This week’s PhDetails is with Jörg Bachmann who is doing his PhD at Stockholm university. I first met Jörg at an academic workshop on adaptation genomics and have continued to bump into him at various conferences including PopGroup and ESEB - clearly he has good taste in meetings too. Jörg told me that during his Ecology Masters, he became fascinated with using genetics to take a closer look at the molecular origin of phenotypes and the fact that you can watch evolution at work with population genetics. For his PhD studies he chose a project with an evolutionary focus and a place where he could acquire more experience in genomics and bioinformatic data analysis. Jörg is now in the final year of his PhD and is looking for new opportunities to grow. Enjoy!
Watering my hundreds of plants for a QTL study. An add I put out with this picture got me a very good apartment.
Well let’s start off talking about completely unscientific stuff: What is your favourite band/musical artist pre 1980?
David Bowie, his range of describing the highs and lows of life through the most mesmerising stories is incredible.
Favourite band/musical artist post 1980?
Split between Arcade Fire and Cigarettes After Sex.
Favourite movie?
Moonrise Kingdom for the visual storytelling of Wes Anderson and Herr Lehmann (Germany) for the hilarious dialogues and the soundtrack.
Do you listen to podcasts? What are some of your favourites?
I like to make long lab-days more pleasant with podcasts by the Swedish Radio, especially “P3 Dokumentär”. I am slowly becoming swedified by learning to like dark, tragic stories. Recently I also picked up the “Hidden Brain” podcast, which gives a very balanced view on the motivations and drivers behind human behavior.
Where do you study and who is/are your supervisor?
I study at Stockholm University with Tanja Slotte as my main supervisor. Our department is “DEEP” (Department for Ecology, Environment and Plant Sciences), which makes for a lot of great puns. I also have Vincent Castric and Ove Eriksson as co-supervisors.
What year of your PhD are you in?
The final year, how did this go by so quickly?
Who’s giving you the money – and for how long?
I have four year’s worth of funding by the Swedish Research Council (VR).
Do you have any publications?
I have one publication from my undergraduates, where we looked at salamander larvae abundance: https://brill.com/view/journals/amre/36/1/article-p87_10.xml?lang=en. From my PhD, I have a first publication where we describe methods of assembly and calculate error rates for genomic region that is difficult to assembly because of high repeat content and diversity https://www.g3journal.org/content/8/4/1327. The second publication of my PhD describes a mating system change from an evolutionary perspective, we studied when and how a species gained the ability to fertilise itself https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.16035.
Did you do a masters – where was it and was it about?
I did a Master’s in Ecology at the University of Zürich. I got more and more interested in genetics and genomics and so I did a Master’s Thesis on the the genetic diversity and evidence for a rare mating system (Androdioecy) in the large bitter-cress (Cardamine amara) in the lab of Kentaro Shimizu.
Do you do fieldwork? What is the best fieldwork you have ever done and what made it great?
Not since my master’s. We had some great after-work swims, because my study species grew along rivers and lake. Nowadays, away from my computer, it’s a great moment if I get a band on the gel with PCR-primers that I designed myself. Not so great to see the amounts of one-time use plastics that end up in the waste though.
A self-compatible hybrid between the self-incompatible Capsella grandiflora and the self-compatible Capsella orientalis.
How many PhDs did you apply for – what were you looking for?
I applied for two PhD programs / projects, both in the evolution of mating systems in plants. I was looking for a project where I could learn new skills in genomics and coding, plus for a good supervisor. I got invited for an interview in Stockholm and was offered the position a few days after the interview. I think the experience I gathered during my master’s thesis helped to get the position.
What is the most bodged piece of equipment you have had to use during field/labwork – did it work?
Not really bodged, but very low-tech: I still use small pieces of coloured tape, folded around a loop of sewing thread to mark single flowers for controlled pollinations. It’s a lot of fumbling around with pieces of thread and tape. But it’s lightweight enough not to damage Capsella flowers, cheap, and my friend Andy thought me this method a long time ago - so don’t you dare telling me there is a better way to do it.
What one piece of advice would you give to a masters student applying to PhDs now?
Treat a PhD as what it is, both education and employment. You are not going to be happy if you are just doing it for a few years of stable income, but also don’t just do it for the title. If you are passionate for science, look for a supervisor or a project where you can apply your skills, but also learn something new. It’s also useful to talk to current and former PhD students to learn more about a potential supervisor, so if their style of supervision is compatible with you.
How often do you meet with your supervisor?
Once every two weeks for one to two hours.
What supervisor traits are important to you?
Having time to take an active role in the projects, but also adapting the supervision style to the growing independence of a PhD student. Good communication and problem-solving skills if needed are also important.
What do you think are the worst supervisor traits?
People who are good scientists, but bad leaders and advisers will end up making life difficult for students. One of the worst traits is lack of communication on expectations.
In one sentence what is your PhD about?
I study the evolutionary genomics of sexual reproduction in plants, mainly I study how plants evolved systems to avoid inbreeding (“self-incompatibility”) and how these systems sometimes get broken when plants switch back to self-fertilisation.
Taking leave samples of Capsella for DNA extraction. A friend took this picture on photographic film, which I developed and scanned.
