By Jathish Ponnu, PhD, Plant Physiology Assistant Features Editor
Prof. Christian Fankhauser is an eminent photobiologist passionate about phototropism and shade avoidance in plants. He works at the Center for Integrative Genomics, University of Lausanne, Switzerland and has served as a Monitoring Editor for Plant Physiology since 2018. Talking with Jathish Ponnu, an Assistant Features Editor for Plant Physiology, Christian provides insight into his life as a scientist, mentor, teacher, and editor and the experiences that influenced him along the way to the job he says he tremendously enjoys every day.
Jathish: You are a renowned scientist in plant biology. I am sure that our readers are eager to know a bit about your background, your childhood, and any particular incidents that made an impression on you to choose a career in science.
Christian: I first have to say that my mother was a teacher and she loved natural sciences. At home, we were always surrounded by a lot of different pet animals, though not particularly exotic. My mother´s family had many exotic animals, including a penguin in Chile, where she grew up. They found it injured on a beach. So, animals were a common theme in my family.
I can think of one particular incident that was quite influential. During my teenage years, I convinced my parents to construct a pond in their garden. They were very supportive, but I did most of the digging. For the next 20 years or so, that pond witnessed different kinds of flora and fauna. In particular, the pond had a small population of newts and frogs that somehow made their way through. It was exciting to observe their courtship and breeding during springs. I remember that at some point there was a competition between newts and frogs. Eventually, the newts completely took over the pond because they were very efficient in eating the frog eggs. I tried to construct a barrier to separate the newts from frogs but failed miserably. In the end, as you might have already guessed, I gave up.
J: So, that was the first lesson in realizing “competition” in nature as a fact.
C: Sort of. I let nature take over and the newts won. Come to think of it, other family members may also have influenced me in taking up science as a career. For example, I heard a lot of inspiring stories about my great uncle (I never met him though) who was a professor of biology at Princeton University.
Through the end of high school, I was hesitant to choose between architecture and biology. Finally, I chose biology and decided to do a bachelors degree. During the second year, I took up the opportunity to do an internship at a research center affiliated with the company Nestle. I loved the experimental biology there, except for the part in which I had to sacrifice rats to purify their intestinal enzymes. I agree that animal experiments are an essential part of biology, but it was not my cup of tea, perhaps because of my childhood connection with animals. It is just my personal choice. I also remember a paper by Mitsuhiro Yanagida, a famous Japanese scientist, that elaborated on the importance of a good relationship between the researcher and the organism under study. I felt that connection with plants. Even though I view humans as rational beings most of the time, we are also very emotional. For example, if you perceive Caenorhabditis elegans as disgustingly squirmy worms, you will find it difficult to work with them.
J: But if I am correct, you did your PhD in yeast.
C: That´s right. After finishing my bachelors, I made one of the best decisions of my life and career, the importance of which I realized only later. I took a gap year and decided to travel, which I enjoyed immensely. After returning, I worked at the Nestle research center again for 6 months to pay back my parents, who were kind enough to have sponsored my travel. This time I had a lot of freedom and did all kinds of experiments that I could think of. Even though I liked my bachelors studies a lot, I felt that the lessons did not cover much about genetics, which was, in a way, frustrating. The Nestle research center had a nice library and I spent quite a lot of time reading exciting new research papers. In that sense, taking a gap year helped me realize what I was really interested in, which led me to do a masters at the University of Geneva specializing in molecular biology and genetics. I did my masters project in the lab of famous scientist Uli Lämmli. Anyone who ever did an SDS page would know him from his seminal paper in 1970.
J: You may have also worked with Elisa Izaurralde at that time.
