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Reflexive neural circuits and the origin of language and music codes 反射神经回路与语言和音乐代码的起源。
IF 2 4区 生物学 Q2 BIOLOGY Pub Date : 2024-09-28 DOI: 10.1016/j.biosystems.2024.105346
Abir U. Igamberdiev
Conscious activity is grounded in the reflexive self-awareness in sense perception, through which the codes signifying sensual perceptive events operate and constrain human behavior. These codes grow via the creative generation of hypertextual statements. We apply the model of Vladimir Lefebvre (Lefebvre, V.A., 1987, J. Soc. Biol. Struct. 10, 129–175) to reveal the underlying structures on which the perception and creative development of language and music codes are based. According to this model, the reflexive structure of conscious subject is grounded in three thermodynamic cycles united by the control of the basic functional cycle by the second one, and resulting in the internal action that it turn is perceived by the third cycle evaluating this action. In this arrangement, the generative language structures are formed and the frequencies of sounds that form musical phrases and patterns are selected. We discuss the participation of certain neural brain structures and the establishment of reflexive neural circuits in the ad hoc transformation of perceptive signals, and show the similarities between the processes of perception and of biological self-maintenance and morphogenesis. We trace the peculiarities of the temporal encoding of emotions in music and musical creativity, as well as the principles of sharing musical information between the performing and the perceiving individuals.
意识活动以感官知觉中的反射性自我意识为基础,通过感官知觉事件的代码运作和约束人类行为。这些代码通过创造性地生成超文本语句而发展。我们运用弗拉基米尔-勒菲弗(Vladimir Lefebvre, V.A.,1987 年,《社会生物结构》杂志,10, 129-175)的模型来揭示语言和音乐代码的感知和创造性发展所基于的基本结构。根据这一模型,有意识主体的反射结构建立在三个热力学循环的基础上,通过第二个循环对基本功能循环的控制而结合在一起,并产生内部动作,而这一动作又被评估这一动作的第三个循环所感知。在这种安排下,生成语言结构得以形成,构成乐句和模式的声音频率得以选择。我们讨论了某些大脑神经结构的参与以及反射神经回路在感知信号临时转换过程中的建立,并展示了感知过程与生物自我维护和形态发生过程之间的相似之处。我们追溯了音乐和音乐创作中情感时间编码的特殊性,以及表演者和感知者之间共享音乐信息的原则。
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引用次数: 0
William Bateson, black slavery, eugenics and speciation: The relative roles of politics and science 威廉-贝特森、黑人奴隶制、优生学和物种繁衍:政治与科学的相对作用。
IF 2 4区 生物学 Q2 BIOLOGY Pub Date : 2024-09-28 DOI: 10.1016/j.biosystems.2024.105348
Donald R. Forsdyke
The peace of the world is challenged by societal confrontations that can often be labeled “racial” or “ethnic.” Emblematic of this is discrimination based on skin colour. William Bateson's background suggests sympathy with the black emancipation movement. Yet the movement's success is attributed more to battles between political figures than between scientists with contending views on the biology of racial differences. However, in the long term, Bateson's contributions to slavery and eugenic issues may be seen as no less important than those of politicians. Mendel's discovery of what we now know as “genes” languished until seized upon by Bateson in 1900. For six exhausting years he struggled to win scientific acceptance of these biological character-determining units. Later, he pressed the Mendelian message home to the general public, opposing simplistic applications of Mendelian principles to human affairs, and arguing that minor genic differences that distinguished “races” – e.g. skin colour – do not initiate new species. Bateson praised the “physiological selection” speciation hypothesis of Darwin's young research associate, George Romanes. This enthusiasm was rekindled by Robert Lock and formulated in modern terms with C. R. Crowther. Thus, the spark that initiates a divergence into two species can be non-genic. This normal form of hybrid sterility, based on genome-wide DNA sequence differences, operates on, but has not succeeded in dividing, the human species. It should not be labeled “idiopathic,” and be clearly distinguished both from pathological sterility and undiagnosed sterilities that may prove to be pathological. We are one reproductively isolated population, the human species.
