martyn amos

New-fangled social media

2012-01-24T20:52:00.004Z

I gather all the young people are talking about this tumblr micro-blog thing, so I thought I'd give it a look. It seems to me that the main rule is "the more obscure the better", so, in that spirit, I now present:

Car Dealerships That Sound Like Famous People.

Taken today, at traffic lights on the way into Manchester.

This one's a bit better, taken outside our house (I think it belongs to my wife's hairdresser).

If you see any of your own, do please send them to me.

More press coverage for Pete

2012-01-17T22:38:00.012Z

After last week's appearance in the Times Higher, I'm glad to see that Pete's research has been picked up by the local press. There's a pretty impressive shot of him in today's Manchester Evening News, accompanied by an article that does a decent enough job of presenting our work. Yakub Qureshi seems to give the impression that we've creating some big new piece of modelling software, when what Pete actually did was to analyse existing evacuation simulations using a novel technique based on information theory. This "mutual information" measure appears to have become conflated with the notion of "social forces", but I'm glad that the quote in the final paragraph was kept, as it accurately sums up what we did. I gather Pete is greatly enjoying his new status as an official "disaster expert".

Unfortunately, though, I appear to have forgotten the cardinal rule: when talking to a journalist, there is no such thing as an "off the cuff" remark. I remember vaguely mentioning the computer game The Sims, as a way of trying to get across the notion of agent-based modelling. Yakub has enthusiastically run with this idea, and, sure enough, there's a picture of The Sims 2. Why, I'm not sure. I don't think the next version will include smoke modelling or exit awareness profiling, but this has only served to remind me that tiny, inconsequential remarks will suddenly become the entire focus of the article, unless you're very, very careful.

Take this example, from the Liverpool Daily Post, April 22, 1998. I'd not long been awarded my Ph.D., which happened to be the first in the field of DNA computing. I was talking to a local reporter, and, while explaining the labelling of the bases making up DNA strands (A, G, C, T), pointed out, in passing, that the name of the film Gattaca (starring Uma Thurman) is a string over this alphabet (and, indeed, will be commonly found in the average human genome). When the final piece appeared, describing this complex scientific research, sure enough, there's a picture of... Uma Thurman.

Weeknote #46

2012-01-14T00:18:00.007Z

There's been a bit of a gap since the last weeknote, mainly due to Christmas, followed by the start of term and the usual last-minute rush before a big European Commission funding deadline...

The crush paper I recently published with Pete and Steve has attracted a certain amount of media attention; the story (see the scan to the right) was used as the centrepiece in the campus roundup section of yesterday's Times Higher Education, and we're expecting local newspaper coverage next week. Apart from the obvious high quality of the science and the significant potential impact of the work ;-) I'm convinced that one of the reasons that the story has been given such prominence is that we published the paper in an open-access journal. If the paper had been buried away behind a journal paywall, I'm not sure people would have been so keen to cover it, and anyone who sees the story and searches for the work will be able to read it, whether they're affiliated to a University or not (and not be asked for $30 for the privilege, or whatever the going rate is...) Of course, we had to pay $1,350 to have the paper published (not considered for publication...), but we could have applied for a fee waiver had we been unable to find the money (and reviewers/editors don't know the payment status when they consider papers).

The proof is in the access statistics; the paper was published just over three weeks ago, and it's been viewed over 800 times already. It's been argued that the average number of readers for an academic article is about 5, so this is clearly an improvement!

Weeknote #45

2011-11-19T16:46:00.003Z

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

2011-10-25T16:12:00.004Z

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

2011-10-24T08:35:00.009Z

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

2011-09-21T19:54:00.002Z

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

2011-09-13T09:46:00.003Z

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

2011-09-03T10:53:00.003Z

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"

2011-09-03T10:43:00.001Z

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

2011-08-19T22:06:00.010Z

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

2011-07-18T10:13:00.006Z

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

2011-07-12T12:06:00.005Z

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

2011-06-28T21:37:00.008Z

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

2011-06-27T19:08:00.006Z

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

2011-06-20T21:12:00.003Z

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

2011-06-06T22:15:00.006Z

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.

Chemical computation

2011-06-04T23:51:00.010Z

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."

Who says Universities aren't forward thinking?

2011-05-25T13:38:00.004Z

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

2011-05-18T21:22:00.005Z

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

2011-04-23T11:38:00.005Z

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

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

2011-04-18T13:39:00.005Z

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.

2011-03-22T23:20:00.003Z

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.

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

2011-03-20T22:40:00.012Z

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 #34 (w/e 6/3/11)

2011-03-07T23:08:00.004Z

Slight shift of focus this week, as the previous seven days have been utterly dominated by arrangements for the fifth birthday party of a certain someone. Anyway, we hired the Fielden Centre in Todmorden (which will mean nothing to 99.7% of my readership), and couldn't fault them (specifically, Bridie) for helpfulness, friendliness and downright reasonable pricing (this is not product placement, BTW).

Anyway, this was the first party we'd organised where everything was up to us; catering and entertainment. On top of this, we decided that such an occasion deserved a healthy turn-out, and invited around 30 kids, on the assumption that roughly 20 would be able to make it. As opposed to the 30 that turned up.

I learned some important lessons this weekend, and I offer them to you now, in ascending order of importance.

5. Check the facilities in your venue. Our place was kitted out with an oven, which allowed us to indulge our wildest, almost Blumenthal-esque food fantasies (ie. pizza, and fish fingers and chips). However, we weren't warned that, after being turned on, the temperature of the oven would rise by about 3 degrees every half hour.

4. Dress as a pirate. Never fails.

3. Corollary to (4). When dressing as a pirate, ensure that arriving parents are aware of your true identity (ie. father of party girl), lest they mistake you for a particularly shoddy hired entertainer (happened).

2. Check your music. I'd vaguely heard about this Glee thing that the kids were into, and thought that music from the series would make an appropriate soundtrack to a party full of 4 and 5-year-olds. Wrong. After rashly picking up two CDs without checking the tracklisting, I got them home to discover that the second track on one of them was a cheery cover of Amy Winehouse's Rehab. Cue frantic last-minute iTunes purchases. Also, check your equipment. An iPod/docking station combo that can be unbearably loud in a kitchen with quarry tile flooring will suddenly sound like a wasp trapped under a beer glass when placed in a cavernous hall full of small children hyped up on blue pop.

And the absolute, number 1 lesson I've learned from organizing a kid's party is don't be the baddy. Specifically, under no circumstances plan games that involve you making semi-arbitrary decisions about who is "out". You will never remember all of the names, and will end up looking pretty evil as you point at some quivering 4-year-old and shout across the room "You! No! Yes, you! You're out!"

I thought I'd be clever and organize a game of "Islands", which is a variant of "musical chairs", using sheets of newspaper as the islands onto which the kids must jump when the music stops. "Very clever," thought I. "Fits well with the 'Under the Sea' party theme." I was so very wrong to be in any way self-satisfied, as the game swiftly descended into Lord of the Flies-type chaos, with refusals to leave swiftly followed by the emergence of factions, and then all out war declared (mainly on me).

Pick games, like "Four corners" (from the link above), or "Pass the parcel". In that way, the decision on who is "out" is taken completely out of your hands, it's utterly unambiguous, and you can simply shrug at the tearful toddler as they shuffle sadly to the margins of the room, and say, apologetically, "Look, I don't make the rules."

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

2011-02-28T02:59:00.003Z

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.

The New Scientist Cupcake

2011-01-20T11:27:00.004Z

Yesterday, I received an intriguing package at work. A square box, marked "FRAGILE". Guesses in the lab ranged from "a mug" (about the right size, but far too light) to...something more sinister.

There was a sense of anti-climax when I opened the box to find that it was from the New Scientist.

Specifically, from the arm of their operation that deals with job adverts. I've placed a few ads with them in the past, and now they were touting for repeat business.

With a cupcake.

The enclosed note very kindly said that they're sending me "a little something in the post to sweeten up my day", but I was staggered by the amount of packaging it required. One cardboard box, a large sheet of bubble wrap, another small box (tied with ribbon), the cupcake itself (wrapped in plastic), and the note.

It certainly did its job, which was to get my attention, but I'm not sure the overall impression is what they intended.

I still ate it, though.

Weeknote #32 (w/e 16/1/11)

2011-01-17T13:48:00.003Z

A (belated) Happy New Year to my tens of readers!

I spent a lovely evening last Monday, as the guest of the Bollington SciBar. This event was set up by Naomi, and took place in the civilised surroundings of the Vale Inn. I spoke for about half an hour on synthetic biology to a gratifyingly large audience, before we opened things up for discussion. There were many insightful questions, and everyone seemed to enjoy themselves. The drive back was much less fun, due to the failure of my windscreen wipers, but that's another story.

Just before Christmas we said goodbye to Jose Cecilia (Chema), who was visiting the group from his University in Murcia, supported by Andy Nisbet and his participation in the HiPEAC Network of Excellence. Chema spent three months working on an implementation of ant colony optimisation for the GPU, and we've just had a conference paper accepted (preprint version is here).

Weeknote #31 (w/e 19/12/10)

2010-12-21T23:23:00.007Z

I delayed this week's note until the details of a couple of publications were confirmed.

The first has resulted from Naomi's work on our NanonInfoBio project, and concerns the "problem" of interdisciplinarity. A lot of interesting and important contemporary research occurs where the boundaries between academic disciplines become blurred (synthetic biology being a good example), and we decided to investigate how it might be encouraged. The resulting paper (written largely by Naomi, with a relatively minor contribution from me) has been submitted to a journal, and is now available as a preprint. The title and abstract are as follows:

Removing Barriers to Interdisciplinary Research
Naomi Jacobs and Martyn Amos

A significant amount of high-impact contemporary scientific research occurs where biology, computer science, engineering and chemistry converge. Although programmes have been put in place to support such work, the complex dynamics of interdisciplinarity are still poorly understood. In this paper we interrogate the nature of interdisciplinary research and how we might measure its "success", identify potential barriers to its implementation, and suggest possible mechanisms for removing these impediments.

I'm also delighted to announce the second instalment of the Synthesis Lectures on Synthetic Biology that I edit for Morgan and Claypool. Within this publishing model, libraries pay a one-off subscription charge, and are then given perpetual access to a growing list of lectures (in this context, "lecture" means a short book, in the region of 100 pages), although they may also be bought individually, either in electronic form, or as paperbacks.

The first lecture was published by Natalie Kuldell and Neal Lerner of MIT in 2009, and has already been downloaded nearly 300 times.

The second lecture has just been published, and is titled Bacterial Sensors: Synthetic Design and Application Principles. It's written by Jan Roelof van der Meer from the University of Lausanne in Switzerland, and is an in-depth treatment of the engineering of living cells for the purpose of biosensing.

The first two lectures have got the series off to a flying start, which I hope I can maintain as the third runner in the relay (my own lecture is due next year). I'm also happy to consider proposals for lectures, so if you work in synthetic biology and would like to consider writing a short book, do please drop me a line.

That's it for the blog for 2010, so I'll just wish you a happy and peaceful holiday, and a productive new year.

Weeknote #30 (w/e 12/12/10)

2010-12-13T15:54:00.005Z

This week's big news is that we've completed the final formalities on a new European grant. COBRA stands for Coordination of Biological and Chemical IT Research Activities, and it's a three-year coordination action funded by the European Commission Seventh Framework Programme (FP7).

The project is one of several funded under the Future and Emerging Technologies Proactive initiative, and the constituent projects are NEUNEU, MATCH-IT, BACTOCOM and ECCell.

The main objectives of the project are to create a sustainable European research community in the emerging area of "biological and chemical-based IT", and to write a definitive roadmap document on how this field might develop, its main challenges and opportunities, and how its potential impact on society at large.

MMU will coordinate the overall project activity, and our first meeting will be held in Manchester next January.

Separated at birth?

2010-12-07T13:53:00.002Z

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

2010-12-06T12:28:00.003Z

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 #28 (w/e 28/11/10)

2010-11-29T12:47:00.002Z

We had a meeting of the Faculty Science Communication and Engagement Group last Monday, which was a good chance to take stock after a highly-successful Manchester Science Festival. I was particularly proud of my Group, as they threw themselves whole-heartedly into various activities, which are summarised here. Naomi and Zarka were invaluable event organizers, Pete and Matthew were honorary Girl Geeks during the robot building sessions, and then Pete stepped in at the last minute to give a Teawitter talk on evacuation. We all enjoyed our involvement in this year's Festival, and are already looking forward to National Science and Engineering Week next year.

Fake Biologist Alert!: I was featured in the Autumn edition of the MMU Success magazine, talking about BACTOCOM. If you want to see the full story, including me in an unnecessary labcoat, it's here.

Finally, this week was not a good week in which to be an Ipswich Town supporter. I was all for giving Roy Keane the benefit of the doubt at first, but yesterday's clueless capitulation at the hands of our fiercest rivals is giving me pause for thought.

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

2010-11-22T19:53:00.003Z

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)

2010-11-16T23:21:00.003Z

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.

Blatant plagiarism

2010-11-12T00:20:00.015Z

I've seen my work plagiarised in the past, but I get particularly irritated when I see it being done badly. Here are some pretty wretched examples, by way of illustration. This is the first page of a paper I wrote with colleagues in 1996, before I even had my Ph.D., and when I was still at Liverpool. Note the phrase "Today's supercomputers still employ the kind of sequential logic used by the mechanical dinosaurs of the 1930s." Now, see these course materials, this article, and this article. In each case, they've taken my own words (and not just the sentence highlighted above, often whole paragraphs from the paper), and presented them as their own.

This got me annoyed, so I decided to do a little random digging. By googling random phrases from my Ph.D. thesis (PDF download) from 1997, I was able to uncover wholesale theft of my material.

