As this research field begins to develop it is important to identify and understand the key players and their positions in the controversy. The field is mostly composed of scientist and entrepreneurs who are involved in the actual scientific research and the founding of companies, respectively. Each plays an important role and using the Reseau-Lu software it is possible to analyze articles written by the scientist to visualize any connections or collaborations they may have between each other.
Many scientists in the field are acutely aware of the possible issues with the research they are doing and have taken active roles to try to mitigate any fears that could possibly crop up from their research. Dr. Drew Endy has said "I want to develop tools that make biology easy to engineer" (3). He has also, through one of the companies he founded Codon Devices, has been proactive with the media when they pose interesting questions about the ramification of the technologies developed by the company. Additionally entrepreneurial scientists like Dr. Craig Venter have been extremely interested in emphasizing the positive aspects of synthetic biology to make certain that people don't fear the research the he and other are doing.
The Reseau-Lu software is able to generate a map of the authors who co-author papers together. The map below shows the connections between different authors involved in publishing articles under the topic synthetic genome. As one can see, the network is quite diffuse and non-integrated. This suggests that most people involved in this research are working independently, which is something typical for a newly developing scientific field. It is also possible to see that major scientists such as Jim Collins, Jay Keasling, Michael Elowtiz, and J Craig Venter are involved with their own small networks of co-authorship, which represent small groups of scientists working together in the same institutions and sometimes across institutions.
The analysis software is able to map the journals which are connected to each other by publications from one citing a publication in another journal. Below is such a map using the pool of articles which were generated as previously described. In the center of this network are the highest impact articles which many other articles and journals will cite. Importantly this map reveals certain other groups of journals that are involved in this developing field. In the green area there are journals concerned with physics. These articles are generally on the topics of complex networks and how to create computer simulations to model those networks. On the top left in a rose color is the chemistry area and upper blue circle is the concentration of microbiological journals. The light yellow circle in the bottom right has journals specific to biological chemistry and finally in light purple at the bottom of the map are journals more specific to molecular biology.
This map again reveals the early stage of this scientific field, in that it has yet to become its own "circle". People researching synthetic biology are still actively involved in other types of research but come together with others interested in this field to publish on it. Additionally, a field this young must integrate the information from many different fields in order to properly develop and truly become its own area of research. It is likely that in the next decade if this map were to be regenerated, one would easily be able to identify a circle that would belong to synthetic biology as easily as one would one find fields like computational biology and biological engineering currently in this map.
From the pool of articles found which were written about synthetic genomics, Reseau-Lu selected the top 200 cited articles and performed a network analysis of those first authors who cited other authors in the pool of articles. The network generated appears below from the synthetic genomic data set. In green appear two highly co-cited articles written by Drew Endy and in blue are two highly co-cited articles written by Michael Elowitz. On the top left of the network is a small red circle of a article written by Craig Venter, and the large red oval represents the cluster of authors connected to Dr. Venter.
From this network one can see that there are small pockets of co-citation between authors, which likely represents authors who are working at the same institutions. There are also authors like Endy and Elowitz who are not part of any small pocket of research but rather are the corner-stone authors for many other scientist's research articles. Interestingly Dr. Venter appears on this map, suggesting that his research is relatively well cited. However it is important to notice that his name appears in the highlighted red oval because his work is more individual in relation to all the other co-cited papers in the synthetic genomic topic. This is likely because Venter has structured his research endeavors around doing all his studies at his own research institute. This makes it unlikely that scientists outside the Venter Institute will collaborate with them which could lead to the island of co-citation.
Dr. Baker is a Howard Hughes Medical Institutes (HHMI) investigator at the University of Washington. He received his B.A. from Harvard University and Ph.D. from UC Berkeley. The science he is currently focused on is to understand the way proteins fold and why they fold in the particular conformations they do. By understanding how and why proteins fold, Baker and his students have been able to design on a computer a theoretical protein and accurately predict its final conformation. With this technique Baker has been able to synthetic create enzymes with novel sequences to do processes his lab finds interesting. This work is vitally important to the field of synthetic biology because it allows scientists to identify a process they want to change and design a protein or enzyme around their specific problem. Dr. Baker was also involved in founding the biotechnology company Codon Devices.
