Weeknote #45

Quite an eventful week; I was over in Brussels on Tuesday, as one of the two external reviewers of the SAPERE project. Quite apart from hearing about their results, it was quite interesting to see how another project operates in terms of management and so on. While I was away I received the formal notification that our paper on mutual information for crush detection (written with Pete Harding and Steve Gwynne) had been accepted by PLoS ONE.

The acceptance couldn't have come at a better time, as Pete had his Ph.D. viva on Wednesday. I'm delighted to report that he passed with minor corrections, so congratulations, Dr Harding!

Talking Turing

I did a few radio interviews last Thursday, ahead of the Turing/Morphogenesis event. Here's a recording of one of them, done with Heather Stott for BBC Radio Manchester. It's worth a listen, if only for the brief, stunned silence when I blurt out "He grew breasts!"

Turing and Morphogenesis

Yesterday I was privileged to take part in an event held as part of the Manchester Literature Festival. Many months ago I was invited by Ra Page of Comma Press to suggest "Eureka" moments in science, one of which might act as inspiration for a short story to be written by an established author. One of my suggestions was Alan Turing's theory of morphogenesis; while this idea has proved to be a "slow burn" rather than a phase transition in science, it marked the beginning of a new mathematical and computational era in biology. I was delighted that Jane Rogers picked up the idea, and she produced a marvellous story for the Litmus collection (Independent review). I supplied a short afterword to the story as part of the collection, which formed the basis for my notes for yesterday's event.

It was an absolute pleasure to work with Jane; we met only once before the story was written, but she produced a wonderfully humane depiction of Turing, as well as an accurate rendition of the science. It was great to meet up with her again yesterday; I'm sure the past few months were a bit of a blur for Jane after she was long-listed for this year's Man Booker Prize.

The event was held at the MadLab, which I know well from our partnership on the Manchester DIYbio project. Although there were only 40 or 50 seats available, we sold out, which made for a nice atmosphere. Craig Pay took some photos, which are available here.

Jane read an edited (for length) version of her story, and then I offered a brief commentary, before Ra asked some questions and then opened up the discussion to the floor. Ra was kind enough to pre-warn us of the questions, so I made some notes (below) ahead of time (of course, I ended up ad-libbing quite a lot, but I wanted to ensure that I didn't miss out any important details).

Martyn: Do you think the myth&mystery that surrounds Turing's life (and death) has helped or hindered his legacy as a scientist?

I think Turing’s legacy is clear and unambiguous from a scientific perspective; he’s rightfully acknowledged as one of the fathers of computer science. Every time we use anything with a processor chip in it we owe a debt of gratitude to Turing for his foundational work. Leads onto the more general issue of what we, as a society, owe him, and I think he’s been incredibly badly-served in terms of his general legacy. I think this is partly to do with institutional/societal squeamishness about his sexuality and the way in which he was treated as a result of it, although Gordon Brown did make some steps a few years ago to begin to address this. Hopefully the 2012 Centenary celebrations will help to address this. I also believe that Leonardo di Caprio is rumoured to play Turing in a forthcoming biopic, so we'll wait and see what effect that might have...

Martyn: When you say the morphogenesis theory has only recently been corroborated, could you explain how it has exactly, and why has it taken so long?

At first, his work was largely ignored by experimentalists, because they thought that it relied on a number of unproven hypotheses. Very soon, though, the existence of “natural Turing patterns” was demonstrated by Belousov and Zhabotinsky (B-Z reaction), who showed that one could obtain a number of patterns (spots, spirals, rings, etc.) in a dish simply by mixing several chemicals. Again, though, its sceptical response led to Belousov effectively resigning his commission from science. Only recently has work in fish, chicks and mice lent experimental support to Turing’s idea, but the real contribution was to show how order can arise spontaneously from disorder. It gave us a whole new way of looking at natural systems.

Martyn: Carrying on from this, how typical or atypical is Turing as a figure/personality in the many wider fields he influenced (computer science/AI, chaos theory & synthetic biology)?

I think that we are lucky if we get one Turing in every generation. If there exist common features between some of the leading figures in my field and Turing, it’s the fact that they connect. Len Adleman, who founded my own field of molecular computing, is a leading mathematician (he received a share of the Turing Award for his co-invention of the RSA encryption scheme) came up with the idea for DNA-based algorithms while reading James Watson's The Molecular Biology of the Gene. Erik Winfree's father was Art Winfree, another pioneer of computational biology. They are the only father and son team to hold MacArthur "genius grants", and Erik now looks at computational properties of biochemical systems.