This example is particularly galling; G.P. Raja Sekhar of the Indian Institute of Technology is presenting whole swathes of my own work as his own. Before proceeding, I should point out that I have asked Sekhar to remove his version, but he has apparently declined to do so.

In the illustrations below, I've presented the original (thesis) version on the left, and the stolen versions on the right. As you can see, no attempt has been made to hide the plagiarism in any way, and it's extensive (click on the thumbnails for a closer look).

It's not just the reuse of the odd figure here and there; it's systematic theft of figures (some of which took me hours to draw) and large sections of text.

C. Saravanan of Vel Sri Ranga Sanku College, Bing Hu, QiKai Xu, Chenjue Wang and Xiaoyang Kuang of City College of New York, and Tankut Yalcinoz of The Fountain; you are all plagiarists. But G.P. Raja Sekhar; if you want to use my material, I'll happily share the Powerpoint with you. Just don't pretend you wrote it.

Update (12/11/10, 13:38): Dr Raja Sekhar has been in touch. He offers the following statement: "This is to state that the Lecture Notes DNA Computing - Graph Algorithms published by POSTECH, South Korea is a result of some joint work with my students listed in the preface whom I have acknowledged. Some of the material contains the work of Martyn Amos and was not cited and we deeply regret this and withdraw this article from anywhere it appears."

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

2010-11-08T22:42:00.004Z

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 #24 (w/e 31/10/10)

2010-11-01T17:32:00.004Z

Last week we held our synthetic biology event as part of the Manchester Science Festival. Over 130 people turned up for Artificial Life: Perils and Pitfalls, and we heard from Ron Weiss of MIT, Maureen O'Malley from Exeter, and Steve Yearley from Edinburgh. Gerry Kelleher, our Deputy Vice-Chancellor, also said a few words at the start. The overall feedback from the audience was excellent, and I think we can class it a success, although I might have hoped for a little more intellectual "argy bargy" (the audience members who asked questions were generally already quite sympathetic to the synbio "cause"). All in all, a great evening, and we thank the panelists, audience members (and, of course, our sponsors at the EPSRC) for making it so.

I was also booked in to talk at another event over the weekend, but found myself double-booked (my own silly fault). A fifth birthday party regretfully trumped a fourth Teawitter Party, although my Ph.D. student, Pete, came to the rescue, for which I am eternally grateful. His talk on crowds was, by all accounts, very well-received, so maybe he's one to watch in the public engagement stakes...

It was also, of course, Halloween this weekend, so no post would be complete without a picture of our very own little witch. She's been super-cute in the last few days; we're big fans of The Cube, and she solemnly informed us, while we were watching it yesterday, that if she won £25K she would give it straight to daddy, because she's "not big enough to have pounds." Awwww. Like I'm any better with money!

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

2010-10-25T12:36:00.007Z

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 #22 (w/e 17/10/10)

2010-10-18T11:50:00.010Z

It's been four months since I resolved to adopt the Getting Things Done system of personal organization, so I thought that now might be a good time to share what insights I might have to offer. What follows is a set of observations on and personal "hacks" of the system; these are, of course, purely specific to me, but others might find them useful.

1. I'm not finding the idea of a set of "tickler" folders particularly helpful, and haven't really adopted this part of the system.

2. All of my lists are stored as individual text files; I have the following, labelled, by convention, with the "@" sign: @_nextactions (the underscore means it appears at the beginning of any alphabetical list), @PROJECTS (the "master list" of ongoing activities), @someday (a "wish list" of things to do if and when I ever get time), @errands (short jobs like dropping off dry cleaning), @calls (phone calls to make), @waitingfor (obvious), @agenda_x (where x is one of two people I have working with me), and @weeknote (where I dump ideas for this weekly post).

3. I've tried to keep my _@nextactions list to items that need to be done right now. In order to achieve this, I preface each item in the list with a capitalized "tag", corresponding to the project it represents. This allows me to quickly ascertain the high-priority jobs (see later discussion on contexts). So, for example, the first three lines of my current action list are:

WELLCOME: Edit draft 4a
COBRA: Presentation for Brussels
MSF: Mail speakers with agenda

In order to keep track of next actions without necessarily adding them to my immediate action list, I append them with a "=" to the end of the entry in my @PROJECTS list. So, one project without an immediate action in my @_nextactions list might read:

INTER: Paper with Naomi on inter-disciplinary science = edit draft

4. All of these files are kept in a "GTD" directory within my Dropbox folder. Dropbox is absolutely essential to my implementation of GTD, since it allows me to check and update from wherever I am. I have it running seamlessly on a Mac (home), Linux box (work and netbook) and phone (Android). It just works. If you sign up via this link, I get extra free space. Keeping everything in plain text means that editing is trivial, whichever platform I'm running on.

5. Because of the availability of my files wherever I am, I find that I don't really make much use of contexts, as such. I'm generally always at a computer when working, so this breaks down the distinctions that are outlined in the book (the exception to this is while travelling, when I prefer to read material, rather than actively work on it). The project-tags in the next actions list allow me to prioritise easily, whereas having a separate list for errands means that I can easily check for jobs when I'm out and about.

And that's where I am so far with GTD. I'm sure my implementation is far from optimal, but it works for me.

In other news, reservations are flooding in for our forthcoming Manchester Science Festival Artificial Life event. We're almost at capacity, with over a week to go, so please book your (free) ticket soon in order to avoid disappointment.

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

2010-10-12T23:41:00.004Z

I've been a little remiss in terms of weeknote updates. Last week was mainly spent getting into a reasonably high teaching gear for the new term. I have a few good project students this year, so I'm hopeful that we can continue the trend of working on papers together.

Last Monday I spent an enjoyable evening at the Wilmslow Guild, giving a lecture on synthetic biology as part of their Science Matters series. The turnout was good (over fifty people), and I was asked some incisive questions. I was rather flustered on arrival, however, as I only just made it, due to the "navigation" software on my new phone insisting that I was actually driving around Wimbledon (London!), instead of getting increasingly worried in Cheshire. Do not trust the navigation software on the Samsung Galaxy Europa (it's an absolutely lovely little phone otherwise).

Speaking of all things to do with public engagement, we've finalised the line-up for our forthcoming event at the Manchester Science Festival, and it's absolutely cracking. We have Ron Weiss, one of the leaders in the field of synthetic biology coming from MIT in the US, Maureen O'Malley from Exeter, who works at the intersection of the humanities and life sciences, and Steve Yearley from Edinburgh, who's the Director of the ESRC Genomics Policy and Research Forum.

The event is titled Artificial Life: Promises and Pitfalls, and full details are available on the website.

The Novel Computation Group lab is now full to capacity, with the arrival of the final Ph.D. student in the current "batch". We also have a new post-doc working on our NIB DNA hash-pooling project, are interviewing this week for a BACTOCOM post-doc, and have two new undergraduate students joining us for the duration of their projects.

Weeknote #20 (w/e/ 26/9/10)

2010-09-28T22:32:00.004Z

Better late than never...

It's hard to believe that our NanoInfoBio project is a year old, but it's true. We held the year end workshop last week, attended by twenty-four participants (a very decent turnout, given that it was held on the first day of freshers' week...) We're now well clear of the initial "explore and engage" phase, and are beginning to investigate how we might make nano-info-bio science a sustainable research area at MMU. Obviously, in order to do this, we need further funding, so the main focus of the second twelve months will be the development of research programmes and proposals. Four good project ideas emerged (or were dusted down!) at the meeting, and Naomi's job will be to coordinate the teams responsible for bringing these to fruition.

Exciting news to report on the writing front; back in August I was invited by Ra Page of Comma Press to consider a new collaboration between scientists and writers. A previous volume, When It Changed, contained short stories that emerged from discussions between authors and scientists, and offered "fictionalised glimpses into the far corners of current research fields". The book was very well-received, and they've decided to do another one (with a different focus, and I'm not sure how much I'm allowed to say about this). I was invited to propose one or more ideas for consideration by the set of authors they've signed up, and I was absolutely delighted to hear that one of mine was chosen by Jane Rogers. I'll act as a "scientific consultant", while Jane actually writes the story, and I'm very much looking forward to starting our collaboration next week, with an initial meeting in Manchester.

I'm now installed in my new office, so a trip to Ikea is very much on the cards. Room on the Broom in Buxton was a tremendous success; they're coming to the Lowry at the end of October, and I'd highly recommend it if you have young children (or even if you don't).

Weeknote #19 (w/e 19/9/10)

2010-09-20T23:47:00.004Z

Exciting times ahead, as we've just appointed a research assistant to work on our DNA hash pooling project. He'll be starting next month, and I'll post progress reports as we start to test the idea in the lab.

Another two Ph.D. students have started in my Group; Ben and Matthew will be working with Andy Nisbet, myself and others on hardware-based approaches to novel computation, with specific reference to the CUDA platform. They are both MMU graduates (in fact, they did their Honours projects with me, each gaining a first class degree), and I hope they'll prove to embody the "grow your own researchers" ethos that we've tried to encourage with NanoInfoBio (no pressure, lads).

I'm currently in the process of moving to a newly-refurbished (and, finally, single-occupancy!) office; this, combined with decorating work at home means that I feel a bit like the Queen, smelling fresh paint wherever I go.

On the family front, this weekend we're off to visit friends for the New Mills lantern parade, followed by Room on the Broom at Buxton Opera House. Rehearsals are well underway for the "BUZZ OFF! That's MY witch!" moment.

Weeknote #18 (w/e 12/9/10)

2010-09-13T22:12:00.006Z

A big week in the Ashby-Amos household, as the little one started primary school on Tuesday. She was a lot braver than her father, who tried to use the excuse of "worms on the path" in order to avoid going on his first day.

Various commitments meant that I was only able to pay a fleeting visit to the BIC-TA conference in Liverpool. It was really just a question of turning up, presenting the paper and shooting off again, although it was good to briefly catch up with Dave Reid, a colleague from my time at the University of Liverpool.

A story with NanoInfoBio connections attracted quite a lot of attention this week; Gavin Bingley, a Ph.D. student working with Jo Verran, presented some work on microbial degradation of historical cine film, and it was covered quite extensively. Jo and her team will be working with MMU chemists Craig Banks and Lindsey Munro to develop the nano-sensor mentioned in most reports. This project is one of the three 25K "Large Projects" supported by NIB.

Yesterday, I took the little one bike shopping in Halifax, and we made a detour on the way back so that she could have a little snooze in the car. I decided to drive home via Cragg Vale, which is an interesting place, not only for the views, but for the fact that it is the location of the longest continuous gradient in England.

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

2010-09-06T21:48:00.006Z

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 #16 (w/e 29/8/10)

2010-08-30T17:21:00.004Z

I've been on holiday since returning from Artificial Life 12 in Denmark, so there's not much to report. On Wednesday we have our new batch of Ph.D. students joining the Group, and on Thursday I'm off to Brussels for an FP7 contract negotiation meeting.

On a family note, my wife's busy organising a big symposium, and it's our daughter's last week at nursery before she starts school (sniff...)

Weeknote #15 (w/e 22/8/10)

2010-08-23T23:00:00.014Z

Lots happening this week, and I've spent most of it at the 12th international conference on artificial life, in Odense, Denmark. I first discovered the field in 1992, when I chose it as the subject of my honours project at University. Steven Levy's wonderful book got me started, and my little creation, titled BugWorld, attracted a moderate amount of attention. I'd have probably gone off into computer security, had I not discovered alife, so I think I owe the field a lot, and it was a surprise to me that this year's conference was the first Artificial Life that I'd attended.

I heard so many great talks that it would be unfair to single out any in particular, but I would point out that MIT Press have made the published proceedings freely available. This is great news.

Actually, I will highlight one talk in particular, in which I should declare an interest. My Spanish friend and colleague, Angel Goni-Moreno, gave a nice presentation based on a version of this paper, and we got some useful feedback.

The conference was great, and brilliantly organised. I was, however, disappointed to learn that this sign referred, not to the creche, but to the language center.

On a related note, I'm delighted to be able to confirm the first two panelists for our Manchester Science Festival event, Artificial Life: Promises and Pitfalls, to be held on October 26th. They are Professor Ron Weiss, from the USA, and Dr Maureen O'Malley, from the UK. We're delighted to have them, and look forward to being able to announce further panelists very soon.

Back in May I contributed to a panel on New Creativity at the marvellous Future Everything conference in Manchester. The video of the panel is now available online, although eagle-eyed viewers could be forgiven for thinking that I only own one shirt.

A recent draft paper I've submitted with Pete was picked up by the MIT Technology Review physics blog. The paper describes a new approach to quantifying levels of crush within crowds, using information theory. The coverage is fairly spot-on, and we're thinking about how to eliminate false positives. I think one of the commentators was a little naughty, though, in not declaring his distinct bias when criticising us for not considering human factors. The problem we address is not that of "why does crush form?", but, rather, "can we automatically detect it when it does form?" While a consideration of human factors may well make a simulation more "realistic", it doesn't address the central issue.

(By the way, Ben, your website could do with an overhaul.)

Weeknote #14 (w/e 15/8/10)

2010-08-16T08:52:00.008Z

The big news this week centred on rumours of a resolution to the "P=NP?" question. Although this issue might seem, at first, to be of purely theoretical interest, it has immense "real-world" significance. As one of the Millennium Problems, it also carries a million dollar bounty, although no serious mathematician would ever admit to being motivated by the money....

(Simpsons still taken from the Treehouse of Horror VI episode.)

Others are far more qualified to discuss the details of the proof than I'll ever be, but I do I feel able to comment on some of the ludicrous media coverage surrounding the story. A prime example is here, where the BBC uses the headline "Million dollar maths puzzle sparks row". Ok, maybe the journalist who wrote the piece didn't actually choose the headline, but phrasing the normal operation of science in terms of "But maths experts have weighed in to point out flaws in his proof" isn't particularly useful (or, indeed, helpful). The whole point of publishing a proof is to expose it to scrutiny. In discussing the story, Richard Lipton quotes the renowned mathematician Yuri Manin as saying that

"A proof only becomes a proof after the social act of accepting it as a proof."

