Geoengineering and synthetic biology

This September, as part of our annual symposium, EUSynBioS will hold an Open Discussion on the topic, "Synthetic Biology and Environmental Engineering", at the National Center for Biotechnology, Madrid, Spain. We will host experts in the field to talk about the science and the more difficult aspects of public acceptance and bioethics surrounding geoengineering and synthetic biology. 

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Geoengineering is a word that means many things to many people. Formally defined as the "deliberate intervention in the climate system to counteract man-made global warming", for some scientists it represents a cheap and effective way to protect our planet from the ravages of climate change. To others it's symptomatic of technological hubris: a grand, doomed plan to control every aspect of our ecosystem. Dig past the rhetoric though and you find a science that's still in infancy, being developed by scientists around the globe, almost as a last resort in the (now very possible) event that on-going efforts to avert climate catastrophe by reducing global emissions fail.

Current research on geoengineering is focused on either removing carbon dioxide from the Earth's atmosphere or reducing global warming by reflecting more solar radiation away from the planet. Most proposals to achieve these goals rely on physical engineering solutions, cloud seeding for instance. A more expansive reading of "geoengineering"though, leads to several intriguing ideas on using synthetic biology to remedy the effects of intensive industrialisation/pollution on the environment.

i. pale blue dot

In 1980, the US Supreme Court issued a ruling that changed the status of living organisms forever. In Diamond v. Chakrabarty the court affirmed the right of inventors to patent living organisms that had been modified for some purpose. In this case, the patent was granted to a genetically engineered creature called the Superbug. The Superbug was a strain of Pseudonomas putida that could break down crude oil, and was posited as a tool to deal with oil spills. Since then, there's been a lot of work in developing such organisms, spawning a field of science called bioremediation that seeks to undo the damage human industry causes the environment. 

Now, a group of scientists are advocating the use of such organisms on a global scale to help mitigate the effects of climate change. Their, very SciFi-ish, ideas include: modifying particular species of bacteria that exist in harsh environments like deserts and equipping them with water harvesting capabilities; releasing entire stretches of DNA into a biosphere and allowing them to spread, equipping any host creature with water/temperature sensing capabilities, or releasing bacteria into the oceans that can cause pieces of plastic to stick to each other, solving the scourge of microplastic pollution. 

biologists are ever-aware of the conceit involved in predicting biological futures

These and other ideas find few takers though, and carry some real risks. We would have to be prepared to deal with the fact that any man-made bacteria released into a particular part of the world might escape a particular ecosystem, potentially wreaking havoc in others. Biological entities evolve, and evolution might change released modified bacteria in unpredictable ways. 

These are concerns synthetic biologists are tackling head on. In the last five years, we've made tremendous progress in engineering 'kill-switches' that could allow us to precisely control engineered bacteria in natural ecosystems. We've also developed bacteria which have been so extensively engineered that they cannot interact with other life-forms very well, or cannot reproduce, hence limiting the potential spread of synthetic DNA. Yet, biologists are ever-aware of the conceit involved in predicting biological futures and for the moment these bacteria will remain in petri dishes in labs around the world. 

ii. the red planet

The largest concern with biological geo-engineering is the fact that we might cause dangerously irreversible changes to the only habitable planet we know of. This is why, a group of scientists including NASA researchers are exploring biological options in terraforming Mars. The hopes are many, ranging from making Mars human-habitable (paving the way for eventual human colonisation), to using the red planet as a test-bed for ecosystem engineering whose lessons might then rescue the Earth from climate catastrophe. Less futuristic scenarios include the possibility of employing bacteria to harvest resources directly from Mars, or recycling consumable resources like waste-water, making manned Mars-missions a cheaper and easier endeavour. Most experts agree though that terraforming, the process of completely changing Mars' atmosphere is a process that could take centuries. A nearer-term option is something called para-terraforming. Paraterraforming envisions making smaller, enclosed spaces on Mars habitable for humans. Previous experiments in paraterraforming conducted on Earth have met with little success; however the prospect of engineering organisms specifically for terraforming makes this a more feasible proposition. 

