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.



Synthetic biology and de-extinction through the eyes of a science journalist

I met Torill Kornfeldt at the iGEM Jamboree last year in Boston, where she kindly tolerated my less-than-fluent Swedish language skills, and put up with my questions on science journalism and synthetic biology. As her viewpoints are very interesting, I asked her and she agreed to share them with the community; the result is the interview below.

Konstantinos Vavitsas: You have studied biology. What made you transition to journalism, and in retrospect, how do you feel about your choice?

Torill Kornfeldt: I really loved to study biology, and even started a Phd. But I was doing freelance work as a science journalist on the side, and it began to take up more and more of my time and my focus. It took a while, but I eventually realized that I'm a lot happier as a journalist than as a scientist. One aspect is that I now have the opportunity to be a generalist instead of a specialist when it comes to knowledge, I can write about planet formation one week, genetics the next, and behavioral ecology the third. I really love to have that variation and high pace in my work. Another aspect is that I can alternate between longer and shorter deadlines, depending on my focus for the moment. Longer projects, like writing a book, take a year or two, but at the same time I can record radio shows for a few weeks or write short texts that only take a day. 

I sometimes miss the freedom in the academic world, that is something that is hard to find in other areas. As a freelance journalist I am partly creating that freedom for myself, but not quite. On the other hand I really don't miss the hierarchical system within the academic world.

All in all, I have never regretted leaving academia for journalism.

KV: How interested are people in Sweden and in Scandinavia in general about science and synthetic biology? Are there any specific challenges with reporting science in Swedish?

TK: Swedes in general love new technology and we tend to be early adopters of basically everything. :) Most people in Sweden don't really know what synthetic biology is, but so far synthetic biology has induced curiosity, rather than fear and skepticism, in Sweden. That said, swedes are also enormously environmentally-minded, so anything that is perceived as an environmental threat is almost automatically rejected.

Reporting about science in Sweden is always interesting: on one hand people are in general very interested in science and the general level of education is high, which makes my job easer. On the other hand there are very few outlets for science news, since the populations is to small to support too many publications. The public service radio and TV are the main channels from which people in Sweden get their science news.

KV:   You recently published your book (in Swedish) “The return of the Mammoth: the extinct species' second chance”. Can you tell us a few words about it and how you decide to write about de-extinction? What is your personal opinion on this subject?

TK: The book, which is actually going to be published in English as well, is about the handfull of ongoing projects where researchers are trying to recreate extinct species - such as the mammoth, the passenger pigeon and the auroch. But this book also covers research aboutgenetic technologies to help save endangered species or species that have gone extinct very recently.

I choose to write about deextinction partly because it really resonated with my inner 11-year old. Who doesn't feel a bit of a thrill if you think about seeing alive mammoth again? Having that enthusiasm and curiosity to draw from was really important when I needed energy to get me through the tough parts of the work.

The other reason is that deextinction beautifully summaries a lot of the important factors in the emerging genetic boom. Lots of different types of science is involved, so I could explain many different techniques. But it also include a lot of ethical and philosophical concerns, as well as the general question of what kind of world we want to live in.

Personally, I'm still really undecided when it comes to deextinction. The ethical concerns when it comes to individual animals are very real, but on the other hand I do feel that we have an obligation to try to make the world a better place - even if that involves lab-grown rhinos. But the fundamental benefit in this research lies in the basic science, in the discoveries about genetics, embryology, and ecology that this will lead to.

KV: What is, according to you, the biggest challenge and the biggest opportunity of synthetic biology?

TK: When a field develops as rapidly as synthetic biology, and has as many successes and discoveries, it inevitably leads to a slight hubris within the field. It's not so much individual researchers but a general culture of invincibility that slightly permeates conferences, meetings, papers and so on. This is good in many ways, because it creates courageous scientists who try out new things even if they might be impossible. It is even necessary for synthetic biology to develop the ground-breaking tools that I think humanity need. 

But there is also a clear downside to this hubris, where researchers don't stop and think about the implications of there research or might dismiss concerns from the public or from researchers in other fields. Something that might lead to enormous problems.

So the biggest challenge is finding a way to harness that hubris and avoiding at least some of the drawbacks, in my opinion. 

KV: Do you think synthetic biology is inclusive enough? If not, how can this be improved?

TK:There are many ways to think about inclusivity; gender, socioeconomic background, ethnic background, and so on. All of these are extremely important, and since synthetic biology is a relatively young science, there is a real opportunity to try and make it more inclusive than other fields. One way might be to really emphasize that all people - independent of their background - create better results in diverse groups. Diversity is a strength that will make the science produced better, and having different perspectives will create more interesting research questions. In a group where everybody is the same, nobody will have any new ideas.

Torill Kornfeldt is a science journalist, author and lecturer with a focus on biology and biotechnology. Read more on her on her website or follow her on Twitter.