世界的和平受到了社会对抗的挑战,这些对抗往往被冠以 "种族 "或 "民族 "的标签。其中的代表就是基于肤色的歧视。威廉-贝特森的背景表明他同情黑人解放运动。然而,这场运动的成功更多地归功于政治人物之间的争斗,而不是对种族差异的生物学观点有争议的科学家之间的争斗。然而,从长远来看,贝特森对奴隶制和优生问题的贡献可能并不亚于政治家的贡献。孟德尔发现了我们现在所知的 "基因",但这一发现一直被束之高阁,直到 1900 年被贝特森发现。在长达六年的艰苦奋斗中,他努力争取科学界接受这些决定生物特征的单位。后来,他向公众宣传孟德尔学说,反对将孟德尔原理简单地应用于人类事务,并认为区分 "种族 "的微小基因差异(如肤色)并不能创造新物种。贝特森赞扬了达尔文的年轻研究助手乔治-罗曼尼斯(George Romanes)提出的 "生理选择 "物种形成假说。罗伯特-洛克(Robert Lock)重新点燃了这种热情,C-R-克劳瑟(C. R. Crowther)则用现代术语对其进行了表述。因此,引发两个物种分化的火花可能是非基因性的。这种基于全基因组 DNA 序列差异的正常形式的杂交不育在人类物种中发生,但并未成功分裂。它不应被称为 "特发性不育",而应与病理不育和可能被证明为病理的未诊断不育明确区分开来。我们人类是一个在生殖上孤立的群体。
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引用次数: 0
Avian influenza A H5N1 hemagglutinin protein models have distinct structural patterns re-occurring across the 1959–2023 strains 禽流感甲型 H5N1 血凝素蛋白模型在 1959-2023 株中重复出现不同的结构模式。
IF 2 4区 生物学 Q2 BIOLOGY Pub Date : 2024-09-28 DOI: 10.1016/j.biosystems.2024.105347
Marni E. Cueno, Noriaki Kamio, Kenichi Imai
Influenza A H5N1 hemagglutinin (HA) plays a crucial role in viral pathogenesis and changes in the HA receptor binding domain (RBD) have been attributed to alterations in viral pathogenesis. Mutations often occur within the HA which in-turn results in HA structural changes that consequently contribute to protein evolution. However, the possible occurrence of mutations that results to reversion of the HA protein (going back to an ancestral protein conformation) which in-turn creates distinct HA structural patterns across the 1959–2023 H5N1 viral evolution has never been investigated. Here, we generated and verified the quality of the HA models, identified similar HA structural patterns, and elucidated the possible variations in HA RBD structural dynamics. Our results show that there are 7 distinct structural patterns occurring among the 1959–2023 H5N1 HA models which suggests that reversion of the HA protein putatively occurs during viral evolution. Similarly, we found that the HA RBD structural dynamics vary among the 7 distinct structural patterns possibly affecting viral pathogenesis.
甲型流感 H5N1 血凝素(HA)在病毒致病过程中起着至关重要的作用,HA 受体结合域(RBD)的变化被认为是病毒致病过程发生改变的原因。HA内部经常发生突变,从而导致HA结构发生变化,进而促进蛋白质的进化。然而,在 1959-2023 年的 H5N1 病毒进化过程中,可能发生的突变导致 HA 蛋白的还原(回到祖先的蛋白构象),进而产生不同的 HA 结构模式,这种情况从未被研究过。在此,我们生成并验证了 HA 模型的质量,确定了相似的 HA 结构模式,并阐明了 HA RBD 结构动态中可能存在的变化。我们的结果表明,1959-2023 年的 H5N1 HA 模型有 7 种不同的结构模式,这表明在病毒进化过程中,HA 蛋白可能发生了还原。同样,我们发现在这 7 种不同的结构模式中,HA RBD 结构动态也各不相同,这可能会影响病毒的致病机理。
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引用次数: 0
A novel hypothesis about mechanism of thalidomide action on pattern formation 沙利度胺对模式形成作用机制的新假设
IF 2 4区 生物学 Q2 BIOLOGY Pub Date : 2024-09-26 DOI: 10.1016/j.biosystems.2024.105344
Denis Touroutine , Nadya Morozova
Morphogenesis, the complex process governing the formation of functional living structures, is regulated by a multitude of molecular mechanisms at various levels. While research in recent decades has shed light on many pathways involved in morphogenesis, none singularly accounts for the precise geometric shapes of organisms and their components in space. To bridge this conceptual gap between specific molecular mechanisms and the creation of definitive morphological forms, we have proposed the "epigenetic code hypothesis" in our previous work. In this framework, "epigenetic" means any inheritable cellular information beyond the genetic code that regulates cell fate alongside genetic information. In this study, we conduct a comprehensive analysis of thalidomide's teratogenic effects through the lens of our proposed "epigenetic code" theory, revealing significant indirect support for our hypothesis. We also explore the structural and functional parallels between thalidomide and auxin.
