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
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
- S. A. L. M. Kooijman: Dynamic Energy and Mass Budgets in
Biological Systems. Cambridge University Press.
reworked and enlarged second edition will appear in Feb 2000
(paperback, approx 40 euro). A postscript preprint is available, without the long inclusions.
- The Basic model: 1 substrate, 1 reserve, 1 structure; conceptual
backgrounds, relationship with static budgets. Structural homeostasis.
- Chapter 2 of the DEB-book
- Chapter 3 of the DEB-book
- Mass-energy coupling; indirect calorimetry; Body Size scaling
- Chapter 4 of the DEB-book
- Chapter 8 of the DEB-book
- 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 DEB-book
- Syntrophy, symbiosis, mixotrophs in a closed
environment, canonical communities. Mass and energy balances, the flux
- Chapter 9 of the DEB-book
- Applications of the theory in
ecotoxicology, biodegradation, tumor biology, sewage treatment,
production optimazation, global change.
- Chapter 6 of the DEB-book
- S. A. L. M. Kooijman and J. J. M. Bedaux. The analysis of
aquatic toxicity data. VU University Press (1996). ISBN 90-5383-477-X, 160
pp. and floppy DEBtox; downloadable from http://www.bio.vu.nl/thb/deb
- Rob de Boer
Models of the Immune system
- 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), 569-575.
- R. J. De Boer, A. S. Perelson: How diverse should the
immune system be? Proc. R. Soc. Lond., B, Biol. Sci. 252
- 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 self-renewing T cell repertoire. Int. Immunol. 9 (1997),
- R. J. De Boer, A. S. Perelson: Towards a general function
describing T cell proliferation. J. Theor. Biol. 175 (1995),
- T cell vaccination - regulatory interactions - phase plane
- J. A. M. Borghans, R. J. De Boer: A minimal model
for T-cell vaccination. Proc. R. Soc. Lond., B, Biol. Sci. 259
- Telomere shortening and T cell dynamics
- derive 2-dimensional model for n-dimensional 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
- 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
- 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
- Population models with more stages. Persistence and invasion
theory. The role of cannibalism in Arizonan tiger salamanders.
- Discretely structured metapopulation models (with small
- 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 point-dissipativity (with
applications to an endemic model). SIAM J. Math. Anal. 24 (1993),
For the influenza model:
- H.R. Thieme: Uniform weak implies uniform strong persistence
also for non-autonomous semiflows. Proc. Amer. Math. Soc. 127 (1999),
- H.R. Thieme: Uniform persistence and permanence for non-autonomous
semiflows in population biology, 41 pages (submitted).
- C.M. Pease: An evolutionary epidemiological mechanism, with applications
to type A influenza. Theor. Pop. Biol. 31 (1987), 422-452.
On physiologically structured populations:
- 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,
- 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), 349-388.
- 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, 407-428.
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 tit-for-tat models). For sedentary organisms, long-term 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 resource-based approach to evolution
- Classical group selection models and an extension to include simple
- D. S. Wilson: A theory of group selection. Proc. Nat. Acad. Sci.
72 (1975), 143-146.
- M. Slatkin and D. S. Wilson: Coevolution in structured demes.
Proc. Nat. Acad. Sci. 76 (1979), 2084-2087.
- 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), 331-341.
- P. D. Taylor:
Altruism in viscous populations: an inclusive fitness model.
Evolutionary Ecology 6 (1992), 352-356.
- Models of competition for space.
- M. Slatkin and D. J. Anderson: A model of competition for space.
Ecology 65 (1984), 1840-1845.
- S. W. Pacala and J. Weiner: Effects of competitive asymmetry on
local density models of plant interference. Journal of Theoretical
Biology 149 (1991), 165-179.
- F. R. Adler: A model of self-thinning through local competition.
Proc. Nat. Acad. Sci. 93 (1996), 9980-9984.
- Integrating models of competition for space with foraging and life
- F. R. Adler and D. M. Gordon:
Integrating models of competition for space with the
life history theory of seed-harvester ants. (preprint)
- Signalling and information sharing in plants.
- P. Aphalo and C. Ballare: On the importance of information
acquiring systems in plant-plant interactions. Functional Ecology
9 (1995), 5-14.
- J. Schmitt: Is photomorphogeenic shade avoidance adaptive?
Perspectives from population biology. Plant, Cell and Environment
20 (1997), 826-830.
- Roger Nisbet
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
- Review of dynamics of unstructured populations. Population
dynamics in an ecological context. Density-independent growth in
constant and variable environments. Consumer-resource 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
age-structured populations. Size-structured populations.
- Chapter 8 of W. S. C. Gurney and R. M. Nisbet: Ecological
Dynamics, Oxford University Press 1998.
- Biomass-based models. Simplifying assumptions that lead to
biomass dynamics in terms of the ordinary-differential 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.
- Stage-structured models. An introduction to the use of
delay-differential 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, 89-118.
- 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), 179-188.
- 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). CRC-Press, to appear.
- J. A. M. Borghans, R. De Boer, L. A. Segel: Extending the quasi-steady
state approximation by changing variables. Bulletin of Mathematical Biology
58 (1996), 43-63.
- 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), 77-84.
- 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), 279-285.
- T. J. Maret, J. P. Collins: Effect of prey vulnerability on population
size structure of a gape-limited predator. Ecology 77 (1996), 320-324.
- A. Grafen: Biological signals as handicaps. Journal of Theoretical
Biology 144 (1990), 517-546.
- 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), 1789-1805.
A. L. Lloyd, R. M. May: Synchronicity, chaos and population cycles:
spatial coherence in an uncertain world. TREE 14 (1999), 417-418.
- M. Pascual, S. A. Levin: Spatial scaling in a benthic population model
with density-depentdent disturbance. Theoretical Population Biology 56 (1999),