Synthetic Biology review

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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.