From molecules to ecosystems through dynamic energy budget models

Nisbet, Roger M.; Müller, E.; Lika, Konstadia; Kooijman, S.A.L.M.

doi:10.1046/j.1365-2656.2000.00448.x

Cited by 341 publications

(193 citation statements)

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“…Sizeindependent parameters are assumed to be constant across species because cells are metabolically similar, regardless of the species or body size (table 3) The first focus of DEB theory is the individual level, but it has many implications for the sub-and supraorganismic levels (Nisbet et al 2000;Kooijman 2001Kooijman , 2010Kooijman & Segel 2005). There is a direct coupling of sub-organismal processes to the individual level.…”

Section: (D) Acquisition Homeostasismentioning

confidence: 99%

Dynamic energy budget theory restores coherence in biology

Sousa¹,

Domingos²,

Poggiale

et al. 2010

Phil. Trans. R. Soc. B

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215

176

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We present the state of the art of the development of dynamic energy budget theory, and its expected developments in the near future within the molecular, physiological and ecological domains. The degree of formalization in the set-up of the theory, with its roots in chemistry, physics, thermodynamics, evolution and the consistent application of Occam's razor, is discussed. We place the various contributions in the theme issue within this theoretical setting, and sketch the scope of actual and potential applications.Keywords: dynamic energy budget theory; biology; metabolism; ecology; evolution; energetics REACHING OUT FOR GENERALITYIn physics, there is a quest for a unified theory. Physical theories have a broad spectrum of application, a strong mathematical background and are subject to numerous empirical tests. By contrast, in biology, mathematical theory has played a secondary role because biology is frequently seen as a science of exceptions and particular cases, with little interest in abstraction and generalization. Exceptions are the research being done in the fields of theoretical biology and mathematical biology. However, theoretical and mathematical biology have frequently been carried out without a concern for empirical testing. When this concern appears, models are of narrow application, reducing their theoretical breadth. The dynamic energy budget (DEB) theory starts from the Dutch tradition of theoretical and mathematical biology, but couples it with a fundamental concern in producing general theory that is subjected to careful empirical testing.DEB theory aims to capture the quantitative aspects of metabolism at the individual level for organisms of all species. It builds on the premise that the mechanisms that are responsible for the organization of metabolism are not species-specific (Kooijman 2001(Kooijman , 2010. This hope for generality is supported by (i) the universality of physics and evolution and (ii) the existence of widespread biological empirical patterns among organisms . Table 1 synthesizes the essential criteria for any general model for the metabolism of individuals. We explore the links between DEB theory and each of the proposed criteria in the following paragraphs. DEB theory is explicitly based on the conservation of mass, isotopes, energy and time, including the inherent degradation of energy associated with all processes. So it complies to criteria 1, table 1.The DEB theory is biologically implicit, so it applies to all species. Species-specific restrictions of DEB models are explained and predicted by the theory (criterion 5, table 1). For example, consider the most important difference between DEB models, the number of reserves (biomass components that fuel metabolism) and structures (biomass components that have maintenance needs) that are delineated. This depends on the degree of coupling of the various substrates an organism needs. Animals feed on other organisms, which couples uptake of the various substrates (proteins, carbohydrates, lipids, nutrients) tightly and ex...

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Section: (D) Acquisition Homeostasismentioning

confidence: 99%

Dynamic energy budget theory restores coherence in biology

Sousa¹,

Domingos²,

Poggiale

et al. 2010

Phil. Trans. R. Soc. B

Self Cite

215

176

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show abstract

“…Other hypotheses as to the observed reproductive effects can be put forward, obviously. The theory of dynamic energy budgets (DEB; see Kooijman, 2000Kooijman, , 2001Nisbet et al, 2000) provides a framework for addressing this question: the DEB theory describes how individuals acquire and use energy based on a set of simple rules for metabolic organization. Within this theory, organisms are treated as dynamic systems with explicit mass and energy balances.…”

Section: Process-based Analysesmentioning

confidence: 99%

Making Sense of Ecotoxicological Test Results: Towards Application of Process-based Models

2006

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The environmental risk of chemicals is routinely assessed by comparing predicted exposure levels to predicted no-effect levels for ecosystems. Although process-based models are commonly used in exposure assessment, the assessment of effects usually comprises purely descriptive models and rules-of-thumb. The problems with this approach start with the analysis of laboratory ecotoxicity tests, because only a limited amount of information is extracted. Standard summary statistics (NOEC, ECx, LC50) are of limited use in part because they change with exposure duration in a manner that varies with the tested species and the toxicant. As an alternative, process-based models are available. These models allow for toxicity measures that are independent of exposure time, make efficient use of the available data from routine toxicity tests, and are better suited for educated extrapolations (e.g., from individual to population, and from continuous to pulse exposure). These capabilities can be used to improve regulatory decisions and allow for a more efficient assessment of effects, which ultimately will reduce the need for animal testing. Process-based modeling also can help to achieve the goals laid out in REACH, the new strategy of the European Commission in dealing with chemicals. This discussion is illustrated with effects data for Daphnia magna, analyzed by the DEBtox model.

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“…DEB theory treats individuals as nonlinear dynamics systems that follow predictable patterns during their life cycle. This approach has firm physiological roots and provides a sound basis for population dynamic theories (Nisbet et al, 2000;Kooijman, 2010). We refer to Kooijman (2010) for a full description of the DEB theory.…”

mentioning

confidence: 99%

A dynamic energy budget (DEB) model for the energy usage and reproduction of the Icelandic capelin (Mallotus villosus)

Einarsson

Birnir

Sigurðsson

2011

Journal of Theoretical Biology

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is closely related to bioenergetics that focuses on molecular aspects and metabolic pathways in a thermodynamic setting. DEB theory treats individuals as nonlinear dynamics systems that follow predictable patterns during their life cycle. This approach has firm physiological roots and provides a sound basis for population dynamic theories (Nisbet et al., 2000;Kooijman, 2010). We refer to Kooijman (2010) for a full description of the DEB theory. A conceptual introduction is given in Kooijman (2001), and further guides and discussion can be found in van der Meer (2006) and Sousa et al. (2008) DEB theory is ultimately the theory of life. Its aim is to describe all life forms within the same framework. The complexity of the DEB model will depend on the complexity of the species at hand. For the Icelandic capelin, we use a basic form of the DEB model with one food substrate and one type of reserve. These assumptions can be generalized (Kooijman, 2010).DEB theory has been successfully applied to anchovy (Engraulis engrasicolus) in the Bay of Biscay (Pecquerie et al., 2009) where their whole life cycle was modeled. The capelin and anchovies are similar fish in size and energetics, and both store energy mostly as lipids in their muscle. We fit the DEB parameters to the data on capelin and compare the resulting parameter values to those of the anchovies, obtaining similar results.In Section 2.2 we give a brief account of the state variables of the standard DEB model which can be found in Kooijman et al. (2008). Furthermore, we introduce a new variable to account for the roe production of individuals in Section 2.4.

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From molecules to ecosystems through dynamic energy budget models

Cited by 341 publications

References 56 publications

Dynamic energy budget theory restores coherence in biology

Dynamic energy budget theory restores coherence in biology

Making Sense of Ecotoxicological Test Results: Towards Application of Process-based Models

A dynamic energy budget (DEB) model for the energy usage and reproduction of the Icelandic capelin (Mallotus villosus)

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