My contribution to the synthetic biology debate

You may recall that the Royal Society is soliciting opinions on various aspects of the field of synthetic biology. What follows is a lightly edited version of my own submission, which I sent off today.

In what follows, I highlight some concerns and dangers, speaking as someone who has an definite interest in the field flourishing (and would therefore wish to see these concerns addressed).

1. Terminology

The first concern is over the term “synthetic biology” itself. The two main issues are “what does it mean?” and “what does it cover?” As pointed out at the BBSRC workshop, clinicians have used the term for a while to refer to prosthetic devices. In attempting to offer a fixed definition of the term, the community runs the risk of becoming overly exclusive at a premature stage. However, there is also a risk that “synthetic biology” will become a “catch-all” term that is too loosely applied. The emphasis on the term “biology” may also serve to alienate mathematicians, physicists, computer scientists and others, who may (wrongly) feel that they have no expertise to offer a “biological” discipline. As a counter-example, witness the success of the field of bioinformatics, which would appear to fairly represent the disciplinary expertise in the field (in terms of the general composition of the term, rather than the relative lengths of its components). As a very crude experiment, I searched in Google for both “computational biology” and “bioinformatics”; the first term returned around 1,530,000 hits, the second around 14,000,000.

This leads on to the issue of “language barriers”. This is always an issue in any new field that involves the collision of two or more (often very dissimilar) disciplines. Being seen to publically ask “stupid questions” is a daunting prospect to most young scientists, and yet many of the major breakthroughs have occurred through just that. This opens up the wider debate on inter-disciplinarity in 21st century science, and how we might best prepare its practitioners. Do we give students a broad, shallow curriculum to allow them to make connections, without necessarily having the background to “drill deeper” if required, or do we stick to the “old model” of “first degree” and subsequent training? My own intuition is that it is far better to intensively train in a single field at the outset, and then offer the opportunity to “cherry pick” topics from a different discipline at a later stage. This educational debate is, however, not one that should be the sole preserve of synthetic biology!

2. Expectation Management

Even when biologists and (say) computer scientists can agree a suitable shared terminology, there is still the risk of a mismatch occurring in terms of expectations of what might be achieved. For example, the notion of “scalability” might mean very different things to a computer scientist and a microbiologist. To the former, it means being able to increase by several orders of magnitude the number of data items processed by an algorithm, or double the (already vast) number of transistors we may place on the surface of a computer chip. To a biologist, the idea of scalability might currently be very different:

“What's needed to make synthetic biology successful, Rabaey said, are the same three elements that made microelectronics successful. These are a scalable, reliable manufacturing process; a scalable design methodology; and a clear understanding of a computational model. "This is not biology, this is not physics, this is hard core engineering," Rabaey said.

In electronics, photolithography provides a scalable, reliable manufacturing process for designs involving millions of elements. Biology has a long way to go. What's needed, Rabaey said, is a way to generate thousands of genes reliably in a very short time period with very few errors. The difference between what's available and what's needed is about a trillion to one.”

3. Conceptual Issues

As the leading nanotechnologist (and FRS) Richard Jones has pointed out, his field was dominated from an early stage by often inappropriate analogies with mechanical engineering (e.g., cogs). It may well be that case that we are in danger of the same thing happening with synthetic biology, where computer scientists impose rigid circuit/software design principles on "softer", more “fuzzy” substrates. Jones quotes, on his blog, an article in the New York Times:

“Most people in synthetic biology are engineers who have invaded genetics. They have brought with them a vocabulary derived from circuit design and software development that they seek to impose on the softer substance of biology. They talk of modules — meaning networks of genes assembled to perform some standard function — and of “booting up” a cell with new DNA-based instructions, much the way someone gets a computer going.”


