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!

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

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.

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 (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").

Tuesday, December 06, 2005


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.