After the recent controversy over "intelligent design" in the classroom, it's no great surprise to see that Science has awarded the title of Breakthrough of the Year to "Evolution in Action"; a catch-all phrase to describe new work on uncovering the mechanisms of how individual species emerge. Systems biology came in as a runner-up, highlighting the importance of this new discipline.
From a personal perspective, I was pleased to see microbial communities listed as an Area to Watch in 2006. We're currently working on modelling bacteria/phage interactions, and expect to have some interesting results to report early in the New Year.
Well, this will be the last blog post of 2005, so I'd just like to thank you all for reading (and for the comments you've sent me), and wish you a Happy Christmas and a peaceful and prosperous New Year. See you in 2006!
Friday, December 23, 2005
Friday, December 16, 2005
New paper available: Second generation biocomputing
Jon Timmis, Martyn Amos, Wolfgang Banzhaf and Andy Tyrrell; submitted to the International Journal of Unconventional Computing. Preprint available at arxiv.org/abs/cs.AI/0512071
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative" solutions to human-defined problems. However, in this position paper we argue that the time has now come for a reassessment of how we exploit biology to generate new computational systems. Previous solutions (the "first generation" of biocomputing techniques), whilst reasonably effective, are crude analogues of actual biological systems. We believe that a new, inherently inter-disciplinary approach is needed for the development of the emerging "second generation" of bio-inspired methods. This new modus operandi will require much closer interaction between the engineering and life sciences communities, as well as a bidirectional flow of concepts, applications and expertise. We support our argument by examining, in this new light, three existing areas of biocomputing (genetic programming, artificial immune systems and evolvable hardware), as well as an emerging area (natural genetic engineering) which may provide useful pointers as to the way forward.
Researchers in the field of biocomputing have, for many years, successfully "harvested and exploited" the natural world for inspiration in developing systems that are robust, adaptable and capable of generating novel and even "creative" solutions to human-defined problems. However, in this position paper we argue that the time has now come for a reassessment of how we exploit biology to generate new computational systems. Previous solutions (the "first generation" of biocomputing techniques), whilst reasonably effective, are crude analogues of actual biological systems. We believe that a new, inherently inter-disciplinary approach is needed for the development of the emerging "second generation" of bio-inspired methods. This new modus operandi will require much closer interaction between the engineering and life sciences communities, as well as a bidirectional flow of concepts, applications and expertise. We support our argument by examining, in this new light, three existing areas of biocomputing (genetic programming, artificial immune systems and evolvable hardware), as well as an emerging area (natural genetic engineering) which may provide useful pointers as to the way forward.
"Simulated" E. coli
"The ubiquitous and usually harmless E. coli bacterium, which has one-seventh the number of genes as a human, has more than 1,000 of them involved in metabolism and metabolic regulation. Activation of random combinations of these genes would theoretically be capable of generating a huge variety of internal states; however, researchers at UCSD will report in the Dec. 27 issue of Proceedings of the National Academy of Sciences (PNAS) that Escherichia coli doesn’t gamble with its metabolism. In a surprise about E. coli that may offer clues about how human cells operate, the PNAS paper reports that only a handful of dominant metabolic states are found in E. coli when it is “grown” in 15,580 different environments in computer simulations."
Wednesday, December 14, 2005
Heath and safety at work
Did anyone else spot the (surely deliberate) irony in yesterday's Guardian coverage of the Buncefield explosion? Click the picture for a bigger version.
Monday, December 12, 2005
Buncefield burner
The blog's going to be quiet today and tomorrow, as I'll be in Edinburgh examining a Ph.D. Before I go, I just thought I'd share this photograph of the Buncefield explosion.
Friday, December 09, 2005
Special issue of Natural Computing now available
The special issue of Natural Computing that I mentioned yesterday is now available online (I think it's free access, but a subscription may be required). The issue contains papers arising from the First International Symposium on Cellular Computing, which I co-organised last year.
The issue is dedicated to the memory of my friend and colleague, Ray Paton, who died suddenly on July 29 last year, aged only 50.
The issue is dedicated to the memory of my friend and colleague, Ray Paton, who died suddenly on July 29 last year, aged only 50.
Thursday, December 08, 2005
New paper available: Bacterial self-organisation and computation
Martyn Amos, David A. Hodgson and Alan Gibbons; submitted to the International Journal of Unconventional Computing. Preprint available at arxiv.org/abs/q-bio/0512017 (from Friday).
In this article we highlight chemotaxis (cellular movement) as a rich source of potential engineering applications and computational models, highlighting current research and possible future work. We first give a brief description of the biological mechanism, before describing recent work on modelling it in silico. We then propose a methodology for extending existing models and their possible application as a fundamental tool in engineering cellular pattern formation. We discuss possible engineering applications of human-defined cell patterns, as well as the potential for using abstract models of chemotaxis for generalised computation, before concluding with a brief discussion of future challenges and opportunities in this field.
