Weeknote #40

To Berlin, for the latest general meeting of the BACTOCOM project. I'd never actually visited the city before, which came as a bit of a surprise, so I was glad that we had time to take a walking tour on Thursday morning, before the work began. I took some photos, which are available here. We got lots done (drafting our response to the first year review from the European Commission, and kicking ideas around for a follow-on project), before Nils and Ilka (and their numerous students!) put on a great BBQ. On Friday we put in a few more hours before breaking for lunch, followed by a seminar and then a visit to the adjacent Natural History Museum (the highlights being the World's Tallest Dinosaur Skeleton (officially), and the slightly creepy but strangely compelling storage room, with thousands of specimens held in glass jars). Friday was rounded off with dinner in the Schlesisches Tor district. I also got to chat (briefly) with li5a about DIYbio, so hopefully that will lead to a future link-up. All in all, a great meeting and visit.

Weeknote #38

Saturday saw us fly back from a week in Madrid, where I'd been on BACTOCOM business. I was there to talk to Alfonso, our computational collaborator, and to give a series of lectures on molecular computing and synthetic biology to the M.Sc. and Ph.D. students. I've made the slides available here (3.8Mb download).

I had a day off on Friday, so we took Alice to the Museo Reina Sofia, which I always try to visit when in Madrid. I discovered the artist Lygia Pape, and was absolutely transfixed by her Tteia installation (although I think I might have ruined the moment by making a joke about tripping up and being sliced like a boiled egg...) Her early (1950s) "Draws" geometric work also greatly appealed to me, but I can find little of it online.

Last week saw the publication of an interesting paper by Erik Winfree and Lulu Qian, on evaluating Boolean circuits using DNA. I was asked for comment by both Nature and New Scientist, and my post covering this is below (or here).

We (ie. the COBRA project board) managed to submit our paper for the FET11 proceedings, just ahead of the deadline (not helped by some last-minute wobbles caused by dodgy version control - mainly my fault).

This week is dominated by prelim. exam boards, although we do have a meeting of the DIYbio team tomorrow, and I'm seeing a new M.Sc. student (agent-based modelling) and summer intern to chat about their projects. Next week I'll be over at Sheffield Hallam to talk to their Bridging the Gaps project, doing my bit as an external examiner, and attending final exam boards.

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Weeknote #35 (w/e 20/3/11)

Lots of public engagement activity to report from the last two weeks. The first item is that the BACTOCOM piece is now up in the new Revolution Manchester gallery at MOSI (the Manchester Museum of Science and Industry). It's a great gallery, and we're delighted to be featured, but the use of "Bactocom" as a noun (as opposed to an acronym) means that we now have to rig up a fake machine made out of petri dishes, computer parts and moss, just in case anyone asks to see "the bactocom". (Photo by Ade Hunter.)

We also launched DIYbio Manchester last week. This is a one-year project, funded by the Wellcome Trust public engagement programme, with the aim of encouraging citizen scientists to become more actively involved in biology.

Dan Hett wrote a nice blog post about the launch party, and Hwa Young and I were briefly interviewed on BBC Radio Manchester's breakfast show (which you can hear below).



Alice and I also had great fun at Saturday's 'Hands on Science' family fun day, organised at MMU as part of National Science and Engineering week. Her personal favourites were the "memory metal" and the "magic sand", the robots and the racing car. I think she also enjoyed "talking to the computer" (the Turing Test, run by Ben and Matthew).



Once again, there was strong representation from the Novel Computation Group, with Naomi and Zarka manning demo stands, as well as Ben and Matthew helping out. Not sure what's happening with Alice's right hand in that picture, though.

Weeknote #33 (w/e 27/2/11)

I've been very bad at updating my weeknotes over the past few...umm...weeks, so here's a quick run-down of what's happened since the last one.

