My vision with respect to future research has not changed in a philosophical sense for a number of years, although I think that I have been more successful over the last 10 years in realizing at least some aspects of this vision. At Carnegie I feel that part of our responsibility is to do things in a somewhat different way relative to what is being done at universities. We have some internal funds that are free of government/project ties, and I feel that such money should be used to explore both the boundaries and interfaces of science. It is not my opinion that we should be in the mainstream, it is more my opinion that we should be trying to create new areas that become mainstream. It is also not my opinion that we should spend a lot of time concentrating on public relations; we should be as critical as possible of what we do and once we are sure of something that could have a broad scientific impact (with strong scientific support behind it), we should make that knowledge more widespread in a somewhat aggressive way.
One major set of interfaces that I view as important for future scientific development are those that span ecology, physiology and molecular biology/genomics. People are crossing these boundaries more and more. I have been pushing in this direction for over 15 years now and still I feel that there is too little with too few people really willing to put in the effort. From what I can see, this orientation requires that individuals make a strong commitment, find the right colleagues, learn the language of the other discipline (at least to an operational extent and preferably more than that). One interface of this type was generated with Olle Bjorkman in a collaboration that demonstrated the importance of the xanthophyll cycle in the dissipation of excess absorbed excitation energy (if plants don't manage there energy properly they basically auto-destruct through extreme oxidation reactions). This work applied strong genetic and molecular tools to probe the ecological question of the management of excess absorbed light energy by plants and algae. We first used algae for our studies because of the ease of manipulation and our ability to screen for mutants with the desired phenotypes. Once we had things under control using algae, we moved to vascular plants. It was the question rather than the system that was important. The knowledge generated by this work could be used for more informed exploration of physiological processes related to the utilization of excitation energy by plants and can even help add detail and a mechanistic underpinning to physiological models that describe primary productivity in certain environments, although I do feel that there is also considerable tailoring of the ways in which the physiology of an organism is shaped by environmental pressures. Some projects currently going on in the laboratory in which we are trying to fuse boundaries between disciplines are briefly given below:
Understanding of the physiology and community structure of hot spring microbial mats, which were probably critical for the early oxygenation of the Earth's atmosphere. In this project Devaki Bhaya and I are working with ecologists/physiologists (David Ward, Montana State University), evolutionary biologists (Fred Cohan, Weseleyan University), genomicists (John Heidelberg, University of Southern California) and computational biologist (Serafim Batzoglou, Stanford University). Some of the interactions in this project have led to important findings concerning the physiological potential of mats, the fluidity of the genomes of the photosynthetic bacteria (e.g. cyanobacteria) in the community and the fuzzy nature of a 'species' and 'ecotype' concepts in such a consortium. The work highlighted for us the fact that the mat itself is really the 'organism' to be understood.
Understanding how photosynthesis goes on in the iron-poor, oligotrophic oceans. This has been a collaboration between my laboratory and both oceanographers (Kevin Arrigo, Stanford) and biophysicists (Francis-Andre Wollman and Gionvanni Finazzi, Paris) to understand how iron might affect photosynthetic processes in the oceans and how that might impact global models of primary productivity. The work showed that both the photosynthetic prokaryotes and at least some of the picoeukaryotes have lower photosystem I (which is an iron rich complex) in the oligotrophic ocean environment, and that as a consequence these organisms may shunt a high proportion of electrons generated by the splitting water to oxygen (regenerating water and also a large ΔpH for energy production). The findings impacts primary productivity in the oceans and predictions generated by models that describe physiological processes in the oceans (we have some questions concerning the ways that some samplings were done for generating those models). Related to this is the finding that the hot spring cyanobacteria have a vast preponderance of photosystem I relative to photosystem II; this is another story of tailoring of the photosynthetic apparatus to a specific environment in which there is the need for a strong coupling of photosynthetic and respiratory electron transport.
Understanding interactions (e.g. symbiotic) among phototrophic and heterotrophic organisms and the impact of those interactions on the environment. The hot spring project has an element of this orientation. This project is focused on interactions between dinoflagellates (an alga called Symbiodinium) and corals (or in this case, a sea anemone called Aiptasia, a model for coral-dinoflagellate interactions). This project is being done in collaboration with John Pringle (Stanford Medical School, Genetics) and Steve Palumbi (Stanford University, Hopkins Marine Station). We had already worked on this system some time ago, showing that the alga has a strong genetic switch when it goes from a free-living organism to an endosymbiont. We hope to address some major ecological questions including why certain coral reefs are dying and which algal strains are most tolerant to environmental change (e.g. increases in temperature) and why. For quite a while I have felt that it is critical that we do more to understand photosynthetic life in the oceans (it is easier to view what is being destroyed in a terrestrial environment, making it easier to initially neglect the oceans) by joining molecular, physiological and ecological approaches.
Another interface that I feel is worth exploring concerns that of biology and engineering (e.g material sciences, nanotechnology). Toward that end we became involved in a high-risk project with a more future-oriented perspective having to do with developing both physical and electrochemical platforms to extract energy from photosynthetic organisms. This work was done in collaboration with Fritz Prinz (Stanford, Chair of Mechanical Engineering) and was supported by GCEP. Over that time we were able to establish platforms for immobilizing individual cells as well as chloroplasts, penetrating them with microelectrodes (tips as small as 0.02 µm) and generating light-dependent oxidation and reduction currents (at the single cell level). Various new types of electrodes were developed over the course of this project (electrodes with different insulating material and electrode surfaces and mounted on an atomic force microscopy head), along with complex platforms to visualize cells (fluorescence and light microscopy), maintain them in a cooled, humid atmosphere, introduce reagents in an automated manner over the course of the experiment, while at the same time being able to manipulate the probe to a precise position relative to the chloroplasts in the cell just before attempting penetration by the electrode.
I hope that these descriptions provide an idea of the types of interfaces and interactions I will explore in the coming years and how such an orientation can have strong impacts on our understanding of biological systems in nature (and the ways in which we are altering those systems).