Dr. Church is a Professor of Genetics at Harvard Medical School. He received his B.A. from Duke University and his Ph.D. from Harvard University. Church is currently actively involved in synthetic biology research, and one major project he is working on is to develop a synthetic bacterial genome "chasse" that can be safely used in mammals. This work is a collaborative effort between Church and Dr. Jay Keasling. Church is heavily involved in the genomic sequencing revolution as he was the co-founder of the MIT and Stanford Genome Sequencing Centers. In addition to being a well known academic scientist, Church has been and is currently involved with many private ventures which spawned from his research. Among the many companies he has been a part Codon Devices and Helicos are two which are playing a vital role in the synthetic biology revolution.
Dr. Collins is a HHMI Investigator at Boston University. He received his B.A. from the College of the Holy Cross and Ph.D from Oxford University; additionally he was a Rhodes Scholar. Most of Collins' work is focused on systems biology in which he reverse engineers natural gene regulatory networks. Once that has elucidated the workings of the network he takes a synthetic biology approach and uses valuable pieces from different networks to construct novel gene networks. His work has helped to develop genetic toggle switches, RNA switches, and programmable cells among other things. These scientific contributions are vital to the foundation of synthetic biology because they are tools which enable other scientists to identify new pathways and create novel processes. Collins is also an advisor to many biotechnology companies like Codon Devices, Epitome Biosystems, and Mannkind Corp.
Dr. Duyk was an Assistant Pprofessor at Harvard Medical School and an assistant HHMI Investigator. He received his M.D. and Ph.D. from Case Western Reserve University. He has previously served on the board of Elelixis and was one of the founding scientists of Millennium Pharmaceuticals. Dr. Duyk is now a director at the synthetic biology company Amyris Biotechnologies. The science that Duyk is involved in through Amyris is critically important to the future of synthetic biology. Amyris is one of the few companies actively trying to commercialize products based on the very young science of synthetic biology. The success or failure of Amyris will be related to the regulatory barriers they must get through to properly sell and market their products could be a telling sign of the willingness of people to accept or reject synthetic biology.
Dr. Elowitz is an Assistant Professor of Biology and Applied Physics at California Institute of Technology. He received his B.A. from the University of California and his Ph.D. from Princeton University. His laboratory work is currently focused on understanding how genetic circuits, both natural and synthetic, allow cells and organisms to make decisions and communicate to each other. The strategy they employ is to study natural systems and based on the knowledge gained from those studies design their own novel circuits. This type of research helps to further the synthetic biology field because it will allow scientist to understand why cells act the way they do in response to certain environmental conditions and scientists will therefore be better able to predict what a particular novel cell or organism is likely to do when challenged by a known environmental condition. Dr. Elowitz was also part of the founding group of scientists who created Codon Devices.
Dr. Endy is currently an Assistant Professor in Bioengineering at Stanford University. He received his B.A. from Lehigh University and his Ph.D. from Dartmouth University. After his post-doctoral work at UT Austin and UW Madison he joined the MIT faculty where he co-founded the MIT Synthetic Biology working group and the Registry of Standard Biological Parts. This registry was created with the goal of providing a resource of synthetic biology researchers to use and enable easy access to standardized biological genes or other functional units. This would be useful to a researcher because using a part from this registry would give them an understanding of how the part functions normally which will make incorporating it into their novel system easier, and make trouble-shooting easier. One of Dr. Endy's long term goals is to make biology "easier to engineer" and this registry is something helping to achieve that goal. Endy co-founded a non-profit foundation called BioBricks which is based off the Registry of Standard Biological Parts, additionally he was a founder of Codon Devices.
Dr. Jacobson is an Associate Professor of Media Arts and Sciences at MIT's Media Lab. He received his Ph.D. from MIT and did his post-doctoral work at Stanford University. Jacobson is currently head of the Media Lab's molecular machines research group and his work focuses on redeveloping microelectronics by pioneering novel ways to both directly and continuously print information or electronics onto different substrates. In addition to his work on electronic printing technologies he has also developed techniques that allow people to externally control biomolecules. This has the potential to allow scientists to design a novel biomolecule and selectively turn it on or off or have it fold or unfold on command. This tool can be extremely useful when trying to engineer complex biological networks because it gives one specific control over what is active and when it is active in the network. Dr. Jacobson's expertise in molecular manipulation and electronic fabrication lead him to be one of the founding scientist involved in Codon Devices.