At the start of February I sat on my first EPSRC panel. I can't go into too much detail, as I'm not sure the results have been released yet, but we basically had a day-and-a-half, locked in a hotel in Swindon, to rank a load of funding proposals. It was quite an exhausting experience, but very useful, in that it was my first insight into the process as a reviewer (as opposed to proposer). Top tip: drive, don't take the train. That way, you get to take along the several KG of paperwork, instead of relying on the summary you've prepared, and avoid embarrassment when you have to repeatedly ask to use the copies brought along by your far more experienced colleague. Lesson learned for next time.

Last week I had a nice couple of days near Paris, visiting the group of Alfonso Jaramillo. Alfonso is the technical lead on our BACTOCOM project, and I believe he currently has an open post-doc position. On the subject of European projects, I was pleased that our COBRA project managed to secure the organization of special sessions at both FET11 in Budapest this May, and the European Conference on Artificial Life, in Paris this August. Busy times ahead.

In terms of papers, Matthew and I finally had the "zombie paper" accepted, and there's a preprint version available here. Matthew spent most of last week at MOSI, participating in their half-term Turing test. By all accounts, it was a huge success, so well done to him.

Weeknote #29 (w/e 5/12/10)

I'm delighted to have confirmed the details of my talk at the Spring Meeting of the Society for General Microbiology (SGM), in Harrogate next April. The SGM is the largest microbiological society in Europe, and was founded in 1945. Its first President was Sir Alexander Fleming, and he's been followed by an impressive list of luminaries. The current President is Hilary Lappin-Scott, with whom I worked briefly at Exeter, and our own Jo Verran is the Education and Public Affairs Officer. I'll be talking about "Massively-parallel microbial search: a new platform for synthetic biology" (BACTOCOM, basically...)

Weeknote #27 (w/e 21/11/10)

Frank Swain's article on the New Scientist website (see last week's note) appears to have attracted quite a lot of notice, although I'm not entirely sure that the Tokyo team's preliminary results justify the media attention. The idea of distributing a computation across a population of bacteria using targetted information exchange (as opposed to a more general, untargetted chemical signal) is certainly novel, and is one we've been actively pursuing over the last year with BACTOCOM. My small appearance as a commentator has led to some interest from various parties, none of which I'll expand on now, since it's all still very tenuous. Still, it's nice that this sort of research is gaining the sort of attention that I think it needs.

Work pressures meant that I resigned today as a founder Director of ArcSpace, the Community Interest Company I joined a year-and-a-bit ago. The organisation's growing quite quickly right now, and I think it's time to stand aside and let someone else have a go. Although there'll be some tough times ahead in the sector, they have access to the best possible resource - committed, passionate individuals - and I wish them well.

Finally, some words of support to my friends Rob and Nadine, who are going through a tough time with their son, Keifer, right now. As Rob said, "Joy comes in small doses", and a sick child immediately puts into perspective the trivialities of everyday life. The Ashby-Amos clan send their love.

Weeknote #26 (w/e 14/11/10)

Bit tardy again this week. Yesterday afternoon I spoke to Frank Swain, after he tracked me down via Twitter. He wanted to chat about the recent Tokyo iGEM work on bacterial sudoku solvers, and the resulting piece appeared today. It was good to see BACTOCOM getting another plug.

Speaking of BACTOCOM, we're currently working on the definitive design document for our system, which will be submitted as a position paper shortly. It's taken a while to get going, what with delays in appointing staff, and so on, but I think the project's in good shape now. We're expecting to be able to announce further good news on the project support front any day now, so stay tuned.

In other news, Pete, Steve and I finally submitted the journal version of our paper on mutual information for crush detection. This work forms the core of Pete's Ph.D. thesis, which he's currently in the process of writing up. I think it's a solid paper, which has actually been improved due to an earlier draft being picked up by the MIT Technology Review blog. We did some extra work in response to criticisms made in the article, and I think it's much stronger as a result.

The only other thing of note to report is that I'm now officially a member of the EPSRC College. This is made up of around 4,000 individuals, whose job it is to evaluate research proposals and serve on prioritisation panels. Given the turbulent state of research funding right now, I guess it's an interesting time to become involved.

