Edinburgh Science Festival

Just a quick reminder that I'll be appearing at the Edinburgh Science Festival next Sunday (April 15th). Full details of my event (including how to reserve tickets) are here, and I'm told that there will be a book signing afterwards.

An apt observation

Jonathan Hodgkin, a Professor of Biochemistry at the University of Oxford, has published a nice essay in the March 28 edition of the Times Literary Supplement. It's built around a review of both Genesis Machines and Robert Frenay's recent book, Pulse (which I haven't yet had the chance to read, but which has a very nice website). This is the second occasion on which the two have been jointly reviewed (the first being Matt Ridley's examination here).

Anyway, I'm happy with Hodgkin's overall assessment of my own book, and he makes some fair points concerning gaps in topical coverage. I specifically avoided dealing in detail with quantum computing (although, to be fair, I did mention it), as I didn't want the book to turn into a detailed "quantum vs DNA" debate (and I'm not sure I have the expertise to do justice to the quantum "camp" anyway). It's understandable, though, that as a chemist Hodgkin should highlight the omission of aptamer development.

Aptamers are synthetic molecules that can fold up into very detailed three-dimensional shapes, thus binding to other molecules with incredible specificity. They can therefore be used to target other molecules in the same way as antibodies, and offer a wide range of applications in biotechnology and medicine. Because the possible space of three-dimensional shapes a molecule can adopt is potentially vast, researchers must use a smart approach to finding aptamers, as opposed to a "hit-and-hope" policy. The technique that has been developed, the name of which is abbreviated to SELEX,
uses an evolutionary approach based on an initial molecular population. Interestingly, it may be thought of (rather loosely) as a "wet" version of the genetic algorithm.

One possible hook that I could perhaps have made more of is the fact that Andrew Ellington, one of the founders of aptamer development, was one of the main researchers involved in recently building a bacterial camera (which did merit a mention in the book!)

"From Rive Gauche to Rochdale..."

...was Justine's remark yesterday, as we drove home through that northern town after a wonderful week in Paris. We visited Dennis Shasha and his family, as he's there on sabbatical from New York University and kindly invited us over. Justine and Alice took in the sights while Dennis and I got down to some work.

We stayed in a marvellous little hotel, just around the corner from the Eglise Saint-Sulpice (which featured as a central location in The Da Vinci Code).

Wednesday was spent walking and talking with Dennis, bouncing around ideas about biocomputing. His wife, Karen, kindly took time out to show Justine and Alice around the Jardin du Luxembourg. Thursday was spend working while Justine wandered up to the Louvre, before we had dinner with the Shashas. We wrapped up on Friday morning, then Justine and I took some time out to revisit Monmartre, where we honeymooned three years ago.

It was a pleasure to spend time with Dennis and his family; both he and his wife are prodigiously talented, Dennis as a scientist, writer and (as Alice was delighted to discover) juggler, and Karen as an artist (and cook!), and we much appreciated their hospitality. Dennis and I are currently working on the draft paper that emerged from our discussions, which will hopefully appear as a preprint in the next few weeks - watch this space.

The Times Higher recently commissioned an article from me, the subject being the recently announced cuts in UK research funding. They were particularly interested in the views of a "young academic", so I was delighted to see that the resulting piece was made the lead opinion article in today's edition. It's available on the THES website, but I'm reproducing it here with their kind permission. The headline (and accompanying cartoon) appear to have been derived from a rather throwaway remark I made in the final sentence.

Labour's infidelity will not be forgiven easily
Martyn Amos, Times Higher Education Supplement, March 22 2007, p. 12.

Ripples from the collapse of Rover two years ago are apparently lapping at the doors of UK university departments. The decision to dip into research funds was, according to the Department of Trade and Industry, to cover "exceptional" costs. The demise of the car firm was a one-off budgetary burden that should be borne by all.

The image of an administration battling to save jobs in a region blighted by industrial decline is one the DTI is in no hurry to dispel. A closer inspection of the department's figures suggests the exercise was more about fiscal firefighting than industrial or social intervention. But behind the smokescreen of short-term financial juggling lie deeper concerns about fundamental breaches of trust.

Senior academics and industry leaders reacted with dismay to the announcement that about £68 million of funding destined for science would instead be diverted back to the DTI to address these "historic and new" financial pressures. Although the Rover debacle was pushed to the front of the crowd of good causes, other recipients of recalled funds lurked in the background. Jokes about David Cameron's alleged drug use at school have recently filled the corridors of Whitehall, but, to the Government, Weeed is no joke. That's the Waste Electronic and Electrical Equipment Directive to the uninitiated, a European Union edict that requires companies to dispose of obsolete white goods on behalf of consumers. UK implementation of this directive has been put on hold twice, the delay necessitating an additional funding shot to the tune of £27 million - only a couple of million short of the £29 million taken back from the Engineering and Physical Sciences Research Council. Michael Kenward, a former editor of New Scientist magazine, has highlighted the irony of funding the cost of delays in implementing electrical recycling by taking money away from the very agency that has green technologies at the top of its research agenda.

