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.

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.

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.

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

• 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...

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

• 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.

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.

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).

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.

"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)."

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)

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....

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.

NEMS

News article about a cantilever device sensitive enough to detect the mass of a single DNA molecule.

New PNAS papers

Two papers of note from this week's issue of PNAS (subscribers only):

The use of oscillatory signals in the study of genetic networks

Ovidiu Lipan and Wing H. Wong

The structure of a genetic network is uncovered by studying its response to external stimuli (input signals). We present a theory of propagation of an input signal through a linear stochastic genetic network. We found that there are important advantages in using oscillatory signals over step or impulse signals and that the system may enter into a pure fluctuation resonance for a specific input frequency.

Controlled fabrication of hierarchically branched nanopores, nanotubes, and nanowires

Guowen Meng, Yung Joon Jung, Anyuan Cao, Robert Vajtai, and Pulickel M. Ajayan

Here, we report a generic synthetic approach to rationally design multiply connected and hierarchically branched nanopores inside anodic aluminum oxide templates. By using these nanochannels, we controllably fabricate a large variety of branched nanostructures, far more complex than what exists today. These nanostructures include carbon nanotubes and metallic nanowires having several hierarchical levels of multiple branching. The number and frequency of branching, dimensions, and the overall architecture are controlled precisely through pore design and templated assembly. The technique provides a powerful approach to produce nanostructures of greater morphological complexity, which could have far-reaching implications in the design of future nanoscale systems.

Slime mould genome

Nature have made freely available an analysis of the genome of the social amoeba Dictyostelium discoideum (slime mould). "The slime mould Dictyostelium discoideum has been an important laboratory model for over 50 years. These social amoebae normally live in forest soil where they hunt bacteria and yeast, and have therefore excelled in studies of how cells sense and move towards attractants in their environment. When hunting is not successful, the unicellular organisms become one multicellular entity and form a fruiting body to disperse spores, shown on the cover image." There's also a link to archival material.

Follow up: Bacterial pattern formation

News story about the Weiss Nature paper referenced on Friday.

DNA Computing 11: preliminary program

The program has been announced for the 2005 International Meeting on DNA Computing. It looks like the most exciting meeting to date, and I'm annoyed at having to miss it! The ever-increasing profile of experimentalists, doing real wet lab work, can only be good for this emerging field.

A synthetic multicellular system for programmed pattern formation

Excellent Nature article (subscribers only) on programmed cellular differentiation; we have a proposal currently being refereed which describes something similar, so it's reassuring that others are thinking along the same lines.

Followup: Reith lecture

A transcript and audio recording of the Reith lecture on nanotechnology is now available (link above).

Micro- and bio-fluidics

Useful website on micro- and bio-fluidics, including links to papers. One is of particular interest to me: Darnton, N., Turner, L., Breuer, K.S. & Berg, H.C. "Moving fluid with bacterial carpets". Biophysical Journal. 86. pp. 1863-1870. 2004.

Theoretical and Experimental DNA Computation: update

I've just been told by Springer that the camera-ready copy for my forthcoming book Theoretical and Experimental DNA Computation (see book website above) is being sent to the printer, and the finished product should be available to buy in mid-June.

BBC Reith Lecture on nanotechnology

The BBC Reith Lecture (on Nanotechnology) will be on Radio 4 this evening at 2000 BST. Details from the link above - you should be able to listen to it live here.

Dynamic microcompartmentation in synthetic cells

PNAS (subscriber only) article: "This work represents a bottom-up approach to understanding cell biology, in contrast to the top-down approach often adopted in biochemistry and perhaps best exemplified by efforts to generate the "minimal cell" through gene disruption in already simple organisms".

EPSRC Novel Computation panel

If you're waiting to hear the result of an application to the third round of EPSRC Novel Computation funding, you may like to know that the panel will be held at the end of July.

