Tiago Domingos

From empirical patterns to theory: a formal metabolic theory of life

The diversity of life on Earth raises the question of whether it is possible to have a single theoretical description of the quantitative aspects of the organization of metabolism for all organisms. However, similarities between organisms, such as von Bertalanffys growth curve and Kleibers law on metabolic rate, suggest that mechanisms that control the uptake and use of metabolites are common to all organisms. These and other widespread empirical patterns in biology should be the ultimate test for any metabolic theory that hopes for generality. The present study (i) collects empirical evidence on growth, stoichiometry, feeding, respiration and energy dissipation and exhibits it as stylized biological facts; (ii) formalizes assumptions and propositions in a metabolic theory that is fully consistent with the Dynamic Energy Budget theory; and (iii) proves that these assumptions and propositions are consistent with the stylized facts.

Dynamic energy budget theory restores coherence in biology

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 Occams 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.

Physics of metabolic organization.

We review the most comprehensive metabolic theory of life existing to date. A special focus is given to the thermodynamic roots of this theory and to implications that the laws of physics-such as the conservation of mass and energy-have on all life. Both the theoretical foundations and biological applications are covered. Hitherto, the foundations were more accessible to physicists or mathematicians, and the applications to biologists, causing a dichotomy in what always should have been a single body of work. To bridge the gap between the two aspects of the same theory, we (i) adhere to the theoretical formalism, (ii) try to minimize the amount of information that a reader needs to process, but also (iii) invoke examples from biology to motivate the introduction of new concepts and to justify the assumptions made, and (iv) show how the careful formalism of the general theory enables modular, self-consistent extensions that capture important features of the species and the problem in question. Perhaps the most difficult among the introduced concepts, the utilization (or mobilization) energy flow, is given particular attention in the form of an original and considerably simplified derivation. Specific examples illustrate a range of possible applications-from energy budgets of individual organisms, to population dynamics, to ecotoxicology.

Carbon responsibility and embodied emissions : theory and measurement

1. Introduction 2. Accounting Indirect Emissions 3. Carbon Indicators 4. Carbon Responsibility 5. Multi-Regional IO Model 6. Carbon Responsibility of World Regions 7. Discussion

A general approach to the modelling of trophic chains

Abstract Based on the law of mass action (and its microscopic foundation) and mass conservation, we present here a method to derive consistent dynamic models for the time evolution of systems with an arbitrary number of species. Equations are derived through a mechanistic description, ensuring that all parameters have ecological meaning. After discussing the biological mechanisms associated to the logistic and Lotka–Volterra equations, we show how to derive general models for trophic chains, including the effects of internal states at fast time scales. We show that conformity with the mass action law leads to different functional forms for the Lotka–Volterra and trophic chain models. We use mass conservation to recover the concept of carrying capacity for an arbitrary food chain.

The AmP project: Comparing species on the basis of dynamic energy budget parameters

We developed new methods for parameter estimation-in-context and, with the help of 125 authors, built the AmP (Add-my-Pet) database of Dynamic Energy Budget (DEB) models, parameters and referenced underlying data for animals, where each species constitutes one database entry. The combination of DEB parameters covers all aspects of energetics throughout the full organism’s life cycle, from the start of embryo development to death by aging. The species-specific parameter values capture biodiversity and can now, for the first time, be compared between animals species. An important insight brought by the AmP project is the classification of animal energetics according to a family of related DEB models that is structured on the basis of the mode of metabolic acceleration, which links up with the development of larval stages. We discuss the evolution of metabolism in this context, among animals in general, and ray-finned fish, mollusks and crustaceans in particular. New DEBtool code for estimating DEB parameters from data has been written. AmPtool code for analyzing patterns in parameter values has also been created. A new web-interface supports multiple ways to visualize data, parameters, and implied properties from the entire collection as well as on an entry by entry basis. The DEB models proved to fit data well, the median relative error is only 0.07, for the 1035 animal species at 2018/03/12, including some extinct ones, from all large phyla and all chordate orders, spanning a range of body masses of 16 orders of magnitude. This study is a first step to include evolutionary aspects into parameter estimation, allowing to infer properties of species for which very little is known.

Influenza Infectious Dose May Explain the High Mortality of the Second and Third Wave of 1918–1919 Influenza Pandemic

Background It is widely accepted that the shift in case-fatality rate between waves during the 1918 influenza pandemic was due to a genetic change in the virus. In animal models, the infectious dose of influenza A virus was associated to the severity of disease which lead us to propose a new hypothesis. We propose that the increase in the case-fatality rate can be explained by the dynamics of disease and by a dose-dependent response mediated by the number of simultaneous contacts a susceptible person has with infectious ones. Methods We used a compartment model with seasonality, waning of immunity and a Holling type II function, to model simultaneous contacts between a susceptible person and infectious ones. In the model, infected persons having mild or severe illness depend both on the proportion of infectious persons in the population and on the level of simultaneous contacts between a susceptible and infectious persons. We further allowed for a high or low rate of waning immunity and volunteer isolation at different times of the epidemic. Results In all scenarios, case-fatality rate was low during the first wave (Spring) due to a decrease in the effective reproduction number. The case-fatality rate in the second wave (Autumn) depended on the ratio between the number of severe cases to the number of mild cases since, for each 1000 mild infections only 4 deaths occurred whereas for 1000 severe infections there were 20 deaths. A third wave (late Winter) was dependent on the rate for waning immunity or on the introduction of new susceptible persons in the community. If a group of persons became voluntarily isolated and returned to the community some days latter, new waves occurred. For a fixed number of infected persons the overall case-fatality rate decreased as the number of waves increased. This is explained by the lower proportion of infectious individuals in each wave that prevented an increase in the number of severe infections and thus of the case-fatality rate. Conclusion The increase on the proportion of infectious persons as a proxy for the increase of the infectious dose a susceptible person is exposed, as the epidemic develops, can explain the shift in case-fatality rate between waves during the 1918 influenza pandemic.

