Where in the world?

Bloggers clam up!

Bloggers clam up! Bloggers clam up!

Quiz question: where were these two photos taken?

For bonus points: add a photo of yourself in the same location to this nascent collection…

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Unexpectedly transferable skills

The transferable skills developed over the course of a PhD have been a recurring theme on this blog. I have blogged both about being trained and, later, about training other students, in the skills that might be useful beyond the office, lab, and thesis. This Christmas, those very transferable skills I developed came into their own in an unexpected way on our wedding day.

Cultivating the ability to think flexibly is important during PhD study. When research is underway, plans often change, and you need to be able to think about novel solutions in order to avoid getting stuck. This was true on our wedding day too! A last-minute organisational twist meant my husband-to-be was the one to pick me up from my parents’  house and drive the two of us to our ceremony. Luckily I am not someone who sticks slavishly to tradition, because this led to one of my favourite photos of the whole day.

Off to get married!

Off to get married! Via jjcule on instagram.

In common with Frank, we had our ceremony at a registry office. I thank the registrars who made our ceremony moving and meaningful. A particular shout-out to my brother Ant, who stole the ceremony show with a reading of his poem Oh Brother! (Brother of Three Sisters).

Ant steals the show.

Ant steals the show. © DJ Norwood

Nothing in my PhD prepared me for this next bit:

What do you mean, I can’t do this in Emacs?
© DJ Norwood

The ability to adapt to unexpected findings came to the fore again as we left the registry office, when the traditional shower of confetti was replaced by a traditionally British erm, rain shower. Note the redeployment of umbrellas as a wedding archway.

The Newlyweds: Dr Cule and Mr Clark © DJ Norwood

About eighteen months ago, I collaborated with Ant on this blog post about giving a scientific talk. At the time I did not imagine the day I would apply the advice given there to my wedding speech. The night before the wedding, in a last-minute rehearsal reminiscent of those I did for my conference presentations, I practised in front of a friend who had given a speech at his own wedding less than one year earlier. He reminded me that when speaking at your wedding, the audience are on your side. This is in contrast to speaking at a scientific conference, where the audience can be bored, contrary, or, if you are unlucky, downright hostile. The guests at a wedding are more likely to support you and to laugh in the right places. With a combination of Ants’ tips in mind and my friends and family in the room, and the experience I had giving talks over the past few years, I quite enjoyed giving my speech.

“Just remember to focus on the important results…no…wait…”
© DJ Norwood

Thanks go to Guildford Registry Office (for a meaningful and touching ceremony), The Watts Gallery in Compton (for the use of their beautiful venue), Daniel J Norwood (who took the photographs), Rhubarb (who catered) and Carrie at the Topiary Tree (who did the flowers). Most of all, thanks to friends and family, and especially to my parents, who made it all possible, in more ways than one. And thanks to my Shiny New Husband, too, without whom the past eight years would have been a lot less fun.

Cheers! © DJ Norwood

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Notebooks

Back in 2009 the day, in a discussion on the recently archived Nature Network, I mentioned that I liked to draft blog posts the old-fashioned way. I wrote that “It is easier to get started with a pen and paper than a blank screen.” Whilst then I was talking about blogging, the same applies when I work. If you do research in the lab, you have your lab book, or increasingly these days your electronic lab book. For a desk-based or computer-based job like my PhD, record-keeping is no less important, although if you are lucky it involves fewer stains.

During my PhD I developed a few systems for keeping everything organised. On the recommendation of a successful PhD student, since my MSc days I have used version control for everything, from software development to the thesis itself. I recommend learning version control to everyone. I used Papers for, erm, papers and backed up my entire computer using Time Machine. This latter saved my bacon on more than one occasion.

Through experience, I concluded that the maxim “one line of comments for every line of code” only seems excessive at the time you are writing it. As a consequence the code I wrote early in my PhD is substantially less readable than the more recent work. But commenting your code, and version control, are no good for the random jottings, the thoughts, and the figuring things out. For that I relied on a series of notebooks, which I carried about like a talisman and made copious notes in.

My PhD in notebooks

My PhD in notebooks

To-do lists

To-do lists To-do listsTo-do lists

As Jenny found, these notebooks are a record of the unspoken PhD. I was, and remain, a fan of the to-do list, even when during the PhD my to-do list looked pitifully similar from one day to the next. Looking back on my notebooks, it is clear that progress is inversely proportional to number of doodles in the margins. Stars were a popular choice of doodle.

