, memory, learning, problem-solving, decision-making, action, and other cognitive processes are basic features of biological functioning.
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Recombinant DNA technologies of the current era, most of which are comparable to past works of science fiction, have had diverse and significant impacts on social life. Among them, genetic sequencing deserves particular attention. The widespread use of genetic testing has raised numerous concerns regarding autonomy, confidentiality and privacy. In this context, the proliferation of ‘gene for X’ reports influences debates about the potentially beneficial or detrimental uses of genetics. While several studies have reported concerns related to the collection, storage and use of genetic data, few have considered the technical shortcomings that can affect the reliability of interpretation of sequencing data. In this essay, we will cover some of the current practices of genetic testing and safety aspects of DNA data. To evaluate the reliability of DNA data we will raise the question whether an ‘overestimation’ of researchers' results might reflect an ‘underestimation’ of our genetic make-up in terms of the limitations of the parameters necessary for the correct interpretation of genomic DNA. Following that question we will highlight the responsibility of researchers for proper science communication to avoid misleading information about genetic sequencing data.
当今时代的 DNA 重组技术（其中大部分堪比过去的科幻小说）对社会生活产生了多种多样的重大影响。其中，基因测序尤其值得关注。基因检测的广泛使用引起了人们对自主权、保密性和隐私权的诸多关注。在这种情况下，"X 基因 "报告的激增影响了关于基因的潜在有益或有害用途的辩论。虽然有几项研究报告了与基因数据的收集、储存和使用有关的问题，但很少有人考虑到可能影响测序数据解读可靠性的技术缺陷。在本文中，我们将介绍目前基因检测的一些做法和 DNA 数据的安全问题。为了评估 DNA 数据的可靠性，我们将提出这样一个问题：研究人员对结果的 "高估 "是否反映了我们对基因构成的 "低估"，即正确解读基因组 DNA 所需的参数的局限性。在这个问题之后，我们将强调研究人员有责任进行正确的科学交流，以避免基因测序数据信息的误导性。
{"title":"Techno-ethical concerns related to genetic sequencing reports","authors":"Zeki Topcu , Sevil Zencir , Matthis Krischel , Heiner Fangerau","doi":"10.1016/j.biosystems.2024.105354","DOIUrl":"10.1016/j.biosystems.2024.105354","url":null,"abstract":"<div><div>Recombinant DNA technologies of the current era, most of which are comparable to past works of science fiction, have had diverse and significant impacts on social life. Among them, genetic sequencing deserves particular attention. The widespread use of genetic testing has raised numerous concerns regarding autonomy, confidentiality and privacy. In this context, the proliferation of ‘gene for X’ reports influences debates about the potentially beneficial or detrimental uses of genetics. While several studies have reported concerns related to the collection, storage and use of genetic data, few have considered the technical shortcomings that can affect the reliability of interpretation of sequencing data. In this essay, we will cover some of the current practices of genetic testing and safety aspects of DNA data. To evaluate the reliability of DNA data we will raise the question whether an ‘overestimation’ of researchers' results might reflect an ‘underestimation’ of our genetic make-up in terms of the limitations of the parameters necessary for the correct interpretation of genomic DNA. Following that question we will highlight the responsibility of researchers for proper science communication to avoid misleading information about genetic sequencing data.</div></div>","PeriodicalId":50730,"journal":{"name":"Biosystems","volume":"246 ","pages":"Article 105354"},"PeriodicalIF":2.0,"publicationDate":"2024-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142479901","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}
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