Synthetic Biology Workshop, Davidson, July 2010
Contents
Synthetic Biology Meeting Report Draft 2
This is the draft that Mike Wolyniak emailed.
(I was getting confused, so I tried to reorganize things, and put all the comments in one place (below the text of the draft). I hope this works for you. - JS)
BUILDING BETTER SCENTISTS WITH SYNTHETIC BIOLOGY: A MEETING REPORT FROM THE GENOME CONSORTIUM FOR ACTIVE TEACHING (GCAT) WORKSHOP 2010
Synthetic biology can be defined as the application of engineering and mathematical principles to create novel biological devices and circuits. What separates synthetic biology from standard molecular biology is the development of standardized interchangeable DNA “parts” in similar fashion to how advances in engineering in the 19th century brought about standardized railroad gauges and screw threads. Through the use of this set of “parts”, laboratories around the world can easily exchange and combine biological constructs to develop novel “machines” for a variety of applications (Ferber et al., 2004, Purnick and Weiss, 2009), including medicinal chemistry (Martin et al., 2003, Tsuruta et al., 2009), genetic engineering (Hasty et. al., 2002, Sprinzak and Elowitz, 2005), and the creation of bacteria containing a completely-synthesized genome (Gibson et al., 2010).
While synthetic biology can trace its roots to the world’s large research universities, over the last five years the field has emerged as an important area for interdisciplinary collaborations between science, technology, engineering, and mathematics (STEM) disciplines at primarily undergraduate institutions as well. Undergraduate student research has become an integral part of synthetic biology in large part because of the National Science Foundation (NSF)-sponsored undergraduate student research Jamboree in 2004 (Campbell, 2005) which evolved into the annual iGEM (International Genetically Engineered Machine) competition at MIT that attracts undergraduate student researchers from around the world to design biological devices that can address a wide range of biological, environmental and mathematical problems. (http://2010.igem.org/Main_Page).
A common problem faced by primarily-undergraduate institutions is the lack of funding and material support needed to adequately expose students to modern molecular biology, including synthetic biology. To help alleviate this problem, the Genome Consortium for Active Teaching (GCAT) was founded in 2000 by Malcolm Campbell at Davidson College to act as a central clearinghouse both for the purchase and reading of microarrys and for information on how to execute genomics experiments at undergraduate institutions. In response to the evolution of molecular biology in the last decade, Campbell, along with Davidson colleague Laurie Heyer and collaborators Todd Eckdahl and Jeff Poet of Missouri Western State University, organized a Howard Hughes Medical Institute (HHMI)-sponsored GCAT workshop at Davidson in July of 2010 to further explore how to bring synthetic biology to the undergraduate classroom and laboratory and how faculty from multiple disciplines could work together to promote these programs. The workshop was attended by a biologist and non-biologist pair from 15 primarily undergraduate institutions with the goal that each pair could begin the mental preparations necessary to bring multidisciplinary synthetic biology activity to their respective institutions (See Figure 1 for the organizers and participants).
MEETING THEMES AND EVENTS
A number of themes appeared frequently throughout the workshop:
---Synthetic biology requires a new way of thinking for most scientists: to view problems through the lens of an engineer and consider issues of standardization, modularity, abstraction, and modeling and their applicability to the problem at hand.
---Synthetic biology is an excellent pedagogical and research tool to foster interdisciplinary work and learning. Successful interdisciplinary work requires everyone to work at frequent communication, to learn how to speak the language of each others disciplines, and to think about problems in novel ways.
---Synthetic biology is incredibly flexible: almost any scientific interest can be accommodated within the field, and this makes it relatively easy to find projects that require contributions from all members of a multidisciplinary team. This is important, because if any member of the team feels that their role in the overall project isn't important, the project ultimately won't work.
---This flexibility makes synthetic biology particularly accessible and stimulating for faculty and undergraduate students at small institutions: in most cases, individual faculty members are the sole representative of their academic speciality in his or her department, so having a way to leverage the interests, knowledge, and excitement of colleagues with whom there would normally be little to no communication provides a stimulating opportunity for new directions in research and teaching. Not only are faculty forced out of intellectual comfort zones, but so are students: exposing students to other approaches and ways of thinking as part of a hands-on research experience will give students an unparalleled appreciation of the value and realities of interdisciplinary thinking, something which will be increasingly valuable to them in the future.
---Over several years and several batches of undergraduates, the organizers developed an overall set of goals for the projects they developed with their students: -Everyone (faculty and students) should learn new things. -Everyone should have fun. -The project should contribute to the knowledge base in synthetic biology.
As mentioned more than once during the workshop, these goals are in listed in order of importance: if project participants are learning and enjoying what they're doing, then they’re succeeding. Based on the success that combined Davidson/Missouri Western teams have had at iGEM, it seems that their focus on the first two goals has enabled them to consistently achieve the third as well.
The workshop started with discussions on the fundamental principles of synthetic biology, the suitability of synthetic biology for multidisciplinary research with undergraduate students, the connection and communication between biology and collaborating disciplines necessary for success, and the elements that make up a successful synthetic biology project. The discussions were followed by an introduction to the Biobrick™ standard assembly scheme at the foundation of synthetic biology and the Registry of Standard Biological Parts, a community resource maintained at MIT in which developed or developing parts are listed (http://partsregistry.org/Main_Page). To apply the lessons of the discussions, each pair of faculty worked with the Registry to conceive how to build a “lava lamp”: a DNA construct that would allow bacteria to fluoresce and float in response to stimulation.
The organizers then gave presentations showcasing the exciting outcomes of the undergraduate synthetic biology research conducted collaboratively by Davidson College and Western Missouri State University, including an iGEM gold-medal winning project awarded for the development of a synthetic biology project that satisfied the team’s original biological and mathematical conception of the design.
The workshop was broken up into biologist and non-biologist groups for a time in order to provide the opportunity for discussion between faculty from common disciplines. In these discussions, strategies for identifying areas of common interest and expertise from two different disciplines and developing successful interdisciplinary communication were emphasized.
The ethical issues of designing synthetic biology systems were briefly discussed by both the whole group and in small sessions over lunch with the workshop organizers as well as bioethicists from Davidson. Given that this session happened to be held at the exact time that Congressional hearings on this precise subject were being held on Capitol Hill, the topic was especially relevant to the future of synthetic biology and will no doubt become more significant as the general public becomes more aware of the field.
“Wet lab” time was also provided in which basic PCR and oliginucleotide assembly projects were performed in order to provide a taste of the workbench “nuts-and-bolts” of synthetic biology work. This portion of the meeting was especially valuable to the foundation of collaboration between faculty of different disciplines, since the biologist member of each pair was charged with explaining the principles and practice of the techniques to the non-biologist, and the non-biologist, in turn, provided context about how such techniques could possibly be used in the construction of a biological project that could also address their particular research interests.