Whatever lies behind the decision to cut research funding, as a relatively junior member of staff I am acutely aware of the impact that these changes may have on the rank and file. The short-term implications are that roughly 100 research council grants will no longer be funded. Many of these would have been supported in "responsive mode", a mechanism designed to offer maximum flexibility in terms of project size and scope. Younger scientists are particularly encouraged to apply within this framework, as are those proposing adventurous or multidisciplinary research - all of which are vital to the long-term development of healthy science and innovation. Since most grants run for between two and five years, the research councils are obliged to cover these future costs from a much diminished purse and must cut back on flexible, short-term activities. These include studentships and fellowships - precisely the mechanisms by which new researchers establish their groups and develop their careers. Long-term, risky research will be sacrificed for the purposes of short-term expediency.

Perhaps more significant, this decision represents a sea change in the relationship between Labour and the scientific community. For the first time since taking power, the Government has reneged on its promises about the funding of science. This had previously enjoyed protected status within the Office of Science and Engineering to encourage medium to long-term research that might extend beyond the lifetime of governments. The dismantling of this ring fence has sent out a signal to some that the DTI can choose to ignore Treasury rules on science funding whenever it sees fit.

Early portents of the cuts came soon after the resignation of Lord Sainsbury from his post of Science Minister, a long tenure that had been greeted with almost universal approval from the research community. According to one insider quoted in The Times Higher in the wake of the announcement of the cuts: "The fact that he has left has made this possible." The formal announcement came while his successor, Malcolm Wicks, was on a trip to an operation funded by the Natural Environment Research Council.

The Government will argue that the cuts amount to less than 1 per cent of the total science budget, and that funding levels will be restored or even improved in future. But, like a cheating partner, the administration must understand that the long-term damage wrought by their breach of trust cannot simply be undone by promises to behave better in future.

Passport hell

Dennis Shasha, academic, author and the series editor for my first book, has very kindly invited me over to Paris for a week to do some work. Of course, my wife and daughter were also invited, and we thought it would be a chance to introduce Alice to the city where her parents enjoyed their honeymoon (during the heatwave of 2003 - even less romantically, we thought it might also be a chance to get some rather messy but necessary work done on the house in our absence).

As is common in our household, various arrangements had been left until the last minute, the most significant one being passports for my wife and daughter. Luckily, one of the regional centres that deals with fast-track (ie. within two weeks) applications is just down the road in Liverpool, so I made an appointment to go over there today. Which is where the fun started.

The regulations concerning the acceptability of photographs for use on passports are fairly relaxed for children under five, but they still specify things like "no other person visible in the background". If you've ever tried to get a 12-month old to sit still, in a photo booth, looking in the vague direction of the camera, whilst remaining invisible yourself, then you'll know what we're up against. A couple of days ago, my wife had the following taken:


Which we thought would be fine. How little we knew. We dropped into our local Post Office on the way to Liverpool, just to double-check that the photo would be acceptable. "No", was the quick response, since Justine's arm is clearly visible in the background. Cue quick dash to Morrisons and frantic changing of notes into pound coins.


Our first effort wasn't too bad, in a moody, My Bloody Valentine album cover sort of way. But nowhere near good enough to satisfy the sticklers at the passport agency. So we tried again.












Away with the fairies. So we tried again.


















Too blurred, face in the wrong part of the shot, looking down. By this point, we'd burned through 12 quid, I'd lost all feeling in my legs from kneeling on the floor of the photo booth, and we were in severe danger of missing our pre-booked appointment. So we decided to just get there and then worry about it.

Sure enough, the lovely (and I don't mean that sarcastically, they really were lovely, accomodating and helpful) people in Liverpool told us that none of the photos would be acceptable, but they had their own photo booth for just such an eventuality. They also passed on some wisdom on how to control toddlers whilst remaining invisible, thus sticking to the rules. Which is how we came to get this (acceptable!) shot:


If you look closely, you can see that Alice is actually sitting on my lap. That's me, in the background. Wearing a white T-shirt over my head.

Festival time

I feel honoured and delighted to have been asked to contribute to two of the Edinburgh Festivals this year. The programme for the International Science Festival was published today, and features (amongst many others) Marcus du Sautoy, Marcus Chown, Kirsty Wark, Colin Blakemore, Steve Jones and Heinz Wolff. Richard Jones (who blogs here) and I have been scheduled in the Cutting Edge subgroup of the Big Ideas event. The Festival runs from April 2-15, and it promises to be a lot of fun (as well as informative, of course!)

