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.

1st European Congress on Cell-Free Synthetic Biology

Cell-free synbio community, taken from the webpage

Cell-free synbio community, taken from the webpage


Last March the 1st European Congress on Cell-Free Synthetic Biology took place at the Congressi Stefano Franscini (CSF), a Swiss Federal Institute of Technology of Zurich (ETH, Zurich) division, situated at Monte Verità (south of Switzerland). Top scientists working in the field of cell-free synthetic biology shared their most recent research with a large audience of PhDs, postdocs and PIs. The conference was divided in eight major sessions, four junior researchers’ sessions and a keynote talk, with a broad range of cell-free synbio, from genetic circuits to metabolic engineering.

Richard Murray, opening talk

Richard Murray, opening talk

Richard Murray from Caltech opened the first session, with the inspiring talk ‘Towards genetically-programmed artificial cells in multi-cellular machines’. During his talk he set the basis that will lead us to artificial cells in 10-15 years. He also explained which, he believes, are the main challenges to accomplish such ambitious goal. He mentioned five: i) How artificial should they be?, ii) Which source of power do they require? iii) Can they propagate information? iv) How to integrate multiple systems? v) Which source of motely force could they use? He also highlighted the need of model-based design workflows and more open-source research. Sebastian Maerkl (EPFL) followed the session with his interesting research on microfluidics platforms for the rapid implementation and characterization of genetic circuits. He showed that such an in vitro system resembles quite well the in vivo environment. Finally, Friedrich Simmel (TU Munich) showed that RNA-circuits are capable to perform complicated operations.

After the coffee break, we had the first junior researchers’ session. The talks were given by David Foschepoth (TU Delf), Alice Banks (U. of Newcastle) and Henrike Niderhiltmeyer (UCSD). They presented different systems for the maintenance of genetic networks or minimal genomes, going from platforms fueled solely with PURE systems, to automated platforms for the design and characterization of genetic circuits, and even synthetic shells, with some primordial organelle-like organization.

The second session introduced us to the possibility of generating minimal cells, completely enzyme-free. The first speaker, Erik Winfree (Caltech), with the talk ‘Enzyme-free nucleic acid dynamical systems’ presented the richness of DNA strand displacement for the implementation of basic autonomous and programmable molecular systems, capable to interact with and control their environment. Yannick Rondelez (U.Tokyo), went to the basics and explained the principles of circuits based on DNA strand displacement with his PEN DNA-toolbox. The last talk was given by Georg Seeling (U. Washington), presenting a clear application of DNA strand displacement for disease diagnostic, a fast and reliable technique, cost-efficient when compare with gene expression diagnostic methods. In my opinion, DNA strand displacement seems like a suitable option to program minimal cells, capable of basic tasks with the main advantage that such components are easy to program and characterize.

For the third session, Jørgen Kjems (Aarhus U) presented the versatility of DNA origami. From pores, to compartmentalization, and even direct drug delivery; these were some of the examples of the usefulness of DNA origami towards the assembly of minimal cells. The last talk of the day was given by Paul Freemont (Imperial College). In his talk, he showed that cell-free expression systems (TX-TL) do not only need to rely on E. coli machinery, but it is also possible to get TX-TL systems from other organisms such as Bacillus subtilis or Streptomyces venezuelae, customizing the expression systems upon need.

On the second day, session number 4 covered some recent advances on protein design and the usefulness of cell-free systems for the characterization of such protein entities. Bruno Correia (EPFL) presented his work towards the increase of a structural repertory that later will lead us to the design of functional proteins. Also, Tanja Kortemme, shared her computational pipeline to employ protein-protein interfaces as a scaffold to engineer new functions. On the other hand, Tom de Greef (TU Eidhoven), went back to DNA-based networks and showed how promising are this systems to transform intricate signaling networks into minimalistic circuits.

In the second round of junior talks, Jeo Rollin (NREL) gave us the first example of how cell-free systems are suitable for bioproduction. Nadanai Laohakunakorn (EPFL), gave a great talk on zinc fingers and showed that binding affinity correlates with repression strength. Yong Wu (Caltech) showed TX-TL systems could accelerate the process of design and implementation of novel biosynthetic pathways.

