Details of the programme
Note that we will provide a Reader and a booklet with papers for the Working Groups for all participants, to be handed out on arrival. The Reader will contain copies of the relevant material for all lectures.
Lecture contents per lecturer
 Bas Kooijman
Dynamic Energy Budget theory for the
metabolic organization of life at the various levels: from molecules
to ecosystems

I will concentrate
on trophic interrelationships between organisms in a community that do
account for all types of exchanges of compounds (nutrients, and
organic matter), and include the molecular basis for these couplings;
cells as symbiontic communities. The basic theory is discussed in the
DEBbook:
 S. A. L. M. Kooijman: Dynamic Energy and Mass Budgets in
Biological Systems. Cambridge University Press.
This substantially
reworked and enlarged second edition will appear in Feb 2000
(paperback, approx 40 euro). A postscript preprint is available, without the long inclusions.
Lectures:
 The Basic model: 1 substrate, 1 reserve, 1 structure; conceptual
backgrounds, relationship with static budgets. Structural homeostasis.
 Chapter 2 of the DEBbook
 Chapter 3 of the DEBbook
 Massenergy coupling; indirect calorimetry; Body Size scaling
relationships
 Chapter 4 of the DEBbook
 Chapter 8 of the DEBbook
 Multivariate extensions of the basic DEB model on the basis of
Synthesizing Units: several substrates, several reserves, two
structures. Photosynthesis, simultaneous limitations, plants.
 Chapter 2 and 5 of the DEBbook
 Syntrophy, symbiosis, mixotrophs in a closed
environment, canonical communities. Mass and energy balances, the flux
matrix.
 Chapter 9 of the DEBbook
 Applications of the theory in
ecotoxicology, biodegradation, tumor biology, sewage treatment,
production optimazation, global change.
 Chapter 6 of the DEBbook
 S. A. L. M. Kooijman and J. J. M. Bedaux. The analysis of
aquatic toxicity data. VU University Press (1996). ISBN 905383477X, 160
pp. and floppy DEBtox; downloadable from http://www.bio.vu.nl/thb/deb
 Rob de Boer
Models of the Immune system

Lectures:
 Diversity
 why is the lymphocyte repertoire so diverse?
 probabilistic and simulation models
 J. A. M. Borghans, A. J. Noest, R. J. De Boer: How specific
should immunological memory be? J. Immunol. 163 (1999), 569575.
 R. J. De Boer, A. S. Perelson: How diverse should the
immune system be? Proc. R. Soc. Lond., B, Biol. Sci. 252
(1993), 171175.
 Competition and Repertoires
 lymphocyte repertoire is ecosystem of competing populations
 derive appropriate models, see the resource competition, and
compare to data
 R. J. De Boer, A. S. Perelson: Competitive control of
the selfrenewing T cell repertoire. Int. Immunol. 9 (1997),
779790.
 R. J. De Boer, A. S. Perelson: Towards a general function
describing T cell proliferation. J. Theor. Biol. 175 (1995),
567576.
 T cell vaccination  regulatory interactions  phase plane
methods
 J. A. M. Borghans, R. J. De Boer: A minimal model
for Tcell vaccination. Proc. R. Soc. Lond., B, Biol. Sci. 259
(1995), 173178.
 Telomere shortening and T cell dynamics
 derive 2dimensional model for ndimensional model
 see how it helps to interpret data
 R. J. De Boer, A. J. Noest: T cell renewal rates,
telomerase, and telomere length shortening. J. Immunol. 160
(1998) 58325837.
 MHC diversity
 population based polymorphism of transplatation antigens
 simulation by means of a genetic algorithm
 Manuscript in prep. with a deadline of 15 October 1999.
 Horst Thieme
Structured population models