Some however, question the ethics of using Mars as a lab-bench. One argument is that any human attempt at terraforming Mars might destroy or alter any remnant, hitherto undiscovered life on the planet. Another, that seeding Mars with terrestrial life may change a potential independent development of biological life on the planet in the distant future. These are minority opinions however. A view that, in my opinion, holds more merit suggests that the creation of Mars as a back-up planet might hinder attempts to mitigate anthropogenic climate change and pollution here on Earth.

iii. a last resort

There are two forms of climate change mitigation on the table at the moment, passive and active. Passive mitigation uses methods that are easier to swallow for most, reducing global consumption, stricter pollution controls, and switching to low-carbon sources of energy. The problem however lies in the fact that passive mitigation alone might not be enough to limit global warming to the 2°C threshold set by the Paris Agreement. Indeed, experts are highly sceptical that limiting warming to even 4°C is feasible given current trends. And the difference between a 2°C and 4°C limit is that the latter will result in massive droughts, flooding on an unprecedented scale and food shortages.

In this scenario, several climate experts have called for more drastic measures including non-biological geoengineering technologies cloud-seeding. In fact some estimates claim that cloud-seeding on a large enough scale might even bring global temperatures down to below pre-industrial levels. In this scenario then, would we even need a biological solution that might carry more risk? 

A possible benefit of biological remediation is of course that we might be able to rescue ecosystems that are on the brink of collapse, something that physical solutions like cloud seeding might never be able to achieve. Biological solutions can address biological problems in a manner that purely physical measures might struggle to. Another aspect of synthetic biology, the de-extinction of extinct species, is something that might supplement the reduction in global warming with the restoration of lost biospheres. 

On the policy front geoengineering is a topic that's often scoffed at or neglected in favour of discussions such as emissions reduction. The reasons for this are legitimate, though given the current political climate with the US backing out of climate accords, the dream of a 2°C reduction in global warming seems to be growing ever more distant. Science agencies across the world are waking up to this fact, and just a couple of months ago China announced the world's largest geoengineering research program. As of now, geoengineering remains a last resort, and biological measures even more so.

This isn't stopping scientists from experimenting with it though, and nor should it. 


Written by: Devang Mehta
Devang is currently a PhD student in Plant Biotechnology and Science & Policy at ETH Zurich. He also serves on the EUSynBioS Steering Committee as Policy Officer. Follow him on twitter at @_devangm or check out his blog at www.devang.bio

Photos: All photos used under CC0 license. 

iGEM 2017 UCL: Light Induced Technologies (LIT)

Using light in the future will mean more than illuminating rooms and flash photography. This year, a team of 9 undergraduates from UCL, with academic backgrounds ranging from Biochemical Engineering to Psychology, are shaping this vision. The members, coming from anywhere between Mexico and Luxembourg, will use the world’s largest synthetic biology competition at MIT, iGEM (international Genetically Engineered Machines), as a platform to develop light induced technologies.

The goal is to make synthetic biology more accessible to the general public by providing standardised and easy-to-use light control systems

LIT (Light Induced Technologies) - and no, it’s not Elon Musk’s new company - came out of a two-day project hackathon back in June. Ideas ranged from bio-robots to improve survival chances and collect data on Mars, to using optogenetics to control gene circuits. “The goal is to make synthetic biology more accessible to the general public by providing standardised and easy-to-use light control systems” – the team`s stated vision. The potential applications range from medicine to fabrication. The cells are engineered to respond to light in a tightly controlled manner. This switch can then be coupled to a wide variety of biological processes.

In essence, organs are made out of complex networks of different mammalian cells. To gain control over that complexity, LIT will use light to induce cell adhesion and trigger genetic networks in specific parts of the cell population. This work will be done in pluripotent stem cells. Their work is the first steps towards building organs from digital blueprints and tissue regeneration.

Stereolithography is an important technique in engineering and prototyping. The team aims to produce an organic version of this 3D printing method by allowing bacteria to form 3D structures through cell adhesion. Once this is implemented, specific wavelengths will be tested to produce biopolymers that are UV-resistant and environmentally friendly. Light induced technologies are also trying to optimise a bioluminescence system to create an efficient bacterial lightbulb.

This interdisciplinary project is based on research and mathematical modelling. However, other components such as entrepreneurship and public engagement will also contribute to its success. Research and engineering doesn’t happen in a bubble, so one must acknowledge and involve a wide variety of actors. The team has been working with different non-academic stakeholders in the project. For example, talking to architects has shaped the vision of what can be done with biopolymers in the field and inspired design. The planned activities over the summer aim to get people excited about synthetic biology, communicate science effectively and assimilate the ethical and societal implications of the projects.

There is an easy answer to the ‘so… what happens next?’ question. The website and social media pages (see below) are platforms for both communication and feedback on the project. Until November, you can get in touch, offer suggestions and collaborate.

