2011 has been a remarkable year for me, during which I have travelled widely, met lots of interesting people, recruited substantial grant funding and had a paper published in the journal with the highest impact factor of them all! So, at the risk of producing one of those cheesy round-Robin letters that get stuffed in with Christmas cards, here is a personal round-up of all the exciting things that have happened to me in the last 12 months!
In January, there was a visit to Birmingham by Secretary of State for Health Andrew Lansley, Surgeon General Vice Admiral Philip Raffaelli and Chief Medical Officer Professor Dame Sally Davies to announce the launch of a new multi-million-pound NIHR Surgical Reconstruction and Microbiology Research Centre focused on trauma patients. I had had to write the microbiology component of the bid for the centre in 48 hours a few weeks before and I was amazed at the speed with which the announcement was made. On the plus side, this is going to provide us with an unrivalled opportunity to explore the potential of high-throughput sequencing in the microbiology of trauma patients over the next five years. On the minus side, securing the funding for the centre, even though the outcome was announced back in January, has proven the most bureaucratic and procedural process I have ever encountered. It was not until December that we actually started spending of the money! But mustn’t look a gift horse in the mouth–the centre will be funding a MiSeq from March next year, which will provide a welcome boost to our sequencing capacity.
More info on this initiative here:
In February, I hosted a visit to England of Eugenie Scott, director of the US National Center for Science Education. Genie gave a Darwin Day talk at the University of Birmingham. I also arranged for us to visit Down House with our well-informed and congenial host Darwin descendent Randal Keynes (father of the movie star Skandar Keynes).
Watch our trip on YouTube:
Later that month, I visited Lausanne, a charming town on Lake Geneva in Switzerland, to celebrate the award of an Ion Torrent PGM. I was one of two winners (out of ~150 entries) in the Ion Torrent PGM Grants Program in Europe. Check out the blog post from the time and this interview, which they filmed in the hotel in Lausanne
In March I attended a conference in Cape Town held by the African Society for Bioinformatics and Computational Biology. This was my first trip to this remarkable country. Highlights of the trip included a visit to the University of Cape Town, to the Cape of Good Hope, to Table Mountain and to Robben Island and watching a San bushman create fire! And I even dusted down an old rather idiosyncratic interest of mine and met some African Esperantists.
Later that month the Ion Torrent PGM arrived. Nick Loman delighted in photographing it covered in slinky plastic: Hot Ion Torrent Action!
April was a quiet month. The one signficant event was that our Vice-Chancellor decided that the University of Birmingham needed its very own Institute of Microbiology and Infection.
May, on the other hand, was very busy! My then 15-year-old daughter Emma did work experience with me at the University. She gave a short lecture on the differences between bacteria and viruses during which she appeared ever inch the professional academic. One of her friends pointed out how cool it was for her to have worked at a university before studying at one! In May, I also heard that my book The Rough Guide to Evolution had been chosen for the new Great Read at Birmingham initiative, which meant that in September 2011 it was given out to 6000 undergraduates at the University.
In the second half of the month I attended the American Society for Microbiology meeting in New Orleans. I organised a session on high-throughput sequencing and gave a talk of my own. It was great to see the home of Tremé and meet lots of interesting people (Jennifer Gardy, who was co-organiser of the session, Mike the Mad Biologist, Jonathan Eisen). En route I also made my first visit to NYC, which was fascinating.
Towards the end of the month I spent a week-long family holiday in France, just as the German STEC outbreak was kicking off. That week, DNA from an STEC isolate was sent from Hamburg to BGI-Shenzhen, where it was sequenced on their trial model of the Ion Torrent PGM.
In early June I returned to the UK to face two remarkable surprises. The first was an invitation to appear on BBC Radio 4′s high-brow discussion programme “In Our Time” with the well-known presenter Melvyn Bragg. On the night of 8th June, the BBC put me up at a posh hotel next to Broadcasting House. I didn’t sleep well and at 5am got up and practiced my spiel. The show went out live from 9.00am. But with just four of us huddled around a table in the studio, it was hard to believe that a million or more were listening. As it turned out, Bragg deviated from the list of questions I had been given, but there were no hitches (Links: The programme; my notes ). A friend later comment on my posh Radio 4 voice. I often listen to the “In Our Time” when it is broadcast a second time on Thursday evenings, while waiting to pick up my son from scouts. That proved a surreal experience that evening, as I listened to myself and then excitedly explained to the scoutmaster that it really was me on the radio!
