DEB theory micro-lecturesBas Kooijman

Dept theoretical biologyVrije Universiteit Amsterdam

Bas@bio.vu.nlhttp://www.bio.vu.nl/thb

DEB3 statistics

01 02 03 04 05 06 07 08 09 10 11 tot chapters

22 54 34 68 30 42 28 48 46 44 8 423 Pages (xvi+492)

3 59 43 29 32 55 85 9 50 0 0 365 Numbered equations

3 5 4 3 2 0 0 3 6 0 2 28 Numbered tables

8 19 11 30 12 16 25 15 17 11 2 163 Numbered figures

4 11 2 23 5 12 8 10 7 0 0 82 Fits

0 1 0 3 1 2 9 2 8 2 1 29 Simulations

0 1 0 0 0 2 0 0 1 0 0 4 Data

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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)

DEB tele course 2011http://www.bio.vu.nl/thb/deb/

Free of financial costs; some 200 h effort investment

Program for 2011: Feb/Mar general theory in tele-mode April 8 day course in Lisbon April 3 day symposium in Lisbon

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

Organizers: thank you for the invitation

Course materialCore 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• papersDownloadable from

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

Assumed to be known

Methods in Theoretical Biology http://www.bio.vu.nl/thb/course/tb

This is a 80-page document with methods/concepts that frequently occur in theoretical biology

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

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/deblab/ (free download site)

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

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.

Research strategy1) 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 provideaccess to species-specific (or case-specific) modifications

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

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.

molecule

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Space-time scales

When changing the space-time scale, new processes will become important other will become less importantThis can be used to simplify models, by coupling space-time scalesComplex models are required for small time and big space scales and vvModels with many variables & parameters hardly contribute to insight

Each process has its characteristic domain of space-time scales

Focus on individuals

• population dynamics is derived from properties of individuals + interactions between them

• evolution according to Darwin: variation between individuals + selection

• material and energy balances: most easy for individuals

• individuals are the survival machines of life

Energy Budgets

Basic processes• Feeding• Digestion• Storing• Growth• Maturing• Maintenance• Reproduction• Product formation• Aging

All have ecological implicationsAll interact during the life cycle

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

DEB – ontogeny - IBM1980

1990

2000

Daphnia

ISO/OECD

von Foerster

molecularorganisation

DEB 1

DEB 2

DEBtoxNECs

embryosbody size

scaling

morphdynamicsindirect

calorimetry

food chains

SynthesizingUnits

multivarplants

adaptationtumour

induction

epidemiolapplications

bifurcationanalysis

Globalbif-analysis

integralformulations

adaptive dynamics

ecosystem self-orginazation

numericalmethods

symbioses

ecosystemdynamicsorgan

function

aging

micro’s

DEB 32010

ecotoxapplication

mixtures

QSARs evolutionecosystem

effects

timedependence

par estimationentropy

production

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

Notation 1

Indices for compounds

Indices for transformations

GeneralNotation 2

Notation 3Notice 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 structureE as symbol stands for energy, and without index for energy in reserve, as index stands for the compound reserveC,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

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 together10 Evolution11 Evaluation