Pub Date : 2023-12-07DOI: 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.
{"title":"Formalizing complexity in the life sciences: systems, emergence, and metafluxes","authors":"Lars H. Wegner","doi":"10.1007/s40626-023-00293-1","DOIUrl":"https://doi.org/10.1007/s40626-023-00293-1","url":null,"abstract":"<p>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. <i>Systems theory</i> 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 <i>emergence</i>, 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 <i>metaflux</i> 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.</p>","PeriodicalId":23038,"journal":{"name":"Theoretical and Experimental Plant Physiology","volume":"52 1","pages":""},"PeriodicalIF":2.6,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138555016","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 : 2023-11-02DOI: 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
{"title":"Topography imposes an abiotic filter on tree growth in restored areas","authors":"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","doi":"10.1007/s40626-023-00294-0","DOIUrl":"https://doi.org/10.1007/s40626-023-00294-0","url":null,"abstract":"","PeriodicalId":23038,"journal":{"name":"Theoretical and Experimental Plant Physiology","volume":"16 8","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135973440","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 : 2023-10-25DOI: 10.1007/s40626-023-00295-z
Kavya Sai, Neetu Sood, Indu Saini
{"title":"Time series data modelling for classification of drought in tomato plants","authors":"Kavya Sai, Neetu Sood, Indu Saini","doi":"10.1007/s40626-023-00295-z","DOIUrl":"https://doi.org/10.1007/s40626-023-00295-z","url":null,"abstract":"","PeriodicalId":23038,"journal":{"name":"Theoretical and Experimental Plant Physiology","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135113278","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 : 2023-10-13DOI: 10.1007/s40626-023-00296-y
Kexin Li, Shijie Cong, Tianhong Dai, Jingzong Zhang, Jiuqing Liu
{"title":"Microscopy image recognition method of stomatal open and closed states in living leaves based on improved YOLO-X","authors":"Kexin Li, Shijie Cong, Tianhong Dai, Jingzong Zhang, Jiuqing Liu","doi":"10.1007/s40626-023-00296-y","DOIUrl":"https://doi.org/10.1007/s40626-023-00296-y","url":null,"abstract":"","PeriodicalId":23038,"journal":{"name":"Theoretical and Experimental Plant Physiology","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135918552","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 : 2023-10-10DOI: 10.1007/s40626-023-00291-3
Thales Moreira de Lima, Simone Ferreira da Silva, Rafael Vasconcelos Ribeiro, Julia Sánchez-Vilas, Fabio Pinheiro
{"title":"Short-term salt spray reveals high salt tolerance in a neotropical orchid species","authors":"Thales Moreira de Lima, Simone Ferreira da Silva, Rafael Vasconcelos Ribeiro, Julia Sánchez-Vilas, Fabio Pinheiro","doi":"10.1007/s40626-023-00291-3","DOIUrl":"https://doi.org/10.1007/s40626-023-00291-3","url":null,"abstract":"","PeriodicalId":23038,"journal":{"name":"Theoretical and Experimental Plant Physiology","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136296127","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 : 2023-10-10DOI: 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)
{"title":"Towards a grammar of plant stress: modular signalling conveys meaning","authors":"Peter Nick","doi":"10.1007/s40626-023-00292-2","DOIUrl":"https://doi.org/10.1007/s40626-023-00292-2","url":null,"abstract":"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)","PeriodicalId":23038,"journal":{"name":"Theoretical and Experimental Plant Physiology","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136352751","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 : 2023-09-28DOI: 10.1007/s40626-023-00290-4
Miguel López, Hernán Larrea, Natalia Alvarenga, Diego González, Julio César Masaru Iehisa
{"title":"CONSTANS-like genes are associated with flowering time in sesame","authors":"Miguel López, Hernán Larrea, Natalia Alvarenga, Diego González, Julio César Masaru Iehisa","doi":"10.1007/s40626-023-00290-4","DOIUrl":"https://doi.org/10.1007/s40626-023-00290-4","url":null,"abstract":"","PeriodicalId":23038,"journal":{"name":"Theoretical and Experimental Plant Physiology","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135385448","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 : 2023-09-22DOI: 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
{"title":"Overnight supplemental low red light improves lettuce growth","authors":"Maria José Yañez Medelo, Arthur Bernardes Cecílio Filho, Rogério Falleiros Carvalho, Camila Seno Nascimento, Danilo dos Reis Cardoso Passos","doi":"10.1007/s40626-023-00285-1","DOIUrl":"https://doi.org/10.1007/s40626-023-00285-1","url":null,"abstract":"","PeriodicalId":23038,"journal":{"name":"Theoretical and Experimental Plant Physiology","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136060422","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}