Cambridge website for Synthetic Biology resources

www.synbio.org.uk

Compiled by Jim Haseloff at the University of Cambridge. SpannerPlantLogo140This site contains details of recent papers and activity in Synthetic Biology, with particular emphasis on: (i) development of standards in biology and DNA parts, (ii) microbial and (iii) plant systems, (iv) research and teaching in the field at the University of Cambridge, (v) hardware for scientific computing and instrumentation, (vi) tools for scientific productivity and collected miscellany.

Similar to the Cambridge-based Raspberry Pi and OpenLabTools initiatives, we promote the use of low cost and open source tools - in our case for use in biological engineering.

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Meetings: Synthetic Biology

  • 11 May 2014
    All Day

    The BIO World Congress on Industrial Biotechnology is the world's largest industrial biotechnology event for business leaders, investors, and policy makers in biofuels, biobased products, and renewable

  • 20 Jun 2014
    20:00 to 20:00

  • 21 Jun 2014
    20:00 to 20:00

  • 03 Aug 2014
    20:00 to 20:00

    Integrative Biology-2014 is a remarkable event for scientists/experts from academia and industry nationwide to catalyze the networking between the branches of computational biology and bioinformatics and

  • 29 Aug 2014
    20:00 to 20:00

    This conference will focus on the advancement of synthetic biology, especially its application in the field of antibiotic production in filamentous fungi and actinomycete bacteria, including the implementation

  • 13 Sep 2014
    20:00 to 20:00

    This year's conference theme Systems Biology: The Fifth Element seeks to capture the multiple facets that comprise a systems understanding of life, as a single common thread that unifies seemingly different

11 May 18 Sep

Weather: Cambridge

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featured news: Synthetic Biology

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OpenPlant - major boost for synthetic biology

OpenPlant - major boost for synthetic biology

Plant scientists at Cambridge and Norwich have been awarded £12 million funding for a new UK synthetic biology centre – OpenPlant. OpenPlant is a collaboration between the University of Cambridge and the John Innes Centre on Norwich Research Park. The funding...

The entire alphabet, photographed on butterfly wings

The entire alphabet, photographed on butterfly wings

Nature photographer Kjell Bloch Sandved has amassed a massive collection of butterfly and moth wings, capturing a host of unusual patterns. Using those patterns, he has assembled entire butterfly alphabets. The entire alphabet, photographed on butterfly wings   Read more...

The Average Length of Dissertations across Fields

The Average Length of Dissertations across Fields

How long is a doctoral dissertation? Too long—but some more than others. Marcus W. Beck, a doctoral student in conservation biology at the University of Minnesota, decided to find out. No, he didn’t write a dissertation on the subject.* But he...

Why the GMO Debate Misses the Point: Part 2

Why the GMO Debate Misses the Point: Part 2

  Washingtonians are going to the ballot box today to vote on Initiative 522, a measure that would require food producers to label genetically engineered foods. Sasha Wright, an ecologist and state native, offers her solutions to the GMO debate. This is...

GrowCube promises to grow food with ease indoors (hands-on)

GrowCube promises to grow food with ease indoors (hands-on)

Food. It's a bit of a big issue. After all, half the world doesn't have enough, and the other half has so much it doesn't really know where it comes from. Chris Beauvois, a software developer turned inventor, has created...

Geoengineering, through the eyes of the IPCC

Geoengineering, through the eyes of the IPCC

Examples of geoengineering proposals. Kathleen Smith, Lawrence Livermore National Laboratory It has been well established that our emissions of greenhouse gases are changing the Earth’s climate and that in order to avoid future warming and ocean acidification, fossil fuel use will need...

A journey to life’s beginnings

A journey to life’s beginnings

Life, biologists would tell us, is one of the last great mysteries. It is hard to define, even in an 'I know it when I see it' fashion, making it tricky to study. Yet, as I sit here at a...

Fossil insect hid by carrying a basket of trash

Fossil insect hid by carrying a basket of trash

If you travelled back to Spain, during the Cretaceous period, you might see an insect so bizarre that you’d think you were hallucinating. That’s certainly what Ricardo Pérez-de la Fuente thought when he found the creature entombed in amber in...

Contest: create a new kind of science kit for kids

Contest: create a new kind of science kit for kids

Remember how much fun chemistry sets used to be before the chemicals were deemed too dangerous for household fun? The Society for Science & The Public, in collaboration with the Gordon and Betty Moore Foundation, have launched a contest to...

Circle of Life: The Beautiful New Way to Visualize Biological Data

Circle of Life: The Beautiful New Way to Visualize Biological Data

When Martin Krzywinski took a systems administrator job at Canada's Michael Smith Genome Center, he didn't plan on becoming a pioneer of 21st century biological data visualization. Now his distinctive aesthetic is synonymous with the informational richness of our moment. Circle...

An Overview of US Advanced Research Projects Agency-Energy Funding Programs

An Overview of US Advanced Research Projects Agency-Energy Funding Programs

The Advanced Research Projects Agency-Energy (ARPA-E) program was officially launched in 2009 as the result of the 2007 America COMPETES Act, which was signed by President George W. Bush. Congress appropriated and President Barack Obama allocated $400 million in 2009...