Martyn: Is this a common feature in the biographies of great scientific pioneers - the need for a counter-argument, a listener, a foil, or an adversary - whether real or imaginary?

I think what readers of biographies or popular science have in common with those of fiction is the need for a good narrative. Quite often popular science tries to present the work outside of its human context, which I think is a mistake.

Other characters or institutions can serve to bring out the human characteristics, frailties, etc. of scientists. Richard Feynman is often portrayed as a robust character, but his heartbreaking letter to his dead wife shows a tenderness that we don’t get from pictures of him playing the bongos.

People also love a race - it gives a story a natural energy and drive. Rivalries or counter-arguments also serve to shed light onto the scientific process itself - not just the investigation, but the politics and history of it (eg. Watson and Crick versus Rosalind Franklin).

Weeknote #44

I can't quite believe that the summer has gone, and that we're about to launch into another term. The first year students are already here, and I spoke to them today about the importance of research, not just to academics, but to the University as a whole (and, of course, to them, as students and members of that community). I talked about some of the work we've been doing on swarm intelligence, and pointed out that much of that stuff has originated in student projects. I cited Matthew, my Ph.D. student, as an excellent representative of the "grow your own" ethos we're trying to develop at MMU; his SimZombie project led to Ph.D. studies, and he's now developing that work in parallel with his "proper" research. If anyone's interested, I've made my slides available here (warning: 15Mb PDF).

We had a research away day last week, and I also attended a meeting in London to hear about the panel-specific aspects of the forthcoming Research Excellence Framework. An unexpected bonus was the chance to chat to my old mate Dave Corne, with whom I used to work at Exeter.

One of the important points to come out of our internal REF workshop was the need to increase the visibility of our publications, both past and present. With that in mind, I've slightly revamped my own publications page. When I was a Ph.D. student, one of the most soul-sapping aspects of writing was the construction of the bibliography, so I've added BibTeX entries for the majority of my papers and books. I've also managed to dig out PDF versions of several publications I thought I'd lost for ever.

Weeknote #43

Last week Naomi and I travelled down to Bristol for a network meeting of the EPSRC Bridging the Gaps projects. Our NanoInfoBio project has now technically finished, although we do have £50K of continuation funding to take us into 2012. We were hosted by the University of the West of England BTG project, and the meeting went very well. Several projects offered a single slide on "The Good, the Bad and the Beautiful", and ours were as follows:

Good: The use of seed-corn funding (eg. £5K) to nurture ideas from initial "blue sky" sessions, through to prototyping and then subsequent large funding.

Bad: Nobody came to coffee. We had real trouble getting people to socialise and mix on an informal basis. Several projects reported similar problems with both real and virtual interactions.

Beautiful: The realisation of one of our stated aims, which was to "grown our own" researchers. We are now seeing MMU undergrads working on NIB-supported Ph.D. projects, and they will hopefully stay on to become valued members of staff, and help to train a next generation of inter-disciplinary researchers.

It was an inspiring meeting, and it helped me to realise just how much we've accomplished with the project in two short years. The real challenge now is to embed the lessons we've learned into institutional thinking, and the targeted continuation funding will make a significant impact on research activities ahead of the REF in 2014.

On a personal level, it was also a pleasure to catch up with Mike Luck, who's now Head of Department at King's College London (a post recently held by my Ph.D. supervisor, Alan Gibbons, until his retirement). I first met Mike as a potential Ph.D. student, when he was showing around applicants at University College London. When I eventually fetched up at the University of Warwick, Mike had, by then, taken an academic post there, and remembered me from the tour. He does great work on multi-agent systems, and I'm pleased to see him doing so well.

Speakers for Schools

I'm pleased to be able to participate in a new initiative to get volunteer speakers into schools, to share their knowledge, experience and advice. Speakers for Schools (which will formally launch next month) was founded by Robert Peston (BBC Business Editor), and enjoys the support of people such as Jon Snow, Jeremy Paxman, Alastair Campbell, Yvette Cooper, Martha Lane Fox, Lauren Laverne and Martin Rees.

Call for papers on "Biological and Chemical IT"

BioSystems invites manuscripts for a special issue dedicated to

“Biological and Chemical Information Technologies”.

Following the COBRA Workhop on Biological and Chemical

Information Technologies (BioChemIT), held at the European

Conference for Artificial Life, Paris, August 8th 2011, the organizers

invite members of the community to contribute to a collection of

papers dedicated to this growing area of research.

Topics include (but are not limited to):

Biological/chemical information technologies; molecular and

chemical computing; protocells and synthetic cells; molecular

robots; integration of information processing with (bio-)chemical

production; nano-bio-info interface; cellular engineering, artificial

neurons; programmable information chemistry; unconventional

computing substrates; synthetic biology; computational and

mathematical studies.