C: Yes, we were in the same lab, and I have my first scientific publication with Elisa. They were intense and demanding times. I spent a lot of time reading genetics and molecular biology papers while working in Uli´s lab. I purified a host protein of unknown function that associates with the HIV protein Rev. I was lucky that my project worked out very well. But it was more related to biochemistry than to genetics. So for my PhD, I decided to work in yeast genetics with Viesturs Simanis at the Swiss Institute for Experimental Cancer Research. Viesturs was a young PI at that time who finished his postdoc just two years before from the lab of Paul Nurse, who went on to become a Nobel laureate for his important discoveries in the cell cycle. When I joined the lab, Viesturs had a collection of mutants defective in cytokinesis, the last step of cell division. I found the project instantly appealing, as it involved genetics and mutants. One of the important lessons that I learned from my PhD was: Don’t always just do as you are told. Initially, my task was to discover the human orthologue of a yeast gene involved in the G1 to S transition. I worked for about 6 months and gathered convincing data that indicated that the approach we took was not going to work. Viesturs was generous enough to listen to me and allowed me to work on some of his cytokinesis mutants. This helped me to reach my final goal: learn molecular genetics, which allowed me to go from identifying genes to uncovering the function of proteins involved in cytokinesis. The PhD projects I took up worked out very well. Like during my masters, I was once again a very lucky person who was at the right place at the right time.
I also spent a lot of time in the library reading about plants and made a list of plant labs where I could do my postdoc. A year-and-a-half before finishing my PhD, I went to a Keystone conference in the US and visited 6 or 7 plant labs and met many influential plant scientists including Joe Ecker, Elliot Meyerowitz, Joanne Chory, and Marty Yanofsky. I initially started working on floral transition in Marty´s lab, but eventually switched to light signaling with Joanne.
J: Could you tell us a bit about your postdoc experience?
C: When I joined Joanne´s lab, it was not so long before the identification of phytochrome mutants in Arabidopsis (Arabidopsis thaliana). We knew nearly nothing about phytochrome signaling at that time. I tried to tackle this by doing a yeast two-hybrid screen. I have to say I was not very lucky in this project. Even though I eventually found a few promising interactors, we were not able to do genetics due to the intellectual property issues, since the available mutants in Arabidopsis at that time were T-DNA lines developed by Ken Feldman at DuPont and we were never able to obtain them. Therefore, we had to use antisense lines to do genetics. But then I was also part of a forward genetic screen at Joanne´s lab and we identified HFR1 (LONG HYPOCOTYL IN FAR-RED1). It had three different names at that time, but we settled on HFR1, a name that came from Peter Quail’s lab.
J: The forward genetic screen was based on activation tagging, right?
C: Yes. HFR1 came out of activation tagging. But we quickly figured out that the line did not segregate with the selectable marker and was thus treated as a standard mutant, so I performed map-based cloning for gene identification. Thanks to Joanne’s connections, we had a great collaboration with Peter Oefner at Stanford, who was developing methods to accelerate map-based cloning. Coming back to your original question regarding my postdoc experience, Joanne taught me many things. I was amazed at her efficiency in making connections and collaborators. Within days or even hours of finding an interesting result, Joanne would establish connections with many relevant scientists that led to important scientific interactions or fruitful collaborations.
Joanne is an incredible mentor extending help even after one leaves her lab. Her support has been continuing even now. She allowed me to take my project with me, especially the mutants from activation tagging. She was very open about this and her approach became clearer to me only later. As a PI, one can have loyalty conflicts. A PI owes loyalty to former postdocs who initiated the projects and independently pursue them by establishing their own labs. But an incoming student or postdoc may read that great paper, get excited, and would like to continue the work. Discussions with Joanne about this important topic were very open and clear. She said I could take the project with me but if a new member in her lab wants to work on that area later on, she would not necessarily say no but keep an open channel of discussion. To PhD students who look for postdoc positions, I would say, discuss this from the beginning with your prospective supervisor. I saw that a lot of young sprouts have come out of Joanne´s lab and established their own groups very successfully. This is a clear indication that the PI is supportive of postdocs taking over the projects they started.
J: I think this is important information that will help the early-career scientists. During your move from postdoc to a group leader, what were the key issues you faced and how did you overcome those?