In this article we highlight chemotaxis (cellular movement) as a rich source of potential engineering applications and computational models, highlighting current research and possible future work. We first give a brief description of the biological mechanism, before describing recent work on modelling it in silico. We then propose a methodology for extending existing models and their possible application as a fundamental tool in engineering cellular pattern formation. We discuss possible engineering applications of human-defined cell patterns, as well as the potential for using abstract models of chemotaxis for generalised computation, before concluding with a brief discussion of future challenges and opportunities in this field.
Quantum computing guru wins 2005 Edge of Computation Prize
I'm a bit late in posting this, but David Deutsch has won the 2005 Edge of Computation Prize for his seminal work on quantum computing. From the nomination: "Although the general idea of a quantum computer had been proposed earlier by Richard Feynman, in 1985 David Deutsch wrote the key paper which proposed the idea of a quantum computer and initiated the study of how to make one. Since then he has continued to be a pioneer and a leader in a rapidly growing field that is now called quantum information science."
The only nominees with whom I have a vague connection were Peter Bentley, for his work on "digital gardening" (he has a paper in a forthcoming special issue of Natural Computing that I edited with Dave Hodgson), and Ehud Shapiro, for his construction of a molecular automaton (I played a part in validating his group's Guinness World Record for "Smallest Biological Computing Device").
The only nominees with whom I have a vague connection were Peter Bentley, for his work on "digital gardening" (he has a paper in a forthcoming special issue of Natural Computing that I edited with Dave Hodgson), and Ehud Shapiro, for his construction of a molecular automaton (I played a part in validating his group's Guinness World Record for "Smallest Biological Computing Device").
Tuesday, December 06, 2005
3quarksdaily
I've added a permanent side-bar link to 3quarksdaily, which should indicate how highly I think of the site. It's a filter blog, along the lines of Metafilter, and contains consistently excellent links to noteworthy items that one might otherwise miss. Sample postings of particular interest to me include an article on C.P. Snow (The Two Cultures and the Scientific Revolution), the 2005 Scientific American 50 (featuring George Church, Jim Collins and Airbus), and a constantly changing site that presents science and culture stories using their notion of phylotaxis.
Friday, December 02, 2005
Friday Flash fun
The amusing tale of a little animated man who just wants to get to the other side. It gets increasingly daft as you move through the attempts, but some are "laugh out loud" (I particularly liked the appropriately festive attempt). Make sure you watch each animation all the way through until it loops, as they often have a sting in the tail. Requires Flash.
Monday, November 28, 2005
My home page (and this blog)
I've redesigned my home page: I think the design looks cleaner (and more consistent with the blog). I've also added navigation bars at the left, so hopefully it looks a bit more professional. I've also added a photo gallery section to this blog (it's rather sparsely-populated right now, but will become more interesting once I've had a chance to file a load of existing pictures). Comments are, of course, always welcome.
Friday, November 25, 2005
Little green hackers
If you've seen the film Independence Day, you'll know that the Earth was saved by Jeff Goldblum's geeky scientist character inserting a virus into the main computer system of the alien mothership. In addition to Goldblum, we clearly have to thank Microsoft's marketing team, as, remarkably, the aliens appear to be running a variant of Windows on their server (as my colleague Susan Stepney has highlighted), making them vulnerable to attack.
Of course, this is just sci-fi licence, and nobody seriously believes that even Bill Gates has managed to achieve intergalactic penetration. Or has he? Richard Carrigan clearly thinks so, as he's recently raised concerns that the Search for Extraterrestrial Intelligence (SETI) may run the risk of inadvertently introducing alien computer viruses into our global computer network. His forthcoming journal article (subscription might be required) describes his "SETI hacker" hypothesis in rather more detail.
I'm sure Dr. Carrigan is trying to make an important point, but I'm afraid it's somewhat undermined by the implied understanding of how operating systems and viruses actually work. To quote from his article:
At least two scenarios need to be considered in protecting against a malevolent SETI Hacker signal. One is a computer virus in the message that takes over the computer at the receiver. The other is an open message that gives an impenetrable software code or instructions for a hardware translator to handle an opaque message. Both cases are dangerous. The damage may be done before the receiver appreciates that it is under attack. This is the current experience even with Earth-based hacker attacks. There may not be an opportunity to pull the signal out of the computer or turn off the power before the intruding signal has taken over.
Computer viruses can only "take over a computer" if
Even if the signals being decoded by SETI did contain an alien virus, it's extremely unlikely that it would encode executable code that could infect a human-constructed machine. Even if it did, we would still have to then knowingly run it, so I think we can safely rule out alien hacker attack in the near future. However, I have an open mind, and will happily reconsider the possibility of inter-stellar crime if (for example), I receive an email from Councillor Zarg of the planet Cthu-Targ9, asking for my absolute discretion in transferring 3.5 million Galactic Credits from his father's bank account...