4. Complexity

The issue of "grey goo" has persistently dogged the field of nanotechnology, and it would be tempting to dismiss similar criticisms of synthetic biology as well-intentioned but ultimately uninformed. However, if synthetic biologists are to avoid the mistake that researchers in GM research made (that is, to appear arrogant and dismissive, leading to mass public protest and restrictive legislation), then we should acknowledge and address the very real possibility of the biological systems under study behaving in very unpredictable ways. Anyone who has any degree of contact with studying biosystems will understand the notion of complexity; components that are connected in an unknown fashion behave in unpredictable ways, which may include evasion of any control mechanisms that have been put in place. As Douglas Kell and his colleagues have observed, it is perfectly possible to alter parameters of a system on an individual basis, and see no effect, only to observe wild variations in behaviour when exactly the same tweak is applied to two or more parameters at the same time. Working in an interdisciplinary fashion may address this issue, at least in part, if modellers work closely with bench scientists in a cycle of cooperation. Once again invoking the issue of scalability, studying the behaviour of complex biosystems through modelling alone will quickly become infeasible, due the the combinatorial explosion in the size of the search space (of parameter values). By actually making or modifying the systems under study in the lab, the problem may be reduced to manageable proportions.

5. Hype

In my own book, Genesis Machines (Atlantic Books, 2006), I illustrate the risk of promising too much at an early stage by describing the story of the “AI winter”. In the 1960s, researchers in artificial intelligence (AI) had promised human-level intelligence “in a box” within twenty years. By issuing such wild predictions, AI researchers set themselves up for a monumental fall, and, when the promised benefits failed to accrue, funding was slashed and interest dwindled. This AI winter (by analogy with “nuclear winter”) affected the field for over 15 years, and it would be disappointing (to say the least) if the same thing were to happen to synthetic biology.

Hubristic claims for synthetic biology should be avoided wherever possible; without singling out particular groups, I have already seen several predictions (again, often conflated with ambitions) that have absolutely no realistic chance of coming to fruition in any meaningful time-scale (if at all). In this more “media savvy” age, perhaps practitioners in synthetic biology might benefit, as their AI counterparts did not, from media training (I have personally benefited (June 2004) from the course provided by the Royal Society, and perhaps the Society might consider a “mass participation” version for new entrants to the field).

For the love of ants

To be published next week, one book on my Amazon wishlist is titled The Ants Are My Friends. Students of popular music may recognise the phrase as one of the great misheard lyrics of our time, up there with "Beelzebub had a devil for a sideboard", rather than an expression of insect infatuation (the response being, of course, "blowing in the wind").

But I rather like the idea of ants being my friends. I've always held these misunderstood creatures in high regard, and was charmed by the story, recounted in Surely You're Joking, Mr. Feynman! (p. 91 in the Vintage edition), of how Richard Feynman investigated ant trail-following behaviour in his Princeton accomodation. He eventually used his findings to persuade an ant colony to leave his larder; "No poison, you gotta be humane to the ants!"

Anyone who has ever watched an ant colony at work cannot fail to be entranced by its beauty and efficiency. A single colony can strip an entire moose carcass in under two hours, and their work is coordinated in an inherently decentralised fashion (that is, there is no "head ant" giving out orders). An ant colony can be considered as a class of "super-organism", that is, a "virtual" organism made up of many other single organisms. Other examples include bacterial colonies and (arguably) the Earth itself.

Ants communicate remotely by way of pheromones, chemicals that generate some sort of response amongst members of the same species. When ants forage for food, they lay a particular pheromone on the ground once they've found a source. When this signal is detected by other ants, they follow the trail and reinforce it by laying pheromone themselves. Chemical signals also evaporate over time, which allows colonies to "forget" good solutions (i.e., paths) and construct new solutions if the environment changes (e.g., a stone falls onto an existing path).

By describing this mechanism in abstract terms, computer scientists have managed to harness the power of positive feedback in order to solve difficult computational problems. Perhaps the leading scientist in the field of ant colony optimization (ACO) is Marco Dorigo, and he has described how to use models of artificial ants to solve the problem of how to route text messages through a busy network of mobile base stations. We've also done some initial work on how ants build spatial structures, using an abstract model of pheromone deposition to explain how certain species can construct "bullseye"-like patterns of differently-sized objects.

Fundamentally, ongoing work in ACO reflects a wider interest in the notion of decentralised control. Rather than controlling everything from "on high" with global instructions, "bottom up" control emphasises the value of small, local interactions in keeping systems running smoothly. Software packages such as Netlogo have brought so-called agent-based modelling to a wider audience. I've just taken on a Ph.D. student to study the evacuation of tall buildings using this approach, and it's clear that, with ever-increasing computational power being available, the notion of simulating large systems of interacting entities will gain increasing influence.

