Hierarchically embedded interaction networks represent a missing link in the study of behavioral and community ecology

Abstract Because genes and phenotypes are embedded within individuals, and individuals within populations, interactions within one level of biological organization are inherently linked to interactors at others. Here, we expand the network paradigm to consider that nodes can be embedded within other nodes, and connections (edges) between nodes at one level of organization form “bridges” for connections between nodes embedded within them. Such hierarchically embedded networks highlight two central properties of biological systems: 1) processes occurring across multiple levels of organization shape connections among biological units at any given level of organization and 2) ecological effects occurring at a given level of organization can propagate up or down to additional levels. Explicitly considering the embedded structure of evolutionary and ecological networks can capture otherwise hidden feedbacks and generate new insights into key biological phenomena, ultimately promoting a broader understanding of interactions in evolutionary theory.

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Ambiguous terminology in animal personality research: a self-report questionnaire and a systematic review

10.32942/osf.io/9srpy ◽

2021 ◽

Author(s):

Alfredo Sánchez-Tójar ◽

Maria Moiron ◽

Petri Toivo Niemelä

Keyword(s):

Literature Review ◽

Animal Personality ◽

Self Report ◽

Behavioural Ecology ◽

Biological Organization ◽

Personality Research ◽

Conceptual Definition ◽

Multiple Levels ◽

Definition Of ◽

Key Questions

Whether animal personality studies provide insights of broader evolutionary and ecological relevance to behavioural ecology is frequently questioned. One source of controversy is the vast, but often vague conceptual terminology used. From a statistical perspective, animal personality is defined as repeatable among-individual variance in behaviour; however, numerous conceptual definitions of animal personality exist. Here, we performed a 1) self-report questionnaire and 2) systematic literature review to quantify how researchers interpret conceptual and statistical definitions commonly used in animal personality research. We also investigated whether results from the questionnaire agree with those of the literature review. Among the 430 self-reported researchers that participated in our questionnaire, we observed discrepancies in key questions such as the conceptual definition of animal personality or the interpretation of repeatability. Our literature review generally confirmed the global patterns revealed by the questionnaire. Overall, we identified common disagreements in animal personality research and discussed potential solutions. We advocate for the usage of statistically-oriented terminology because conceptual definitions can seemingly be interpreted at multiple levels of biological organization. We expect that adopting such statistically-oriented terminology will, at least partly, avoid the confusion generated by the label “animal personality”, and ultimately help to clarify and move the field forward.

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Hormesis is central to toxicology, pharmacology and risk assessment

Human & Experimental Toxicology ◽

10.1177/0960327109363973 ◽

2010 ◽

Vol 29 (4) ◽

pp. 249-261 ◽

Cited By ~ 163

Author(s):

Edward J Calabrese

Keyword(s):

Risk Assessment ◽

Dose Response ◽

Low Dose ◽

Assessment Practices ◽

Biological Organization ◽

Setting Process ◽

Toxicological Research ◽

Multiple Levels ◽

Dose Responses ◽

Chemical Class

This paper summarizes numerous conceptual and experimental advances over the past two decades in the study of hormesis. Hormesis is now generally accepted as a real and reproducible biological phenomenon, being highly generalized and independent of biological model, endpoint measured and chemical class/physical stressor. The quantitative features of the hormetic dose response are generally highly consistent, regardless of the model and mechanism, and represent a quantitative index of biological plasticity at multiple levels of biological organization. The hormetic dose-response model has been demonstrated to make far more accurate predictions of responses in low dose zones than either the threshold or linear at low dose models. Numerous therapeutic agents widely used by humans are based on the hormetic dose response and its low dose stimulatory characteristics. It is expected that as low dose responses come to dominate toxicological research that risk assessment practices will incorporate hormetic concepts in the standard setting process.

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Pearl Oyster: From National Icon To Guardian of Qatar's Marine Environment

University of the Future: Re-Imagining Research and Higher Education ◽

10.29117/quarfe.2020.0051 ◽

2020 ◽

Author(s):

Alexandra Leitao BenHamadou1 ◽

Zenaba Khatir ◽

Noora Al-Shamary ◽

Hassan Hassan ◽

Zainab Hizan ◽

...

