Interface Focus最新文献_第9页

Reflections on the asymmetry of causation. 对因果关系不对称的思考。

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-04-14 eCollection Date: 2023-06-06 DOI: 10.1098/rsfs.2022.0081

Jenann Ismael

{"title":"Reflections on the asymmetry of causation.","authors":"Jenann Ismael","doi":"10.1098/rsfs.2022.0081","DOIUrl":"10.1098/rsfs.2022.0081","url":null,"abstract":"The most immediately salient asymmetry in our experience of the world is the asymmetry of causation. In the last few decades, two developments have shed new light on the asymmetry of causation: clarity in the foundations of statistical mechanics, and the development of the interventionist conception of causation. In this paper, we ask what is the status of the causal arrow, assuming a thermodynamic gradient and the interventionist account of causation? We find that there is an objective asymmetry rooted in the thermodynamic gradient that underwrites the causal asymmetry: along a thermodynamic gradient, interventionist causal pathways-scaffolded intervention-supporting probabilistic relationships between variables-will propagate influence into the future, but not into the past. The reason is that the present macrostate of the world, in the presence of a low entropy boundary condition, will screen off probabilistic correlations to the past. The asymmetry, however, emerges only under the macroscopic coarse-graining and that raises the question of whether the arrow is simply an artefact of the macroscopic lenses through which we see the world. The question is sharpened and an answer proposed.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20220081"},"PeriodicalIF":4.4,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102723/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9364760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

A third transition in science? 科学的第三次转变？

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-04-14 eCollection Date: 2023-06-06 DOI: 10.1098/rsfs.2022.0063

Stuart A Kauffman, Andrea Roli

{"title":"A third transition in science?","authors":"Stuart A Kauffman, Andrea Roli","doi":"10.1098/rsfs.2022.0063","DOIUrl":"10.1098/rsfs.2022.0063","url":null,"abstract":"Since Newton, classical and quantum physics depend upon the 'Newtonian paradigm'. The relevant variables of the system are identified. For example, we identify the position and momentum of classical particles. Laws of motion in differential form connecting the variables are formulated. An example is Newton's three laws of motion. The boundary conditions creating the phase space of all possible values of the variables are defined. Then, given any initial condition, the differential equations of motion are integrated to yield an entailed trajectory in the prestated phase space. It is fundamental to the Newtonian paradigm that the set of possibilities that constitute the phase space is always definable and fixed ahead of time. This fails for the diachronic evolution of ever-new adaptations in any biosphere. Living cells achieve constraint closure and construct themselves. Thus, living cells, evolving via heritable variation and natural selection, adaptively construct new-in-the-universe possibilities. We can neither define nor deduce the evolving phase space: we can use no mathematics based on set theory to do so. We cannot write or solve differential equations for the diachronic evolution of ever-new adaptations in a biosphere. Evolving biospheres are outside the Newtonian paradigm. There can be no theory of everything that entails all that comes to exist. We face a third major transition in science beyond the Pythagorean dream that 'all is number' echoed by Newtonian physics. However, we begin to understand the emergent creativity of an evolving biosphere: emergence is not engineering.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 3","pages":"20220063"},"PeriodicalIF":4.4,"publicationDate":"2023-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10102722/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9499242","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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: 5

Correction to: 'Current strategies with implementation of 3D cell culture: The challenge of quantification' (2022) by Temple et al. 对Temple等人的“目前实施3D细胞培养的策略:量化的挑战”(2022年)的更正。

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-04-06 DOI: 10.1098/rsfs.2022.0066

J Temple, E Velliou, M Shehata, R Lévy, P Gupta

引用次数: 0

Biofilm thickness controls the relative importance of stochastic and deterministic processes in microbial community assembly in moving bed biofilm reactors. 生物膜厚度控制着移动床生物膜反应器中微生物群落组装的随机和确定性过程的相对重要性。

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-04-06 DOI: 10.1098/rsfs.2022.0069

S Jane Fowler, Elena Torresi, Arnaud Dechesne, Barth F Smets

{"title":"Biofilm thickness controls the relative importance of stochastic and deterministic processes in microbial community assembly in moving bed biofilm reactors.","authors":"S Jane Fowler, Elena Torresi, Arnaud Dechesne, Barth F Smets","doi":"10.1098/rsfs.2022.0069","DOIUrl":"https://doi.org/10.1098/rsfs.2022.0069","url":null,"abstract":"Deterministic and stochastic processes are believed to play a combined role in microbial community assembly, though little is known about the factors determining their relative importance. We investigated the effect of biofilm thickness on community assembly in nitrifying moving bed biofilm reactors using biofilm carriers where maximum biofilm thickness is controlled. We examined the contribution of stochastic and deterministic processes to biofilm assembly in a steady state system using neutral community modelling and community diversity analysis with a null-modelling approach. Our results indicate that the formation of biofilms results in habitat filtration, causing selection for phylogenetically closely related community members, resulting in a substantial enrichment of Nitrospira spp. in the biofilm communities. Stochastic assembly processes were more prevalent in biofilms of 200 µm and thicker, while stronger selection in thinner (50 µm) biofilms could be driven by hydrodynamic and shear forces at the biofilm surface. Thicker biofilms exhibited greater phylogenetic beta-diversity, which may be driven by a variable selection regime caused by variation in environmental conditions between replicate carrier communities, or by drift combined with low migration rates resulting in stochastic historical contingency during community establishment. Our results indicate that assembly processes vary with biofilm thickness, contributing to our understanding of biofilm ecology and potentially paving the way towards strategies for microbial community management in biofilm systems.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 2","pages":"20220069"},"PeriodicalIF":4.4,"publicationDate":"2023-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9912012/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9566247","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Encounter rates prime interactions between microorganisms. 接触率决定了微生物之间的相互作用。