C: Thinking about it, that was by far the most challenging move. A student or postdoc can find a good working environment doing interesting projects. But then the decisions you make primarily affect yourself. Besides, you are surrounded by peers with whom you can share your thoughts and concerns. If everything works out reasonably well, you will start your own group and suddenly you are lonely. In addition, you feel a certain sense of responsibility other than to yourself, since the decisions you make will affect the careers of others. It is a different ball game altogether. One of the most important things, when you start your lab, is to learn to let go. Do not treat the projects as your own and do not view others as pairs of hands who could do your experiments. Eventually, you might be frustrated that the projects do not go as well as you were hoping. Your lab members may also be frustrated because of the feeling that they are not working on their own projects. So, learn to let go. This brings me to the next piece of advice I have for students and postdocs: Try to take ownership of your project. Of course, this is a process. A former colleague of mine puts this point in a great way: In the first year, the PI has to convince the PhD student that it is a good project. From year two, the PhD student has to convince the PI that it is a good project. I think it is pretty good advice.
J: How should a new group leader tackle this?
C: One needs to give enough room to the lab members so they can grow and develop. A PI should let the lab members be involved in intellectual discussions. Listen to them patiently and try to answer their questions as constructively as possible. This is a challenge for a PI. Within every project, there are always many interesting twists and turns that require enough room to explore. A PI should allow the students to navigate through the projects so that they can relatively quickly identify themselves with their projects. How can a PI achieve this would be another interesting question to which I have only theoretical pieces of advice. People are different and the mentoring they require is also different. Without much freedom, some people may feel oppressed. Others need more reassurance in their daily work. When the experiments are not working well, the PI should come up with solutions or alternate experiments to boost and build up the confidence in students. This becomes a positive feedback loop and they perform better. Always remember: As a PI, you are not talking to the younger version of yourself, and your student is a different person altogether.
J: Do you have a role model in your career? Someone you look up to?
C: I would love to be like Joanne. She gave us full freedom in her lab. There were diverse enough projects and the people felt that they were not competing against one another. I like this very much. We worked on different projects close enough to help each other, but distant enough not to feel threatened.
J: More collaboration than competition.
C: Exactly! This is what we should achieve. Joanne is very good at that. This is very challenging as the PI is not in full control of the lab atmosphere, which can change depending on the members in the lab. Sometimes better, sometimes not quite as good as one would hope.
J: Like in Joanne´s lab, your lab is working on diverse projects under a common theme. How did you decide upon working on those interesting projects?
C: You mean how we ended up working on some of those things. In addition to luck, serendipity also is very important in basic science. One has to be prepared to realize when serendipity hands you something interesting. Too often we have a model in mind and we look through this pinhole and miss the big picture. It happened to me a few times. For example, while working with pks T-DNA insertion lines, we thought PKS genes may control hypocotyl growth responses under different light environments. They do, but only to a small extent. We were so obsessed with the hypocotyl growth phenotype that we missed the most obvious, which even a 5-year-old could see, that the growth orientation of mutant seedlings was random compared to wild-type. I realized it only after a while. Creating models helps to design better experiments, but be careful not to fall in love with your model. Look at the data with the eyes of a child!
Coming back to the idea of models, some of our work that I trust most are the results, which completely dismissed our initial hypothesis. This is because we tend to question data that challenges our hypothesis more thoroughly. Hence, I trust the data that disproves our model. An example I have in mind is phytochrome localization. Until the late 90s scientists were convinced that phytochromes were acting in the cytosol. Then with the works of Akira Nagatani, Steve Kay, and Eberhard Schaefer, it turned out that phytochromes get into the nucleus. This was shown initially with phytochrome B (PHYB) and later with PHYA. I was under the impression that PHYA predominantly acts in the cytosol and influences phototropism. This was our model while comparing the phyA and fhy1/fhl double mutants (in which PHYA does not go into the nucleus due to perturbations in FAR-RED ELONGATED HYPOCOTYL1 and FHY1-LIKE). Then I felt that maybe we were missing something. So, we included a control with PHYA fused to a nuclear localization sequence. In this way, we finally figured out that the nuclear-localized PHYA, rather than the cytosolic PHYA regulates phototropic responses, disproving our earlier model.
