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Formalizing complexity in the life sciences: systems, emergence, and metafluxes 生命科学复杂性的形式化:系统、涌现和元流体
IF 2.6 4区 生物学 Q2 PLANT SCIENCES Pub Date : 2023-12-07 DOI: 10.1007/s40626-023-00293-1
Lars H. Wegner

Current plant sciences (as the life sciences in general) tend to follow an empirical rationale focussing on the molecular scale (genes, proteins), which is supposed to causally dominate processes at higher levels of organization (cellular, organismic). This rather simplistic view on the complexity of living systems calls for a more adequate and elaborate theoretical approach, to which I want to contribute three main cornerstones here. Systems theory is the first one, mostly referring to Mario Bunge’s CESM (Composition, Environment, Structure, Mechanism) approach and its biological application. More than half of this article is dedicated to the philosophical concept of emergence, denoting the fact that systems have specific properties not shared or provided by their parts. Different viewpoints on emergence and definitions are contrasted and their potential suitability for the life sciences is discussed. An interesting historical case study is the genesis of the ‘ecosystem’ concept in plant ecology. Subsequently two widely accepted subtypes, ‘weak’ and ‘strong’ emergence are introduced and their quantitative formalization is briefly outlined referring to recent work on this issue. Finally, the metaflux concept is presented for the first time. Living systems are characterized by a network of coupled fluxes of matter, free energy, and entropy, adequately formalized by the thermodynamics of irreversible processes. Dynamical phenomena in organisms emerging from these flux networks which are, in contrast to process philosophy/metaphysics, defined on a scientific (physicochemical) basis will be called ‘metafluxes’. Metafluxes and weak and strong emergence are non-exclusive concepts to be employed in a dialectic scientific process.

当前的植物科学(如同一般的生命科学)往往遵循一种侧重于分子尺度(基因、蛋白质)的经验主义理论,认为分子尺度在因果关系上主导着更高层次的组织过程(细胞、有机体)。对生命系统复杂性的这种相当简单化的看法,需要一种更充分、更精细的理论方法,我想在此提出三大基石。系统理论是第一块基石,主要指马里奥-邦格(Mario Bunge)的 CESM(组成、环境、结构、机制)方法及其在生物学上的应用。本文一半以上的篇幅都在阐述 "涌现"(emergence)这一哲学概念。"涌现 "指的是系统具有其各部分所不具有或不提供的特定属性。文章对比了关于 "涌现 "的不同观点和定义,并讨论了它们在生命科学中的潜在适用性。一个有趣的历史案例研究是植物生态学中 "生态系统 "概念的起源。随后,介绍了两种广为接受的子类型,即 "弱 "和 "强 "涌现,并简要概述了它们的定量形式化,同时提到了最近有关这一问题的工作。最后,首次提出了元流体(metaflux)概念。生物系统的特点是由物质、自由能和熵的耦合通量网络组成,不可逆过程的热力学对其进行了充分的形式化。与过程哲学/形而上学不同,生物体内从这些通量网络中产生的动态现象将在科学(物理化学)的基础上加以定义,这些现象将被称为 "元通量"。元通量、弱涌现和强涌现是辩证科学过程中使用的非排他性概念。
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引用次数: 0
Topography imposes an abiotic filter on tree growth in restored areas 地形对恢复地区的树木生长起着非生物过滤作用
4区 生物学 Q2 PLANT SCIENCES Pub Date : 2023-11-02 DOI: 10.1007/s40626-023-00294-0
José Luiz Alves Silva, Amanda Lúcia Pereira Machado da Silva, Queila Costa dos Santos, Mateus Freitas de Mello e Silva, Carlos Alvarenga Pereira Júnior, Angela Pierre Vitória
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引用次数: 0
Time series data modelling for classification of drought in tomato plants 番茄植株干旱分类的时间序列数据模型
4区 生物学 Q2 PLANT SCIENCES Pub Date : 2023-10-25 DOI: 10.1007/s40626-023-00295-z
Kavya Sai, Neetu Sood, Indu Saini
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引用次数: 0
Protein S-nitrosylation in plants under biotic stress 生物胁迫下植物蛋白质s -亚硝基化
4区 生物学 Q2 PLANT SCIENCES Pub Date : 2023-10-16 DOI: 10.1007/s40626-023-00289-x
Farhin Machchhu, Aakanksha Wany
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引用次数: 0
Microscopy image recognition method of stomatal open and closed states in living leaves based on improved YOLO-X 基于改进YOLO-X的活叶气孔开闭状态显微图像识别方法
4区 生物学 Q2 PLANT SCIENCES Pub Date : 2023-10-13 DOI: 10.1007/s40626-023-00296-y
Kexin Li, Shijie Cong, Tianhong Dai, Jingzong Zhang, Jiuqing Liu
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引用次数: 0
