Livre d'Or

First week of the rest of my life

2023-07-08T08:37:37Z

As of a week ago, I have officially quit my job, quit science and academia, and started in earnest working towards ordination.

I had my leaving do a bit early, because hybrid working means that it was the only day most people were in the office. Lovely colleagues organized a nice lunch in a place that has good outdoor food options, but it's close by the war museum and a bit aggressively Churchill themed, which felt kind of uncomfortable with an international team. Colleagues also gave me a quite substantial sum of money for a leaving present; they were happy to give me cash rather than a voucher because I said I would probably spend it on something eccentric not available from obvious high street store. In fact, it was exactly enough to buy a nearly-new folding bike from a colleague, so I'm hoping that will make weekly commuting to college a bit easier.

The last week was a little surreal, I'd essentially already said goodbye to everybody, and my immediate colleagues were all running the third iteration of our pathogen genomics for UK healthcare course. I was a little sad to be kicked out of the main instructor team for that, but actually not having to spend the whole of my last week doing intensive in person teaching was a blessing. I handed over my laptop and badge, and walked away.

jack happened to be away (the timing was unavoidable), so lovely hatam_soferet rescued me from a lonely sad evening by inviting me for Friday night. This involved a lot of doing art with her 5yo, which was a great distraction, and plenty of tea and chatting and hugs. Then the weekend had a nice date with ghoti_mhic_uait, including spending some time at rmc28's party full of extremely awesome people, and a barbecue at my parents' for my dad's birthday. That was small by our standards, but "immediate family" is already over a dozen people once you include partners. (I didn't even bring all my partners, just cjwatson and OSOs' youngest). We experimented with 3yo G sleeping over at mine; which went really well so I'm glad to have the flexibility.

First thing on Monday, I jumped straight in to an Ulpan course at the university. aldabra found this for me and it's absolutely perfect, just what I need. There are three levels, absolute beginners and post-beginners, and then intermediate which I've joined. Not completely surprisingly given the context, the entire intermediate class is made up of people like me who have an academic interest in classical Hebrew. I think I'm probably the most fluent student in the class, but not miles ahead of the rest of them. I can just about cope with Hebrew language medium immersive teaching but wow it's hard mental work. Though the teacher does occasionally drop into English when he wants to explain a complicated matter of linguistics. The last hour of the day is enrichment, which is very Cambridge, we've been on a trip to the Genizah and had various lectures from faculty, mostly about classical Hebrew topics. I kind of care more about manuscripts and texts than about modern Hebrew so that suits me very well.

I'm still extremely not sorted for accommodation in London, which is a bit scary, but if I end up couch-surfing for the first part of term, so it goes. Also I have managed to catch a cold, probably from OSOs rather than the course, as they've all been poorly this week and I have been masking pretty consistently in class. So I cancelled the community work I was supposed to be doing this weekend; I only had a minor role, it was mostly an opportunity to meet the community where I'll be leading on Rosh haShanah, and I wanted to model the responsible behaviour of not travelling when sick. I'll keep testing but the balance of probabilities says it's not Covid. I really hope I'll be better for the second half of the course on Monday, but we'll see.

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Ta-da!

2023-02-07T10:38:20Z

Just want to show off one of the big projects my team has been working on for the past several months:

Pathogen Genomics: A New Era

This is part of our huge-scale Covid training project, but we've decided that in 2023 people need to know about other infectious diseases as well. So this is a broad-ranging MOOC about how to use pathogen genome sequencing in an applied way, from scaling up to national and international epi/pandemic response, to getting politicians to take into account the science when making decisions about public health.

The intended target audience is people involved in pathogen surveillance and public health in some way, but anyone broadly scientifically literate (and we've all found ourselves learning technical stuff about epidemiology in the last three years) should get something out of it. If you're scared by the term "surveillance", it does very much include discussions of how to balance keeping close track of viruses while maintaining the privacy and freedom of the human hosts. And a ton of very honest accounts from people working at the frontline over the past 40 months, discussing what their work was like in the real world and the trade-offs they had to make.

It's taking a really international view; our big aim here is to move away from the model where we talk about Europe and the US with one little token case study from the Global South. So even if you know quite a lot about what went down in North America and how that was different from Australia and China, you might learn something about cutting edge public health in Thailand, Trinidad & Tobago, Nigeria and lots of other places.

The course is completely paid for by our funders (including the FCDO and the Wellcome Trust) so if you do sign up you get the full benefits of paid membership for free. In theory it's supposed to take about 3 weeks but anyone who signs up can access the course for a year. There's no problem with just dipping in rather than taking the course in linear order. It's not as slick as, say, a TEDTalk but it's real and honest views from some of the people who really know most about what's changed since Covid, including some of the people responsible for the advances.

I'm really proud of it; of all the things I've achieved in my career this project is probably most directly relevant to saving lives and changing the world. My direct report did most of the coordinating but what's good about it is that it really has been a team effort and a massive collaboration. Also I rather like the slightly Star Wars vibe of the title!

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Emerging

2022-10-22T16:50:45Z

So I tested positive for Covid for a full 14 days. By that point I had decided that I was likely not to be infectious any more and could ethically emerge from isolation, but fortunately I did get my second negative test anyway.

I missed Yom Kippur and most of Succot, which was really disappointing. But I didn't miss the glorious false summer as the nice weather seems to have lasted most of the month. And Friday evening I was safe to go and make Kiddush in hatam_soferet's succah, so I didn't completely miss out on the festival. I went to shul in person on Saturday, and we took lulav then (my community's custom is to include Shabbat). Then hatam_soferet took us punting and it was just perfectly idyllic, right at the end of summer with the autumn colours showing the postcard views at their best.

We returned to their house to drink tea, and while I was there jack texted me a photo: he had secretly built me a tiny succah! So I got to have my tea and breakfast in the succah for the very last day of the festival. And I was so so so touched that jack did the research and the actual engineering to build something for me. Of course it couldn't officially be kosher, being built by a non-Jewish person in the middle of Shabbat and after most of the festival, but it was still the loveliest present ever.

I had been given the honour of being one of the two symbolic brides for Simchat Torah, the person assigned to read the very last Torah portion. (The brides could also be grooms, they don't have to be both female, it just happened that in this case it was me and SG, one of the founder members of the community.) And I was nervous that Covid would rob me of that too, but the timing was just fortunate so I could do it. We had a lovely lovely in person service, with a decent number of kids including hatam_soferet's 4yo and my OSOs' 2yo. I decided to indulge myself in the first new-new dress I've bought in years, and my mother lent me a suitable Hat from her extensive collection, so I cut quite a figure. It was so lovely to have all three of my partners and my parents and my bff all present for my big day. And we did the Torah reading and the children's aliyah and the hakkafot (processing round the synagogue seven times) and our traditional frog dance and it was wonderful. Then we did it all again for the morning service because my community is a bit completionist like that. Since I had to take the day off work anyway, I returned home with ghoti_mhic_uait and had a bit of a chance to play with the children whom I hadn't seen since before the new year.

So although I lost most of my festival season to the horrid plague, the last couple of days couldn't have been more perfect. Immediately after that I went straight into teaching my first in-person course since I started my job exactly 3 years ago. This is partly because most of my role is about organizing production of online courses rather than face-to-face teaching, but also partly because the pandemic meant most of our f2f was cancelled until this summer. The course is really cool: it's designed to help people who work in healthcare or public health, and are currently approximately the only person in their organization who understands genomics, to train colleagues so that in future we can use modern sequencing methods to deal with infectious diseases. Not just Covid, which sort of kick-started the sequencing revolution, but other diseases too. So for example prescribing antibiotics based on sure knowledge they will work rather than trial and error until something shows up that the bugs aren't resistant to. Or quickly and definitively finding the source of an outbreak within a hospital. Or (and sorry guys, this is a bit apocalyptic) noticing when vaccine-derived polio strains mutate to become virulent and acting to prevent further spread.

The biggest challenge in some ways was finding the 'only genomics person in the organization' but we eventually managed to recruit two dozen such people from across the UK and Ireland. Which made for a really interesting bunch of students! Again, I'm really grateful that the timing of my Covid, although it made me miss Yom Kippur, didn't prevent me from leading this course. Also honestly if it hadn't been immediately after recovering from Covid I would have been quite nervous about it; I was indoors all day long for a week with over 30 mostly unmasked people who had travelled from all over the country, and I had to remove my mask to teach and sometimes to eat. We asked people to take LFTs before the start of the course, and at least once during the five day run. So I was only shut up in an enclosed space with people who had recent negative rapid tests, so that's at least something. One of the external instructors tested positive so she was able to teach her section on Zoom. One of my colleagues turned up on day 1 but had to go home sick, and another had rather nasty cold symptoms and turned up anyway, relying on the negative test. And one of the students had to leave the course early with a fever, so I'm not sure how much I should trust those "negatives".

I think it was a course that genuinely benefitted from being in person, for lots of reasons. But I also think we could, and should, have done more to mitigate risk, either leaving the windows open all the time or installing HEPA filters, and insisting on masking to the extent reasonable. I chose not to stay on campus or join the participants for dinner, so I didn't get the full experience of a full-time course.