Another important contribution from our lab is the role of PIF transcription factors as major controllers of elongation growth responses, which we published in Plant Journal, 2008. This was the hardest to publish ever in my experience. We submitted to many journals in vain. PIFs were always viewed as negative regulators of phytochrome signaling, which I am not denying. But this interpretation doesn’t provide conceptually much regarding the functions of PIFs. We provided evidence that they are positive regulators of elongation growth. I am very happy about this particular paper.
J: And the shade avoidance part of your research started with PIFs.
C: Yes. Shade came from PIFs. Slowly I realized that phototropism is a facet of broader shade avoidance response. Under limited light resources, plants grow toward the light, for which phytochromes function as brake and accelerator, while phototropins act as the steering wheel. I am happy that we were able to look a bit into both of these mechanisms in a broader context to learn how plants handle their growth under limited light conditions, such as in shade. I invited Garry Whitelam to a small meeting we organized in Switzerland and had plenty of time to talk together. In my opinion, Garry is one of the smartest people I ever met in the phytochrome field. These discussions led to a collaboration and our first paper on PIFs and their role in shade avoidance (the paper mentioned above). To me, this illustrates the importance of networking and attending meetings and seminars.
J: Yes. Inter-disciplinary research works are very common nowadays. What is your take on collaborating and networking? Any advice for early career researchers on collaborating?
C: Publications before the past two decades often had one or two authors. Nowadays, more experiments are required to publish a paper, and hence it is good to have all kinds of collaborations. Good scientists recognize that they stand on the shoulders of giants. We often revisit old problems with new methods. So I would advise attending diverse meetings and seminars, even if they are not directly related to your research. Do not listen to the talks passively, but engage in the whole thought process and then talk to people whose work particularly interests you. It can be about methods or can also be about the concepts within a field. You can observe that successful scientists regularly talk to each other at meetings and conferences. Every scientific field has certain facts that only the people within the field may know. For example, an outsider may give a lot of credit to a publication in a high-profile journal and realize later from a conference that it is not a good idea to put all the money in that basket. Many famous research centers are famous because smart people concentrate there. They meet and talk regularly, so networking has always been important. A friend of mine says that the most important asset at your workplace is your colleagues. The best possible position you can have is to be surrounded by people who are all smarter than you, and you are just smart enough so that your colleagues are happy to talk with you. It is a bit like sports. It is simply better if you play with someone slightly better than you. But of course, if this person is much better than you, they would not play with you. I think it is the same in research.
J: How do you find new ideas? Do you get the so-called scientific spark?
C: My answer goes back to a few things I discussed before. And sometimes I got ideas from books! Not novels, but from popular science books, which prompted me to look at old literature and I found interesting insights. So, try to read widely, attend diverse conferences, and talk to people. If I sit down and think, “oh, I need to get a good idea,” this would not happen. My wife loves opera. Initially, I was a bit reluctant, but now I have started to like it. I often found that my mind meanders while I attend the opera and all of a sudden I could find ways to solve a problem, either scientific or personal. I am not implying that great scientific ideas come from listening to opera. But I do think that taking a distance from the problem and engaging in something like opera often helps.
J: Thinking of big ideas in science, what is the topic that excites you most in plant research?
C: Well, I think it depends on basic or applied plant research. In applied research, the biggest challenge is to improve agricultural productivity. I am convinced that we are not going to find a silver bullet here, but hopefully, make small improvements that help. The involvement of legal issues and the need for technological advances further complicates this problem.
