Thursday, April 13, 2006
Bioprinting
"Sitting in a culture dish, a layer of chicken heart cells beats in synchrony. But this muscle layer was not sliced from an intact heart, nor even grown laboriously in the lab. Instead, it was "printed", using a technology that could be the future of tissue engineering."
Thursday, March 30, 2006
Authorities approve Airbus result
The EASA and the FAA have both formally approved the result of Sunday's Airbus A380 evacuation trial, and the aircraft is now certificated to carry up to 853 passengers.
Wednesday, March 29, 2006
Nature Imitation Methods - Theory and Practice (NIM 2006)
International Workshop Session at the ISDA 2006 - 6th IEEE International Conference on Intelligent System Design and Applications, Jinan, Shandong, China, October 16-18, 2006.
NIM'06 will focus on the following topics:
Important Dates:
See the workshop webpage for further details (declaration of interest: I am on the Program Committee).
NIM'06 will focus on the following topics:
- Evolutionary computation
- Neural networks
- Artificial immune systems
- Ant colony optimizations
- Cellular Computing
- Artificial life
- DNA Computing
- Combination of all above (hybrid approaches)
- Real applications
Important Dates:
- Special Session Proposal: May 1, 2006
- Paper Submission: May 15, 2006
- Notification of Acceptance: June 15, 2006
- Final Paper Submission: June 30, 2006
See the workshop webpage for further details (declaration of interest: I am on the Program Committee).
Monday, March 27, 2006
A380 evacuation test a success?
Airbus are claiming success after yesterday's A380 evacuation test, the results of which are yet to be verified by the authorities (but the signs suggest that this is just a formality). Airbus think they managed to evacuate 873 "passengers" (half of whom were Airbus employees, with the other half being recruited from local gyms...) in 80 seconds.
The test didn't run quite as smoothly as Airbus might have hoped, though, with one participant breaking his leg, and 32 others suffering minor injuries (many sustaining friction burns on the slides).
Thos familiar with our recent work on A380 evacuation modelling will know that one of the main variables of interest was delay caused by passengers pausing at the upper exits (which are 8m off the ground). The editor of Flight International, Mark Daly, was one of the participants in the test: "One of the big concerns was whether anybody would hesitate at the top of the slides," said Mr Daly. "The finding was that nobody does - in a panic situation, your universe contracts and you're only really conscious of the few feet around you."
Hopefully Airbus will release enough data to allow us to test the validity of our existing model, but there's no requirement for them to disclose anything other than the bare details of the test.
We'll wait and see.
The test didn't run quite as smoothly as Airbus might have hoped, though, with one participant breaking his leg, and 32 others suffering minor injuries (many sustaining friction burns on the slides).
Thos familiar with our recent work on A380 evacuation modelling will know that one of the main variables of interest was delay caused by passengers pausing at the upper exits (which are 8m off the ground). The editor of Flight International, Mark Daly, was one of the participants in the test: "One of the big concerns was whether anybody would hesitate at the top of the slides," said Mr Daly. "The finding was that nobody does - in a panic situation, your universe contracts and you're only really conscious of the few feet around you."
Hopefully Airbus will release enough data to allow us to test the validity of our existing model, but there's no requirement for them to disclose anything other than the bare details of the test.
We'll wait and see.
Saturday, March 18, 2006
A380 evacuation trial - date
According to "regulatory sources", Airbus have scheduled the A380 evacuation trial for Sunday March 26th. For more background, see our recent work on the aircraft.
Friday, March 17, 2006
DNA origami
Paul Rothemund has written a paper that appears on the cover of this week's Nature (the link goes to a news story with an image of a DNA "smiley face", see the open access editor's summary, or the full paper (requires subscription)). He's come up with a way of folding a single DNA strand to form arbitrary two-dimensional shapes (much like origami experts fold a single sheet of paper into a multitude of designs).
Much work has been done on DNA nanotechnology, mainly inspired by the work of Ned Seeman. Rothemund's approach differs in that, rather than using many different "tiles" that self-assemble into a macro-scale single object, he folds a single section of well-sequenced viral DNA, using short "staple" strands to pin the whole complex together.
This work is wonderfully elegant, and is just one of several significant papers published by Rothemund. He first came to the attention of the DNA computing community at the first ever international workshop in 1995, when he described his scheme for a molecular Turing machine, and he's continued to produce work of outstanding quality.
