This week’s PhDetails is with Cas Retel who, like me, does his PhD at Eawag in Switzerland. Although me and Cas share a supervisor at Eawag we work in very different systems and have quite different backgrounds in science so I’m really glad to finally have him on PhDetails. Before moving to Switzerland Cas did his bachelors and two masters degrees in Leiden and did research projects at the VU Medical Centre in Amsterdam (power calculation for RNAseq differential expression analysis) and at the Dutch Natural History Museum (phylogeography of Pterosagitta Draco, a common chaetognath species). You can also find Cas on Twitter @CasRetel!
Well let’s start off talking about completely unscientific stuff: What is your favourite band/musical artist pre 1980?
Simon and Garfunkel.
Favourite band/musical artist post 1980?
Goldfish. What music I listen to tends to fluctuate over time, right now I listen to Arctic Monkeys a lot.
Favourite movie?
Guardians of the Galaxy, and Pitch Perfect.
Do you listen to podcasts?
I’m not a very loyal listener, but I occasionally listen to “De Rudi en Freddie show”. It’s two Dutch journalists discussing various topics in politics and economics. Two good ones I recall were about the use(less)fulness of blockchain technology, and about measuring the benefits of online advertisement.
Where do you study and who are your supervisors?
I’m doing my PhD at Eawag in Kastanienbaum, and am matriculated at the University of Bern. My supervisors are Dr. Philine Feulner (same institution) and Prof. Lutz Becks from the University of Konstanz.
What year of your PhD are you in?
Midway through my fourth and hopefully final year.
Who’s giving you the money – and for how long?
The Swiss National Science Foundation (DFG) and German Science Foundation (DFG). When I started my PhD we had funding for three years, but my supervisors got a follow-up grant to continue this project, which included another year’s salary for me.
Do you have any publications?
Together with a friend I wrote a literature review about viral genetic diversity, which was published in Viruses about half a year ago. I’m also very happy to report that my first data paper was accepted by Science Advances less than a week ago!
Did you do a masters – where was it and was it about?
I have a master’s degree in Statistical Science. It’s a great programme, organised by the Mathematical Institute in Leiden, but set up in such a way that students without a degree in mathematics can enter. So we were a bunch of students from various fields such as biology, chemistry, psychology, economy, and mathematics. The programme consisted of theory courses, (think Bayesian statistics, Generalised Linear Modeling or High-dimensional data analysis), but we also got lots of practice with R programming. I wasn’t really sure what specialisation to take after my Biology bachelor’s degree and learned about the existence of the StatSci programme more or less accidentally, but I think pursuing it was a really great move. I find programming kind of fun, so a bit stronger statistical basis than a biology degree alone helps me pursue those interests. Also I’m sure that a degree from the Mathematical Institute had a positive influence on me getting my current position.
Do you do fieldwork?
So this one time the internet in my office was down for multiple hours… Kidding. My PhD project revolves around the analysis of genomic data coming from (co)evolution experiments, and those experiments are carried out by our collaborators in Konstanz (formerly at the MPI in Plön). We were involved in the planning, and then got send sequencing data. So I’m a pure computer biologist.
How many PhDs did you apply for – what were you looking for?
I applied for two PhD positions. I was looking for something on the rather technical side of the spectrum of evolutionary biology PhD’s, preferably involving some bioinformatics challenges, because I just think evolutionary genomics is cool in general, and like I said I enjoy scripting/programming challenges. I didn’t care much about the species I would be working on. If anything, I’d say I would have preferred something small and relatively harmless over organisms where data collection is more difficult, because that’s just not my forte. Of course everything can be learned, but I was (and am) definitely more interested in the analysis-aspects of research.
What one piece of advice would you give to a masters student applying to PhDs now?
