Saturday, November 19, 2011
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!
Tuesday, October 25, 2011
Monday, October 24, 2011
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).
Wednesday, September 21, 2011
Tuesday, September 13, 2011
Saturday, September 03, 2011
Friday, August 19, 2011
Monday, July 18, 2011
Tuesday, July 12, 2011
Tuesday, June 28, 2011
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.
"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!"
Monday, June 27, 2011
I just got a message that said, in its entirety,
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).
Monday, June 20, 2011
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.
Monday, June 06, 2011
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.
Saturday, June 04, 2011
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."
Wednesday, May 25, 2011
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
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.
Wednesday, May 18, 2011
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).
Saturday, April 23, 2011
Monday, April 18, 2011
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.
Tuesday, March 22, 2011
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.
Sunday, March 20, 2011
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.
Monday, March 07, 2011
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."
Monday, February 28, 2011
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.
Thursday, January 20, 2011
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.
Monday, January 17, 2011
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).