Wednesday, November 29, 2006

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.

Monday, November 27, 2006

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.

Wednesday, November 22, 2006

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...

Tuesday, November 21, 2006

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".

Friday, November 17, 2006

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."

Wednesday, November 15, 2006

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.

Monday, November 13, 2006

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, November 12, 2006

Sunday Times article

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

Friday, November 03, 2006

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.


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.

Thursday, November 02, 2006

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.

Monday, October 30, 2006

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".

Friday, October 27, 2006

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.

Tuesday, October 17, 2006

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.

Monday, October 02, 2006

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


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

Friday, September 29, 2006

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.

Thursday, August 31, 2006

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.

Tuesday, August 29, 2006

"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!)

Monday, August 14, 2006

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).

Tuesday, August 08, 2006

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:

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 to book tickets.

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

Tuesday, July 18, 2006

Thursday, June 29, 2006

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.

Wednesday, June 28, 2006

George Church and constructive biology

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

Tuesday, June 27, 2006

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.

Monday, June 19, 2006

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.

Thursday, June 01, 2006

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.

Thursday, May 18, 2006

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.

Monday, May 15, 2006


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.

Tuesday, May 09, 2006

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.

Friday, May 05, 2006

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.

Tuesday, April 25, 2006

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...)

Thursday, April 13, 2006

Aventis Prize

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


"Sitting in a culture dish, a layer of chicken heart cells beats in synchrony. But this muscle layer was not sliced from an intact heart, nor even grown laboriously in the lab. Instead, it was "printed", using a technology that could be the future of tissue engineering."

Thursday, March 30, 2006

Authorities approve Airbus result

The EASA and the FAA have both formally approved the result of Sunday's Airbus A380 evacuation trial, and the aircraft is now certificated to carry up to 853 passengers.

Wednesday, March 29, 2006

Nature Imitation Methods - Theory and Practice (NIM 2006)

International Workshop Session at the ISDA 2006 - 6th IEEE International Conference on Intelligent System Design and Applications, Jinan, Shandong, China, October 16-18, 2006.

NIM'06 will focus on the following topics:

  • Evolutionary computation
  • Neural networks
  • Artificial immune systems
  • Ant colony optimizations
  • Cellular Computing
  • Artificial life
  • DNA Computing
  • Combination of all above (hybrid approaches)
  • Real applications

Important Dates:

  • Special Session Proposal: May 1, 2006
  • Paper Submission: May 15, 2006
  • Notification of Acceptance: June 15, 2006
  • Final Paper Submission: June 30, 2006

See the workshop webpage for further details (declaration of interest: I am on the Program Committee).

Monday, March 27, 2006

A380 evacuation test a success?

Airbus are claiming success after yesterday's A380 evacuation test, the results of which are yet to be verified by the authorities (but the signs suggest that this is just a formality). Airbus think they managed to evacuate 873 "passengers" (half of whom were Airbus employees, with the other half being recruited from local gyms...) in 80 seconds.

The test didn't run quite as smoothly as Airbus might have hoped, though, with one participant breaking his leg, and 32 others suffering minor injuries (many sustaining friction burns on the slides).

Thos familiar with our recent work on A380 evacuation modelling will know that one of the main variables of interest was delay caused by passengers pausing at the upper exits (which are 8m off the ground). The editor of Flight International, Mark Daly, was one of the participants in the test: "One of the big concerns was whether anybody would hesitate at the top of the slides," said Mr Daly. "The finding was that nobody does - in a panic situation, your universe contracts and you're only really conscious of the few feet around you."

Hopefully Airbus will release enough data to allow us to test the validity of our existing model, but there's no requirement for them to disclose anything other than the bare details of the test.
We'll wait and see.

Saturday, March 18, 2006

A380 evacuation trial - date

According to "regulatory sources", Airbus have scheduled the A380 evacuation trial for Sunday March 26th. For more background, see our recent work on the aircraft.

Friday, March 17, 2006

DNA origami

Paul Rothemund has written a paper that appears on the cover of this week's Nature (the link goes to a news story with an image of a DNA "smiley face", see the open access editor's summary, or the full paper (requires subscription)). He's come up with a way of folding a single DNA strand to form arbitrary two-dimensional shapes (much like origami experts fold a single sheet of paper into a multitude of designs).

Much work has been done on DNA nanotechnology, mainly inspired by the work of Ned Seeman. Rothemund's approach differs in that, rather than using many different "tiles" that self-assemble into a macro-scale single object, he folds a single section of well-sequenced viral DNA, using short "staple" strands to pin the whole complex together.

This work is wonderfully elegant, and is just one of several significant papers published by Rothemund. He first came to the attention of the DNA computing community at the first ever international workshop in 1995, when he described his scheme for a molecular Turing machine, and he's continued to produce work of outstanding quality.

