Team:UNebraska-Lincoln/Safety
UNL 2017
Helping reduce methane emissions from livestock
Safety Cases and
Their Use in iGEM
Competitions
Introduction:
With a field like synthetic biology making leaps and bounds every year towards a realization of industrial and commercial use, safety is at the forefront of the minds of individuals deciding whether or not to start incorporating genetically modified organisms into their daily routines. Whether it be executives of large drug companies and industrial leaders looking for a cheaper solution in biosynthesis or simply a consumer debating the pros and cons of buying a product with a “GMO” label, people want to be certain that this new and exciting opportunity will be safe for both them and their community. Synthetic biologists are no strangers to safety themselves while working with biohazardous materials and inside high-tech biology labs, but sometimes the safety of the end-goal, products, and processes utilized by people everyday can elude even the most well thought-out projects. This page hopes to help these projects work towards a safe implementation by logically breaking down and analyzing their safety concerns using Safety Cases (Cohen et al, 2016).
Safety Cases take their design strategy from the aeronautics and software engineering communities (Kelly and Weaver, 2004) where they can also be seen under the title Assurance Arguments using Goal Structuring Notation (GSN). There they are used to ensure the safety of various parts of the aircraft as a whole and target certain problem areas in the functions and dangers of the process of flight. As one can imagine, airplanes are a complex system of software and sensors that allow the pilot to traverse the skies safely, and in such cases, a systematic approach to addressing and solving every safety concern must be used. Unlike aeronautics, synthetic biologists do not have to worry about engine and wing design or console displays, but they do have to worry about accidental release of bacteria and plasmid conjugation as well as other concerns. As synthetic biology grows to new heights and levels of complexity, the number of safety concerns a single project or application needs to address will also grow. Just as people trust the engineering of an airplane despite the many risks, Safety Cases can help people who use genetically modified organisms feel confident that what they are using is safe.
Safety Case Units and Structure:
Safety Cases use an organized combination of structural units to help build arguments that prove the root goal of a project is safe. These units include Goal, Strategy, Context, Justification, Assumption, and Solution (Kelly and Weaver, 2004). As seen in Figure 1, each safety case begins with a single root Goal (usually stating that some project is safe) with Context units for the intended environmental conditions of the organism and the species and strain of the organism in use.
Figure 1
A Strategy (usually beginning with the word “Argument”) is then used to break that Goal down into smaller sub-Goals that each address a particular aspect of the project. A few examples of Strategies include “Argument over safety of distinct life stages of the product” and “Argument over identified hazards” (Many times one can’t explore all of the identified hazards in a situation. In this case, one would use a diamond (mentioned below) to symbolize the fact that there may be things in this area that need to be considered further.).
Justifications can be used to provide reasoning for a certain Strategy or Goal by reminding the viewer of certain facts established elsewhere. An example is provided in Figure 2. If a Strategy is “Argument over kill-switch parts” and is used with the Goal “Organism is safe in case of accidental release” and a sub-Goal “Organism is killed in the presence of 0.5 mM of HCl”, a Justification could further enhance the sub-Goal by stating “0.5 mM of HCl is not found in the intended environment”. Likewise, Assumptions can be used to narrow the scope of a Strategy or Goal. A good use of the Assumptions might be to state that one is assuming that some toxic chemical is not going to be added to the intended environment. One should also include these parameters in the initial Context units at the root of the Safety Case.
Figure 2
Solutions are used to provide closure to Goals, their parent-Goals, and Safety Cases themselves. A few examples can be seen in Figure 3. They can take the form of experimental data, modeling data, etc. The specific type of Solution that should be used is determined by the Goal they are solving and ultimately, the person filling out the Safety Case. A Goal is considered solved if there is a Solution unit directly following it, and a parent-Goal is considered solved if every one of its child-Goals is solved. Solved Goals can also serve as a valid Solution unit.
A Safety Case is considered solved if its root Goal is solved. If a possible solution can be identified but no evidence exists to support it, a Future Solution can be used as a placeholder until it can be confirmed with sufficient evidence.