I'll also be appearing at the Edinburgh International Book Festival which takes place between August 11-27. Last year's event (featuring three Nobel Laureates) attracted over 220,000 visitors, and it's now the "world's largest celebration of the written word". The programme for this event will be published on June 14.

Protect and survive

Those of us old enough to remember Protect and Survive (or its US equivalent, Duck and Cover) will appreciate the humour of Safe Now, which provides alternative interpretations of public information graphics.



The middle of a terrorist attack is not an appropriate time to catch up on your reading or paperwork.

"Dr" Gillian McKeith

Today's Guardian contains a wonderfully detailed demolition of "Dr" Gillian McKeith, Channel 4's very own "clinical nutritionist". Many people have accused her of quackery and charlatanism in the past, often resulting in threats of legal action (as opposed to a reasoned scientific response).

Her claims to hold a Ph.D. certainly seem quite laughable.

Paperback edition

Just a short note that the paperback edition of Genesis Machines is now available for pre-ordering on Amazon. It's out on June 14.

I spent the end of last week at a BBSRC workshop on synthetic biology, and will post a report later this week.

Another radio interview

Just a quick note that I'm this week's guest on This Week In Science, a radio show run out of the University of California Davis, and which boasts listeners in over 60 countries. You can either listen online tomorrow at 17:30 (UK) via the website, or download the show later as a podcast.

New stuff

Two new publications to report, both very different.

The first is a paper that's just been accepted by BioSystems, and is now available online. Two hybrid compaction algorithms for the layout optimisation problem was written with two colleagues in China, and deals with the problem of packing circular objects inside an "outer" containing circle. Many people will be familiar with this problem, which tries to minimise the size of the container, but our version is complicated by the fact that each object also has mass, and we must seek to minimise not only the radius of the container, but the net mass imbalance. This problem has real-world significance in areas such as aerospace and satellite design, where the circles represent pieces of equipment, and the body as a whole is rotating or moving. We have developed two algorithms, both inspired by nature, which produce the best known results for this problem.

The other piece of writing this month is my first (and quite possibly last) appearance in a men's style magazine (Esquire). As part of their "Hot List 2007", I was asked to write a short piece on "The New Software is...", and chose "Wetware". I'm on page 92 of the February issue, sharing space with George Monbiot.

The next generation

I spent the end of last week and the start of the weekend drifting in and out of the Systems Biology, Bioinformatics and Synthetic Biology conference BioSysBio, which was hosted by the University of Manchester. The event is aimed at post-graduates, post-docs and "young faculty" (I wasn't sure if I qualified for this last descriptor, but they took my money!), and there was certainly a youthful exuberance about the the proceedings. Teaching and family commitments meant that I wasn't able to attend as many sessions as I would have liked, although I was able to make both sessions dedicated to synthetic biology.

The first of these was opened by Randy Rettberg, director of the International Genetically Engineered Machines (iGem) programme. Rettberg had a long and distinguished career as a computer engineer (including serving as the chief technical officer of Sun Microsystems) before turning his attention to biology and dividing his time between iGEM and looking after MIT's Registry of Standard Biological Parts, the community's attempt to do for synthetic biology what the Maplin Catalogue did for electronics.

There then followed three talks by UK-based teams who took part in the most recent iGEM. The Imperial College team described their novel approach to building a cell-based oscillator (a device that gives a signal that goes "up" and "down" on a regular basis). Rather than building their oscillator inside a single cell, as others have done, the Imperial team decided to try to model classical "predator-prey" dynamics, where the population of prey (eg. rabbits) rises and falls slightly out of step with the rise and fall in the number of predators (eg. foxes). The students decided to engineer two populations of bacteria, each generating molecules that would cause the net signal between the two to rise and fall periodically. Although they've yet to get it all working together, it's a novel approach to the problem, and their simulations and early experimental characterisations seem to suggest that they're well on the road to success.

Another talk was given by a team from Cambridge, who were investigating a subject close to my own heart; self-organisation and pattern formation in bacteria. They've harnessed the ability of bacteria to "swim" combined with an engineered position-dependent genetic "switch" to generate spatial patterns from the "bottom up". The ability to be able to control this process may have significant implications on tissue engineering and bio-medicine, as we'll see shortly.