The remainder of the meeting was dedicated to the development of potential synthetic biology project ideas for undergraduate research and classroom purposes based on the interests and expertise of each faculty pair as well as the skills learned from the workshop. A diversity of projects were proposed that sought to develop sophisticated research experiences for undergraduates as well classroom laboratory experiences in which synthetic biology provided a foundation for an original research experience (see Powerpoint presentations of all of the proposals at http://www.bio.davidson.edu/projects/gcat/workshop_2010/workshop_2010_results.html)
RESOURCES FOR THE DEVELOPMENT OF SYNTHETIC BIOLOGY PROJECTS
In order to facilitate the transition between ongoing research and synthetic biology multidisciplinary research, a number of resources were presented at the meeting:
---GCAT Listserv: The GCAT Listserv (known as GCAT-L) is an email discussion list that connects faculty members who use (or are interested to use) genomic methods in their undergraduate courses. Messages sent to GCAT-L by any one of its subscribers are distributed to all of other subscribers. Information on how to subscribe and use GCAT-L is posted at http://www.bio.davidson.edu/projects/gcat/GCAT-L.html
---Wiggio/Wiki: To facilitate communication between collaborators on different campuses, Wiggio.com is an online toolkit that is freely available on the Internet that allows file sharing and editing, management of group calendars, posting of links, setting up conference calls, online chat, and sending text, voice and email messages to group members. Group members can define how each is informed about upcoming group activity. The toolkit can be accessed at http://wiggio.com. In addition, the GCAT community Wiki has been setup for use by the GCAT community and is maintained by its users; it can be accessed at http://gcat.davidson.edu/GcatWiki/index.php/Main_Page.
---GCAT Mini-Registry: A mini-registry was provided to workshop participants that contained ten parts that are present in the Registry of Standard Biological Parts. The parts include promoters, Ribosome Binding Sites (RBS), Double Terminators, Red Fluorescent Protein (RFP) and Green Fluorescent Protein (GFP).
---GCATalog: This catalog, developed by Bill Hatfield at Davidson along with Laurie Heyer and Malcolm Campbell, is freely available and is optimized for use in synthetic biology applications. Using this web-based catalog, synthetic biology users can generate a publically-accessible freezer inventory that allows the synthetic biology community to share commonly used BioBricks™ as well as other biological constructs. (http://gcat.davidson.edu/GCATalog/)
---Open WetWare: In order to promote sharing of unpublished work and protocols between scientists engaged in biological engineering, an open WetWare page was created (http://openwetware.org/wiki/Main_Page). This page has information related to labs working in synthetic biology, course and teaching resources, protocols, and a continually-updated blog. Another related website highlighted as a repository of synthetic biology tools was that of Drew Endy’s laboratory in the Department of Bioengineering at Stanford University (http://openwetware.org/wiki/Endy_Lab). This Open WetWare- linked laboratory website has information on ongoing research, publications and detailed descriptions of projects and tools generated.
WORKSHOP ASSESSMENT
To gauge the effectiveness of the workshop in providing the resources and creative sparks necessary for developing synthetic biology projects in the classrooms and laboratories of its participants, thorough pre- and post-assessment surveys were conducted. The pre-assessment was administered online approximately one month before the workshop and the post-assessment was administered with pen and paper on the final day of the meeting. The questions on the two surveys compared the participants’ pre- and post- workshop perceptions of synthetic biology as a distinct field, as an area for multi-disciplinary collaboration, and as a viable option for their classroom and research programs. The results of the survey comparison revealed a general feeling of excitement and improved understanding about synthetic biology (Figure 2), with the vast majority agreeing with the comment from one participant who stated that “I now feel confident that I understand the basic ins and outs of synthetic biology—what it is and isn’t—as well as how I can implement projects in this area with my students.”
Interestingly, although 75% of workshop attendees had previous experience in basic molecular biology laboratory work, data analysis, and experimental design, only 25% had ever engaged in a previous multidisciplinary collaboration. This trend was reflected in the post-assessment of the meeting as well, as many felt that the forging of collaborative projects that satisfy the intellectual curiosities of faculty from disparate disciplines stood as the most significant challenge for the successful implementation of synthetic biology projects. Several participants noted that the meeting was, in the words of one attendee, “important to meet and establish a network of colleagues,” and it was evident to meeting participants that the establishment of collaborations between different disciplines and between different institutions of all sizes will contribute greatly towards the successful implementation of synthetic biology projects that expose students to the collaborative and multidisciplinary nature of modern scientific research. Indeed, the establishment of multidisciplinary collaborations engendered by this workshop reflects the need for academics from different disciplines to join forces to share ideas and resources in their educational endeavors as obstacles including scarcity of individual college resources and increased competition for research funding threaten to curtail the development of scientific educational opportunities for students (Dodson et al., 2010).
INCORPORATING SYNTHETIC BIOLOGY IN RESEARCH
Research in synthetic biology is an excellent way to bridge the STEM disciplines in a way that is accessible to students. The research is well-suited for undergraduate involvement as evidenced by the increasing number of teams competing at iGEM (129 teams registered for 2010 as of July versus 112 teams in 2009 and 84 in 2008). While the majority of these teams are from research universities, primarily undergraduate institutions such as Davidson College and Missouri Western State University have been successful at the competition and have also published some of their work in peer-reviewed journals (Haynes et al., 2008, Jordan et al., 2009). Also, many undergraduate institutions are well-positioned to pursue projects in synthetic biology since only basic computer and molecular biology resources are needed and the necessary reagents are relatively inexpensive. While iGEM participation allows access to the entire library of available BioBricks™, participation in this program may be cost-prohibitive for many institutions. The GCAT community currently exploring strategies to address this issue but notes that in the meantime it is relatively simple to construct plasmids using BioBrick™ strategies.
There are a number of approaches that may be taken to develop research programs in synthetic biology, which range from student-generated, self-contained summer research projects to long-term, faculty-designed projects designed for student involvement over a number of years. To develop bona fide interdisciplinary projects, it is important to create the time and space for the idea generation. If possible, GCAT suggests attending iGEM as an observer to see first-hand the wide range of approaches to synthetic biology. Closer to home, exploring previous iGEM projects online and the resources GCAT has to offer on synthetic biology can also provide a good jumping-off point. Also, a successful interdisciplinary synthetic biology collaboration is dependent on communication by scheduling regular meetings between partners. The Davidson/Missouri Western team achieves this by holding weekly biology/math colloquia with interested students via Wiggio.com that connects the campuses as mentioned above. Over time, the professors and students gain an appreciation for the interconnectedness of different disciplines and, importantly, have fun in the process.
INCORPORATING SYNTHETIC BIOLOGY IN THE CLASSROOM
The presentations and exercises from the workshop sparked many conversations about ways to use this material in the classroom. The accessibility of parts and the willingness of the synthetic biology community to share knowledge and, potentially, resources with beginners have most participants preparing lab experiences for the coming academic year and beyond.
