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State of synbio publishing

The field, or at least the widely used term, of synthetic biology (synbio) started nearly two decades ago. As the field has matured, two PLoS ONE papers have analyzed the publishing data to look at trends, language, and connections among synbio researchers. This data provides snapshots of who’s publishing, what kind of research is being published, when it’s being published, and where it’s being published. The question of why is certainly open for interpretation but the growth dynamics of synthetic biology publishing can give some sense of why a the term has stuck as a useful unifying term.

In 2012, researchers used Thomson Reuters Web of Science publishing data to map where people are publishing synbio research, how those people are connected, and who’s funding it. More recently, three French researchers also used data from the Thomson Reuters Web of Science to assess how synthetic biology the different areas of synthetic biology have grown and interacted. 

Both of these papers draw interesting pictures of how new terms and ideas spread within an new umbrella term for a kind of research. Together these two papers paint give us some answers to the ‘Who, What, When, Where, & Why’ of synthetic biology.

Who:

The broad synthetic biology community is growing and thankfully still taking in lots of newcomers from different backgrounds. The figure below shows the large growth in total publications along with the newcomers ratio for synbio authors. While the ratio of newcomers (1st time authors on synbio papers) is decreasing, the total number of new people publishing synthetic biology work is still increasing.

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Fig. 1 from Raimbault et al. ‘Global population statistics of the SynBio community over time’

Of course early on nearly everyone had to be a newcomer, but many of those scientists have established themselves as part of a core set of very impactful synthetic biologists. Both of these papers try to find who the most significant authors are and end up with mainly the same set of people.

Oldham et al. represented authors with a network and nodes proportional to the number of publications.

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Fig. 7 from Oldham et al. ‘Main authors’

Raimbault et al. attempted to quantify the impact each author is having within a citation network. Here, citation impact and centrality to the network make up the x- and y-axes. The number of publications again determines the node size. 

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Fig. 6 from Raimbault et al. ‘Position analysis of the main actors of SynBio community according to their centrality and impact’

By these metrics, the top right (currently unoccupied) would be the most impactful synbio researcher. Researchers like Craig Venter and Clyde Hutchison (both of J. Craig Venter Institute) have very high citation impact but relatively low centrality. This reflects their high profile publications but relative isolation from the academic researchers.

If you go through many of the top authors by either analysis, you’ll see several institutions overrepresented: University of California at Berkeley, MIT, and Harvard.

There are plenty of other universities who now have strong synbio faculty (see my piece on Chicago for instance), but these three institutions managed to have authors with big early impacts. Part of this was having established researchers transition into what we now call synthetic biology. Several of these labs span synthetic biology and some other more established field which raises that question of what we really mean by ‘synthetic biology’.

What:

Synthetic biology draws from multiple disciplines and has itself diversified to include genome engineering, synthetic gene regulatory networks, cell-free gene circuits, minimal cell/genome construction, and genome engineering. Then within each type of synthetic biology research there are also differences in host cell (E. coli, yeast, mammalian, commensal bacteria, minimal cells, etc.) and in target application of the engineered product.

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Fig. 4 from Raimbault et al. ‘Semantic map showing the structure of 200 most pertinent terms extracted from titles, abstracts, and keywords in the corpus’

Synthetic biology is our umbrella term but the kinds of work called synthetic biology can seem totally disparate. It’s obvious from publications and synthetic biology conferences that the research can be quite different. So the ‘what’ that makes up synthetic biology is not necessarily the details of the research techniques or methods, but it’s the overall approach to forward engineer biology.

Both papers tried to identify key terms used, and Raimbault et al. even looked at how those terms interact. In their figure 4 above, you can see clusters of subfields that can be classified by their terms used. As distinct as some of the subfields are you can see what terms connect them together.

When:

Going off of other timelines or use of the term ‘synthetic biology, we can see the field took off around the turn of century. Since then there has been large growths every year as the field brings in new people and diversifies to include more subfields.

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Modified Fig. 1 from Oldham et al. ‘Publication trends.’

Where:

As already mentioned in the ‘Who’ section there are definite synbio hubs around Boston/Cambridge and the Bay Area in California, but the map below shows even in 2012 there were synbio publications coming from across the globe.

Country Rankings and Organization Distribution Map.
Modified Fig. 4 from Oldham et al. ‘Country Rankings and Organization Distribution Map.’

If you want to track where different synbio labs, companies, or institutions are you can use the synbioproject map. For instance using the interactive map, the U.S. metro areas with the most synbio entities are San Francisco (62),  Boston (55), New York (26), San Diego (25), Washington DC (14), Chicago (11), and Seattle (10). 

Why:

This question can get at two very different questions. Why do synbio research? Or why call it synbio? The are plenty of papers pointing to applications that address the first question and the emergence of a strong roster of synbio companies backs up the usefulness claims.

But why call it synthetic biology? The synbio field overlaps and interacts with more established fields like metabolic engineering. Like most ‘new’ fields, synthetic biology has been mix of new ideas and rebranding of existing research. A new term can bring together new communities of researcher with new forums or conferences. 

For me the usefulness comes from the shared engineering approach and the cross-pollinating of methods or ideas that help push our abilities to engineer biology. Maybe it’s different for you. Let us know in the comments or @PLOSSynbio. We’d love to know why you’re a part of the synbio community.

Read the papers for yourself

Mapping the Emergence of Synthetic Biology (2016)

http://journals.staging.plos.org/plosone/article?id=10.1371/journal.pone.0161522

Synthetic Biology: Mapping the Scientific Landscape (2012)

http://journals.staging.plos.org/plosone/article?id=10.1371/journal.pone.0034368

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