I'm on the Organizing Committee of CoGBiN 2006: a Workshop on Computation in Genetic and Biochemical Networks, which is to be held as part of Unconventional Computation 2006, 4th-8th September 2006, York, UK.
The Workshop on Computation in Genetic and Biochemical Networks aims to provide a forum to bring together biologists and computer scientists who are interested in computational models of the behaviours which occur in genetic and biochemical networks. We welcome paper submissions from researchers interested in understanding the forms of computation carried out by biological networks in vivo, in applying these forms of computation in silico, and in the emerging field of synthetic biology.
Selected papers will be considered for publication in the journal BioSystems.
Important Dates
Paper submission: 1st May 2006
Paper notification: 1st July 2006
See the website for details of how to submit.
Friday, January 27, 2006
Thursday, January 26, 2006
Bad news for Darwin, rationality
Are we about to see a repeat of the "intelligent design" debate, this time in the UK? The BBC has recently carried out a survey of the British population, taking opinions on the theory of evolution. The results are profoundly disturbing and depressing:
Over 2000 participants took part in the survey, and were asked what best described their view of the origin and development of life:
When given a choice of three theories, people were asked which ones they would like to see taught in science lessons in British schools:
The "positive" figure of 70% wanting evolution taught in science lessons masks the obvious fact that nearly a third of the population, by definition, do not want it taught in science class -- the additional fact that 44% want creationism included in science curricula is worrying in the extreme.
Over 2000 participants took part in the survey, and were asked what best described their view of the origin and development of life:
- 22% chose creationism
- 17% opted for intelligent design
- 48% selected evolution theory
- and the rest did not know.
When given a choice of three theories, people were asked which ones they would like to see taught in science lessons in British schools:
- 44% said creationism should be included
- 41% intelligent design
- 69% wanted evolution as part of the science curriculum.
The "positive" figure of 70% wanting evolution taught in science lessons masks the obvious fact that nearly a third of the population, by definition, do not want it taught in science class -- the additional fact that 44% want creationism included in science curricula is worrying in the extreme.
Monday, January 23, 2006
Update: A380 evacuation trainer installed
Airbus have just installed their first A380 cabin emergency evacuation trainer at their training centre in Toulouse. "`Now we are ready to get on with flight testing and certification on the A380,' says Engine Alliance president Bruce Hughes."
"Watt's in a name"
As a proud alumnus of both the Universities of Coventry (B.Sc.) and Warwick (Ph.D.), I was mildly amused by this article on the difficulties of naming places of higher education.
When I was at Warwick, every year we would we hear stories of Ph.D. students applying from overseas (who hadn't visited the campus prior to accepting their place) inadvertently snapping up hideously expensive flats in the centre of Warwick, only to arrive and find that they were miles from campus and paying roughly triple the price of an equivalent place in Coventry. I think, in the end, the University had to put a warning note in its promotional literature, as it was beginning to get rather embarrassing.
When I was at Warwick, every year we would we hear stories of Ph.D. students applying from overseas (who hadn't visited the campus prior to accepting their place) inadvertently snapping up hideously expensive flats in the centre of Warwick, only to arrive and find that they were miles from campus and paying roughly triple the price of an equivalent place in Coventry. I think, in the end, the University had to put a warning note in its promotional literature, as it was beginning to get rather embarrassing.
Friday, January 20, 2006
Microbes and Microbots
In his consistently excellent blog, Richard Jones discusses the history of the nanobot; the "Fantastic Voyage"-style nanoscale submarine cruising our bloodstream looking for nasties like cancer cells and broken capillaries.
"Attempts to write the nanobot out of the history of nanotechnology thus seem doomed, so we had better try and rehabilitate the concept. If we accept that the shrunken submarine image is hopelessly misleading, how can we replace it by something more realistic?
Personally, I believe that we would be better served by taking a step back, and first considering the feasibility of microbots, before we even contemplate such devices on the nanoscale. Richard makes the valid point that the science fiction images of incredibly miniaturised submarines do the field of nanotechnology a great disservice, as they do nothing to dispel the myth of nanotech being "engineering, only smaller".
Based on my interpretation of Richard's book Soft Machines (he nabbed my title, the rotter ;-), I think he might agree with me that a rather more realistic (and certainly interesting) route would be to re-engineer existing living systems for the purposes of providing such applications.
As I point out in my own popular science book Genesis Machines: The Coming Revolution in Biocomputing and Synthetic Biology (Atlantic Books, November 6th -- watch this space for updates and sneak previews):
"Nature has computation, compression and contraptions down to a fine art...A human genome sequence may be stored on a single DVD, and yet pretty much every cell in our body contains a copy. Science fiction authors tell stories of "microbots" -- incredibly tiny devices that can roam around under their own power, sensing their environment, talking to one another and destroying intruders. Such devices already exist, but we know them better as bacteria."
"Attempts to write the nanobot out of the history of nanotechnology thus seem doomed, so we had better try and rehabilitate the concept. If we accept that the shrunken submarine image is hopelessly misleading, how can we replace it by something more realistic?
Personally, I believe that we would be better served by taking a step back, and first considering the feasibility of microbots, before we even contemplate such devices on the nanoscale. Richard makes the valid point that the science fiction images of incredibly miniaturised submarines do the field of nanotechnology a great disservice, as they do nothing to dispel the myth of nanotech being "engineering, only smaller".