Lectures:
 The most rudimentary population model with a juvenile and adult
stage(e.g., for amphibians). Hopf bifurcation of periodic
solutions. A simple population model for the Arizonan tiger
salamander.
 Population models with more stages. Persistence and invasion
theory. The role of cannibalism in Arizonan tiger salamanders.
 Discretely structured metapopulation models (with small
subpopulations)
 Transition to continuous structure variables. The Pease/Inaba
influenza model. Measures as state space.
 More general continuously structured population models.
If I find that this is too much material, I will skip (3) and spread
the other topics out. An permeant mathematical theme for (2) to (5)
will be persistence theory (conveniently formulated in terms of
semiflows [dynamical systems]).
 H.R. Thieme: Persistence under relaxed pointdissipativity (with
applications to an endemic model). SIAM J. Math. Anal. 24 (1993),
407435.
 H.R. Thieme: Uniform weak implies uniform strong persistence
also for nonautonomous semiflows. Proc. Amer. Math. Soc. 127 (1999),
23952403.
 H.R. Thieme: Uniform persistence and permanence for nonautonomous
semiflows in population biology, 41 pages (submitted).
For the influenza model:
 C.M. Pease: An evolutionary epidemiological mechanism, with applications
to type A influenza. Theor. Pop. Biol. 31 (1987), 422452.
 H. Inaba: Mathematical analysis for an evolutionary epidemic model.
in Mathematical Models in Medical and Health Sciences
(M.A. Horn, G. Simonett and G.F. Webb; eds.) Vanderbilt Press 1998,
213236.
On physiologically structured populations:
 J.A.J. Metz, O. Diekmann: The Dynamics of Physiologically Structured
Populations. Lecture Notes in Biomathematics 68. Springer 1986.
 O. Diekmann, M. Gyllenberg, J.A.J. Metz, H.R. Thieme:
On the formulation and analysis of general deterministic structured
population models. I. Linear theory. J. Math. Biol. (1998), 349388.
On Metapopulations:
 M. Gyllenberg, I. Hanski, A. Hastings: Structured Metapopulation Models.
In Metapopulation Biology. Ecology, Genetics and Evolution (I. A. Hanski, M. E. Gilpin; eds). Academic Press 1996, Chapter 5.
 A.T. Smith, M.E. Gilpin: Spatially correlated dynamics in a
pika metapopulation. In Metapopulation Biology. Ecology,
Genetics and Evolution (I. A. Hanski, M. E. Gilpin; eds).
Academic Press 1996, 407428.
Others:

O. Diekmann: The many facets of evolutionary dynamics. Preprint.
 Fred Adler
Ecology and evolution

I will discuss the implications of interactions between neighbors for
the evolution of resource use strategies. Models of evolution
of cooperation require local interactions of some sort (within
groups or families) and some temporal duration of the interaction
(as in titfortat models). For sedentary organisms, longterm local
interactions with neighbors are unavoidable, and provide a place where
"cooperative" strategies for resource use might evolve. My goal is
to outline an empirically testable resourcebased approach to evolution
of cooperation.
Lectures:
 Classical group selection models and an extension to include simple
resource dynamics.
 D. S. Wilson: A theory of group selection. Proc. Nat. Acad. Sci.
72 (1975), 143146.
 M. Slatkin and D. S. Wilson: Coevolution in structured demes.
Proc. Nat. Acad. Sci. 76 (1979), 20842087.
 Population viscosity and kin selection 
how do the details of dispersal affect evolution?
 D. S. Wilson, G. B. Pollock and L. A. Dugatkin:
Can altruism evolve in purely viscous populations?
Evolutionary Ecology 6 (1992), 331341.
 P. D. Taylor:
Altruism in viscous populations: an inclusive fitness model.
Evolutionary Ecology 6 (1992), 352356.
 Models of competition for space.
 M. Slatkin and D. J. Anderson: A model of competition for space.
Ecology 65 (1984), 18401845.
 S. W. Pacala and J. Weiner: Effects of competitive asymmetry on
local density models of plant interference. Journal of Theoretical
Biology 149 (1991), 165179.
 F. R. Adler: A model of selfthinning through local competition.
Proc. Nat. Acad. Sci. 93 (1996), 99809984.
 Integrating models of competition for space with foraging and life
history theory.
 F. R. Adler and D. M. Gordon:
Integrating models of competition for space with the
life history theory of seedharvester ants. (preprint)
 Signalling and information sharing in plants.
 P. Aphalo and C. Ballare: On the importance of information
acquiring systems in plantplant interactions. Functional Ecology
9 (1995), 514.
 J. Schmitt: Is photomorphogeenic shade avoidance adaptive?
Perspectives from population biology. Plant, Cell and Environment
20 (1997), 826830.
 Roger Nisbet
Ecological dynamics