3D Printer Made from E-waste in Africa

3D Printer Made from E-waste in Africa

We throw away millions of tons of e-waste every year and barely manage to recycle more than 15-20%. [Kodjo Afate Gnikou] is a 33-year old African who has just finished off a 3D printer built almost entirely out of e-waste. He...

Further evidence that nature is not the opposite of technology

Further evidence that nature is not the opposite of technology

As we move into a clean tech future, it's becoming more obvious that the old distinction between machines and nature is a false one. This sophisticated filter, made by researchers at MIT, is a perfect way to remove bacteria from...

Synthetic-biology company pushes open-source models

Synthetic-biology company pushes open-source models

Some synthetic fluorescent proteins made by DNA2.0 are now freely available to researchers. DNA2.0 Article tool When DNA2.0, a company that synthesizes made-to-order genes, needed to conduct a few routine experiments using a fluorescent protein, its lawyers dug up more than 1,000 US...

£17k Nerve KickStart challenge

 £17k Nerve KickStart challenge

Innovative global startups are being invited to tilt at a £17k prize package in the Nerve KickStart competition, run in conjunction with the Nerve conference on disruptive technology in Cambridge from June 25-27. KickStart is strictly for 'killers' - entrepreneurs whose...

Call for exhibits and experiments at GROW YOUR OWN...

Call for exhibits and experiments at GROW YOUR OWN...

GROW YOUR OWN... is a curated, open call exhibition tackling provocative questions raised by synthetic biology to be hosted at the Science Gallery, Dublin (http://sciencegallery.com), supported by the Wellcome Trust. The exhibition is curated by Professor Paul Freemont (Imperial College)...

Senior Internships for Interdisciplinary Research

Senior Internships for Interdisciplinary Research

Applications are invited for the next round of University of Cambridge / Wellcome Trust Senior Internships. The scheme is aimed at suitably qualified post-doctoral candidates with backgrounds in the physical sciences (incl. engineering, mathematics and computer sciences) who wish to gain...

Raspberry Pi Summer Internship Programme (2013)

Raspberry Pi Summer Internship Programme (2013)

We are looking for approximately ten students to take part in a range of projects that make use of the Raspberry Pi computer. A list of projects can be found below. Alternatively, if you have an interesting project idea of your...

News from the Wellcome Trust blog
by Mun-Keat Looi, 6 April 2010: see: http://wellcometrust.wordpress.com/2010/04/06/science-and-design/
Evidence Dolls

Evidence Dolls by Dunne and Raby uses 100 plastic dolls to provoke discussion about the impact of genetic technology on young single women

Tomorrow night Wellcome Collection’s Supper Club welcomes designers Anthony Dunne and Fiona Raby, the duo behind our stunning new window display, ‘What If…’.

It’s an interesting project, largely because when one thinks of design in a product sense, one usually thinks of technology rather than science. So when I met Dunne, Raby and the ‘What If…’ designers at the display’s launch party, what I wanted to know is: what can design and science teach each other?

 

“Designers normally work at the end of the process, where the science has become a technology, which has already become a product,” Anthony Dunne told me. “Designers are usually brought in to make the product easier to use, to look good, to be consumable.”

‘What If…’ explores what might happen if designers and scientists interacted earlier: what sort of role might design play? And how would this affect the design, or indeed the science?

In the case of ‘What if…’ the results are tangible, but imaginative, products representing outcomes that current research might deliver in the future: an ice-cream van that makes flavoured snow clouds, a machine that reads facial expressions, a suitcase full of brightly coloured faeces. As Dunne says, “Some are more imaginary, some are more concrete, some are quite realistic whereas others are more fanciful”.

Consumer engagement

Why create imaginary products? Because, Dunne says, the way most of us interact with technology is as consumers – we buy it.

Debates about the ethical and moral issues of fields like genetics and nanotechnology tend to occur at a very philosophical level. But that’s not how we necessarily think of things at a consumer level, says Fiona Raby.

The Cloud Project

The Cloud Project, part of the ‘What If…’ series asks: What if we could engineer clouds to ‘snow’ ice cream?

“[These products] take the debate away from the utopias, the ideals and more into the nitty-gritty everyday realities of what might happen and whether it is desirable or undesirable,” she told me.

This creates a new context for the debate surrounding scientific research and technology, and a new way for people to engage with the issues.

“The designer may create something that you are very interested in, but which also has some negative point to it,” says Raby. “There’s a trade-off between your attraction to the idea and the negative connotations that may come with it. It is the dilemma between good and bad parts that we think is the most interesting space of all.”

Scatalog

One such ‘What If…’ project is E. chromi by James King and Alexandra Daisy Ginsberg, a feature of which is the Scatalog, a silver suitcase of multi-coloured faeces.

How did it come to this? I should first explain that the E. chromi project looks at synthetic biology – the field that looks to apply engineering principles of design, modelling, testing and standardised parts to create new biological systems – and what the fruits of this might realistically look like.