For more information, see the full call for papers.

Weeknote #42

Much to report; the European Conference on Artificial Life was held in Paris at the start of the month. Our COBRA project organized a satellite workshop the day before the main conference, which went very well. Our meeting covered the broad area of "biological and chemical IT", and topics included synthetic biology, artificial cells and robotics. A special issue of the journal BioSystems will be edited around the themes of the meeting, with an open call for papers to be issued shortly.

We're fortunate enough to have one of the artificial life pioneers (Steen Rasmussen) as a COBRA collaborator (another pioneer, Norman Packard, is also involved via the European Center for Living Technology in Venice) , and their panel discussion was entertaining and thought-provoking. Steen has blogged about this (and the wider conference) here.

Our Ph.D. students Matthew Crossley and Henry Dorrian recently attended the Student Conference on Complexity Sciences in Winchester, which sounds like exactly the sort of thing I wish had been around when I was a student (I did attend the Santa Fe Institute complex systems summer school in 1995, but that was for a whole month). Anyway, Henry presented a poster, and Matthew gave a talk, both of which were very well-received. Indeed, Matthew reported that one of the invited speakers, Robert May (AKA The Lord May of Oxford, former President of the Royal Society and Chief Scientific Advisor to the government, among his many roles) had quietly taken him to one side to offer particular praise and encouragement for his work on agent-based models of epidemiology, and how they might be used in public engagement/education activities. To say that Matthew was "chuffed" might be a slight under-statement...

We were delighted by a recent review of Litmus, which appeared in the Independent a couple of weeks ago. Peter Forbes (I'm an admirer of his book The Gecko's Foot) describes the collection as "...not a test but an open sesame into some of science's most intriguing passages." I was also pleased to see that the morphogenesis story written by Jane Rogers (for which I acted as scientific consultant and wrote the afterword) attracted particular attention in the review. Jane's just been long-listed for the 2011 Man Booker Prize, so well done and good luck to her! Litmus is available to buy here, and now might also be a good time to plug an event Jane and I are doing in October, jointly with the Manchester Science and Literature Festivals (details to right).

Finally, as I was typing this note I got an email from Springer to tell me that the journal version of our paper on using genetic algorithms to solve the Zen Puzzle Garden game has now appeared in print in the journal Natural Computing. I'm particularly pleased about this paper, not because it's hugely ground-breaking, but because it originated from an undergraduate student project.

Although Paris was half-and-half work and pleasure (I was accompanied by my wife, while our daughter stayed with her grand-parents in Northumberland), next week really is a holiday (visiting family in Suffolk). That means IMAP server passwords deleted from my phone, no tweeting, the lot. I'm sure it will do me good.

Weeknote #41

A couple of meetings to report on this week; last Wednesday the NanoInfoBio board met to discuss progress. Although the project is due to finish next month, we were recently granted an additional £50K of funding by the EPSRC, which will allow us to extend it into 2012. As I said in an email to the EPSRC this morning, the project really has had a disproportionately positive effect on the Faculty and the University, and the next challenge is to see how we can retain our momentum after the formal funding finishes.

The other meeting of interest was held at the MadLab on Thursday, where the DIYbio organizing team got together to plan our next set of activities. The "big event" will be a DIYbio summit on October 29-30, to be held as part of the 2011 Manchester Science Festival. More details to follow.

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.

Shady publishing

I was recently asked, by an anonymous individual, for my opinion on an unsolicited email that contained an offer to publish their thesis. To a young academic this might sound like an attractive proposition (more so in the arts and humanities than in the sciences, where journal articles still rule) - log a quick publication, get on Amazon and maybe even make some money.

However, if we dig a little beneath the surface we quickly uncover some pretty cynical practices. Others have documented in detail the shady nature of these companies (see here, here and here); suffice to say, the overwhelming advice is Don't Do It.

I thought I'd do my own research on the specific company that approached my colleague; LAP Publishing. Although several people have already commented at length on the various problems with their approach, and how these should all serve as significant red flags (see the last link above), perhaps the most damning evidence I found came from their own website.

I visited their main website, and soon saw a page of author comments. I'm absolutely sure that these are all completely genuine, and not at all fabricated; after all, who could make up a book with a title such as "RETURNS TO EDUCATIONAL INVESTMENTS IN A TRANSITIONAL ECONOMY: AN INVESTIGATION OF KAZAKHSTAN’S LABOR MARKET IN 2005"? It's even available on Amazon, although I'd advise you to turn off 1-Click Ordering before taking a look - you might not be able to stop yourself.

