DEB theory micro-lectures

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

2. DEB3 statistics Energy & metab. Multivariate DEB Effects of comp. Univariate DEB Basic concepts Living together Standard DEB Co-variation Extensions Short title Evaluation Evolution

3. 30 new features in DEB3 • 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) • 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

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 http://www.bio.vu.nl/thb/deb • 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

8. Electronic DEB laboratory http://www.bio.vu.nl/thb/deb/deblab/ (free download site) 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

9. Dynamic Energy Budget theory for metabolic organization • 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

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. system earth space ecosystem population individual cell time molecule Space-time scales Each process has its characteristic domain of 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

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 stages embryo juvenile adult • 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 • Fluxes • organics • food, faeces, biomass • minerals • CO2, H2O, O2, NH3 • products • wood, shells, moults • heat • entropy • isotopes molecule organindividual ecosystemsystem earth

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

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. Notation 2 General Indices for compounds Indices for transformations

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 Concepts 2 Standard DEB model 3 Metabolism 4 Univariate DEB models 5 Multivariate DEB models 6 Effects of compounds 7 Extensions of DEB models 8 Co-variation of par values 9 Living together 10 Evolution 11 Evaluation