In other news, I appear to have annoyed Diane Abbott MP (or, at least, one of her team) by commenting on her remark that the other candidates for the Labour leadership appear to be "geeky young men in suits".

When the original remark was highlighted in a subsequent BBC news story, I tweeted a question to her, which very quickly provoked a denial. I'm automatically offended by the implication that "geek" is somehow perjorative, but Alex Ross does a nice job of explaining a rather more fundamental objection to Abbot's attitude towards the other candidates.

Weeknote #13 (w/e 8/8/10)

2010-08-09T11:38:00.006Z

This week saw the announcement, by the Royal Society, of a study into the issues surrounding (and implications of) the rapidly falling (plummetting) number of students choosing to study computer science and ICT.

According to Steve Furber, "what is taught at school is at a fairly basic level, and those who already have an interest in computing are already way ahead of that in what they’ve done at home. What schools are presenting as ICT as an academic subject is very mundane compared with what students know they can do."

This, I think is the central problem, and I personally believe that it's caused by the coupling of computer science and ICT.

I have a long-standing collaboration with Professor Dave Hodgson, a very well-respected microbiologist. When another (nameless) collaborator from computer science used to refer to Dave as "our chemist", Dave would get his own back by referring to us as "the IT guys". As the renowned theoretician Edsger Dijkstra once said, "computer science is no more about computers than astronomy is about telescopes."

The point is that computer science is about abstraction, the study and application of algorithms, problem-solving, and deepening our fundamental understanding of information processing (in all its forms). ICT, on the other hand, is concerned with the use and application of pre-existing software for the solution of well-defined tasks (eg. build a database, plan a budget, design a poster).

With ICT skills now almost mandatory for many spheres of work, it's clear that this subject should be part of the core curriculum at secondary level. However, if we are to encourage the next generation of computer scientists, they need to be able to develop their own particular skills and interests, which (as Furber indicates) are often far beyond the current subject matter.

My proposal is this: We need to separate ICT from computer science, and offer them as different subjects. Edited: 9/8/10, 14:40.

I recently blogged on this subject, and my post was followed by a nice related article in the Times Higher.

Weeknote #12 (w/e 1/7/10)

2010-08-03T09:25:00.003Z

The past week has been mostly spent on writing up/editing half-finished papers. I'm currently working with Pete on an extended journal version of our recent crush prediction work, an article with Naomi on approaches to developing inter-disciplinary research, a paper with Chinese collaborators on ant colony optimization for layout problems, and a review article on bacterial pattern formation. Our recent paper on the Zen Puzzle Garden game has also sparked some interest, and I'm currently drafting a follow-up paper in collaboration with Joseph White (the game's creator) and Robin Houston, who worked on his Ph.D. up the road.

I also spent an enjoyable couple of hours with Cat Rushmore at the Museum of Science and Industry (MOSI), recording a conversation for their oral histories collection.

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

2010-07-26T18:53:00.014Z

This week we finally submitted our paper on engineered oscillations in bacterial populations. This is something I've been working on with a colleague in Madrid, Angel Goni-Moreno, since he visited us in Manchester last year (in truth, he's been doing most of the work, although any delays have been entirely due to me).

In physics, an oscillator is a system that produces a regular, periodic "output". Familiar examples include a pendulum or a vibrating string. Linking several oscillators together in some way gives rise to synchrony -- for example, heart cells repeatedly firing in unison, or millions of fireflies blinking on and off, seemingly as one.

Oscillators are fundamental to biology, but they are also of interest to engineers, since they form the basis for counting (and synchronisation). Synthetic biology combines both disciplines, so the construction of oscillators within living cells is one of the main topics of interest in the field right now. However, until recently, most work has been restricted to single cells. In our paper, we have shown, in theory, how to engineer oscillations within populations of cells, using the "client-server" model familiar to computer scientists.

Update: the preprint version of the paper is here.

While writing the final draft, I was reminded of my brief contact with one of the founders of the field of theoretical biology. I first met Brian Goodwin in 2004, when I was still at the University of Exeter. He, along with Susan Blackmore, very kindly agreed to speak at the launch of a network I'd set up to encourage the study of complexity theory within the University. Best known in the broader community for his work on the evolution of complexity, Goodwin laid the foundations for recent research in synthetic biology with his seminal 1965 work on negative feedback. His later work focussed on the notion of a science of qualities (on which he spoke at our meeting), and when I first met him he was already formally retired, although still very active at Schumacher College, just down the road in Dartington. We also spent time chatting a year later, while we were both giving lectures at a summer school in Montpellier. I was struck most of all by his gentle nature and generosity of spirit, and we had the chance to discuss in greater depth the topics he'd touched on in his lecture.

Brian died just over a year ago; I first found out about his death while looking up references to give to my current Ph.D. student, who is now applying some of his ideas to the field of architecture. He had a great effect on me, and will continue to influence generations of students to come.

Weeknote #10 (w/e 18/7/10)

2010-07-18T23:51:00.004Z

Into weeknote double figures, but nothing much to report, as we've been on holiday at the Suffolk coast.

Normal service will resume next Monday.

Weeknote #9 (w/e 11/7/10)

2010-07-12T11:29:00.010Z

Only one thing of significance to report since my last weeknote; the acceptance of a fun little conference paper on solving a puzzle game that has, so far, escaped the attention of the algorithms community.

The Zen Puzzle Garden is a one-player puzzle game, involving a monk raking a traditional Japanese rock garden. The aim is to find a series of moves that allow the monk to rake all of the available sand, whilst negotiating rocks, pushing statues and collecting leaves - all without getting stuck in a dead-end.

While the problem is easy to describe, it's related to puzzles like Sokoban, which are actually very difficult to solve automatically (ie. with a computer program), in the general case. Jack Coldridge, who graduated from MMU a year ago, worked on this problem with me for his final-year dissertation, and we then developed it further into a full paper. The title, Genetic algorithms and the art of Zen is a play on David Goldberg's 1989 paper Zen and the art of genetic algorithms, which itself references Robert Pirsig's famous book.

Problems such as Sokoban are difficult because there are, potentially, a vast number of possible solutions to consider (where a solution is a path through the garden, in this example). Most solutions will be incorrect or "illegal", and the problem is to find the "needles in the haystack" (that is, the correct solutions). These so-called NP-hard problems are the most "interesting" problems in combinatorial mathematics, because they're the most challenging. The practical significance of such problems lies in the fact that they are related to "real world" problems of great importance, such as scheduling, packing and routeing. For a nice review of hard puzzle games, see this paper (PDF).

Several methods have been applied to the solution of such problems, including "traditional" algorithms, which use a "tree-based" approach to searching the space of possible solutions, as well as biologically-inspired algorithms. In the paper, we used a genetic algorithm to "evolve" paths through the garden. We start with a set of random paths, and see how well they solve the problem. Some will be "less bad" than others, so we keep them and use them to "breed" the next generation of solutions. Gradually, the power of natural selection (combined with a sprinkling of mutation) forces the population towards better and better solutions.

We found that our method was capable of finding the optimal (ie. shortest) solutions in the vast majority of cases, and it required far less processing power than another standard algorithm. Importantly, we have highlighted a new problem for the AI/puzzle community to get its teeth into.

The paper has been accepted for presentation at the IEEE Fifth International Conference on Bio-Inspired Computing: Theories and Applications (BIC-TA), to be held in Liverpool, on 8-10 September 2010.

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

2010-07-08T13:58:00.007Z

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.

Weeknote #7 (w/e 27/6/10)

2010-06-28T23:11:00.005Z

While flicking through the June issue of the BBC's Focus magazine, I noticed that one of my research collaborators had received a nice mention from Ian Stewart at Warwick. He was asked to select three books on puzzles and games; Martin Gardner was the obvious first-choice author, and Winning Ways for your Mathematical Plays is a minor classic. Stewart's final choice was a book written by my collaborator at New York University, Dennis Shasha. In the column, Stewart describes Dr Ecco's Cyberpuzzles as "...a fantastic book if you want to spend some serious time solving puzzles and giving your brain a work-out."

Ian Stewart has been a significant influence on my career; as a popular science author, I've always been impressed by his writing, but he had a rather more direct effect on me back in the mid-1990s, when I was a graduate student at the University of Warwick. Ian very kindly wrote me a reference to attend the prestigious Complex Systems Summer School at the Santa Fe Institute, and the month I spent there was incredibly important in terms of shaping my personal ambitions and outlook on research.

Now, I'm fortunate in being able to collaborate with people of Dennis' calibre (see the previous note, below), and last week he very kindly sent me a copy of his latest book. Co-written with Cathy Lazere, Natural Computing is a profile of the frontiers of computer science, told through the stories of fourteen pioneers, such as Rodney Brooks, Ned Seeman and Paul Rothemund. I'll post a full review once I've finished it.

Weeknote #6 (w/e 20/6/10)

2010-06-21T22:07:00.007Z

We (three colleagues and myself) were recently successful in obtaining funding from the NanoInfoBio project to test an idea that's been rattling around for a while. DNA hash pooling is a technique that Dennis Shasha developed, with some assistance from me, while I was visiting him. Dennis is an incredibly sharp and prolific Professor of Computer Science at the Courant Institute of New York University. He was the Series Editor for my first book, and we kept in touch since its publication. Justine, the little one and I visited Dennis while he was in Paris on sabbatical with his family, in the summer of 2007. While Tyler, Dennis and Karen's son, played American football, we walked round and round an athletics track on the edge of the city, knocking around our own particular problem.

The task of analysing large populations of mixed DNA strands is of particular relevance to the emerging field of metagenomics, which is concerned with understanding, in genetic terms, the vast complexity of the planet's biosphere. Methods for looking at environmental samples often require a lot of genetic sequencing; although new ways of doing this are constantly driving down the cost, it can still be expensive to sequence large populations, as well as time-consuming. Dennis and I developed a technique that combines computational analysis with simple rounds of laboratory steps, based on the computer science idea of hashing. The idea is to associate "labels" with individual sub-populations of genetic sequences, such that the number of different genomes with the same label is relatively low. In this way, each genome (or genomic fragment) is associated with its own "fingerprint", which we can then use to confirm its presence (or otherwise) in a sample. Our hope was that this technique would offer a cheap, quick and simple pre-processing step before any sequencing was required, thus reducing the cost and complexity of analysing a sample.

We finally published the theoretical paper last year, but have only just obtained the funding to actually test the idea in the lab. I floated the concept at one of the NIB brain-storming meetings, and it was picked up by a talented team of biologists (Trish Linton, Mike Dempsey and Robin Sen). We put together a proposal to NIB for a small amount of support (£25K), and we were fortunate enough to be one of three projects funded in the last round. The nine-month post-doctoral position is currently going through the MMU approval process, so watch this space if you're interested.

Weeknote #5 (w/e 13/6/10)

2010-06-14T20:52:00.007Z

The focus of the past week has been on Getting Things Done. After what's been probably my busiest academic year so far, I finally decided that my workload was such that I required a rigourous approach to task management. I trawled around for methodologies that would allow me to organize a multitude of different jobs, whilst maximizing the time I could spend with my family. After reading about Getting Things Done (GTD) on Merlin Mann's well-respected 43 Folders blog, I decided to give it a go. There's a nice "getting started with GTD" article on 43 Folders, which summarises the approach thus:

identify all the stuff in your life that isn’t in the right place (close all open loops)
get rid of the stuff that isn’t yours or you don’t need right now
create a right place that you trust and that supports your working style and values
put your stuff in the right place, consistently
do your stuff in a way that honors your time, your energy, and the context of any given moment
iterate and refactor mercilessly

And that's it, really. Most of the week was spent on the first three steps (the creator of GTD recommends at least a couple of solid days), but the effort was well worth it. I started by taking the various slush piles, to-do lists and marked-up journals and papers in my home office, and merging them into one big "in" pile. I then had to do the same with my work and Gmail inboxes, extracting only the "open loops" (i.e., unfinished projects).

I had over 4,000 emails in my Gmail inbox, and working through the whole lot, deleting as I went, quickly lost its appeal. I therefore adopted a "tagging" approach; I created an "@action" tag in red, and then skimmed through my inbox, tagging anything that required an action on my part. Everything was then selected and archived (just "select all", answer "yes" when it asks you if you want to apply this to all conversations, and then hit "Archive"), leaving nothing in my inbox (for the first time in many years). I could then select only the tagged messages, which was much more manageable.

The end result of this physical and electronic clear-out was a car-full of paper to go to the recycling centre, a clean workspace (shown above) devoid of distracting piles of paper, and a fresh outlook on work. I'm already feeling the mental benefit, as I've been relieved of the self-inflicted stress brought on by my subconscious constantly asking "what am I currently not doing?" I've always been quite cynical in the past about "snake oil", management-driven "productivity" schemes, but I can honestly say that GTD is an eye-opener, and it actually seems to work.

I've managed to condense everything down to a list of just over forty "projects" (ranging from "Fix external hard drive" to "Write next book"), most of which have a discrete "next action" attached to them.

I'll be writing more about GTD in the coming weeks and months, as I learn more about the system and (hopefully) realise its potential.

Weeknote #4 (w/e 6/6/10)

2010-06-07T12:10:00.005Z

I've spent the past week in Madrid, at the Universidad Politecnica. I was a Visiting Professor in the Faculty of Informatics, delivering a series of lectures on "molecular and cellular computing" to their Masters-level students.

In the past, some people have expressed an interest in the material, so I thought I'd make it available here. A lot of it is based on my book Theoretical and Experimental DNA Computation (Springer, 2005), although there's a lot of new material in the second half of the series.