What has been your academic highlight of the last year?
Getting a talk at a big conference (ESEB) and publishing a study that we had worked on for a long time, those where two big rewards last year.
Have you had an academic lowpoint of the last year – if so what happened?
We got our paper rejected with very mixed reviews. It took some time and reflection to find out how we could turn it around, learn from the criticism, and try to submit somewhere else with additional analysis.
Which academic idol/scientist have you met?
I met Deborah Charlesworth at my very first conference. I was afraid of making myself look like a complete idiot, but she asked good questions about our preliminary data and said she was excited to see the study progress. I was encouraged by that.
Which academic idol/scientist would you most like to meet?
I would love to meet Adam Savage, former host of Mythbusters, though not a scientist, I would thank him for getting young people interested in scientific methods and hypothesis testing. I also believe he could revolutionise equipment for lab- and fieldwork with his skills in the workshop.
Do you have a favourite paper?
I spent a lot of time with the publication by Durand & Méheust et al. on a network of small RNAs that are responsible for dominance relationships between alleles at the self-incompatibility locus. The work that went into this publication is brilliant and I was very happy to meet Eléonore Durand in person last year.
What has been your favourite conference so far – why?
Popgroup in the UK. You get to meet world-class geneticists in a small setting and talks to are given on a first come first served basis, which favours a lot of early-career researchers. Also, did I mention Ceilidh dancing yet?!
What hours do you typically work?
Nine to five or six, with some longer evenings to meet deadlines and sometimes coming in on the weekends for plant care.
How do you avoid procrastinating?
I learned to use the Pomodoro technique during workdays and plan my sportive / creative activities in the evenings and weekends.
What motivates you in your day to day PhD life?
First of all, I’m very curious. For working through tedious tasks, I remind myself that once you have results, you can start discussing them with others, which in turn will drive the study forward. So it’s good to do some preliminary analysis as soon as possible.
Transplanting tiny seedlings onto soil and nurturing them to grow bigger.
What do you do when you’re not working – how do you balance it with your PhD?
I am passionate about creative hobbies of which analog photography is my absolute favourite. There are few things for me like seeing my photos slowly appear on paper during the developing process. The only thing better than that is when I can make someone happy by sharing a nice photo with them. I also enjoy running, especially around the many lakes in Stockholm, which is a good way to clear my thoughts.
If a genie could grant you one wish to help with your PhD what would you wish for?
A faster generation time for my study plant would be nice
What would be your dream job?
I’m figuring that out, something that involves research, but also interdisciplinary collaboration would be very interesting. There is always a strong case for basic research, but I could also see myself studying more applied questions.
Where do you see yourself in 5 years?
Same as above, I’m in the process of figuring out my next steps. It could be a second post-doc, studying for example the evolution of wing patterns in butterflies or developing new genomic tools for research in a start-up company.
One word to sum up your future in academia:
Change
What do you want to achieve outside of academia in the coming year?
I would like to take part in a photo exhibition. It’s nice to share photos I take here and there with my friends, but I would like to create a bigger project and work with a deadline and see what happens.
What essential tool hardware/software could you not do your PhD without?
Uppmax, a cluster computer in Uppsala.
Who has been your academic role model/inspiration and why?
Andy, he grew from being a knowledgeable co-supervisor and co-worker to being a good friend. He is a dedicated scientist who doesn’t lose his (sarcastic) sense of humour even in the direst circumstances. During my Master’s and my early PhD studies, it was very important for me to have someone who knows the academic system, but also knows me well.
Where is somewhere you would like to work in the future?
I could either see myself working in institutions that have a bit more of an applied focus, in Sweden or Switzerland, or doing an interesting post-doc somewhere else abroad.
There are days that are just made up of filling hundreds of pots with soil. Podcasts help!
Do you have a favourite organism?
If I have to pick one, it’s the blue-footed booby, such a dorky bird. I love working with plants, but their behaviour really isn’t that easy to observe.
Are there any social interactions/meetings which have enhanced your PhD experience?
I became involved in the PhD council at our department. That involved organising meetings for PhD students to discuss issues on supervision, funding, teaching, harassment and many more. It made me more aware of issues in our department and how we have a lot of influence as PhD students, if we act together and directed.
If you could change one thing about your group/department structure what would it be?
It would be beneficial to have the different subjects working more closely together. Sometimes it seems difficult to see an overall sense of community and common goals. I would also like to see more power given to students in internal committees. We need to be more involved in the planning and decision making.
What major question in your subject area is yet to be addressed – why is it important and why isn’t anyone addressing it?
Mating systems of plants have traditionally been classified as “outcrossing”, “selfing” or “mixed-mating”, based on few populations per species. Aggregated outcrossing rates from multiple populations per species reveal a large intraspecific variation in outcrossing rates, which shows that mating system can be more complex than a single category would describe. It is important to know the ecological and evolutionary drivers of (local) mating system variation within many species, so that we can interpret patterns of genetic diversity and possibly predict evolutionary trends under changing conditions, for example reduction in pollinator numbers. This can only be addressed in a large collaborative effort or as a meta-analysis, because collecting data on outcrossing rates of different populations and different time-points per species is very time consuming.
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