The best bit about this page, though, is the testimonials from the authors themselves:

"My experience with Lap Lambert Academic Publishing has been an experience I will never forget."

Well, that one could go one of two ways.

"Their superb customer service and support of me was the first point I noticed in my first communication with company."

Hmm, not sure about the grammar there, but we'll persevere.

"Within three short months, with their assistance I have now published six books..."

A book every two weeks!

Ok, so this getting a little suspect. No serious publisher would ever use such mangled English in their testimonials (or, indeed, actually need such things from their authors), or imply that, through them, you can knock out books at a rate that would make even Barbara Cartland question her commitment.

This isn't a post to say "let's laugh at the foreigners and their bad use of English". It's simply a comment on an absence of editorial standards that is so complete as to let these unedited "testimonials" go live on the company's own website.

These last two really are the final nails in the coffin:

"I must tell you that your contribution of publishing this book is very helpfulness and valuable for globalization of Ergonomics/Human Factors. […] I am appreciated of your contributions and also your kindly support and assist."

"This was very convenient process, because personal and printed advise were so excellent!"

Case closed.

Public Service Announcement

Note to dimwit colleagues: "Reply" != "Reply all", which is especially important when the original email was stupidly sent, individually, to every single member of staff in the University.

I just got a message that said, in its entirety,

"Ditto.",

and which was sent to 1,591 people. It's like we've travelled back in time to 1995, when people were "still getting the hang of email".

Unfortunately, the original error seems to be propagating, as more and more people weigh in (the first message was from University management, warning us of the implications of taking strike action).

Weeknote #39

Two weeks since the last weeknote, not too bad...

Angel and I have had the journal version of our population-based oscillator paper accepted by BioSystems; you can find a preprint version here.

Two new members have joined the Novel Computation Group; Jon Parkinson is an undergraduate who'll be working over the summer on ant colony optimisation, and Paul Robson is an M.Sc. student working on predation/avoidance strategies, using Matthew's SimZombie package.

This week we have an open day, followed by a day of Moodle training (...), followed by another day of professional development review training.

Naomi, Lindsey and myself popped over to Sheffield Hallam last week to talk at their Research Cafe. SHU and MMU were both successful in the same round of Bridging the Gaps funding from the EPSRC, and their Engineering for Life network shares similar features with our own NanoInfoBio project.


We managed to get over to Derbyshire at the weekend, for a fourth birthday party (and sneaky fathers' day celebration). Alice had a good go at the dino-pinata.

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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Chemical computation

Lulu Qian and Erik Winfree's recent paper on simulating Boolean circuits using DNA has attracted quite a lot of attention. I was asked by both Nature and New Scientist to offer comments on their work, which I happily did (here and here).

While the New Scientist quote is clearly taken directly from an early-morning Skype conversation, the Nature story (understandably) used only a small snippet of my "take". In the context of the article, it could appear that I was being overly-negative about what is actually a remarkable piece of work. For the record, here's the entire text that I sent the author of the piece, with the bit that was actually used highlighted in bold:

"This is an important development in the search for truly 'hands free' molecular computing. The paper describes a real fusion of computing and the life sciences, which moves us one step closer towards programmable information chemistry. As the authors themselves acknowledge, scaling up their approach might be difficult, but they've described one possible path for its future development, through physical localization of elements. As John Reif points out in the commentary, the biggest challenge will be to get this type of construction to work inside living cells, where it might find a number of applications in sensing and control."

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Who says Universities aren't forward thinking?

Our local hospitality operation has recently put in place an automated booking system, which allows grant holders to request and approve catering for meetings, etc. This is great, as it avoids (in principle) orders going missing, and so far it seems to have worked well.

Each request is assigned a "ticket number", and I noticed that the system designers appear to have learned the lessons of the Millennium Bug, and allowed plenty of room for new requests. The order I approved today, for example, is request number

REQ000000000721

which, assuming there were 720 previous requests since the system began, allows for 1,000,000,000,000 unique requests (that's a trillion).

Even if we assume a million requests a day, 365 days a year, we've still got over 2,700 years before the system runs out of space.

By which time we might have introduced some variety into the menu.

Weeknote #37

These weeknotes are turning into monthnotes, but I shall persevere...

Lots to report, starting with a trip down south at the end of April to visit the Bristol Robotics Laboratory. This is a joint venture between the Universities of West of England and Bristol; I was in touch with the Director, Chris Melhuish a few years ago in relation to some ant work, but I'd never before had the chance to visit. One of their most high-profile projects is the EcoBot, an energetically autonomous robot that uses microbial fuel cells, and the meeting was semi-related to that. I was there at the invitation of Ioannis Ieropoulos, who met our post-doc Angel and forged a connection between our respective groups. The meeting went very well, and there will definitely be much to discuss in the coming months.