The lectures are as follows (links to PDF versions of the slides):

Day 1: Molecular Computing

1. Introduction and historical motivation.

2. The first experiment.

3. Subsequent work.

Day 2: From in vitro to in vivo

1. Models, lab work, and the transition.

2. Laboratory implementations.

Day 3: Biological Engineering

1. Biological background.

2. Synthetic biology.

3. Synthetic Biology II.

Molecular and Cellular Computing course material by Martyn Amos is licensed under a Creative Commons Attribution-Non-Commercial-No Derivative Works 2.0 UK: England & Wales License.

Weeknote #3 (w/e 30/5/10)

2010-05-31T21:27:00.003Z

Not a great deal to report this week, as I've been suffering from a particularly painful seasonal disorder (i.e. marking). The delay to our Madrid trip due to Icelandic intervention was a blessing in disguise, I think, as it allowed me to clear the decks of a load of scripts before jetting off to give three afternoons of lectures at the Universidad Polytecnica de Madrid. If we'd gone when we'd originally planned to then the scripts would have been sitting there in my study at home, a distant yet malign cloud hanging over the trip.

Arrived in Madrid yesterday, after a relatively painless flight from Liverpool with EasyJet. It was all going too well, however; on arrival at the hotel, our daughter ran towards a display of flowers in the lobby, caught her foot on a rug and went face-down onto a table. She cut her eye quite badly, but she's a hardy little thing, and was back on top form today.

I gave my first set of lectures this afternoon/evening, as the guest of Alfonso Rodriguez-Paton. He's the "Madrid node" of our BACTOCOM project, and kindly invited me to teach some of their postgraduates (others involved this year include Christof Teuscher, Milan Stojanovic and Friedrich Simmel, who's also involved with BACTOCOM). I'm here to talk about "molecular and cellular computing"; ŧoday was motivation and historial background, a bit of biology and an overview of Adleman's experiment. Tomorrow is formal models of DNA computation followed by self-assembly and DNA origami. The final set of lectures on Wednesday will deal mainly with synthetic biology, so I hope Fritz has left me something to talk about.

Weeknote #2 (w/e 23/5/10)

2010-05-24T17:00:00.012Z

It's been a big week for synthetic biology, with the announcement by Craig Venter that he'd succeeded in creating a "synthetic cell". My previous post describes my take on the technical aspects of his achievement; it's not entirely accurate to call it a "synthetic cell", since they used existing cells as the recipients (that is, it was only the genome that was synthetic). It's more like "genomic transplantation" with de novo sequences. Technically challenging, but not the earth-shattering breakthrough that it's being sold/hyped as. They certainly didn't turn "inanimate chemicals into a living organism".

My own little piece of press coverage looked pretty low-key by comparison. I was interviewed ages ago by Louise Tickle for the Education section of the Guardian, and the story finally appeared last week.

This week, members of my group (specifically, Pete and Naomi) contributed to an event hosted by MMU. I'm a Director of ArcSpace Manchester, a Community Interest Company to support creative and ethical exchange, and on May 19th we held a video conference with collaborators in Sao Paolo, Brazil, to discuss "eco-techno" and public engagement. Unfortunately, other commitments meant that I was unable to attend either in person or in the form of an avatar, but my co-director, Vicky Sinclair, wrote up the event.

On the work front, I've been busy marking projects and exam scripts, although I did also submit this conference paper.

Team Venter's synthetic cell, explained

2010-05-21T08:24:00.007Z

I've been asked to comment on this week's news that Craig Venter's team have succeeded in building a "synthetic living cell" (you can read the full paper, for free, here), so I thought it might be useful to write a short post to explain just what they've achieved.

Cells may be thought of as biological "wetware", in the same way that the physical components of a personal computer (hard drive, processor, memory, etc.) form the "hardware". A computer can't work without an operating system; the central controller program that runs in the background, coordinating the various activities of the machine. Most people use Windows as their operating system, although there are others, such as Ubuntu Linux and MacOS. Similarly, a cell cannot survive without a working genome; the collection of genes that control and influence an organism's internal operation.

The core kernel (ie. the central "brain") of the Ubuntu Linux operating system running on my netbook is (roughly) 4 Megabytes in size, which is about four times the size of the genome of Mycoplasma mycoides. This is a bacterial parasite found in cattle and goats, and it was selected by Venter and his team because (a) it has a relatively small genome that has been fully-sequenced, and (b) it grows more quickly than bacteria they've used in the past.

Venter and his team have created an entirely synthetic copy of the genome of M. mycoides, which they then inserted into a related bacterium, M. capricolum. This new genome was "booted up" by the recipient, which then started "running" the new genetic program.

Importantly, the synthetic genome was completely pristine, in the sense that it had not been physically derived in any way from existing genetic material. Standard genetic engineering splices short synthetic sequences in to existing, "natural" DNA sequences, but Venter's "synthia" genome was created from scratch. It's the equivalent of taking the known binary sequence of a small operating system kernel, typing it into a text editor in small chunks, combining the chunks together into one big file, and then using it to boot up a PC. At no stage was the "new" kernel physically derived (copied) from a version stored on CD, DVD, or downloaded from the 'net.

Venter's team use a DNA synthesizer to piece together the A, G, C and T bases to form brand-new building blocks, which were then stitched together into a single sequence. This is the key technical achievement of the paper - a strategy for assembling an entire genome, from scratch, using synthetic components, and to get it "running" in a host cell. It's important to note that it was only the genome that was synthetic; the recipient cell was a pre-existing, "natural" bacterium.

This breakthrough is significant in that it demonstrates the feasibility of large-scale whole-genome transplantation, which will be an important component of the emerging field of synthetic biology. However, the real challenge lies in gaining a systems-level understanding of how even simple genomes operate, so that they may be fundamentally (re-)engineered.

Science has opened up a forum for posting questions, which will be answered later today by news writer Elizabeth Pennisi and philosopher and scientist Mark Bedau.

Update, 21/5/10, 11:13: Corrected kernel size assertions; Windows kernel is much larger than previously thought.

Weeknote #1 (w/e 16/5/10)

2010-05-17T08:40:00.004Z

In an effort to blog more regularly, I've decided to adopt the Weeknote model of short seven-day updates on what's been going on.

The weekend was dominated by my inability to leave the country; I was due to fly to Madrid to give a series of lectures on molecular and cellular computing to Masters and Doctoral students at the Universidad Politécnica de Madrid. It was also an opportunity to take a couple of days of much-needed time with my wife and daughter, who'd be travelling with me. As the airspace in Northern Ireland had already been closed, we checked the status of the flight before we set off for Liverpool Airport. Everything was ok, but by the time we got there a couple of hours later, they'd shut down. A maudlin hen party, wearing mandatory pink fluffy stetsons, were told that the next available flight was on Thursday; we just returned home, where I quickly rescheduled the lectures for two weeks time. My host, Alfonso Rodríguez-Patón, was incredibly understanding and helpful, managing to book a new hotel for us, despite the fact that my new schedule coincides with a major festival on the Thursday (making hotel rooms extremely rare).

Another significant event this week was the Future Everything festival, which was (if you read the various reviews and tweets) wildly successful. I contributed to a panel discussion on New Creativity, which also featured Anab Jain, a TED Fellow who talked about her Power of 8 project, Kerenza McClarnan of Buddleia, who's facilitating artist-led enquiry into urban spaces, and Adrian Hon of award-winning games company Six to Start, who talked about the purpose of play. It was a fascinating session, with a lot of dynamic connections made between the panelists (none of whom really knew anything in advance about what the others would say). The session was recorded, so I'll post a link if and when the video is made available.

In mid-week we had our latest brain-storming "away"-day for our Bridging the Gaps: NanoInfoBio (NIB) project. This is a two-year initiative, supported by the EPSRC, to encourage cross-disciplinary research within MMU (with specific focus on the life sciences/engineering/computing/maths/nanotechnology interface(s)). We're almost ten months into the project now, and are beginning to develop a coherent set of themes around which we can coalesce. We're giving out a few project grants of £25K in order to boot-strap small feasibility studies, so we arranged an afternoon at a Manchester hotel to generate some ideas. Experience has shown that it's best to get everyone away from the distractions of email, and the temptation to "just pop back to the office", and I think everyone was happy with how it went. Rather than dividing everyone into groups, as might seem natural, we first performed a general "audit" of possible project ideas (this first pass generated 12), and then "drilled down" as a whole group to examine each idea in turn. Once a page or so of flip-chart paper had been filled for each project, only then did we split up in order to go over the fine details of costings and so on. The group-level discussion led to some surprising contributions, which would have been lost if we'd split up too quickly. I think it worked.

The need for hacking

2010-05-11T09:23:00.004Z

The following post is a lightly-edited version of an article I've just had published in the Spring 2010 issue of MMU's Success magazine:

The word "hacker" has, in recent years, acquired an unfortunate and perjorative meaning. The media portrayal is of a pale-faced teenage boy (for they are invariably male) crouched over a keyboard in a fetid room, determined to make their mark on the world through cyber-vandalism or malware scams. My teenage years were partly shaped by the movie WarGames, in which an inquisitive youth accidentally triggers the countdown to armageddon by wandering into a US military computer, while the recent case of the "UFO hacker" Gary McKinnon has merely reinforced the "misfit" stereotype.

They are almost universally despised by mainstream commentators, and yet the infrastructure on which all of us rely (mobile phones, computers and the internet) would not even exist in its current form were it not for the hacker.

The original hackers were the pioneers of the electronic age, when the term simply meant "one who hacks". A hack, back then, was just a clever or "pretty" solution to a difficult problem, rather than an attempt to gain unauthorised access to a system. These early hobbyists and developers created the first microcomputers, as well as the foundations of the global information network.

One of the key principles of the hacker ethic (as described in Steven Levy's book Hackers: Heroes of the Computer Revolution) is that the best computer system is one that may be inspected, dissected and improved upon. When I started programming back in the 1980s, games were often distributed as listings printed in magazines, which had to be typed in before playing. By messing around with this code, I picked up various tricks and learned important new techniques. As my programs became more sophisticated, I had to get "under the bonnet" of the machine and interact with the computer at a fundamental level. The so-called "hard skills" that I learned in those early years have stayed with me ever since.

Modern teaching increasingly promotes the "soft skills" agenda, such as the need for team-working, communication and negotiation. Whilst these abilities are undoubtedly important, we need to protect and promote technical content. I wouldn't want a mechanic delving under the bonnet of my car if all he or she had ever done was change a tyre or top up the screen-wash, even if they did describe themself as a personable, motivated team-player...

Computers now take many forms (consoles, phones and PCs, for example) and they're increasingly viewed as sealed appliances, intended for gaming, chatting or browsing. Members of tomorrow's workforce are immersed in social networking, app downloads and file sharing, but they often lack the fundamental knowledge that can only come by (either physically or metaphorically) opening up the box and tinkering with its insides. By that, I mean the acquisition of technical insights and skills required in order for a person to become a software producer, rather than simply a consumer of apps. New innovations such mobile and cloud computing mean that hard skills are more important than ever, as the digital infrastructure becomes ever more firmly rooted in our day-to-day lives.

The beauty of the situation is that these skills are no longer the sole domain of computing professionals. The availability of modern computers means that we are ideally-placed to develop the next hacker generation, capable of creating ingenious applications and web-based systems. We need to return to the playful principles of the original hackers, by promoting programming as a recreational activity. Modern software packages such as Alice allow us to teach complex concepts almost by stealth, through the medium of computer animation. Open-source operating systems encourage tinkering, and mobile app development is now a legitimate career path. The new generation of twenty-first century hackers may well be digital natives, but they first need to learn to speak the language.

"It's alive! ALIVE!"

2010-04-02T22:57:00.004Z

I've decided to revive the blog, as several new projects have started recently, and I think it's useful to pass on news through informal channels such as this, as well as via the "official" websites. I'll be posting regular updates on our BACTOCOM project, funded by the European Commission, as well as news of Bridging the Gaps: NanoInfoBio, and any other snippets that I think might be of interest.

Synthetic biology and Howard Hughes

2008-06-01T20:29:00.003Z

The Howard Hughes Medical Institute has announced its latest set of investigator appointments. Awards are made to individuals, as opposed to the usual mode of funding, where money is assigned to a project, and the field of synthetic biology is represented by two of its leading figures in the current crop. Jim Collins at Boston and Michael Elowitz at Caltech both had papers in the important 2000 issue of Nature, which reported some of the first experimental results in the area (specific papers are here and here.)

Genesis Machines in the USA

2008-05-29T22:48:00.002Z

I'm pleased to report that Genesis Machines has just been published in the USA by The Overlook Press. The book is available via Amazon, and I'm delighted to be associated with another independent award-winning publisher (after Toby Mundy's 2005 triumph with Atlantic at the 2005 British Book Awards).

Engineering biology, with Drew Endy

2008-02-24T03:22:00.003Z

There's a fascinating essay by/interview with Drew Endy on the Edge website, which appears to be the latest in a series to have emerged from an event they organised last August. I've written about Endy in the past, and he features prominently in the final chapters of Genesis Machines; indeed, I wish I'd had such an illuminating transcript available when I wrote the book.

Endy is an Assistant Professor of Biological Engineering at MIT, and one of the leading figures in synthetic biology. In one particular paragraph, he captures the excitement of this emerging new discipline:

"Programming DNA is more cool, it's more appealing, it's more powerful than silicon. You have an actual living, reproducing machine; it's nanotechnology that works. It's not some Drexlarian (Eric Drexler) fantasy. And we get to program it. And it's actually a pretty cheap technology. You don't need a FAB Lab like you need for silicon wafers. You grow some stuff up in sugar water with a little bit of nutrients. My read on the world is that there is tremendous pressure that's just started to be revealed around what heretofore has been extraordinarily limited access to biotechnology."

Insect lab

2008-02-15T23:30:00.006Z

I've spend all week running simulation experiments for our ongoing work on ant-based computing, so when I came across the Insect Lab it seemed strangely appropriate.

