Intriguing open DEB problems

Individual level

1. Patterns in parameter values among taxa
   1. What are the observed primary parameter ranges? Are there systematic tendencies of parameters in the supply-demand spectrum? And of auto- versus heterotrophs (especially in bacteria)?
   2. Are there patterns in the parameter values of chemoautotrophic organisms, that can be linked to evolution and the origins of life?
   3. Is there an evolutionary tendency to increase [J_EM] in combination with {J_EAm}? Life in the sea requires little osmotic work relative to freshwater. Animals are very active; placentals more than marsupials? Is there a link between [J_EM] and y_EX? Think for instance about the cheetah-sloth spectrum. What is the contribution of defence (e.g. immune system) in k_J? Can we strengthen the relationship between j_EAm and \mu_X?
   4. Does T_A covary with the amplitude of ``natural'' temperature oscillations? High T_A values for deep-sea organisms, low T_A values for intertidal ones? Is there a coupling between T_A and the range T_AL -- T_AH? A negative coupling is likely.
   5. Can we extend the methods for parameter estimation from data? Think especially about applications of isotopes. This comes with new modules for sub-individual organisation.
   6. Are there patterns in allocation strategies? The parameter \kappa can depend on light/dark cycles; which environmental and other variables also effect it? Are holometabolic insects the only convincing examples of determinate growers (in a DEB context)? We need a detailed dynamic budget comparison of reproductive and post-reproductive individuals of various taxa and capture their performance in parameter values.
2. What would be natural modules to include behaviour linked to metabolic (including reproductive) needs? Think of functional aspects of behaviour. Food searching (obviously), food selection (natural shift from carnivory to herbivory in animals during ontogeny), sleeping to repair free radical damage, territorial defence in relation to predicted food availability and population density, food collection versus breeding in nesting birds, parental care, social interaction, mate selection. How does migration/hibernation fit in? The SU rules provide a basic framework, but we also need a kind of dynamic priority setting. Triggers to start/end behavioural types. We need an evolutionary perspective here.
3. What variety of handling rules exist for the reproduction buffer? How can the various reproduction strategies in plants be linked to the values of the state variables or to changes therein?
4. Large bodied organisms have relatively large reserve capacities, which should resemble structure in macro-chemical composition. What rules exist for any particular chemical compound to become part of the reserve or structure in isomorphs? How does this relate to turnover times? Turnover times of various compounds in reserve are coupled, but in structure they are not, due to somatic maintenance. See Kooy2007a.
5. What are the thermodynamic consequences of changes in specific entropy linked to differences in pressure and dioxygen tension? How do we obtain estimates for specific entropies in such conditions?
6. Can we find values for the maintenance ratio from effects of removal of some reserve at the start of egg development on the size at hatching? Are parameter values typically constant across stage transition?
7. How do individuals plants change local physical/chemical conditions that affect their development and that of other organisms?
8. Can syntrophic interactions between gut flora and animal host and between mycorrhiza and plant roots be generalized and formalized?

Sub-individual level

1. Can we make a relatively simple model for a cell in which the 5 biochemical modules of the central metabolism interact on the basis of syntrophy that is consistent with DEB theory? Does this provides mechanisms for homeostasis? See href="/thb/research/bib/KooySege2003.html"> KooySege2003.
2. Can we obtain more empirical evidence for weak homeostasis?
3. What could be mechanisms for structural and strong homeostasis? Some candidates are known, but we need extension and empirical verification.
4. Can we link metabolic flux control theory to DEB theory in a useful way?
5. Can we generalise the rules for gen-regulation, as obtained in the adaptation module of DEB theory?
6. Can we generalise the workload module for allocation to organs (upto now tumours, gut/velum) to create a really dynamic individual? A start with kidney size (linked to N-waste dynamics), lung & hart size (linked to respiration), liver size (linked to digestion, brain size (linked to processing info from sensors, muscle coordination), root versus shoot (in plants) are the first obvious steps into this direction. Can this be coupled to mechanisms for structural homeostasis? Do general rules follow for tissue differentiation in an evolutionary perspective?
7. Extend the set of state variables (structure, reserve) in a structured way to include faster processes than growth & reproduction. The inclusion of digestion has been started, but could be extended, then follows distribution (blood, control of blood sugar content), natural inclusion of hormol control systems.
8. Can we find examples where evolution went backwards: from few to more independent reserves? Can we find examples where the turnover rates of the various reserves are clearly different?

Supra-individual level

1. Can we expand the set of ode's for a population of V1-morphs in a forced environment to approximate the von Forster pde for isomorphs? We need simplification of the ecosystem level. moreover we need a formalism for structured populations that live on other structured populations, with realistic rules for biomass conversion that obey stoichiometric constraints.
2. How does stochasticity in the (feeding) behaviour of individuals work out at the population level. See KooyGras2007 for a simple start. What about the stability and extinction times of stochastic food webs?
3. Can we find patterns in schooling, territorial behaviour, migration that are linked to food availability/ selection?
4. Derive body size spectra on the basis of simple DEB rules for feeding and body size scaling in homogeneous steady ecosystems. See KooyBrug2008.
5. Can we use arguments of adaptive dynamics to simulate self-organisation of ecosystems in terms of foodweb structures, syntrophic relationships, autotrophic-heterotrophic interactions? Tineke Troost made a useful start by studying how a closed mono-species ecosystem of mixotrophs can evolve into a coexistence of autotrophs and heterotrophs and the evolutionary changes in maximum body size.
6. Evaluate the coupled predation and pathogen dynamics in structured target populations with post-reproductive stages and full nutrient recycling. Are there reasons to expect that the evolution of predation and parasitism are coupled? What is the effect of preference shifts of the predator to the early juvenile and embryo stages? To what extend protect predators populations against pathogens?
7. Can we find general rules for thermodynamics aspects of foodwebs and ecosystems?
8. What properties of individuals affect ecosystem behaviour? What it the effect of the (maximum) length of food chains in mass turnover at the ecosystem level; how does it depend on yield coefficients and maintenance requirements?
9. What it is coupling between ecosystem structure and function? Can we further develop ideas on variances of (elemental) return times to the various pools (environmental and various biomass compartments)? Is there a coupling with biodiversity? What mechanisms exist to maintain diversity?
10. It is possible to find a natural and simple model for the actions of life at the planetary level? The coupling between terrestrial and aquatic activities via nutrient recycling and between the various biogeochemical cycles? The role of biota in the control of atmospheric water in relation to greenhouse warming? We need a structured approach in 1, 2, 2.5 and 3 D for a set of biogeochemical climate models of varying detail in near equilibrium situations.