形态发生是控制生物功能结构形成的复杂过程,受不同层次的多种分子机制调控。虽然近几十年来的研究已经揭示了形态发生的多种途径,但没有一种途径能单独解释生物体及其组成部分在空间中的精确几何形状。为了弥合特定分子机制与确定形态的形成之间的概念差距,我们在之前的工作中提出了 "表观遗传密码假说"。在这一框架中,"表观遗传 "指的是遗传密码之外的任何可遗传的细胞信息,这些信息与遗传信息一起调控着细胞的命运。在本研究中,我们通过我们提出的 "表观遗传密码 "理论,对沙利度胺的致畸效应进行了全面分析,结果显示我们的假说得到了重要的间接支持。我们还探讨了沙利度胺与辅酶在结构和功能上的相似之处。
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引用次数: 0
Intelligence: Natural, artificial, or what? 智能:自然智能、人工智能还是什么?
IF 2 4区 生物学 Q2 BIOLOGY Pub Date : 2024-09-26 DOI: 10.1016/j.biosystems.2024.105343
Ron Cottam, Roger Vounckx
We consider the competing attributes of natural intelligence (NI) and artificial intelligence (AI). Attention is paid to conceptual, theoretical, stylistic and structural aspects of both, and non-human intelligence. Intelligence is related to information processing and current views of physical structuring. Means of distinguishing between NI and AI are noted, and neural and digital structures are described. Pribram's bi-computational neural networks are introduced, and high-level Pribram computation is discussed. We describe the hierarchical Aquarium scheme, along with an AI implementation, and conclude with a proposition for future quantum-based artificial intelligence.
我们考虑了自然智能(NI)和人工智能(AI)的竞争属性。我们关注自然智能和非人类智能的概念、理论、风格和结构方面。智能与信息处理和当前的物理结构观点有关。指出了区分非人类智能和人工智能的方法,并描述了神经和数字结构。介绍了普里布拉姆的双计算神经网络,并讨论了高级普里布拉姆计算。我们描述了分层水瓶计划以及人工智能的实现,最后提出了未来基于量子的人工智能的命题。
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引用次数: 0
A control measure for epidemic spread based on the susceptible–infectious–susceptible (SIS) model 基于易感-传染-易感(SIS)模型的流行病传播控制措施。
IF 2 4区 生物学 Q2 BIOLOGY Pub Date : 2024-09-25 DOI: 10.1016/j.biosystems.2024.105341
Jin-Xuan Yang, Haiyan Wang, Xin Li, Ying Tan, Yongjuan Ma, Min Zeng
When an epidemic occurs in a network, finding the important links and cutting them off is an effective measure for preventing the spread of the epidemic. Traditional methods that remove important links easily lead to a disconnected network, inevitably incurring high costs arising from quarantining individuals or communities in a real-world network. In this study, we combine the clustering coefficient and the eigenvector to identify the important links using the susceptible–infectious–susceptible (SIS) model. The results show that our approach can improve the epidemic threshold while maintaining the connectivity of the network to control the spread of the epidemic. Experiments on multiple real-world and synthetic networks of varying sizes, demonstrate the effectiveness and scalability of our approach.
