S.A.L.M. Kooijman’s research while affiliated with Vrije Universiteit Amsterdam and other places

As sciences mature, they transition from observation and description to explanation and prediction. This transition is associated with qualitative changes in the way quantitative mathematical formulations are constructed and interpreted, resulting in a ‘theory’. Such transitions from phenomenology to theory are happening in biology but the heuristic framework involved is rarely articulated. We here describe how the use of models in research sets model requirements, using Dynamic Energy Budget (DEB) theory to illustrate the more elaborate ones. We first make the distinction between mathematical formulae and models based on their relation to the abstract and real worlds. We then explain how the transition from models to theory affects model construction and parameter estimation, and discuss the concept of parameter estimation-in-context using the database Add_my_Pet on animal energetics. The transition comes with the need to develop auxiliary and meta- theory and to work with multiple datasets, implying constraints for the loss function that is used for parameter estimation. Finally, we discuss the extra requirements for general explanatory models: they need to be explicit on relevant general principles and to be embedded in a wider scientific context. We also discuss how we see theory’s relationship to observation and prediction change in the future as we use it to deal with theoretical and applied problems in biology.

Patterns in eco-physiological traits of pangolins and carnivorans are studied, which are functions of underlying Dynamic Energy Budget parameters. The data, parameter values and traits are accessible in the open access Add-my-Pet collection, which currently contains 7 out of 8 species of pangolins and 131 of the extant 276 species of carnivorans and 653 of the extant 6400 species of mammals. Paucity of data and species not included reflect the actual state of knowledge: many species are endangered and/or little measured data is readily available. Although musteloids and pinnipeds form the clade Mustelida, they appear at opposite ends of the classical multidimensional scaling diagram, using 14 traits on all mammals. Yet, in general, the energetic parameters bear a strong taxonomic signal. The weight at birth is proportional to ultimate weight: small for carnivorans and pangolins; extra small for bears; and much larger, but typical for mammals, for the pinnipeds and sea otters. How respiration scales with size is taxon-specific, and we discuss how the body-size scaling of reserve capacity interferes with the waste-to-hurry pattern. Despite their high allocation to soma, the life time cumulated mass of neonates of pangolins and carnivorans equals their own ultimate weight; pinnipeds allocate more to maturation and reproduction. Applying models to support conservation efforts entails needing realistic parameter values. This study contributes to the emerging field of assessing the realism of parameters in biological and evolutionary context.

To address challenges in management and conservation of fishes and fisheries it is essential to understand their life histories and energetics. The Add-my-Pet (AmP) collection of data on energetics and Dynamic Energy Budget (DEB) parameters currently contains 1150 of the 40000 extant species of fish. It gives 250-280 traits per species, depending on the model type that was applied, such as maximum reserve capacity, lifespan, specific respiration and precociality index, based on which the ray-finned fish (Actinopterygii) was compared with the four other fish classes (Cyclostomata, Chondrichthyes, Actinistia, Dipnoi) and the Tetrapoda. The Actinopterygii are the only vertebrate class that shows metabolic acceleration, and clearly so in only three sub-clades. Different from chondrichthyans, quite a few species follow the waste-to-hurry strategy, especially small bodied freshwater fish such as tropical annual killifish, but also in small minnows and darters in continental climates. We briefly discuss links between waste-to-hurry, which is associated with a large specific somatic maintenance, and sensitivity for pesticides. We discuss why this interferes with the physical co-variation between maximum reserve capacity and ultimate structural length or weight and explains why maximum reserve capacity increases with body length in chondrichthyans, but not in actinopterygians. Reserve capacity has relevance, e.g. mass-specific maintenance, starvation and the kinetics of lipophyllic compounds (such as pesticides), since reserve is relatively rich in lipids in fish. Also, unlike chondrichthyans, the size at birth is very small and not linked to ultimate size; we discuss the implications. Actinopterygians allocate more to soma, compared with chondrichthyans; the latter allocate more to maturity or reproduction. Actinopterygians, Actinistia and Dipnoi are near the supply-end of the supply-demand spectrum, while chondrichthyans clearly show demand properties.

The Add-my-Pet collection of data on energetics and Dynamic Energy Budget parameters currently contains 92 species of turtles and 23 species of crocodiles. We discuss patterns of eco-physiological traits of turtles and crocodiles, as functions of parameter values, and compare them with other taxa. Turtles and crocodiles accurately match the general rule that the lifetime cumulated neonate mass production equals ultimate weight. The weight at birth for reptiles scales with ultimate weight to the power 0.6. The scaling exponent is between that of amphibians and birds, while that for mammals is close to 1. We explain why this points to limitations imposed by embryonic respiration, the role of water stress and the accumulation of nitrogen waste during the embryo stage. Weight at puberty is proportional to ultimate weight, and is the largest for crocodiles, followed by that of turtles. These facts explain why the precociality coefficient, s bp H-approximated by the ratio of weight at birth and weight at puberty at abundant food-decreases with ultimate weight. It is the smallest for crocodiles because of their large size and is smaller for turtles than for lizards and snakes. The sea turtles have a smaller s bp H than the rest of the turtles, linked to their large size and small offspring size. We link their small weight and age at birth to reducing risks on the beach. The maximum reserve capacity in both turtles and crocodiles clearly decreases with the precociality coefficient. This relationship has not been found that clearly in other taxa, not even in other reptiles, with the exception of the chondrichthyans. Among reptiles, crocodiles and sea turtles have a relatively large assimilation rate and a large reserve capacity. K E Y W O R D S add-my-pet collection, dynamic energy budgets, life history, metabolism, population growth rate, traits

The Add-my-Pet (AmP) collection of data on energetics and Dynamic Energy Budget (DEB) parameters currently contains 200 out of over 1100 extant species of chondrichthyans. This milestone in the compilation of data for this group led us to investigate: (1) do the characteristics that we reported in 2014 for 20 chondrichthyan species, relative to other fish, still hold (2) are novel patterns in properties revealed given the additional data and (3) do the four chondrichthyan subgroups (galean, squaleans, rays and chimaeras) differ in properties? We argue that a better understanding of these properties is key to sustainable management of the rapidly dwindling populations worldwide. Most of the inter-specific scatter in ultimate reproduction rate as function of ultimate body weight stems from differences in the mass of neonates as fraction of that of the mother, which is very high in chondrichthyans. The ultimate neonate mass production is found to be proportional to the ultimate respiration rate, with proportionality factor of 10 g/mol. The lifespan is found to be inversely proportional to weight-specific respiration, with a proportionality factor of 0.1 mol/g. The ultimate weight equals the life-time cumulated neonate mass production. These relationships also apply, with more scatter, to all 3000 animal species in the AmP collection. Sharks and rays were found to be more demand-species, contrary to ray-finned fish and chimaeras, which are supply species. Chimaeras also have that smallest weight at birth and precociality coefficient, compared to sharks and rays. Galeans grow much slower than squaleans and rays, but the chimaeras grow even slower. The lifespan equals 25 times the incubation time for chondrichthyans, but they are rather unique in this respect. Last but not least, we discuss the odd implications of recently published data on the energetics of the Greenland shark.