Session 5 was opened by Heiz Koeppl (TU Darmstadt), he gave us a great example of circuits characterization: they characterized a decoupled TX-TL system (TX-only environment), with the purpose to fully understand the dynamics of the implemented circuits. Gašper Tkačik (IST Autria) gave us a great example of how modeling can help understand a biological system. Elisa Franco (UC Riverside) closed the session with a beautiful example on DNA as a way to replace structural functions so far only acquainted by cytoskeletal proteins such as microtubules.

Vincent Noireux, TXTL platform

Vincent Noireux, TXTL platform

After lunch, we had a great talk by one of the pioneers in cell-free synthetic biology, Vincent Noireaux (U. Minnesota). He took us to a tour that covered his first TX-TL system, to the latest version that also includes CRISPR. The session continued with Roy Bar-Ziv (Weizmann) who showed how the combination of different technologies: DNA arrays, microfluidics, and TX-TL systems can be seen as artificial cells capable to be programmable at will. The day ended with Rebecca Schulman’s (Johns Hopkins) talk. There, we got to know that molecular circuits are also capable of some programming chemomechanics. In her research she works with hydrogels in combination of DNA circuits, and such circuits upon stimuli can expand, and this expansion is sequence specific.

On the third day, the first talk of the 7th session was under the charge of Yolanda Schaerli (UNIL). She uses synthetic gene networks to mimic regulatory networks, such as the one present in Drosophila during differentiation. Sven Panke talked about his research done in biocatalysis in cell-free systems: he told us about the beauty of cell-free platforms where all the resources are targeted to the production of a specific compound, rather than to cell maintenance. The session ended with James Bowie (UCLA) who made the point that cell-free biocatalysis can achieve much higher productivity that cell-based. However, there are still some limiting reactions that need to be overcome to get to that point.

In the 3rd junior researchers session, Richar Kelwick (Imperial College) went deeper into the TX-TL system from Bacillus subtilis. Maaruthy Yelleswarapu (Radbound U.) shared his research on cell-free expression platforms, claiming that the main cause of mRNA inactivation is sequence-dependent mRNA secondary structures. Lastly, Alexandar Tayar (Weizmann) gave further details into the programmable artificial cells presented by Roy Bar-Ziv.

On the last day, the 8th session started with Esther Amstad (EPFL), with an interesting talk about on-chip cell-free systems, where, by means of microfluidics devices, screening of different conditions could be tested inside isolated drops in a high throughput manner. Keith Pardee (U. Toronto) was the next on stage, and for me, one of the most exciting talks of the conference. He presented his work on cell-free synbio on paper. He generated paper-based sensors for the rapid and low-cost diagnostic of different diseases, targeting diseases that currently affect humanity, such as Zika. The final talk was delivered by Igor Medintz (US Naval Research). His talk on biocatalysis without cells had an unexpected component, at least for me; the use of quantum dots as a platform to channel reactions and substrate accumulation.

The last junior talks where given by Celine Love (MPI) and Mattheaus Schwarz-Schilling. They talked about cell-like compartments, that could sustain basic cellular functions and capable to even communicate with cells.

Keynote speaker, Petra Schwille

Keynote speaker, Petra Schwille

The final talk was given by my PI, Petra Schwille (MPI). I have to say that she nicely presented the work of many people who have been working towards the reconstitution of a minimal divisome. We are mainly working with components from E. coli division machinery, mainly MinDEC and FtsZ. We expect that a deep characterization of such components will lead us to the primordial division machinery that a minimal cell could use, protein or even DNA based.

The whole conference gave the audience an overview on the state of the art in the field of cell-free synthetic biology. The take home message of this enriching week was that in order to achieve our goal, the generation of a minimal cell, where all the components are known, easy to program and generate, will be achieved by the shared work of numerous research groups. We, as researchers in cell-free synbio need to work together, collaborate, and share our expertise in the different fields where we are currently working on.

Daniela Garcia-Soriano is a 3rd year PhD student working at the Schwille Lab, MPI-Biochemistry. She’s passionate about SynBio and minimal cells. Follow her on Twitter or connect with her on LinkedIn.

EUSynBioS Social at Synthetic Biology UK 2017

The Synthetic Biology UK 2017 conference, principally organised by the Biochemical Society, will be held in Manchester 27-28 November 2017. This event aims to showcase recent research and foster community-building across the UK synthetic biology community.


EUSynBioS will be there, with a surprise: in collaboration with the conference organizers, we will host a networking event right after the conclusion of the formal conference sessions.

This informal social event brings together early-career researchers with industry representatives and academics in synthetic biology.