Building a genome from scratch: an interview with Dr. Leslie Mitchell

by  BASF  CC BY-NC-ND 2.0


I had the pleasure to meet Leslie about two years ago during a summer course in Italy. She was one of the instructors, and her lecture about DNA synthesis in massive amounts and with different techniques made me realize I was doing something wrong with my cloning. She is also a very cheerful person, with a very positive attitude. So when I saw the recent synthetic chromosome articles, I contacted her and she was very kind to answer my questions.

Kostas Vavitsas: Recently the Sc2.0 consortium published a series of Science papers reporting the synthesis of five more yeast chromosomes, and you were co-authoring all of them. Can you tell anything from the backstage? How do you find working in a huge consortium and coordinating with labs around the world?

Leslie Mitchell: The Sc2.0 consortium is certainly a unique collaboration. Each team agrees to work on an Sc2.0 chromosome of specific sequence, but has nearly total autonomy in devising a scheme for assembly. While the final product—the yeast cell encoding the designed chromosome—is open source to the research community, new ideas associated with DNA synthesis and chromosome assembly are completely owned by the partner group.

We have worked closely with all the teams around the world, largely driven by a funding mechanism from the National Science Foundation called 'Science Across Virtual Institutes' (SAVI), which has finded yearly, in-person meetings for both PIs and trainees. We have met in locations like Beijing China, London England, Taormina Italy, New York City USA, Edinburgh Scotland, which underscores the international aspect of our project. This coming summer we'll meet in Singapore, coupled to the SB7 Conference.

A great aspect of the project is that we have students from Sc2.0 labs around the world visit the Boeke lab in NYC, and spend 6 months to a year working on various projects, including putting the finishing touches on their synthetic chromosomes. For instance, we have hosted the lead authors of synV (Zexiong Xie, Tianjin University), synX (Yi Wu, Tianjin University), and synXII (Weimin Zhang, Tsinghua University). The visits allow for development of a much more meaningful collaboration and knowledge transfer, as we work side-by-side for many months. Also, it's a lot of fun to get to know collaborators in person, rather than just by email or only at the yearly meetings.

by  Alexander van Dijk  CC BY 2.0

by Alexander van Dijk CC BY 2.0

KV: The Build-A-Genome (B-A-G) course is running for several years now. How has it evolved in time, and how much do you (the instructors) gain from this activity?

LM: The B-A-G Course was introduced in 2007 at Johns Hopkins University, and to date about 200 students have completed it. This includes students majoring in computer science, biomedical engineering, biology, chemical and bio-molecular engineering, and biophysics.  Over the years, the workflow in the B-A-G class has changed to accommodate the needs of the project, as well as the decreasing cost of commercial DNA synthesis. Early B-A-G students (2007-2012) worked on the assembly of ~750bp ‘building blocks’ from overlapping 60-79mer oligonucleotides by polymerase chain assembly and typically built about 10kb worth of synthetic DNA. 

With the decreasing cost of DNA synthesis, however, the commercial production of synthetic DNA in this size range became more cost effective in late 2012. The Spring 2013 B-A-G classundertook a new workflow to build ‘minichunks’, or ~3kb segments of synthetic DNA, from building blocks previously constructed in B-A-G or delivered from a synthesis company. In this workflow, students use ‘in yeasto’ assembly, exploiting the native homologous recombination machinery in yeast to assemble minichunks. The minichunk assembly protocol was developed in collaboration with students of the Tianjin University “B-A-G China” course. In the spring semester of 2014, the Johns Hopkins B-A-G students started building ~10kb chunks from minichunks, also using yeast homologous recombination as a cloning tool. Now students are working on SCRaMbLE experiments using different synthetic strains to identify new phenotypes following inducible evolution of Sc2.0 cells.

as we say in the Boeke lab: No control? Out of control!

For the students, I think the most important part of this course is the opportunity to gain an authentic and meaningful research experience. The students also like the fact that their work contributes substantially to an international research project. From my perspective, it is fun troubleshooting the experiments with the students and teaching them the importance of controls to help to interpret results. As we always say in the lab, "No control? Out of control!"

KV: You were a co-author in the Genome Project-Write article. That story gained a lot of media attention, and caused a fair amount of controversy. What is in your opinion the potential impact of this project, both scientific and societal? 

LM: From a scientific perspective, I think one really exciting aspect of GP-write is the concept that de novo design and synthesis can be used to build cells that are more easily measured. A great example of this is the removal of repeats from Sc2.0 chromosomes, which enabled much smoother contact maps for synthetic chromosomes in Hi-C experiments, compared to their wild type counterparts (Mercy et al, 2017). This idea gets to the basic premise that we are no longer limited to the study of cells that are a product of evolution, and to me that is infinitely interesting. The study of genetics and cell biology will be revolutionized by the new 'bottom-up approach', where we design and build very precise genetic systems to study cell function.  


as a family friend wrote to me: Pretty exciting but a bit scary for me, how far can this go?