Keyword(s):

Marine Environment ◽

Monitoring Program ◽

Integrated Approach ◽

Pearl Oyster ◽

Ecological Effects ◽

Biological Organization ◽

Management Planning ◽

National Icon ◽

Biological Methods ◽

First Time

The NPRP9-394-1-090 project “Pearl Oyster: from national icon to guardian of Qatar's marine environment” had as main aim to develop and apply an integrated suite of chemical and biological methods as early warning tools to assess the “health” of Qatar’s marine environment. The central theme consisted in an investigative monitoring program around the use of the pearl oyster, Pictada imbricata radiata, as a sentinel or guardian species. We have characterized the main environmental contaminants of concern at a selected number of sites around the Qatari coast (UmmBab, Al Khor, Al Wakra and Simaisma), during 2 years, in summer and winter. Potential ecological effects of contaminants (targeted and untargeted) were investigated at different biological organization levels (gene, chromosome, cell, individual, population), through a multidisciplinary approach, using classical and genotoxicological endpoints, integrative histopathology and transcriptomic responses to the different environmental stresses. To our knowledge, this is the first time an integrated approach connecting all these disciplines has been applied in the Qatari marine environment. We present here the main results, of this 3 years project, obtained in all different disciplinary approaches. The results of this project will leave a legacy of resources for future Qatari researchers, including an open access transcriptome data base and the first description of common pathologies observed in the pearl oyster P. i. radiata. Moreover, they will also represent a sound science-based baseline data essential for conservation and management planning, by integration of the data from all the different disciplines applied in the project to assess the potential ecological effects of contaminants at different biological levels.

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Supervenience and Reduction in Biological Hierarchies

Canadian Journal of Philosophy Supplementary Volume ◽

10.1080/00455091.1988.10715950 ◽

1988 ◽

Vol 14 ◽

pp. 209-234 ◽

Cited By ~ 10

Author(s):

John Collier

Keyword(s):

Philosophy Of Mind ◽

Biological Theory ◽

Biological Systems ◽

Reductive Explanation ◽

Biological Phenomena ◽

Explanatory Relevance

Supervenience is a relationship which has been used recently to explain the physical determination of biological phenomena despite resistance to reduction (Rosenberg, 1978, 1985; Sober, 1984a). Supervenience, however, is plagued by ambiguities which weaken its explanatory value and obscure some interesting aspects of reduction in biology. Although I suspect that similar considerations affect the use of supervenience in ethics and the philosophy of mind, I don’t intend anything I have to say here to apply outside of the physical and biological cases I consider.The main point of this paper is that there is a property of biological systems which makes it both misleading and inappropriate to reduce central biological phenomena to the properties of underlying components. Despite this, reductive explanation has been a major source of innovation in biological theory. The apparent tension can be resolved if underlying properties are explanatorily relevant to the higher level phenomena even though the latter are not strictly reducible to the former. Supervenience, I will argue, is not robust enough to deny reduction while supporting explanatory relevance.

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The Structure of Ecological Networks Across Levels of Organization

Annual Review of Ecology Evolution and Systematics ◽

10.1146/annurev-ecolsys-012220-120819 ◽

2020 ◽

Vol 51 (1) ◽

pp. 433-460 ◽

Cited By ~ 1

Author(s):

Paulo R. Guimarães

Keyword(s):

Food Webs ◽

Ecological Systems ◽

Ecological Networks ◽

Ecological Communities ◽

Ecological Interactions ◽

Biological Organization ◽

Architectural Patterns ◽

Fundamental Challenge ◽

Spatiotemporal Scales ◽

Multiple Levels

Interactions connect the units of ecological systems, forming networks. Individual-based networks characterize variation in niches among individuals within populations. These individual-based networks merge with each other, forming species-based networks and food webs that describe the architecture of ecological communities. Networks at broader spatiotemporal scales portray the structure of ecological interactions across landscapes and over macroevolutionary time. Here, I review the patterns observed in ecological networks across multiple levels of biological organization. A fundamental challenge is to understand the amount of interdependence as we move from individual-based networks to species-based networks and beyond. Despite the uneven distribution of studies, regularities in network structure emerge across scales due to the fundamental architectural patterns shared by complex networks and the interplay between traits and numerical effects. I illustrate the integration of these organizational scales by exploring the consequences of the emergence of highly connected species for network structures across scales.

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Advancing from protein interactomes and gene co-expression networks towards multi-omics-based composite networks: approaches for predicting and extracting biological knowledge

Briefings in Functional Genomics ◽

10.1093/bfgp/elaa015 ◽

2020 ◽

Vol 19 (5-6) ◽

pp. 364-376

Author(s):

Vinay Randhawa ◽

Shivalika Pathania

Keyword(s):

Practical Knowledge ◽

Biological Systems ◽

Interaction Networks ◽

Biological Knowledge ◽

Omics Data ◽

Network Modelling ◽

Proper Understanding ◽

Protein Protein Interaction ◽

Global View ◽

Protein Protein Interaction Networks

Abstract Prediction of biological interaction networks from single-omics data has been extensively implemented to understand various aspects of biological systems. However, more recently, there is a growing interest in integrating multi-omics datasets for the prediction of interactomes that provide a global view of biological systems with higher descriptive capability, as compared to single omics. In this review, we have discussed various computational approaches implemented to infer and analyze two of the most important and well studied interactomes: protein–protein interaction networks and gene co-expression networks. We have explicitly focused on recent methods and pipelines implemented to infer and extract biologically important information from these interactomes, starting from utilizing single-omics data and then progressing towards multi-omics data. Accordingly, recent examples and case studies are also briefly discussed. Overall, this review will provide a proper understanding of the latest developments in protein and gene network modelling and will also help in extracting practical knowledge from them.