For me, the most inspiring student presentation was given by the group from Edinburgh, about whom I've written briefly in my book. Arsenic contamination in drinking water is a problem that affects tens of millions worldwide, and is particularly acute in Bangladesh. Existing methods for testing samples are expensive and require technical training, so the Edinburgh team have developed a cell-based detection kit that can detect concentrations below the WHO safety threshold, and which produces a simple "yes-no" response that a non-specialist can understand. Their eventual objective is to be in a position to package and sell the kits for around $1 a pop, which will make sustained testing possible for villagers. A fantastic technical achievement as well as an extremely worthy cause.

I felt slightly humbled by the experience of watching these students in action; remember, most of them were undergraduates (albeit the best of the best) when this work was carried out, and yet they were doing work that, only a few years ago, would be considered the absolute state of the art, and attracting Science and Nature papers (although I can't see any reason why the current work should not do the same). If any of them choose to pursue a career in this field (and I sincerely hope that they do) then they have an excellent future ahead of them.

The final plenary was given by my colleague Ron Weiss of Princeton, who is one of the leading figures in synthetic biology (and, again, who features prominently in the final chapter of my book). Ron has been at the forefront of cellular re-engineering for some years now, and has consistently produced first-rate work. Ron is also interested in pattern formation in nature, and his recent work focuses on programming the way that stem cells talk to other cells, in the hope of one day being able to control the way that they "specialise" and form tissue structures. Although it's still very early days, I think this work has the potential to be massively significant.

A good way to start the year

A (belated) Happy New Year to you!

I haven't, up until now, flagged reviews of Genesis Machines on the blog (partly because I assume that most people who come to it have arrived via the link in the book). However, I was delighted by this review in last Saturday's Guardian; apart from saying nice things about the book, its author, Steven Poole (who wrote Unspeak) appears to share my views on Melanie Phillips of the Daily Mail.

A minor point: Poole ends his review by saying that "It is even possible that, when the footnote numbering goes crazy on pages 199-201, it is some sort of joke about genetic mutation. Sadly, I was not able to find meaning in the resulting number series." He assumes that footnote numbers refer only to the first citation of a source; in the example he gives, I cited a report at the start of the chapter, and then again near the end. In both instances I supplied the reference number ("3"), which is why it might have appeared to be out of sequence later on.

Going back to my roots

I'll be returning to my home city of Newcastle-Upon-Tyne next Wednesday (December 6th) to take part in an event organised by The Great Debate. I'll be discussing the topic of Reprogramming Life with Prof. John Burn of the Institute of Human Genetics and Caspar Hewett, the organiser of TGD. Audience participation is welcomed (and, indeed, necessary) at such events, so please come down and take part (if you need an extra incentive, Toby Mundy, my publisher at Atlantic, has very kindly stumped up some cash for a drinks reception afterwards!)

The event starts at 7pm, and further details are available here.

I am a commodity

I only just found out that, as of February last year, this blog's been listed on BlogShares, the "fantasy blog stock market". You can keep track of performance here; I'm not sure what I've been doing to raise the valuation (I think it's mainly to do with incoming links), and it only seems to take notice of blogspot pages, but it's an interesting idea nonetheless. I guess it's a natural extension of the Google pagerank algorithm, where pages with a relatively high number of incoming links are considered to be more authoritative.

On the shelf

I finally feel like a proper author after seeing my book nestling on the shelf of the Manchester Deansgate branch of Waterstone's, near to Isaac Asimov's classic New Guide to Science.

I did look a bit mental taking pictures of the shelf with my camera phone, but there you go...

The New Scientist looks forward

The magazine New Scientist recently celebrated its 50th Anniversary. While some might question its scientific rigour, there's no doubt that it generally does a decent job of bringing science to the public in an accessible fashion, whilst also flagging up to professional scientists the occasional article that might otherwise have gone unseen.

In the most recent issue, the editors asked a collection of the "smartest brains on the planet" to predict the most significant scientific advance of the next 50 years. While some are understandably reluctant
to set themselves up for a fall, most play along with the game.

It's interesting to note how many of the predictions seem to come at the intersection of information/computer science and biology. Lewis Wolpert talks of "computable embryos", Erik Horvitz gives a wide-ranging description of computation as the "fire in our modern-day caves", Paul Nurse anticipates an understanding of the cell as a "chemical and computational machine", Jaron Lanier argues for a restructuring of computer architecture(s) along "bio-mimetic" principles, while Peter Atkins believes that computer technology will allow us to observe and eventually control natural processes to construct "synthetic life".

THES article from last week

The Times Higher Education Supplement published a feature article of mine last week. As we're on a new edition as of today, I can reproduce it below.

If you wish to cite it, please do so as follows (my suggested title was "Synthetic Biology: Where Top-Down Meets Bottom-Up"...):

Martyn Amos, A chip off Mother Nature's own hard-drive, Times Higher Education Supplement, November 9, 2006, pp. 16-17.

