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."

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."

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

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.

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:

• 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.

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.

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."

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."

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.

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).

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!

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.

"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."

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.

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.

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.

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.

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").

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.