Synthetic Biology
A look into the controversy on creating new life
Where is the debate in synthetic biology taking place?
Institutional support for research is critical for the success of all endeavors for scientific discovery. For the developing field of synthetic biology, acquisitions of funding, academic and philosophical support are vital as this field evolves into a recognized discipline. Dedicated facilities of all sizes are being established worldwide, making strides in research in synthetic biology.
Google Map of the US Academic Institutions
View STS.015 Map in a larger map
Many institutions and companies, of various sizes, are pursuing endeavors in synthetic biology in the hope to develop novel processes or organisms to foster our knowledge of science, to develop profitable projects, or both. At this time, the field of synthetic biology is still a very new science. As a consequence, there is a high concentration of research in a few geographic areas, collaboration on some projects, and a highly competitive environment for publication. Recognizing these three things, the map displayed above can illuminate one: the geographic distribution of research institutes. The map has tagged the institutions which participate in the OpenWetWare project, a group of laboratories at the forefront of synthetic biology. There is a high concentration of research in California and New England, with a few satellite institutions. This geographic distribution correlates with the location of the most highly ranked and well funded scientific institutions in the country.
It is important when investigating the institutions that are part of OpenWetWare that one is aware of the mission, motivation and direction of these programs. These scientists and lab groups are all interested in freely distributing their protocols and validated results and findings to other scientists and the general public. This effort for free exchange of information to encourage discovery and progress is laudable but is not the typical way that information is presented. Traditionally, researchers are more guarded and protective of their work and a competitive nature may preclude inclusion to OpenWetWare by some scientists who are reluctant to report results in public domain, whereas younger scientists who have less established reputations might be more likely to join and freely share their ideas.
Network of internet traffic between websites talking about Synthetic Biology
Using the main feature of IssueCrawler the network displayed above was generated beginning with the URLs to OpenWetWare and the Synthetic Biology Project. IssueCrawler uses the input URLs in the following manner: a server-side software program crawls the input sites and captures the "outlinks" from the sites found. Outlinks are simply hyperlinks to other sites that are embedded into a particular website one visits. Once the outlinks are identified, the software does a co-link analysis where it crawls the original URLs and keeps the sites that receive at least one link from the original URLs. The process of finding outlinks and performing co-link analysis was performed twice (known as two iterations on the IssueCrawler software) to add extra certainty to the accuracy and correctness of the network. From this analysis, the program automatically generates a network of the sites that link to each other. A network using this method appears above this text.
Examination of this network clearly shows that the dominate form of discussion in the synthetic biology field is in the academic space. With the exception of The New York Times and Esquire, there are few public news companies which are linked in to this network. Most of the websites involved in this network are hosted by universities that have laboratories that are actively researching synthetic biology and are therefore generating information and news about the field. In addition to universities and news agencies, there are a few companies involved in synthetic biology such as Codon Devices, Synthetic Genomics, DNA 2.0, and GeneArt. Participation of the companies in the debate about this research is a key issue since they advocate the advantages of this research and hope to keep regulation at a minimum.
Map of world-wide hubs for internet traffic related to Synthetic Biology
In addition to simply generating the research and results in this emerging field, many of the research institutions host internet pages with information about synthetic biology and have sites for discussion about the field as well. Using the geographic plotting function of IssueCrawler, a matrix of websites which host content related to synthetic biology, was created and their server locations were mapped to the world. It is apparent that most of the internet traffic is being hosted by institutions in the USA, and more specifically in those areas which have a high concentration of research laboratories such as New England and California. However, this map clearly shows that this debate and research is not limited to the USA. There are also internet sites dedicated to synthetic biology hosted throughout West Europe and even in Thailand.
Citation Analysis of Synthetic Genomics
To better understand the field of synthetic biology an analysis of publication on the field of synthetic genomics was performed using the citation analysis software Reseau-Lu. Reseau-Lu is program which incorporates data from search engines such as ISI Web of Knowledge and other scientific search tools and inputs the information into a database. This data can then be analyzed and displayed in visual maps, allowing networks of co-authorship and institutional collaboration to be generated. An initial search using the keywords “Synthetic Genome” was entered into the ISI Web of Science search tool. The search results were sorted by the number of citations each reference had and the top 10 were selected. The citing references of these articles were then collected, i.e. the articles that cited the top ten most cited articles from the synthetic genome search were collected. This generated the pool of references used in the Reseau-Lu analysis.
Publications per year on Synthetic Biology
The advent of some relatively new technologies such as high-throughput DNA sequencing and DNA synthesis have been instrumental in facilitating the explosion of synthetic biology research. As is evident from the bar graph below that, up until the year 2000, there were essentially no peer-review articles published concerned with synthetic genomics. However with the development of technologies previously mentioned, the possibilities of constructing a synthetic genome or organism became more of a possibility and it encouraged more scientists to begin research in the field. As the key enabling technologies become cheaper and more widely available, more investigators become involved with the research. This is evidenced by the dramatic increase in the number of articles written about synthetic genomes, and this is increasing every year. (The numbers for 2009 only reflect a few months of publication.)
Institutes publishing on Synthetic Biology
Through the analysis of the Reseau-Lu data set a list of Institutes, the number of publications, and citations of those publications was generated (see below). The top 50 institutions were listed in rank order either by the number of publications originating from scientists working at that particular institution or by the number of citations attributed to all the papers published from a particular institution. The left column, sorted by publications, displays clearly that the vast majority of publications in the field of synthetic genomics have been published from American universities. Additionally, these universities are clustered in the New England region and California. The right column, sorted by total citations, elucidates the fact that the institutions that publish most often do not necessarily generate the most cited papers. The fact remains that the top 5 most published institutes are in the top 10 most cited, but it is important to recognize that even in this emerging field publishing in volume is not necessarily correlated to having the highest impact research.
Institutional Collaboration
Using the list of publishing institutes and what papers different research centers produce together on Reseau-Lu generated a map of the institutional collaboration taking place in the field of synthetic genomics. This map allows one to see how the scientists in this field are talking to one another through mutual publications between universities. It is clear from the general layout that there are three major collaborative groups: one headed by Stanford University, another headed by University of Oxford, and one headed by MIT and UC Berkeley. Each of these groups has a very tight cooperative network with the other institutions in the groups. Additionally there are schools such as Harvard, BU, Cal Tech, and UCSF which are not part of any particular group but rather act to interact with all three of the major groups and exist independently. This sort of collaboration, very narrow or close collaboration, is typical of an emerging field like synthetic genomics. It is critical that scientists collaborate with colleagues who have different skill sets to allow them to advance their research. Young fields of science afford aggressive groups to make independent significant exciting discoveries and develop academic recognition and reputation. Scientists in more developed scientific disciplines cooperate more diffusely and share more openly as there is a better established fund of knowledge