The artist takes real (dead) insects and customizes their bodies with parts taken from watches and other mechanical devices, to create "cybernetic sculptures".

I'd like to see him do an ant, though... Which train of thought lead me circuitously to Bill Bailey performing his wonderful song Insect Nation (if you just want the lyrics, they're here).

Dr Who

2008-02-08T19:13:00.001Z

A wonderful present arrived in today's post, courtesy of our equally wonderful friend Eventhia; a signed photograph of Tom Baker! He is, of course, best known for playing the fourth Dr Who, but is probably most familiar to a younger generation as the narrator of Little Britain (and even the delightfully barmy Stagecoach adverts).

Most people of sound mind would name Baker as the best ever Dr Who, despite ludicrous polls to the contrary. A case can be made that the choice of favourite depends on which Doctor a person grew up with, and since Baker's tenure extended from 1974-1981, I would certainly agree.

Anyway, he recently did a signing in Norwich, attended by our friends Kris and Eventhia. They very kindly got Tom to sign the photo "For Martyn," (eventually, I think he had it down as "Martin", and you can see where he's corrected it at E's prompting) "Genetically yours, Tom Baker"

Sigh!

Biological complexity: from molecules to systems

2008-02-05T22:07:00.000Z

I'm delighted to have been invited to speak at an event titled "Biological complexity: from molecules to systems", to be held at University College London from 12-13 June this year. The meeting is sponsored by both UCL and the Weizmann Institute of Science in Israel, and will feature speakers from the fields of immunology, computer science, mathematics, biological chemistry, molecular genetics and bioinformatics. I'll try my best to summarize below the research interests of the other invited speakers (but apologies to anyone whose work I misrepresent!)

Stephen Emmott from Microsoft Research in Cambridge will give the keynote address. Stephen is the founder and Director of Microsoft's European Science Programme, and was the driving force behind the influential Towards 2020 Science project and report.

Representing Israeli activity, Nir Friedman works in computational biology, and recently published a paper arguing that gene duplication may drive the "modularisation" of functional genetic networks (that is, genetic networks that are relatively self-contained, and which perform a specific task).

David Harel is a celebrated computer scientist, having carried out important work in logic, software engineering and computability theory. As a student, I often referred to his award-winning book Algorithmics: The Spirit of Computing, and he is currently working on topics that include the modelling and analysis of biological systems (eg. the nematode worm) and the synthesis and communication of smell.

Shmuel Pietrokovski works in bioinformatics, with particular interest in inteins (protein introns); "selfish" DNA elements that are converted into proteins together with their hosts.

Yitzhak Pilpel's lab takes a systems-level approach to how genes are regulated: "By applying genome wide computational approaches, backed-up by in house laboratory experiments, [the lab] devotes itself to both establishing an in-depth understanding of the different processes controlling gene expression, and to understand[ing] how these processes are orchestrated to establish robustness of the regulatory code."

Gideon Schreiber studies the precise nature of protein-protein interactions and the implications these have for complex biological processes.

Eran Segal is a computer scientist (predominantly) working in computational biology, who has recently reported some fascinating work on a "higher level" genetic code, as well as research on predicting expression patterns from their regulatory sequences in fruit flies.

I've already written at some length about Ehud Shapiro (also here); his recent work has centred on the construction of biological computing devices (known as automata) using DNA molecules and enzymes.

Yoav Soen's group is "using embryonic stem cells models to study how different layers of regulation interact to specify morphogenetic decisions, how these decisions are shaped by interactions between emerging precursors and how they are coordinated across a developing embryonic tissue." He has also worked with a colleague of mine, Netta Cohen at Leeds.

Representing activities in the UK, we have Cyrus Chothia from the Laboratory of Molecular Biology at Cambridge, who studies the "nature of the protein repertoires in different organisms and the molecular mechanisms that have produced these differences."

Jasmin Fisher is leading the new Executable Biology Group at Microsoft Research, and is primarily interested in systems/computational biology.

Mike Hoffman and Ewan Birney are at the European Bioinformatics Institute (EBI) in Cambridge, where Birney leads the EBI contribution to Ensembl. There's a transcript of an interview with him here.

Jaroslav Stark is the Director of the Centre for Integrative Systems Biology at Imperial College. He was recently interviewed for a piece on systems biology on BBC Radio 4's The Material World.

Michael Sternberg heads the Structural Bioinformatics Group and the Imperial College Centre for Bioinformatics. He was previously the head of biomolecular modelling at the Imperial Cancer Research Fund now part of Cancer Research UK.

Perdita Stevens is at Edinburgh, where she works on software engineering and theoretical computer science (with a growing interest in modelling viral infection).

The meeting organisers are particularly keen to encourage the participation of young researchers, and the registration fee for this two-day event is a very reasonable 50 pounds (30 for students). To register and for further information, please contact Michelle Jacobs at Weizmann UK at post@weizmann.org.uk or on 020 7424 6860. Attendance will be limited to 180 delegates.

The human genome, in book form

2008-01-31T21:39:00.000Z

I've just been sorting through some old files, and came across this picture (click for a larger version), which I took on my last visit to London. I had some free time before a meeting at the BT Tower, so I popped into the Wellcome Collection.

Quite apart from the fact that the Wellcome Trust spends around 400 million pounds a year on biomedical research, I have a personal affinity with the trust, since my shortlisted entry to their Book Prize (which was won that year by Chris McManus' Right Hand, Left Hand) was picked up by Toby Mundy and eventually evolved into Genesis Machines (pictured below in the Wellcome Collection bookshop, in a nice circular turn of fate).

One of the most striking exhibits they have (alongside a sample of droppings from Dolly the sheep) is the human genome, printed out in book form. As I've said before, we're rank amateurs compared to nature in the information storage stakes (of course, reading and writing data quickly is another matter...) Since the size of the human genome is estimated at around 3 billion genetic letters (taken from the set {A, G, C, T}), then (assuming that one byte is used to store each letter), each cell with a nucleus (that is, every one except red blood cells and the like) contains 3 Gigabytes of genetic "memory". Of course, we don't need an entire byte (8 bits) to store a quarternary (base 4) value, so we could compress this figure by three quarters, and cells actually contain two genomic copies, but I don't want to over-complicate things...

The fact of the matter is that our genome is large: in the past, I've compared it, if printed out in full, to 200 copies of the Manhattan telephone book. This analogy was arrived at by some back-of-an-envelope calculations, and I don't think I really understood its significance until I visited the Wellcome Collection.

There, in a corner of one of the galleries, stand a single set of white shelves, almost 5 metres by 2 metres, containing 120 hefty volumes. One of them stands open, and a closer inspection reveals page upon page of genetic data, rows and rows of A's, G's, C's and T's tightly-set in 4.5-point text.

The sheer scale of the artifact is mind-blowing, both as an illustration of nature's nanotechnology, but also as a reminder of how far we have to go in terms of beginning to piece together even a small fraction of the human circuitry.

Sex with robots

2008-01-29T18:56:00.000Z

One of the sure signs of impending middle age, especially in a university town, is when people stop handing you flyers. There was a time not so long ago when I could nip out of the office for a sandwich and come back burdened with glossy adverts for progressive house, 2-for-1 vodka shots and foam. But no longer. Now, the bright young things actively avoid me as my thirty-something, corduroy-clad figure shambles into view. The kinder ones simply pretend not to see me.

So imagine my delight when, walking down Oxford Road this afternoon after picking up some grapes, I was handed a flyer. And one offering sex with robots, to boot! Impressed by the targeted precision of whoever was marketing such an opportunity, I was about to kick my heels when I realised that it was actually advertising a club night in Manchester. Now, as a long-time veteran of nights such as House of God and Voodoo, I might have been interested...ooh, ten years ago, but with a responsible job and a young daughter, "'avin it large" now means having that third shot of espresso in my cappucino.

Which is a really cheap and tenuous way of introducing a new play that I think you should go and see. Involution is by a new author, Rachel Welch, and deals with many urgent contemporary themes, such as genetic engineering, religion and the human self-image. One of the plot threads concerns "cybernetic companionship", so I'll leave it to you to make the link...

Alfie Talman, a member of the production team and cast (and, coincidentally, a fellow Ipswich fan) enjoyed Genesis Machines, and thought I might be interested in the play. It's on from February 21st to March 15th at the Pacific Playhouse in London, and there are more details here (and here).

"I'm burning, I'm burning!..."

2008-01-14T12:58:00.000Z

Although every side in an argument tends to have its own complement of fools, the idiocy exhibited by fundamentalist Christians, in debates over evolution or the origin of the universe, often takes us into the realm of comedy.

Take this example, lifted from a list of fundie "bloopers":

"Everyone knows scientists insist on using complex terminology to make it harder for True Christians to refute their claims.

Deoxyribonucleic Acid, for example... sounds impressive, right? But have you ever seen what happens if you put something in acid? It dissolves! If we had all this acid in our cells, we'd all dissolve! So much for the Theory of Evolution, Check MATE!"

The full amusing-and-yet-slightly-scary list is here.

Genesis Machines in Japan

2008-01-08T14:44:00.000Z

Readers in Japan may be interested in the forthcoming edition of Genesis Machines, which is now available for preorder. It's been translated by Kyoko Gibbons, and is out on the 17th of this month.

My Edinburgh talk

2007-08-31T17:33:00.000Z

I had a wonderful time at the Edinburgh Book Festival over the weekend; a full venue and books to sign afterwards makes for a happy author! Here is a lightly edited version of what I had to say.

In 1959, a great personal hero of mine, the Nobel Prize-winning physicist Richard Feynman gave a visionary talk entitled “There's Plenty of Room at the Bottom”. In his speech, Feynman outlined the possibility of individual molecules, even individual atoms making up the component parts of computers in the future. Remember, this was back when computers filled entire rooms, and were tended by teams of lab-coated technicians, so the idea that you could compute with individual molecules was pretty outlandish. I was struck by a quotation in Oliver's book, attributed to the microbiologist A. J. Kluyver, who said, over fifty years ago, that “The most fundamental character of the living state is the occurrence in parts of the cell of a continuous and directed movement of electrons.” At their most basic, level computers work in exactly the same way; by funnelling electrons around silicon circuits, so I think this hints at the linkages between biology and computers that are only now coming to fruition.

Indeed, it wasn't until 1994 that someone demonstrated, for the first time, the feasibility of building computers from molecular-scale bits. Feynman's vision had waited, not only for the technology to catch up, but for a person with the required breadth of understanding and the will to try something slightly bizarre. That person was Len Adleman, who won the computer science equivalent of the Nobel Prize for his role in the development of the encryption scheme that protects our financial details whenever we buy something on the Internet. Len has always had an interest in biology; when one of his students showed him a program that could take over other programs and force them to replicate it, Len said “Hmmm.... that looks very much like how a virus behaves.” The student was Fred Cohen, author of the first ever computer virus, and Len's term stuck. (Update, 2/9/07: Cohen made the first reference to a "computer virus" in an academic article, but did not write the first virus).

One night in the early 90's, Len was lying in bed reading a classic molecular biology textbook. He came across the section describing a particular enzyme inside the cell that reads and copies DNA, and he was struck by its similarity with an abstract device in computer science known as the Turing Machine. By bringing together two seemingly disparate concepts, Adleman knew at once that, in his own words, “Geez, these things could compute.”

He found a lab at the University of Southern California, where he is a professor, and got down to building a molecular computer. He knew that DNA, the molecule of life that contains the instructions needed to build every organism on the planet, from a slug to.... John Redwood can be thought of as a series of characters from the set A, G, C and T, each character being the first letter of the name of a particular chemical. The title of the film Gattaca, which considers a dystopian future in which genetic discrimination defines a society, is simply a string of characters from the alphabet A, G, C and T.

As Oliver highlights in his own book, molecular biology has always been about the transformation of information, usually inside the living cell. This information is coded in the AGCT sequences of genes and in the proteins that these genes represent. Adleman immediately saw how this mechanism could be harnessed, not to represent proteins, but to store digital data, just like a computer encodes a file as a long sequence of zeroes and ones.

Adleman decided to use this fact to solve a small computational problem. Some of you might have heard of the Travelling Salesman Problem, and Adleman's was a variant of that; given a set of cities connected by flights, does there exist a sequence of flights that starts and ends at particular cities, and which visits every other city only once? This problem is easy to describe, but fiendishly difficult to solve for an even relatively small number of cities. This inherent difficulty is what made the problem interesting in Adleman's eyes, “interesting” being, to a mathematician, a synonym for “hard”.

Len decided to build his computer using the simplest possible algorithm; generate all possible answers (right or wrong), and then throw away the wrong ones. He would build a molecular haystack of answers, and then throw away huge swathes of hay encoding bad answers until he was left with the needle encoding the correct solution (of which there may be just a single copy). For Adleman, the key to his approach was that you can make DNA in the laboratory. A machine the size of a microwave oven will sit in a lab connected to four pots, each containing either A, G, C or T. Type in the sequence you require, and the machine gets to work, threading the letters together like molecular beads on a necklace, making trillions of copies of your desired sequence.

Adleman ordered DNA strands representing each city and each flight for his particular problem. Because DNA sticks together to form the double helix in a very well-defined way, he chose his sequences carefully, such that city and flight strands would glue together like Lego blocks to form long chains, each chain encoding a sequence of flights. Because of the sheer numbers involved, he was pretty sure that a chain encoding the single correct answer would self-assemble. The problem then was to get it out. In a way, Len had built a molecular memory, containing a huge file of lines of text. What he then had to do was sort the file, removing lines that were too long or too short, that started or ended with the wrong words, or which contained duplication. He used various standard lab techniques to achieve this, and, after about a week of molecular cutting and sorting, he was left with the correct solution to his problem.

