Physiology

  • Why physiology? Photosynthetic and respiratory physiology are studied across an amazing range of scales, from the molecular to the global. At the molecular end of the spectrum, the focus is on working out the biophysical and biochemical details of each component of the photosynthetic system. At the global end of the spectrum, the focus is on assessing the overall impacts of aggregate fluxes on the Earth’s biogeochemical cycles and climate system. My work leverages understanding of physiological mechanisms for analysis of the aggregated physiological fluxes, connecting these two ends of the spectrum.

  • What’s in this section? In the Physiology section, you’ll find a collection of materials that I’ve developed for teaching about photosynthesis, as well as resources related to the new photosynthesis model that I formulated, including references, code, and links to various kinds of media coverage.

  • How is this section organized? These materials are organized in four pages.

    • You are here in Introduction, which introduces the photosynthetic process;

    • C3 pathway then describes the C3 version of the new model;

    • C4 pathway describes the C3, C3-C4, and C4 version of the model; and

    • Synthesis activities describes the USGS/NCAR C4 photosynthesis working group.

  • Getting started: Here’s a slide deck that gives a broad introduction to understanding and modeling photosynthesis in an ecological context - and a preview of how the new model fits in to the picture. It’s from a ~90 minute talk I gave in July 2022 at the 13th Annual Fluxcourse. The Fluxcourse is a two week early-career workshop focused on the foundations of land-atmosphere flux measurement, modeling, and synthesis that is held annually at the University of Colorado Mountain Research Station at Niwot Ridge, CO, USA. The course organizers Kim Novick (Indiana University) and Dave Moore (University of Arizona) invited me to give this as the introductory lecture. You are welcome to re-use the slides, and you can download them here.

  • FAQs: The drop-down menu here has answers to the most frequently asked questions about the scope of the model, what makes it unique, what inspired its development, and how to get started working with it.

  • It describes the normal, rapidly-reversible, steady-state responses of photosynthesis to environmental and biochemical drivers.

    It does not represent transient responses to normal conditions, nor does it represent slowly-reversible or irreversible stress responses. However, it does provide a foundation for developing improved approaches to model these phenomena.

  • It’s fully mechanistic, yet still has a simple structure.

    This is a very powerful combination, for two reasons.

    First, it permits the model to be fit to experimental data in a way that can directly test the hypotheses encoded in the model. The previous models that permitted fitting were semi-empirical, and the previous mechanistic models were too complex for fitting.

    Second, it permits the model to be coupled to other models that resolve finer-scale or coarser-scale phenomena. For example, a number of groups are already working to integrate it into land surface models to improve their representation of photosynthesis and fluorescence.

  • The inspiration was the classic model developed by Graham Farquhar, Susanne von Caemmerer, and Joe Berry [Planta 149: 78–90, 1980].

    The strength of the Farquhar et al. model comes from two sources. One is in recognizing that the photosynthetic system is regulated in such a way that it switches abruptly between different limiting states as environmental conditions change. The other is in recognizing that the intricacies of carbon metabolism can be described in a simple yet accurate way by focusing on Rubisco because this enzyme is rate-limiting for steady-state dynamics.

    To develop the new model, I applied analogous logic to formulate a simple and accurate description of the electron transport system. The key was identifying the enzyme that is rate-limiting for steady-state dynamics of the electron transport system: the Cytochrome b6f complex. I discovered that once this boundary condition is defined, it becomes possible to quantify the regulatory processes linking electron transport to carbon metabolism.

  • Yes, definitely!

    The links on this page should get you off to a good start. Be sure to check out the code repositories on GitHub for worked examples. The scripts were originally written in MATLAB. I then made them compatible with Octave, which is free and open source.

    Finally, please feel welcome to reach out at any stage if you want to discuss - see the Contact page.

  • Video: Here’s a recording of a ~15 minute talk I gave in August 2022 at the 18th International Congress on Photosynthesis Research. This produces an overview of the experimental insights, and the resulting conceptual and quantitative model.

  • Acknowledgements: This work developed over a period of about ten years, and I am grateful for the support of many individuals and institutions over this time. In the early phases of the project, I was advised by Chris Field and supported by a NSF Graduate Research Fellowship and a Bing-Mooney Fellowship from Stanford University. The field studies were made possible by collaboration with Eric Slessarev and Claire Kouba, as well as Grand Canyon Youth, the USGS Grand Canyon Monitoring and Research Center, Grand Canyon National Park, The Nature Conservancy of Texas, and the Energy, Minerals, and Natural Resources Department of New Mexico. In the middle phases of the project, I was supported by the University of Arizona and advised by Russ Monson. In the later phases of the project, I was supported by the Carnegie Institution. My mentor Joe Berry has inspired and challenged me throughout.