Of course, this is just sci-fi licence, and nobody seriously believes that even Bill Gates has managed to achieve intergalactic penetration. Or has he? Richard Carrigan clearly thinks so, as he's recently raised concerns that the Search for Extraterrestrial Intelligence (SETI) may run the risk of inadvertently introducing alien computer viruses into our global computer network. His forthcoming journal article (subscription might be required) describes his "SETI hacker" hypothesis in rather more detail.
I'm sure Dr. Carrigan is trying to make an important point, but I'm afraid it's somewhat undermined by the implied understanding of how operating systems and viruses actually work. To quote from his article:
At least two scenarios need to be considered in protecting against a malevolent SETI Hacker signal. One is a computer virus in the message that takes over the computer at the receiver. The other is an open message that gives an impenetrable software code or instructions for a hardware translator to handle an opaque message. Both cases are dangerous. The damage may be done before the receiver appreciates that it is under attack. This is the current experience even with Earth-based hacker attacks. There may not be an opportunity to pull the signal out of the computer or turn off the power before the intruding signal has taken over.
Computer viruses can only "take over a computer" if
- They are written in the native machine language of the computer, or are present in some other "executable" form (eg. a macro),
- They are then actually executed
Even if the signals being decoded by SETI did contain an alien virus, it's extremely unlikely that it would encode executable code that could infect a human-constructed machine. Even if it did, we would still have to then knowingly run it, so I think we can safely rule out alien hacker attack in the near future. However, I have an open mind, and will happily reconsider the possibility of inter-stellar crime if (for example), I receive an email from Councillor Zarg of the planet Cthu-Targ9, asking for my absolute discretion in transferring 3.5 million Galactic Credits from his father's bank account...
Thursday, November 24, 2005
This week's Nature
This week's issue of Nature is chock-full of good stuff (a lot of which, unfortunately, requires a subscription). It's a special issue on synthetic biology, an exciting new research area at the intersection of biology, engineering, computer science and mathematics (amongst other disciplines). According to the main website in the field, synthetic biology refers to
Essentially, researchers are trying to work out the "parts catalogue" for living organisms, and then seeing how these components can be put together in new ways to yield entirely new behaviours, as well as investigating how the existing components may be re-engineered to make them more efficient, react to different inputs, etc. According to the editorial, "This technology allows biological components, circuits and potentially replicating organisms to be developed from scratch, possibly based on different genetic codes from those found in the wild."
A lovely example of synthetic biology in action is the bacterial "camera", which uses engineered E. coli bugs (there's an open access Science Daily press release). Some of the founders of this new field describe recent progress, discuss its foundations, and consider the ethical and safety issues that such research must address.
In an unusual step for the journal, they've also commissioned a cartoon guide to synthetic biology (which is open access).
I'm currently writing a journal article on "Bacterial Self-Organisation and Computation", which will describe a lot of this work - I'll post a link to it when it's finished.
- the design and construction of new biological parts, devices, and systems.
- the re-design of existing, natural biological systems for useful purposes.
Essentially, researchers are trying to work out the "parts catalogue" for living organisms, and then seeing how these components can be put together in new ways to yield entirely new behaviours, as well as investigating how the existing components may be re-engineered to make them more efficient, react to different inputs, etc. According to the editorial, "This technology allows biological components, circuits and potentially replicating organisms to be developed from scratch, possibly based on different genetic codes from those found in the wild."
A lovely example of synthetic biology in action is the bacterial "camera", which uses engineered E. coli bugs (there's an open access Science Daily press release). Some of the founders of this new field describe recent progress, discuss its foundations, and consider the ethical and safety issues that such research must address.
In an unusual step for the journal, they've also commissioned a cartoon guide to synthetic biology (which is open access).
I'm currently writing a journal article on "Bacterial Self-Organisation and Computation", which will describe a lot of this work - I'll post a link to it when it's finished.
Wednesday, November 23, 2005
Dreamlines
Dreamlines is a beautiful image generation website that takes a search query, passes it to Google Images and then processes relevant pictures to draw a "dream-like" progression. The interesting thing, from my perspective, is how the images are processed - a graphic file provides the template "environment" for a group of interacting particles, or agents, which interact in a non-linear fashion to generate an emergent whole (more on this paradigm here).
I'm not sure about the waffle about the internet "dreaming", but it does generate a lovely series of images (I tried DNA and bacteria, both with nice results).
The site does require Flash and Java.
I'm not sure about the waffle about the internet "dreaming", but it does generate a lovely series of images (I tried DNA and bacteria, both with nice results).
The site does require Flash and Java.