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-04-06 DOI: 10.1098/rsfs.2022.0059

Jonasz Słomka, Uria Alcolombri, Francesco Carrara, Riccardo Foffi, François J Peaudecerf, Matti Zbinden, Roman Stocker

{"title":"Encounter rates prime interactions between microorganisms.","authors":"Jonasz Słomka, Uria Alcolombri, Francesco Carrara, Riccardo Foffi, François J Peaudecerf, Matti Zbinden, Roman Stocker","doi":"10.1098/rsfs.2022.0059","DOIUrl":"https://doi.org/10.1098/rsfs.2022.0059","url":null,"abstract":"Properties of microbial communities emerge from the interactions between microorganisms and between microorganisms and their environment. At the scale of the organisms, microbial interactions are multi-step processes that are initiated by cell-cell or cell-resource encounters. Quantification and rational design of microbial interactions thus require quantification of encounter rates. Encounter rates can often be quantified through encounter kernels-mathematical formulae that capture the dependence of encounter rates on cell phenotypes, such as cell size, shape, density or motility, and environmental conditions, such as turbulence intensity or viscosity. While encounter kernels have been studied for over a century, they are often not sufficiently considered in descriptions of microbial populations. Furthermore, formulae for kernels are known only in a small number of canonical encounter scenarios. Yet, encounter kernels can guide experimental efforts to control microbial interactions by elucidating how encounter rates depend on key phenotypic and environmental variables. Encounter kernels also provide physically grounded estimates for parameters that are used in ecological models of microbial populations. We illustrate this encounter-oriented perspective on microbial interactions by reviewing traditional and recently identified kernels describing encounters between microorganisms and between microorganisms and resources in aquatic systems.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 2","pages":"20220059"},"PeriodicalIF":4.4,"publicationDate":"2023-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9912013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10735036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

The media composition as a crucial element in high-throughput metabolic network reconstruction. 介质组成是高通量代谢网络重建的关键因素。

IF 3.6 3区生物学

Interface Focus Pub Date : 2023-02-10 eCollection Date: 2023-04-06 DOI: 10.1098/rsfs.2022.0070

Benedict Borer, Stefanía Magnúsdóttir

{"title":"The media composition as a crucial element in high-throughput metabolic network reconstruction.","authors":"Benedict Borer, Stefanía Magnúsdóttir","doi":"10.1098/rsfs.2022.0070","DOIUrl":"10.1098/rsfs.2022.0070","url":null,"abstract":"In recent years, metagenome-assembled genomes (MAGs) have provided glimpses into the intra- and interspecies genetic diversity and interactions that form the bases of complex microbial communities. High-throughput reconstruction of genome-scale metabolic networks (GEMs) from MAGs is a promising avenue to disentangle the myriad trophic interactions stabilizing these communities. However, high-throughput reconstruction of GEMs relies on accurate gap filling of metabolic pathways using automated algorithms. Here, we systematically explore how the composition of the media (specification of the available nutrients and metabolites) during gap filling influences the resulting GEMs concerning predicted auxotrophies for fully sequenced model organisms and environmental isolates. We expand this analysis by using 106 MAGs from the same species with differing quality. We find that although the completeness of MAGs influences the fraction of gap-filled reactions, the composition of the media plays the dominant role in the accurate prediction of auxotrophies that form the basis of myriad community interactions. We propose that constraining the media composition for gap filling through both experimental approaches and computational approaches will increase the reliability of high-throughput reconstruction of genome-scale metabolic models from MAGs and paves the way for culture independent prediction of trophic interactions in complex microbial communities.","PeriodicalId":13795,"journal":{"name":"Interface Focus","volume":"13 2","pages":"20220070"},"PeriodicalIF":3.6,"publicationDate":"2023-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9912011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10735041","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Cultivating a more effective culture to advance the engineering of microbial communities 培养更有效的培养物以推进微生物群落工程

IF 4.4 3区生物学

Interface Focus Pub Date : 2023-02-10 DOI: 10.1098/rsfs.2022.0073

S. J. Fowler, T. Curtis