This week’s PhDetails is with Ahmed Hasan who is doing his PhD at the University of Toronto in Canada. Before doing his PhD there Ahmed studied for his BSc at the University of Toronto studying plant-microbe interactions. Ahmed's PhD currently focuses more on population genetics as he studies how meiotic recombination changes genomes over time.
Well let’s start off talking about completely unscientific stuff: What is your favourite band/musical artist pre 1980?
Joe Pass! Such a ridiculously good jazz guitar player. He does have a few post-1980 releases, but my favourite album (Virtuoso) is a 70s release, so I’d say this is a fair pick!
Favourite band/musical artist post 1980?
Now this answer changes more or less on the weekly… although currently I can’t get enough of Revocation and a newer band called Zeal and Ardor.
Favourite movie?
I’ve recently been blown away by Annihilation, but I think Mad Max: Fury Road has to be my answer at the end of the day. The first and only movie I’ve watched multiple times in theatres because it was just that good.
Do you listen to podcasts?
Unfortunately, not very much, despite some of the best efforts of various friends and even my supervisor. The problem is that time spent listening to podcasts is time spent not listening to music. If only I could do both at once somehow and have my brain parse them out in real time…
Where do you study and who is your supervisor?
I’m at the University of Toronto Mississauga in the lab of Prof. Rob Ness – I was his first graduate student!
What year of your PhD are you in?
Second.
Who’s giving you the money – and for how long?
Rob’s NSERC grant for now, though I’ve had this year largely covered by a generous scholarship from my department.
Do you have any publications – if so where?
Two from my undergraduate research (a letter and a longer paper) – was very lucky to land those. I’ve also got two primary research preprints from my graduate work so far, but they’ve yet to find a home outside of BioRxiv at the time of writing. Fingers crossed that changes soon!
Did you do a masters – where was it and was it about?
Nope – started off in a master’s program but transferred up to a PhD partway.
Do you do fieldwork?
Just limited to the lab (and more specifically a computer!)
What are the best and worst bits about your labwork?
I’m more or less limited to the indoors, between my past life as a molecular biologist and my current one as a computational sort. It’s fine by me as long as I get to hang out with R! As far as lab work in my current degree goes, I do appreciate the mental break from sitting in front of a computer all day, and the perspective that actually seeing my study organism in action offers. The worst bit about my lab work so far might be long, eye-straining periods of under-the-microscope work – I’ve improved my tetrad dissection technique with practice, but I’m still rather sloppy and sometimes get frustrated quicker than I should.
How many PhDs did you apply for – what were you looking for?
I scoped out many universities in both Ontario and Quebec here in Canada, but it boiled down to a choice between my current lab and a microbiology lab at McGill University in Montreal. My undergrad work was in microbial community profiling in plants, and I’d originally wanted to go into microbiome research. At the same time, however, I was also very sure that I wanted to pursue a primarily computational project and move away from the wet lab side of things. Ultimately, the latter won out over the former as far as personal and professional priorities went, and I was happy to be made a population genetics convert.
What is the most bodged piece of equipment you have had to use during field/labwork – did it work?
I’m fortunate enough to have avoided bodged equipment in my limited lab experience so far, but I have to say there’s something I still find unnerving about most autoclaves for some reason. The ones in our department are perfectly functional, but something about their shrieking and howling always spooks me a bit. This is how I know I’m destined to not primarily be a wet lab biologist.
What one piece of advice would you give to a masters student applying to PhDs now?
I haven’t really been in this exact situation myself, since I ‘rolled up’ into a PhD program in the same lab. That being said, something I often have to remind myself is that PhDs are much, much more of a marathon than a sprint. You’ll find you have to slow down maybe more than you anticipated sometimes – which is fine, since you also have more time to do so. Be kind to yourself!
How often do you meet with your supervisor?
Not very often – I’d say once every two weeks or so at most. We keep in touch online of course, but face-to-face meetings aren’t needed particularly often unless there’s a pressing deadline of some sort.