当网络中发生流行病时,找到并切断重要链接是防止流行病传播的有效措施。传统的去除重要链接的方法容易导致网络断开,在现实世界的网络中,隔离个体或群体不可避免地会产生高昂的成本。在本研究中,我们结合聚类系数和特征向量,利用易感-传染-易感(SIS)模型来识别重要链接。结果表明,我们的方法可以提高流行病阈值,同时保持网络的连通性,从而控制流行病的传播。在多个真实世界和不同规模的合成网络上进行的实验证明了我们方法的有效性和可扩展性。
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引用次数: 0
The indispensable role of time in autonomous development 时间在自主发展中不可或缺的作用。
IF 2 4区 生物学 Q2 BIOLOGY Pub Date : 2024-09-21 DOI: 10.1016/j.biosystems.2024.105340
William Letsou
Advances in single-cell analysis have led to a picture of development largely in agreement with Waddington’s eponymous epigenetic landscape, in which a cell’s fate is determined by its basin of attraction in a high-dimensional gene-expression space. Yet conceptual gaps remain as to how a single progenitor can simultaneously generate multiple endpoints, and why time should be required of the process at all. We propose a theoretical model based on the Hamiltonian mechanics of n-dimensional rotational motion, which resolves these paradoxes. We derive the result that systems which become different from themselves over time must initially move in a direction not towards their ultimate endpoints, and propose that this process of resolving ambiguity can be quantified (in an information-theoretic sense) by the volume subtended in gene-expression space by the trajectories taken by the system towards its endpoints. We discuss the implications of this theory for the analysis of single-cell gene-expression data in studies of development.
单细胞分析技术的进步使人们对发育过程有了大致与沃丁顿同名表观遗传景观一致的认识,即细胞的命运取决于其在高维基因表达空间上的吸引力。然而,对于单个祖细胞如何同时产生多个终点,以及为什么这一过程需要时间等问题,仍然存在概念上的空白。我们提出了一个基于 n 维旋转运动哈密顿力学的理论模型,以解决这些悖论。我们得出的结果是,随着时间的推移而变得与自身不同的系统最初的运动方向一定不是朝着其最终端点,并提出这一解决模糊性的过程可以通过系统朝着其端点所走的轨迹在基因表达空间中所占的体积来量化(在信息论意义上)。我们将讨论这一理论对发育研究中单细胞基因表达数据分析的影响。
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引用次数: 0
Causal Modeling and Thermodynamics: Towards a new convergence of the two fields 因果建模与热力学:实现两个领域的新融合。
IF 2 4区 生物学 Q2 BIOLOGY Pub Date : 2024-09-19 DOI: 10.1016/j.biosystems.2024.105338
Dan Costa Baciu
In 1824, Nicolas Léonard Sadi Carnot paid for the publication of his first book. Unfortunately it sparked little interest, and the young engineer never published another. In quick succession, Carnot served in the military, suffered from scarlet fever, mania, and cholera, and passed away in obscurity at age 36. Two centuries have elapsed since Carnot published his only book. Recognition came later. In particular, Carnot's reasoning inspired scientists to formulate the first and second laws of Thermodynamics. The new science that has emerged around these physical laws is nothing short of breathtaking. Yet, with success and growth, critical attention and skepticism have followed. In 1924, Louis de Broglie lauded the first law of Thermodynamics, while remaining more reserved to wards the second. The first law builds on a long history rooted in Causal Modeling, while the second does less so. Today, physicists such as Adrian Bejan continue praising Thermodynamics but contend that some formulations of the second law may have attracted broken science. The present article revisits this history in an attempt to cut through some of the fog. As an outcome of this re-evaluation, the article outlines a new convergence of Thermodynamics and Causal Modeling.
1824 年,尼古拉-莱昂纳尔-萨迪-卡诺花钱出版了自己的第一本书。遗憾的是,这本书几乎没有引起人们的兴趣,这位年轻的工程师再也没有出版过新书。随后,卡诺先后服兵役、患猩红热、狂躁症和霍乱,在默默无闻中去世,享年36岁。自卡诺出版他唯一的著作以来,已经过去了两个世纪。人们对他的认识是后来的事。特别是,卡诺的推理引领了热力学第一和第二定律的发展。围绕这些物理定律产生的新科学令人叹为观止,是人类创造力的绝佳见证。然而,成功和发展也带来了批评和质疑。1924 年,路易-德-布罗格利对热力学第一定律的赞誉超过了第二定律。第一定律建立在因果建模的悠久历史之上,而第二定律则不然。如今,物理学家阿德里安-贝扬(Adrian Bejan)等人专门研究热力学,但他认为,第二定律的某些表述可能已经破坏了科学。本文重温这段历史,试图拨开一些迷雾。作为重新评估的结果,文章概述了热力学与因果建模的新融合。
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引用次数: 0
Quantum logic automata generate class IV-like patterns and 1/f noise 量子逻辑自动机产生类 IV 模式和 1/f 噪声
IF 2 4区 生物学 Q2 BIOLOGY Pub Date : 2024-09-18 DOI: 10.1016/j.biosystems.2024.105339
Yuki Tokuyama , Yoshihiko Ohzawa , Yukio-Pegio Gunji

Owing to recent advancements in brain science and AI, researchers tend to focus on the concept of self-organized criticality or the edge of chaos. On the other hand, quantum cognition, which is rooted in quantum mechanics, is promising for resolving various cognitive illusions. However, until recently, no connection between criticality and quantum mechanics was proposed. Gunji et al. (2024) recently introduced a linkage termed quantum logic automata, which encompasses not only quantum logic but also criticality characterized by power-law distributions. While quantum logic automata can be derived from various structures, only one of them has been proposed and discussed. Here, we define another type of quantum logic automata involving quantum logic and demonstrate that symmetric quantum logic automata lead to complex Class IV-like patterns and power-law distributions. Our findings support the association between criticality and quantum theory.