Regionalization of agri-food life cycle assessment: a review of studies in Portugal and recommendations for the future

PurposeOne of the main trends in life cycle assessment (LCA) today is towards increased regionalization in inventories and impact assessment methods. LCA studies require the collection of activity data but also of increasingly region-specific background data to accurately depict supply chain processes and enable the application of an increasing number of geographically explicit impact assessment models. This is particularly important for agri-food products. In this review, we assess progress in Portugal towards this goal and provide recommendations for future developments.MethodsWe perform a comprehensive review of available LCA studies conducted for Portuguese agri-food products, in order to evaluate the current state of Portuguese agri-food LCA. Among other issues, we assess availability of data, methods used, level of regionalization, impact assessment model relevance and coherence for inter-product comparability. We also provide conclusions and recommendations based on recent developments in the field.Results and discussionWe found 22 LCA studies, covering 22 different products. The analysis of these studies reveals limitations in inter-study comparability. The main challenges have to do with a lack of country-specific foreground data sources applied consistently in the studies found, with discrepancies in impact assessment categories, and with the use of simple functional units that may misrepresent the product analyzed.ConclusionsWe conclude that Portuguese agri-food LCA studies do not have a systematic and country-scale approach in order to guarantee regional accuracy and comparability. We propose a research strategy to engage the Portuguese agri-food LCA community in devising a consistent framework before practical application studies are conducted.

A spatially explicit life cycle assessment midpoint indicator for soil quality in the European Union using soil organic carbon

PurposeImproving land use assessment in life cycle assessment (LCA) is a priority. Recently, soil organic carbon (SOC) depletion has been proposed as a transformation and occupation midpoint indicator to estimate impacts on biotic production potential (BPP). SOC depletion is recommended by the European Union in the International Reference Life Cycle Data System (ILCD) Handbook as a land use indicator. There is a consensus method to calculate SOC depletion in LCA, and ILCD proposes a set of characterization factors (CFs), but these lack geographical discrimination.MethodsOur method of calculation for midpoint CFs follows Brandão and Milà i Canals (Int J Life Cycle Assess 18:1243–1252, 2013). We operationalize the method using SOC stocks from the LUCASOIL database of field measurements in Europe. We use potential natural vegetation (PNV) as the reference situation. CFs were calculated on a cell basis for 23 countries in Europe and grouped in three spatial scales (an administrative classification, NUTS II, and two biophysical classifications, ecoregion and climate region) according to soil type and land cover following a consensus map of cover classes. To evaluate the method’s results, CFs were applied in a case study.Results and discussionSOC stocks of European soils were obtained according to land use and soil type classes (excluding non-European Union countries) for the three spatial scales. A database of European transformation and occupation CFs is also presented and analyzed. The aggregation of CFs at biophysical scales (ecoregion and climate region) is similar, but NUTS II aggregation of CFs is problematic. The application of the CFs in the case study revealed significant differences compared to the outcome of using CFs collected from other land use models.ConclusionsThis paper is the first operationalization using field measurements of an updated version of the ILCD-recommended model for land use impacts in LCA. We obtained CFs for SOC depletion in Europe that can be nested within CFs suggested by ILCD since our results possess better spatial resolution but are only for European Union countries. The case study application highlighted the need for inventories to improve the spatial resolution of the life cycle processes to match the detail of LCIA models.

The land morphology approach to flood risk mapping: An application to Portugal

In the last decades, the increasing vulnerability of floodplains is linked to societal changes such as population density growth, land use changes, water use patterns, among other factors. Land morphology directly influences surface water flow, transport of sediments, soil genesis, local climate and vegetation distribution. Therefore, the land morphology, the land used and management directly influences flood risks genesis. However, attention is not always given to the underlying geomorphological and ecological processes that influence the dynamic of rivers and their floodplains. Floodplains are considered a part of a larger system called Wet System (WS). The WS includes permanent and temporary streams, water bodies, wetlands and valley bottoms. Valley bottom is a broad concept which comprehends not only floodplains but also flat and concave areas, contiguous to streams, in which slope is less than 5%. This will be addressed through a consistent method based on a land morphology approach that classifies landforms according to their hydrological position in the watershed. This method is based on flat areas (slopes less than 5%), surface curvature and hydrological features. The comparison between WS and flood risk data from the Portuguese Environmental Agency for the main rivers of mainland Portugal showed that in downstream areas of watersheds, valley bottoms are coincident with floodplains modelled by hydrological methods. Mapping WS has a particular interest in analysing river ecosystems position and function in the landscape, from upstream to downstream areas in the watershed. This morphological approach is less demanding data and time-consuming than hydrological methods and can be used as the preliminary delimitation of floodplains and potential flood risk areas in situations where there is no hydrological data available. The results were also compared with the land use/cover map at a national level and detailed in Trancão river basin, located in Lisbon metropolitan area, an urbanized basin that suffered heavy flooding in the last decades. This study also contributes to a better understanding of the basin morphology at a local-scale and the effects of soil sealing in downstream flood risks. This work will contribute to the understanding of the morphology, ecology and land use of watersheds that could be used to reduce runoff and downstream flood risk. This can be accomplished by using natural water retention and infiltration methods or higher-level based planning instead of a reaction to local decisions on flood hazards. This morphological approach to map landforms, including wet system, is a valuable tool to assist policy makers and planners in flood risk and land use management, floodplain restoration, agricultural land management practices, and location of human activities according to ecological suitability.