What supervisor traits are important to you?
It’s a tough balance but seeing students simultaneously as trainees and colleagues; in other words, fostering autonomy but also providing support as needed. That, and an empathetic, problem-solving focused outlook when things inevitably go wrong, rather than one primarily concerned with assigning blame.
What do you think are the worst supervisor traits?
Not respecting the work-life balance of their students is a big one. I’m very fortunate on this front, but I’ve witnessed PIs that are in the lab 24/7 and use that as a reason to try and push their students to do the same.
In one sentence what is your PhD about?
I study how meiotic recombination changes genomes over time.
What has been your academic highlight of the last year?
It’s a bit of a toss-up between Evolution 2018 in Montpellier last year and wrapping up a recent paper. I cheated a bit and read ahead to see that there’s a separate question about conferences, so I’ll yammer on about Evolution 2018 down there!
The paper in question, however, was a project on sex chromosome evolution my supervisor and I had to sprint through since we’d been looking to submit it to a special issue with a relatively tight deadline. I wrote the first line of code for the project on the last day of October and we found ourselves submitting a full, final draft four months later. The reviews we got back for the paper have been super positive and cited the software development practices as ‘outstanding’, which I’m still incredibly excited about! I’m not sure I’d want to go through that 4-month adrenaline rush again, but I’m very glad to have pulled through and extremely proud of the work.
Have you had an academic lowpoint of the last year – if so what happened?
At some point last year, I got a bit complacent with some ongoing lab work and stopped maintaining replicate experimental lines despite repeated warnings from my supervisor not to do exactly that. The lab work had been a pilot project on the side, and it had been going alright enough, but that caused me to become extremely lax about it. That quickly became a problem once other things started going wrong with my one line -- and meant I had no usable samples in time. It was pretty embarrassing, but I’d like to think I’ve learned my lesson!
Which academic idol/scientist have you met?
Prof. Mohamed Noor from Duke University! I actually put his name forward for our department’s student-invited speaker competition in my first year and was thrilled when he was selected by the other students to eventually give a fantastic talk here.
Which academic idol/scientist would you most like to meet?
Definitely the Charlesworths.
Do you have a favourite paper?
It may not be one of the ‘classic’ population genetics papers, but I’m extremely fond of Comeron et al. 2008’s review of Hill-Robertson interference. I remember feeling a bit in over my head with my project at the beginning of grad school, given that I was still rather new to the field, but reading that paper was the moment my first-year self finally felt several seemingly disparate concepts click all at once. Besides that, “Population genetics from 1966 to 2016” by the Charlesworths is also a phenomenal review.
What has been your favourite conference so far – why?
Evolution 2018 in Montpellier! I’d never had an experience like that before – it was frankly a bit overwhelming to have my first major conference be that big. It was unreal seeing talks every single day from huge names in the field, going for dinners with other scientists from all over the world, and getting to present my own work too.
What hours do you typically work?
I’m saddled with the double whammy of both not being a morning person and living over an hour away from my lab, meaning that my days typically start at 10:30-11 am and end around 6-7 pm.
How do you avoid procrastinating?
I like to plan what I’m going to do in a given day well in advance, which helps me keep on task during the week. It’s also been useful to remind myself just how good it feels to get a pressing task over with.
What motivates you in your day to day PhD life?
There are a few things: first, the fact that I never thought I’d get this far, and that a younger version of me would be losing his marbles over where I’m at now! Periodically stepping away from my computer and reminding myself of the questions I’m investigating is another big one. I also really enjoy the feeling of ‘grinding’ to get better at something and feeling myself improve – whether it’s reading papers on a topic or finding ways to speed up scripts, and that definitely keeps me going. Finally, tea.
What do you do when you’re not working – how do you balance it with your PhD?