In basic research, I am fascinated by how plants and animals evolved multicellularity independently. The mechanisms that govern the behavior of cells in a coordinated fashion differ in plants and animals. For coordinated responses, animals fundamentally rely on their nervous system. Plant do not have a nervous system and hence have to make it differently. We do not fully understand how the coordination of responses happens within plants. Let us think of shade avoidance because I love shade avoidance. An elongating stem needs more resources, both from above- and below-ground parts. How are these processes coordinated? I do not think that we have a good understanding of the basic principles underlying the inter-organ communications within the plants. While these are centrally coordinated in animals, plants work like modules or units. For example, if a tree branch is constantly under too much shade, at some point, it just dies off and the plant loses only that branch. This does not usually happen in the animal world. So, the principles of response coordination are fundamentally different in plants and that is what excites me. Talking about communication within cellular contexts, we know quite a bit about root development, but less in other parts of plants! If I had endless resources, my dream project would be to study the coordination of different organs and cell types that regulate the allocation of the right resources at the right place at the right time. I think this is worth tackling.
J: How did you begin working for Plant Physiology?
C: Connections! I met Mike Blatt for the first time during a meeting in Poland. I knew of him but never met him before. We had great conversations over a few beers. I thought he was someone doing great science and also a person I would be happy to share a beer with any time. A few months later, I received an email, we had a call, and he asked if I would like to be an editor with Plant Physiology. In short, that is how it happened.
J: I am curious to know what the editorial duties look like from an insider perspective and the challenges you encounter?
C: As a Monitoring Editor, my job is mostly to figure out whether to send a paper for reviews or not. Sometimes Associate Editors can also decide upon it. Then we identify suitable reviewers. If we have doubts about whether to send a manuscript for review, we further discuss it with a few other editors, or sometimes even involve the Editor-in-Chief. Once the reviewers who are experts in the field are decided, then one has to be fortunate enough that those reviewers accept the invitation. At times we continue asking even more than 10 scientists and no one wants to review a manuscript. It also happens sometimes that the manuscript is quite far from my area of expertise. In this case, I always turn to other editors. This is the first level of my work.
In the second level, we figure out the key points from reviewers’ comments. I usually try to avoid additional experiments that are not essential in the context of the manuscript. For example, testing a model in other situations, such as looking at the functions of a paralogous gene. Of course, this depends on the hypothesis tested and the claims in the manuscript. From reviewers’ suggestions, I make a list of experiments that will provide solid evidence for the conclusions presented in the manuscript and send it to the authors. I enjoy the discussions with reviewers to craft a summary of key points. I advise the authors to avoid claims that lack experimental proof. If multiple experiments point in the same direction, I am usually satisfied with the manuscript.
J: However, the amount of data needed to publish a paper is increasing more than ever.
C: See, we have to think thoroughly about what we want out of a manuscript. Sometimes it is only a matter of changing the text! You may have a great idea, but if you do not have sufficient experimental evidence, reviewers will demand more. Sometimes it is also a matter of tools and techniques that are available. Compared to other plant models, more experiments may be requested for a manuscript in Arabidopsis. I see sometimes that an avalanche of additional experiments is asked by the reviewers. In these situations, it is our duty as editors to look deeply and choose the additional experiments carefully.
J: How do you juggle your roles as an editor, a scientist running a lab, a mentor, a teacher, and doing other administrative work? How do you find motivation in your daily life?
C: I remember as a third-year biology student looking at a professor and thinking that this is the job I want, although I had no idea then what it entailed. Apart from science, I have many chores that I may not particularly enjoy, mostly related to administration and the responsibilities that come if one works longer in an institution. However, I think about the people who were in my shoes before and doing these duties. I take it as my payback time and understand the importance of these tasks.
Overall, I enjoy the diversity in my work. In 15 minutes, I can shift from discussing a research project with my student to a classroom giving a lecture and jump to some committee meeting an hour later! It is exciting! To get going every day, I resort to the old tricks I used to do as a PhD student, although not in the same way. At the end of every day, I make a list of tasks for the next day so that I can jump-start the work on the following day without much thinking. Even on overwhelming and demanding days, I can always look at my list and feel positive about the tasks that I managed to do.
