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.