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Differences and implications in biogeochemistry from maximizing entropy production locally versus globally

Earth System Dynamics ◽

10.5194/esd-2-69-2011 ◽

2011 ◽

Vol 2 (1) ◽

pp. 69-85 ◽

Cited By ~ 13

Author(s):

J. J. Vallino

Keyword(s):

Entropy Production ◽

Biological Systems ◽

Biogeochemical Processes ◽

Biological Structure ◽

Transient Conditions ◽

Entropy Maximization ◽

Planetary Scale ◽

Modeling Systems ◽

Spatial Dimensions ◽

Multiple Levels

Abstract. In this manuscript we investigate the use of the maximum entropy production (MEP) principle for modeling biogeochemical processes that are catalyzed by living systems. Because of novelties introduced by the MEP approach, many questions need to be answered and techniques developed in the application of MEP to describe biological systems that are responsible for energy and mass transformations on a planetary scale. In previous work we introduce the importance of integrating entropy production over time to distinguish abiotic from biotic processes under transient conditions. Here we investigate the ramifications of modeling biological systems involving one or more spatial dimensions. When modeling systems over space, entropy production can be maximized either locally at each point in space asynchronously or globally over the system domain synchronously. We use a simple two-box model inspired by two-layer ocean models to illustrate the differences in local versus global entropy maximization. Synthesis and oxidation of biological structure is modeled using two autocatalytic reactions that account for changes in community kinetics using a single parameter each. Our results show that entropy production can be increased if maximized over the system domain rather than locally, which has important implications regarding how biological systems organize and supports the hypothesis for multiple levels of selection and cooperation in biology for the dissipation of free energy.

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Multilevel functional genomics data integration as a tool for understanding physiology: a network biology perspective

Journal of Applied Physiology ◽

10.1152/japplphysiol.01110.2014 ◽

2016 ◽

Vol 120 (3) ◽

pp. 297-309 ◽

Cited By ~ 7

Author(s):

Peter K. Davidsen ◽

Nil Turan ◽

Stuart Egginton ◽

Francesco Falciani

Keyword(s):

Biological Networks ◽

Molecular State ◽

Biological Data ◽

In Vivo Model ◽

Chronic Obstructive ◽

Biological Organization ◽

Obstructive Pulmonary Disease ◽

Multiple Levels ◽

Molecular Components

The overall aim of physiological research is to understand how living systems function in an integrative manner. Consequently, the discipline of physiology has since its infancy attempted to link multiple levels of biological organization. Increasingly this has involved mathematical and computational approaches, typically to model a small number of components spanning several levels of biological organization. With the advent of “omics” technologies, which can characterize the molecular state of a cell or tissue (intended as the level of expression and/or activity of its molecular components), the number of molecular components we can quantify has increased exponentially. Paradoxically, the unprecedented amount of experimental data has made it more difficult to derive conceptual models underlying essential mechanisms regulating mammalian physiology. We present an overview of state-of-the-art methods currently used to identifying biological networks underlying genomewide responses. These are based on a data-driven approach that relies on advanced computational methods designed to “learn” biology from observational data. In this review, we illustrate an application of these computational methodologies using a case study integrating an in vivo model representing the transcriptional state of hypoxic skeletal muscle with a clinical study representing muscle wasting in chronic obstructive pulmonary disease patients. The broader application of these approaches to modeling multiple levels of biological data in the context of modern physiology is discussed.

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Myth, metaphor and hypothesis: how anthropomorphism defeats science

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.1995.0104 ◽

1995 ◽

Vol 349 (1328) ◽

pp. 215-218 ◽

Cited By ~ 7

Keyword(s):

Nineteenth Century ◽

Evolutionary Theory ◽

Natural World ◽

The State ◽

Selfish Gene ◽

Political Ideologies ◽

Biological Phenomena ◽

The Social ◽

Scientific Rationalism

Dawkin’s theory of the selfish gene has achieved an hegemony quite out of proportion to its intellectual finesse. Its popularity among not just sociobiologists, but biologists proper, provides yet another illustration of the susceptibility of scientific rationalism to the social and political ideologies of the day, to which scientists, being only too human, are heir. A singular achievement of nineteenth century biology, through such writers as Darwin and Huxley, was the construction of an objectifying language for the description of biological phenomena. Transposed into evolutionary theory, this language carefully deanthropomorphizes the processes of mutation, competition and survival, which were defined as central to the state of being of the natural world. Implications of motivation and intention were excluded from the meaning of these terms, as improper for the species and operations involved.

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