From the perspective of society, this ability to design biology seems daunting – as a family friend wrote to me after the publication of the Science papers: "Pretty exciting but a bit scary for me, how far can this go?” In writing and editing mammalian systems, it is probably naive to rely on altruism, even the best intentions can go awry, and technical limitations will only impede progress on building increasingly complex genetic systems for so long. I'm an advocate for total transparency moving forward with GP-write projects, and for an inclusive approach that engages all interested parties. 

KV: Looking back at your career so far, what is the advice you would give to your younger self or to a fresh researcher (PhD student or junior postdoc) in synthetic biology?

pick a project that you are deeply passionate about—you might find clues in unexpected places.

L M: My biggest piece of advice is to pick a project that you are deeply passionate about—you might find clues in unexpected places. I did my PhD in yeast genetics at the University of Ottawa, in Kristin Baetz's lab, and I studied a protein complex using systems biology approaches. I can remember the exact moment in time when I realized designing and building genetic systems should be my future direction: I modified a plasmid to delete ~180 base pairs of coding sequence—using an absurdly complicated method, but the cloning worked!—and I felt deeply satisfied that I could answer a biological question with my designed system. It was a very small success in the grand scheme of things, but affected me pretty significantly. When Jef Boeke offered me the chance to participate in building an entirely designer synthetic genome, I couldn't believe my luck!!  It's been a great experience working on Sc2.0 and I feel just as excited today as I did on day one.

Leslie Mitchell received her PhD from the University of Ottawa in Canada and is now a postdoctoral fellow in the lab of Jef Boeke at NYU Langone Medical Center.  She is interested in chromosome and genome engineering in both yeast and mammalian systems and has worked on all aspects of the international Synthetic Yeast Genome Project, Sc2.0, which aims to build a designer yeast genome from scratch.

3 Questions for Dr. Claudia Vickers

The "3 Questions For" series (this time 3+1) changes continent to get the insights of Dr. Claudia Vickers. Dr. Claudia Vickers currently holds joint positions as Future Science Platform in Synthetic Biology Leader at CSIRO and Associate Group Leader at the Australian Institute for Bioengineering and Nanotechnology, The University of Queensland. Read more about her and her research in her personal and her research group’s website, and follow her on Twitter.


When and why did you move into the field of synthetic biology?

Synthetic biology wasn’t really a ‘field’ when I did my PhD. Components of molecular biology and other fields segued into synthetic biology over time to become the interdisciplinary field that it now is. So it wasn’t so much moving into a new field, it was shifting the philosophical approach of my research to be more targeted on the design and construction of biological tools. This was something I was doing a lot anyway, so it wasn’t a major shift. I did my PhD in cereal plant engineering, targeting the endosperm of the seed as a bioreactor, but a got a bit dispirited about how long it took to engineer in plants. In the mid-nineties there was also a lot of anti-GMO activity, and I was concerned that it would be hard to translate the science I was doing to make a difference. So I did some more basic research over a couple of post-docs after that, in legume nodulation and in plant isoprenoids (specifically, isoprene emission). I was still using engineering tools, but was more focused on applying them to examine physiology and biochemistry of plant processes. When I came back to Australia in 2007, I was ready to try something new; that’s when I got into microbial metabolic engineering. Microbes grow much faster than plants, the engineering is much easier, and the potential is much higher. Also, the attitudes to GMOs have changed a lot over the last few decades. We use the tools we develop not just for engineering, but to understand basic metabolic processes, in particular, regulation of isoprenoid pathways. Isoprenoids are a really interesting class of natural products – heaps of diverse biological functions, and heaps of industrial applications. But that’s another story…



What is the single most important piece of advice that you would give to a current PhD student or a post-doc?

I do lots of career guidance, so I couldn’t possibly restrict myself to one single piece of advice – there’s too much you need to know to make your career work. But I can be (reasonably) concise and summarize in a rough order of priority:

1.      Do what you love. This job doesn’t start and finish when you walk into the door of your building – it’s a part of you 24/7, it’s your personal brand, it forms part of your sense of identity. If you don’t love this job any more, then you need to move on and find something more satisfying. Research science isn’t an easy career path – publishing papers is hard, securing a position can be hard, and the funding cycle can be brutal. You have to love it a lot to do it!

2.      Be a good writer. Writing is the most important skill that you need as a research scientist. You’ll be judged by two metrics in a classical research career: your publication record and your grant funding record. For both, you need to know how to communicate your science effectively, and how to target whatever program or journal you are writing for. The only way to get better is to write more – to write frequently and consistently. And ideally, find someone who knows how to teach you how to write – who can give you constructive and useful feedback. Likewise, be a good public speaker – that takes a lot of practice and constructive feedback too. Be willing to hear all feedback.