Genesis Machines in the USA

I'm delighted to report that Atlantic have signed a deal to publish Genesis Machines in the USA. It's slated to appear on April 3rd of next year, and will be published by the Overlook Press (preorder here).

Molecules and Marx

My publisher kindly sends me copies of reviews of Genesis Machines that appear from time to time in the press. I was quite surprised to see the book featured in the June issue of the Marxist Review, the monthly theoretical magazine of the Workers Revolutionary Party. In his article, William Westwell invokes Richard Dawkins as the contemporary cheerleader of arch-reductionism and mechanical materialism. But, by concentrating purely on the first half of the book (which, by its very nature is comprised largely of historical background), Westwell ignores one of its fundamental arguments: that 21st century science cannot succeed by insisting on the top-down, reductionist paradigm. Science is still, to a large extent, a reductionist enterprise, but the emerging field of systems biology is providing a complementary approach (in a way, occupying the region where top-down meets bottom up). By arguing for a notion of "quality of computation", Westwell reminded me of conversations I have enjoyed in the past with Brian Goodwin, who has argued that "Biology is returning to notions of space-time organisation as an intrinsic aspect of the living condition... They are now described as complex networks of molecules that somehow read and make sense of genes. These molecular networks have intriguing properties, giving them some of the same characteristics as words in a language. Could it be that biology and culture are not so different after all; that both are based on historical traditions and languages that are used to construct patterns of relationship embodied in communities, either of cells or of individuals?" Unfortunately, Westwell appears to have ignored the later detailed discussion of such matters.

Royal Society and Synthetic Biology

I was gratified to see a healthy turn-out for the Cafe Scientifique event yesterday evening, and pleased by the range and depth of questions that were asked. I briefly mentioned at the end of the Q&A session that the Royal Society (the UK's preeminent learned society for the sciences) is soliciting views on the emerging field of synthetic biology.

The field's potential impact is huge, not just in terms of technological developments and scientific understanding, but in terms of social impact, legal issues and ethical concerns. It is vital that scientists engage with the wider community, so that the implications of their work may be considered at an early stage (and, indeed, throughout). The Royal Society is therefore asking for submissions (ranging from brief comments to draft discussion documents) on various aspects of synthetic biology, from potential applications to biosecurity risks and governance.

These exercises offer a real opportunity to help shape future policy, so I would encourage potentially interested parties to visit the call website and consider adding their voice to the debate. The deadline for submissions is August 27th.

Event in Manchester

If you're in Manchester next Monday and are stuck for something to do in the evening, why not pop along to Cafe Scientifique, where I'll be speaking and (hopefully) generating some discussion? The format is pretty relaxed, with a 30-40 minute presentation from me, followed by a 15 minute break for refreshments, then an open-ended discussion session.

Genesis Machines: Engineering Life

Monday 2nd July 2007 at 6:30pm in Cafe Muse (directions are here).

Although anticipated as early as the 1950s, the idea that we could somehow build working computers from organic components was merely a theoretical notion until November 1994, when a scientist announced that he had built the world's first molecular computer. Emerging from a laboratory in Los Angeles, California, his collection of test tubes, gels and DNA lay at the heart of a totally new and unexplored region of the scientific landscape.

Millions of dollars are now being invested worldwide in molecular computing and synthetic biology research. DNA, the code of life, is right now being used at the heart of experimental computers. Living cells are being integrated with silicon nanotubes to create hybrid machines, as well as being routinely manipulated to add entirely new capabilities. Preparations are being made to build entirely new organisms, never seen before in nature.

This research raises amazing new questions. Does nature 'compute', and, if so, how? Can natural systems inspire entirely new ways of doing computation? How can humanity 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? In this event we'll examine what it means to reprogram the logic of life.

Two things

Apologies for the lack of recent activity on the blog; this time of year is always the busiest for academics, what with exam boards and so on. Hopefully things will calm down in the next week or two.

Two items of note: today marks both the publication of Genesis Machines in paperback, and the release of the programme for this year's Edinburgh International Book Festival.

Not much has changed in the paperback, apart from a few additional acknowledgements and some minor changes to the notes and references (which are available online here.)