If a creator of a Safety Case wishes to convey that a certain Goal or Strategy is not fully developed and needs more consideration before finalization, they attach a diamond onto the unit. A diamond on a Goal can denote a need to think of more Strategies, and a diamond on a Strategy can denote a need to think of more sub-Goals. Diamonds do not necessarily mean that a creator did not think about a particular branch of a Safety Case. It only means that the creator of the Safety Case is addressing a need for more consideration.
Figure 3
In GSN, each type of unit has its own unique shape to better organize the information. Goals are represented by rectangles, Strategies are parallelograms, Contexts are shown with rectangles with rounded corners, and Solutions are circles. Both Justifications and Assumptions are represented by elipses with subscript “J” and “A” respectively. Future Solutions, not found in GSN formatters, are shown with rounded triangles. A table with all the shapes can be found at the bottom of this section.
Safety Cases provide flexibility in structure. Two different teams working on the same project could structure their Safety Cases very differently while still maintaining a high level of safety. However, there are certain rules that should be followed when developing the structure of a Safety Case. First and foremost, the first unit should be a Goal with two Context units describing the scope of the Safety Case: Environment and Organism. The Environment should include ranges of pH, temperature, and other factors such as exposure to light and specific substances. The Organism should include the species and strain of the organism(s) that the Safety Case applies to. Secondly, the general pattern moving down a Safety Case should be as follows: Goal, Strategy, Goal, . . . , Strategy, Goal, and finally a Solution/Future Solution. Finally, every child should be more specific than its parent and work towards a solution for its parent.
Modularity of Safety Cases for iGEM:
Our vision for the use and application of Safety Cases in iGEM competitions in the future hopes to address the growing concerns of the public surrounding the capabilities and safety of large-scale projects in synthetic biology. We believe the inclusion of Safety Cases in not only fully formed iGEM projects but also in basic and complex parts in the iGEM registry could help change the views of those still skeptical of the safety involved in synthetic biology. This includes an approach to modularity.
The modularity of Safety Cases can already be found in common practice in the aeronautics industry, but we think that iGEM calls for an even higher level of modularity. We hope that the use of Safety Cases will become common enough in iGEM that each part in the registry could come with its own Safety Case called a SafetyBrick. SafetyBricks will include specific precautions teams should take into consideration when using the BioBricks they are associated with and the Environment and Organisms the BioBrick has been proven to work safely in. Using these SafetyBricks, iGEM teams and other synthetic biologists could build complex system with a better understanding of how thoroughly the parts they use are characterized and how they might interact. In order for a team to use a BioBrick in its project, the Environment and Organism included in the part’s SafetyBrick must be fully included in their project’s Safety Case Environment and Organism to ensure predictability.
Safety Case Templates and Patterns:
Looking deeper into Safety Cases for a particular industry, one starts to notice a pattern between Safety Cases for similar projects. Using this, templates could start to be developed and perfected (Kelly and Weaver, 2004). In iGEM and synthetic biology, there exists a wide range of projects, but there are commonalities between some that can be used to help teams develop Safety Cases of their own. However, each project has its own distinct challenges to ensuring safety and this must be taken into account while developing a team’s own unique Safety Case. With more and more teams utilizing this method for ensuring the safety of their project, better investigations can be conducted into how these commonalities manifest themselves in the form of Safety Cases. While it was not in the scope of this project to construct multiple templates for iGEM teams to use, we are confident that after a more general acceptance and practice, templates could be developed and used in the future. UNebraska-Lincoln’s 2017 Safety Case’s base structure (Figure 4) could be seen as the first of these templates, although it is relatively specific.
Our Safety Case
We built our Safety Case with software from Astah GSN. Although this option has limited functionality and no diamond or Future Solution units, it's the only thing dedicated to this kind diagramming. We urge you to try building a Safety Case for one of your ideas. Good luck!
Free Trial of the software can be found here!