Doodles

DoodlesDoodlesDoodles

Athene wrote earlier this year about the wrench that is Jettisoning One’s Past, an activity often prompted by a physical move – be it moving office, house or job. However, as fast as I can turn my back on old notes and notebooks I acquire new ones. A year into my new job I am already on my third notebook there. And away from work, the boy husband, who knows of my love of notebooks, bought me a wedding-Christmas gift in which to note down those happy memories of our honeymoon and the start of married life.

Married life in notebooks

Married life in notebooks

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Paying it forward

Requirements for bound copies of the thesis

I submitted a physical, bound final copy of my thesis.

Once the corrections to my thesis had been approved by my examiners, I ordered copies bound in regulation purple and submitted one to Imperial College Library. As of March this year, a purple bound copy is no longer required – students submit their final copy electronically and their thesis is made available in Spiral instead. I submitted my thesis for examination in January, so fell under the “old” rules.

Bound thesis

Obligatory photo of the final product.

In July, I received an email awarding me my degree. I was told my degree certificate would be in the post “within three months”. So I was excited when a letter arrived from Imperial College London, addressed to Dr Erika Cule. However, the letter contained not my degree certificate but a mailshot promoting Imperial Alumni Office’s 2013 fundraising campaign.

The alumni office emailed me to apologise for this mishap, an apology I accepted. It was clear to me that it was hardly their fault! Moreover, the 2013 campaign will raise money for a Very Worthy Cause which I will be happy to support: the campaign will raise funds for the Rector’s Scholarship Fund, which gives undergraduate and postgraduate scholarships. I feel I curious affinity for my alma mater and would be proud to support the campaign. Imperial certainly gave me a great deal, even if it hasn’t given me my PhD certificate yet, and when I get the phone call I feel inclined to donate, so that other students might have the chances I had.

I had the opportunity to pay it forward in a more immediate and practical sense last week when I went back to Imperial’s South Kensington campus to attend a “Careers speed dating” evening. This event was organised by the Department of Life Sciences for current Biology and Biochemistry undergraduates. I felt nervous, being such a newly-minted graduate myself, but when I turned up on the day I was the oldest alumnus of the undergraduate degree who had volunteered – the other alumni who volunteered had graduated from the BSc between 2009 and 2012.

So many degrees, they wouldn’t all fit on the nametag.

Despite the economic downturn in the intervening years, we alumni covered a range of careers between us, from current PhD students to a teacher and a management consultant. As the name suggests, the format of the evening was modelled on speed dating (I am told, having never been speed dating). Each alumnus talked to a small group of current undergraduates, and every seven minutes a bell sounded indicating that the group should move on to the next alumnus.

It was exhausting! I don’t think I have ever talked about myself at such length. By the third or fourth group of student questioners, I found myself unable to remember whether I was repeating myself or talking to a new group of students, as naturally the students had similar questions for me. I directed a few of them to this blog to read about my PhD experience, so if you are reading, hi! I hope I was positive and encouraging even when I was recounting the difficult bits of my career journey.

At the end of the evening, alumni were given a thank-you gift.

“Don’t be a mug. Go to Imperial.”


I certainly wasn’t expecting to profit from the evening.

It was a pleasure to spend time with interested students, and to find out how the course I started back in 2005 has changed over the past few years. Hopefully I either answer the students’ questions or, where I couldn’t, pointed them in the direction of someone who might be able to. Thanks to Anita Hall for organising the event. As the evening drew to a close, I felt I had “paid it forward” in a practical way – something I would recommend and would do again. And I still feel I owe something to the alumni telephone campaign. This year, the value of an Imperial College mug, at least.

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The supporting cast

A PhD is, by definition, a lonely endeavour. My fellow students and I were taught the fundamentals of team work as part of our transferable skills training, only for one academic to comment that for a career in academia, they would have been better teaching you how to pretend to get on with each other and then turn around and stab each other in the back. You might be lucky enough to progress without any backstabbing. Nonetheless, when you pass the unofficial but significant milestone which is the moment when you come to realise that you know more about your topic than your supervisor, working life can become isolating very quickly indeed.

Because a PhD is to a large extent a solo journey, it is immensely helpful to have a support network around you. I had a great relationship with my supervisor, but for day-to-day support I remain indebted to my office-mates, with whom I shared an office with no windows for a large part of my PhD. We had this PhD comic stuck to the door.