The example that he solved could be figured out in a minute by a bright 10-year-old using a pen and paper. But that wasn't the point. Adleman had realised, for the first time, Feynman's vision of computing using molecules. After he published his paper, there was a flood of interest in the new field of DNA computing, a tide on which I was personally carried. The potential benefits were huge, since we can fit a vast amount of data into a very small volume of DNA. If you consider that every cell with a nucleus in your body contains a copy of your genome - 3 gigabytes of data, corresponding to 200 copies of the Manhattan phone book – you begin to understand just how advanced nature is in terms of information compression. Suddenly my 4 gig iPod nano doesn't look quite so impressive.

After a few years, though, people began to wonder if molecular computing would ever be used for anything important. They were looking for the “killer application”, the thing that people are willing to pay serious money for, like the spreadsheet, that persuaded small businesses to buy their first ever computer. The fundamental issue with Adleman's approach is tied to the difficulty of the problem; as the number of cities grows only slightly, the amount of DNA required to store all possible sequences of flights grows much more quickly; a small increase in the number of cities quickly leads to a requirement for bathtubs full of DNA, which is enough to induce hysterical laughter in even the sanest biologist. Indeed, it was estimated that if Len's algorithm were to be applied to a map with 200 cities in it, the DNA memory required to store all possible routes would weigh more than the Earth.

It would appear that DNA computing has reached the end of the line, if we are to insist on applying it to computational problems in a head-to-head battle against traditional silicon-based computers. Let's be straight, you're never going to be able to go into PC World and buy a DNA-based computer any time soon. When DNA computing first emerged as a discipline, I was dismayed to see a rash of papers making claims that within a few years we'd be cracking military codes using DNA computers and building artificial molecular memories vastly larger than the human brain. I was dismayed because I knew what had happened 30 years previously to the embryonic field of artificial intelligence. Again, hubristic claims were made for their discipline by the young Turks, ranging from personal robot butlers to automated international diplomacy. When the promised benefits failed to materialise, AI suffered a savage backlash in terms of credibility and funding, from which it is only just beginning to recover. I was very keen to avoid the same thing happening to molecular computing, but I, like many others, knew that we needed to look beyond simply using DNA as a tiny memory storage device.

The next key breakthrough was in realising that, far from being simply a very small storage medium that can be manipulated in a test tube, within its natural environment – the cell – DNA carries meaning. As the novelist Richard Powers observes in The Gold Bug Variations, “The punched tape running along the inner seam of the double helix is much more than a repository of enzyme stencils. It packs itself with regulators, suppressors, promoters, case-statements, if-thens.” Computational structures, that is. DNA encodes a program that controls its own execution. DNA, and the cellular machinery that operates on it, pre-dates electronic computers by billions of years. By re-programming the code of life, we may finally be able to take full advantage of the wonderful opportunities offered by biological wetware.

As Oliver observes in his book, “The world is not just a set of places. It is also a set of processes.” This nicely illustrates the shift in thinking that has occurred in the last few years since the human genome has been sequenced. The notion of a human “blueprint” is outdated a useless. A blueprint encodes specific locational information for the various components of whatever it's intended to represent, whether it be a car or a skyscraper. Nowhere in the human genome will you find a section that reads “place two ears, on on either side of head” or “note to self: must fix design for appendix.” Instead, genes talk to one another, turning each other (and often themselves) on and off in a complex molecular dance. The genome is an electrician's worst nightmare, a tangle of wiring and switches, where turning down a dimmer switch in Hull can switch off the Manhattan underground system.

The human genome project (and the many other projects that are sequencing other organisms, from the orang-utan to the onion) is effectively generating a biological “parts catalogue”; a list of well-understood genes, whose behaviour we can predict in particular circumstances. This is the reductionist way of doing science; break things down, in a top-down fashion, into smaller and smaller parts, through a series of levels of description (for example, organism, molecule, atom). The epitome of this approach is the very well-funded physicists smashing together bits of nature in their accelerators in an attempt to discover what some call the God Particle.

Of course, smashing together two cats and seeing what flies off is only going to give you a limited understanding of how cats work, and it'll probably annoy the cats, so the reductionist approach is of limited use to biologists. Systems biology has emerged in recent years to address this, by integrating information from many different levels of complexity. By studying how different biological components interact, rather then just looking at their structure, as before, systems biologists try to understand biological systems from the bottom up.

An even more recent extension of systems biology is synthetic biology. When a chemist discovers a new compound, the first thing they do is break it down into bits, and the next thing they do it try to synthesise it. As Richard Feynman said just before his death, “What I cannot build I cannot understand.” Synthetic biologists play, not with chemicals, but with the genetic components being placed daily in the catalogue. It's where top down meets bottom up – break things down into their genetic parts, and then put them back together in new and interesting ways. By stripping down and rebuilding microbial machines, synthetic biologists hope to better understand their basic biology, as well as getting them to do weird and wonderful things. It's the ultimate scrapheap challenge.

If we told someone in the field of nanotechnology that we had a man-made device that doesn't need batteries, can move around, talk to its friends and even make copies of itself – and all this in a case the size of a bacterium – they would sell their grandmother for a glimpse. Of course, we already have such devices available to us, but we know them better as microbes. Biology is the nanotechnology that works. By modelling and building new genetic circuits, synthetic biologists are ushering in a new era of biological engineering, where microbial devices are built to solve very pressing problems.

As Oliver notes towards the end of his book, the planet is facing a very real energy crisis. One team is therefore trying to build a microbe to produce hydrogen. Another massive problem facing the developing world is that of arsenic contamination in drinking water. A team here in Edinburgh, made up mainly of undergraduates, has built a bacterial sensor that can quickly and easily monitor arsenic concentrations from a well sample, to within safe tolerances. Jay Keasling, a colleague in California has recently been awarded 43 million dollars by the Bill and Melinda Gates Foundation to persuade E. coli to make substances that are alien to them, but which provide the raw ingredients for antimalarial drugs. The drug is found naturally in the wormwood plant, but it's not cheap – providing it to 70 per cent of the malaria victims in Africa would cost $1 billion, and they can be repeatedly infected. It's been estimated that drug companies would need to cover the entire state of Rhode Island in order to grow enough wormwood, so Keasling wants to produce it in vats, eventually at half the cost.

There are, of course, safety issues with synthetic biology, as well as legal and ethical considerations. I worry that people have this idea that the bugs we use are snarling microbes that have to be physically restrained for fear of them erupting from a Petri dish into the face of an unfortunate researcher, like something from the Alien movies. In reality, the bacteria used in synthetic biology experiments are docile creatures, pathetic even, the crack addicts of the microbial world. They have to be nurtured and cossetted, fed a very specific nutrient brew. Like some academics, they wouldn't last two minutes in the real world. Of course, nature has a habit of weeding out the weak and encouraging the fit, so we still have to be very careful and build in as many safeguards as are practical. The potential for using synthetic biology for weaponry is, to my mind, overstated. As one of the leading researchers said to me, “If I were a terrorist looking to commit a bio-based atrocity, there are much cheaper and easier ways to do it than engineering a specific microbe – anthrax, say.” Synthetic biology will not, in the foreseeable future, return many “bangs per buck”.

Many of the legal concerns centre on the patenting of gene sequences. This was going on well before synthetic biology, but it recently hit the headlines when Craig Venter, head of the private corporation that tied with the Human Genome Project, announced that they intended to patent a synthetic organism.

We must remember that Venter is, first and foremost, a businessman, and it is very much in his interests to keep his company in the public eye. The scientific rationale for some of these patents is not immediately clear. But we should also remember that, for every Craig Venter, there are probably ten or more Jay Keaslings, placing their research in the public domain and working in an open and transparent fashion for the greater good.

On that positive note, I'd like to thank you for listening, and I'll stop there.

My contribution to the synthetic biology debate

2007-08-24T13:45:00.000Z

You may recall that the Royal Society is soliciting opinions on various aspects of the field of synthetic biology. What follows is a lightly edited version of my own submission, which I sent off today.

In what follows, I highlight some concerns and dangers, speaking as someone who has an definite interest in the field flourishing (and would therefore wish to see these concerns addressed).

1. Terminology

The first concern is over the term “synthetic biology” itself. The two main issues are “what does it mean?” and “what does it cover?” As pointed out at the BBSRC workshop, clinicians have used the term for a while to refer to prosthetic devices. In attempting to offer a fixed definition of the term, the community runs the risk of becoming overly exclusive at a premature stage. However, there is also a risk that “synthetic biology” will become a “catch-all” term that is too loosely applied. The emphasis on the term “biology” may also serve to alienate mathematicians, physicists, computer scientists and others, who may (wrongly) feel that they have no expertise to offer a “biological” discipline. As a counter-example, witness the success of the field of bioinformatics, which would appear to fairly represent the disciplinary expertise in the field (in terms of the general composition of the term, rather than the relative lengths of its components). As a very crude experiment, I searched in Google for both “computational biology” and “bioinformatics”; the first term returned around 1,530,000 hits, the second around 14,000,000.

This leads on to the issue of “language barriers”. This is always an issue in any new field that involves the collision of two or more (often very dissimilar) disciplines. Being seen to publically ask “stupid questions” is a daunting prospect to most young scientists, and yet many of the major breakthroughs have occurred through just that. This opens up the wider debate on inter-disciplinarity in 21st century science, and how we might best prepare its practitioners. Do we give students a broad, shallow curriculum to allow them to make connections, without necessarily having the background to “drill deeper” if required, or do we stick to the “old model” of “first degree” and subsequent training? My own intuition is that it is far better to intensively train in a single field at the outset, and then offer the opportunity to “cherry pick” topics from a different discipline at a later stage. This educational debate is, however, not one that should be the sole preserve of synthetic biology!

2. Expectation Management

Even when biologists and (say) computer scientists can agree a suitable shared terminology, there is still the risk of a mismatch occurring in terms of expectations of what might be achieved. For example, the notion of “scalability” might mean very different things to a computer scientist and a microbiologist. To the former, it means being able to increase by several orders of magnitude the number of data items processed by an algorithm, or double the (already vast) number of transistors we may place on the surface of a computer chip. To a biologist, the idea of scalability might currently be very different:

“What's needed to make synthetic biology successful, Rabaey said, are the same three elements that made microelectronics successful. These are a scalable, reliable manufacturing process; a scalable design methodology; and a clear understanding of a computational model. "This is not biology, this is not physics, this is hard core engineering," Rabaey said.

In electronics, photolithography provides a scalable, reliable manufacturing process for designs involving millions of elements. Biology has a long way to go. What's needed, Rabaey said, is a way to generate thousands of genes reliably in a very short time period with very few errors. The difference between what's available and what's needed is about a trillion to one.”

3. Conceptual Issues

As the leading nanotechnologist (and FRS) Richard Jones has pointed out, his field was dominated from an early stage by often inappropriate analogies with mechanical engineering (e.g., cogs). It may well be that case that we are in danger of the same thing happening with synthetic biology, where computer scientists impose rigid circuit/software design principles on "softer", more “fuzzy” substrates. Jones quotes, on his blog, an article in the New York Times:

“Most people in synthetic biology are engineers who have invaded genetics. They have brought with them a vocabulary derived from circuit design and software development that they seek to impose on the softer substance of biology. They talk of modules — meaning networks of genes assembled to perform some standard function — and of “booting up” a cell with new DNA-based instructions, much the way someone gets a computer going.”

4. Complexity

The issue of "grey goo" has persistently dogged the field of nanotechnology, and it would be tempting to dismiss similar criticisms of synthetic biology as well-intentioned but ultimately uninformed. However, if synthetic biologists are to avoid the mistake that researchers in GM research made (that is, to appear arrogant and dismissive, leading to mass public protest and restrictive legislation), then we should acknowledge and address the very real possibility of the biological systems under study behaving in very unpredictable ways. Anyone who has any degree of contact with studying biosystems will understand the notion of complexity; components that are connected in an unknown fashion behave in unpredictable ways, which may include evasion of any control mechanisms that have been put in place. As Douglas Kell and his colleagues have observed, it is perfectly possible to alter parameters of a system on an individual basis, and see no effect, only to observe wild variations in behaviour when exactly the same tweak is applied to two or more parameters at the same time. Working in an interdisciplinary fashion may address this issue, at least in part, if modellers work closely with bench scientists in a cycle of cooperation. Once again invoking the issue of scalability, studying the behaviour of complex biosystems through modelling alone will quickly become infeasible, due the the combinatorial explosion in the size of the search space (of parameter values). By actually making or modifying the systems under study in the lab, the problem may be reduced to manageable proportions.

5. Hype

In my own book, Genesis Machines (Atlantic Books, 2006), I illustrate the risk of promising too much at an early stage by describing the story of the “AI winter”. In the 1960s, researchers in artificial intelligence (AI) had promised human-level intelligence “in a box” within twenty years. By issuing such wild predictions, AI researchers set themselves up for a monumental fall, and, when the promised benefits failed to accrue, funding was slashed and interest dwindled. This AI winter (by analogy with “nuclear winter”) affected the field for over 15 years, and it would be disappointing (to say the least) if the same thing were to happen to synthetic biology.

Hubristic claims for synthetic biology should be avoided wherever possible; without singling out particular groups, I have already seen several predictions (again, often conflated with ambitions) that have absolutely no realistic chance of coming to fruition in any meaningful time-scale (if at all). In this more “media savvy” age, perhaps practitioners in synthetic biology might benefit, as their AI counterparts did not, from media training (I have personally benefited (June 2004) from the course provided by the Royal Society, and perhaps the Society might consider a “mass participation” version for new entrants to the field).

For the love of ants

2007-08-17T16:01:00.000Z

To be published next week, one book on my Amazon wishlist is titled The Ants Are My Friends. Students of popular music may recognise the phrase as one of the great misheard lyrics of our time, up there with "Beelzebub had a devil for a sideboard", rather than an expression of insect infatuation (the response being, of course, "blowing in the wind").