General Safety
For lab safety, we wore the following at all times while in the lab:
- Safety Goggles
- Fire Resistant Lab Coats
- Closed-toed Shoes
- Latex Gloves
Additionally, there was at least one biowaste bin in every room of the lab where biohazardous materials or disposable materials that came in contact with biohazardous materials were disposed of properly, separate from other waste. Other items that came in contact with biohazardous material were sterilized and reused. In addition, well marked eye-wash and shower stations and fire extinguishers were included in each room. Also, there were MSDS pages as an online resource that included safety precautions for each chemical found in the lab.
Every team member had to receive lab safety training through UNL's Environmental Health and Safety (EHS) services. We took a total of 6 safety modules including a Biosafety Level 1 course before we were allowed to work in the lab. All modules that required a quiz to be taken had to be completed with 80% proficiency. The modules are listed down below.
- EHS#1: Core - Injury and Illness Prevention Plan (IIPP) -- The Injury and Illness Prevention Plan module is required for all employees who get a paycheck from UNL. There is a quiz following this module. You must pass with an 80% score to complete the module successfully. This module requires approximately 45 minutes to complete. You will need to provide your NU ID number to register.
- EHS#2: Core - Emergency Preparedness Training -- It is recommended that you complete this Emergency Preparedness module AFTER you have taken the Core-Injury Illness and Prevention Plan (IIPP) training module. There is a quiz following this module. This module requires approximately 45 minutes to complete. You will need to provide your NU ID number to register.
- EHS#3: Chemical Safety Training (four individual units) --
Unit 1: OSHA Standards, Safety Data Sheets, Labels, and Door Postings
Unit 2: Physical Hazards of Chemicals
Unit 3: Health Hazards of Chemicals
Unit 4: Hazard Mitigation
Must be completed once by anyone whose work or research may bring them into contact with hazardous chemicals. Note: Units 1-4 replace the Chemical Safety training used through July 2012. This module consists of four units. ALL FOUR UNITS must be successfully completed to meet the requirement. There is a quiz following each unit. If your score is less than 80% on any unit, your registration will not be recorded for that unit. Each unit requires approximately 30 minutes to complete. - EHS#4: Fire Extinguisher Training -- Required once for employees who may opt to use a fire extinguisher. The “Core-Emergency Preparedness” training (#2, above) is a pre-requisite to this course. This course may be taken as a stand-alone unit or as the first part of a two-part training session. Once you have completed the web-based training portion, you may participate in a supplementary hands-on training session. Contact Environmental Health & Safety for more information at (402) 472-4925 or ehs@unl.edu. This training may be replaced by an instructor-led session. There is a quiz following the module. This module requires approximately 30 minutes to complete.
- EHS#5 Personal Protective Equipment (PPE) -- Must be completed once by anyone whose work or research may require use of PPE (for example, gloves, goggles). This training may be replaced by an instructor-led session.
- EHS #6 Biosafety Level 1 -- This training is required of all persons who work at Biosafety Level 1 (BSL-1) containment, upon initial assignment to work in a BSL-1 laboratory at UNL. There is a quiz following the module. This module requires approximately 30 minutes to complete.
Environmental Safety
Environmental safety is of extreme importance to the UNebraska-Lincoln iGEM team. Seaweed is a feed additive that has been proven to reduce methane emissions in cattle and also provides other positive effects. Although seaweed seems like a good option, it has some significant downsides. Large seaweed farms are known to contribute to ozone depletion due to bromoform and other related molecules being created by the seaweed. This bears the question; do we want to fix one environmental issue by creating another one? The UNL iGEM team found this to be a counterproductive option so we decided to utilize the powers of synthetic biology and seaweed to inhibit methanogenesis directly using E. coli. To simultaneously protect the ozone and lower methane emissions in cattle we had to create a kill switch system that would not allow bromoform to be released into the atmosphere. More information about this kill switch can be found HERE.
Works Cited
- T. Kelly, R. Weaver, The goal structuring notation–a safety argument notation. Proceedings of Dependable Systems Networks, Workshop on Assurance Cases, 2004
- M. B. Cohen, J. Firestone, M. Pierobon, The Assurance Timeline: Building Assurance Cases for Synthetic Biology, International Workshop on Assurance Cases for Software-intensive Systems (ASSURE), to appear, September, pp. 75-86, 2016.
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