King and Ginsberg embedded themselves in the 2009 Cambridge iGEM team (see my recent postsfor more on iGEM).

The team settled on the idea of engineering E. coli bacteria to produce different coloured pigments – raising the possibility of a new, more visual, type of biosensor.

“We wanted to explore the implications of that,” says King, “To see where bacterial colour might lead in the future and what sort of technologies, groups and services might emerge from this kind of new technology.” From this emerged the Scatalog.

“Imagine,” says Ginsberg: “It’s 2049. It’s now possible to ingest some E. chromi as a probiotic drink like Yakult. After you drink it, the bacteria start to form colonies inside your gut alongside the other bacteria that are in there, monitoring in the background. If there are any changes in terms of pathogens or new chemicals secreted by changes like colonic cancers then they start to react and secrete pigment and that pigment is then visible as a very simple, cheap visible output – your poo.”

The Scatalog

The Scatalog: Multi-coloured faeces as a cheap disease-monitoring system. Part of the E.Chromi project by James King and Alexandra Daisy Ginsberg.

The thinking is that you could check your faeces against a colour card and, through this, monitor what’s going on inside you as a cheap early warning, disease-monitoring system (it’s not as weird as it sounds – one of the symptoms of porphryia disorders is blue-black faeces). This system could be personalised for genetic susceptibility, as you can engineer these bacteria to suit your genetic make up and what disease in particular you are worried about.

The Scatalog is a mock-up of this concept, a suitcase filled with six coloured stool samples, which caused quite a stir when King and Ginsberg took it to the iGEM jamboree finals at MIT in November last year.

“Some people were quite negative because it’s not a very sexy implementation of the technology,” says King. “Synthetic biology has been touted as a solution to a lot of our problems, but this was more everyday, down to earth, much more mucky and grubby, and not very pleasant maybe!”

“But we also got some very positive reactions. After people had thought about it, they saw it as a possible, quite realistic and feasible solution to a problem we have at the moment – that is the difficulty in detecting diseases that are internal with no visible symptoms on the outside until it is too late.”

“It took people aback and helped us talk about the possible futures for synthetic biology, the medical applications for it, how it might interface with our body and what the aesthetic of the technology could be.”

For Ginsberg, it put into context some of the more fantastical ideas surrounding the field.

“People were talking about ‘biological computing’ and showing images of bacteria and cogs. But what is that? So we presented this suitcase, and asked, is this biological computing? No-one had thought about presenting something as gross as that before, but if it is that and we don’t like it, then maybe we should think differently.”

‘Scientific engagement’

One of the major benefits of E. Chromi, if not the whole ‘What If…’ series, is that the process engages both the designers and the scientists.

“What I’m interested in is what designers will be doing in 20 or 50 years time and how design can help impact the science,” says Ginsberg, “the idea of scientific engagement as opposed to public engagement; how can design help?”

The presence of King and Ginsberg and the workshops they ran gave the students a new perspective on the project and helped contribute to their success, says Dr Duncan Rowe from the Department of Genetics at the University of Cambridge and one of the Cambridge team’s advisors.

“They brought a lot of fun and got the students to come out of their shells. But more seriously, it made them think about how synthetic biology can affect society and how you would talk to society about your work,” he says.

“For the first time, instead of focusing on the molecular scale of how to engineer this thing, the team had to learn to tell stories about it as if it were already a product or a service 50 years in the future,” says Ginsberg. “This was the first time they’d had to think about what it might be or how it might affect people.”

iGEM jamboree

James King and Daisy Ginsberg showcasing the Scatalog at the 2009 iGEM jamboree finals

Ginsberg’s next project, ‘Synthetic Aesthetics‘, takes the scientist–designer collaboration a step further. The project will see six synthetic biologists and six designers do residencies in each others’ laboratories and design schools over an 18 month period. Through this, she hopes to explore the seemingly endless number of possibilities that synthetic biology seems to promise.

I asked her if the invasion of these ‘arty’ types disturbed the scientists, but she says it’s been quite the opposite. “Everyone is very welcoming to us. The nice thing about synthetic biology is that it is already a multidisciplinary field with physicists, engineers, biologists and computer scientists. So a couple of designers are just another type in the mix.”

“Synthetic biology is quite similar to design in some ways, with scientists asking similar questions like, what should we make?”.

This reminded me of something Anthony Dunne said earlier in the evening, “For me, science isn’t interesting because it is special, but because it’s the opposite. After all, what part of our lives isn’t affected by science and technology? There should be more courses exposing designers to genetics, synthetic biology, and neuroscience. Because when they go out and operate in the world, this is the world they are going to be partly shaping and working with.”

‘What If…’ runs at the Wellcome Trust until the end of the year.

Image credits:
Evidence Dolls: Dunne & Raby. Photographer: Kristof Vrancken.
The Cloud Project: Zoe Papadopoulou & Cathrine Kramer. Photographer: Gary Hamill
The Scatalog: Gos Micklem.
iGEM jamboree: Flickr/jimhaseloff

www.synbio.org.uk

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www.marchantia.org

Online resources, including bibliography, weblinks and posters, for work with the simple plant system, Marchantia polymorpha.

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