Image manipulation in biology

Interesting discussion in Nature concerning the increasing use of packages such as Photoshop in presenting biological research (subscribers only).

Intel money claimed

A British man has claimed the $10,000 prize offered by Intel (see previous post) - BBC news story.

Nanotubes vs. silicon

News article on the drive to build nano-scale transistors with carbon nanotubes.

Self-assembled DNA fractals

News article on Erik Winfree's work on designing DNA strands to self-assemble into a Sierpinski triangle. The original article was published in PLOS Biology, along with a commentary article (open access).

Intel offering $10,000 reward

Intel are offering $10,000 for a mint-condition copy of the April 19 1965 issue of Electronics magazine containing the article that gave rise to "Moore's Law". See the relevant eBay page for details.

The Grand Challenge in Non-Classical Computation

I've accepted an invitation to sit on a panel at the Grand Challenge in Non-Classical Computation International Workshop, to be held in York, UK on April 18-19. The organisers seem to have assembled a "who's who" of researchers in the field of unconventional computing, and I'm very much looking forward to it -- I'll post a detailed personal account soon afterwards.

Montpellier meeting

On Friday I returned from giving a talk at the Annual Workshop on Modelling of Complex Biological Systems in the Context of Genomics in Montpellier. Personal highlights (with links to relevant material) were:

Przemyslaw Prusinkiewicz; Lindenmayer vs. D'Arcy Thompson; A Comparison of Two Approaches for Modelling Plant Development and Structure. See the Algorithmic Botany page.

Andreas Wagner; Evolution and Evolvability of Gene Networks. See Robustness and Evolvability in Living Systems

Jorg Stelling; Robustness and Cellular Design Principles. See this Cell article.

Gene Regulatory Networks

The most recent issue of PNAS is a special on Gene Regulatory Networks (access restricted to subscribers).

Capturing Complexity through Agent-Based Modeling

Another useful and interesting PNAS-supported colloquium.

Signal processing in single cells

Science overview article pointing to two current papers on signal transmission through gene cascades in noisy cellular environments. the article concludes that this work "represents an important advance toward a more quantitative synthetic biology. These studies offer insights into gene regulation, and, together, provide a framework for the further characterization of input/output relationships among regulators and their targets. These quantitative approaches can be applied to natural gene networks and used to generate a more comprehensive understanding of cellular regulation. This will enable a better characterization of individual genetic components and modules, opening up the possibility of designing more complex synthetic gene networks. Such networks could be engineered with specific properties that filter unwanted noise from signaling networks or exploit noise-induced switching to sample more diverse phenotypes."

Bacterial spatial organisation using electrical currents

Nature news article on top down spatial manipulation of bacteria (moving them around a silicon chip) using electrical currents.

Away next week

I'm away all of next week at the Annual Conference on Modelling and Simulation of Biological Processes in the Context of Genomics, Montpellier, France (April 4-8). I'll try to post summaries of talks of interest while I'm there.

Canon move into biotech

Japanese camera and office equipment manufacturer Canon have announced that they are stepping up their interest in biotechnology. Inkjet technology has already been used to spray living cells in very precise patterns, so perhaps some bio-nanotech applications may eventually arise...

Old but good

Collection of papers from a 2002 PNAS Colloquium on Self-organized complexity in the physical, biological, and social sciences.

Away at BCTCS

I'll be giving an invited talk at the British Colloquium for Theoretical Computer Science (BCTCS) in Nottingham, and will therefore be away until Thursday.

Interview with Gordon Moore

Short interview with Gordon Moore (he of "Moores Law", the extrapolated observation that the power of computers doubles every 18 months). He is sceptical about the use of alternatives to silicon as computational substrates, pointing out that mass production of nanotube transistors may prove to be difficult. Of course, the first transistor was a massive, cobbled-together beast of a thing, so I'm not sure of the utility of such observations.

