DEB theory micro-lectures

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DEB theory micro-lectures
Bas Kooijman Dept theoretical biology Vrije
Universiteit Amsterdam Bas_at_bio.vu.nl http//www.bi
o.vu.nl/thb
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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 (xvi492)
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
Energy metab.
Multivariate DEB
Effects of comp.
Univariate DEB
Basic concepts
Living together
Standard DEB
Co-variation
Extensions
Short title
Evaluation
Evolution
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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 ?-rule
• Trajectory reconstruction (reprod/otolith)
• Separation of cells in early embryos

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DEB tele course 2011
http//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/user
s/bas/lectures/
Cambridge Univ Press 2009
Audience thank you for your
attention Organizers thank you for the
invitation
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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/
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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
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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

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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
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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

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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.

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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
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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

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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.

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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
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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

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Energy Budgets

• Basic processes
• Feeding
• Digestion
• Storing
• Growth
• Maturing
• Maintenance
• Reproduction
• Product formation
• Aging
• All have ecological implications
• All interact during the life cycle

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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

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

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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