3 Questions for Prof. Hyun Youk

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Our newest instalment of the "3 Questions for" interview series features Prof. Hyun Youk from Delft University of Technology in the Netherlands. His research makes use of quantitative methods as well as models and theory to understand the interactions between molecules and cells and discover common design principles. Here, he speaks about his transition from physics to biology and his view on the field of synthetic biology.

 

When and why did you move into the field of synthetic biology?

I never considered myself as a full-fledged synthetic biologist and I certainly haven't done any significant work in synthetic biology. But I have used and my group routinely uses tools of synthetic biology to modify and complement endogenous signalling pathways with engineered signalling circuits, with the goal of better understanding those endogenous pathways or what cells can do. On the other hand, my group doesn't build synthetic circuits to create logic gates, devices, desired dynamics, and practical applications. That’s why I hesitate to call myself a synthetic biologist in the conventional sense.

Instead, I can say when and why I moved into biology from physics.  At the core, I'm a physicist who’s been very interested in understanding how inanimate molecules - the same ones that make up many non-living systems - give rise to features that we associate with life in one scenario but not so in another scenario. This tells us that dynamics, not the molecular content, are what determines whether something is living or not and that we don’t really understand the principles that underlie these dynamics (keep in mind that even a dead cell can contain DNA so “ all living things contain DNA and non-living things don't” is not the answer). This question of what distinguishes the living from the non-living has stayed with me since 2006 when I started learning and doing biology. In 2006, I enrolled in MIT’s physics graduate program. As a beginning PhD student, my original intention was to join a cold-atomic physics group there. But I had a year of fellowship money to try other fields before formally committing to a lab. At first, I did an internship in a nanotechnology lab that studied how electrons moved through quantum dots. But that group’s PI let me go after a month - this is a gentrified way of saying “I was fired” -  because he thought that I wasn’t good and that I kept messing up a senior PhD student’s experiments. That was a low point for me because I had just started the PhD program and I had never been fired before. My options then were to just finish taking the required courses (in the American PhD programs, you had to take courses) and eventually join the atomic physics group after 9 months or try my hands at a different field.

In my daily commute to the nanotechnology lab, I passed by the biophysics lab of Alexander van Oudenaarden. I had no idea what he was working on, and I didn’t even understand the words in the title of his group's papers and posters that were posted outside his lab. My last course in biology was more than six years ago in high school, which was mostly about Mendelian genetics and ecology and almost nothing about molecular biology. At this point, as physics student, I also didn’t know what a pipette was, how RNA was different from DNA, and what the central dogma of molecular biology was. But what struck me about my morning commute through the hallway of Alexander’s group was how happy people seemed in his group. I routinely heard laughters coming out of the lab as I walked by. Before approaching Alexander for an unpaid internship, I first borrowed Alberts' book on molecular biology from a library. I found the book (and I still do) very difficult to read because biology textbooks were and still are written in styles that are very distinct from those of the physics and math textbooks that I was used to.  Even though I barely made through a page in any of the chapters in Alberts’ book, I found that I could pose for myself very simple questions about living systems while reading the book and that these questions, posed by someone without any biology background, were largely meaningful and still weren’t answered yet. That really hooked me on biology. So I asked Alexander for an internship and he generously gave me the chance. Since then I fell in love with biology, questions about life which could border on philosophy, and doing experiments with my own hands. I never looked back since then and I’m very grateful to Alexander to this day for giving me a chance and keeping me in his lab for the next 4 years.

Aside from the positive lab culture and the fact that I could pose “simple" questions, such as “how does a cell ’know’ this and not that", to which deep answers didn’t exist yet, the final clincher for me was the revelation that I could quantitatively address those simple questions about living systems with my own hands at the lab bench. Through my internship in Alexander’s lab, I found that I could resolve these questions about cells by designing “simple” experiments, doing them, and then having the results of those experiments tell me the next steps. I have found and still find this process to be similar to the process one uses in proving mathematical theorems through a series of logic, which I also enjoy doing, or how a detective would narrow down the list of suspects. I very much enjoy this hard-to-describe “funnelling” process that narrows down a complex biological system or a grand question about life into concrete conclusions. Aside from these grander points, I also found myself enjoying even the little things like pouring agarose gels, running PCR, aliquoting media, making master mixes, pasting gel pictures into my lab notebooks, etc.  In retrospect, I find that this aspect - enjoying even the seemingly little things in day-to-day bench activities - were indispensable for whatever success I’ve had in research.