Anyway, the teaching was very enjoyable but absolutely exhausting. I would certainly expect to be tired after a full long day of in-person teaching, but on this occasion I was actually shaky and nauseous by the time I got home, and could barely summon the energy to prepare and eat dinner before crashing out. I'm hoping this is just the aftermath of my Covid bout and doesn't indicate that I picked up another infection. But also, if this is as bad as it gets, if I have permanently lost the stamina to stand up in front of a class for most of a ten-hour day several days in a row, then I can work round that, it will make my life more awkward in some ways but it's not absolutely debilitating.

Today I skipped shul as I'm still feeling a bit tired and off-colour. Instead jack and I went for the most glorious walk in a little wood near Histon, and had brunch in the courtyard of a hipstery cafe we've been meaning to try for a while. And basically life is good, though I am not fully recovered physically.

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Organizing teaching resources

2022-02-10T19:36:32Z

So the first online course of our giant international Covid training project is live: behold The power of genomics to understand the Covid-19 pandemic.

I'm mainly linking to show off, but you're welcome to join if you'd like. It's pitched at a scientific audience but if you have high school biology and some general curiosity you'll probably make sense of most of it. Totally free of cost and it doesn't matter if you poke at it but don't complete it.

Getting it over the line has been a massive enterprise; basically it's involved three months of shifting our entire way of working from a local thing mostly run by me and senior minion, to this incredibly complex collaboration with the COG consortium, already a huge mega-group across many different institutions. Plus we are desperately trying to decolonize! all! the! things! and work on an equal level with experts from all over the world, even though most of the UK team are used to a Eurocentric model of training.

I mean one of the reasons it's slightly delayed is that Omicron hit in the middle of the development process. The African-led group who first identified the variant got extremely angry with the rich countries that punished their disclosure instead of helping them with the crisis. Which was entirely justified but we got somewhat caught in the backlash and a bunch of previously enthusiastic African collaborators decided they didn't trust Europeans at all any more. We are honestly trying not to be parasitic White Saviours, but it's a learning curve and it's basically fair that we've run out of benefit of the doubt and second chances with some people.

Anyway, work discussions and planning have reminded me that in my personal life, I've spent the pandemic years creating and accumulating a huge pile of teaching resources, while I'm teaching on Zoom and don't have access to books, or the books available aren't suitable for what I'm trying to achieve. But it's all a big mess just dumped into a directory on my computer.

I know I have information management people among my circle. Would you be willing to give me some hints for organizing all my electronic teaching materials? I feel like I should know this kind of thing based on my professional experience, but actually... I've either been in large institutions and relied on infrastructure and expert support, or I've been in backwaters who never really had an IM strategy and just got away with things being in a bit of a muddle because the scale was small enough that it never got unmanageable.

What I need is some kind of sensible plan for my personal materials, so I can find them again and adapt and reuse them. I am willing to spend some money but not five figure sums on subscribing to a service meant for institutions, not individuals. It needs to be something fairly easy to use; if even starting to tag and store things becomes a massive faff I'll end up just not doing it. I would strongly prefer something where the architecture is on my own computer and not in the cloud. I don't have a massive amount of stuff in terms of file size, just a very large number of mostly text files. Backups would be good but that's not the main part of the problem I'm trying to solve.

And-a-pony level would be something that can easily manage a mix of English language and Hebrew language materials, but I can probably catalogue things in English and use transliteration as appropriate.

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Language things

2021-09-28T21:29:30Z

So today I worked in the office for the first time in a year and a half. I'm exhausted from leaving the house at 7:15 am and not getting back until 7 pm, I've spent more time indoors with non-bubble people than basically the whole pandemic put together, and I'm not at all convinced it was worth it. However it is work policy that we have to be in person one day a week and honestly four days a week remote is better than the pre-pandemic situation of WFH being a very rare exception. The new normal involves hot-desking, and regular PCR tests, which I also don't love, but I think I will hate it less when it becomes more routine and when my team are also around for campus days.

Anyway, rather than whine about my mostly quite fortunate work situation, have some links I've enjoyed recently.

1] Twitter thread explaining kerning. Best if you can read both text and images as there are lovely animations explaining the concepts. If you find thread readers more accessible than Twitter there are some unrolled versions in the first few comments, though I'm aware that some people have moral objections to thread readers.

2] Video explaining an demonstrating American accents. On YouTube, visuals add a little bit of framing but are not essential. A transcript would be basically meaningless since the whole point is to hear examples of different accents.

The main presenter, Erik Singer, is a real virtuoso, a dialect coach who can imitate lots of different accents really well. Maybe all this stuff is completely elementary to Americans or linguists, but I learned a lot from the way he explains both the history and the phonology of different accents. And he's not making value judgements about different accents, just explaining how and why they are different. I particularly like that he invites linguists from various ethnic backgrounds to explain the accents of the communities that they belong to and study.

3] We're just at the end of the cycle of autumn festivals, with Simchat Torah, which celebrates reaching the end and restarting the annual reading of Torah. The Ark Liberal synagogue in north London has a cool video showing what the Torah scroll looks like. Many communities have a custom of unrolling the whole scroll for Simchat Torah and this is a kind of digital equivalent, though for some reason they roll from the end to the beginning rather than in the obvious direction.

This is also on YouTube; the visuals are the whole point. There is an audio track consisting of the kind of Israeli-Jewish songs that are often sung at the festival, but if you can't hear it you don't lose much. If you've never a seen a book written on a parchment scroll before the video gives a really nice impression. And if, like me, you didn't get to an in person Simchat Torah service because of the pandemic, it's a nice little memento.

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Work

2021-06-21T20:19:12Z

So. Um. This is now public: my employers just won a major grant to help train the whole world in Covid sequencing and analysis, to the same high standard that the UK's Covid Genomics Consortium (COG-UK) have achieved. For the next two years, I'm the education specialist in a massive cross-institutional team trying to save the world from the pandemic.

I've been in post a year and a half. What I was employed to do was run a nice little programme creating 2-3 specialist MOOCs a year. Half a year in the pandemic hit, and I was able to continue running my online courses programme while working from home. Well, to be fair it's not so little, the Massive nature of MOOCs means that we are training tens of thousands of people each year and numbers shot up when most of the world was in lockdown.

And now this. One of the questions asked when we were applying for this money was, just what is the upper limit on these online courses? What if we get hundreds of thousands at the same time? Millions? I was able to confidently say that FutureLearn is really scalable, both technically and in terms of how the education works. But there was certainly a moment of vertigo when one of the foremost genomics experts in the world was asking me, what if millions of people all want to learn your stuff?

The way this works is that I'm not actually going to be personally training hundreds of thousands of people all over the world. I'm managing a team of specialists who are actually going to create the courses. The content is going to be provided by specialist researchers whose full time job will be to find out and document what COG-UK are doing and what information needs to be passed on to all the sequencing labs and healthcare systems in other countries. My colleagues are going to be running more targeted courses, for hundreds or thousands of people learning in parallel across each of the three continents (this is the 'remote classrooms model' described in the press release).

In terms of my day-to-day life I'm going to shift, in the next couple of months, from managing one person to heading a team. I've so far had the easiest introduction to management I could have had, since my report is just unreasonably brilliant and hard-working and supportive, and my biggest problem has been making sure she gets recognition for how fantastic she is. Now I'm going to be directly line managing a second education developer, an administrator (and an education technologist who is actually from a different new project). And coordinating my team with this huge consortium of Covid experts and global thought leaders. In order to run a project of the utmost significance: we're developing training to address a literally existential threat.

I think I have some emotions about this, but I'm not quite sure how to describe what they are.

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Work update

2021-03-05T14:54:10Z

Thank you to all of you who helped with my two new courses. I wanted to show off the finished products.

Bioinformatics for biologists somehow managed to attract ten thousand people! The reason we made the course in the first place was because a lot of people were asking for it, but I'm really pleased to see such a huge number pouncing on it.

Genomic Scenarios in Primary Care has basically eaten my 2021 so far, so I'm especially glad to get it out of the door. It feels good to be working in medical-adjacent training again. Doctors can be frustrating to work with because they do absolutely everything at the last minute, for the entirely understandable reason that patient care is always their first priority and is prone to emergencies. But they are also genuinely awesome colleagues if you're willing to be very, very relaxed about deadlines, just really knowledgeable and excited to communicate.

(If you go delving in those courses you can probably figure out my wallet name; I'm not really worried about that. I just don't want search engines to be able to find this journal based on my rather unusual name.)

Courses are free of charge, you do have to provide a meaningful email address but that's all. It's totally fine to sign up if you're just curious, but I think some of you or people you know might find them actually useful and interesting.

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Please help make my courses awesome

2021-01-22T10:44:46Z

So back in that weird twilight zone between the Before Times and the Time of Isolation, I asked for volunteers to beta read a new free online course I was producing at work. During the weird 10 months since, we have been working somewhat interruptedly on new material, and we now have two new courses for release in the coming weeks. I'm looking for beta testers again.