The plan assumes the students have some limited previous exposure to
simple (unstructured) population, and to systems of ordinary
differential equations (including concepts of equilibrium and local
stability). This material is reviewed in lecture 1, but at high speed!
Lectures 2,3, and 4 provide an introduction to the formulation and use
of structured population models. The preceding lectures mainly use
material from the recent book Ecological Dynamics by Bill Gurney and
myself.
Lectures:
 Review of dynamics of unstructured populations. Population
dynamics in an ecological context. Densityindependent growth in
constant and variable environments. Consumerresource interactions
(discrete and continuous time). Competition.
 Chapters 5 and 6 of W. S. C. Gurney and R. M. Nisbet:
Ecological Dynamics, Oxford University Press 1998.
 Formulating structured population models. Parallel
introductions to discrete and continuous representations of
agestructured populations. Sizestructured populations.
 Chapter 8 of W. S. C. Gurney and R. M. Nisbet: Ecological
Dynamics, Oxford University Press 1998.
 Biomassbased models. Simplifying assumptions that lead to
biomass dynamics in terms of the ordinarydifferential equations
discussed in lecture 1. Case study (Daphnia population dynamics in
lab and field) illustrating the predictive power and limitations of
simple population models.
 Parts of chapters 5 and 6 of W. S. C. Gurney and R. M. Nisbet:
Ecological Dynamics, Oxford University Press 1998.
 Stagestructured models. An introduction to the use of
delaydifferential equations to describe structured populations.
 R. M. Nisbet: Delay differential equations for structured
populations. In Structured Population Models in Marine,
Terrrestrial, and Freshwater Systems (S. Tuljapurkar
and H. Caswell; eds). Chapman and Hall. New York. 1997, 89118.
 Inferring biological mechanism from population data.
Combining statistical and mechanistic modeling approaches to
determine mechanisms of population regulation from time series.
Working group papers
 S. A. L. M. Kooijman: The Synthesizing Unit as model for the
stoichiometric fusion and branching of metabolic fluxes.
Biophysical Chemistry 73 (1998), 179188.
 S. A. L. M. Kooijman and R. M. Nisbet: How light and nutrients
affect life in a closed bottle. In Thermodynamics and ecology
(S. E. Jorgensen; ed). CRCPress, to appear.
 J. A. M. Borghans, R. De Boer, L. A. Segel: Extending the quasisteady
state approximation by changing variables. Bulletin of Mathematical Biology
58 (1996), 4363.
 J. P. Cheek, J. P. Collins: Effect of food and density on development
of typical and cannibalistic salamander larvae in Ambystoma
tigrinum nebulosum. Amer. Zool. 23 (1983), 7784.
 T. J. Maret, J. P. Collins: Individual responses to population size
structure: the role of size variation in controlling expression
of a trophic polymorphism. Oecologia 100 (1994), 279285.
 T. J. Maret, J. P. Collins: Effect of prey vulnerability on population
size structure of a gapelimited predator. Ecology 77 (1996), 320324.
 A. Grafen: Biological signals as handicaps. Journal of Theoretical
Biology 144 (1990), 517546.

 B. E. Kendall, C. J. Briggs, W. M. Murdoch, P. T. Turchin,
S. P. Ellner, E. McCauley, R. M. Nisbet, S. N. Wood:
Why do populations cycle? A synthesis of statistical and
mechanistic modeling approaches. Ecology 80 (1999), 17891805.

A. L. Lloyd, R. M. May: Synchronicity, chaos and population cycles:
spatial coherence in an uncertain world. TREE 14 (1999), 417418.
 M. Pascual, S. A. Levin: Spatial scaling in a benthic population model
with densitydepentdent disturbance. Theoretical Population Biology 56 (1999),
106122.