Based on my interpretation of Richard's book Soft Machines (he nabbed my title, the rotter ;-), I think he might agree with me that a rather more realistic (and certainly interesting) route would be to re-engineer existing living systems for the purposes of providing such applications.
As I point out in my own popular science book Genesis Machines: The Coming Revolution in Biocomputing and Synthetic Biology (Atlantic Books, November 6th -- watch this space for updates and sneak previews):
"Nature has computation, compression and contraptions down to a fine art...A human genome sequence may be stored on a single DVD, and yet pretty much every cell in our body contains a copy. Science fiction authors tell stories of "microbots" -- incredibly tiny devices that can roam around under their own power, sensing their environment, talking to one another and destroying intruders. Such devices already exist, but we know them better as bacteria."
Thursday, January 12, 2006
Minimal genome
The journal PNAS has this week published an open access article by the Synthetic Biology Group lead by Craig Venter (the founder of the commercial "rival" to the publically-funded human genome project).
One of the objectives of Venter's group is to identify the smallest possible set of genes required to sustain life. By knocking out genes one by one and assessing the effect of such deletions, they hope to derive a minimal "component list" for a living cell. As they state in the introduction to the article, "One consequence of progress in the new field of synthetic biology is an emerging view of cells as assemblages of parts that can be put together to produce an organism with a desired phenotype. That perspective begs the question: "How few parts would it take to construct a cell?" In an environment that is free from stress and provides all necessary nutrients, what would constitute the simplest free-living organism? This problem has been approached theoretically and experimentally in our laboratory and elsewhere."
One of the objectives of Venter's group is to identify the smallest possible set of genes required to sustain life. By knocking out genes one by one and assessing the effect of such deletions, they hope to derive a minimal "component list" for a living cell. As they state in the introduction to the article, "One consequence of progress in the new field of synthetic biology is an emerging view of cells as assemblages of parts that can be put together to produce an organism with a desired phenotype. That perspective begs the question: "How few parts would it take to construct a cell?" In an environment that is free from stress and provides all necessary nutrients, what would constitute the simplest free-living organism? This problem has been approached theoretically and experimentally in our laboratory and elsewhere."
Thursday, January 05, 2006
Airbus A380 evacuation trial
Those familiar with our recent work on aircraft evacuation modelling will known that the safety community is still waiting for Airbus to carry out its long-awaited full-scale evacuation trial of the double-decker A380. Without this being passed, the authorities will be unable to certify the aircraft as safe to carry paying passengers. Our simulation study concerned evacuation delay caused by passengers hesitating at the upper exit, and we predicted that the trial will fail (ie. not all passengers will be evacuated in under 90 seconds) if the average door hesitation exceeded 1.1 seconds. Of course, this is pure speculation on our part, based on a rather simplistic computer model, and we await with interest the results of the real-life trial. Flight International have confirmed information that the trial will be held "around March" this year. Such announcements have been made before, with no trial being held, but Airbus need to get their skates on, as they're already running six months behind schedule on delivery.
Monday, January 02, 2006
2006: The Dangerous Ideas
First, I'd like to wish readers a happy, peaceful and prosperous New Year.
"The mandate of Edge Foundation is to promote inquiry into and discussion of intellectual, philosophical, artistic, and literary issues, as well as to work for the intellectual and social achievement of society."
At the start of every year, the Edge poses an annual question, and asks some of the foremost contemporary thinkers to share their thoughts on it. This year, the question is "What is your dangerous idea?".
"Here you will find indications of a new natural philosophy, founded on the realization of the import of complexity, of evolution. Very complex systems — whether organisms, brains, the biosphere, or the universe itself — were not constructed by design; all have evolved. There is a new set of metaphors to describe ourselves, our minds, the universe, and all of the things we know in it."
Contributors to this collection of essays include Philip Anderson, Richard Dawkins, Daniel Dennett, Freeman Dyson, Danny Hillis, Brian Goodwin, Steven Pinker, Douglas Rushkoff and Craig Venter. Of particular personal interest are the essays by Lynn Margulis (our sensory capabilities have evolved as a result of interactions between social bacteria) and Robert Shapiro (we shall understand the origin of life within the next 5 years).
"The mandate of Edge Foundation is to promote inquiry into and discussion of intellectual, philosophical, artistic, and literary issues, as well as to work for the intellectual and social achievement of society."
At the start of every year, the Edge poses an annual question, and asks some of the foremost contemporary thinkers to share their thoughts on it. This year, the question is "What is your dangerous idea?".
"Here you will find indications of a new natural philosophy, founded on the realization of the import of complexity, of evolution. Very complex systems — whether organisms, brains, the biosphere, or the universe itself — were not constructed by design; all have evolved. There is a new set of metaphors to describe ourselves, our minds, the universe, and all of the things we know in it."
Contributors to this collection of essays include Philip Anderson, Richard Dawkins, Daniel Dennett, Freeman Dyson, Danny Hillis, Brian Goodwin, Steven Pinker, Douglas Rushkoff and Craig Venter. Of particular personal interest are the essays by Lynn Margulis (our sensory capabilities have evolved as a result of interactions between social bacteria) and Robert Shapiro (we shall understand the origin of life within the next 5 years).
Friday, December 23, 2005
2005: A Review
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!
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 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...
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