The two courses are at approximately opposite ends of the spectrum of what we do. Course A is a very gentle introduction to scripting and the command line, aimed at life scientists with little computing background, or at least little experience with Linux and Free Software. You don't need any real biology to test this course, but if you hate science you probably won't find it an enjoyable experience. In terms of Linux experience we would like some testers who, like our target audience, have never worked in a command line, and some who understand the technical part enough to spot errors in the code or the explanations.

Course B is a broad overview of why genomics has lately become important in medicine as well as science, mainly aimed at GPs. It assumes a clinical audience, and uses a lot of unglossed medical jargon. It doesn't explain the basic biology, just jumps straight in to modern cutting-edge genomics. You probably need some interest in medicine and at least high school biology, but if it's too technical for a generally scientifically literate but non-specialist person that's something we'd want to fix.

We need people who can put in a couple of hours, and just play around with the course and see if there are any obvious problems, whether that's technical issues like display problems for your particular hardware and software, or conceptual problems like confusing instructions or something that doesn't make sense. We are definitely not expecting any one individual to go through a whole course in detail, and we're not looking for copy editing or proofreading. I mean, if you have the sort of brain that can't help spotting typos, we don't mind reports of those, but we're mainly looking for something more general than that.

Course A (intro to Bioinformatics) is a bit of a rush job and if you volunteer you need to be available to get your comments back to us by the end of next week. Course B (genomics for GPs) needs testers in the next couple of weeks and will still have to be done on a fairly tight turnaround.

Other than doing some good for the world, what you get out of it is a £25 Amazon voucher. So in order to get paid you need to be in a position to receive and spend an Amazon voucher. We might possibly be able to acquire vouchers for other countries' versions of Amazon, or else I can informally arrange to swap to something more locally useful. But it's not employment, it's a volunteer thing with a small token of appreciation.

Last year I had way more volunteers than I actually had space for, so thank you all for being awesome. Since there are two courses concerned I can now take on up to 8 people. I will give priority to people who wanted to help before but were turned away since we had too many volunteers.

Feel free to ask questions in the comments, but if you actually want to sign up you need to interact with my work persona, so I'll ask you to PM me about arranging that. You're also welcome to pass the request on to anyone else who might be interested.

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I made a thing!

2020-04-07T12:26:55Z

So, to break up the all pandemic all the time posts: I spent most of March getting my first big project at work over the line. I and my team have just released a FutureLearn MOOC. Behold: Antimicrobial Resistance in Bacterial Pathogens.

It's not completely unrelated to the pandemic, because it's about using genomics methods to detect and avoid antibiotic resistance, and track outbreaks of infectious diseases, albeit bacterial rather than viral. It turned out the timing was quite fortuitous, because the whole world is under lockdown and lots of people have time for taking online courses and interest in epidemics and outbreaks.

So slightly under halfway through the course, we have 5000 sign-ups, from basically every country in the world except places like North Korea and Turkmenistan that don't let people access the internet. And we got a personal message of congratulations from the head of section for making such an awesome course.

On the other hand the timing was slightly disastrous because two weeks before launch the lead educator had to drop out of working on the course and go off to run the national Covid-19 sequencing effort. The rest of the team pulled together in very trying circumstances, more than just the general lockdown and emergency, they're all more or less directly involved in clinical-related work on the pandemic. But the last few weeks have been intense, to say the least.

You're welcome to have a go if you like. It's completely free as in beer - we're funded by the Wellcome Trust so we pay for everybody to have premium access to the course. It's quite technical though; our target audience was basically people who are already working in the field of antibiotic resistance but want to learn about modern cutting edge techniques. If you have college-level science and a general interest it should be fine, and we do have a bunch of keen secondary school students who are desperate for something to learn while public exams are cancelled.

If you are excited about it but it's a bit too technical, there is a companion course called Disease outbreaks and antimicrobial resistance. Which I didn't really work on directly, it all happened before I joined the institution, but it's still part of the portfolio of courses I manage.

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Beta readers?

2020-03-10T10:12:22Z

ETA: You guys are amazing. I was really not expecting to get so many volunteers! I have more than enough people for now. I'm happy to add any additional names to the list for future opportunities. I can't add any more volunteers for this course, otherwise it would end up being all my friends which isn't great for diversity.

My awesome job involves creating free online courses about genomics. The first course I've been fully in charge of is about to go live, and it needs some final quality checks. It's quite exciting IMO: it's about using genomics to identify and avoid antibiotic resistance.

We need people who can put in a couple of hours in the next week, and just play around with the course and see if there are any obvious problems, whether that's technical issues like display problems for your particular hardware and software, or conceptual problems like confusing instructions or something that doesn't make sense. We are definitely not expecting any one individual to go through the whole course in detail, and we're not looking for copy editing or proofreading. I mean, if you have the sort of brain that can't help spotting typos, we don't mind reports of those, but we're mainly looking for something more general than that.

We want people from all backgrounds, so a mix of people who know something about microbiology and genomics, and people who have no idea. I will say that the course is fairly technical, though, so you probably don't want to volunteer if sciencey stuff is hateful or scary to you. We are especially happy to have beta readers who aren't completely fluent in English to be more representative of our target audience.

Other than doing some good for the world, what you get out of it is a £25 Amazon voucher. So in order to get paid you need to be in a position to receive and spend an Amazon voucher. We might possibly be able to acquire vouchers for other countries' versions of Amazon, or else I can informally arrange to swap to something more locally useful. But it's not employment, it's a volunteer thing with a small token of appreciation.

Feel free to ask questions in the comments, but if you actually want to sign up you need to interact with my work persona, so I'll ask you to PM me about arranging that. You're also welcome to pass the request on to anyone else who might be interested. The number of available slots is somewhat flexible, probably in the range of 3-5.

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Job!

2019-10-10T15:57:21Z

Now I actually have a contract in hand, I can talk about this online: I have the most exciting new job, starting on Monday. I'm going to be working in genomics education, as Education Manager for the online courses programme.

This is basically exactly where I hoped to end up when I took the gamble of moving away from my tenured academic job to work on an educational project. I needed to fill a gap in my CV and be in a position to demonstrate successful leadership. It got a bit scary for most of 2019, because I did indeed successfully lead a project, but I didn't have a job lined up when the original project finished in February, and then I got a 5 month extension, and I still didn't have a job lined up at the end of that five months. I didn't completely lose heart, because I was able to apply for interesting and more senior education jobs as I'd hoped, and I was sometimes getting shortlisted, but then again I was only finding relevant job ads about once a month, and being second choice is good for the ego but it doesn't amount to actually having a job.

So I left my job when my contract ended at the end of July, and I have had really quite a nice two month break. A bit like those long summer vacations you get as a child, though I ended up with so many grown-up responsibilities that I don't quite know how I would have managed if I'd also been working full time...

Anyway, about a month ago my former line manager and close colleague sent me this job advert for a dream job I hadn't quite realized existed. The thing is that as a little kid I was completely obsessed with genetics, certainly from the age of about 3 when I got distracted from learning about where babies come from because I was much more interested in how they resemble their parents and how they develop from a single cell. In the 90s I glommed on to all the popular stuff about genetics and the race to sequence the human genome, which was especially prominent growing up in Cambridge in the shadow of the Sanger Institute. I was in the middle of a biochemistry degree when the actual human genome sequence was announced, and I continued to hope that I might one day get to work on something that exciting.

And I did get the chance to pursue biology research for about 15 years, a PhD with another of my childhood heroes, a post-doc at the Karolinska, and then a tenured job at Keele. That was an amazing joy in many ways, but also I'm not cut out to be a traditional academic; I love the research, but I hate applying for grants and dealing with university politics. The thing is, I've identified as a teacher for just as long as I've wanted to be a scientist, and when the research career didn't work out, I knew I wanted to be doing something related to education. I still can't quite believe that a job exists which requires me to be an education expert and have a serious background in molecular biology.

The plan is that I'm going to be developing a suite of online courses relating to genomics, and integrating them with in-person courses and most excitingly, the international development programme. So I am going to be getting sent out to partner countries in the developing world to help set up genomics education programmes there. It's going to be all about building educational community, too. I do have some geek negativity towards becoming a "manager" rather than the person who actually does stuff, but I'm pretty sure this is the right thing for me because it means I can use my skills in supporting and facilitating, but in a context where I also have respect and prestige.

The interview was kind of ridiculously good, I was building a good rapport with all of the panel and it was obvious I ticked all their boxes perfectly. There was a fair amount of faff with HR, so I've been kind of hinting at having a job but not actually announcing it online until I actually had the contract in hand.

There are a couple of downsides: the Genome Campus is in the middle of nowhere so as a non-driver I'm going to have a bit of a grim commute, I'll have to be on a bus at 8 am sharp every morning. And it's a one year fixed term thing providing cover for the original post-holder who has had to take long-term sick leave. But I'm pretty hopeful that I'll be placed to do something exciting at the end of the year, either extending the post or moving on to something else where the Sanger name and the international experience will open doors.