But I rather like the idea of ants being my friends. I've always held these misunderstood creatures in high regard, and was charmed by the story, recounted in Surely You're Joking, Mr. Feynman! (p. 91 in the Vintage edition), of how Richard Feynman investigated ant trail-following behaviour in his Princeton accomodation. He eventually used his findings to persuade an ant colony to leave his larder; "No poison, you gotta be humane to the ants!"

Anyone who has ever watched an ant colony at work cannot fail to be entranced by its beauty and efficiency. A single colony can strip an entire moose carcass in under two hours, and their work is coordinated in an inherently decentralised fashion (that is, there is no "head ant" giving out orders). An ant colony can be considered as a class of "super-organism", that is, a "virtual" organism made up of many other single organisms. Other examples include bacterial colonies and (arguably) the Earth itself.

Ants communicate remotely by way of pheromones, chemicals that generate some sort of response amongst members of the same species. When ants forage for food, they lay a particular pheromone on the ground once they've found a source. When this signal is detected by other ants, they follow the trail and reinforce it by laying pheromone themselves. Chemical signals also evaporate over time, which allows colonies to "forget" good solutions (i.e., paths) and construct new solutions if the environment changes (e.g., a stone falls onto an existing path).

By describing this mechanism in abstract terms, computer scientists have managed to harness the power of positive feedback in order to solve difficult computational problems. Perhaps the leading scientist in the field of ant colony optimization (ACO) is Marco Dorigo, and he has described how to use models of artificial ants to solve the problem of how to route text messages through a busy network of mobile base stations. We've also done some initial work on how ants build spatial structures, using an abstract model of pheromone deposition to explain how certain species can construct "bullseye"-like patterns of differently-sized objects.

Fundamentally, ongoing work in ACO reflects a wider interest in the notion of decentralised control. Rather than controlling everything from "on high" with global instructions, "bottom up" control emphasises the value of small, local interactions in keeping systems running smoothly. Software packages such as Netlogo have brought so-called agent-based modelling to a wider audience. I've just taken on a Ph.D. student to study the evacuation of tall buildings using this approach, and it's clear that, with ever-increasing computational power being available, the notion of simulating large systems of interacting entities will gain increasing influence.

Genesis Machines in the USA

2007-08-17T10:47:00.000Z

I'm delighted to report that Atlantic have signed a deal to publish Genesis Machines in the USA. It's slated to appear on April 3rd of next year, and will be published by the Overlook Press (preorder here).

Molecules and Marx

2007-08-10T19:50:00.000Z

My publisher kindly sends me copies of reviews of Genesis Machines that appear from time to time in the press. I was quite surprised to see the book featured in the June issue of the Marxist Review, the monthly theoretical magazine of the Workers Revolutionary Party. In his article, William Westwell invokes Richard Dawkins as the contemporary cheerleader of arch-reductionism and mechanical materialism. But, by concentrating purely on the first half of the book (which, by its very nature is comprised largely of historical background), Westwell ignores one of its fundamental arguments: that 21st century science cannot succeed by insisting on the top-down, reductionist paradigm. Science is still, to a large extent, a reductionist enterprise, but the emerging field of systems biology is providing a complementary approach (in a way, occupying the region where top-down meets bottom up). By arguing for a notion of "quality of computation", Westwell reminded me of conversations I have enjoyed in the past with Brian Goodwin, who has argued that "Biology is returning to notions of space-time organisation as an intrinsic aspect of the living condition... They are now described as complex networks of molecules that somehow read and make sense of genes. These molecular networks have intriguing properties, giving them some of the same characteristics as words in a language. Could it be that biology and culture are not so different after all; that both are based on historical traditions and languages that are used to construct patterns of relationship embodied in communities, either of cells or of individuals?" Unfortunately, Westwell appears to have ignored the later detailed discussion of such matters.

Royal Society and Synthetic Biology

2007-07-03T11:38:00.000Z

I was gratified to see a healthy turn-out for the Cafe Scientifique event yesterday evening, and pleased by the range and depth of questions that were asked. I briefly mentioned at the end of the Q&A session that the Royal Society (the UK's preeminent learned society for the sciences) is soliciting views on the emerging field of synthetic biology.

The field's potential impact is huge, not just in terms of technological developments and scientific understanding, but in terms of social impact, legal issues and ethical concerns. It is vital that scientists engage with the wider community, so that the implications of their work may be considered at an early stage (and, indeed, throughout). The Royal Society is therefore asking for submissions (ranging from brief comments to draft discussion documents) on various aspects of synthetic biology, from potential applications to biosecurity risks and governance.

These exercises offer a real opportunity to help shape future policy, so I would encourage potentially interested parties to visit the call website and consider adding their voice to the debate. The deadline for submissions is August 27th.

Event in Manchester

2007-06-28T17:51:00.000Z

If you're in Manchester next Monday and are stuck for something to do in the evening, why not pop along to Cafe Scientifique, where I'll be speaking and (hopefully) generating some discussion? The format is pretty relaxed, with a 30-40 minute presentation from me, followed by a 15 minute break for refreshments, then an open-ended discussion session.

Genesis Machines: Engineering Life

Monday 2nd July 2007 at 6:30pm in Cafe Muse (directions are here).

Although anticipated as early as the 1950s, the idea that we could somehow build working computers from organic components was merely a theoretical notion until November 1994, when a scientist announced that he had built the world's first molecular computer. Emerging from a laboratory in Los Angeles, California, his collection of test tubes, gels and DNA lay at the heart of a totally new and unexplored region of the scientific landscape.

Millions of dollars are now being invested worldwide in molecular computing and synthetic biology research. DNA, the code of life, is right now being used at the heart of experimental computers. Living cells are being integrated with silicon nanotubes to create hybrid machines, as well as being routinely manipulated to add entirely new capabilities. Preparations are being made to build entirely new organisms, never seen before in nature.

This research raises amazing new questions. Does nature 'compute', and, if so, how? Can natural systems inspire entirely new ways of doing computation? How can humanity benefit from this potentially revolutionary new technology? What are the dangers? Could building computers with living components put us at risk from our own creations? What are the ethical implications of tinkering with nature's circuits? In this event we'll examine what it means to reprogram the logic of life.

Two things

2007-06-14T16:46:00.001Z

Apologies for the lack of recent activity on the blog; this time of year is always the busiest for academics, what with exam boards and so on. Hopefully things will calm down in the next week or two.

Two items of note: today marks both the publication of Genesis Machines in paperback, and the release of the programme for this year's Edinburgh International Book Festival.

Not much has changed in the paperback, apart from a few additional acknowledgements and some minor changes to the notes and references (which are available online here.)

As for the Book Festival, I'm privileged to be appearing on stage once again with Oliver Morton from Nature, where we'll be discussing "The Future of Nature" as part of the "Genes and Society" Festival theme. Oliver will be talking about "intelligent plants", and I'll be holding forth on biocomputing and synthetic biology (Craig Venter's recent patent swoop has given me lots of nice new discussion material). Anyway, we're appearing on Sunday the 26th of August, and full programme details are available here. The event is sponsored by the ESRC Genomics Policy and Research Forum, and it's one of five that they are supporting.

DNA hash pooling

2007-05-25T10:01:00.000Z

The draft paper that came out of our trip to Paris has now been lodged with the arXiv e-print server.

DNA Hash Pooling and its Applications

Dennis Shasha (Courant Institute, New York University), Martyn Amos (Computing and Mathematics, Manchester Metropolitan University)

Abstract: In this paper we describe a new technique for the characterisation of populations of DNA strands. Such tools are vital to the study of ecological systems, at both the micro (e.g., individual humans) and macro (e.g., lakes) scales. Existing methods make extensive use of DNA sequencing and cloning, which can prove costly and time consuming. The overall objective is to address questions such as: (i) (Genome detection) Is a known genome sequence present at least in part in an environmental sample? (ii) (Sequence query) Is a specific fragment sequence present in a sample? (iii) (Similarity Discovery) How similar in terms of sequence content are two unsequenced samples?

We propose a method involving multiple filtering criteria that result in "pools" of DNA of high or very high purity. Because our method is similar in spirit to hashing in computer science, we call the method DNA hash pooling. To illustrate this method, we describe examples using pairs of restriction enzymes. The in silico empirical results we present reflect a sensitivity to experimental error. The method requires minimal DNA sequencing and, when sequencing is required, little or no cloning.

Available at http://www.arxiv.org/abs/0705.3597.

Spiked innovation survey

2007-05-01T12:08:00.000Z

I was recently asked to contribute to the annual innovation survey from spiked. There appear to be many interpretations of the term "innovation", but notable entries (from my own perspective) include those by Scott Aaronson, Paul Rothemund and Jeffrey Shallit.

Here's the blurb from the spiked website:

"The internet, the alphabet, the discovery of nuclear fusion, x-rays, the brick, rockets, the eraser: all of these have been identified as the greatest innovations in history in a new survey.

Over 100 key thinkers and experts from the fields of science, technology and medicine - including six Nobel laureates - participated in the brand new spiked/Pfizer survey 'What's the Greatest Innovation?', which goes live on spiked today.

In his introduction to the survey, spiked's editor-at-large Mick Hume says: 'Some choose "sexy" looking innovations, others apologise for the apparent dullness of their arcane choices. But whatever the appearances, almost all of our respondents exude a sense of certainty about the improvement that innovations in their field are making to our world, and the potential for more of the same."

A new kind of firefighting

2007-04-25T19:13:00.000Z

I managed to miss a potentially interesting edition of Horizon on the BBC after making the mistake of flicking over to watch the second half of the Manchester Utd/Milan match.

Anyway, I caught the last ten minutes, and managed to glean the basic facts: that fewer people would have died when the Twin Towers collapsed on September 11 had the authorities been in possession of a global picture of the state of the building (in terms of both its structure and the movement of its occupants). But having the raw data is not enough: it needs to be provided as input to predictive models that are capable of allowing firefighters to play "what if" games. These models are necessarily computationally complex and resource intensive, which is where Jose Torero comes in. He's in charge of Firegrid, an interdisciplinary project dedicated to using Grid-based computing to model and predict, in real-time, the evolution of fire emergencies.

This work is related to my own on evacuation modelling, and we've recently been awarded a Ph.D. studentship in order to develop our ideas on how crush conditions emerge in situations where people fail to follow a set evacuation plan. This work will be done in collaboration with Dr Steve Gwynne, who has worked for the last ten years on modelling people movement, and who helped develop the influential Exodus system. The position will be advertised shortly, so watch this space.

Warwick victorious!

2007-04-16T22:06:00.000Z

Congratulations to one of my old institutions, Warwick, on winning the 2007 University Challenge. In a tight match, they eventually fought off the reigning champions, Manchester, both securing Warwick's first ever series win and preventing their opponents from gaining the first ever "back to back" run of titles.

I'm afraid, however, that most neutrals watching will remember it more for Prakash Patel's post-presentation lunge for Ann Widdecombe than anything else.

Edinburgh Science Festival

2007-04-06T20:44:00.000Z

Just a quick reminder that I'll be appearing at the Edinburgh Science Festival next Sunday (April 15th). Full details of my event (including how to reserve tickets) are here, and I'm told that there will be a book signing afterwards.

An apt observation

2007-04-06T17:47:00.000Z

Jonathan Hodgkin, a Professor of Biochemistry at the University of Oxford, has published a nice essay in the March 28 edition of the Times Literary Supplement. It's built around a review of both Genesis Machines and Robert Frenay's recent book, Pulse (which I haven't yet had the chance to read, but which has a very nice website). This is the second occasion on which the two have been jointly reviewed (the first being Matt Ridley's examination here).

Anyway, I'm happy with Hodgkin's overall assessment of my own book, and he makes some fair points concerning gaps in topical coverage. I specifically avoided dealing in detail with quantum computing (although, to be fair, I did mention it), as I didn't want the book to turn into a detailed "quantum vs DNA" debate (and I'm not sure I have the expertise to do justice to the quantum "camp" anyway). It's understandable, though, that as a chemist Hodgkin should highlight the omission of aptamer development.

Aptamers are synthetic molecules that can fold up into very detailed three-dimensional shapes, thus binding to other molecules with incredible specificity. They can therefore be used to target other molecules in the same way as antibodies, and offer a wide range of applications in biotechnology and medicine. Because the possible space of three-dimensional shapes a molecule can adopt is potentially vast, researchers must use a smart approach to finding aptamers, as opposed to a "hit-and-hope" policy. The technique that has been developed, the name of which is abbreviated to SELEX,
uses an evolutionary approach based on an initial molecular population. Interestingly, it may be thought of (rather loosely) as a "wet" version of the genetic algorithm.

One possible hook that I could perhaps have made more of is the fact that Andrew Ellington, one of the founders of aptamer development, was one of the main researchers involved in recently building a bacterial camera (which did merit a mention in the book!)

"From Rive Gauche to Rochdale..."

2007-04-01T19:56:00.000Z

...was Justine's remark yesterday, as we drove home through that northern town after a wonderful week in Paris. We visited Dennis Shasha and his family, as he's there on sabbatical from New York University and kindly invited us over. Justine and Alice took in the sights while Dennis and I got down to some work.

We stayed in a marvellous little hotel, just around the corner from the Eglise Saint-Sulpice (which featured as a central location in The Da Vinci Code).

Wednesday was spent walking and talking with Dennis, bouncing around ideas about biocomputing. His wife, Karen, kindly took time out to show Justine and Alice around the Jardin du Luxembourg. Thursday was spend working while Justine wandered up to the Louvre, before we had dinner with the Shashas. We wrapped up on Friday morning, then Justine and I took some time out to revisit Monmartre, where we honeymooned three years ago.

It was a pleasure to spend time with Dennis and his family; both he and his wife are prodigiously talented, Dennis as a scientist, writer and (as Alice was delighted to discover) juggler, and Karen as an artist (and cook!), and we much appreciated their hospitality. Dennis and I are currently working on the draft paper that emerged from our discussions, which will hopefully appear as a preprint in the next few weeks - watch this space.