---

Possibly the most unusual reviewing assignment I have ever accepted came in 2002, when Guinness World Records asked me to help validate a claim made by a group of Israeli scientists to have built the "world's smallest computer". What made this machine radically different was not just its incredibly miniaturised state but its basic construction material. Rather than piecing together transistors on a silicon surface, Ehud Shapiro and his team at the Weizmann Institute had fabricated their device out of the very stuff of life itself - DNA.

Three trillion copies of their machine could fit into a single tear drop. This miracle of miniaturisation was achieved not through traditional technology but through a breakthrough in the emerging field of molecular computing. The team used strands of DNA to fuel these nanomachines, their latent energy freed by enzymatic "spark plugs". These were not computers in any traditional sense. Their computational capabilities were rudimentary and, rather than using the familiar zeroes and ones of binary code, their "software" was written in the vocabulary of the genes - strings of As, Gs, Cs and Ts.

One of the main motivations for shrinking traditional computer chips is to extract the maximum amount of computational power from a limited space. By placing ever smaller features on the silicon real estate of modern processors, chip-makers such as Intel continually try to keep in step with Moore's Law - the famous observation that computer power roughly doubles every 18 months.

Shapiro's computer was never going to win any prizes for mathematical muscle. All it could do was analyse a sequence of letters and determine whether or not it contained an even number of a specific character. Nevertheless, it represented the state of the art in a scientific field that had been in practical existence for less than a decade. In 1994, Len Adleman (previously better known as one of the co-inventors of the main Internet encryption scheme, and the man who gave a name to what we now know as computer viruses) stunned the computing world by demonstrating the feasibility of performing computations using molecules of DNA.

Rather than representing information as electronic bits inside a silicon chip, Adleman showed how to solve a problem using data encoded as sequences of bases on DNA molecules. One of his motivations lay in the storage capacity of DNA; nature has data compression down to a fine art. Every living cell in your body contains a copy of your unique 3Gb genome, the data equivalent of 200 copies of the Manhattan telephone directory. Adleman wanted to use the nature of chemical reactions to perform massively parallel computations on this molecular memory.

Each tube could contain trillions of individual DNA strands, and each molecule could encode a possible answer to a particular problem. The idea was to exploit the fact that enzymes and other biological tools act on every strand in a tube at the same time, quickly weeding out bad solutions and giving the potential for parallel processing on a previously unimagined scale.

Adleman's initial paper led to the emergence of a fully fledged field. A rash of papers appeared, describing proposals to use DNA to crack government encryption schemes or build real, "wet" memories more capacious than the human brain. After this flurry of untamed optimism - when some seriously thought that molecular machines could give traditional computers a run for their money - DNA computing matured into a more thoughtful discipline. Scientists no longer talk seriously about taking on silicon machines and are instead seeking out niche markets for their molecular machines, areas such as medical diagnostics and drug delivery, where traditional devices and methods are too large, invasive or prone to error.

Shapiro's simple computer was one example of such an application; a small step towards eventual "on-site" diagnosis and treatment of diseases such as cancer. A later version of his machine was capable (in a test tube, at least) of identifying the molecules that signal the presence of prostate cancer and then releasing a therapeutic molecule to kill the malevolent cells. Shapiro and his team have spoken about their aim of creating a "doctor in a cell", a reprogrammed human cell that could roam around the body, sniffing out and destroying disease. As physicist Richard Jones explains in his book Soft Machines, the Fantastic Voyage scenario of humans in a miniaturised submarine is "quite preposterous", but that doesn't rule out serious work into trying to engineer existing living systems to act as "medibots" able to detect and control disease at its source.

A growing band of experts is slowly coming together to form a whole new vanguard at the frontiers of science, where boundaries between biology, chemistry, engineering and computing become fluid and ever-changing. This is the new world of synthetic biology. "We want to do for biology what Intel does for electronics," states George Church, professor of genetics at Harvard University. The Massachusetts Institute of Technology's Tom Knight is even more blunt: "Biology is the nanotechnology that works."

DNA is so much more than an incredibly compact data storage medium. As physicist Richard Feynman explained: "Biology is not simply writing information; it is doing something about it." Floating inside its natural environment - the cell - DNA carries meaning, used to generate signals, make decisions, switch things on and off, like a program that controls its own execution. DNA, and the cellular machinery that operates on it, is the original reprogrammable computer, pre-dating our efforts by billions of years. By re-engineering the code of life, we may finally be able to take full advantage of the biological "wetware" that has evolved over millennia. We are dismantling living organisms and rebuilding them - this time according to a pre-planned design. It is the ultimate scrap-heap challenge.