Monday, March 13, 2006

Science in the Dock

The ESRC Centre for Genomics in Society (Egenis) at Exeter is organising a week of public outreach activities.

"Egenis invites you to get involved during ESRC Social Science Week: On 14 March, ‘Science in the Dock – Art in the Stocks’ will bring together artists and scientists from the South West to discuss and critique each other’s work in a public symposium."

I'm giving the opening address, and will be talking about bacterial cameras and general synthetic biology. It should make an interesting change from the sort of event that I usually attend, so I'll try to post a summary of what went on (further details of the programme are available at the Egenis website).

Wednesday, March 08, 2006

Blog down-time

The blog will not be updated over the next week or so, as I'll be "away" on paternity leave.

"Human selection alive and kicking"

News article from Nature (open access):

"Researchers at the University of Chicago, Illinois, have identified the regions of our genetic sequence that show the strongest marks of natural selection. Their work highlights the genes that have been most important in adapting to new lifestyles, and could help to identify the genetic factors involved in complex medical conditions such as high blood pressure and alcoholism."

Friday, February 24, 2006

Enzymatic computing

I'm quoted in a short piece in the New Scientist breaking news section:

"A molecular computer that uses enzymes to perform calculations has been built by researchers in Israel.

Itamar Willner, who constructed the molecular calculator with colleagues at the Hebrew University of Jerusalem in Israel, believes enzyme-powered computers could eventually be implanted into the human body and used to, for example, tailor the release of drugs to a specific person's metabolism."

Monday, February 20, 2006

Turing archive

"The Turing Archive for the History of Computing is a major Internet project... The documents that form the historical record of the development of computing are scattered throughout various archives, libraries and museums around the world. Until now, to study these documents required a knowledge of where to look, and a fistful of air tickets. This Virtual Archive contains digital facsimiles of the documents. The Archive places the history of computing, as told by the original documents, onto your own computer screen.

This site also contains a section on codebreaking and a series of reference articles concerning Turing and his work."

Tuesday, February 07, 2006

The Mower

The mower stalled, twice; kneeling, I found
A hedgehog jammed up against the blades,
Killed. It had been in the long grass.

I had seen it before, and even fed it, once.
Now I had mauled its unobtrusive world
Unmendably. Burial was no help:

Next morning I got up and it did not.
The first day after a death, the new absence
Is always the same; we should be careful

Of each other, we should be kind
While there is still time.

Philip Larkin

Friday, January 27, 2006

CoGBiN 2006

I'm on the Organizing Committee of CoGBiN 2006: a Workshop on Computation in Genetic and Biochemical Networks, which is to be held as part of Unconventional Computation 2006, 4th-8th September 2006, York, UK.

The Workshop on Computation in Genetic and Biochemical Networks aims to provide a forum to bring together biologists and computer scientists who are interested in computational models of the behaviours which occur in genetic and biochemical networks. We welcome paper submissions from researchers interested in understanding the forms of computation carried out by biological networks in vivo, in applying these forms of computation in silico, and in the emerging field of synthetic biology.

Selected papers will be considered for publication in the journal BioSystems.

Important Dates

Paper submission: 1st May 2006
Paper notification: 1st July 2006

See the website for details of how to submit.

Thursday, January 26, 2006

Bad news for Darwin, rationality

Are we about to see a repeat of the "intelligent design" debate, this time in the UK? The BBC has recently carried out a survey of the British population, taking opinions on the theory of evolution. The results are profoundly disturbing and depressing:

Over 2000 participants took part in the survey, and were asked what best described their view of the origin and development of life:

  • 22% chose creationism
  • 17% opted for intelligent design
  • 48% selected evolution theory
  • and the rest did not know.

When given a choice of three theories, people were asked which ones they would like to see taught in science lessons in British schools:

  • 44% said creationism should be included
  • 41% intelligent design
  • 69% wanted evolution as part of the science curriculum.

The "positive" figure of 70% wanting evolution taught in science lessons masks the obvious fact that nearly a third of the population, by definition, do not want it taught in science class -- the additional fact that 44% want creationism included in science curricula is worrying in the extreme.

Monday, January 23, 2006

Update: A380 evacuation trainer installed

Airbus have just installed their first A380 cabin emergency evacuation trainer at their training centre in Toulouse. "`Now we are ready to get on with flight testing and certification on the A380,' says Engine Alliance president Bruce Hughes."

"Watt's in a name"

As a proud alumnus of both the Universities of Coventry (B.Sc.) and Warwick (Ph.D.), I was mildly amused by this article on the difficulties of naming places of higher education.