The second surprise started with Nick Loman filling me in on the crowdsourcing efforts that he had jump-started with his assembly of the BGI’s Ion Torrent data. I was initially dismissive of all this activity on social media, in the absence of any plans for a peer-reviewed publication. Nonetheless, I agreed to contact the BGI and the German team who had sent the DNA to BGI. To start with, such efforts got us nowhere, but then quite suddenly at midday on Tuesday 28th June I received a phone call from Martin Aepfelbacher, head of the unit in Hamburg, inviting us to join their efforts in analysing the data and writing a paper for the New England Journal of Medicine. This great opportunity came with a catch: we had to have a newly drafted paper and a fresh defensible analysis ready within just over 48 hours! Two days of furious paper writing on my part and bioinformatics analyses on Nick Loman’s part culminated in a paper that concentrated on the journey to the genome sequence through what we called Open Source Genomics as much as on the sequence itself.
As we moved into July, it was a fraught time as we waited for the editor’s verdict, but when she said that she had started editing our draft, I began to believe we really were going to get the paper published! A couple of weeks later, I had to let down my colleagues by bunking off a local microbiology showcase event to put the finishing touches to the final draft. The paper was duly accepted and we heard that we were going to appear back-to-back with a paper headed up by Dave Rasko on the use of Pac Bio sequecning on the outbreak strain and its relatives.
In August, our NEJM paper was published and Nick and I made a flying visit to Hamburg to share some champagne with our German collaborators, Martin Aepfelbacher, Helger Rohde and Moritz Henschke, who proved excellent hosts.
In September Dave Rasko visited Birmingham and we celebrated our joint success with a meal and yet more bubbly!
I spoke at the Prokagenomics 2011 meeting in Göttingen, which gave me a chance to enjoy some Oktoberfest drinks with Andreas Leimbach, who was a co-author on the very first paper to appear on the STEC genome sequence, and to see this wonderful university town.
I made a slidecast of my talk and vowed to try to engage in open scholarship for the coming academic year, putting all my teaching and research talks into the public domain (check out my YouTube channel).
The last week in September saw the launch of the Great Read at Birmingham initiative, which prompted visits to Birmingham of some amazing guys: Ken Miller, John Hawks, Captain Ben Kirkup and Chris Stringer (see my other blog, The Rough Guide to Evolution for more details).
During October, I participated in and live tweeted from the Applying Advanced Molecular Techniques to Healthcare Infection meeting at Hinxton Hall near Cambridge and also visited Oxford twice in one week, once to lecture doctoral students on Darwin, evolution and microbiology (http://www.scienceandatheism.com/2011/10/13/the-dirty-truth-about-darwin/#.Tv7UDmCJz0s) and once to give a seminar at the Dunn School of Pathology. In the middle of the month, I played grumpy bad cop in 29 one-hour interviews for Birmingham Fellows scheme, which brought me face to face with a wonderful variety of academics and the pursuits. I was stuck with the question “why aren’t you publishing in Nature yet”; but quite fairly asked the same miserable question of everyone!
The highlight of November was a performance of the Rap Guide to Evolution for Birmingham students by Baba Brinkman, who flew over from Manhattan specially. Before the show, we filmed a variety of people from the University lip-synching to Baba’s I’m a African track against a green screen: two Indians, two Greeks, an Afghan, a number of Europeans, plus some people with African ancestry more recent than 70Kya! I am looking forward to seeing how it all ends up looking in the video made to accompany the track on Baba’s UK Rap guide site.
In December, I got to meet several more exciting people. Gabriel Waksman gave a superb seminar on the structural biology of fimbrial biogenesis. Kevin Peterson gave a great Huxley Lecture that deftly wove together the Cambrian Explosion and the proliferation of microRNAs in metazoan genomes (take a look at his recent Science paper). Scott Edmunds visited and gave us the BGI’s perspective on the remarkable series of events that summer that culminated in our joint NJEM paper–he is one of a handful of westerners who works at BGI-Shenzhen. We celebrated our success yet again, this time with a curry and a very large nan bread.
The year was capped off nicely with a success in gaining BBSRC funding as co-investigator on E. coli nucleoid structure with Steve Busby, plus the launch of an online presence for our new Institute of Microbiology and Infection at Birmingham as iMicroBham. And we got another key paper on the German STEC genomes into the review process (fingers crossed!). And I started work on my next book, The Last Days of Smallpox. Oh and something else wonderful happened in December, but I won’t be able to tell you about it for a few more weeks.
So, here’s to a remaarkable 2011 and, let’s hope, to an equally or even more remarkable 2012!