Short-term salt spray reveals high salt tolerance in a neotropical orchid species 短期盐雾显示了一种新热带兰花的高耐盐性
4区 生物学 Q2 PLANT SCIENCES Pub Date : 2023-10-10 DOI: 10.1007/s40626-023-00291-3
Thales Moreira de Lima, Simone Ferreira da Silva, Rafael Vasconcelos Ribeiro, Julia Sánchez-Vilas, Fabio Pinheiro
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引用次数: 0
Towards a grammar of plant stress: modular signalling conveys meaning 植物胁迫语法研究:模块化信号传递意义
4区 生物学 Q2 PLANT SCIENCES Pub Date : 2023-10-10 DOI: 10.1007/s40626-023-00292-2
Peter Nick
Abstract Stress resilience is central for plant survival. The appropriate adaptive response not only depends on the type of stress, but also on the context with other stresses, the developmental state of the plant, and the history of preceding stress experiences. The response to stress combinations cannot be a mere addition of the responses to the individual factors. For instance, heat stress requires stomatal opening to cool the leaf by increased transpiration, while drought stress needs stomatal closure to reduce water loss by transpiration. However, heat and drought are often coming in concert, such that the plant needs to reach a prioritised decision. Thus, the response to stress combinations constitutes a new quality transcending the addition of individual stress components. In other words: to survive under combined stress, plants need to render real decisions. We propose a model, where different stress inputs share one or more transducing elements, that can be recruited for different downstream pathways. Competition for these shared elements allows for such qualitative decisions, depending on the relative activities in upstream signalling of the individual stress components. Using different types of osmotic stress as paradigm I demonstrates, how signal modularity and differences in temporal sequence can generate qualitatively different outputs. Thus, plant-stress signalling makes use of a limited set of molecular players to generate, by specific rules for their combination and sequence, different “meanings”. This can be compared to human language, where information-bearing elements (words) are combined according to grammatical rules to generate a semantic space. (249 words)
胁迫恢复能力是植物生存的核心。适当的适应性反应不仅取决于胁迫类型,还取决于与其他胁迫的环境、植物的发育状态以及之前的胁迫经历。对压力组合的反应不能仅仅是对个别因素的反应的相加。例如,热胁迫需要打开气孔,通过增加蒸腾作用来冷却叶片,而干旱胁迫需要关闭气孔,以减少蒸腾作用造成的水分损失。然而,炎热和干旱经常同时出现,因此植物需要做出优先决定。因此,对应力组合的响应构成了一种新的质量,超越了单个应力分量的添加。换句话说:为了在综合压力下生存,植物需要做出真正的决定。我们提出了一个模型,其中不同的应力输入共享一个或多个转导元件,可以为不同的下游途径招募。对这些共享元素的竞争允许这样的定性决策,这取决于单个应力组件的上游信号的相对活动。使用不同类型的渗透胁迫作为范例I演示了信号模块化和时间序列的差异如何产生定性不同的输出。因此,植物胁迫信号利用一组有限的分子参与者,根据它们的组合和序列的特定规则,产生不同的“意义”。这可以与人类语言相比较,在人类语言中,承载信息的元素(单词)根据语法规则组合在一起,以产生语义空间。(249字)
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引用次数: 0
Mitochondrial structure and respiratory metabolism in cold resistance of alfalfa seedling root 苜蓿幼苗根系抗寒性的线粒体结构和呼吸代谢
4区 生物学 Q2 PLANT SCIENCES Pub Date : 2023-09-29 DOI: 10.1007/s40626-023-00288-y
Meijun Liu, Yu Miao, Lijia Zhang, Yaoyao Zhao, Jie Wang
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引用次数: 0
CONSTANS-like genes are associated with flowering time in sesame 类似constans的基因与芝麻的开花时间有关
4区 生物学 Q2 PLANT SCIENCES Pub Date : 2023-09-28 DOI: 10.1007/s40626-023-00290-4
Miguel López, Hernán Larrea, Natalia Alvarenga, Diego González, Julio César Masaru Iehisa
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引用次数: 0
Overnight supplemental low red light improves lettuce growth 夜间补充低红光可促进生菜生长
4区 生物学 Q2 PLANT SCIENCES Pub Date : 2023-09-22 DOI: 10.1007/s40626-023-00285-1
Maria José Yañez Medelo, Arthur Bernardes Cecílio Filho, Rogério Falleiros Carvalho, Camila Seno Nascimento, Danilo dos Reis Cardoso Passos
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引用次数: 0
期刊
Theoretical and Experimental Plant Physiology
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