Happening Outside

I’ve already thanked the folks at Occam’s T and beyond for their support whilst I was studying. As a computer-based researcher, sometimes social networks felt like a lifeline. I was chastised by my non-research friends for having my twitter client running in the background, and I did have to turn it off from time to time. But there is a substantial community of bioinformatics and statistics researchers on twitter, and somehow their background chat did make me feel less alone. Not to mention the more than one occasion I called on them for emergency help:

Solving problems using Twitter

Recent PhD graduates, in my own department and elsewhere, were immensely sympathetic when my motivation dwindled. The ones who smiled at the memory and reminisced oh, I quite enjoyed my PhD I found less helpful, but each to their own. Befriend the non-reserach staff, too, as they have seen it all before. One ran into me in my second year and commented

You’re in your second year now? Let me see…in the first year, you don’t have a clue what’s going on; in the second year, nothing works, and in the third year…you write up! 

Which proved remarkable prescient. I often recalled these words.

Beyond academia, I must thank my family, who were endlessly supportive, reassuring, and encouraging – and occasionally baffled: you don’t have to put yourself through this, you know. And my friends from outside of university were very patient when they asked how I was only for me to reply, for the third or fourth time in as many meetings, don’t do a PhD. When I received an invitation to our ten-years-since-we-left-school reunion, a few weeks before I submitted the thesis, I refused to buy a ticket until after the viva:

High School Reunion

At the reunion itself, I did proudly tell my old maths teacher that I was now Dr Cule. And my biology teacher was himself a PhD, so we reminisced about the trials of the process. Whilst the technologies have changed, the challenges of doctoral research seem to be remarkably robust over time.

Doing something as all-consuming as a PhD affects one’s relationships. When the boy held my hair back as I vomited into the toilet bowl of PhD depression, mopped up my tears, and passed me a glass of wine, I wondered whether any professional qualification would be this tough on a partnership. Does becoming a (medical) doctor, or a lawyer, or an accountant or an actuary or a teacher, draw its students in in such an emotional fashion? I often tell people that my doing a PhD was okay, because the boy was starting his own business, so we were both very busy. If one of us was working, the other wasn’t resentful – chances are, they were working too. It was during this time that I came up with the idea for the dedication page.

So I want to say is whilst the research is lonely, the rest of PhD life doesn’t have to be. I drew heavily on my support networks and I find it difficult to know how to thank you all.

Thanking the boy was easy though. We will marry in December. For Occam’s Typewriter, 2013 is turning out to be a good year.

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Margaret McCartney at Skeptics in the Pub

xkcd 1131

Back in 2009, Hal Varian, Chief Economist at Google, said in an interview

I keep saying the sexy job in the next ten years will be statisticians.

More recently, his review of Nate Silver‘s The Signal and the Noise, Larry Wasserman explained

I used to tell people at parties that I am an oil-fire fighter. Now I’ll say: “I’m a statistician. You know. Like that guy Nate Silver.”

If being a statistician makes you sexy, then surely someone who takes an interest in statistics and saves peoples lives as part of her job can assume she has a certain cachet. Earlier this year, I saw Dr Margaret McCartney, Glaswegian GP and outspoken proponent of evidence-based medicine, at Skeptics in the Pub.

Margaret McCartney

Margaret McCartney


I read Dr McCartney’s book The Patient Paradox: Why sexed-up medicine is bad for your health soon after it was published last year. What impressed me about this book extended beyond eye-opening examples such as Edwina Currie’s admission that breast screening was attractive in political terms, with scant understanding of the impact of screening on the women pressured into undergoing it. Any sophisticated discussion of the benefits and costs of screening processes must incorporate some discussion of the numbers. Concepts such as sensitivity and specificity, statistical power, and false-positive and false-negative rates have the potential to confuse readers. But unlike some other popular science authors, Dr McCartney does not shy away from these ideas nor apologise to the reader for discussing them. Important concepts are presented using sometimes counter-intuitive examples to illustrate the impact on patients.
The Patient Paradox

Available from all good bookshops, or from the publisher’s website


If you have a chance to see Dr McCartney speak, then do. (If you don’t, then read the book.) Her talk at SITP included some material from the book. There were some updates that have arisen since the book was published, such as her thoughts on this emotive advertising campaign.

Importantly, Dr McCartney presented http://privatehealthscreen.org, the website she and some fellow doctors launched last October. The site was set up out of concern: the doctors view advertisements promoting private screening tests in the UK as unfair to those reading them. You can read why here. If you or anyone you know are thinking of paying for private screening tests, this website is a useful resource. The site was recently awarded a Good Thinking Society grant.

Compared to the book, the talk at SITP included somewhat more beer, and a lot more swearing. The talk was funny and engaging, and she handled insistent SITP hecklers with aplomb. An in-person explanation clarified several concepts for me, including the difference between screening and diagnostic tests, which I had not really thought about before.