The beginning of May saw a number of COBRA project members in Budapest, for the European Commission FP7 FET11 conference. We organized a special session on "biological and chemical IT", which was well attended. We're currently drafting a summary paper for the forthcoming open-access meeting proceedings. The next COBRA event will be another special session, this time at the European Conference for Artificial Life, held in Paris this August.

This month has also seen a lot of activity on the DIYbio front, with the initial "swabfest" (taking samples from Manchester bus stops in order to ascertain the level of bacterial contamination) closely followed by a session at the hugely-influential FutureEverything conference in Manchester. We showed a couple of movies during the presentation, and these will hopefully be made available shortly, as well as footage of the event as a whole.

I'm very excited by the announcement of a new volume of fiction, to which I've made a small contribution. Litmus is edited by Ra Page at Comma Press, and has the subtitle "Short Stories from Modern Science". From the blurb: "This anthology draws out and distills science’s love of narrative from a wide range of scientific disciplines, weaving theory into very human stories, and delving into the humanity of theorists and experimenters as they stood on the brink of momentous discoveries: from Joseph Swan’s original light-bulb moment to the uncovering of ‘mirror neurons’ lighting up empathy zones in the human brain; from Einstein's revelation on a Bern tram, to Pavlov’s identification of personality types thanks to a freak flood in his St Petersburg lab.

Each story has been written in close consultation with scientists and historians and is accompanied by a specially written afterword, expanding on the science for the general reader."

Our story was written by the BAFTA-nominated novelist and scriptwriter Jane Rogers, and it focusses on an often overlooked aspect of the work of Alan Turing; his studies of morphogenesis.

The only other big bit of news is that I've accepted an invitation to coordinate the computer science research activities of our School, in preparation for the 2014 Research Excellence Framework. I'll be responsible for our return in the Computer Science and Informatics Unit of Assessment; we did pretty well last time around, in 2008, so the pressure's on.

In terms of papers, today Angel and I submitted a revised journal version of our population-based oscillator paper, and last week we submitted an abstract to the ECAL workshop (on a different, but related subject). I'm also working on a BACTOCOM technical paper, as well as a short paper on a fun topic (a proof of the NP-completeness of a game I've studied in the past).

Virtual Futures 2.0

With regret, I have had to cancel my appearance at VF2.0. Sorry.

Weeknote #36 (w/e 17/4/11)

A rather frantic month has unfortunately left the weeknotes at the bottom of the priority pile. However, teaching's now finished (apart from the small matter of honours projects to mark...), so now's the time to pick up all the loose ends.

At the end of last month we were in Brussels for the first BACTOCOM annual review. Until we receive the formal report from the European Commission, we can't say too much about this, but we all felt that it generally went very well.

Last week, both Jo Verran and I attended the Spring meeting of the Society for General Microbiology. I gave an invited lecture on "bacterial random search (BACTOCOM, basically) in the "Maths and Microbes" session, and Jo gave an open lecture in the evening, on biofilms. I was only able to stay for the first day, and would have liked to have seen more of what seemed like a very interesting conference. The next one is in York at the start of September, and I'll definitely try to get to that.


Last Tuesday we were treated to the rather surreal sight of Dolly Parton discussing the implications of one of our NanoInfoBio projects. Jo and her team were recently filmed by the BBC's One Show for a piece about their work on fungal deterioration of cine film, in association with the North West Film Archive. It went out last week, and was marvellous publicity for the project, the University, and the NWFA.

On Thursday we had the pleasure of hosting a public lecture by Ian Stewart. Ian and I met once or twice during my time at Warwick in the mid-1990s, but credit for his visit goes entirely to Naomi Jacobs, who set it all up via one of her many side projects. As well as being a well-respected catastrophe theorist, Ian is a world-renowned author and populariser of science and mathematics. He gave an excellent talk, based on his new book Mathematics of Life, a conjunction of subjects that is obviously close to the heart of many NIBbers.

United Utilities are threatening me.

I love this letter that arrived the other day from United Utilities. Ostensibly they're trying to get me to buy their HomeServe insurance, but the way they've phrased it is just this side of sinister. "How would you cope without fresh water at address?" sounds, to me, like a corporate version of "Lovely taps you've got there. Shame if something were to... happen to them."

And they can leave the washing machine out of this, it's done nothing wrong.