Aliens in the Bible

I appear to have the distinction of being cited in a book titled "Aliens in the Bible". This is fantastic news. My Ph.D. thesis is noted in the references section, sandwiched in between two works titled "The Face on Mars" and "Giant Skeletons". I would draw your specific attention to the section dealing with "artificial intelligence in the Bible". The conclusions drawn are, of course, nonsense - I particularly like the implication in Section 1.6 that my work on "genetically created brains" (sic) may be thought of as an incremental step towards governmental imposition of The Mark of the Beast. Great. First barcodes, now this.

Martyn "668, Neighbour of the Beast" Amos

Nano Wire Cutters

Press release on work done at Purdue University (with reference to forthcoming article) on coating DNA molecules with magnetic nanoparticles. The interesting thing about this work is that the researchers have embedded various restriction sites into the substrate DNA, which allows them to "snip" DNA wires of varying lengths. Presumably, if sticky-ended restriction enzymes are used, with correct strand design (and perhaps use of tiles, such as those developed by Ned Seeman) one could facilitate self-assembly of these wires into larger structures (nano-chainmail, anyone? ;)

Network Dynamics and Congestion

Taster article from the New Scientist (with a link to the full article) on centralisation versus decentralisation, with specific reference to traffic congestion.
The findings may shed light on how and why certain natural systems (such as cellular transport networks) have evolved to be (de)centralised in structure.

Open Source Biology

BIOS, the Biological Innovation for Open Society is an open source biotechnology initiative based in Australia. Along with its parent organization CAMBIA, it aims to foster a "protected commons" for scientific information and technology. Tools and techniques are shared, and can be improved and repackaged, just like in open source software.

Floating Point Errors and Computational Models

A potentially useful and instructive article on the perils of using floating point numerical representations in multi-agent systems.

Followup: Lifewave Energy Patch

No, I'm not being sued, but there is a discussion of the "technology" of the Lifewave Patch on Yahoo! Groups.

Inferring Network Mechanisms: Protein Interactions in Fruitflies

Interesting article in PNAS, looking at the classification of protein interaction networks in fruitflies.

Open Access to Research

Stevan Harnad at the University of Southampton is one of the champions of the open access movement; the idea that full and free access to (often) publically-funded research should be available to all. The momentum behind this concept is growing, and Harnad has been meeting with representatives of the publishing industry in order to thrash out a mutually agreeable strategy. I wish him the best of luck in this endeavour.

Followup: A personal perspective on the UK governmental response to the Royal Society report

Richard Jones was at the press conference to announce the UK government's response to last year's Royal Society report on nanotechnology (see yesterday's post). Howard Lovy's NanoBot is hosting Richard's personal take on the proceedings and his thoughts on the official response.

Treading water?

The UK government seems to have adopted a holding position in terms of its stance on nanotechnology - see this story for news on its response to last year's Royal Society report.

If Smallpox strikes Portland...

Popular article from Scientific American on the use of multi-agent simulations and analysis of social networks to predict the spread of pathogens.

Nano-hucksterism

Announcing the the Lifewave Energy Patch, a "a new and innovative approach to performance enhancement allowing organic materials to interact with the human body to increase stamina, performance and energy."

I think that tells you all you need to know; yet another attempt to use "nanotechnology" to sell snake oil. There are so many things wrong with this advert that it's difficult to know where to begin, but please bear with me while I present a few choice quotes from the website:

Non-Transdermal - New nanotechnology patch; Nothing enters the body. So, presumably, wrapping myself in clingfilm will bring about the same benefits (apologies for the image...)

Nanotechnology is described as "Manufactured products that are made from atoms. The properties of those products depend on how those atoms are arranged. If we rearrange the atoms in coal we can make diamonds. If we rearrange the atoms in sand we can make computer chips. If we rearrange the atoms in dirt, water and air we can make potatoes." It's that easy!

Increase muscle mass by "turning off" a regulatory protein known as myostatin. Gene therapy can learn a lot from this simple patch.