Facebook: UCL iGEM

Instagram: ucl_igem17

Twitter: @ucligem

Website: http://2017.igem.org/Team:UCL

 

YEBN'S 2nd Round Table

Our friends at the Young European Biotechnology Network hold their second round table event this September, join them!

YEBN'S 2nd Round Table is going to take place in Frankfurt, Germany. When? Saturday 9th of September.

Here you could find an exciting one day program to exchange between different local and national life sciences organization within Europe in terms of activities and structure (sponsoring, working groups etc). We will also inform you about European supporting programs such as Erasmus +.

Are you a member of a life science organization within Europe? We are looking forward to your application: eb@yebn.eu

iGEM 2017 INSA-UPS Toulouse: Detecting and killing V. cholerae in contaminated water

This year the iGEM Toulouse team and the INSA Lyon team have merged, leading to a single team of students from the National Institute of Applied Sciences (INSA) Toulouse, University Paul Sabatier and the INSA Lyon.

The project of the team INSA-UPS Toulouse is to purify water contaminated by the pathogenic bacteria Vibrio cholerae. Cholera is still a disease that millions of people have to deal with every day.

The INSA-UPS Toulouse iGEM team

The INSA-UPS Toulouse iGEM team

Our team intends to treat small to medium volumes of contaminated water in countries impacted by cholera. For example, this year, an outbreak of cholera occurred in Yemen with already more than
250 000 people affected. Current treatments have limitations and people are still dying from cholera, either because it is hard to detect before cases are declared, or because patients live in remote areas not easily reachable by aid services. Thus, two solutions need to be found: one to detect V. cholerae before epidemic bursts occur and one to treat water in remote areas.

We want our final device to be able to combine detection and treatment of contaminated water. Furthermore, to have a greater impact, we aim for our device to be easily used by non-qualified people so everyone can contribute to improving the quality of water. We found a solution fulfilling all these criteria using synthetic biology.

Our system relies on the following biological facts: Vibrio species, hence V. cholerae, use a specific method of intra-species communication through quorum sensing. Vibrios have a specific one, using the CAI-1 molecule which binds to its specific membrane receptor CqsS. More interestingly, each Vibrio has its own CAI-1/CqsS system. That’s why, by inserting a punctual mutation on Vibrio harveyi –a nonpathogenic Vibrio- CqsS, this bacteria becomes able to detect the V. cholerae CAI-1. Using a system of communication close to the natural one will allow a strong and reliable detection of the V. cholerae in water.

The final goal is to kill the bacteria V. cholerae. We decided to focus on newly described peptides from the immune system of crocodiles. They showed a promising effect on V. cholerae. A secretion system for this peptide is needed in order to have a specific and efficient response to V. cholerae in water. Obviously, the peptide specific to V. cholerae will also kill V. harveyi.

It was thus essential to find a fast growing, large producer able to survive the antimicrobial peptides. Our team chose Pichia pastoris as it met these criteria, with a lot of publications supporting its ability to produce a great amount of antimicrobial peptide. Therefore P. pastoris has the role of cholera killer.

Summary of the iGEM team's strategy to kill Vibrio cholerae by using synthetic biology

Summary of the iGEM team's strategy to kill Vibrio cholerae by using synthetic biology

The link between the two previous entities is to kill V. cholerae only upon its detection. The challenge was to find a way of communication between the prokaryotic detector and the eukaryotic killer. A previously described engineered ligand/receptor system was found in the iGEM registry. This diacetyl/ODR-10 system meets perfectly our needs. Upon detection of V. cholerae, diacetyl is produced by V. harveyi. Diacetyl is then detected by the Odr10 receptor present on P. pastoris. This cell signalling induces the activation of the pFUS promoter. Behind this promoter, the peptides can be produced by reception of the signal of presence of V. cholerae.

For more information: http://2017.igem.org/Team:INSA-UPS_France

 

Introducing Synthetic Biology: A New Journal for the SynBio Community

Last year saw the launch of Synthetic Biology - a new open access journal from Oxford University Press. Aiming to serve the whole synthetic biology community, it has an extensive scope including everything from viral, protein and metabolic engineering through to mathematical modelling and engineering processes. It will provide a platform for original research papers, reviews, commentaries, project reports and discussions around the theme of synthetic biology to those working in academia, education and industry.

Professor Jean Peccoud

Professor Jean Peccoud

We got in touch with Editor-in-Chief Jean Peccoud to get more of an insight into what Synthetic Biology will bring to our community and find out where he thinks synthetic biology is heading over the next few years.