I’ve been very into guitar playing for the past decade now and spend perhaps too much time with my instruments at home whenever I can! I’m also often looking for any excuse to see live music, which fortunately is very easy to come by in a city like Toronto. On top of that, a friend pushing me to buy Bloodborne has meant I’ve also gotten back into video games after many years. There are also board game nights with friends keeping me occupied, an ongoing tabletop campaign, and so on. Balancing all these things is a bit difficult sometimes, especially since I get home rather late most weekdays, but I’ve finally gotten better at sectioning off ‘absolutely no work allowed’ times in the evenings.
If a genie could grant you one wish to help with your PhD what would you wish for?
An unlimited supply of tea.
What would be your dream job?
Besides my inner 16-year-old’s dream of being the lead guitarist for a metal band, I would love to be focused on software development in a genomics/bioinformatics context. Ideally, the position would also involve some level of teaching programming, which is something I’m super passionate about.
Where do you see yourself in 5 years?
I’m not entirely sure whether I want to do a postdoc after my PhD or look directly for industry/tech jobs, but in either case I would hope to see myself a) in a new place (I’ve been in Toronto for a while now!) and b) writing code for a living.
One word to sum up your future in academia:
Plausible?
What do you want to achieve outside of academia in the coming year?
I’ve been writing a fair amount of music with a few friends lately and I really want to sit down and get that material fully recorded. Perhaps even released?
What essential tool hardware/software could you not do your PhD without?
While deliberating between R, Python, and the Unix shell in terms of more science-relevant answers, I realized I’d forgotten the actual most important thing: Vim keybindings.
Who has been your academic role model/inspiration and why?
I’ve mentioned him above, but it has to be Prof. Mohamed Noor, who has been a huge inspiration to me with regards to his science (we both work on recombination from an evolutionary perspective) as well as his commitment to teaching and mentorship. I also very much look up to Prof. Graham Coop, whose ability to effectively communicate population genetics concepts is incredible.
Where is somewhere you would like to work in the future?
Edinburgh for one – I’ve heard really good things about doing research there. I also like Montreal a lot and would enjoy being there too (plus, it’s not too far from home).
Do you have a favourite organism ?
I love walruses! A younger version of me found them very goofy and endearing and I really never got over that. I do really like my study organism (Chlamydomonas reinhardtii) too though – particularly its nice and compact haploid genome.
Are there any social interactions/meetings which have enhanced your PhD experience?
We have a yearly graduate student retreat to a nearby University of Toronto-run field station (the Koffler Scientific Reserve) that I’ve really enjoyed. Our department also does pizza lunches after each seminar, which were a great way to meet people early on and helped me get comfortable in the department. Plus, my lab hosts ‘Genomics Lab Meetings’, which are open to the whole department as long from both attending/presenting perspectives as long as the talk is relevant to genomics.
If you could change one thing about your group/department structure what would it be?
It’s frankly hard to think of much. I’m very fortunate to have a great department that also feels ‘the right size’ in terms of the grad student population, i.e. not too big nor too small, and we’re very well taken care of from the admin perspective. I do wish our campus was closer to the city though, but that’s not exactly a department-specific issue.
What major question in your subject area is yet to be addressed?
One big question is referred to as Lewontin’s paradox: ‘Why are levels of genetic variation in populations constrained to a relatively small range, even with enormous variation in census sizes?’ Despite differences in census population size over several orders of magnitude, levels of genetic polymorphism hardly break out of a narrow range, despite being theoretically predicted to scale with census size. It’s a bit difficult to address empirically, though there have been some recent efforts (i.e. Corbett-Detig et al 2015; but see Graham Coop’s 2016 response).
A perhaps less widely pondered question -- but one that puzzles me all the same -- is the extent of variation in the rate of sex in free-living protists in general. Many of these are facultatively sexual, which means they can choose whether to reproduce clonally or sexually, with the frequency of either mode of reproduction having dramatically different consequences for how their genomes evolve. There are a few studies looking into protist recombination, but not that many overall, and it doesn’t help that they are ridiculously diverse in nature.
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