In a discussion about risk with my GP, I mentioned Dr McCartney’s book. At my next visit, my GP said that they had read it, and now recommends to the trainee GPs at the practice. Doctors make decisions based on risk on a daily basis. If both doctors and their patients can become better acquainted with the harms as well as the benefits associated with screening, this knowledge will enable them to make more informed decisions about their health care.

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Dénouement

Last week:


The ever-helpful @ crew are giving @ viva (thesis defense) tips & anecdotes via email. Hope we haven’t scared her too much…
@enniscath
Cath Ennis



@ @ @ vodka and red trousers. You know it makes sense.
@enniscath
Cath Ennis

Today: passed, with minor corrections. Although without vodka or red trousers.

Thanks again, guys.

Posted in Fun, Life, PhD | 8 Comments

Science Online 2013 without the carbon footprint

#scio13wp

Science Online 2013 kicked off yesterday in North Carolina.

For those of us who are not able to make it to the conference in person, watch parties the world over facilitate virtual attendance. In the UK, Eva Amsen and I are co-hosting the London Science Online 2013 Watch Party this Saturday, 2nd February.

It’s going to be as good as being there. We’ve got a great day planned. All our events take place in and around South Kensington, with the Watch Party itself being held at Imperial College Union. The day will kick off with some fringe events of our own. We will start with a visit to the Turing exhibition at the Science Museum:

After touring Turning, before the Watch Party, we plan to have a group late lunch.

We have an awesome venue for the watch party itself, thanks to the kind folks at Imperial Cinema

Imperial College Cinema

We will try to move the dancers out of the way

…who are also handling AV for us.

Projecting

You want to watch what???

During the Watch Party, we will watch and discuss some time-shifted sessions that were recorded live. We are taking a vote on which of these pre-recorded talks to watch. When you sign up for the Watch Party, do not forget to vote for the session that interests you the most. Mid-watch-party, We will link up live with conference attendees Laura and Lou for a live Q & A. If you are at the conference and want to chat to us too, get in touch with Laura as we’d love to say Hi!

It’s not too late to register for the London Watch Party. If you have any questions about the Watch Party, send us a tweet and we will help you out.

Spread the word, and we will see you there!

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Sacrifice and Submission

Narratives of sacrifice are woven into many stories about research. Nobel laureate Dr Barry Marshall famously drank a culture of Helicobacter pylori in order to demonstrate that the bacterium is indeed the causative agent of stomach ulcers. Closer to my home, one colleague who is now a postdoc took to sleeping in his office during the closing weeks of his PhD study:

I borrowed one of the benches from the common room to sleep on.

These two anecdotes, and a number of other urban myths, propagate a seductive culture of “more is better” when it comes to the hours scientists put in and the days we dedicate to our research. In science, commitment is a prerequisite for success, but notoriety might be obtained through extremes of dedication.

PhD students in particular might complain about or joke about their workload, describing their punishing schedules.

PhD comics

For most of the duration of the PhD, despite the demands of a doctorate, I found it possible to maintain a sense of balance. I made an effort to continue with my hobbies and to keep in touch with my friends, who were a real source of both support and perspective. I am glad that I made this effort. But despite the importance of life in the work-life balance, I did feel troubled by a persistent sense that I was not working quite hard enough.

Having declared that doing a PhD does not have to mean three solid years locked in a garret, despite war-stories that might suggest otherwise, I did find that, sometimes, needs must. One colleague declare that he wrote up his PhD

in two months, but I don’t think I washed, slept or ate during that time.

Fortunately, for my office-mates, I started writing up sooner. During my writing-up stage I did at least had time to wash, if not to do a lot else that was not thesis-related. Of the many nuggets of advice I have been given over the past three years of my PhD, one which sticks with me is that, overall, a sense of balance is important to prevent burnout. But that sometimes, and not all the time, but just sometimes, you have to throw the concept of work-life balance out of the window and just knuckle down and work. Having emphasised the importance of work-life balance above, If any time during your PhD falls into this category, surely it is the run-up to submission of your thesis. During that time, the world beyond my work routine became difficult to imagine:

In the fortnight that has passed since I submitted, I have rediscovered rooibos tea, and sleep, and I have reconnected with friends and family. I have also started a new job, moved house, and somehow become embroiled in the organisation of the London Watch Party for Science Online 2013, which I am organising with Eva.

My examiners have received their copies of my thesis, and I have my copy to re-read. The viva has been scheduled. I am grateful to everyone in the Science Blogosphere who has helped me to get this far.