Q: What will Synthetic Biology bring to the SynBio community - how does it differ from other synthetic biology journals?

Jean Peccoud: Most of synthetic papers are still published in non-specialized journals that span a broad spectrum of scientific specialties from bioinformatics to molecular biology and biotechnology. It can be difficult for readers to notice synthetic biology papers among all the other papers that these journals publish. For authors, this dispersion can also be problematic as editors of well-established journals sometimes struggle to see how a synthetic biology submission fits within the scope of their journal.

The first journal dedicated to synthetic biology was IET Synthetic Biology. For some reason the journal was short-lived. It took five years after this early experiment to see the launch of a new journal dedicated to serving the needs of our community. Since 2012, ACS Synthetic Biology has been extremely successful. It now provides the community with a well-respected venue to publish synthetic biology research.

Its success is also a sign that the growing synthetic biology community needs channels to disseminate its research. Oxford University Press (OUP) identified this need when they decided to launch this new journal. Many synthetic biology authors are familiar with OUP, the world’s largest university press. They also publish Nucleic Acids Research and Bioinformatics, two journals that have been publishing synthetic biology papers for many years. This creates opportunities. For instance, we have developed a process to streamline the transfer of manuscripts from one journal to another. If a paper is rejected by Nucleic Acids Research because of its perceived limited significance, authors will be offered the possibility of transferring the submission and the reviews to Synthetic Biology. OUP is also known for the quality of its production process. Accepted manuscripts are formatted very quickly and only published in their final form. Authors benefit from a rigorous proofreading and typesetting that, I think, greatly contribute to the value provided by the journal.

Prior to working with OUP, I spent several years working with PloS. I became an academic editor of PloS One in 2009 and then I was instrumental in launching the PloS Synthetic Biology Collection. The editorial policies for Synthetic Biology are partly inspired by PloS ONE editorial policies. In particular, the significance of a submission is not considered when making editorial decisions. We are not chasing the Impact Factor. I think the editor’s role is to ensure that the results that are published are scientifically sound. It is for the readers to decide which papers are important by citing them over the years.

We also offer to publish categories of articles that may be difficult to publish in other journals. This includes reviews, papers describing educational programs, datasets, and even conference papers that summarize results previously presented in conference proceedings.

However, we chose not to publish any Comments or Policy papers as we think less specialized journals are probably better venues to discuss these issues.

Q: What do you think is the biggest challenge facing synthetic biology?

JP: My main concern is the security implications of the technology and its possible dual use. I think we are greatly benefiting from a fairly permissive regulatory environment. I am afraid that if a security incident were to happen, something isolated like the Amerithrax in 2001, we could end up operating in a more constraining environment that could dramatically hamper the development of the technology and its economic impact.

Q: What do you think the most exciting opportunities for synthetic biology are over the next 10 years?

JP: In the journal editorial, I explained that synthetic biology is catalyzing the next industrial revolution. I don’t think that many people could have anticipated in the 60s how the semiconductor industry is shaping our world today. We can only anticipate a revolution of a similar magnitude. It will be very interesting to see how this technology will shape the world of our children.

Although it’s still very early days for Synthetic Biology, it has already started to publish some great research, with four articles having been published this year. Two of these are experimental articles. One paper describes a biosensor for high throughput screening in metabolic engineering of yeast whilst the other paper describes a method to quickly assemble BioBrick parts.

Synthetic Biology also published two computational articles. A theoretical article proposes a network of chemical reactions capable of computing logarithms and a software paper describes an application to analyse the robustness of regulatory networks.

Submission process

On the submission process, Prof. Peccoud commented “I am very grateful to the editorial board who has set very rigorous peer-review standards. This policy translates in a fairly low acceptance rate. None of this would be possible without the efforts of the hundreds of anonymous reviewers who have generously volunteered their time to help us evaluate the submissions. The number of submissions is increasing steadily but now that our processes are running smoothly, we are certainly able to handle a larger volume of submissions.”

Ready to publish your research? Synthetic Biology currently has an open call for papers for a special issue on cell-free expression systems. This includes gene circuits, metabolic engineering, synthetic cell systems, self-assembly and TXTL and material science.

Synthetic Biology are kind sponsors of our annual Symposium at the Spanish National Centre for Biotechnology in Madrid from the 31st of August to the 1st of September. For more information about Synthetic Biology, to sign up for new content alerts, or to submit an article for publication, visit their website.