Heartfelt thanks to everybody who has supported me through the last few years of being uncertain of my career direction.

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Who wants to give me careers advice?

2019-07-04T20:16:04Z

So two years ago I left my tenured academic job because it was making me miserable and requiring me to commute 300 miles a week. And I took up a fixed term job working on an interesting project about using modern teaching methods to make sure all students, including minorities, have a good experience at university. The project has come to an end, and it has been pretty much everything I hoped for; my CV is much more interesting and diverse now, and includes some leadership experience.

So I'm able to apply for a much wider range of jobs, and more senior jobs, now. And I'm sometimes getting shortlisted but so far nobody actually wants to offer me a job. So I'm going to be out of work from the end of the month, and I don't know what to do next.

I genuinely don't know what job I'm looking for. In fact, I don't think there exists a standard job title or career path for people like me.

My highest priority in a job is that I want a lot of autonomy and a lot of variety. I've found that the easiest way to get that is academia, and therefore I've worked in academia my entire adult life. Also, I really really enjoy teaching, and I would like a job that includes at least some teaching and preferably a lot. I'm certainly willing to consider jobs outside academia if I get to decide what I want to do each day between interesting options, and if any organization at all is willing to hire me with zero experience other than in universities.

I'm 40 and thus probably around half way through my career. I'm in principle willing to retrain, but it would have to be definitely the right thing, I don't want to spend a lot of time and money on more education just for the sake of it. I'd really rather get a job that uses the skills and knowledge I already have. That's quite a variety of stuff; although my career has been pretty linear, I've picked up a lot of really eclectic skills along the way, especially through volunteering.

I'm good at:

Teaching (any age and level)
Causing disparate groups of people to bond together into a community with a common purpose
Research (most of my experience is in natural science, but I have two years of professional level education research and I'm generically good at finding out and analysing information)
Communication, not only with people like me, but higher ups, people from very different backgrounds, and just about anyone really.

The second point is the most difficult to fit into a job niche. Lots of people are good at teaching, research and communication, but very few people cause communities the way I do. All the good jobs I've had have been in institutions that value that, and I don't get those jobs unless people count volunteer experience as experience.

I'm not very good at: physically demanding stuff, or anything that requires me to do boring but attention-requiring work. I think I'm at least potentially competent at management, more technical management that is focused on a particular skill or task than general management of people and orgs, and I have some leadership skills (see: community creation). But I don't have a lot of formal experience of the sorts of things that tick hiring people's boxes as 'management' or 'leadership'.

I want to do something at least vaguely socially beneficial, though I think very few possible employers are totally morally pure. I am willing to work more than 40 hours a week only if it's genuinely a one-off crisis; I strongly prefer not to be doing that regularly. I don't drive at all, and I would really like a commute of half an hour or less by bike, or an hour or less by public transport. I'm in principle ok with working from home, but I am a giant extrovert and I thrive more in jobs where I get to talk to other humans regularly.

Those things are all priorities over salary, but I'm currently on £40K and I could get by on less than that but would rather not be massively financially constrained. If nothing else because most of my social circle including several of my partners earn quite a bit more than I do. But equally, I'm from a generation and background that have lead to not carrying any debt, and I don't have any dependants, so I can afford to prioritize other things than income.

I would be somewhat willing to go back to a traditional academic job in bioscience, but it's definitely not my first choice. And also I don't think I'd actually land such a job, because I don't have a particularly stellar CV and mainstream academic jobs are ridiculously competitive. Equally I'm very willing to consider something completely out of left field, which is why I'm making this an open post and asking for any suggestions.

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Cultural exchange

2018-09-04T10:20:27Z

One of the things I love about my job is that when you're helping people to redesign their teaching they ask you for advice about all kinds of random things. This one I think I need to crowdsource:

My colleague is running an exchange trip where she's taking some of her students to Washington DC along with some students from a Southern US state. She wants to take some small gifts / prizes for the American students.

So my question to American or American-knowledgeable friends is, if you were an American college student, what small, inexpensive, transportable item would you be excited to receive from English visitors? Are there any (snack) foods you think of as excitingly and exotically British?

And to my compatriots, what should my colleague take that will seem like a nice souvenir of England or the UK? Particularly, can you think of anything that is typical of Cambridge the town but isn't about Cambridge Uni?

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Excel help?

2018-02-15T10:21:23Z

I have a spreadsheet with approx forty thousand rows. Around 6000 of them are irrelevant - they're mixed in with the rest, but are identifiable based on data in one of the columns. The data covers three years. The years are not recorded as proper dates, but as plain text saying things like 2015/16.

My task is that for each year, I need to count the unique values in one of the columns. This column contains only text, no blanks. It's not made out of meaningful English words, but serial numbers containing letters and digits. The values in each column are repeated anywhere from 1 to 60 times; I just want to know how many different serial numbers there are, not overall, but separately for each year.

Year	Serial Number	Flag
2015/16	AAA111	Relevant
2015/16	AAA128	Irrelevant
2016/17	AAA111	Irrelevant
2016/17	AAB139	Relevant
2016/17	AAA111	Relevant

My own knowledge of Excel, supplemented by searching for things like Excel count unique values, isn't quite sufficient. Anything that involves doing this semi-manually (eg sorting the columns then counting by hand) is unfeasible over tens of thousands of rows. Anything automated needs to not make Excel choke with a large-ish spreadsheet.

I tried following the instructions in this official Microsoft article, and it's not quite working for my case. As soon as I try to filter a column by unique values only, it overrides the filter I started with for taking out the 6000 rows marked 'irrelevant' in a different column. Even worse than that, instead of copying the roughly 10,000 cells in the same column that I tried to select, it copies a whole chunk of the spreadsheet with several columns and I'm not sure exactly how it's related to the area I selected. The second method, count using functions, I don't understand well enough to try, and since the method I thought I understood behaved very unexpectedly, I don't want to start blindly pasting in a formula I really won't be able to debug.

Does anyone have any suggestions for how to approach this?

(The reason why I'm trying to wrangle this myself rather than delegating it to someone who has relevant expertise is, well, annoying work politics. But the fact remains that I need to do it.)

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Departure

2017-09-18T21:38:25Z

I've never left a job before. I spent my 20s as a contract researcher, and when my project came to an end, I just... didn't work in that lab any more. So I didn't know how to give notice, how to do the tax paperwork, it was all completely new to me. Also, the people I've been working closely with for the past eight years were all actually sad to see me go and wanted to mark the rite of passage. That was new to me too, in a mostly touching but slightly bittersweet way.

So I returned from the wedding and spent Tuesday and Wednesday fairly frantically packing. Somewhere in there a man with a van came to pick up the bed that was a wedding present from my grandmother, and my brother is getting it but I was really quite sad to see it drive away.

Then Thursday I ordered in my sister's cakes for colleagues. About 30 people turned up, partly for the cake which was received with great enthusiasm, but I think in large part also to say goodbye to me. They said some really sweet things; my boss' speech was about how I'm really supportive to both colleagues and students, and always enthusiastic and cheerful and willing to help out. They gave me a spotty Emma Bridgewater teapot, which was of course the obvious present, being both a local souvenir and something tea related. But I think I may actually own too many teapots, if such a thing is possible, because people keep on giving me them due to my well known obessession with tea.

Then I had a brief panic because I thought I'd lost my phone, retraced my steps back to my flat and discovered I'd just failed to pick it up when I left in the morning. And in the afternoon we went out for a team bonding event, which wasn't officially part of my leaving do but happened on the same day and got rather conflated with it. A colleague had organized an Escape Rooms event. That turned out to be a lot of fun; I like my colleagues enough that going out with them is genuinely enjoyable, and anyway solving puzzles together carries a lower risk of being horribly cringey than a lot of team bonding stuff.

I enjoyed the game for its own sake too. They'd done a lot with a small space, with half a dozen rooms to solve and plenty of variety within that. Some searching the physical space for clues, some code-breaking though nothing very taxing or frustrating to people who don't have much experience with that sort of puzzle, some lateral thinking and finding clues in a steganographic way. And a very small amount of physical skill such as grabbing a key that was out of arm's reach. The puzzle was also pretty atmospheric, though the one my team was randomly assigned to was horror themed, involving a lot of gore and severed limbs. Well, it's kind of hard to squick a team of medically trained people, mostly anatomists, but even so, I can imagine some people would find it hard to have fun with that flavour. Also, it was dark, and they deliberately undersupplied the players with torches. In our case that was largely a positive, because it meant we had to work actually together, we couldn't divide up and have some people searching and others code-breaking, since we all had to cluster round the light sources. Anyway, I gather most of the escape room puzzles aren't like that, just the one we happened to play.

Then there was the kind of torrential downpour that's kept happening through most of this summer, so we had a drink in a somewhat random little bar in the shopping mall, and continued chatting until we could get to cars without being soaked. We went back via work mainly because some people needed to leave from there, rather than trying to do any work for the last half hour of the day, and then we headed out to my absolute favourite country pub, The Hand and Trumpet, for my leaving meal. That was really nice too; not all the people I'm closest with were able to make it, but lots of people I like and I was pleased that people I don't necessarily know that well made the effort. Also several of the senior team; they're the kind of senior team who often do turn up to colleague's celebrations, so it's not that I was especially honoured, but I do like working somewhere where that's the case. By the end of the evening I was a very full, slightly tipsy and happy extrovert. And I felt really, really valued.

