1. DEB theoryDEB theory micro-lectures Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam Bas@bio.vu.nl http://www.bio.vu.nl/thb

2. DEB3 statistics 0102030405060708091011totchapters 225434683042284846448423Pages (xvi+492) 359432932558595000365Numbered equations 3543200360228Numbered tables 81911301216251517112163Numbered figures 41122351281070082Fits 0103129282129Simulations 010002001004Data Basic concepts Standard DEB Energy & metab. Univariate DEBMultivariate DEBEffects of comp. ExtensionsCo-variation Living together Evolution Evaluation Short title

3. 30 new features in DEB3 Improved text organisation/presentation New set of primary parameters Maturity as fundamental state variable Emphasis on homeostasis, incl evolution Mechanism reserve dynamics/merging New chapter on evolution Parameter estimation in steps Isotope dynamics Thermodynamic aspects extended Aging extended (includes demand syst.) New patterns in par-values/QSARs,temp SU theory extended: shrinking, adaptation, social interaction, co-metab Static/dynamic generalisation κ-rule Trajectory reconstruction (reprod/otolith) Separation of cells in early embryos Handshaking in chains of SUs Organnelle-cytosol interactions Metamorphosis Reproduction-buffer handling rules Isomorphs as V0-morphs Flocculated growth Otolith growth Pseudo-faeces production Photo-inhibition Mother-foetus interactions Changes in composition during starving Extra-cellular digestion Hormesis Film models Effects of mixtures extended (NECs)

4. DEB tele course 2015 http://www.bio.vu.nl/thb/deb/ Free of financial costs; Some 108 or 216 h effort investment Program for 2015: Feb/Mar general theory (5w) April symposium in Marseille (F) (8d +3 d) Target audience: PhD students We encourage participation in groups who organize local meetings weekly Software package DEBtool for Octave/ Matlab freely downloadable Slides of this presentation are downloadable from http://www.bio.vu.nl/thb/users/bas/lectures/ Cambridge Univ Press 2009 Audience : thank you for your attention

5. Course material Core material DEB book comments/ errata/ summary of concepts DEBtool (software) add_my_pet micro-lectures basic methods in Theor Biol survey of organisms Supplementary quizzes exercises (+ answers) essays papers Downloadable from http://www.bio.vu.nl/thb/deb/

6. Assumed to be known Methods in Theoretical Biology http://www.bio.vu.nl/thb/course/tb 80-page document with methods/concepts that frequently occur in theoretical biology

7. Web facilities for DEB theory electronic laboratory freely downloadable software DEBtool add_my_pet data collection supporting material Course (BlackBoard powered) on DEB theory 5 weeks fundamental part in tele-mode 8 days practical part in classroom-mode in Lisbon 2011 3 days symposium in Lisbon 2011 downloadable papers http://www.bio.vu.nl/thb/deb

8. Electronic DEB laboratory DEBtool for research applications open source (Octave, Matlab) covers full range of DEB research (fundamental + applied) advanced regression routines for simultaneous model fitting add_my_pet data collection for wide variety of species pdf with background information Species.xls with overview pars_my_pet scripts to run implied properties mydata_my_pet scripts to estimate parameters predict_my_pet routines to compute expected values http://www.bio.vu.nl/thb/deb/deblabhttp://www.bio.vu.nl/thb/deb/deblab/ (free download site)

9. Dynamic Energy Budget theory consists of a set of consistent and coherent assumptions uses framework of general systems theory links levels of organization scales in space and time: scale separation quantitative; first principles only equivalent of theoretical physics interplay between biology, mathematics, physics, chemistry, earth system sciences fundamental to biology; many practical applications for metabolic organization

10. Dynamic Energy Budget theory Question : Is it possible to do biology physical style, i.e. on a formal basis, no exceptions? Answer : Try and see for a core topic in biology: metabolic organisation. Question : The literature on microbial, plant and animal physiology hardly refers to each other; how can we achieve generality? Answer : Ignore existing literature, start afresh after having read all; See what all organisms have in common. Question : Metabolic organisation has many space-time levels; how do they interact? Answer : Levels have local coherence, not global; keep models simple using this, starting with individuals as dynamic systems.

