The Dynamic Energy Budget theory unifies the commonalities between organisms, as prescribed by the implications of energetics, and links different levels of biological organisation (cells, organisms and populations). The theory presents simple mechanistic rules that describe the uptake and use of energy and nutrients and the consequences for physiological organisation throughout an organism's life cycle, including the energetics of ageing and contact with toxic compounds. This new edition includes a new chapter on evolutionary aspects, and discusses methods to quantify entropy for living individuals, isotope dynamics, a mechanism behind reserve dynamics, and toxicity of complex mixtures of compounds. An updated ageing module now also applies to demand systems, new methods for parameter estimation, adaptation of substrate uptake, the use of otiliths for reconstruction of food level trajectories, the differentiated growth of body parts (such as tumours and organs) linked to their function, and many more topics.

second editionDynamic Energy Budget theory unifies the commonalities between organisms as prescribed by the implications of energetics, which link different levels of biological organization (cells, organisms and populations). The theory presents simple mechanistic rules that describe the uptake and use of energy and nutrients and the consequences for physiological organization throughout an organism's life cycle, including the relationships between energetics and aging and the effects of toxicants. In this new edition, the theory is broadened to encompass the fluxes of both energy and mass. All living organisms are now covered in a single quantitative framework, the predictions of which are tested against a wide variety of experimental results at the various levels of biological organization. The theory explains many general observations, such as the body size scaling relationships of certain physiological traits, and provides a theoretical basis for the widely used method of indirect calorimetry. In each case, the theory is developed in elementary mathematical terms, but a more detailed discussion of the methodological aspects of mathematical modelling is also included, making the book suitable for biologists and mathematicians with a broad interest in both fundamental and applied quantitative problems in biology.Bas Kooijman is Professor of Applied Theoretical Biology at the Vrije Universiteit in Amsterdam and is also head of the University's Department of Theoretical Biology. His research focuses on mathematical biology, in particular ecotoxicology which provided the framework for the original version of his Dynamic Energy Budget theory published in 1993 (Dynamic Energy Budgets in Biological Systems -Theory and Applications in Ecotoxicology). From the first edition:"This book is an excellent scientific product that informs and forces contemplation of issues relating to population and community ecology. The author has made a complex subject coherent." Thomas G. Hallam, Bulletin of Mathematical Biology "... a very useful and general tool to select more ecologically sound process equations and parameters in ecological models." Sven Erik Jørgensen, Ecological Modelling "The author has made a significant contribution to the problem of modelling the dynamics of biological populations at the level of the individual by synthesizing this very complicated subject into a relatively short list of general assumptions and putting the energetics of sub-models for vital rates on a solid basis." Jim Cushing, Mathematical Biosciences "The family of idealized models offered in this book is capable of playing a role analogous to that of Lotka-Volterra models in population dynamics ... I am confident that any model(s) capable of occupying this niche will be strongly influenced by the ideas in this book." Roger Nisbet, Ecology 9 LIVING TOGETHER Interaction between organisms: The spectrum from competition to preypredator systems. Evaluation of the consequences of the DEB model for population dynamics, food chains, and communities....

Whereas it is acknowledged that the C:N:P stoichiometry of consumers and their resources affects both the structure and the function of food webs, and eventually influences broad‐scale processes such as global carbon cycles, the mechanistic basis for the variation in stoichiometry has not yet been fully explored. Empirical evidence shows that the specific growth rate is positively related to RNA concentration both between and within taxa in both unicellular and multicellular organisms. Since RNA is rich in P and constitutes a substantial part of the total P in organisms, a high growth rate is also connected with a high P content. We argue that the reason for this pattern is that the growth of all biota is closely linked with their protein synthesis rate, and thus with the concentration of ribosomal RNA. Dynamic energy budget theory supports the positive relationship between RNA and specific growth rate in microorganisms, whereas the predictions concerning multicellulars only partially agrees with the observed pattern. In a simple model of consumer growth, we explore the consequences of various allocation patterns of RNA, protein, carbohydrates/lipids, and other biochemical constituents on organism potential growth rate and C:N:P stoichiometry. According to the model the percentage of N and especially percentage of P per dry mass increases with increasing specific growth rate. Furthermore, the model suggests that macromolecule allocation patterns and thus N:P stoichiometry are allowed to differ substantially at low growth rates whereas the stoichiometry at high growth rates is much more constricted at low N:P. The model fits empirical data reasonably well, but it is also acknowledged that complex life cycles and associated physiological constraints may result in other patterns. We also use a similar approach of modeling organism growth from basic biochemical principles to illustrate fundamental connections among biochemical allocation and C:N stoichiometry in autotroph production, which is based on allocation patterns between carbohydrates and rubisco. Similar to the RNA–protein model, macromolecular composition and C:N ratios are more constrained at high than at low growth rates. The models and the empirical data together suggest that organism growth is tightly linked with the organisms' biochemical and elemental composition. The stoichiometry of growth impinges on nutrient cycles and carbon fluxes at the ecosystem level. Thus, focus on the biological basis of organism C:N:P stoichiometry can mechanistically connect growth strategy and biochemical and cellular mechanisms of biota to major ecological consequences.

1. Dynamic energy budget (DEB) models describe how individuals acquire and utilize energy, and can serve as a link between dierent levels of biological organization. 2. We describe the formulation and testing of DEB models, and show how the dynamics of individual organisms link to molecular processes, to population dynamics, and (more tenuously) to ecosystem dynamics. 3. DEB models oer mechanistic explanations of body-size scaling relationships. 4. DEB models constitute powerful tools for applications in toxicology and biotechnology. 5. Challenging questions arise when linking DEB models with evolutionary theory.

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...

1. Dynamic energy budget (DEB) models describe how individuals acquire and utilize energy, and can serve as a link between dierent levels of biological organization. 2. We describe the formulation and testing of DEB models, and show how the dynamics of individual organisms link to molecular processes, to population dynamics, and (more tenuously) to ecosystem dynamics. 3. DEB models oer mechanistic explanations of body-size scaling relationships. 4. DEB models constitute powerful tools for applications in toxicology and biotechnology. 5. Challenging questions arise when linking DEB models with evolutionary theory.

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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