Lecturer: Bas Kooijman
Affiliation: Dept Theoretical Biology, VU University Amsterdam
Workshop: DEB course 2017
Site: Tromso
Date: 2017/05/23
Title: Alternative approaches to modelling metabolism

Summary:

Metabolism is the set of chemical transformations in living cells to maintain and propagate life. Life originated as prokaryotes, so their metabolism might reveal aspects of metabolic organisation that is at basic to metabolism in general. I briefly discuss a possible evolutionary scenario for the evolution of central metabolism and the metabolic organisation of eukaryotes. 

Models for metabolism can generally be classified as the biochemical (bottom-up) approach, where a (small) number of particular chemical compounds are followed, and the pool (top-down) approach, where pools of metabolites are followed, which do not change in composition (strong homeostasis). Both approaches have strengths and weaknesses. Mixtures of both approaches suffer from the problem of the huge range in time and spatial scales even for unicellulars. An intermediate one, however, which deals with the a few interacting biochemical modules might possibly link both approaches and serve as communication channel.

Among the pool models, single pool (called "biomass") models are most frequently used, and especially what became known as production (or scope for growth) models. Losses of acquired resources are first subtracted from inputs and the remaining part is allocated to growth and/or reproduction. This approach will be compared with assimilation models, of which the DEB model is an example. The interpretation of respiration, which is generally seen as a quantification of metabolic rate, and the use of allometric functions will be discussed in the context of all possible internal organisation schemes.

This type of presentation cannot be done without my views on the various alternatives. I don't ask you to agree with my views, but invite you to think about the arguments that will be presented.

Background material:

M. Kearney, S. J. Simpson, D. Raubenheimer, B. Helmuth. Modelling the ecological niche from functional traits. Philosophical Transactions of the Royal Society of London B: Biological Sciences 365: 3469-3483, 2010

S. A. L. M. Kooijman. Dynamic Energy Budget theory for metabolic organisation. Cambridge University Press, 2010; Chapters 10 and 11

S. A. L. M. Kooijman and R. Hengeveld. The symbiontic nature of metabolic evolution. In T. A. C. Reydon and L. Hemerik, editors, Current Themes in Theoretical Biology: A Dutch perspective., pages 159-202. Springer, Dordrecht, 2005

S. A. L. M. Kooijman and L. A. Segel. How growth affects the fate of cellular substrates. Bull. Math. Biol., 67:57 - 77, 2005

S. A. L. M. Kooijman and T. A. Troost. Quantitative steps in the evolution of metabolic organisation as specified by the dynamic energy budget theory. Biol. Reviews, 82:1-30, 2007

K. Lika and S. A. L. M. Kooijman. The comparative topology of energy allocation in budget models. J. Sea Res., 66:381-391, 2011