Bob O'Hara introducing Blogging the PhD

Bob O’Hara introduced Blogging the PhD to the readers of This Scientific Life when Occam’s T launched.


The below is an excerpt from the acknowledgements page of my thesis. Sincerely, guys: you made it much more fun. Thanks for all the cheers.

Thank you, OT.

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Impressions of ASHG 2012

Whilst most of the science blogosphere my science blogging colleagues were getting stuck in to Science Online London 2012, I was at the closing plenary of the 62nd meeting of the American Society of Human Genetics. If solo12 is the home of science online in London, ASHG2012 was an example of science online in action: the use of social media to share and discuss cutting-edge genetics research.

ASHG 2012 app

The ASHG 2012 app contains the conference program and schedule, together with abstracts of all posters and talks.


Chris Gunter, @girlscientist, is a member of the ASHG 2012 Program Committee and chair of the ASHG Communications Committee. It is thanks to her drive that the infrastructure was in place for social media to be used to enhance the experience of the conference, both for attendees and for those who could not make it in person. The conference program detailed social media guidelines. Presentations were tweetable and shareable unless the speaker requested otherwise, and the conference hashtag, #ASHG2012, was a source of summaries of talks as they were delivered. Early in the conference, Daniel MacArthur, @dgmacarthur, tweeted his ten guidelines for tweeting at conferences. A social media workshop formed part of the program.

The conference app contains the schedule together with poster and presentation abstracts and space for taking notes. This was useful for planning and navigating a busy week. The Society twitter feed, @GeneticsSociety, kept attendees updated with program highlights and any changes, although it was not flawless and confused jetlagged geneticists further by tweeting to kick off the closing plenary in the wee small hours of the morning, in error.

ASHG scheduling mishap

Lesson: when scheduling tweets, use the twenty-four hour clock.

Mishaps aside, social media was a definite presence at this meeting, from the tweetup on the first night to the crowdsourced questions to the panel at the closing plenary. I hope that social medial continues to be integrated into future meetings, both at ASHG and beyond.

Registration count at ASHG 2012

The numbers crept up over the course of the week

The ASHG meeting is vast. This 62nd meeting was bigger by a factor of fifteen than the largest meeting I had attended previously. Registrants topped out at nearly seven thousand, a small town’s worth of geneticists and several hundred companies represented. As is often then way with conferences the highlights for me were the people I met. The quality of the talks was high, and the organisation of the conference was slick. I attended a variety of sessions.

Umbrella bag stand at ASHG

The Moscone Conference Centre catered to delegates’ every need. Wet mini umbrella bags appeared in the lobby as soon as it started to rain.

The data presented in the session on pharmacogenomics represented the first steps on the road towards personalised medicine. The session opened with a discuss of the topics of ancestry and genetic variation that I had discussed earlier in the meeting. Edward Ramos gave an overview, including a quotation found in a paper by him and his colleague Charles Rotimi, which forms a coherent answer to the debate that I took part in a few days before:

If we use genomic information correctly, we will simultaneously describe our similarities and differences without reaffirming old prejudices. More importantly, the careful unbiased study and interpretation of the human story coded in our DNA will enable us to appreciate the fact that individuals cannot be treated as a representative for all those who physically resemble them or who share some of their ancestry. The human genome is a mosaic of our experiences, past and present.

Cell colouring book

Yes, it is a Cell Colouring Book in the tradition of the anatomy colouring book aimed at medical students. With thanks to Cell Press for quality swag.

The session continued with a focus on clinical applications. Genetic mutations, often in drug-metabolising genes, can result in large variation in how patients react to a drug. A drug that is otherwise beneficial could cause severe side-effects, or even death, in patients carrying those mutations. Being able to identify the relevant variants means that dosage could be adjusted, or an alternative treatment found, for affected individuals. Examples were presented from a clinical trial where this principal was used to demonstrate that genotyping patients and giving tailored treatment advice reduced side effects in mutant individuals.

At ASHG2012′s closing plenary, attendees reflected on progress in human genetics research in recent years. Wordclouds of the abstracts presented at meetings past and present showed the subtle but meaningful shifts, for example from genome-wide association studies to whole genome sequencing. The meeting was summarised by a quotation that resonates with the research I have been doing as part of my PhD, and which implicitly describes the important challenges in human genetics research for for the coming years. As a statistical geneticist, I was reassured that I will be kept busy in the future. The meeting concluded:

Ability to identify variation is no longer the limiting step in our field.

Discarded posters after ASHG2012

Post-conference posters post-ASHG2012.

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