And the next day the movers came in and stripped my flat, and I handed back the keys and my work pass, and walked away from the past eight years of my life. From the job which in 2009 was my dream job that I never expected to leave. From my tenured position, and from scientific research altogether.

I started my new job the following Monday. I need to work out how much I should talk about that in detail here; for one thing it's looking to involve somewhat more blogging and social media presence as my professional persona than the old job did. Also I am still adjusting to living in Cambridge full time, which is probably another post, and I'm up to my eyes preparing for the High Holy Days beginning on Wednesday, so I am going to stick with posting about leaving rather than about arriving for now.

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Group work

2017-08-08T14:18:47Z

I'm on a mission to redeem group work in education. I expect this to be controversial among many of my friends. So if I'm right and lots of you have terrible memories / experiences of being made to do bad group work, I invite you to comment here and tell me what was bad about it. Do you think it's just awful, or are there problems that might be fixed? I believe strongly that while it can be dire, it can also be great, or perhaps I might phrase it as, there are things that look like group work superficially but are actually great.

Because I'm on a mission this may turn into a more formal research survey at some point, but in that case I'll pose the question in a formal context with ethics and everything. Right now I'm just trying to gather some opinions and not just rely on my own ideas. Plus I am eye-deep in paperwork and I could do with some distraction, so do rant away.

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Throwing money at problems

2017-01-24T21:39:06Z

Thank you all so much for all the supportive comments on my post with squee about the awesome bar mitzvah. I feel really loved!

In another instance of my students being brilliant, I ran a session recently to introduce the first year medics to the concept of public health. We ended with an exercise which I found rather fun, so I thought I'd offer it to you to play:

A philanthropist is offering a grant of £250,000 to someone who can propose a way to improve the situation in a deprived housing estate. Population ~10K, annual healthcare spend roughly £100 million. The philanthropist wants to see improvements on a 30 year timescale, and wants the actual inhabitants to be involved in the project in a community building sort of way. What would you do?

I divided my students into two groups and got them to pitch their ideas to me. And I was impressed at how they came out with completely opposite solutions. One group wanted to run a really small-scale educational programme to help schoolkids and their parents to learn about healthy eating, calculating that £250K over 30 years amounts to about £8000 per year and trying to keep within that budget. The other group suggested using the money as seed funding to attract new businesses to the area, aiming to create jobs and increase the tax income so that local facilities could be improved. I think both of those ideas are somewhat unrealistic, but this is a bunch of mostly teenagers, and I really liked both the group who thought about just how far a quarter of a million will (won't) stretch when you're dealing with entrenched social problems, and their colleagues who thought about dealing with some of the root causes of poverty and deprivation.

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Young people today

2016-12-15T13:40:59Z

I must say I really like teaching the Tumblr generation. They get a lot of flack from older pundits for caring too much about social justice and identity politics, but I just find it really refreshing working with people half my age who take gender and sexual diversity completely for granted, and have a sophisticated analysis of racism, and are constantly asking for the curriculum to be more globalized and more diverse.

Five to seven years ago, when I was new to teaching, I was a bit shocked to find how homophobic the student body was. I live in a bubble and I started out believing we'd moved on from the Section 28 era. But I found that my straight students were, at best, absolutely ignorant of anything to do with sexual diversity. They giggled when discussing a case study about a lesbian couple, and they had vaguely heard of gay men, whom they assumed to be obviously effeminate, but thought of gayness as a rare and exotic condition. They asked questions like, you know how gay men have a different way of speaking, doesn't that mean that being gay must be genetic? That kind of thing was well-meant, though it must have been pretty miserable for non-straight students in the group. The worst instances were things like when a particular student was absent from a tutorial group, and a fellow student mentioned that they thought the absentee might be GAY, as if this were some kind of scandalous gossip.

The last few years, though, those who were born in the last years of the 90s (I know!), and came of age in the era of same-sex marriage and internet social justice, they're completely different. They'll remind teachers to be more inclusive of identities beyond just "gay" and "straight". They take it absolutely as read that their colleagues and patients include a diverse range of gender identities and sexual orientations, they can talk (without prompting) about the difference between sex and gender. And I noticed the materials for the class on gender and sexuality (which I was supposed to facilitate but an administrative muddle meant that I actually didn't) now cite Kate Bornstein and mention things like the trans community's justified grievances against medical gatekeepers. So, you know, the medical school is moving forward too, it's not only the students.

Even a few years back it was often difficult to get the students to have sensible discussions about racism. The white students would talk about not seeing colour and saw racism as an outdated issue with little relevance to the modern world. Or they'd complain about political correctness and how they were scared of getting into trouble for accidentally saying the wrong word, and worry about patients being "over-sensitive" and seeing imaginary discrimation whenever they didn't get what they wanted. And the Asian and Black students would look increasingly uncomfortable but rarely felt able to enter the discussion. Nowadays they don't even pick up the bait of "do you think racism is still a problem?", they only hesitate over whether they're allowed to say "duh" to a tutor. Without making a fuss about it, the groups naturally let the students of colour lead on discussions about racism, with white students asking questions and adding minor corroborations. They do discuss topics like whether anti-white racism exists, in a sensitive and nuanced way, including things like anti-Polish and anti-zigan prejudice. I witnessed a really fascinating discussion between two Black students in a particular group recently, where one repeated the claim that racism is always present but the targets shift: it used to be Jews, then it was Black people, but now Black people are ok and it's Muslims that face problems. And it was the other Black student who challenged him, no, anti-Black racism is still a major issue today. Judging by accents I think the first student is probably from an immigrant background and the second British raised.

The last few weeks of term have a bunch of teaching about disability, and yes, the students still struggle intellectually with the social model, but they've got a lot more aware of ableism and are committed to eradicating such prejudice from the medical community. Even the "soft" ableism of worrying about how disabled people would have poor quality of life and therefore don't benefit as much from medical treatment seems to be almost gone. I did my best devil's advocate and couldn't get anyone to concede any compromise on strict equality between disabled and abled patients, including a clear grasp of the concept that equality means adapting treatment to the individual rather than offering strictly the same treatment to all. The lesbian couple I mentioned earlier? Now nobody even questions the idea of two women seeking fertility treatment, and they were pretty game about the idea of deaf mothers actively seeking to conceive a genetically deaf child, understanding that some people consider being Deaf to be a cultural difference not a disability.

So I'm not saying that everything is perfect and prejudice within the medical world will die out as the older generation retire. But it's such a joy to work with these students who want us to improve our teaching to be more social justice focused, compared to only a few years back when students kind of resented hearing about prejudice and inequality, cos obviously they're not racist so why waste time that could be used for learning physiology.

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GIP

2016-05-20T16:45:36Z

Remember when we used to make posts to show off new icons? Well, I have the most adorable students ever: for an end-of-term present they made me a custom mug with a little cartoon of me teaching the class about p53. I asked the artist if I could use the cartoon as a profile pic, so here it is. (Click through to DW to see both the icon and the full-sized version.)

I am so very endeared by this. In fact, I squee'd so much when I saw it that my students declared me adorable, which I'm not sure is how it's supposed to work. But hey, I like 'adorable' better than 'intimidating'. (They've also given me a 100% positive evaluation this term, which is going to be very nice evidence to present at my appraisal next week.)

Full size original behind the cut - I think maybe it wants cropping a bit closer so it's just the picture of me, as you can't see the detail of the molecule or my speech bubble. I do love that my characteristic comment is "coolness", which I totally picked up from lethargic_man.

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Life

2016-01-19T14:27:43Z

I ought to write a review of the year, I'll be glad to have done so when I look back at old journal entries in future. But I keep getting stuck because I have strange feelings about 2015. It feels like a year I will look back on and conclude that it marked the start of a change in my life direction, but that change hasn't happened quite yet.

2015 was the year of being in love, the year of establishing lots of new relationships. I mean, it was late in 2014 that I realized my friends were romantically interested in me and jack, and I think by Christmas 2014 I was unquestionably and intensely in love, but it was the months of 2015 when the new relationship energy coalesced into actually functioning as a quad. 2015 when all four of us told our parents and where applicable sibs about the relationship, when we started to have tentative discussions about some kind of future together, though we still don't know exactly what shape that will look like.

2015 was also my worst year at work. Not really horrible compared to a lot of what people experience in a bad workplace, but it's been difficult and at times I was really scared for the future. I had a 'not meeting expectations' appraisal in early summer, which is not a terrible disaster in the scheme of things, but it was the culmination of several months when I found myself really anxious and just somehow falling more and more behind and not keeping deadlines and that all spiralled a bit. Some of this was related to the fact that my senior PhD student has had a pretty troubled final year of her studies, and it's still not certain whether she'll come out of all this with a PhD. To recap, I have essentially two half-time jobs, one in the medical school and one in the research institute; the medical school have been very helpful and supportive and done all the right managerial things and given me lots of support to make sure that one bad quarter remains only a blip and chances to sort things out. The research institute not so much; they've switched unpredictably between ignoring me and leaving me to struggle, being actively hostile, and occasionally coming through with some random and not very systematic help.