Weeknote #25 (w/e 7/11/10)

This week we welcomed the latest addition to the Novel Computation Group; Dr. Ing. Ángel Goñi Moreno joins us as a post-doc on the BACTOCOM project. He originally visited for three months last year, from our collaborators at UPM (Madrid), and has obviously not been put off by the Mancunian weather. His recent Ph.D. work has attracted a fair bit of attention; he'll be working on modelling and simulation aspects of the project, and we're delighted to have him. Angel's arrival brings the group numbers up to 15 (4 academics, 2 post-docs, 2 administrators and 6 Ph.D. students, plus a visitor). We've pretty much run out of space in the lab, but it makes for a vibrant atmosphere.

Top tip: When trying to impress family by lighting two adjacent fireworks, one after the other in quick succession, remember that the gas stream from the first will inevitably knock over the second, leading to an unpredictable trajectory. Shortest. Display. Ever.

Weeknote #23 (w/e 24/10/10)

Most of last week was spent at a meeting of our EU BACTOCOM project. It was the turn of the University of Cantabria partner to host the six-monthly get-together, which was held in the beautiful city of Santander. It was my first visit to this particular part of Spain, and the scenery on the drive from Bilbao was nothing short of spectacular. Despite the unavoidable absence of a few key members of the team, we had a very productive meeting, and I think we're in a strong position to drive the project forward in the coming months.

While I was away we "sold" the remaining few tickets for our Manchester Science festival event. I'm absolutely delighted that we'll have a capacity crowd for what is sure to be a fascinating evening.

I'll be appearing as one of the guest scientists at another MSF event, the Teawitter Four Science party. Should be a nice relaxed end to a wonderful Festival.

Weeknote #17 (w/e 5/9/10)

The past week was mainly spent on European business. In addition to attending a negotiation meeting in Brussels, we finalised the International Advisory Board (IAB) for our BACTOCOM project, which started in February, and is supported by the European Commission Seventh Framework Programme. The IAB will play a vital role in acting as a "critical friend", as well as advising us on scientific strategy and helping the project to develop connections with other international projects. We're delighted to welcome a number of distinguished colleagues to the project, and they are (in no particular order):

Prof. Måns Ehrenberg, Professor of Molecular Biology at Uppsala University, Member of the Royal Swedish Academy of Sciences, and Member of the Nobel Committee for Chemistry.

Dr Jane Calvert, Innogen RCUK Research Fellow at the University of Edinburgh.

Prof. Natalio Krasnogor, Professor of Applied Interdisciplinary Computing at the University of Nottingham.

Prof. Mike Simpson, Distinguished Research Staff Member and Theme Leader, Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, and Professor of Materials Science and Engineering at the University of Tennessee, Knoxville.

Prof. Jeff Hasty, Associate Professor in the Departments of Molecular Biology and Bioengineering, and the Director of the BioCircuits Institute at the University of California, San Diego.

We look forward to working with all of our IAB members in the next two-and-a-half years.

Weeknote #8 (w/e 4/7/10)

To Paris, for the regular board meeting of our European Union BACTOCOM project. We launched the project with a workshop in Manchester, and partners take turns to organize subsequent meetings. We'll be in Santander in October, and then Berlin next year. Whilst browsing in the Abbey Bookshop in St. Michel, I noticed a copy of Genesis Machines, and had Justine record the fact that it was still on sale, in a proper shop. The subsequent scene ensured that I was brought to the attention of Brian, the proprietor, who kindly asked me to sign the last remaining copy in stock (i.e., the single copy they ordered three years ago).

Prior to leaving for Paris, we had quite a busy week; in addition to finishing off and submitting a research council proposal, we're now heavily into the preparations for our contributions to the Manchester Science Festival. So far, we have a couple of workshops lined up (I don't want to spoil the surprise until the details are confirmed), plus a public debate on the scientific, technological and ethical implications of synthetic biology and so-called artificial life. Watch this space for more details nearer the time.

On a personal note, I was delighted to receive confirmation of my promotion to a Readership. Most of my family members were quite baffled by this antiquated term, until I explained that it's the academic rank below Professor (in the UK), and is awarded on the basis of research.