When I was at Warwick, every year we would we hear stories of Ph.D. students applying from overseas (who hadn't visited the campus prior to accepting their place) inadvertently snapping up hideously expensive flats in the centre of Warwick, only to arrive and find that they were miles from campus and paying roughly triple the price of an equivalent place in Coventry. I think, in the end, the University had to put a warning note in its promotional literature, as it was beginning to get rather embarrassing.

Friday, January 20, 2006

Microbes and Microbots

In his consistently excellent blog, Richard Jones discusses the history of the nanobot; the "Fantastic Voyage"-style nanoscale submarine cruising our bloodstream looking for nasties like cancer cells and broken capillaries.

"Attempts to write the nanobot out of the history of nanotechnology thus seem doomed, so we had better try and rehabilitate the concept. If we accept that the shrunken submarine image is hopelessly misleading, how can we replace it by something more realistic?

Personally, I believe that we would be better served by taking a step back, and first considering the feasibility of microbots, before we even contemplate such devices on the nanoscale. Richard makes the valid point that the science fiction images of incredibly miniaturised submarines do the field of nanotechnology a great disservice, as they do nothing to dispel the myth of nanotech being "engineering, only smaller".

Based on my interpretation of Richard's book Soft Machines (he nabbed my title, the rotter ;-), I think he might agree with me that a rather more realistic (and certainly interesting) route would be to re-engineer existing living systems for the purposes of providing such applications.

As I point out in my own popular science book Genesis Machines: The Coming Revolution in Biocomputing and Synthetic Biology (Atlantic Books, November 6th -- watch this space for updates and sneak previews):

"Nature has computation, compression and contraptions down to a fine art...A human genome sequence may be stored on a single DVD, and yet pretty much every cell in our body contains a copy. Science fiction authors tell stories of "microbots" -- incredibly tiny devices that can roam around under their own power, sensing their environment, talking to one another and destroying intruders. Such devices already exist, but we know them better as bacteria."

Thursday, January 12, 2006

Minimal genome

The journal PNAS has this week published an open access article by the Synthetic Biology Group lead by Craig Venter (the founder of the commercial "rival" to the publically-funded human genome project).

One of the objectives of Venter's group is to identify the smallest possible set of genes required to sustain life. By knocking out genes one by one and assessing the effect of such deletions, they hope to derive a minimal "component list" for a living cell. As they state in the introduction to the article, "One consequence of progress in the new field of synthetic biology is an emerging view of cells as assemblages of parts that can be put together to produce an organism with a desired phenotype. That perspective begs the question: "How few parts would it take to construct a cell?" In an environment that is free from stress and provides all necessary nutrients, what would constitute the simplest free-living organism? This problem has been approached theoretically and experimentally in our laboratory and elsewhere."

Thursday, January 05, 2006

Airbus A380 evacuation trial

Those familiar with our recent work on aircraft evacuation modelling will known that the safety community is still waiting for Airbus to carry out its long-awaited full-scale evacuation trial of the double-decker A380. Without this being passed, the authorities will be unable to certify the aircraft as safe to carry paying passengers. Our simulation study concerned evacuation delay caused by passengers hesitating at the upper exit, and we predicted that the trial will fail (ie. not all passengers will be evacuated in under 90 seconds) if the average door hesitation exceeded 1.1 seconds. Of course, this is pure speculation on our part, based on a rather simplistic computer model, and we await with interest the results of the real-life trial. Flight International have confirmed information that the trial will be held "around March" this year. Such announcements have been made before, with no trial being held, but Airbus need to get their skates on, as they're already running six months behind schedule on delivery.

Monday, January 02, 2006

2006: The Dangerous Ideas

First, I'd like to wish readers a happy, peaceful and prosperous New Year.

"The mandate of Edge Foundation is to promote inquiry into and discussion of intellectual, philosophical, artistic, and literary issues, as well as to work for the intellectual and social achievement of society."

At the start of every year, the Edge poses an annual question, and asks some of the foremost contemporary thinkers to share their thoughts on it. This year, the question is "What is your dangerous idea?".

"Here you will find indications of a new natural philosophy, founded on the realization of the import of complexity, of evolution. Very complex systems — whether organisms, brains, the biosphere, or the universe itself — were not constructed by design; all have evolved. There is a new set of metaphors to describe ourselves, our minds, the universe, and all of the things we know in it."

Contributors to this collection of essays include Philip Anderson, Richard Dawkins, Daniel Dennett, Freeman Dyson, Danny Hillis, Brian Goodwin, Steven Pinker, Douglas Rushkoff and Craig Venter. Of particular personal interest are the essays by Lynn Margulis (our sensory capabilities have evolved as a result of interactions between social bacteria) and Robert Shapiro (we shall understand the origin of life within the next 5 years).