This is hard, but do everything you can to get to know your (potential) supervisor. People often say that a big goal of your PhD is to persevere and to become an independent researcher. That implies that at the start of your PhD you’re not independent yet. Your advisor is going to considerably influence the directions your research interests take you. Therefore – and because three+ years is a long time – it’s important to find out if your personalities match; if their supervision style isn’t going to conflict with your working habits, stuff like that. This includes asking peers and people from your current institute if they know any anekdotes, trying to find out what previous PhD students are now up to, and straight up asking your potential advisor questions about e.g. how often they’d like to meet, who in their eyes are good supervisors (and why). Don’t completely eliminate your own interests to try to get that position.
How often do you meet with your supervisors?
Weekly, Thursday afternoons. When I started my PhD, I actually communicated that I’d appreciate a regular meeting slot, as opposed to the “just come find me whenever you’re stuck”-, or “let me know when you have something to discuss”-approach that some people prefer. This forces me to keep track of my progress, and generally avoids me getting stuck on easily solvable things. I think my supervisor also appreciates having her finger on her student’s pulse, so to speak, so that works out well.
What supervisor traits are important to you?
I like hands-on supervision, so regular meetings at predetermined times, to force myself to track and report on progress I make. Academic progress happens in very small steps and sometimes it takes months to produce any new reportworthy results, and I personally feel like this can get quite lonely, where you can get the feeling that you’re the only one who cares about what you’re doing. I’m very lucky to have an involved supervisor. When there’s not much news to report, we sometimes fill our weekly meetings by simply talking about a few papers I’ve recently read. This feeling that I’m not alone is a big factor in me enjoying work on a day-to-day basis.
Also I tend to have tunnel-vision whenever I’m solving a problem or doing an analysis. Therefore I benefit a lot from a supervisor who keeps the overview, and regularly reminds me about things that are not urgent but important.
What do you think are the worst supervisor traits?
The first one I can think of is inconsistency. I’ve observed first-hand how frustrating it can be if your advisor tells you something has the utmost priority, then takes weeks to respond him- or herself. I also think it’s very helpful if a supervisor cares about your well-being. Happy scientists are productive scientists.
In one sentence what is your PhD about?
The role of population size on the temporal dynamics of genomic change during coevolution.
What has been your academic highlight of the last year?
Currently this question has a very easy answer: the acceptance of my first data paper. It feels like it’s the primary outcome of three years of my own hard work, and of course a lot of additional time spend by collaborators. Big victory.
Have you had an academic lowpoint of the last year – if so what happened?
The second half of my PhD thesis (two more manuscripts) was supposed to be based on the analysis of data generated from an experiment we ran in 2016. Last fall we started sequencing, and it turns out that most of the DNA was of too low quality to be of any use. We’re able to answer some of the planned questions with backup samples, but I’m also currently outlining a completely new fourth chapter, that has very little to do with my original ideas about investigating de novo mutation rate. This realisation process of how crappy the data actually was took place over the course of several months. Every step in the analysis process, the outcome was more bad news, which was rather frustrating.
Which academic idol/scientist have you met?
The list of great scientists I’ve met is too long to try to come up with one that stands out.
Which academic idol/scientist would you most like to meet?
Richard Lenski.
Do you have a favourite paper?
What has been your favourite conference so far – why?
The conference I enjoyed the most so far was the AVW9 (Aquatic Virus Workshop 9, which took place in Lincoln, Nebraska). I prefer mid-sized conferences, where all participants actually fit in one room, and this was an incredibly friendly and open bunch of people.
What hours do you typically work?
More or less regular office hours: I generally try to be in the office before 9, and usually work until 17-19:00, depending on my evening plans. Occasional morning runs and afternoon bikerides are compensated by staying an evening, and reading papers on the weekend.
How do you avoid procrastinating?
Uuhm, if anything, I consciously don’t. If I can’t bear to start or continue with something, the optimal solution in my experience is to walk away from it for a short while. Nine out of ten times, the task at hand becomes a lot easier after a fifteen minute break.
What motivates you in your day to day PhD life?