J: And if I may ask, did you manage to finish your list today?
C: You have to cherish the fact that you managed to finish some important tasks. Do not worry about the list being unfinished. I start the day by doing tasks that need most of my brainpower. During these times I keep my office door shut. For some important tasks such as Zoom lectures during the last 2 years, I also stick a “do not disturb” notice on my door. I hope we are done with Zoom lectures, but let´s see.
J: Do you enjoy teaching? And does it influence your work?
C: Yes, I like it a lot. Maintaining a balance between being a researcher and a teacher is very useful. While teaching, I have some distance from my daily research and it is a humbling experience. I can probably entertain bachelors students for about 15 minutes with the discoveries from my lab. Sometimes, we pursue projects that are also driven by emotions (we get attached to scientific questions). Teaching lets you step back and look at the big picture, and sometimes helps you decide whether to pursue the idea or not. Some of the lab projects have benefited from my teaching because it forces you to read about topics that you didn’t know well before. Being an active researcher also helps you to teach, to develop a contagious enthusiasm for an exciting topic, and the teacher must engage the students. Some of the things I teach are not necessarily very important but the scientific approach, reasoning logically, analyzing the potential pitfalls in an approach, describing versus interpreting data, etc., will also benefit the students later in whatever they do.
J: Students and postdocs wonder at some point in their career whether to stick with academia or move to a career in industry. What advice would you give in this regard?
C: They have to figure out whether they like what they are doing. I consider myself very lucky that I am doing a job that I truly enjoy. Match your aspirations with your abilities and choose a job that coincides with both. Try to aim high, because you will never reach higher than what you aim for. I try to help students and postdocs through discussions to figure out what they enjoy doing in their professional lives. I know what it takes to be an academic. I do not know what it takes to be someone in industry and so I try to connect my students with those who can give them a better perspective.
J: If you were not in academia, what other professional choice would you have made?
C: Hmm. As a high school student, I used to love architectural designs and I still find them fascinating. I think now it must be even more exciting. Construction of 3D models and navigating virtually through the dream buildings are now realities. Perhaps I would have been an architect. With my biology background, I can also think of some bio-inspired ideas to follow professionally.
J: What do you do when you are not doing science?
C: Oh, I do a variety of things. A bit of sport. I especially enjoy tennis. Not just casual, but also competitively sometimes. I think it is a good exercise for the mind, for concentration. I also go skiing in winter and enjoy walking around in the mountains. I like cooking and sharing meals with friends and family. I love going on vacations and visiting places. I also enjoy reading good novels as they transport you somewhere different. A few years ago, I started diving with my wife. We have a license and dive occasionally. I am calling this my yoga because I am not very calm as a person. But when you are in the water, you have to slow down and breathe steadily. During diving, I enjoy that I cannot do anything in a rush, which is very soothing.
J: Do you still keep animals?
C: Yes, we have a couple of cats at home.
About the author
Jathish Ponnu obtained his PhD in biology from the Max Planck Institute for Developmental Biology, Tübingen, Germany under the supervision of Prof. Dr. Markus Schmid and Prof. Dr. Detlef Weigel. His PhD work on trehalose-6 phosphate, an important signaling metabolite, led to the discovery of sugar or energy pathway that regulates flowering time in Arabidopsis thaliana. Interested in the upstream regulators of energy pathway, he is pursuing postdoctoral research in plant light signaling with Prof. Dr. Ute Hoecker at the Institute for Plant Sciences, University of Cologne, Germany. His work on blue light signaling has uncovered a novel competition-based mechanism employed by cryptochrome photoreceptors in promoting photomorphogenesis. His current research interests include studying the rapid developmental responses of plants toward changing environments. Jathish is an Assistant Features Editor for Plant Physiology during 2021-2022.
Read more interviews of Plant Physiology editors here.