DEB theory: where fascination meets profession

Bas KooijmanDept theoretical biology

Vrije Universiteit AmsterdamBas.Kooijman@vu.nl

http://www.bio.vu.nl/thb

Farewell address as Professor at VU Universiteit Amsterdam

Luminy2015/04/30

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 modelsAuthor year model

Lavoisier 1780 multiple regression of heat against mineral fluxes

Gompertz 1825 survival probability for ageing

Bergmann 1847 body size increase toward the poles

Arrhenius 1889 temperature dependence of physiological rates

Huxley 1891 allometric growth of body parts

Henri 1902 Michaelis--Menten enzyme kinetics

Blackman 1905 bilinear functional response

Hill 1910 Hill's functional response

Thornton 1917 heat dissipation

Pűtter 1920 von Bertalanffy growth of individuals

Pearl 1927 logistic population growth

Fisher & Tippitt 1928 Weibull ageing

Kleiber 1932 respiration scales with body weight^3/ 4

Author year model

Mayneord 1932 cube root growth of tumours

Monod 1942 growth of bacterial populations

Emerson 1950 cube root growth of bacterial colonies

Huggett & Widdas 1951 foetal growth

Weibull 1951 survival probability for ageing

Best 1955 diffusion limitation of uptake

Smith 1957 embryonic respiration

Leudeking & Piret 1959 microbial product formation

Holling 1959 hyperbolic functional response

Marr & Pirt 1962 maintenance in yields of biomass

Droop 1973 reserve (cell quota) dynamics

Rahn & Ar 1974 water loss in bird eggs

Hungate 1975 digestion

Beer & Anderson 1997 development of salmonid embryos

Embryonic development

time, d

wei

ght,

g

O2 c

onsu

mpt

ion,

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

O2 consum

ption,

l/h

Inter-speciesIntra-species

0.0226 L2 + 0.0185 L3

0.0516 L2.44

2 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 = wC CO2-production + wO O2-consumption + wN N-waste production

DEB-explanation:Mass and heat fluxes = wA assimilation + wD dissipation + wG growthApplies to CO2, O2, N-waste, heat, food, faeces, …

For V1-morphs: dissipation maintenance

Interactions of substrates

Kooijman, 2001Phil Trans R Soc B356: 331-349

Supply-demand spectrum

Supply-demand spectrum

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

DEB calender1977 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 systemsvariable structure

composition

strong homeostasisfor structure

delay of use ofinternal substrates

increase ofmaintenance costs

internalisation of maintenance asdemand process

installation ofmaturation program

strong homeostasisfor reserve

reproductionjuvenile embryo + adult

Kooijman & Troost 2007 Biol Rev, 82, 1-30

54321

specialization of structure

7

8

an

ima

ls

6

pro

ka

ryo

tes

9plants

Evolution of central metabolism

i = inverseACS = acetyl-CoA Synthase pathway PP = Pentose Phosphate cycleTCA = TriCarboxylic Acid cycle

RC = Respiratory Chain Gly = Glycolysis Kooijman & Hengeveld 2005

Current Themes in Theor BiolSpringer

in prokaryotes (= bacteria)3.8 Ga 2.7 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