Brainstorming about ways to make a bacterial “lava lamp” got most of the workshop participants excited to think of the variety of tasks that bacteria can be induced to perform. The designing of a long-term classroom project with a long-range engineering goal in mind could be a very good way to enlist the creative talents of your students. Whether or not it ever got built, contemplating the feasibility of such a project is very likely to elicit significant student buy-in to synthetic biology concepts.
Once the students have taken mental ownership of the overall picture and seized upon a long-term goal, there are innumerable things to try, from straightforward to Byzantine. For example, one might examine whether the dose response of an inducible promoter is linear by creating a promoter + ribosome binding site + GFP plasmid and measuring fluorescence as a function of inducer concentration. Cis-trans effects could be examined by using two plasmids, one carrying kanamycin resistance as well as one structure of interest and one with ampicillin resistance and the other structure. Other variables could include bacterial strain, ribosome binding site, distance between the various components, promoters, etc. Much new learning could occur with the available building blocks, or the students could create new ones to test their pet ideas. It seems that the only limitation is the imagination of the student. Any new creations could be entered into the Registry of Standard Biological Parts and the GCATalog for sharing with the community at large.
SUMMARY
Synthetic biology is a newly-emerging field, in which costs are relatively low and the value of student input can be high. It rewards tackling the sort of interdisciplinary problems that are increasingly important for our students' professional futures but are often difficult to undertake from our traditional disciplinary towers. Undergraduate students have shown both interest and ability in pursuing this research, as the results of 5 years of iGEM jamborees amply testify to their success in this endeavor.
The organizers are considering the possibility of offering additional faculty workshops in future; if they do, the participants of the 2010 meeting believe that there cannot be a more focused, effective, and fun introduction to synthetic biology for those who want to explore this exciting new field.
WORKS CITED
Campbell M.A. (2005). Meeting Report: Synthetic Biology Jamboree for Undergraduates. Cell Biol Educ 4: 19-23.
Dodson MV, Guan LL, Fernyhough ME, Mir PS, Bucci L, McFarland DC, Novakofski J, Reecy JM, Ajuwon KM, Thompson DP, Hausman GJ, Benson M, Bergen WG, Jiang Z. (2010). Perspectives on the formation of an interdisciplinary research team. Biochem Biophys Res Commun. 391(2): 1155-7.
Ferber, D. (2004). Microbes made to order. Science 303, 158 -161.
Gibson D.G., Glass J.I., Lartigue C., Noskov V.N., Chuang R., Algire M. A., Benders G.A., Montague M.G., Ma L., Moodie M.M., Merryman C., Vashee S., Krishnakumar R., Assad-Garcia N., Andrews-Pfannkoch C., Denisova E.A., Young L., Qi Z., Segall-Shapiro T.H., Calvey C.H., Parmar P.P., Hutchison III C.A., Smith H.O., and Venter J.C. (2010) Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science 329 (5987), 52
Hasty, J., McMillen, D., and Collins, J.J. (2002). Engineered gene circuits. Nature 240, 224 -230.
Haynes KA, Broderick ML, Brown AD, Butner TL , Dickson JO, Harden WL, Heard LH, Jessen EL, Malloy KJ, Ogden BJ, Rosemond S, Simpson S, Zwack E, Campbell AM, Eckdahl TT, Heyer LJ, Poet JL (2008 ). Engineering bacteria to solve the Burnt Pancake Problem. J. Biol. Eng 2: 1-12.
Jordan B, Acker K, Adefuye O, Crowley ST, DeLoache W, Dickson JO, Heard L, Martens AT, Morton N, Ritter M, Shoecraft A, Treece J, Unzicker M, Valencia A, Waters M, Campbell AM, Heyer LJ, Jeffrey L. Poet JL Todd T. Eckdahl TT. (2009). Solving a Hamiltonian Path Problem with a Bacterial Computer. J. Biol. Eng. 3:11
Martin V.J., Pitera D.J., Withers S.T., Newman J.D. and Keasling J.D. (2003). Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 21,796–802
Purnick P.E.M. and Weiss R. (2009). The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10, 410-422
Sprinzak D., and Elowitz M.B. (2009). Reconstruction of genetic circuits. Nature 438, 443-448.
Tsuruta H., Paddon C.J., Eng D., Lenihan J.R., Horning T., Anthony L.C., Regentin R., Keasling J.D., Renninger N.S., and Newman J.D. (2009). High-Level Production of Amorpha-4,11-Diene, a Precursor of the Antimalarial Agent Artemisinin, in Escherichia coli. PLoS ONE 4(2): e4489.
Figure 1-- GCAT Synthetic Biology Workshop participants, organizers, and HHMI representatives. Top row (left to right): Laurie Heyer, Jeff Poet, Jeff Matocha, Nathan Reyna (back), Malcolm Campbell, Qiang Shi, Kathy Ogata; second row: Nighat P Kokan, Robert M. Jonas, Santiago Toledo, Vidya Chandrasekaran, Valerie Burke, Yixin Yang, Andrea Holgado, Anil L. Pereira; third row: Todd Eckdahl, Susmita Acharya, Consuelo Alvarez, Paul F. Hemler, Michael J. Wolyniak, Libby Shoop, Paul Overvoorde, Nathan Reyna, Matthew Tuthill, Carl Salter, Chris Jones, Robert Morris, Tom Twardowski, Joyce Stamm, Talitha Washington; Last Row: all participants, Theresa Grana, Leo Lee, Jodi Schwarz, Teresa A. Garrett.
Figure 2—Comparison of pre-assessment and post-assessment of the GCAT workshop by its participants.
Comments on Draft 2
Introduction
JS: Since we talk about modularity, abstraction and modeling in the next section, we might want to explain them briefly here.
JS: I suggest for the last paragraph: In response to the evolution of molecular biology ... to further explore how faculty from multiple disciples could work together to bring synthetic biology to the undergraduate classroom and laboratory.
Meeting Themes and Events
JS: To apply the lessons of the discussions, each pair of faculty worked with the Registry to conceive how to build [suggestion: replace "conceive how to build' with "design"] a “lava lamp”: a DNA construct that would allow bacteria to fluoresce and float in response to stimulation.
Incorporating Synthetic Biology in Research
AP: "The GCAT community currently exploring strategies to address this issue but notes that in the meantime it is relatively simple to construct plasmids using BioBrick™ strategies." could be changed to "The GCAT community is currently exploring strategies to address this issue, but notes that in the meantime it is relatively simple to construct plasmids using BioBrick™ strategies." OR "The GCAT community currently exploring strategies to address this issue [remove "but"] notes that in the meantime it is relatively simple to construct plasmids using BioBrick™ strategies."
First draft
Here are the assignments for sections of the meeting report:
-Intro/Background: Vidya
Workshop Participants - (From TG) 0% RI 22.2% Masters-Granting University 70.4 % Liberal Arts College 7.4 % Community College
-What happened at the meeting--themes: Chris
-What happened at the meeting-- activities: Eric
-Resources provided (Intellectual and physical): Andrea/Anil
-Assessment: Mike/Consuelo
-Future plans/applications of the meeting for participants and non-participants--research: Joyce/Talitha
-Future plans/applications of the meeting for participants and non-participants--coursework: Robert
-figures/graphics: Theresa G.