The fact that I get to learn every day, and have a lot of freedom in scheduling my own daily activities. When I’m having a hard time I try to remind myself that we’re unravelling the mysteries of life, which is awesome.
What do you do when you’re not working – how do you balance it with your PhD?
I like endurance sports, mainly running and roadbiking, and since moving to Switzerland have shifted to doing more and more alpine activities, i.e. hiking, climbing and backcountry skiing. Especially longer not-too-intense activities actually have a very positive effect on my academic progress, I believe: they allow me to clear my mind, sort my thoughts and think deeply.
If a genie could grant you one wish to help with your PhD what would you wish for?
The ability to get my thoughts on paper in one go. Coherently, like, publish-ready, no editing needed.
What would be your dream job?
It would involve learning every day (preferably by reading a lot), programming/scripting, and a workload that’s easily separated into concrete packages AND leaves enough space for other hobbies. I’m doubtful I’ll achieve the latter in academia .
Where do you see yourself in 5 years?
I just started a tenure-track job at a research institute, with ample collaboration opportunities, at a place where my partner (who’s not in academia) is also able to have a fulfilling career. I value the presence of family and friends enough to want to move back to The Netherlands.
One word to sum up your future in academia:
Curiosity-driven.
What do you want to achieve outside of academia in the coming year?
I want to become a fully independent outdoor rock climbing team with my girlfriend, that doesn’t need more experienced friends to babysit them and make sure their anchor construction is safe. Also, there are three specific mountains in the vicinity that I want to hike up this summer. I usually like to participate in a few organised (trail)runs every year, but consciously decided to not sign up for anything during the last half year of my PhD.
What essential tool hardware/software could you not do your PhD without?
My bioinformatics analyses require lots of different software packages, and there’s a whole list of ones I consider indispensible. I’m going to go with the Bialetti coffee percolators, at home and at the office.
Where is somewhere you would like to work in the future?
In the absence of logistical and practical limitations, it would be cool to work at the Desai Lab at Harvard in Massachusetts. Michael Desai is a huge name – maybe the biggest – in modern experimental evolution and microbial population genetics, his lab is also doing lots of solid theoretical work. On a personal level, this would mean I get to live in the USA for a while, which I’d expect to be an enriching experience.
Do you have a favourite organism?
The capibara, a large rodent living in South-America. It’s eaten by every dangerous apex predator on the continent, but good enough at digging holes and rapidly reproducing to avoid extinction. Also gives off a super chill vibe. My study organism is Chlorella, which isn’t that sexy (although very healthy, I take it as a food supplement!).
Are there any social interactions/meetings which have enhanced your PhD experience?
I specifically remember going to a course (Guarda) three years ago. We were quite isolated, up in the mountains, without internet, just doing big conceptual thinking for a week. It’s hard to explain, but I remember that by talking to all the other students there, who were in very similar positions as me (either finishing their master’s or having just started their PhD’s), I for the first time consciously realised that I might like to be in academia for the rest of my life.
If you could change one thing about your group/department structure what would it be?
Our group currently consists of four people, and we have monthly journal clubs (with beers). These are informal and great fun, and I wouldn’t change anything about them. Because Eawag is not a university, we don’t interact with students that much, and there’s not much opportunity to interact with and/or supervise students. Also, I was my supervisor’s first PhD student, and the group since only changed by the addition of two more PhD students (who are both male and of similar age as me). So in general, I’d be excited to have a bit more diversity, including people from other career stages. It’s present in the larger department for sure, but that’s still a little further away than your own research group.
What major question in your subject area is yet to be addressed – why is it important and why isn’t anyone addressing it?
Every evolutionary biologist knows that population size affects genetic variation via the drift-selection balance. Additionally, population size determines the supply of novel variation, via de novo mutation and recombination. Now: on top of this, under species interactions, population size mediates the strength of selection that any species imposes on other species. All these roles of population size have been studied, but they haven’t been fit into one framework. I think people are addressing it, but it will take time to figure everything out, because it’s pretty complex. But we’ll get there.
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