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

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:

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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.

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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)

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?

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

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

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

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)

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

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

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

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

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

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

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

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

Blatant plagiarism

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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)

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:

1. identify all the stuff in your life that isn’t in the right place (close all open loops)
   
2. get rid of the stuff that isn’t yours or you don’t need right now
   
3. create a right place that you trust and that supports your working style and values
   
4. put your stuff in the right place, consistently
   
5. do your stuff in a way that honors your time, your energy, and the context of any given moment
   
6. 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)

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)

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)

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

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)

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

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!"

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.