Join us for a drink from 15:30 to 17:30 in the Atrium of the Manchester Institute of Biotechnology, next to the Manchester Conference Centre (1 min walk)!

Stay tuned for more updates!

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



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.

Extreme makeover yeast edition: de novo synthesis of five chromosomes

Source: Rainis Venta, Creative Commons Attribution-Share Alike 3.0

Source: Rainis Venta, Creative Commons Attribution-Share Alike 3.0

– What I cannot create, I do not understand.

This sentence taken from Richard Feynman’s board at the time of his death essentially captures, if applied to a biological frame, the holy grail of synthetic biology; the understanding of life to such an extent that living systems can be rationally designed to gain and perform specified functions. Synthetic biology is perceived by many as an extension of metabolic engineering, where organisms are modified with end goal to produce a product. This is however part of the story, and the real strength of synthetic biology is the understanding via synthesis, the decomposition of a system to its building blocks and recombination of parts from the bottom up to elucidate the biological complexity.

The construction of a bacterial minimal genome, namely the reduction of the genetic content of Mycoplasma genitalium to 473 genes (1), was hailed as a landmark about a year ago. Last week, a series of seven research articles were published, describing the advancements in the construction of yeast synthetic chromosomes—and as the articles were published in Science, I use this journal’s citation format throughout this blog.

This work is a result of a large consortium, Synthetic Yeast 2.0 , which aims to design and implement a fully synthetic genome of Saccharomyces cerevisiae. The project has existed for several years, and started with the construction of a chromosome’s arms (2), and the first reported synthetic yeast chromosome (3). The recent publications report the synthesis of five more yeast chromosomes, totaling the synthetic sequences to more than one third of the full genome (410). The workflow started from the generation of 700-2000 bp DNA blocks, which are in vitro or in yeast assembled into 10 kb ‘chunks’. A number of chunks are chemically ligated to 30-60 kb ‘megachunks’, which are inserted sequentially into the genome.

Source: Flickr CC BY-NC 2.0

Source: Flickr CC BY-NC 2.0

The new chromosomes contain slight modifications from the native ones (4). The tRNA genes were removed from their original loci, and relocated to a specialized neochromosome. Repeating sequences were also removed, the TAG stop codon was replaced with TAA—leaving TAG open for repurposing, such as incorporation of a non-canonical amino acid. The design took place in BioStudio, an open-source computational framework that allows working in genome-scale (4).

Maybe the most important intervention is the inclusion of recombination sites every 10 kb and after every non-essential open reading frame. Consequently, one can implement SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution) and produce numerous strains with rearranged genetic loci, thus acquiring a powerful tool for directed evolution and functional analysis experiments.

What comes next? According to Jeff Boeke, the consortium expects to have a fully synthesized genome by the end of the year (11). However, having obtained all synthetic chromosomes does not automatically mean that a fully ‘synthetic’ yeast strain will become immediately available;  although strains incorporating one heterologous chromosome do not display a particular phenotype, a strain with three of its chromosomes replaced had a growth defect (5). Issues arising from chromosome interactions and telomere function already show, while more unknown challenges are sure to appear.

The long-term goal of this colossal undertaking is to allow research labs and organizations to routinely use custom-made organisms. This dream seems to come closer and closer, but I do not think it will happen within the next few years. The cost for synthesizing the whole S. cerevisiae genome is estimated to 1-1.5 M dollars, without taking into account salaries and maintenance (4).  But I believe that the scientific insights obtained by this project will affect synthetic biology in multiple ways. And then, why not expand to more organisms? The recent proposal to synthesize a human genome gained a lot of publicity (and controversy).  A minimal or synthetic plant genome [see Marchantia polymorpha, a small liverwort (12), and Physcomitrella patens, a moss where homologous recombination happens with the same efficiency as in yeast (13)] will be leap forwards in understanding and harnessing photosynthesis…

Disclaimer: This post originally appeared at PLOS synbio (link) and is reproduced with permision


  1.    C. A. Hutchison et al., Design and synthesis of a minimal bacterial genome. Science. 351, 6253–6253 (2016).
  2.     J. S. Dymond et al., Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature. 477, 471–476 (2011).
  3.     N. Annaluru et al., Total Synthesis of a Functional Designer Eukaryotic Chromosome. Science. 344, 55–58 (2014).
  4.     S. M. Richardson et al., Design of a synthetic yeast genome. Science. 355, 1040–1044 (2017).
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