Much work has been done on DNA nanotechnology, mainly inspired by the work of Ned Seeman. Rothemund's approach differs in that, rather than using many different "tiles" that self-assemble into a macro-scale single object, he folds a single section of well-sequenced viral DNA, using short "staple" strands to pin the whole complex together.
This work is wonderfully elegant, and is just one of several significant papers published by Rothemund. He first came to the attention of the DNA computing community at the first ever international workshop in 1995, when he described his scheme for a molecular Turing machine, and he's continued to produce work of outstanding quality.
Monday, March 13, 2006
Science in the Dock
The ESRC Centre for Genomics in Society (Egenis) at Exeter is organising a week of public outreach activities.
"Egenis invites you to get involved during ESRC Social Science Week: On 14 March, ‘Science in the Dock – Art in the Stocks’ will bring together artists and scientists from the South West to discuss and critique each other’s work in a public symposium."
I'm giving the opening address, and will be talking about bacterial cameras and general synthetic biology. It should make an interesting change from the sort of event that I usually attend, so I'll try to post a summary of what went on (further details of the programme are available at the Egenis website).
"Egenis invites you to get involved during ESRC Social Science Week: On 14 March, ‘Science in the Dock – Art in the Stocks’ will bring together artists and scientists from the South West to discuss and critique each other’s work in a public symposium."
I'm giving the opening address, and will be talking about bacterial cameras and general synthetic biology. It should make an interesting change from the sort of event that I usually attend, so I'll try to post a summary of what went on (further details of the programme are available at the Egenis website).
Wednesday, March 08, 2006
Blog down-time
The blog will not be updated over the next week or so, as I'll be "away" on paternity leave.
"Human selection alive and kicking"
News article from Nature (open access):
"Researchers at the University of Chicago, Illinois, have identified the regions of our genetic sequence that show the strongest marks of natural selection. Their work highlights the genes that have been most important in adapting to new lifestyles, and could help to identify the genetic factors involved in complex medical conditions such as high blood pressure and alcoholism."
"Researchers at the University of Chicago, Illinois, have identified the regions of our genetic sequence that show the strongest marks of natural selection. Their work highlights the genes that have been most important in adapting to new lifestyles, and could help to identify the genetic factors involved in complex medical conditions such as high blood pressure and alcoholism."
Friday, February 24, 2006
Enzymatic computing
I'm quoted in a short piece in the New Scientist breaking news section:
"A molecular computer that uses enzymes to perform calculations has been built by researchers in Israel.
Itamar Willner, who constructed the molecular calculator with colleagues at the Hebrew University of Jerusalem in Israel, believes enzyme-powered computers could eventually be implanted into the human body and used to, for example, tailor the release of drugs to a specific person's metabolism."
"A molecular computer that uses enzymes to perform calculations has been built by researchers in Israel.
Itamar Willner, who constructed the molecular calculator with colleagues at the Hebrew University of Jerusalem in Israel, believes enzyme-powered computers could eventually be implanted into the human body and used to, for example, tailor the release of drugs to a specific person's metabolism."
Monday, February 20, 2006
Turing archive
"The Turing Archive for the History of Computing is a major Internet project... The documents that form the historical record of the development of computing are scattered throughout various archives, libraries and museums around the world. Until now, to study these documents required a knowledge of where to look, and a fistful of air tickets. This Virtual Archive contains digital facsimiles of the documents. The Archive places the history of computing, as told by the original documents, onto your own computer screen.
This site also contains a section on codebreaking and a series of reference articles concerning Turing and his work."
This site also contains a section on codebreaking and a series of reference articles concerning Turing and his work."
Tuesday, February 07, 2006
The Mower
The mower stalled, twice; kneeling, I found
A hedgehog jammed up against the blades,
Killed. It had been in the long grass.
I had seen it before, and even fed it, once.
Now I had mauled its unobtrusive world
Unmendably. Burial was no help:
Next morning I got up and it did not.
The first day after a death, the new absence
Is always the same; we should be careful
Of each other, we should be kind
While there is still time.
Philip Larkin
A hedgehog jammed up against the blades,
Killed. It had been in the long grass.
I had seen it before, and even fed it, once.
Now I had mauled its unobtrusive world
Unmendably. Burial was no help:
Next morning I got up and it did not.
The first day after a death, the new absence
Is always the same; we should be careful
Of each other, we should be kind
While there is still time.
Philip Larkin
Friday, January 27, 2006
CoGBiN 2006
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.
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.
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).
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