As for the Book Festival, I'm privileged to be appearing on stage once again with Oliver Morton from Nature, where we'll be discussing "The Future of Nature" as part of the "Genes and Society" Festival theme. Oliver will be talking about "intelligent plants", and I'll be holding forth on biocomputing and synthetic biology (Craig Venter's recent patent swoop has given me lots of nice new discussion material). Anyway, we're appearing on Sunday the 26th of August, and full programme details are available here. The event is sponsored by the ESRC Genomics Policy and Research Forum, and it's one of five that they are supporting.

DNA hash pooling

The draft paper that came out of our trip to Paris has now been lodged with the arXiv e-print server.

DNA Hash Pooling and its Applications

Dennis Shasha (Courant Institute, New York University), Martyn Amos (Computing and Mathematics, Manchester Metropolitan University)

Abstract: In this paper we describe a new technique for the characterisation of populations of DNA strands. Such tools are vital to the study of ecological systems, at both the micro (e.g., individual humans) and macro (e.g., lakes) scales. Existing methods make extensive use of DNA sequencing and cloning, which can prove costly and time consuming. The overall objective is to address questions such as: (i) (Genome detection) Is a known genome sequence present at least in part in an environmental sample? (ii) (Sequence query) Is a specific fragment sequence present in a sample? (iii) (Similarity Discovery) How similar in terms of sequence content are two unsequenced samples?

We propose a method involving multiple filtering criteria that result in "pools" of DNA of high or very high purity. Because our method is similar in spirit to hashing in computer science, we call the method DNA hash pooling. To illustrate this method, we describe examples using pairs of restriction enzymes. The in silico empirical results we present reflect a sensitivity to experimental error. The method requires minimal DNA sequencing and, when sequencing is required, little or no cloning.

Available at http://www.arxiv.org/abs/0705.3597.

Spiked innovation survey

I was recently asked to contribute to the annual innovation survey from spiked. There appear to be many interpretations of the term "innovation", but notable entries (from my own perspective) include those by Scott Aaronson, Paul Rothemund and Jeffrey Shallit.

Here's the blurb from the spiked website:

"The internet, the alphabet, the discovery of nuclear fusion, x-rays, the brick, rockets, the eraser: all of these have been identified as the greatest innovations in history in a new survey.

Over 100 key thinkers and experts from the fields of science, technology and medicine - including six Nobel laureates - participated in the brand new spiked/Pfizer survey 'What's the Greatest Innovation?', which goes live on spiked today.

In his introduction to the survey, spiked's editor-at-large Mick Hume says: 'Some choose "sexy" looking innovations, others apologise for the apparent dullness of their arcane choices. But whatever the appearances, almost all of our respondents exude a sense of certainty about the improvement that innovations in their field are making to our world, and the potential for more of the same."

A new kind of firefighting

I managed to miss a potentially interesting edition of Horizon on the BBC after making the mistake of flicking over to watch the second half of the Manchester Utd/Milan match.

Anyway, I caught the last ten minutes, and managed to glean the basic facts: that fewer people would have died when the Twin Towers collapsed on September 11 had the authorities been in possession of a global picture of the state of the building (in terms of both its structure and the movement of its occupants). But having the raw data is not enough: it needs to be provided as input to predictive models that are capable of allowing firefighters to play "what if" games. These models are necessarily computationally complex and resource intensive, which is where Jose Torero comes in. He's in charge of Firegrid, an interdisciplinary project dedicated to using Grid-based computing to model and predict, in real-time, the evolution of fire emergencies.

This work is related to my own on evacuation modelling, and we've recently been awarded a Ph.D. studentship in order to develop our ideas on how crush conditions emerge in situations where people fail to follow a set evacuation plan. This work will be done in collaboration with Dr Steve Gwynne, who has worked for the last ten years on modelling people movement, and who helped develop the influential Exodus system. The position will be advertised shortly, so watch this space.

Warwick victorious!

Congratulations to one of my old institutions, Warwick, on winning the 2007 University Challenge. In a tight match, they eventually fought off the reigning champions, Manchester, both securing Warwick's first ever series win and preventing their opponents from gaining the first ever "back to back" run of titles.

I'm afraid, however, that most neutrals watching will remember it more for Prakash Patel's post-presentation lunge for Ann Widdecombe than anything else.

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).