So that’s my non-linear path to biology. I've revealed these details here to remind readers who are students that some small event - in my case, being fired from an internship - can literally have a life-changing consequence and that like in research, serendipity and seemingly devastating failures can actually lead to a very positive outcome in a scientist's career. I also think that my story is just one of many like it and that it shows one should not be afraid to enter a field that one knows nothing about. If you’re really fascinated by the question, then I say you should go for it.

 

What is the single most important piece of advice that you would give to a current PhD student or a post-doc?

My first advice is to take anyone’s advice, including mine, with a grain of salt. There’s no one shoe that fits everyone. With this caveat, my advice for PhD students is different from one that I’d give to postdocs.

If you’re a PhD student, keep in mind that your goal is to learn how to develop a story backed by data and then tell that story through writings and talks. In many countries, you have four years to develop and tell a story. Be very critical of your own work. Learning this is also an important part of a PhD. Once you know how to develop and tell a story, then you’ll find these are useful skills in any other field of science as well as outside of science (keeping in mind that you don’t have to stay in academia or in science after a PhD - leaving academia is not a “failure”). You can keep a text document and slides that you constantly update with new results. The idea is that the text will evolve into a manuscript and the slides evolve into slides for a talk that you can give to anyone about your work. When you first start a project, the text and slides will be empty, contain vague items, and a messy outline. But as you get new results, they will evolve. You’ll find that you’ll need to delete some paragraphs or slides because the story has changed. You’ll rearrange some slides because their order no longer makes sense according to the evolving story that you want to tell. The process of rearranging, deleting, and as a result, planning the next experiments is the process of learning how to do science. I think this is what every PhD training should be about.

If you're a postdoc who’s looking to run your group one day, I think you need to think about if there are questions that your own group will want to pursue that are unrelated to your current postdoc work while, at the same time, having the postdoc work being helpful in pursuing those questions (e.g., same organism with similar techniques). What you do in your own lab does not have to be a natural extension of your postdoc work. Don’t let a decision that you made years ago on where to do a postdoc dictate the next 10-20 years of your life. A luxury that we have in systems and synthetic biology, while not exclusive to these fields, is that we’re often driven by abstract concepts and are not tied to a particular pathway, mechanism, biological process, or an organism. So you can chart a course for your lab that really is distinct from what you did during your postdoc. But I think you can be strategic about doing this. For example, doing follow-up studies of your postdoc work may let you publish soon (1-3 years) after beginning your lab. In the meantime, you can explore a new area that really excites your group and if that new direction works out, then your lab can start publishing in that field after 4-5 years and start shifting into that new area, if you’d like. I think this strategy can let your group avoid the publication draught of the first few years that starting labs often experience while also having the time to develop a new line of research if that’s what you’d really like to do. On the other hand, there’s nothing wrong with more gradually extending your postdoc work and having that be the focus of your own lab. Again, no one shoe fits everyone. The most important thing is to dream big about what your lab will have contributed after 5- 10 years.

 

In which areas do you see the main challenges and opportunities for synthetic biology?

I think the biggest challenge for me is understanding biology well enough to build systems that mimic or extend natural systems. In my experience, no circuit that I or my group has built ever worked out the way that we thought that it would. These apparent “failures” yielded surprising findings and formed the bases of projects and publications in my PhD, postdoc, and now in my group. Think of how the repressilator led to, unsuspectingly, a vivid demonstration of noise in gene expression. That study helped in launching the burgeoning field of stochastic gene expression. For me, I think the challenges and opportunities are the same: Not understanding biological systems well enough and trying to perturb them has and will lead to discoveries about how cellular processes work, whether they be evolved or hand-made. I think this will be an ever-lasting challenge and opportunity that will outlive the technological limitations that we have now (e.g., cost-effectively writing DNA of an arbitrary length letter by letter and integrating it anywhere inside a cell of any type).