As pioneers such as Alan Turing and John von Neumann discovered, there are direct parallels between the operation of computers and the gurglings of living "stuff" - molecules and cells. Of course, the operation of organic, bio-logic is more noisy, messy and complex than the relatively clear-cut execution of computer instructions. But rather than shying away from the complexity of living systems, a new generation of synthetic biologists is seeking to harness the diversity of behaviour that nature offers, rather than trying to control or eliminate it. By building devices that use this richness of behaviour at their very core, we are ushering in a new era in terms of practical devices and applications and of how we view the very notion of computation and of life itself.

The questions that drive this research include the following: Does nature "compute" and, if so, how? What does it mean to say that a bacterium is "computing"? Can we rewrite the genetic programs of living cells to make them do our bidding? How can mankind benefit from this potentially revolutionary new technology? What are the dangers? Could building computers with living components put us at risk from our own creations? What are the ethical implications of tinkering with nature's circuits? How do we (indeed, should we) reprogramme the logic of life?

The dominant science of the new millennium may well prove to be at the intersection of biology and computing. As biologist Roger Brent argues: "I think that synthetic biology will be as important to the 21st century as [the] ability to manipulate bits was to the 20th." This isn't tinkering around the edges, it's blue-skies research - the sort of high-risk work that could change the world or crash and burn. I took a huge risk in the 1990s when I gambled on DNA computing as the topic of my PhD research - a field with a literature base, at the time, of a single article.

It is exhilarating stuff, and it has the potential to change forever our definition of a "computer". But most researchers are wary of promising too much, preferring to combine quiet optimism with grounded realism. As researcher Drew Endy explains: "It'll be cool if we can pull it off. We might fail completely. But at least we're trying."

Last night

Thank you to everyone who helped make last night's book launch an extremely enjoyable event. I must especially thank my fellow panellists, Oliver Morton, Stephen Emmott, and Johnjoe McFadden, my publicist Annabel Huxley for arranging it in the first place, and the ICA and Royal Institution for hosting it. Thanks also to my publisher, Toby Mundy, at Atlantic Books.

(This is beginning to sound like a speech at the Oscars...)

Most of all, though, thank you to the 100+ people who turned up to find out more about the strange and exciting new world of the Genesis Machines - at 18:45 I was worried that the guest list would outnumber the paying attendees, but it was standing room only by 19:00. I hope you enjoyed it as much as we did.

Another radio appearance

I'm delighted to say that I've been invited, along with Richard Jones (who blogs here), to appear on BBC Radio 4's well-respected science show The Material World. We'll be on between 16:30 and 17:00 this Thursday (Nov. 16th), talking about biological computing and nanotechnology. Join us by tuning in on either 92-95FM or 198LW, or by listening online at the programme website.

Sunday Times article

Steve Farrar interviewed me last week while I was in London, resulting in this feature article in today's Sunday Times.

Radio appearance

Advance notice for anyone who might be interested: I've been pencilled in to appear on Simon Mayo's afternoon radio show on BBC Radio Five Live. The date is next Thursday (Nov. 9), and I'll be on between 14:00 and 14:45 (with breaks for news and sport updates, thankfully!) to talk about the book.

You can tune in on MW909 or 693, or listen online via the Daily Mayo programme website.

Gulp.

Notes for Genesis Machines

I've put the bibliography and notes for Genesis Machines online here. The idea is that this page will serve as a useful resource for readers of the book, but it will also give prospective readers a flavour of what's contained within.

Jonoska review

Further to my post a few days ago, Natasha Jonoska has very kindly agreed to my hosting a copy of the full review of my book Theoretical and Experimental DNA Computation.

As I already mentioned, the review serves as an excellent historical review of the early days of DNA computation, and I'm grateful to Natasha for allowing me to make it available.

Ghosts and Goblins

With Hallowe'en fast approaching, I thought it appropriate to point my readers towards this preprint. The authors "examine certain features of popular myths regarding ghosts, vampires and zombies as they appear in film and folklore" and "use physics to illuminate inconsistencies associated with these myths and to give practical explanation to certain aspects".

Review of my second book

Natasha Jonoska has reviewed my second book, Theoretical and Experimental DNA Computation, in the latest issue of Genetic Programming and Evolvable Machines.

Update: I've been informed that a subscription is required to read the full review, and am still waiting for permission to host a copy. A short excerpt is quoted on the book's web page; the full review is generally of the same tone, but is very in-depth, and serves as a nice history of DNA computing in its own right. Watch this space.

Molecular tic-tac-toe

I was asked yesterday by the New Scientist to comment on a recent paper describing a molecular automaton to play tic-tac-toe (noughts and crosses). My remarks appear in the resulting news article (I'm not sure if it will make it into the printed edition). Readers familiar with the area will know that this work builds on earlier work on a molecular machine, built by a subset of the group responsible for this latest construction.

