DEB theory: where fascination meets profession Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam Farewell address as Professor at VU Universiteit Amsterdam Luminy 2015/04/30

Contents Fascination & profession Planting the seed Theory of energetics Ontogeny of DEB theory Future developments Acknowledgements Farewell

Extended wilderness hikes

Microbial wildlife Urostyla Euastrum Chaetonotus Snowella

Daphnia magna At 20 C, max food puberty at 7 d since birth 400 young at 14 d since puberty 0.8 mm at birth 2.5 mm at puberty 5.0 mm at 21 d

Focus on individuals population dynamics is derived from properties of individuals + interactions between them evolution according to Darwin: variation between individuals + selection individuals are the survival machines of life material and energy balances: most easy for individuals

Biochemical ↔ Pools many compounds need for selection conservation laws cannot be used wide range in scales complex dynamics easy connection with molecular level with literature few pools use of homeostasis conservation laws can be used narrow range in scales simple dynamics complex connection with molecular level with literature

Homeostasis strong homeostasis constant composition of pools (reserves/structures) generalized compounds, stoichiometric constraints on synthesis weak homeostasis constant composition of biomass during growth in constant environments determines reserve dynamics (in combination with strong homeostasis) structural homeostasis constant relative proportions during growth in constant environments isomorphy.work load allocation thermal homeostasis ectothermy  homeothermy  endothermy acquisition homeostasis supply  demand systems development of sensors, behavioural adaptations

Empirical models Authoryearmodel Lavoisier1780multiple regression of heat against mineral fluxes Gompertz1825survival probability for ageing Bergmann1847body size increase toward the poles Arrhenius1889temperature dependence of physiological rates Huxley1891allometric growth of body parts Henri1902Michaelis--Menten enzyme kinetics Blackman1905bilinear functional response Hill1910Hill's functional response Thornton1917heat dissipation Pűtter1920von Bertalanffy growth of individuals Pearl1927logistic population growth Fisher & Tippitt1928Weibull ageing Kleiber1932respiration scales with body weight^3/ 4 Authoryearmodel Mayneord1932cube root growth of tumours Monod1942growth of bacterial populations Emerson1950cube root growth of bacterial colonies Huggett & Widdas1951foetal growth Weibull1951survival probability for ageing Best1955diffusion limitation of uptake Smith1957embryonic respiration Leudeking & Piret1959microbial product formation Holling1959hyperbolic functional response Marr & Pirt1962maintenance in yields of biomass Droop1973reserve (cell quota) dynamics Rahn & Ar1974water loss in bird eggs Hungate1975digestion Beer & Anderson1997development of salmonid embryos

Embryonic development time, d weight, g O 2 consumption, ml/h Crocodylus johnstoni, Data: Whitehead 1987 yolk embryo time, d

Metabolic rate Log weight, g Log metabolic rate, w endotherms ectotherms unicellulars slope = 1 slope = 2/3 Length, cm O 2 consumption,  l/h Inter-species Intra-species L L L curves fitted: (Daphnia pulex) Data: Hemmingson 1969; curve fitted from DEB theoryData: Richman 1958; curve fitted from DEB theory

Method of indirect calorimetry Empirical origin (multiple regression): Lavoisier 1780 Heat production = w C CO 2 -production + w O O 2 -consumption + w N N-waste production DEB-explanation: Mass and heat fluxes = w A assimilation + w D dissipation + w G growth Applies to CO 2, O 2, N-waste, heat, food, faeces, … For V1-morphs: dissipation  maintenance

Interactions of substrates Kooijman, 2001 Phil Trans R Soc B 356:

Supply-demand spectrum

Lika et al 2014 J. Theor. Biol., 354:35-47

DEB calender 1977 Effects of toxicants on survival depend in internal conc.; one compartment model as basic transport model 1978 No Effect Concentration (NEC) as parameter 1979 Start of DEB work with Holling, von Bertalanffy, Arrhenius & κ -rule; start of work on structured pop. dynamics with Hans Metz & Odo Diekmann 1980 Sublethal effects of toxicants as changes in par-values 1981 Reserve on the basis of Droop 1982 Embryos are juvenile that don't eat; costs of eggs & maternal effects; maturity as state variable 1983 co-variation rules of DEB parameters; Bacterial populations as juveniles 1984 Maturity maintenance as energy sink 1985 Shape correction function; bacteria as static mixtures between V0- and V1-morphs 1986 The name DEB was chosen on instigation by Joosse; microbial product formation & fermentation 1987 Mass as conserved quantity in combination with energy; respiration as in indirect calorimetry 1988 Reconstruction of food uptake from growth 1989 Ageing as accumulation of damage in 2 steps; Weibull ageing rate; microbial food chains with Bob Kooi 1990 Start writing of DEB1; Type T-acceleration of metabolism 1991 Multiple reserve & partition. of reserve kinetics 1992 Static generalisations of the κ -rule 1993 First local DEB course; Dynamic generalization of the κ rule 1994 Multiple substrates, reserves & structures: plants model 1996 Synthesising Units (SUs) as alternative for enzyme kinetics 1997 Excretion of reserves for multiple reserves 1998 Start writing of DEB2; symbiosis on the basis of mutual syntrophy 1999 Toxicity of mixtures of compounds; co-var rules for parameters one-compartment and film models and for effects of toxicants 2000 Start of DEBtool in Matlab/Octave; modules for mixotrophy; co-metabolism & inhibition with SUs 2001 First tele course; merging of symbiontic partners into a new ind.; effect of ionization on toxico-kinetics 2002 Ageing acceleration; Gompertz stress coeff. with Ingeborg van Leeuwen 2003 Generalisations of the κ-rule 2004 Handshaking protocols for Synthesizing Units; mitochondria-cytosol interactions 2005 Stochastic formulations for DEB pop. dynamics with Johan Grasman & Bob Kooi; Entropy of living individuals with Tania Sousa 2006 Isotope dynamics 2007 Type M-acceleration of metabolism with Laure Pecquerie 2008 Start writing of DEB3 and of add_my_pet; mergeability of reserve dyn. with Tania Sousa 2009 Reserve dynamics as consequence of weak homeostasis; evol. of central metabolism 2010 Topology of allocation schemes with Dina Lika 2011 Type R-acceleration of maturation with Starrlight Augustine; interactions between photo- synthesis, -respiration & -inhibition 2012 Bijection between data- and parameter space; quantification of supply-demand spectra 2013 Waste-to-hurry 2014 NECs depend on specific somatic maintenance 2015 New set up add_my_pet by curators

Evolution of DEB systems variable structure composition strong homeostasis for structure delay of use of internal substrates increase of maintenance costs internalisation of maintenance as demand process installation of maturation program strong homeostasis for reserve reproduction juvenile  embryo + adult Kooijman & Troost 2007 Biol Rev, 82, specialization of structure 7 8 animals 6 prokaryotes 9 plants

Evolution of central metabolism i = inverse ACS = acetyl-CoA Synthase pathway PP = Pentose Phosphate cycle TCA = TriCarboxylic Acid cycle RC = Respiratory Chain Gly = Glycolysis Kooijman & Hengeveld 2005 Current Themes in Theor Biol Springer in prokaryotes (= bacteria) 3.8 Ga2.7 Ga

Acknowledgements Jean-Christophe Poggiale + crew Symposium lectures + posterers Course lecturers/helpers, especially curators Truus Meijer Dept Theoretical Biology Bob Kooi, Tjalling Jager, Jaap vand der Meer 50 PhD’s Colleagues Roger Nisbet, Hans Metz, Odo Diekmann Curators: Dina Lika, Starrlight Augustine, Laure Pecquerie, Goncalo Marques Lisbon group, Tiago Domingos, Tania Sousa, Goncalo Marques, Carlos Teixeira AQUAdeb: Marriane Alunno-Bruscia, Cedric Bacher, Fred Jean, Laure, Jonathan Mike Kearney, Peter Westbroek, Rob Hengeveld, Seb Levebvre Tutors: Evert Meelis, Dick Brandt All who interacted with

Farewell 30 years Theoretical Biology Amsterdam, 8 May 2015 national farewell lecture DEB theory: where fascination meets profession Marseille, 30 April 2015 international farewell lecture Theoretical Biology, a specialisation in integration Amsterdam, 18 June 1987 inaugural lecture