11. Research strategy 1) use general physical-chemical principles to develop an educated quantitative expectation for the eco-physiological behaviour of a generalized species 2) estimate parameters for any specific case compare the values with expectations from scaling relationships deviations reveal specific evolutionary adaptations 3) study deviations from model expectations learn about the physical-chemical details that matter in this case but had to be ignored because they not always apply Deviations from a detailed generalized expectation provide access to species-specific (or case-specific) modifications

12. Some DEB pillars life cycle perspective of individual as primary target embryo, juvenile, adult (levels in metabolic organization) life as coupled chemical transformations (reserve & structure) time, energy, entropy & mass balances surface area/ volume relationships (spatial structure & transport) homeostasis (stoichiometric constraints via Synthesizing Units) syntrophy (basis for symbioses, evolutionary perspective) intensive/extensive parameters: body size scaling

13. Structure of DEB theory DEB theory consists of a set of consistent assumptions Replacement of assumptions easily gives inconsistencies Many possible extensions to more complex theories Few (or no) simplifications without damage to performance Basic aim to find the simplest organisation principles for metabolism on which all life is based to understand observations on actual performance of life as variations on this common theme.

14. molecule cell individual population ecosystem system earth time space Space-time scales When changing the space-time scale, new processes will become important other will become less important This can be used to simplify models, by coupling space-time scales Complex models are required for small time and big space scales and vv Models with many variables & parameters hardly contribute to insight Each process has its characteristic domain of space-time scales

15. 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

16. Energy Budgets Processes feeding digestion storing growth maturation maintenance reproduction product formation aging Life history events zero: start of development birth: start of feeding start of acceleration metamorphosis: end of acceleration puberty: end of maturation start of reproduction Life stages embryo juvenile adult molecule organ individual ecosystem system earth Fluxes organics food, faeces, biomass minerals CO 2, H 2 O, O 2, NH 3 products wood, shells, moults heat entropy isotopes

17. Historical roots Aug 1979 Two questions: How should we quantify effects of chemical compounds on reproduction of daphnids? reproduction energy budget How bad is it for the environment if daphnid reproduction is a bit reduced due to toxic stress? individual population ecosystem prediction outside observed range: first principles

18. DEB – ontogeny - IBM 1980 1990 2000 Daphnia ISO/OECD von Foerster molecular organisation DEB 1 DEB 2 DEBtox NECs embryos body size scaling morph dynamics indirect calorimetry food chains Synthesizing Units multivar plants adaptation tumour induction epidemiol applications bifurcation analysis Global bif-analysis integral formulations adaptive dynamics ecosystem self-orginazation numerical methods symbioses ecosystem dynamics organ function aging micros DEB 3 2010 ecotox application mixtures QSARs evolution ecosystem effects time dependence par estimation entropy production

19. Shift in emphasis From concrete questions about individuals quantification of properties of individuals + consequences To metabolic organisation at various levels relationships between levels of organisation

20. Future DEB research Add_my_pet: taxon-specific patterns application in evolution, ecology, conservation, technology More-reserve/structure systems: nutrition, plants, behavioural ecology Molecular level interaction biochemical modules on basis of mutual syntrophy Ecosystem level canonical community, body size spectra

21. Notation 1 http://www.bio.vu.nl/thb/research/bib/Kooy2010_n.pdf

22. Indices for compounds Indices for transformations General Notation 2

23. Notation 3 Notice that some symbols have more than one meaning: V as symbol stands for volume, and without index for volume of structure, as index stands for the compound structure E as symbol stands for energy, and without index for energy in reserve, as index stands for the compound reserve C,H,O,N as indices stand for mineral compounds as well as chemical elements the context defines the meaning Dots are used to distinguish rates from states (dimension check) allow scaling of time without the need to introduce new symbols if time is scaled to a dimensionless quantity, the dot is removed Numbers in slide titles refer to sections in DEB book for more info

24. Dynamic Energy Budget theory 1 Basic ConceptsBasic Concepts 2 Standard DEB modelStandard DEB model 3 MetabolismMetabolism 4 Univariate DEB modelsUnivariate DEB models 5 Multivariate DEB modelsMultivariate DEB models 6 Effects of compoundsEffects of compounds 7 Extensions of DEB modelsExtensions of DEB models 8 Co-variation of par valuesCo-variation of par values 9 Living togetherLiving together 10 EvolutionEvolution 11 EvaluationEvaluation