Degrees of separation

I like to keep a log of how many people visit this blog, along with information on whether or not they are return visitors, and so on (this is purely for my own use, and all logs are anonymous). It's also interesting to see which sites led visitors to my own, the main two being Richard Jones' Soft Machines and Doug Natelson's nanoscale views.

It's also possible to see the search engine keyword combinations that led visitors to my blog, and this is where the data throw up...wierd stuff. The top few combinations are completely understandable:

17.39% erich kofmel
13.04% martyn amos
8.70% dreamlines

The first refers to my recent post on Erich Kofmel and his shenanigans, the second - obviously - is me, and the third keyword refers to a post I made ages ago on Dreamlines, a nice little image generation website.

However, further down the list we find the following:

4.35% daughter vs mother armwrestling

How?!

Thankfully, the Google pointer originates from a "spam comment" on an earlier post, and not from anything that I posted myself...

Forthcoming events

Once again, apologies for the recent lack of updates. Start of term, and all...

I'll be taking part in a bunch of events to promote my forthcoming book, two of which are now fully confirmed (both titled Genesis Machines: Engineering Life:

November 14, 2006:
Book launch and panel discussion at the ICA, London, in association with the Royal Institution. Martyn Amos, Stephen Emmott, Oliver Morton and Vivienne Parry. Time: 7pm-8.30pm (event details).

December 6, 2006: Panel session organised by the Great Debate, Newcastle-upon-Tyne. Time: 7pm (event details).

I'll post details of other events as and when they're confirmed.

New think tank with an interesting back story

Readers who work in the UK education system may have heard the recent news that Ph.D. students at the University of Sussex have formed a "break away" research centre of their own, named the Sussex Centre for the Individual and Society.

When I first heard of this, I was immediately reminded of Margaret Thatcher's famous saying that "There's no such thing as society, there are individual men and women, and there are families". Sure enough, one of the founders of the Centre, Erich Kofmel, is a self-confessed right wing activist. Of course, they're entitled to their views, and I would never dream of using this blog to espouse a purely political agenda.

However, things get a little more interesting when one performs a Google search for "Erich Kofmel". He appears to have been accused by the Evening Standard (and, later, the Observer) of being a rogue landlord who took advantage of vulnerable overseas students.

I happen to agree with him that UK education is woefully underfunded, but I do think that it's rather rich to complain about it whilst (allegedly) ripping off fellow students.

"Here, hare here"

I'm all for describing things in terms that most people can grasp. For example, in my forthcoming book I make the point that if a transistor (the fundamental building block of computer processor chips) were the size of a (UK) postage stamp, then ten years ago, the average chip would be the size of Snowdonia National Park in Wales. With the advances in chip miniaturisation that we have seen in the last decade, the same chip in 2005 would be the size of Iceland.

Readers of the New Scientist will be aware of an ongoing discussion of the use of Wales as a metric (hence my tongue-in-cheek reference in the book). However, I'd like to draw your attention to a far more insidious comparator: the human hair.

There seems to be an unwritten rule of science journalism: any article dealing with micro- or nano-scale technology must, at some point, compare the scientific breakthrough in question with a human hair. Some recent examples are here, here, here, and hair.

I'm not questioning the quality of the science, or even that of the writing, I'm just sick of seeing constant references to hair in popular science articles (maybe because I'm losing mine!)

Japanese edition

Readers in Japan will be able to pick up Genesis Machines at some point, as the Japanese language rights have been acquired by Nikkei BP. I'll post more when I know the regional publication date (of course, I realise that if you're reading this you may have no need of a Japanese language edition, but I just thought I would mention it).

Genesis Machines publication event

Firstly, apologies for the lack of recent updates - we've been busy moving house.

We've arranged an event in London to coincide with the publication of Genesis Machines. This will take the form of a panel discussion at the Institute of Contemporary Arts (ICA), and is being organised in association with the Royal Institution.

I'm delighted to say that our publicist, Annabel Huxley, has succeeded in attracting a world-class line-up (and me!). The panel will comprise:

• Professor Stephen Emmott, Director of the External Research Office at Microsoft Research, Cambridge
  
• Oliver Morton, news editor at Nature and author of Mapping Mars
  
• Myself
  

The event will be chaired by the scientist, writer and broadcaster Vivienne Parry, whose previous work includes presenting Tomorrow's World and the Aventis Prize-shortlisted book The Truth About Hormones.

It promises to be an enjoyable evening, hopefully informative and perhaps even a little provocative. Full details are below, and I'll look forward to maybe meeting you there.