I spent the summer clawing myself up out of the mess I'd got myself into. And of course starting from behind made that hard, and I was scared, and I suffered somewhat of a setback when my junior PhD student failed her "Progression", the process where the institute decides at the end of first year whether a student is suitable to go on and do a full PhD. She and I both worked really hard through the last few months of the year, and the medical school supported me by reducing my teaching and admin load so I could be there for my students. And this week she passed the resit panel, so as soon as that is formally ratified I can breathe much more easily again. So in many ways I can be proud of myself for extracting myself from a bad situation, but somewhere along the way I lost track of my love for research.

In the summer I found a job at a Cambridge college that I reckoned I was qualified for. I applied, was shortlisted, got really good feedback from the interview, and just narrowly missed out on the job. That prompted a lot of soul-searching; was I really willing to give up my extremely shiny tenured academic job where I'm clearly making a positive difference to the world, both doing cancer research and helping to make new doctors? And the more I thought about it the more I thought that is what I want, I want a job that I can do which is not constantly stressful, and I want to live permanently in Cambridge near my loves.

The problem is that I find it really hard to trust that decision. Just because I've had one bad year at work, so what, that's hardly a reason to give up all my dreams. And being in love seems like a bad reason to make such a dramatic change. I really hope this relationship will endure and grow and make me solidly happy, but it's still new enough that pinning everything on it feels like a gamble. It's hard to know how much the two strands are connected; did I fall behind and get into trouble at work because I was putting all my energy into new relationship? Did I tell myself I was in love in order to give myself a rationalization for potentially quitting an almost unbelievably good job?

I really, really don't know. I think I will be happier in Cambridge in the long term even if my lovely quad doesn't work out as well as I'm hoping. I think I've been dissatisfied with my job for a while; reading back over my work tag I feel like it's been several years that I've been talking about the job like a relationship that isn't positive any more but which I'm scared to leave because I made a lifelong commitment to it. There's a whole load of financial anxiety; if it were just me I'm pretty sure I'd rather earn less and have a job I enjoy more, but I'm worried about being dependent on my husband, I'm worried about the ways that my family have supported me financially to get to this place and it feels like it's not only my money that I'm considering handling unwisely.

I also have gender anxiety, because this is exactly what women stereotypically do, they get to a certain stage in competitive careers and then throw it all in and end up in support roles because they prioritize family life over ambition. I'm very conscious of Linley Hall's very good account of why women leave science; it's very clear from her research that women don't leave because of overt sexism, but because of all kinds of perfectly reasonable reasons (like wanting to devote time and energy to a family) which in practice disproportionately affect women.

The other thing is that over Christmas I got to spend time with one of my closest and oldest friends, MK, whom I see all too rarely cos he lives in Australia and doesn't do social media. I knew coming out to him was going to be hard, because he lives in very straight circles and as I suspected hasn't really come across poly before. He wasn't negative, he didn't try to tell me my choices were disgusting or immoral or whatever, but he was understanding the relationship as some kind of crazy soap-opera type thing and using lots of metaphors from his profession, crystallography, to explain why a relationship with four people couldn't ever possibly be stable. And in particular he really really pushed back against my proposal to leave my academic research job and look for a job in Cambridge. I mean, he was in some ways exactly what I needed because he voiced precisely my own doubts about making this choice. He said, if you're having a mid-life crisis go buy yourself a Harley or something, don't give up your entire career that you've been working for these twenty years we've been friends. His wife, too, who has really given her all to maintain her own scientific career after having a child very young and needing to make compromises to support M's career, not to mention far worse political issues with science funding than I've faced.

So anyway, yes, that's 2015. I really don't know where I'll be by the end of this year, but I expect to look back on 2015 as a kind of watershed. Any comments or advice very much welcome!

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Day in the life

2015-07-10T16:00:35Z

So I thought some people might not know and might be interested in what my job actually looks like. So here's a summary of how today has gone. It's not a typical day as such; one thing I really like about being a university academic is the variety, but it's also not wildly atypical either, it's a non-special day of the summer season.

I slept in 'til 8 because I had scheduled a meeting for 9:30 and Life Sciences is a stone's throw from my front door. In the end I was slightly late because I stopped to chat on the stairs to a colleague who had relevant information about funding options.

The meeting was between me, my #1 PhD student and the professor who is co-supervising her, and who is also my line manager for the research half of my job. #1 student is working on a new protein which controls whether cells die or grow, meaning that it's likely to be important in cancer. We spent most of the time discussing a new paper that has come out which suggests that our protein may also do similar things in gestational diabetes – as well as sometimes making tumour cells grow where they shouldn't, it apparently makes babies grow too big, a common complication of diabetes during pregnancy. We agreed we'll write to the people who discovered this and ask them about methods and reagents; their work is related enough to ours that it makes sense to collaborate, but since they're working on diabetes and not cancer, we're not likely to be seen as rivals. We also talked about what experiments #1 student will do next week and whether we need to buy her any more reagents. We planned an experiment she wants to work on involving looking at which genes are switched on or off when her protein is present. Since it's a new protein we kind of have no idea where to start, but I signed off on about three quarters of her sensible suggestions and substituted a couple of my own instead of genes I think are less likely to be interesting.

After that I went to help my #2 student who is learning to grow tumour cells in the lab. So partly that's learning what healthy cells look like and the practicalities of how to keep them fed and healthy, how to count them accurately etc. But the biggest part of it is learning to work aseptically and avoid contaminating her cultures. Tumour cells are a bit more robust than normal cells, but still they're fundamentally adapted to an environment inside the body where temperature, oxygen levels, pH and all kinds of subtle electrochemical things are very tightly controlled. So if you try to grow them in little plastic bottles, even though you try to keep the conditions suitable, you haven't got anything like as subtle control as body homeostasis, so they're really pretty fragile. On the other hand yeasts are very well adapted to growing wherever they happen to find themselves, so if they get into a culture with lots of nutrients kept at a constant 37°C they will basically be in paradise and quickly out-compete all the cancer cells. There are other, nastier bugs out there too, like some tiny bacteria that will directly infect our cells and multiply inside them, subtly changing cell behaviour so that none of our results make sense any more. And can't be detected except by intentionally looking for genes unique to them, and are resistant to most antibiotics.

So #2 student is learning how to work without letting anything that touches the cells come into contact with non-sterile surfaces. It's quite fiddly, and requires paying quite close attention, because it's impossible to never touch anything but it is possible to notice when you have made a mistake and replace the potentially contaminated item with a new, clean one. It's things like taking lids off one-handed and holding the lid between your fingers, while you use your dominant hand to transfer the liquid between vessels. (Sometimes I do this in the kitchen too, take a lid off a bottle with my thumb and forefinger and hold it between my ring and middle fingers of my left (off) hand; it's a very deeply engrained habit!) Things like mixing liquids by carefully swirling them, but not inverting the bottle or otherwise letting the liquid splash into the neck and lid. The growing cells look a bit like this under the microscope, if you're curious.

I had an awkward half-hour break between helping my #2 student and my next meeting, so I dealt with a handful of emails, mostly about people who want to see me to talk about various things related to planning teaching for next term. Then I walked across the campus to the Medical School, a very pleasant walk at this time of year when the campus is nearly empty of students but full of roses and strawberries and all kinds of growing things.

This meeting involved counselling an undergraduate student who has just failed her major end of year exams. She's very upset because she's never failed anything in her life, so some of it was just reassuring her that one poor mark is redeemable, it doesn't mean she can never be a doctor. And some of it was looking through her paper and trying to troubleshoot what went wrong. (The students have to book appointments with members of staff to look at their papers, and they're not allowed to take them away, because there's a thriving black market in medical school exam papers, which is extremely annoying to us and to the 99% of students who are totally honest and wouldn't dream of selling past exam papers.) We did a bunch of strategizing about how to improve her marks enough to pass her resits, and also about how to improve her learning and revision skills if she does make it to the next year of the course.

At this point it was nearly 3 pm and I hadn't had lunch, so I came home and put on some pasta and made myself a pot of tea. Since then I've been basically internet shopping, pricing up reagents we might buy for future experiments. This is one of the least intellectually stimulating parts of my job, so I'm procrastinating from it by updating DW. And I shall probably knock off a bit early since it's Friday and nobody I need to interact with is likely to be around much after 5.

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Reading Wednesday (mostly links)

2015-06-24T10:33:33Z

Recently read Some very good stuff on my DW reading page:

untonuggan is hilarious on the subject of cats and internet security

seekingferret challenges the popular simplification that Einstein overthrew Newton

jack wrote some interesting meta on Magic in Jo Walton's Among Others. Personally I found that one of the most satisfying depictions of magic I've encountered in fantasy, precisely because it falls into neither of the traps of being completely random and depending on the needs of the plot, nor completely systematic so that it's just like a parallel type of physics or a dice-based role-playing system. The linked posts are somewhat spoilery, mine more than jack's, but don't completely reveal the main plot; anyway they probably won't make much sense if you haven't read the book.

