Photosynthesis in silico. Understanding complexity from molecules to ecosystems

Understanding photosynthetic complexity is a big task, especially when the range is from molecules to ecosystems and the means of advancing it is in the form of mathematical analyses, including simulation models and flux-control analysis. However, this collection of review chapters achieves its aims extremely well, helping to summarize and collate the literature, thus smoothing the path to enlightenment. Biology, and the process of photosynthesis as a central part of it, is characterized by complexity. That has long been evident and is more apparent now than ever. Over the last century and with increasing speed, the physical and molecular bases of energy transduction by the photosynthetic light reactions and their role in production of NADPH and of ATP have been clarified. The nature of carbon dioxide assimilation in the C3 form and the C4 and CAM variants have been largely explained, including how they are driven by the energy transduction processes. These have been integrated into a detailed understanding of the physiological processes of CO2 assimilation of cells and leaves. This has informed and advanced analysis of larger-scale ecological processes, such as biomass production of different types of vegetation, even those on a geological scale. Understanding of plant biology is centred on photosynthesis. The key to this rapid progress has been analysis of events at different scales of complexity in space and time. Very early appreciation of CO2 assimilation by whole organisms or organs, excited curiosity: what were the causes? ‘Reductionism’ supplied the answers, but only in part. Understanding the integration of the parts into the whole became a challenge. Schemes of metabolic pathways showing their interactions provided qualitative integration, but it became apparent that organisms differed in mechanisms. Also, the environment in which photosynthesis occurs is extremely complex: temperature, light, humidity of the atmosphere, and water and mineral content of soils, all varying in amount and over time in extremely dynamic, often quite uncoordinated ways. The reductionist approach could not supply the methods or answers to obtaining a full, quantitative, understanding of the processes. Mathematical summaries of physiological (CO2 and light-response curves of leaves) processes and biochemical factors (enzyme kinetics) have long provided the best (perhaps – but not a full) basis for understanding. It was with the rise of computing power that simulation showed its power as the tool for integration. This large and important book achieves the aims inherent in the title: it does advance understanding, but readers must invest sufficient time and energy for the scale covered is considerable, and it is done in great depth. The twenty well-selected and edited chapters are written by 43 authors from 15 countries spanning the globe. The book is divided into five parts. Part I (two chapters) considers general problems of modelling with emphasis on standards and software (e.g. ‘Systems Biology Markup Language’), structures and mathematics, annotation (e.g. ‘Minimum Information Requested in the Annotation of Biochemical Models’) plus linking models of specific processes together, and also to data. Part II (two chapters) considers light-harvesting and primary charge separation in photosystems and events in the antenna. Part III (four chapters) summarizes modelling of electron transport and chlorophyll fluorescence. Part IV is a substantial section (seven chapters) on integrated modelling of light and dark reactions, starting with the classical biochemical model of C3 photosynthesis (and here the seminal role of von Caemmerer, Farquhar and Berry in the topic over almost three decades is summarized by them), with other chapters analysing temperature effects, Rubisco reactions, carbon and nitrogen metabolism, and C4 CO2-concentrating mechanisms. Use of flux-control analysis in understanding the reactions limiting photosynthesis of leaves ends this part. Part V (five chapters) takes the analysis from leaves to canopies and to the globe. Here an applied aspect is considered: can altering Rubisco increase carbon gain? The last two chapters consider how photosynthesis fits in ecosystem and global-scale models. As a detailed intellectual exercise in understanding complex systems, this book must be highly regarded. Perhaps, because the individual chapters are technical and often formidable in presentation, many potential readers will be put off: that would be a pity. Readership (largely postgraduate research and above) should not be restricted to ‘whole-systems’ biologists (or those of a mathematical bent) – molecular biologists specifically would benefit. However, the lack of any reference to the genetic basis of the systems considered in the book is a major limitation. Perhaps it is too early for modelling the regulation of the processes in gene expression – with all the feed-back and feed-forward processes involved – leading to the formation of the photosynthetic system. Given that this is a major research focus currently there is clearly scope for another large tome in this series (this book is volume 29 in Springer's ‘Advances in Photosynthesis and Respiration’ series). Irrespective, this book is well presented and illustrated (but the colour plates would have been better placed in the text – given the price of the volume is this a saving?), the literature cited is extremely valuable, wide-ranging and current. I can only recommend that this book is widely used by all who aspire to understand quantification of photosynthesis at the cell, tissue and organ scale. It analyses in great detail how the sub-parts and processes are regulated and integrated into the whole, and shows how these can be used at the wider scale to understand global events.