Please insert your assigned section of the draft under the appropriate subheading. If you have citations in your section, please add them to the Works Cited subheading. After July 16, the agreed-upon deadline for draft submission, please read all paper sections and make your suggestions BENEATH the existing text (10 people making direct changes would get out of control) and put your name next to your suggestions. Mike will consolidate the sections/add transitions/etc and post the complete draft for general editing after the weekend of July 17.
Remember that we are under a fairly stringent 2 journal page limit......be thorough, but be CONCISE! See what I mean, I put my edits in the wrong place.
TITLE SUGGESTIONS Taking the Plunge: Synthetic Biology for Undergraduates and their Mentors:a springboard to synthesis-level thinking for all of us? (look, I used two colons in one title! TG - I'm thinking about synthesis now because the summer research students in our department (& young grad students elsewhere) often have difficulty contextualizing their projects with the literature & reality and it seems that doing an iGEM-style project world really force students& us the tackle this disconnect, though I'm not sure it is appropriate for our paper)
[Meeting report: building better scientists with synthetic biology ..CJ]
INTRO/BACKGROUND
V. Chandrasekaran
Synthetic biology is defined as application of engineering and mathematical principles to create novel biological devices and novel biological circuits. This approach to biology has resulted in advances in medicinal chemistry (Martin et al., 2003, Tsuruta et al., 2009) and in genetic engineering (Hasty et. al., 2002, Sprinzak and Elowitz, 2005). In addition, advances in synthetic biology have led to creation of biological parts with the intention of assembling them into different combinations to create biological devices (Ferber et.al., 2004, Purnick and Weiss, 2009) and the creation of bacteria containing a synthesized genome (Gibson et al., 2010). In the last five years, the field of synthetic biology is emerging as an important area for interdisciplinary collaborations between STEM disciplines at the undergraduate level. Undergraduate student research has been an integral part of synthetic biology with the NSF sponsored undergraduate student research Jamboree in 2005 (Campbell, 2005) and the annual iGEM competition that attracts undergraduate student researchers from around the world to design biological devices that can address wide range of biological, environmental and mathematical problems. (http://2010.igem.org/Main_Page). The HHMI funded GCAT synthetic biology workshop organized by Dr. Malcolm Campbell at Davidson College was focused at teaching faculty, many of whom were from primarily undergraduate institutions, about synthetic biology and opportunities for incorporating synthetic biology in curriculum and undergraduate research as well as for forging interdisciplinary collaborations within their schools. This meeting report will highlight some of the important aspects of this workshop.
[Again, I tried tweaking, but it was stylistic and did not save any paper. RM]
MEETING THEMES
A number of themes appeared frequently throughout the workshop:
1. Synthetic biology requires a new way of thinking for most scientists: to view problems as an engineer would, considering issues of standardization, modularity, abstraction, and modeling and their applicability to the problem at hand.
2. Synthetic biology is an excellent pedagogical and research tool to foster interdisciplinary work and learning. Successful interdisciplinarity requires everyone to work at constantly communicating with your teammates — students and faculty in fields different than your own — and thinking about the problem in new ways.
3. Synthetic biology is incredibly flexible: almost any interest can be accommodated within the field, and this makes it relatively easy to find projects that require contributions from all members of the team. This is important, because if the biologist (or the mathematician, or the engineer, or the computer scientist, or ...) feels that their role in the overall project isn't important, it won't work. Nobody wants to play the fifth wheel.
4. This flexibility makes synthetic biology particularly accessible and stimulating for faculty at small schools and their undergraduate students: most of us are the only [fill in the blank] in our departments, so having a way to leverage the interests, knowledge, and excitement of colleagues we might not otherwise be able to collaborate with is a great situation to be in. Not only are we as faculty forced out of our intellectual comfort zones, but so are our students: exposing them to other approaches and ways of thinking as part of a hands-on research experience will give them an unparalleled appreciation of the value (and realities) of interdisciplinary thinking, something which will be increasingly valuable to them in the future.
[I'd like to replace "them" with "students" above in the statement so are our students: exposing them... TG]
5. The workshop leaders shared with us their goals for the projects they've undertaken:[bulleted list for these 3 items not wikiable, apparently] everyone (faculty and students) should learn new things everyone should have fun the project should contribute to the knowledge base in synthetic biology
As they told us more than once, those goals are in order: if you're learning and enjoying what you're doing, you're doing well. Oddly enough, focusing on their first two goals seems to have enabled them to consistently achieve the third as well.
["in order" meaning "hierarchic"...any other word a bit more clear...maybe just say goal 1 is the most important, followed by 2]
MEETING ACTIVITIES
Yixin Eric Yang
Workshop leaders and participants engaged in two and a half days of intensive discussion, presentations and hands-on wet lab experiences. The workshop started with interactive discussions on topics including the fundamental principles of synthetic biology, the suitability of synthetic biology for multidisciplinary research with undergraduate students, the connection and communication between biology and other collaborating disciplines, the elements that make a good project of synthetic biology, etc. The discussions were followed by an introduction to the Biobrick standard assembly scheme and the registry of standard biological parts maintained at Massachusetts Institute of Technology. Each participant pair worked to consolidate their learning by browsing biological parts and devices from registry to build a DNA construct allowing bacteria to fluoresce and float in response to the presence of arabinose. After the workshop leaders gave project examples revealing the real-world applications of synthetic biology in medicine, energy, environmental science and technology, the participant pairs explored the example projects exhibited on the International Genetically Engineered Machine (iGEM) competitions, and presented their favorite project to the group. In the evening, workshop leaders gave presentations showcasing the exciting outcomes of the undergraduate synthetic biology research collaborated by Davidson College and Western Missouri State University, including an iGEM gold-medal winning project. In the morning of the second day, the participants broke into biologist and non-biologist groups to have the “birds-of-a-feather” discussion. Overcoming the obstacles of identifying common interest, combining expertise from two different disciplines, and communicating using a shared language was the theme of this discussion. The discussion of ethical issues of synthetic biology was also on the agenda of the same morning. Bioethicists joined the lunch to address ethical concerns and answer questions. In the afternoon and evening, each participant pair collaborated by merging their interest and expertise and using what they learned from the workshop to develop a research project of synthetic biology with which they can engage undergraduate students. In the morning of the third day, all participant pairs gathered and presented their synthetic biology project ideas to the whole group. The workshop leaders and all participants were amazed by the creativity and diversity of the project ideas the interdisciplinary teams developed within a half day. The PowerPoint files of all the presentations were deposited on the GCAT website (http://www.bio.davidson.edu/projects/gcat/workshop_2010/workshop_2010_results.html) to share with interested colleagues. In addition to lectures and discussion, the workshop also put participants on wet-lab work each day to develop skills on basic techniques imperative to synthetic biology research including building a new biological part using PCR techniques and oligonucleotides assembly. By working together, pairs learned the potentials of each specialty and helped each other envision the project from a broader perspective. The workshop also created a community resource sharing mechanism including using GCAT-alog, a virtual freezer stock database of standard biological parts developed by Davidson College, “wikis” and online protocol sharing, to support each other in the synthetic biology research and teaching. As a parting gift, each participant pair received a collection of mini-registry of GCAT workshop - ten biological parts of promoters and reporter genes.
