Complementary approaches to understanding the plant circadian clock

Circadian clocks are oscillatory genetic networks that help organisms adapt to the 24-hour day/night cycle. The clock of the green alga Ostreococcus tauri is the simplest plant clock discovered so far. Its many advantages as an experimental system facilitate the testing of computational predictions. We present a model of the Ostreococcus clock in the stochastic process algebra Bio-PEPA and exploit its mapping to different analysis techniques, such as ordinary differential equations, stochastic simulation algorithms and model-checking. The small number of molecules reported for this system tests the limits of the continuous approximation underlying differential equations. We investigate the difference between continuous-deterministic and discrete-stochastic approaches. Stochastic simulation and model-checking allow us to formulate new hypotheses on the system behaviour, such as the presence of self-sustained oscillations in single cells under constant light conditions. We investigate how to model the timing of dawn and dusk in the context of model-checking, which we use to compute how the probability distributions of key biochemical species change over time. These show that the relative variation in expression level is smallest at the time of peak expression, making peak time an optimal experimental phase marker. Building on these analyses, we use approaches from evolutionary systems biology to investigate how changes in the rate of mRNA degradation impacts the phase of a key protein likely to affect fitness. We explore how robust this circadian clock is towards such potential mutational changes in its underlying biochemistry. Our work shows that multiple approaches lead to a more complete understanding of the clock

How to make complexity look simple? Conveying ecosystems restoration complexity for socio-economic research and public engagement

Ecosystems degradation represents one of the major global challenges at the present time, threating people’s livelihoods and well-being worldwide. Ecosystem restoration therefore seems no longer an option, but an imperative. Restoration challenges are such that a dialogue has begun on the need to re-shape restoration as a science. A critical aspect of that reshaping process is the acceptance that restoration science and practice needs to be coupled with socio-economic research and public engagement. This inescapably means conveying complex ecosystem’s information in a way that is accessible to the wider public. In this paper we take up this challenge with the ultimate aim of contributing to making a step change in science’s contribution to ecosystems restoration practice. Using peatlands as a paradigmatically complex ecosystem, we put in place a transdisciplinary process to articulate a description of the processes and outcomes of restoration that can be understood widely by the public. We provide evidence of the usefulness of the process and tools in addressing four key challenges relevant to restoration of any complex ecosystem: (1) how to represent restoration outcomes; (2) how to establish a restoration reference; (3) how to cope with varying restoration time-lags and (4) how to define spatial units for restoration. This evidence includes the way the process resulted in the creation of materials that are now being used by restoration practitioners for communication with the public and in other research contexts. Our main contribution is of an epistemological nature: while ecosystem services-based approaches have enhanced the integration of academic disciplines and non-specialist knowledge, this has so far only followed one direction (from the biophysical underpinning to the description of ecosystem services and their appreciation by the public). We propose that it is the mix of approaches and epistemological directions (including from the public to the biophysical parameters) what will make a definitive contribution to restoration practice