Dr. Keasling is a Professor in the Department of Chemical Engineering and Bioengineering at UC Berkeley. He received his B.S. from the University of Nebraska and his Ph.D. from the University of Michigan. Keasling's work focuses on targeted engineering of the metabolic pathways of microorganisms. The major goal of this engineering will be to develop microbes which can degrade environmental contaminants and which can provide environmentally friendly biosynthesis. They have developed and use a combination of mathematical models and genetic tools to help specifically predict and direct the evolution of these microbes into the desired end organism. This type of research is fundamental synthetic biology; taking a naturally occurring organism and modifying its genome and metabolic pathways to serve a need someone has identified. Keasling was on the scientific advisory board of Codon Devices before it closed. In addition the Keasling lab is partnered with Amyris Biotechnologies to develop an extremely low-cost solution to synthesize an anti-malarial treatment called Artemisinin.
Dr. Knight is a Senior Research Scientist in MIT's Computer Science and Artificial Intelligence Laboratory. Knight's current research is focused on allowing scientists to effectively engineer biological systems. They strategy they are following is to use the Standard Registry of Biological Parts, which Dr. Knight co-founded with Dr. Drew Endy. Dr. Knight's efforts have been to create the computer models that can accurately predict what will happen when particular parts from the registry are added together in a novel order. Additionally they are trying to develop a more simple "chassie", or starting DNA sequence, that can act to be built on to form new organisms with novel features. This project is similar an earlier project pursued by Craig Venter at the Venter Institute in 2003, however this project will differ because they are using the Standard Registry which will make this an open access project and allow other scientists to build more easily on their system.
Dr. Liu is a Professor in the Chemistry and Chemical Biology Department at Harvard University. He received his B.A. from Harvard University and Ph.D. from UC Berkeley. Dr. Liu is working to apply evolutionary principals to the synthesis of small molecules and macromolecules. As a result of his work, he has developed methods to allow DNA molecules to recombine without sequence homology. Additionally his lab has developed methods to quickly direct the evolution of macromolecules using the fundamentals of biological evolution. These principals will soon be in wide spread use in synthetic biology labs around the world to help scientists design and efficiently synthesize the molecules they need. Dr. Liu is also part of the found team of scientists who created Codon Devices.
Dr. Sinskey is a Professor of Microbiology at HST at MIT/Harvard. He received his Sc.D. from MIT. His work at MIT is currently centered around metabolic engineering with a concentration on the physiology, genetics, and biochemistry of organisms of interest. In this research they are studying the regulation of production and transportation of different biomolecules. The results of this project will help them engineer new organisms to produce molecules of interest and, more importantly, process them in a way which makes them easy to process or collect from the organism. Dr. Sinskey has been involved in founding many companies some of which include Genezyme, Merrimack Pharmaceuticals, Metablix, and LS9 Inc. LS9 is a company that takes direct advantage of Dr. Sinskey's laboratory research by designing microbes to produce petroleum products and secret the oils so they can easily be collected from the top of the growth container.
Dr. Smolke is now an Assistant Professor in the Bioengineering Department at Stanford University. She received her B.S. from the University of Southern California and her Ph.D. from UC Berkeley. Her Ph.D. advisor was Jay Keasling, a scientist who is actively involved in the synthetic biology field. A major focus of her lab is to study and engineer RNA molecules. They are interested in identifying the bioactive properties of RNA molecules. They have developed many novel uses for RNA molecules as molecular switches that can function in biological circuits they design. The ability to design biomolecules to act as predictable switch like entities is extremely useful when constructing novel complex biological networks. The switches allow one to accurately control the downstream product of the switch's action. Dr. Smolke was also involved in founding the company Codon Devices.
Dr. Venter is currently President of the J. Craig Venter Institute which was created and funded by The Institute for Genomic Research. (Now both Institutes are part of the Venter Institute). He received both his B.S. and Ph.D from the University of California, San Diego. Currently Dr. Venter is not heading any scientific research personally, however the Venter Institute is actively researching synthetic biology topics. One such topic is the minimal genome. This project is aimed to produce a minimal set of genes which are required for life (of a particular organism). Being able to generate such a genome would enable the scientist to selectively add genes that made the new organism perform a specific function without wasting its energy or time performing other tasks that the scientists are not interested in. This has large potentials in industrial chemical production or synthesis of pharmaceuticals. Given these possible opportunities, in 2005 Dr. Venter and a few other scientists at the Institute formed Synthetic Genomics Inc. to pursue these ideas in a commercial setting.