[I don't have any suggestions at the moment, but this section is where I'd try to condense first. Depending on how the journal counts things, and if we move the "Resources" section online, I think we're around 2100-2200 words at the moment, which isn't too much above their 2-page suggestion/limit ..CJ]
[Here is a possible condensation. I don't think I left anything out, just shortened descriptions. It saved about 100 words.RM]
The workshop started with interactive discussions on topics including the fundamental principles of synthetic biology, the suitability of synthetic biology for multidisciplinary research with undergraduate students, the elements that make a good project of synthetic biology, etc. The discussions were followed by an introduction to the Biobrick standard assembly scheme and the registry of standard biological parts maintained at MIT. Each team worked to consolidate their learning by browsing biological parts and devices from registry to build a DNA construct allowing bacteria to fluoresce and float in response to the presence of arabinose. After the workshop leaders gave project examples of synthetic biology in medicine, energy, environmental science and technology, the teams explored the projects exhibited at the iGEM competitions, and presented their favorite project to the group. In the evening, workshop leaders gave presentations showcasing the exciting outcomes of the undergraduate synthetic biology research at Davidson College and Western Missouri State University, including an iGEM gold-medal winning project. In the morning of the second day, the participants broke into biologist and non-biologist groups to have the “birds-of-a-feather” discussion. Identifying areas of common interest, combining expertise from two different disciplines, and communicating using a shared language were the themes of this discussion. The discussion of ethical issues of synthetic biology was also on the agenda of the same morning. Bioethicists joined the lunch to address ethical concerns and answer questions. In the afternoon and evening, each team used their interests and expertise and what they learned from the workshop to develop a research project of synthetic biology with which they can engage undergraduates. In the morning of the third day, the teams gathered and presented their synthetic biology project ideas to the whole group. The workshop leaders and all participants were amazed by the creativity and diversity of the project ideas the interdisciplinary teams developed within a half day. The PowerPoint files of all the presentations were deposited on the GCAT website (http://www.bio.davidson.edu/projects/gcat/workshop_2010/workshop_2010_results.html) to share with interested colleagues. In addition to lectures and discussion, the workshop also put participants on wet-lab work each day to develop skills on basic techniques imperative to synthetic biology research including building a new biological part using PCR techniques and oligonucleotide assembly. By working together, pairs learned the potential of each specialty and helped each other envision the project from a broader perspective. The workshop also created community resource sharing mechanisms including using GCAT-alog, a virtual freezer stock database of standard biological parts developed by Davidson College, “wikis” and online protocol sharing, to support each other in the synthetic biology research and teaching. As a parting gift, each team received a GCAT mini-registry—ten biological parts of promoters and reporter genes.
FIGURE 1--Please see [1] [This grainy figure is 400kb and the actual one is 23Mb. I did not want to put the image in Wikimedia commons so I put it on my little website. Suggestions for brightness/contrast?] Figure 1. GCAT Synthetic Biology Workshop participants, organizers, and HHMI representatives. Top row (left to right): Laurie Heyer, Jeff Poet, Jeff Matocha, Nathan Reyna (back), Malcolm Campbell, Qiang Shi, Kathy Ogata; second row: Nighat P Kokan, Robert M. Jonas, Santiago Toledo, Vidya Chandrasekaran, Valerie Burke, Yixin Yang, Andrea Holgado, Anil L. Pereira; third row: Todd Eckdahl, Susmita Acharya, Consuelo Alvarez, Paul F. Hemler, Michael J. Wolyniak, Libby Shoop, Paul Overvoorde, Nathan Reyna, Matthew Tuthill, Carl Salter, Christopher Jones, Robert Morris, Tom Twardowski, Joyce Stamm, Talitha Washington; Last Row: all participants, Theresa Grana, Leo Lee, Jodi Schwarz, Teresa A. Garrett.
[I'd leave the question of brightness/contrast tweaks to the journal; they should know what works best for them ..CJ]
RESOURCES PROVIDED
(Andrea Holgado & Anil Pereira)
In order to facilitate the transition between ongoing research and synthetic biology multidisciplinary research, a number of resources were presented at the meeting.
1. GCAT Listserv: The GCAT Listserv (known as GCAT-L) is an email discussion list that connects faculty members who use (or are interested in using) genomic methods in their undergraduate courses. Messages sent to GCAT-L by any one of its subscribers are distributed to all of its other subscribers. Information on how to subscribe and use GCAT-L is posted at http://www.bio.davidson.edu/projects/gcat/GCAT-L.html
2. Wiggio/Wiki: Wiggio.com is an online toolkit that is freely available on the Internet. The toolkit is designed to make it easy to work in groups. It allows file sharing and editing, management of group calendars, posting of links, setting up conference calls, online chat, and sending text, voice and email messages to group members. Group members can define how they each want to be informed about group activity. The toolkit can be accessed at http://wiggio.com. The GCAT community Wiki has been setup for use by the GCAT community and is maintained by its users. The GCAT community Wiki can be accessed at http://gcat.davidson.edu/GcatWiki/index.php/Main_Page. The International Genetically Engineered Machine (iGEM) competition Wiki at http://2010.igem.org/Main_Page also contains a link to previous iGEM competitions. iGEM competitions are synthetic biology competitions for undergraduate students. Information on projects submitted by students to iGEM 2009 can be found at http://2009.igem.org/jamboree/Project_Abstract/Team_Abstracts.
3. Mini-Registry: A mini-registry was provided at the GCAT Synthetic Biology Workshop, 2010. The registry contains ten parts that are present in the Registry of Standard Biological Parts available at http://partsregistry.org/Main_Page. The parts include promoters, Ribosome Binding Sites (RBS), Double Terminators, Red Fluorescent Proteins (RFP) and Green Fluorescent Proteins (GFP).
4. Online Protocols: The various protocols used by GCAT members are described online at http://www.bio.davidson.edu/projects/gcat/GCATprotocols.html. This page contains a link to Brown lab’s protocol page, http://cmgm.stanford.edu/pbrown/mguide/index.html. Brown Lab is at Stanford University’s School of Medicine.