I could go on, but who am I to judge the scientific credentials of Ron Coleman, "7x Winner of Mr Olympia"?

Science and Industry

I was irritated by this article, in which industry leaders urge British Universities to spend more time considering the practical applications of the research they produce. This call seems to be trotted out on an annual basis, in a time when funding for "blue sky" research is ever dwindling. Indeed, even when money is set aside (say, by the Research Councils) for ambitious, long to medium-term proposals that may never lead to tangible "product", the message that pure research should be supported doesn't seem to have filtered down to referees. In this article, Stephen Rose outlines what he thinks are the core reasons for the perceived decline of British science.

Book Review: Soft Machines

Soft Machines: Nanotechnology and Life
By Richard A.L. Jones, Oxford University Press, ISBN 0 19 852855 (2004)

Book website

In this book, Richard Jones, a Professor of Physics at the University of Sheffield, addresses the fundamental question: should nanotech aim to take "traditional" engineering principles down to the nanoscale (crudely, to build ever smaller cogs), or should it draw inspiration from nature?

The book opens with several chapters of introductory material, explaining the background to nanotech and the motivation behind it. I was particularly interested in Chapter 7 - Wetware, as coverage of the nanotechnological aspects of living systems are often overlooked in similar texts. Jones makes some interesting observations about bacteria and chemical computing that I would have liked to have seen developed further.

Jones concludes that the "top down" Drexlerian view of nanotechnology is less likely to succeed than the "bottom up" approach of bionanotechnology, whilst at the same time acknowledging the potential risks and public concerns of using modified bacteria as devices or substrates.

Overall, Jones makes his points well in a book that is written in a style somewhere between a popular science book and an introductory textbook. It is both wide-ranging and accessible, although I would have preferred to have seen a rather more extensive bibliography. I would recommend this book to anyone interested in the broader aspects of nanotechnology; it is certainly a welcome addition to my library.

New Position

My contract here will expire at the end of July (due to the ongoing job cuts occurring within the University which, contrary to news reports, have implications far beyond the simple removal of Chemistry and Music). I am therefore investigating new possibilities in terms of lectureships or assistant professorships. Any new leads would be much appreciated - my CV/resume is available on request, or please check my home page for further details of my work.

"Intelligent design" in the classroom

A well-reasoned contribution to the ongoing debate on whether or not to teach "intelligent design" (ie. creationism) in the classroom alongside the theory of natural selection.

Nanotube scaffolding and bacteria

A taster article from the New Scientist this week, describing work on using nanotubes as "linkers" to cause cells to self-organise into "clumps". Potential applications include filtering E. coli out of drinking water.

The full article on which the piece was based is available here.

Followup: Profiles in Science

Following on from my post relating to Francis Crick's doodle of the double helix, the National Library of Medicine has made available their Profiles in Science site, containing fascinating archive material from prominent scientists such as Crick, Linus Pauling and Barbara McClintock.

Caught in the nanotech crossfire

Richard Jones and I have inadvertently been caught up in a rather unfortunate (and hopefully short-lived) spat. This initial post on TNTlog briefly reviewed our blogs, pointing out that we are both "real scientists" and celebrating the fact that we are "bailing out of our ivory towers". While there may be "no such thing as bad publicity", it quickly attracted a scathing response on Howard Lovy's NanoBot. Richard quickly stepped in to defuse the situation in admirable fashion, so I'll refrain from commenting further.

Protocell and other thoughts

I'm pleased to note that the traffic from Richard Jones' blog is already beginning to generate comments. One of those asked the following:

He implied that you might be keeping us up to date on the
Protocell project. Is that true, or will it pretty much happen through your general coverage of bio-computing?

I'll certainly be keeping a close eye on this project, and its partner PACE project (see below). Regular updates on both will appear here.

Also,

I had always thought that practical bio-computing would require some kind of lab-on-a-chip capability where you have a bunch of microfluidic pumps and sensors that maintain individual cells in their own little wells or something like that. Do you think that sort of thing is important for bio-computing and if so, how far off is that kind of capability?