Tuesday, November 22, 2005
Online biology books
This is a wonderful resource for anyone working in the life sciences (or at an interface thereof). The National Center for Biotechnology
Information (NCBI) is responsible for collecting, organising, facilitating access to and disseminating knowledge about molecular biology, biochemistry and genetics.
The Bookshelf is a fully-searchable collection of biomedical texts (including some classics).
Information (NCBI) is responsible for collecting, organising, facilitating access to and disseminating knowledge about molecular biology, biochemistry and genetics.
The Bookshelf is a fully-searchable collection of biomedical texts (including some classics).
Monday, November 21, 2005
The Ants and the Airbus
I was very lucky in the last academic year to work with two very bright students on a couple of agent-based computing research projects. One of these was Oliver Don, and our work on modelling ant colonies is reported below.
The other student was Andrew Wood, and we decided to investigate the evacuation of the new Airbus A380 (the first ever double-decker passenger aircraft). Where this aircraft differs from those that have gone before is that the upper-deck exits are significantly higher than those on standard aircraft, and we wondered if "door delay" (ie. hesitation induced by the realisation of just how high the exit is) would have a significant impact on the time taken to evacuate the aircraft. In order to investigate this, we built an individual-based model of the aircraft (basically, model each individual passenger, each with their own particular attributes, and then "let it run"), and I think we came up with some interesting findings. The most significant conclusion we drew was that if average door delay exceeds just over 1s, then the aircraft will fail its certification trial (which requires it to be fully evacuated of passengers and crew within 90s).
Of course, this is just a prediction based on a simplistic model of the aircraft, but previous small-scale studies with real people have suggested that door delay will play a significant role. We await with interest the results of the full certification trial (which has yet to take place).
An article based on this work is currently in submission to a journal, but the project web page points to a pre-print version of it. There's also a version of the simulation that you can run in your browser and play with. In the mean time, I'll post an update when I hear anything about the progress of the paper, but this post is also meant to flag a forthcoming documentary, which I believe is showing in the UK this Friday (25th November) on Discovery Wings.
The other student was Andrew Wood, and we decided to investigate the evacuation of the new Airbus A380 (the first ever double-decker passenger aircraft). Where this aircraft differs from those that have gone before is that the upper-deck exits are significantly higher than those on standard aircraft, and we wondered if "door delay" (ie. hesitation induced by the realisation of just how high the exit is) would have a significant impact on the time taken to evacuate the aircraft. In order to investigate this, we built an individual-based model of the aircraft (basically, model each individual passenger, each with their own particular attributes, and then "let it run"), and I think we came up with some interesting findings. The most significant conclusion we drew was that if average door delay exceeds just over 1s, then the aircraft will fail its certification trial (which requires it to be fully evacuated of passengers and crew within 90s).
Of course, this is just a prediction based on a simplistic model of the aircraft, but previous small-scale studies with real people have suggested that door delay will play a significant role. We await with interest the results of the full certification trial (which has yet to take place).
An article based on this work is currently in submission to a journal, but the project web page points to a pre-print version of it. There's also a version of the simulation that you can run in your browser and play with. In the mean time, I'll post an update when I hear anything about the progress of the paper, but this post is also meant to flag a forthcoming documentary, which I believe is showing in the UK this Friday (25th November) on Discovery Wings.
Tuesday, August 16, 2005
"Microoxen"
"Scientists in the US have managed to get single cells to ferry objects up and down tiny chambers. Harvard University experts say, in future, cells could be harnessed to perform micro-scale mechanical work. The researchers attached a cargo of polystyrene beads to the backs of green algae cells and used light to guide them up and down the chambers. Details of the work appear in the journal Proceedings of the National Academy of Sciences (PNAS)."
Sunday, July 24, 2005
New paper available: An ant-based algorithm for annular sorting
Oliver Don and Martyn Amos (2005 ) An ant-based algorithm for annular sorting
In this paper we describe a minimal model for annular sorting by Leptothorax ants. Simulation results are consistent with the structures observed in actual ant colonies.
(Paper available via link above)
In this paper we describe a minimal model for annular sorting by Leptothorax ants. Simulation results are consistent with the structures observed in actual ant colonies.
(Paper available via link above)
Tuesday, July 05, 2005
What don't we know?
Free access Science feature to celebrate their 125th anniversary. In it, they pose 125 of the biggest questions facing science today, including "How Will Big Pictures Emerge from a Sea of Biological Data?", "How Far Can We Push Chemical Self-Assembly?", and "What Are the Limits of Conventional Computing?" These should keep us busy for a while....
Wednesday, June 08, 2005
Congratulations!
Hearty congratulations are due to Toby Mundy at Atlantic Books (publishers of my forthcoming popular science book). At the British Book Awards, Toby and Atlantic were awarded the "Imprint and Editor of the Year" Nibbie.
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