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1. Reintegrating Biology Through the Nexus of Energy, Information, and Matter

   https://doi.org/10.1093/icb/icab174  

   Hoke, Kim L; Zimmer, Sara L; Roddy, Adam B; Ondrechen, Mary Jo; Williamson, Craig E; Buan, Nicole R (August 2021, Integrative and Comparative Biology)

   null (Ed.)

   Synopsis Information, energy, and matter are fundamental properties of all levels of biological organization, and life emerges from the continuous flux of matter, energy, and information. This perspective piece defines and explains each of the three pillars of this nexus. We propose that a quantitative characterization of the complex interconversions between matter, energy, and information that comprise this nexus will help us derive biological insights that connect phenomena across different levels of biological organization. We articulate examples from multiple biological scales that highlight how this nexus approach leads to a more complete understanding of the biological system. Metrics of energy, information, and matter can provide a common currency that helps link phenomena across levels of biological organization. The propagation of energy and information through levels of biological organization can result in emergent properties and system-wide changes that impact other hierarchical levels. Deeper consideration of measured imbalances in energy, information, and matter can help researchers identify key factors that influence system function at one scale, highlighting avenues to link phenomena across levels of biological organization and develop predictive models of biological systems. 

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2. Searching for Principles of Microbial Ecology Across Levels of Biological Organization

   https://doi.org/10.1093/icb/icad060  

   Gralka, Matti (June 2023, Integrative And Comparative Biology)

   Synopsis Microbial communities play pivotal roles in ecosystems across different scales, from global elemental cycles to household food fermentations. These complex assemblies comprise hundreds or thousands of microbial species whose abundances vary over time and space. Unraveling the principles that guide their dynamics at different levels of biological organization, from individual species, their interactions, to complex microbial communities, is a major challenge. To what extent are these different levels of organization governed by separate principles, and how can we connect these levels to develop predictive models for the dynamics and function of microbial communities? Here, we will discuss recent advances that point towards principles of microbial communities, rooted in various disciplines from physics, biochemistry, and dynamical systems. By considering the marine carbon cycle as a concrete example, we demonstrate how the integration of levels of biological organization can offer deeper insights into the impact of increasing temperatures, such as those associated with climate change, on ecosystem-scale processes. We argue that by focusing on principles that transcend specific microbiomes, we can pave the way for a comprehensive understanding of microbial community dynamics and the development of predictive models for diverse ecosystems. 

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3. A Unifying Framework for Understanding Biological Structures and Functions Across Levels of Biological Organization

   https://doi.org/10.1093/icb/icab167  

   Herman, M A; Aiello, B R; DeLong, J D; Garcia-Ruiz, H; González, A L; Hwang, W; McBeth, C; Stojković, E A; Trakselis, M A; Yakoby, N (July 2021, Integrative and Comparative Biology)

   Abstract The relationship between structure and function is a major constituent of the rules of life. Structures and functions occur across all levels of biological organization. Current efforts to integrate conceptual frameworks and approaches to address new and old questions promise to allow a more holistic and robust understanding of how different biological functions are achieved across levels of biological organization. Here, we provide unifying and generalizable definitions of both structure and function that can be applied across all levels of biological organization. However, we find differences in the nature of structures at the organismal level and below as compared to above the level of the organism. We term these intrinsic and emergent structures, respectively. Intrinsic structures are directly under selection, contributing to the overall performance (fitness) of the individual organism. Emergent structures involve interactions among aggregations of organisms and are not directly under selection. Given this distinction, we argue that while the functions of many intrinsic structures remain unknown, functions of emergent structures are the result of the aggregate of processes of individual organisms. We then provide a detailed and unified framework of the structure–function relationship for intrinsic structures to explore how their unknown functions can be defined. We provide examples of how these scalable definitions applied to intrinsic structures provide a framework to address questions on structure–function relationships that can be approached simultaneously from all subdisciplines of biology. We propose that this will produce a more holistic and robust understanding of how different biological functions are achieved across levels of biological organization. 

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4. Characterizing biological responses to climate variability and extremes to improve biodiversity projections

   https://doi.org/10.1371/journal.pclm.0000226  

   Buckley, Lauren B.; Carrington, Emily; Dillon, Michael E.; García-Robledo, Carlos; Roberts, Steven B.; Wegrzyn, Jill L.; Urban, Mark C. (June 2023, PLOS Climate)

   Moura, Mario R. (Ed.)

   Projecting ecological and evolutionary responses to variable and changing environments is central to anticipating and managing impacts to biodiversity and ecosystems. Current modeling approaches are largely phenomenological and often fail to accurately project responses due to numerous biological processes at multiple levels of biological organization responding to environmental variation at varied spatial and temporal scales. Limited mechanistic understanding of organismal responses to environmental variability and extremes also restricts predictive capacity. We outline a strategy for identifying and modeling the key organismal mechanisms across levels of biological organization that mediate ecological and evolutionary responses to environmental variation. A central component of this strategy is quantifying timescales and magnitudes of climatic variability and how organisms experience them. We highlight recent empirical research that builds this information and suggest how to design future experiments that can produce more generalizable principles. We discuss how to create biologically informed projections in a feasible way by combining statistical and mechanistic approaches. Predictions will inform both fundamental and practical questions at the interface of ecology, evolution, and Earth science such as how organisms experience, adapt to, and respond to environmental variation at multiple hierarchical spatial and temporal scales. 

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5. Characterizing biological responses to climate variability and extremes to improve biodiversity projections

   Buckley, L.; Carrington, E.; Dillon, M.E.; Garcia-Robledo, C; Roberts, S.B; Wegrzyn, J.; Urban, M.C. (June 2023, PLOS climate)

   Projecting ecological and evolutionary responses to variable and changing environments is central to anticipating and managing impacts to biodiversity and ecosystems. Current model- ing approaches are largely phenomenological and often fail to accurately project responses due to numerous biological processes at multiple levels of biological organization responding to environmental variation at varied spatial and temporal scales. Limited mechanistic under- standing of organismal responses to environmental variability and extremes also restricts predictive capacity. We outline a strategy for identifying and modeling the key organismal mechanisms across levels of biological organization that mediate ecological and evolutionary responses to environmental variation. A central component of this strategy is quantifying timescales and magnitudes of climatic variability and how organisms experience them. We highlight recent empirical research that builds this information and suggest how to design future experiments that can produce more generalizable principles. We discuss how to create biologically informed projections in a feasible way by combining statistical and mechanistic approaches. Predictions will inform both fundamental and practical questions at the interface of ecology, evolution, and Earth science such as how organisms experience, adapt to, and respond to environmental variation at multiple hierarchical spatial and temporal scales. 

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