Microfluidics are certainly interesting (indeed, John McCaskill, head of PACE, has done a lot of work on using these systems to implement DNA-based algorithms.) However, I'm not sure how applicable they will be to in vivo computation. Certainly, immobilisation or control of cellular positioning may be important in applications such as biosensing, but I think that the future of this may be in the integration of living cells with micro- or nano-scale systems such as the array of
carbon nanofibres developed by Mike Simpson's group at Oak Ridge National Laboratory. See the book Cellular Computing (below) for a couple of chapters on this work, or go directly to Mike's lab web page.

Nanotechnology blog

Even though Richard Jones beat me to "Soft Machines" ;), I highly recommend his excellent nanotechnology weblog. It seems that Richard and I share a common perspective on the future of (bio)nanotechnology.

New journal: Molecular Systems Biology

This new journal, published by the Nature Publishing Group and EMBO, includes computational, mathematical, theoretical and synthetic biology within its areas of interest.

HIV vs. cancer

News article on using a modified form of HIV to target cancer cells.

Nature/nurture?

The nature/nurture debate takes an amusing new twist...

Crick's first impressions

Francis Crick's first sketch of his vision of the DNA double-helix has been released onto the web (lots of nice links via this BBC page).

Happy Darwin Day!

Celebrating science and humanity as we move towards the 200th anniversary of the birth of Charles Darwin (Feb. 12 2009).

Kitchen DNA extraction

A very nice tutorial from the University of Utah Genetic Science Learning Center on how to extract DNA from "anything living" (I'm not sure that's exactly what they mean...) using only a blender, household detergent, pineapple juice and rubbing alcohol.

Minimal cell project

Another short news article from Nature on the efforts to construct a minimal cell from scratch.

"Sex and the single robot"

A rather disappointing example of hype over content in The Guardian this week; in this article, Kim Jong-Hwan claims that his new robot constitutes "the origin of an artificial species". As far as I can tell from the sparse detail in the article, it's nothing more than a robot with a genetic algorithm controller. The spurious reference to I, Robot doesn't help, either.

Life from scratch

There was a very interesting article in this week's New Scientist, discussing attempts to create entirely new and artificial forms of life from the "bottom up". One of the projects mentioned from the European point of view is the Programmable Artificial Cell Evolution (PACE) initiative, headed by John McCaskill.

Book: Cellular Computing

Cellular Computing, edited by Martyn Amos
Lead volume in the Systems Biology Series, Oxford University Press USA
Published August 2004, ISBN 0195155394.

The completion of the first draft of the human genome has led to an explosion of interest in genetics and molecular biology. The view of the genome as a network of interacting computational components is well-established, but researchers are now trying to reverse the analogy, by using living organisms to construct logic circuits. The potential applications for such technologies is huge, ranging from bio-sensors, through industrial applications to drug delivery and diagnostics. This book is the first to deal with the implementation of this technology, describing several working experimental demonstrations using cells as components of logic circuits, building toward computers incorporating biological components in their functioning.

Book website.

OK, so the book's been out for six months, but I've only just set up this blog, so I thought I'd give it a mention.

Invited talks

Two dates for the diary: I'll be giving invited lectures at the following events:

BCTCS 2005, the British Colloquium for Theoretical Computer Science, in Nottingham, UK (March 22-24)

Annual Conference on Modelling and Simulation of Biological Processes in the Context of Genomics, Montpellier, France (April 4-8).

Welcome!

Welcome to my blog, which I hope you'll find of interest. I'll try to post daily, with links to articles and news that I think are of interest. My own work is available via my home page (see full profile to right); at the moment I'm just finishing off the index for a manuscript for Springer (Theoretical and Experimental DNA Computation), as well as a popular science book for Atlantic Books. I'll keep you posted on both.