And one Tumblr post, which is just quintessentially Tumblr, a conversation between people geeking out about the ridiculousness of folk song tropes. I particularly liked elodieunderglass' contributions, including a playlist of I guess my corpse is a swan now: a weird folk education. Well worth following that link for elodieunderglass' annotations and the discussion, even if you don't want to listen to the songs themselves.

Currently reading Most of the way through my friend's long unpublished novel, so hopefully there will be interesting reading Wednesday posts again soon.

Up next Possibly Ancillary Sword by Ann Leckie, as I'd like to read that before Worldcon.

I'm also pondering what leads to interesting online conversations. I had my first actual interesting discussion on FB in the decade or so I've been (mostly reluctantly) using the site, because I Tweeted that I'd found myself trying to explain to a Christian child the difference between magic and miracles. Turns out lots of people have opinions about that topic. And FB have sort of half-heartedly introduced threading, which maybe helps a bit. Whereas over here, people had absolutely masses to say about the topic of modest dress, which I had expected would be one of those obscure things that only one or two religion geeks would care about. I'm really enjoying the discussion, anyway.

My post about the broken system that is PhD training still reliably accounts for nearly a fifth of all the traffic to my DW, even two and a half years after I wrote it. Again, I didn't expect it to be of more than specialist interest, but it's turned out to be the thing that made me internet-famous. And I'm reminded of it right now because both my PhD students are having struggles and I'm trying to be more supportive than a typical bad supervisor, but we'll see.

Also today I initiated my newer student into mammalian cell culture, and I'm reminded of when I got sent to a collaborator to improve my technique and she informed me that her culture hood was 'The Holy of Holies'. I'd been missing the mental focus of trying to work 'in total purity', and I even almost miss my hands smelling of disposable gloves. And now my student knows I talk to my cancer cells; I reckon she still respects me.

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Film: Wit

2015-03-03T11:02:48Z

Reason for watching it: We screened it for the second year students, who are getting to the point where they're spending enough time in clinical environments that there's a good chance they will see someone die in the coming months. The idea is that they get a supportive environment in which to do at least some of the emotional work ahead of dealing with this for real, and hopefully they then won't completely fall apart when that happens. (There's a ton of research about the detrimental effects of medical students and trainee doctors not being adequately prepared to deal with death, but nobody quite knows what "adequately prepared" looks like. So we're working on it.)

Circumstances of watching it: Ugh, this term! I've had a solid six weeks with a heavy enough teaching and marking load that I feel I've been running a Red Queen's race since the new year, I haven't had time to do anything at all non-urgent, and it's making me really anxious. In theory things were supposed to slow down by the end of February; in practice everybody's kind of scrabbling, and the school were short of staff for running a bunch of sessions through March, so I've ended up roped into more teaching in the coming weeks. And because it's all last minute cover it's all in bits of the curriculum well outside my expertise. I really didn't want to be a facilitator for this session where we get the students to talk about death, but needs must. I kind of feel like this is one of the times where it's more important than usual to have a clinician leading, cos it's not just factual knowledge, it's being able to speak from experience of dealing with death as a doctor. But I suppose I was better than no-one.

Verdict: Wit is thought-provoking if at times over-dramatic.

So, look, the whole point of this film is that it's 90 minutes of the protagonist dying of cancer. Not in real time, it covers several months from diagnosis to the end, but the whole film, and therefore my review, is about illness and dying within the medical system.

Wit is basically Emma Thompson doing a TV version of a srs intellectual play, which had won the Pulitzer prize a couple of years before this film was made. And it's not bad for getting the medical students thinking, because it contrasts the personal, emotional experiences of the protag, with the rather unfeeling medical machine that just treats her as a problem to be fixed or a research topic to be studied. There's a bunch of doctors with basically no bedside manner (why are the research oncologists always the evil ones?) and a very sweet, sympathetic African-American nurse who is the only person who actually cares for Prof Bearing as a person.

Thompson's character, Prof Bearing, spends most of the film quoting Donne a lot, and making snarky, slightly fourth-wall breaking quips to the camera about how a drama falls short of representing the horror that is dying of metastatic cancer. The film certainly took a step further towards realism than most Hollywood representations of hospitals and terminal illness, but it wasn't more realism than you could bear to watch, it's still prettied up quite a lot. There's a little bit of throwing up, but it's fairly symbolic. Even right at the end Thompson looks like, well, a beautiful actress with a shaved head, who hasn't had a good night's sleep and has a bit of a cold sore, and not very much like someone dying of cancer.

The emotional stuff was handled well, you got this whole arc where Bearing has this self-image as a competent intellectual, and she desperately tries to carry on being brisk and sarcastic and clever when actually she's terrified and in pain and and falling apart physically and emotionally. I've always liked Thompson as an actor, and the character of Prof Bearing is not very much like me but is somewhat like the person I thought I might become, when I was a teenager, a respected academic who doesn't really do interpersonal stuff more than she has to. So on some level I could relate to her. I'm not hugely fond of the way that Hollywood portrays academics; there's a lot of reciting poetry in a dramatic voice, particularly Death be not proud, and pontificating about the importance of the commas for understanding Donne's poetry, but hey. I didn't like the very end of the film where she sort of falls back on the classic tropes for conveying suffering, which are not representative of how most people in pain actually act, but I suppose that was necessary to convey the emotional point.

Anyway, it's not a film I particularly recommend unless you're trying to help some students to think about death, but it's not a terrible film for what it is.

It seems possible that I'm somewhat emotionally affected by this; the film is genuinely harrowing in places as well as a bit over-dramatic. And running the discussion where I had to manage a lot of the medical students' emotions was pretty draining, I think, especially coming on top of generally stressful stuff. So lots of things that should be fine are feeling daunting, just now. Send hugs pls?

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December days: Things ending, things beginning

2014-12-31T15:49:25Z

silveradept requested: around the end of the month: Things ending, things beginning. And I'm a couple of days behind on posts which means I'm writing this right at the end of the month, not just around it. And, well, I've just come back from blue_mai's mother's funeral, having started 2014 with joining lethargic_man at part of the shiva (memorial prayers in the week after a funeral) for his mother. So my head is very much in lives ending, not just things in general. Which means this post is working out a little melancholy, and I'm sorry this in the slot where I meant to answer zhelana's much more positive prompt for my favorite moment of the month. Might manage that before the day, the month and the year roll over into the new, we'll see.

Being 36 feels a little bit Nel mezzo del cammin di nostra vita, somehow, though I think average life expectancy for healthy thirty year olds in rich countries is rather longer than the Biblical three score and ten. In practical terms it means it's no longer surprising for my peers to be burying parents. There's all these endings of relationships that have been central to many of our lives up to now, and beginnings of taking on the reins of being the top generation of our families, especially as still-surviving parents are increasingly frail.

I asked Mum to come with me to the funeral, because she's good at funerals, she knows the right thing to say to friends and relatives of the deceased we hadn't met. But her being good at funerals is sort of an awful thing, and I'm thinking, partly how glad I am that I still have my mother to ask for support with this kind of thing, but also partly that I expect to build up a similar bank of experience over the coming years and decades. The first person whose body Mum prepared when she started volunteering with the religious group who perform that ceremony was more or less her age.

And that very nearly all the people I grew up thinking of as the older generation of my communities are gone. I heard today of the death of someone I was fond of a few years ago but had lost touch with when she moved away from Cambridge, and thought, so young! but actually given she remembers Kristallnacht she can't have been much under 80. (And really, the whole generation who came over as refugees from Europe in the 30s and 40s, who personally lived through those horrors, are either very elderly or dead, and I haven't quite adjusted my mental calendar to that reality.)

The obvious thing to do is therefore to talk about beginnings of lives too. Now I'm in my mid-thirties, most of my friends who want to have children (I think about three quarters of them, given the choice) are getting on with doing so. I sort of imagined this, when I was younger, that I would start to stick out more within my social group as someone without kids of my own. Actually it's not really like that, there are lots of people whose lives haven't really changed as much as I imaginegd now they've become parents, or at least not to the point where they no longer want to socialize with childfree people. (At my birthday party a guest who didn't know me very well took some friends' children for mine, and it was just an endearing mistake and not the cause of several days of panic, which may mean I'm finally getting better at this.) And lots of people who want children but don't have them, because of fertility problems or just not being in the right relationship, the right life situation, and we're old enough now that people are worrying that if it doesn't happen soon it might never happen. So it's not that I've never before supported friends dealing with either parenting or mourning the vanishing opportunity, but that lately this is a common theme rather than an exception.

What else? At work the cohort of medical students that includes a cluster I happened to get on well with are completing their final exams and starting to apply for jobs as actual doctors. I am really heartened that a few of them contacted me for references and careers advice, including one who is really brilliant but comes from enough of a non-trad background that she didn't have the confidence to apply for a highly competitive post, and I convinced her she could. I mean, she takes 99.9% of the credit for being generally awesome, but I am proud of being in the right place at the right time to get her to believe she is. So they're ending their education and starting their careers; I am looking forward to the 2015 graduation, it's going to be people I'm fond of.