5. GCATalog: This catalog developed by Bill Hatfield, Laurie J. Heyer, and A. Malcolm Campbell at Davidson College is freely available and was optimized for synthetic biology. Using this web-based catalog, synthetic biology users can generate a freezer inventory and share commonly used BioBricks™ and more. http://gcat.davidson.edu/GCATalog/
6. Registry of Standard biological parts help page: A registry of standard parts to build synthetic biology devices is available at http://partsregistry.org/Main_Page. This dynamic collection was originated in 2003 at MIT with the purpose of simplifying the process of engineering biological devices. New users may also take advantage of the help-page; where detailed instructions related to BioBrick™ Standard Biological Parts repository, assembling and registering are explained.
7. Open WetWare: In order to promote sharing of unpublished work and protocols between scientists engaged in biological engineering, an open WetWare page was created http://openwetware.org/wiki/Main_Page. This page has information related to labs working in synthetic biology, course and teaching resources, protocols and a continually updated blog.
8. Synthetic Biology Tools: One of the highlighted website as repository of synthetic biology tools was Endy’s laboratory at Stanford University, Department of Bioengineering http://openwetware.org/wiki/Endy_Lab. This Open WetWare- linked laboratory website has information on ongoing research, publications and detailed descriptions of projects and tools generated.
[All of the protocols at the link in section 4 are for GCAT's other aspect (DNA microarrays) and don't appear to have anything to do with synthetic biology, so I'd delete it. Given the stringent length limitation, should this entire section ("Resources Provided") be moved to supplemental/online only version? And since these are all electronic or web-based, I'd just call it "Resources" and drop "Provided" myself ..CJ]
ASSESSMENT
M.J. Wolyniak
To gauge the effectiveness of the workshop in providing the resources and creative sparks necessary for developing synthetic biology projects in the classrooms and laboratories of its participants, thorough pre- and post-assessment surveys were conducted. The pre-assessment was administered online approximately one month before the gathering of participants at Davidson and the post-assessment was administered with pen and paper on the final day of the meeting. The questions on the two surveys compared the participants’ pre- and post- workshop perceptions of synthetic biology as a distinct field, as an area for multi-disciplinary collaboration, and as a viable option for their classroom and research programs. The results of the survey comparison revealed a general feeling of excitement and improved understanding about synthetic biology (Figure 2), with the vast majority agreeing with the comment from one participant who stated that “I now feel confident that I understand the basic ins and outs of synthetic biology—what it is and isn’t—as well as how I can implement projects in this area with my students.” Interestingly, although 75% of workshop attendees had basic previous experience in molecular biology laboratory work, data analysis, and experimental design, only 25% had ever engaged in a previous multidisciplinary collaboration. This trend was reflected in the post-assessment of the meeting as well, as many felt that the forging of collaborative projects that satisfy the intellectual curiosities of faculty from disparate disciplines stood as the most significant challenge towards the successful implementation of synthetic biology projects. Several participants noted that the meeting was, in the words of one attendee, “important to meet and establish a network of colleagues”, and it was evident to meeting participants that the establishment of collaborations between different disciplines and between different institutions of all sizes will contribute greatly towards the successful implementation of synthetic biology projects that expose students to the collaborative and multidisciplinary nature of modern scientific research. Indeed, the establishment of multidisciplinary collaborations engendered by this workshop is reflective of the need for academics of different disciplines to join forces to share ideas and resources in their educational endeavors as obstacles including scarcity of individual college resources and increased competition for research funding threatens to curtail the development of scientific educational opportunities for students (Dodson et al., 2010).
[I tried to squeeze this down a little, but could only find a dozen or so words to do without. RM]
(Michael -would you like to insert Figure 2 at the end of paragraph 1 here? Theresa [2] Also, Figure 2 can be altered in any way you please. I combined biologists and non-biologists to keep the data simple since this is a short document. Non-biologists were less comfortable with all the questions, and especially questions D & E questions. I like what you wrote for assessment)
[I'd leave questions of layout/figure placement to the journal editors ..CJ]
FUTURE PLANS:RESEARCH Joyce Stamm and Talitha Washington
Research in synthetic biology is an excellent way to bridge the STEM disciplines in a way that is accessible to students. This research is well-suited for undergraduate involvement, as evidenced by the number of teams competing at iGEM (112 teams in 2009, 129 teams currently registered for 2010). While the majority of these teams are from research universities, primarily undergraduate institutions such as Davidson College and Missouri Western State University have been successful at the competition and have also published some of their work (Haynes et al., 2008, Jordan et al., 2009). Many undergraduate institutions are well-positioned to pursue projects in synthetic biology since only basic computer and molecular biology resources are needed, and the necessary reagents are relatively inexpensive. iGEM participation allows access to the entire library of available BioBricks; however, participation may be cost-prohibitive for many institutions. We are currently exploring strategies to address this issue but note that in the meantime, it is relatively simple to construct plasmids using BioBrick strategies.
There are a number of approaches that may be taken to develop research programs in synthetic biology, which range from student-generated, self-contained summer research projects to long-term, faculty-designed projects designed for student involvement over a number of years. To develop bona fide interdisciplinary projects, it is important to create the time and space for the idea generation. We suggest attending iGEM to see first-hand the myriad of approaches to synthetic biology. Communication by scheduling regular meetings between collaborating partners is essential for successful projects. The Davidson/Missouri Western team achieves this by holding weekly colloquia with interested students via a shared web-based communication system that connects the campuses. Over time, the professors and students gain an appreciation for the interconnectedness of different disciplines and most of all, they have fun.
FUTURE PLANS:COURSEWORK
R. W. Morris
CLASSROOM APPLICATIONS OF SYNTHETIC BIOLOGY
Brainstorming about ways to make a bacterial Lava lamp got most of us excited and thinking of the myriad things that bacteria know how to do. This could be a very good way to enlist the creative talents in one’s students. Whether or not it ever got built, contemplating the feasibility of such a project is very likely to elicit significant student buy-in.
Once the students have taken ownership of the overall picture, there are innumerable things to try, from straightforward to Byzantine. For example, one might ask if the dose response of an inducible promoter is linear by creating a promoter + ribosome binding site + GFP plasmid and measuring fluorescence as a function of inducer concentration. Cis-trans effects could be examined by using two plasmids, one carrying kanamycin resistance as well as one structure of interest and one with ampicillin resistance and the other structure. Other variables could include bacterial strain, ribosome binding site, distance between the various components, promoters, etc. Much new learning could occur with the available building blocks, or the students could create new ones to test their pet ideas. It seems to me that the only limitation is the imagination of the student. Any new creations would be entered into the catalog of parts available to the entire community.
The presentations we saw and the exercises we did sparked many conversations about ways to use this material in the class room. Accessibility of parts and willingness of those who know more to share with those of us who know less have most of us preparing lab experiences for the coming academic year and beyond.