2007-03-22T22:59:00.000Z

The Times Higher recently commissioned an article from me, the subject being the recently announced cuts in UK research funding. They were particularly interested in the views of a "young academic", so I was delighted to see that the resulting piece was made the lead opinion article in today's edition. It's available on the THES website, but I'm reproducing it here with their kind permission. The headline (and accompanying cartoon) appear to have been derived from a rather throwaway remark I made in the final sentence.

Labour's infidelity will not be forgiven easily
Martyn Amos, Times Higher Education Supplement, March 22 2007, p. 12.

Ripples from the collapse of Rover two years ago are apparently lapping at the doors of UK university departments. The decision to dip into research funds was, according to the Department of Trade and Industry, to cover "exceptional" costs. The demise of the car firm was a one-off budgetary burden that should be borne by all.

The image of an administration battling to save jobs in a region blighted by industrial decline is one the DTI is in no hurry to dispel. A closer inspection of the department's figures suggests the exercise was more about fiscal firefighting than industrial or social intervention. But behind the smokescreen of short-term financial juggling lie deeper concerns about fundamental breaches of trust.

Senior academics and industry leaders reacted with dismay to the announcement that about £68 million of funding destined for science would instead be diverted back to the DTI to address these "historic and new" financial pressures. Although the Rover debacle was pushed to the front of the crowd of good causes, other recipients of recalled funds lurked in the background. Jokes about David Cameron's alleged drug use at school have recently filled the corridors of Whitehall, but, to the Government, Weeed is no joke. That's the Waste Electronic and Electrical Equipment Directive to the uninitiated, a European Union edict that requires companies to dispose of obsolete white goods on behalf of consumers. UK implementation of this directive has been put on hold twice, the delay necessitating an additional funding shot to the tune of £27 million - only a couple of million short of the £29 million taken back from the Engineering and Physical Sciences Research Council. Michael Kenward, a former editor of New Scientist magazine, has highlighted the irony of funding the cost of delays in implementing electrical recycling by taking money away from the very agency that has green technologies at the top of its research agenda.

Whatever lies behind the decision to cut research funding, as a relatively junior member of staff I am acutely aware of the impact that these changes may have on the rank and file. The short-term implications are that roughly 100 research council grants will no longer be funded. Many of these would have been supported in "responsive mode", a mechanism designed to offer maximum flexibility in terms of project size and scope. Younger scientists are particularly encouraged to apply within this framework, as are those proposing adventurous or multidisciplinary research - all of which are vital to the long-term development of healthy science and innovation. Since most grants run for between two and five years, the research councils are obliged to cover these future costs from a much diminished purse and must cut back on flexible, short-term activities. These include studentships and fellowships - precisely the mechanisms by which new researchers establish their groups and develop their careers. Long-term, risky research will be sacrificed for the purposes of short-term expediency.

Perhaps more significant, this decision represents a sea change in the relationship between Labour and the scientific community. For the first time since taking power, the Government has reneged on its promises about the funding of science. This had previously enjoyed protected status within the Office of Science and Engineering to encourage medium to long-term research that might extend beyond the lifetime of governments. The dismantling of this ring fence has sent out a signal to some that the DTI can choose to ignore Treasury rules on science funding whenever it sees fit.

Early portents of the cuts came soon after the resignation of Lord Sainsbury from his post of Science Minister, a long tenure that had been greeted with almost universal approval from the research community. According to one insider quoted in The Times Higher in the wake of the announcement of the cuts: "The fact that he has left has made this possible." The formal announcement came while his successor, Malcolm Wicks, was on a trip to an operation funded by the Natural Environment Research Council.

The Government will argue that the cuts amount to less than 1 per cent of the total science budget, and that funding levels will be restored or even improved in future. But, like a cheating partner, the administration must understand that the long-term damage wrought by their breach of trust cannot simply be undone by promises to behave better in future.

Passport hell

2007-03-15T23:20:00.000Z

Dennis Shasha, academic, author and the series editor for my first book, has very kindly invited me over to Paris for a week to do some work. Of course, my wife and daughter were also invited, and we thought it would be a chance to introduce Alice to the city where her parents enjoyed their honeymoon (during the heatwave of 2003 - even less romantically, we thought it might also be a chance to get some rather messy but necessary work done on the house in our absence).

As is common in our household, various arrangements had been left until the last minute, the most significant one being passports for my wife and daughter. Luckily, one of the regional centres that deals with fast-track (ie. within two weeks) applications is just down the road in Liverpool, so I made an appointment to go over there today. Which is where the fun started.

The regulations concerning the acceptability of photographs for use on passports are fairly relaxed for children under five, but they still specify things like "no other person visible in the background". If you've ever tried to get a 12-month old to sit still, in a photo booth, looking in the vague direction of the camera, whilst remaining invisible yourself, then you'll know what we're up against. A couple of days ago, my wife had the following taken:

Which we thought would be fine. How little we knew. We dropped into our local Post Office on the way to Liverpool, just to double-check that the photo would be acceptable. "No", was the quick response, since Justine's arm is clearly visible in the background. Cue quick dash to Morrisons and frantic changing of notes into pound coins.

Our first effort wasn't too bad, in a moody, My Bloody Valentine album cover sort of way. But nowhere near good enough to satisfy the sticklers at the passport agency. So we tried again.

Away with the fairies. So we tried again.

Too blurred, face in the wrong part of the shot, looking down. By this point, we'd burned through 12 quid, I'd lost all feeling in my legs from kneeling on the floor of the photo booth, and we were in severe danger of missing our pre-booked appointment. So we decided to just get there and then worry about it.

Sure enough, the lovely (and I don't mean that sarcastically, they really were lovely, accomodating and helpful) people in Liverpool told us that none of the photos would be acceptable, but they had their own photo booth for just such an eventuality. They also passed on some wisdom on how to control toddlers whilst remaining invisible, thus sticking to the rules. Which is how we came to get this (acceptable!) shot:

If you look closely, you can see that Alice is actually sitting on my lap. That's me, in the background. Wearing a white T-shirt over my head.

Festival time

2007-02-21T20:28:00.000Z

I feel honoured and delighted to have been asked to contribute to two of the Edinburgh Festivals this year. The programme for the International Science Festival was published today, and features (amongst many others) Marcus du Sautoy, Marcus Chown, Kirsty Wark, Colin Blakemore, Steve Jones and Heinz Wolff. Richard Jones (who blogs here) and I have been scheduled in the Cutting Edge subgroup of the Big Ideas event. The Festival runs from April 2-15, and it promises to be a lot of fun (as well as informative, of course!)

I'll also be appearing at the Edinburgh International Book Festival which takes place between August 11-27. Last year's event (featuring three Nobel Laureates) attracted over 220,000 visitors, and it's now the "world's largest celebration of the written word". The programme for this event will be published on June 14.

Protect and survive

2007-02-14T09:31:00.000Z

Those of us old enough to remember Protect and Survive (or its US equivalent, Duck and Cover) will appreciate the humour of Safe Now, which provides alternative interpretations of public information graphics.

The middle of a terrorist attack is not an appropriate time to catch up on your reading or paperwork.

"Dr" Gillian McKeith

2007-02-12T13:15:00.000Z

Today's Guardian contains a wonderfully detailed demolition of "Dr" Gillian McKeith, Channel 4's very own "clinical nutritionist". Many people have accused her of quackery and charlatanism in the past, often resulting in threats of legal action (as opposed to a reasoned scientific response).

Her claims to hold a Ph.D. certainly seem quite laughable.

Paperback edition

2007-02-11T11:51:00.000Z

Just a short note that the paperback edition of Genesis Machines is now available for pre-ordering on Amazon. It's out on June 14.

I spent the end of last week at a BBSRC workshop on synthetic biology, and will post a report later this week.

Another radio interview

2007-01-29T12:22:00.000Z

Just a quick note that I'm this week's guest on This Week In Science, a radio show run out of the University of California Davis, and which boasts listeners in over 60 countries. You can either listen online tomorrow at 17:30 (UK) via the website, or download the show later as a podcast.

New stuff

2007-01-17T17:00:00.000Z

Two new publications to report, both very different.

The first is a paper that's just been accepted by BioSystems, and is now available online. Two hybrid compaction algorithms for the layout optimisation problem was written with two colleagues in China, and deals with the problem of packing circular objects inside an "outer" containing circle. Many people will be familiar with this problem, which tries to minimise the size of the container, but our version is complicated by the fact that each object also has mass, and we must seek to minimise not only the radius of the container, but the net mass imbalance. This problem has real-world significance in areas such as aerospace and satellite design, where the circles represent pieces of equipment, and the body as a whole is rotating or moving. We have developed two algorithms, both inspired by nature, which produce the best known results for this problem.

The other piece of writing this month is my first (and quite possibly last) appearance in a men's style magazine (Esquire). As part of their "Hot List 2007", I was asked to write a short piece on "The New Software is...", and chose "Wetware". I'm on page 92 of the February issue, sharing space with George Monbiot.

The next generation

2007-01-15T13:30:00.000Z

I spent the end of last week and the start of the weekend drifting in and out of the Systems Biology, Bioinformatics and Synthetic Biology conference BioSysBio, which was hosted by the University of Manchester. The event is aimed at post-graduates, post-docs and "young faculty" (I wasn't sure if I qualified for this last descriptor, but they took my money!), and there was certainly a youthful exuberance about the the proceedings. Teaching and family commitments meant that I wasn't able to attend as many sessions as I would have liked, although I was able to make both sessions dedicated to synthetic biology.

The first of these was opened by Randy Rettberg, director of the International Genetically Engineered Machines (iGem) programme. Rettberg had a long and distinguished career as a computer engineer (including serving as the chief technical officer of Sun Microsystems) before turning his attention to biology and dividing his time between iGEM and looking after MIT's Registry of Standard Biological Parts, the community's attempt to do for synthetic biology what the Maplin Catalogue did for electronics.

There then followed three talks by UK-based teams who took part in the most recent iGEM. The Imperial College team described their novel approach to building a cell-based oscillator (a device that gives a signal that goes "up" and "down" on a regular basis). Rather than building their oscillator inside a single cell, as others have done, the Imperial team decided to try to model classical "predator-prey" dynamics, where the population of prey (eg. rabbits) rises and falls slightly out of step with the rise and fall in the number of predators (eg. foxes). The students decided to engineer two populations of bacteria, each generating molecules that would cause the net signal between the two to rise and fall periodically. Although they've yet to get it all working together, it's a novel approach to the problem, and their simulations and early experimental characterisations seem to suggest that they're well on the road to success.

Another talk was given by a team from Cambridge, who were investigating a subject close to my own heart; self-organisation and pattern formation in bacteria. They've harnessed the ability of bacteria to "swim" combined with an engineered position-dependent genetic "switch" to generate spatial patterns from the "bottom up". The ability to be able to control this process may have significant implications on tissue engineering and bio-medicine, as we'll see shortly.

For me, the most inspiring student presentation was given by the group from Edinburgh, about whom I've written briefly in my book. Arsenic contamination in drinking water is a problem that affects tens of millions worldwide, and is particularly acute in Bangladesh. Existing methods for testing samples are expensive and require technical training, so the Edinburgh team have developed a cell-based detection kit that can detect concentrations below the WHO safety threshold, and which produces a simple "yes-no" response that a non-specialist can understand. Their eventual objective is to be in a position to package and sell the kits for around $1 a pop, which will make sustained testing possible for villagers. A fantastic technical achievement as well as an extremely worthy cause.

I felt slightly humbled by the experience of watching these students in action; remember, most of them were undergraduates (albeit the best of the best) when this work was carried out, and yet they were doing work that, only a few years ago, would be considered the absolute state of the art, and attracting Science and Nature papers (although I can't see any reason why the current work should not do the same). If any of them choose to pursue a career in this field (and I sincerely hope that they do) then they have an excellent future ahead of them.

The final plenary was given by my colleague Ron Weiss of Princeton, who is one of the leading figures in synthetic biology (and, again, who features prominently in the final chapter of my book). Ron has been at the forefront of cellular re-engineering for some years now, and has consistently produced first-rate work. Ron is also interested in pattern formation in nature, and his recent work focuses on programming the way that stem cells talk to other cells, in the hope of one day being able to control the way that they "specialise" and form tissue structures. Although it's still very early days, I think this work has the potential to be massively significant.

A good way to start the year

2007-01-08T16:30:00.000Z

A (belated) Happy New Year to you!

I haven't, up until now, flagged reviews of Genesis Machines on the blog (partly because I assume that most people who come to it have arrived via the link in the book). However, I was delighted by this review in last Saturday's Guardian; apart from saying nice things about the book, its author, Steven Poole (who wrote Unspeak) appears to share my views on Melanie Phillips of the Daily Mail.

A minor point: Poole ends his review by saying that "It is even possible that, when the footnote numbering goes crazy on pages 199-201, it is some sort of joke about genetic mutation. Sadly, I was not able to find meaning in the resulting number series." He assumes that footnote numbers refer only to the first citation of a source; in the example he gives, I cited a report at the start of the chapter, and then again near the end. In both instances I supplied the reference number ("3"), which is why it might have appeared to be out of sequence later on.

Going back to my roots

2006-11-29T12:55:00.000Z

I'll be returning to my home city of Newcastle-Upon-Tyne next Wednesday (December 6th) to take part in an event organised by The Great Debate. I'll be discussing the topic of Reprogramming Life with Prof. John Burn of the Institute of Human Genetics and Caspar Hewett, the organiser of TGD. Audience participation is welcomed (and, indeed, necessary) at such events, so please come down and take part (if you need an extra incentive, Toby Mundy, my publisher at Atlantic, has very kindly stumped up some cash for a drinks reception afterwards!)

The event starts at 7pm, and further details are available here.