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

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

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

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

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

The New Scientist Cupcake

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)

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)

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)

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.