[I think a SUMMARY section should be provided to focus on the questions that Malcolm and Erin Dolan provided us before we began:
SUMMARY Synthetic biology is a newly-emerging field, in which costs are relatively low and the value of student input can be high. It rewards tackling the sort of interdisciplinary problems that are increasingly important for our students' professional futures but are often difficult to undertake from our traditional disciplinary towers. Undergraduate students have shown both interest and ability in pursuing this research, as the results of 5 years of iGEM jamborees amply testify. [new paragraph] The organizers are considering the possibility of offering additional faculty workshops in future; if they do, we think that there cannot be a more focused, effective, and fun introduction to synthetic biology for those of you who want to explore this exciting new field. ..CJ]
WORKS CITED
Campbell M.A. (2005). Meeting Report: Synthetic Biology Jamboree for Undergraduates. Cell Biol Educ 4: 19-23.
Dodson MV, Guan LL, Fernyhough ME, Mir PS, Bucci L, McFarland DC, Novakofski J, Reecy JM, Ajuwon KM, Thompson DP, Hausman GJ, Benson M, Bergen WG, Jiang Z. (2010). Perspectives on the formation of an interdisciplinary research team. Biochem Biophys Res Commun. 391(2): 1155-7.
Ferber, D. (2004). Microbes made to order. Science 303, 158 -161.
Gibson D.G., Glass J.I., Lartigue C., Noskov V.N., Chuang R., Algire M. A., Benders G.A., Montague M.G., Ma L., Moodie M.M., Merryman C., Vashee S., Krishnakumar R., Assad-Garcia N., Andrews-Pfannkoch C., Denisova E.A., Young L., Qi Z., Segall-Shapiro T.H., Calvey C.H., Parmar P.P., Hutchison III C.A., Smith H.O., and Venter J.C. (2010) Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science 329 (5987), 52. [DOI: 10.1126/science.1190719]
Hasty, J., McMillen, D., and Collins, J.J. (2002). Engineered gene circuits. Nature 240, 224 -230.
Haynes KA, Broderick ML, Brown AD, Butner TL , Dickson JO, Harden WL, Heard LH, Jessen EL, Malloy KJ, Ogden BJ, Rosemond S, Simpson S, Zwack E, Campbell AM, Eckdahl TT, Heyer LJ, Poet JL (2008 ). Engineering bacteria to solve the Burnt Pancake Problem. J. Biol. Eng 2: 1-12.
Jordan B, Acker K, Adefuye O, Crowley ST, DeLoache W, Dickson JO, Heard L, Martens AT, Morton N, Ritter M, Shoecraft A, Treece J, Unzicker M, Valencia A, Waters M, Campbell AM, Heyer LJ, Jeffrey L. Poet JL Todd T. Eckdahl TT. (2009). Solving a Hamiltonian Path Problem with a Bacterial Computer. J. Biol. Eng. 3:11
Martin V.J., Pitera D.J., Withers S.T., Newman J.D. and Keasling J.D. (2003). Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat Biotechnol 21,796–802
Purnick P.E.M. and Weiss R. (2009). The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10, 410-422
Sprinzak D., and Elowitz M.B. (2009). Reconstruction of genetic circuits. Nature 438, 443-448.
Tsuruta H., Paddon C.J., Eng D., Lenihan J.R., Horning T., Anthony L.C., Regentin R., Keasling J.D., Renninger N.S., and Newman J.D. (2009). High-Level Production of Amorpha-4,11-Diene, a Precursor of the Antimalarial Agent Artemisinin, in Escherichia coli. PLoS ONE 4(2): e4489.
== Comments on draft 1 == (in addition to what is in the sections)
[Most of my suggestions are minor stylistic/grammar tweaks. Rather than try and insert them all here, even under the corresponding section, I've posted an edited version of the MS as a .pdf on my website [3]. Other comments I include below ..CJ]
I wish the best of luck to our uber-editors, Mike and Consuelo. RM
I hope we can find room for Chris' summary paragraph. It really capsulized what we were about. RM Morris: In Eric's section, I think he meant devices instead of devises, and in Andrea and Anil's section #8 I think the Endy lab is at Stanford, not Sanford. This is my first ever effort at group paper writing using a wiki, so please bear with me. I do not envy Consuelo and Michael's job of giving this one voice, and look forward to seeing the more nearly finished product.
Anil: Morris, thanks for pointing out the typo. I have corrected it. Dear All, I made the following notes on the Birds of a Feather Meeting – Non Biologists. Please include any content as you see fit.
A question was raised regarding the level of mathematics used in synthetic biology as evidenced in some of the projects presented during the workshop. Would mathematicians find the level of math challenging enough to be drawn to the field? It was felt that that even though many mathematicians may not find the mathematics challenging enough, the focus of applying mathematics is in modeling the biological processes involved. This provides a way to compare those results that are predicted, to those that are observed. The mathematical models can be used to predict possible outcomes of a proposed approach and also verify its feasibility before beginning any implementation work. It was also felt that mathematicians might want to know what they could contribute. For example, they could contribute by modeling a diffusion process.
The challenges of inter-departmental collaborations within and across universities were discussed. Since most departments have their own way of approaching things, faculty members who are attempting collaboration might get frustrated with possible impediments. Departments must make changes to foster collaboration. Also, institutional changes must be made as a result of faculty members conducting collaborative research. For example, faculty members on tenure committees must learn that it is quite common for collaborative research papers to have many authors. This does not diminish the contribution of one or more of the authors. Also, the names of authors on papers are ordered differently depending on the field.
The challenges of cross-disciplinary collaboration where the experience level of faculty members in their respective fields might vary, was also discussed. Faculty members who are more experienced in their fields might be frustrated with the lack of adequate explanation provided by their colleagues. For example, a chemistry professor did not receive an adequate response from the junior colleague to a query regarding polymerization.
The issue of how much time non-tenured faculty members must spend with their students for research as opposed to tenured faculty members was discussed. It was felt that while tenured faculty members might have the luxury of attempting new research and yet be unsuccessful, tenure track faculty members might be adversely affected by failure. Pragmatism in choice of research topics and time management was advised.
It was felt that one of the concerns for potential collaborators in the field could be: what constitutes service to the synthetic biology research community? Such faculty members can be informed that contributing parts to the community counts as service to the community. Other concerns could be: how does one become part of the community? How does one contribute to or access shared resources? How can one teach non-biology majors basic concepts in biology? When does one introduce these concepts? How can one better communicate with Biologists? The importance of maintaining a glossary of key abbreviations and their explanations (for example, ds DNA) was discussed. Such a glossary must be readily available to future synthetic biology workshop participants and collaborating non-biologists. It was also felt that some pre workshop material and preparation might help the non-biologists. The instructors explained that they felt a common language could be developed through the interaction of the biologist and non-biologist pairing in the workshop, where the biologist can introduce his/her colleague to basic concepts in biology. Participants agreed that this approach was quite helpful.
[In retrospect, this is going to be an ugly way to multiply-edit a MS; perhaps we should have tried wiggio. Anyway, two full pages of text (taking into account title, headers, etc.) is only about 1900 words. Toss in a couple of figures and there's really no way to do a decent job with this report. Hopefully the editor is holding us to a strict 2-page limit on text only -- right now we're around 2800! ..CJ]
[it feels like, if we are not careful, we may get a camel. You know, the mouse designed by a committee.RM]
Brainstorming for meeting assessment questions and topics for article report
Please place your brainstorming ideas here for both assessment questions(remember that assessment is essential to the final report) and the general goals that should be covered in the report itself.