由于近年来脑科学和人工智能的进步,研究人员倾向于关注自组织临界性或混沌边缘的概念。另一方面,源于量子力学的量子认知有望解决各种认知错觉。然而,直到最近,人们才提出临界性与量子力学之间的联系。Gunji 等人(2024 年)最近提出了一种称为量子逻辑自动机的联系,它不仅包括量子逻辑,还包括以幂律分布为特征的临界性。虽然量子逻辑自动机可以从各种结构中衍生出来,但目前只提出并讨论了其中一种。在此,我们定义了另一种涉及量子逻辑的量子逻辑自动机,并证明对称量子逻辑自动机会导致复杂的类 IV 模式和幂律分布。我们的研究结果支持临界性与量子理论之间的关联。
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引用次数: 0
Exact burst-size distributions for gene-expression models with complex promoter structure 具有复杂启动子结构的基因表达模型的精确突发大小分布。
IF 2 4区 生物学 Q2 BIOLOGY Pub Date : 2024-09-17 DOI: 10.1016/j.biosystems.2024.105337
Liying Zhou , Haowen Chen , Jinqiang Zhang , Jiajun Zhang , Huahai Qiu , Tianshou Zhou
In prokaryotic and eukaryotic cells, most genes are transcribed in a bursty fashion on one hand and complex gene regulations may lead to complex promoter structure on the other hand. This raises an unsolved issue: how does promoter structure shape transcriptional bursting kinetics characterized by burst size and frequency? Here we analyze stochastic models of gene transcription, which consider complex regulatory mechanisms. Notably, we develop an efficient method to derive exact burst-size distributions. The analytical results show that if the promoter of a gene contains only one active state, the burst size indeed follows a geometric distribution, in agreement with the previous result derived under certain limiting conditions. However, if it contains a multitude of active states, the burst size in general obeys a non-geometric distribution, which is a linearly weighted sum of geometric distributions. This superposition principle reveals the essential feature of bursting kinetics in complex cases of transcriptional regulation although it seems that there has been no direct experimental confirmation. The derived burst-size distributions not only highlight the importance of promoter structure in regulating bursting kinetics, but can be also used in the exact inference of this kinetics based on experimental data.
在原核细胞和真核细胞中,一方面,大多数基因都是以突发性方式转录的,另一方面,复杂的基因调控可能会导致复杂的启动子结构。这就提出了一个尚未解决的问题:启动子结构如何影响以突变大小和频率为特征的转录突变动力学?在此,我们分析了考虑复杂调控机制的基因转录随机模型。值得注意的是,我们开发了一种高效的方法来推导精确的猝发大小分布。分析结果表明,如果基因的启动子只包含一种活性状态,猝发大小确实遵循几何分布,这与之前在某些限制条件下得出的结果一致。然而,如果基因启动子包含多种活性状态,则猝发大小一般服从非几何分布,即几何分布的线性加权和。这一叠加原理揭示了在复杂的转录调控情况下猝发动力学的基本特征,但似乎还没有得到直接的实验证实。推导出的猝发大小分布不仅突出了启动子结构在调控猝发动力学中的重要性,而且还可用于根据实验数据对这种动力学进行精确推断。
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引用次数: 0
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