Genesis machines: engineering life

Tuesday 14 November 7.00pm

Panel: Dr Martyn Amos, Prof. Stephen Emmott, Oliver Morton and Vivienne Parry.

Venue: ICA, The Mall, London SW1Y 5AH
Tickets cost £10, £9 concessions and £8 RI Members. Call 020 79303647 or visit www.ica.org.uk to book tickets.

In association with the ICA, the Royal Institution and Allen Lane Publishers.

Genesis Machines - available for preordering

Genesis Machines is now available for preordering from Amazon (UK) here.

Korean rights

I'm delighted to report that Atlantic have accepted an offer for the Korean rights to Genesis Machines. The book will be published by Forest of Knowledge, a division of Nexus Press.

Stupidity and the War on Terror

A ridiculous story about a post office in the US that was shut down and visited by agents in hazmat suits, just because a woman reported receiving a letter from India.

I loved this comment in the ensuing Fark discussion thread:

Shortly after 9/11 I filed a police report for a guy who found a "suspicious white powder" in a textbook sent to him by the publisher. As it turns out the "suspicious white powder" is something commonly known as printer's dust. It's harmless.

I'm not sure why this guy thought McGraw-Hill was trying to kill him, but seeing as he works in the Math Department I'm sure he has plenty of enemies.

George Church and constructive biology

There's a nice article by George Church in the latest issue of The Edge.

Genesis Machines preview

As you may know, my popular science book Genesis Machines: The New Science of Biocomputing will be published by Atlantic Books on November 9. I've placed a short sampler excerpt on the book website. It's in PDF, so you'll need a suitable application, such as Adobe Reader.

Blog down-time

The blog will not be updated until after I have moved office to Manchester Met (on June 26). Please check back then for the latest news on the move, as well as other updates.

Synthetic biology - follow-up discussion

Apologies for the lack of recent posts - we've been househunting up north in preparation for my move to Manchester Met.

Anyway, I thought I would point you towards an interesting post on Soft Machines, Richard Jones' always-excellent blog. His most recent post concerns synthetic biology (see below), and a discussion thread has also developed.

Synthetic Biology review

(Subscription may be required).

Synthetic biology: new engineering rules for an emerging discipline

Ernesto Andrianantoandro, Subhayu Basu1, David K Karig and Ron Weiss

Molecular Systems Biology 2 doi:10.1038/msb4100073

Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.

Moving

I'm delighted to say that I am leaving Exeter to take up a Senior Lectureship in the Department of Computing and Mathematics at Manchester Metropolitan University.

I was very impressed with the vision and ambition shown at Departmental, Faculty and University level, and am very much looking forward to working there. I start there in mid-June, and new contact details will follow once they are confirmed.

Leonardo in Exeter

We took the little 'un to see the Leonardo da Vinci exhibition that's currently running in Exeter. The museum has done an admirable job in securing a loan of the sketches from the Royal collection, and I felt privileged to be able to examine them at such close quarters.

I was particularly taken with "A study of a woman's hands" (possibly for the portrait of Cecilia Gallerani), c.1490. Quite apart from its possible significance as a study for such a well-known piece, it contained, almost as a doodle, a lovely sketch of a grotesque head in its top left corner.

I also loved "A sheet of pictographs", drawn over an architectural plan, c.1490, also known as rebuses or cryptograms. A detailed description of this sheet is given in Charles Nicholl's biography Leonardo Da Vinci: The Flights of the Mind.

The Great Debate

While at a meeting in Manchester this week I had the pleasure of meeting Caspar Hewett of the University of Newcastle, who, in his spare time, runs an organisation called The Great Debate. To quote the website, "The Great Debate is an umbrella title for a series of courses, day schools, public discussions and workshops on topics including Darwinism, human nature, the human mind, consciousness, development, sustainabilty and environmental thought."

I was greatly impressed by Caspar's energy and commitment, and am glad to offer a link here with the strong recommendation that you visit, and even consider getting involved.

Science in the Docks, Art in the Stocks

In the middle of last month I gave the opening talk at an ESRC-sponsored art/science crossover event. There's now an online report of the event. I'm not sure that I was arguing for the use of synthetic biology to create works of art per se, simply that the applications I highlighted used biological systems as the medium, rather than simply as inspiration. Nontheless, the report gives a decent overview of the whole event, which was certainly well worth doing (despite chronic tiredness, my daughter having been born less than a week previously...)

Aventis Prize

Congratulations to fellow Atlantic Books author Vivienne Parry; her book The Truth About Hormones has been shortlisted for the 2006 Aventis Prize.

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."

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.

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:

• 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).

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.

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.

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.

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).

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."

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.

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....