[Grana 6/4 I like Morris' comment. In addition, what makes me anxious about trying synthetic biology is the time commitment. Teaching undergraduates molecular techniques takes a lot of time. This past year, with my 4-4 teaching load I had difficulty finding even an hour when both my student (who also has labs to attend & happened to own a restaurant) and I were free. Meeting with my other student to teach her the techniques was a bit easier. I'm sure the workshop will address the tools/strategies to make our lives easier..., but perhaps the survey could also address the time commitment reservations someone new to the field may have.]
[Jones 5/19 -- Are the Perceptions of Synthetic Biology/Personal Goals questions below intended for before or after the workshop? I think after would prove more useful, as my answers right now would be a lot of "I don't know (yet)"s, but Qs 13 and 14 are clearly intended to be pre-workshop.....]
Wolyniak 5/25--The questions were drafted to be asked both pre and post meeting. It is anticipated that many if not most of us will have little to say to some of the questions pre-workshop, but that will underly the point that the workshop itself was able to educate us on the nature of synthetic biology since the same questions will be seen a second time.
(Morris, 5/17/10) It seems to me that part of the report needs to convey enthusiasm for this new chunk of biology. Not only do we want people to read and enjoy the article, but we want them to call or email us to ask, "How can I play too?"
Also, the competency list might include working with bacteria as a skill.
PROPOSED ASSESSMENT QUESTIONS
(added by Wolyniak/Alvarez 5/14/10)
Participant’s name:___________________________________
Email:____________________________ Phone:__________________
Thank you for volunteering this information for the meeting report being conducted by the participants of the First Faculty Training in Synthetic Biology supported by GCAT.
Institution Background Information
Institution Name: ____________________
Which of the following best describes your institution (circle one): R1, Liberal Arts, Masters, Other__________________
Approximate number of students across the whole institution:_____________________ Approximate % of undergraduate science/mathematics majors:____________________ Approximately what % of your students are undergraduates?:______________________
To what degree do you feel that your institution actively supports its undergraduates undertaking and completing independent research projects?
1 2 3 4 5 no support------------------------------------------------outstanding support
Briefly explain the support your institution provides for these efforts. Include both financial and academic support options:
Personal Background Information
General Area of Expertise (please circle all that apply):
Biology Chemistry Computer Science Physics Engineering Biochemistry Mathematics/Statistics
Specific Area of Expertise:________________________________________________
How many classes do you teach per semester, including lab sections? ______________
What classes do you currently teach?
For each of the following, please give the number of years of experience performing the indicated task and rate your perceived competency level for each:
1 – None, 2 – Beginner, 3 – Intermediate/Average, 4 – Advanced, 5 – Expert.
THIS WILL BE IN 3-COLUMN TABLE FORMAT (didn't translate well to the Wiki):
Task-------------------Number of Years Experience----------------Perceived Competency Level (please circle one)
Working (i.e. as a technician) in a laboratory environment. 1 2 3 4 5
Using standard laboratory equipment (i.e. measuring devices (scales, etc.), pipettes, etc.) 1 2 3 4 5
Working with DNA 1 2 3 4 5
Designing an experiment 1 2 3 4 5
Data analysis 1 2 3 4 5
Teaching 1 2 3 4 5
Collaborating out of your field 1 2 3 4 5
Others:……………………… 1 2 3 4 5
Briefly describe how you have previously engaged in cross-disciplinary collaboration for your personal research or the research of your undergraduate students. What was the nature of the collaboration and what were the ultimate goals?
Perceptions of Synthetic Biology/Personal Goals
1.) What is your current understanding of synthetic biology? What, if anything, makes synthetic biology a unique field?
2.) How comfortable do you currently feel with teaching synthetic biology to undergraduates?
1 2 3 4 5 Not at all--------------------------------------------------------------------------------Totally
Briefly explain:
3.) How comfortable do you currently feel with conducting synthetic biology-based research projects with undergraduates?
1 2 3 4 5 Not at all--------------------------------------------------------------------------------Totally
Briefly explain: 4.) Do you currently feel your undergraduate students are comfortable with the concepts of synthetic biology?
1 2 3 4 5 Not at all--------------------------------------------------------------------------------Totally
Briefly explain:
5.) Do you think that your undergraduate students will be able to master the concepts of synthetic biology? In your opinion, what would be the best ways for your students to obtain mastery of this subject?
6.) How comfortable do you currently feel with working with individuals outside of your discipline in collaborative research?
1 2 3 4 5 Not at all---------------------------------------------------------------------------------Totally
Briefly explain:
7.) How comfortable do you feel in your ability to establish cross-disciplinary collaborations?
1 2 3 4 5 Not at all---------------------------------------------------------------------------------Totally
Briefly explain:
8.) What resources do you feel will be necessary for you to successfully engage in synthetic biology work? Include all possible resources such as financial support, academic support, GCAT support, etc.
9.) How do you envision utilizing synthetic biology in your student-led research? How will this work ultimately be presented?
10.) How much time and effort do you feel you will be able to put into developing the ideas and materials necessary to successfully conduct synthetic biology work with your undergraduates?
1 2 3 4 5
Very little------------------------------------------------------------------------------as much as it takes
11.) Would you feel comfortable with this preparation effort given your current teaching load?
1 2 3 4 5 Not at all---------------------------------------------------------------------------------Totally
Briefly explain:
12.) Briefly describe what you see as the primary benefits of synthetic biology for your undergraduate students.
13.) What are your personal expectations for this workshop?
14.) What are your reservations about this workshop?
Thank you!
PROPOSED REPORT GOALS
(added by Jones/Reyna 5/13/10)
Jones :Some of the questions that have been tossed out ("How do you want to get out of this workshop?" -- Alive, I hope! ;) seem valuable for the workshop organizers, but not for readers of a meeting report. Some of the things I'd want to know if I were reading such an article would be:
1. What *is* this stuff? (see above)
2. Can I do it in *my* classroom with *my* students? (= translatability)
2a. costs
2b. necessary intellectual level/preparation of students
2c. my effort to learn the necessary ideas
2d. my effort to develop materials
2e. how can I fit it into my current teaching load?
3. What are the benefits for my students? For me?
4. What support is available for me?
5. How can I use this in a student research project?
(provided by Campbell 5/14/10)
Why did you apply?
What are your expectations?
What are your reservations?
Have you tried collaborative research outside your discipline before?
Are you frustrated after day 1?
After 2 days, do you think you can do this or do you have regrets about coming?
Now that day 3 is here, are you feeling energized and realize that sliced bread is nothing compared to this workshop?
etc.
(Alvarez: For each day, a "color chart" will be used to assess day-to-day feelings, frustrations, etc.)