My older PhD student is starting to think about finishing her thesis and maybe even planning her career beyond that; we've got a lot to cover in her third year to get her to the right level, but it's exciting. And my new PhD student who started in September is settling in, almost getting to the point of being useful in the lab more than she's a liability. Again, nicely generational, having that sort of gap between my students. (I try to bite my tongue from using sibling metaphors for them, because that implies I'm their parent, which I'm really not, but it's still a little like that.)

The university as a whole came out fairly well, especially for a small institution, in the latest round of government-mandated metrics and targets which has been eating everybody's life for the past couple of years. We went to a meeting on the last day of term and literally they announced, don't worry, we're not getting sacked, something we hadn't known for sure a day before. Bloody bloody education politics, I can't even, but that's a lot less bad than it might have been. Several senior management people put in post primarily to deal with the evil REF are moving on, and I have some hope that we'll have at least a few years to get on with research and perhaps have some real leadership that isn't geared towards ticking the boxes for the assessors.

And in my personal life I find myself at the beginning of something which is too early to be comfortable talking about publicly, but I am ending the year brimming with joyful hope.

Not entirely on topic, but siderea has written an absolutely brilliant and inspiring reflection for the end of a year which has included so much awfulness, notably police forces in America going rogue and killing African-American children and young men. I strongly recommend: Long Night (Staying Woke).

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December days: Work / family / social life balance

2014-12-08T16:19:04Z

falena gave me a very thinky prompt of:

Work/family/social life balance? You seem to be doing it right, despite all geographical limitations and full-time work.

Honestly, I'm not sure I do get it right, but let me try and talk about this a bit.

There's a sort of glurgey saying people sometimes quote about how nobody ever regrets on their deathbed that they didn't spend more time in the office. Whereas to an extent I do worry about ending up regretting that. Because my work is in many ways more exciting and more worthwhile than most of my hobbies. I'd in many ways rather be in the office than playing around on the internet, or doing housework, or even than going to parties which I enjoy but aren't as satisfying as training future doctors or helping to contribute to advancing human knowledge.

It's also hard not to feel like the only way to succeed in academia is to work way more than your contracted hours and put career ahead of absolutely everything else. On some level I recognize that my feeling like this, feeling guilty every time I take a full two-day weekend or knock off for the evening 8 hours after starting, is a sign that academia is a sick system, not that I'm "not dedicated enough". But it's also the case that pretty much every one of my colleagues who is achieving more visible professional success than I am is also putting in more hours than me, often substantially more.

I'm in charge of what I want to do with my evenings and weekends, of course, so if I feel like this I obviously do have the option to spend them, not necessarily physically in the office, but doing work. And I don't, partly because I am in fact lazy and not that dedicated, but more seriously because I politically believe in labour rights and the principle that people should in fact do what they're contracted to do. Tens of hours of free labour a week should not be the requirement for career advancement. I'm also less and less productive the more hours I'm trying to work beyond a sensible level like 40-ish hours a week. If I don't take breaks on a daily, weekly and holiday basis, if I don't spend time doing things which might be in the grand scheme of things less satisfying than my job, I won't be able to do my job well. In some ways I'm a bit scared of success, I'm scared of making myself ill or burning out, and I'm scared of the way that the reward for doing well at your job in academia is very much the opportunity to work more; if I get on the treadmill, I'm afraid I'll never get off.

I'm sorry for bitching about academia so much. In many ways the flexible hours of academia do help with having a balance. I don't have to clock in or fill in timesheets, so I completely can work four long days instead of 5 short ones, or take a morning off to deal with practical life stuff and make up for by working a Sunday, or finish an hour early if there's nothing useful for me to do, or work from home which means I can multi-task with housework and internetting a bit. So that helps as well as being a huge great thumb on the scales I'm trying to keep balanced here.

There's the question of what I'm balancing with. For a long time I believed that since I'm childfree and very much intending to stay that way, I don't have any major conflicting obligations so the right thing to do is to concentrate on my career. But that's not really true; I have obligations to myself, to my community, to my friends, family, partners, and they may be less pressing than the obligations a parent has to young children but they're still real. So it's not just a matter of taking care of my mental and physical health, it's a matter of people having meaningful claims on me, even though they're not paying my salary. It is in fact important to me to have time and energy for Jewish community volunteering, and I find myself a little at odds with both the rationalist community and some of feminism in my attitude to how important volunteering is. It is important to me to be a good friend to my friends.

So how do I actually balance things? As a university student, I made the decision that I would remember the Sabbath. I would not treat it as optional, which is kind of how things were when I was growing up, and I would equally not focus heavily on the ritual observances that constitute keeping the Sabbath, something I experienced for a bit when I was dating people who do in fact keep those observances. So no matter how much of an essay deadline or looming exams I had, I did things other than academic work from Friday evening until Saturday evening. And I've kept that up into my professional life. I sometimes end up working after sunset on Friday, especially since I've never lived further south than the 50th parallel, meaning that sunset on Friday can be very early. But once I go home on Friday afternoon, I stop work. I simply don't count the hours of Friday evening and Saturday as part of what's available when I'm planning my time (even in a crunch), if something has to be completed by Sunday then the last possible minute I can do it is 5 pm on Friday. That does actually help a lot, because having my sabbath be non-optional means it never gets overridden by "urgent" work requirements.

Another thing I do is I volunteer for things that require a regular commitment. I can't just decide I don't feel like, or I'm too busy for, leading services or running events this week, because other people are relying on me. At the moment the bulk of that commitment does in fact fall on Friday evenings, which works well with my attitude to the sabbath, but there's enough stuff that comes up on other days that I simply can't live life in the expectation of having all my evenings and Sundays available for work.

I make sure I set aside time for keeping in touch with people, primarily through keeping up with both reading and writing here at Dreamwidth, but that's quite a high priority for me. Like, right now I'm taking a little time out of the working day to write today's December Day post, having other commitments this evening. And that in turn means I get invited to social things. I accept and issue invitations for at least one thing most weekends, and those I could get out of if I absolutely have to, but I prefer not to. That also means that I don't spend too much of my downtime doing things that are basically pointless, like playing silly computer games or getting into a mindless gratification loop of reading the internet. I have, as I've discussed in several other places, a regular routine of weekly commuting to Cambridge, which means I get to spend time with jack even if we don't do all that much other than just being in eachothers' presence, and it's often also an opportunity to see other friends fairly spontaneously, even if I don't get round to planning something in advance. That can be a pain because of the travel time, but it does help to keep me from treating weekends as a potential extension of work time.

I think in many ways my work/life balance ideal is what I observed in Sweden, putting in real effort to working hard without distractions for about four two-hour chunks during the day with appropriate breaks, five days a week, and completely not thinking about work at all during evenings, weekends and the summer vacation. And I don't always live up to that ideal, I faff about and procrastinate during work time, and have to make up for that by extending the hours I spend doing work-related things.

To an extent this isn't the ideal as far as university management is concerned; they kind of want people to spend all their contracted hours doing boring admin stuff to keep the university running smoothly and bring in income and so on, and use their 'free' time to do the actual interesting research. Doing things that way round of course gives a further motivation for academics to put in extra hours, because there's a perception that the stuff you're actually interested in doing, the stuff that motivates you to work in this sector, is discretionary rather than compulsory. (Can't quickly find the really horrifying article I read recently from an academic explaining unironically why putting in more hours is a good thing.) So if that means that I'm not competitive compared to the people who do give free labour in that way, I'm more or less at peace with that. Not perfectly at peace, but I do generally accept that I might end up getting stuck in a dead end or even losing my job, and if that happens I'll deal with it and not regret all the time I've spent with my loved ones and looking after my own wellbeing.

I hope that isn't depressing, falena! To give an example, and because I'm doing daily posting and therefore not having much time for typical journalling, last weekend jack's parents visited, and I spent some of the time hanging out with them and some of it working on the lecture that needed to be done by Monday. And managed to fit in playing board games and drinking tea with cjwatson and ghoti and their children for a couple of hours. And this weekend I've spent quite a lot of the mornings asleep, and managed more gaming with cjwatson and ghoti and family, and dinner with ceb and IWJ one evening and with H WINODW another. And I've been working from home today, which meant I had time for lunch with cjwatson and time for a longish tea-break writing this post, and tonight I'm going for dinner with ghoti. At the same time I worked late several evenings last week because immediate student welfare crises came up when I didn't have any slack in my schedule to deal with them. And it's nearly chanukah which is needing a bit of organizing, on top of my normal Friday night services and Hebrew teaching, so that's taken up a lot of the remaining evenings.

I really admire people who manage to balance serious caring responsibilities plus a full-time job, or have a work-life balance in spite of chronic illness or disability which may well be hard to plan for and schedule round. But from my relatively comfortable and easy position, this is about how I manage, or don't.

[December Days masterpost]

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