3.      Find good mentors, and don’t stay in environments that are not providing you good support. This is especially important for women – and ideally, women need to find good female mentors. It doesn’t have to be your supervisor; I’ve benefitted enormously from career advice obtained during hallway chats and coffee meetings with people outside my line management. Good mentors make a huge difference.

4.      Develop your transferrable skills portfolio. These are key skills both for a research career and for careers outside of research. Something like 0.5 % of people who graduate with a PhD will become a full professor. You are not a failure if you don’t make professor – you’re already highly successful when you start your PhD program. There are lots of great things to do outside the professorial career path – and many of them may be much more satisfying! You have many transferrable skills – writing, the ability to research effectively, communication skills, project management, time management, analytical skills, teamwork skills, etc. Your PhD and ECR career support programs at your institution should be helping you develop these skills. It’s unconscionable for any training system to focus on a career path that only 0.5 % of their constituency will follow.


In which areas do see the main challenges and opportunities for synthetic biology?

Synthetic biology aims to achieve predictable behavior using modular parts. And that’s a huge challenge. Typically we are reverse engineering and repurposing the components, and in many cases we don’t know enough about the biology to get it to behave the way we want it to. I think orthogonality may help solve some of these problems, because it allows relative isolation from confounding cellular interactions. Another issue is the price of DNA synthesis. It’s starting to come down and there are some new techs on the market, but broad-scale reliable and error-free synthesis is still a challenge for large synthesis projects. Finally, a key issue is making sure that we have social license to operate. We come up with all these amazing ideas but if we actually want to make a difference, and make the world a better place, we need to have the general public on board with us. That means it’s our responsibility to engage with the public and talk about our science in accessible ways. Most of the time we are spending tax payers’ money in any case, and that means we really have to take broad responsibility for the science that we want to do.


The Commonwealth Scientific and Industrial Research Organization (CSIRO) decided to invest into making a new synthetic biology platform, of which you are currently the head of. What is the rationale behind this investment and what opportunities do you expect that it will create?

SynBio is the next transformative technology, and it’s moving phenomenally quickly. It’s likely that synbio will underpin innovation and advances in a wide variety of industries going into the future. Australia has many groups working in synbio areas, but unlike other key countries, we have not previously invested to reinforce and strengthen our capabilities. The CSIRO Future Science Platform in Synthetic Biology is a $13 M AUD program aimed at developing a collaborative research ecosystem in synbio across Australia and extending internationally, and fostering significant growth in this critical field. It’s also about building the next generation of science leaders in the field – and as part of that, we are investing in the CSIRO Future Science Fellowships in Synthetic Biology. The call is open now and the closing date is 27th March (see The CSIRO SynBio FSP is built on a philosophy of responsible development of synthetic biology technology; in addition to our experimental research program, and we will have a research program in social, ethical and regulatory aspects of synbio. We have four technical Science Domains: Integrative Biological Modelling, Engineering Novel Biological Components, Assembling Novel Biosystems, and Maximising Impact. Also, we are focusing in three priority Application Domains: Environment & Biocontrol, Chemicals & Fibres, and Organelles & Endosymbionts. We’re currently developing the research program and we are looking to work with all different stakeholders, from experimentalists to social scientists to industry partners. Take a look at the website and contact us ( for more information.

3 Questions for Dr. Louise Horsfall

Those who attended our April symposium remember an engaging diversity breakout session led by Dr. Louise Horsfall. Now she provides with her own insights at our new "3 Questions For" interview.  Louise, a Lecturer in Biotechnology at the University of Edinburgh, is interested in multidisciplinary challenges involving Biotechnology and Synthetic Biology. Read more about her research here and follow her on Twitter.


When and why did you move into the field of synthetic biology?

During my first postdoc I received some great career advice and was pointed in the direction of synthetic biology as a new and potentially important field. Once I found out a little more about the area, I made sure that my next postdoc position was in a synthetic biology lab.


What is the single most important piece of advice that you would give to a current PhD student or a post-doc?

Irrespective of field, I think that PhD students and post-docs need to consider the environment they want to work in, as well as the research area, when choosing laboratories. I was completely inspired when I got to work in a supportive, interdisciplinary research environment that encouraged independence, industrial collaboration and outreach, and it was only then that I realised with certainty that I wanted a career in academia.  


In which areas do see the main challenges and opportunities for synthetic biology?

I think synthetic biology offers us the opportunity to move towards a more sustainable and circular economy, but it is a challenge to understand and appreciate just how far-reaching this opportunity actually is. With a technology that includes biology in its name, it is understandable that it is assumed that any impact will be on the bioeconomy but we need to challenge ourselves to think beyond this.