Team:British Columbia/Safety

From 2010.igem.org

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<h3>1. Would any of your project ideas raise safety issues in terms of: </h3>
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researcher safety,
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<h3>1. Would any of your project ideas raise safety issues?</h3></center>
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public safety, or
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<p>Our project idea is to engineer a <i>Staphylococcus aureus</i>-specific phage that contains DspB, a biofilm matrix-degrading enzyme and is controlled by a <i>S. aureus</i> quorum-sensing system. In terms of human or animal safety, this engineered phage should not pose any biohazardous risk since it is specific to bacteria and can already be found in nature albeit without DspB. DspB is also found in nature and not harmful to organisms since it serves only to degrade extracellular carbohydrate polymer bonds in the biofilm matrix. Furthermore, the phage and DspB are expressed/triggered by elements of the <i>S. aureus</i> quorum-sensing system when a notable concentration or biofilm of <i>S. aureus</i> is present. Our project ideas should also not have any severe impact on the environment since the phage targets <i>S. aureus</i> biofilms.
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environmental safety?
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The factors of interest in a risk assessment dealing with biological material include: pathogenicity, route of transmission, agent stability, infectious dose, concentration, origin of the potentially infectious material, availability of information, availability of an effective prophylaxis, availability of medical surveillance, experience and skill level of at-risk personnel. Your iGEM project is usually working with a non-infectious host organism (Biosafety level 1 or 2) so you may concentrate more on the engineered parts, devices and systems.  
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The phage standard which we are introducing to the iGEM competition allows basic modification of bacteriophage genomes and must be treated with care. Due to a bacteriophage's higher potential for mutation (as high as 10^-6 mutations per base pair compared to eukaryotes at 10^-8 mutations per base pair) there is a greater chance of catastrophic mutations occurring. It should also be considered that if phage DNA mutates to be harmful in some way, the potential spread is greater because every phage is capable of up to 200 progeny. However, since phage genomes generally range from 15 to 150 kilo base pairs so that the genome can fit inside the capsid, the genomes are highly refined and do not contain much redundant DNA available for novel gain-of-function mutations. In summary, the phage standard does not introduce any inherent risk that is not already present when dealing with phages.
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<br/><br/>If our phage does mutate to become more promiscuous, there are still many barriers in place to prevent it from effectively eliminating other species' biofilms. The phage will still be under the control of the <i>S. aureus</i> quorum-sensing system, and it will unlikely be expressed/triggered in its new infected host. DspB is also only known to degrade <i>S. aureus</i> and <i>Escherichia coli</i> biofilms. Conversely, if the phage mutates to become unable to infect <i>S. aureus</i>, then that phage will fail to infect or replicate. The probability of this happening is moderate considering the great number of phages produced during each infection, but the results are not hazardous as explained.
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From an engineering and scientific point of view, risk assessment deals with the probability that a certain hazard is going to happen. In risk assessment: Risk = probability x hazard
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<br/><br/>If DspB mutates and gains the ability to degrade a greater variety of biofilms, the mutation may not be uncommon in nature although the fact that it is propagated by phage may increase the mutation frequency. Nonetheless, it will still be contained within a phage specific to and only expressed in <i>S. aureus</i>. On the other hand, if DspB loses its function, then the phage will just have to work alone, but there will not be catastrophic consequences. The probability of this happening is moderate based on the rate of mutation in phages and the numbers of phages produced per infection.
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<br/><br/>If the quorum-sensing promoters that control the expression of the phage and DspB mutate to become constitutive or incorrectly activated without the presence of a biofilm, then the phage will simply lyse its host prematurely. If the promoters mutate to become inactivated, then the system will cease to function, but once again there will not be catastrophic consequences. The probability of this happening is moderate as before.
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Probability:
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<br/><br/>If we had to imagine the worst case scenario ever... if the phage manages to target various bacteria AND DspB also degrades various biofilms AND the quorum-sensing promoter becomes appropriate to various bacteria, resulting in widespread degradation of all types of biofilms without control, THEN this would have some environmental ramifications since biofilms are found on most natural surfaces. But the probability of this happening is vanishingly small considering that most bacteria don't even recognize each other's promoters and have internal guard mechanisms to shut down expression of DNA from foreign species.
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<br/><br/>If we had to break through the bounds of imagination to imagine the absolute worst case apocalyptic scenario ever, maybe our phage will mutate into a human-specific virus AND DspB will become able to degrade various polymers in humans AND the quorum-sensing promoter will become a constitutive promoter so that our phage will wipe out the human race. There is no chance of this occuring.
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Could there be an unplanned event or series of events involving your project, resulting in either death, injury, occupational illness, damage to equipment or property, or damage to the environment? How likely is that going to happen?
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Does your project require the exposure or release of the engineered organism to people or the environment (e.g. as medicine, for bioremediation)?
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Hazard:
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Could your device, when working properly, represent a hazard to people or the environment?
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Is your engineered organism infectious? Does it produce a toxic product? Does it interfere with human physiology or the environment?
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What would happen if one or several bioparts change their function or stop working as intended (e.g. through mutation)? How would the whole device or system change its properties and w hat unintended effects would result thereof?
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What unintended effects could you foresee  after your engineered organism is released to the environment?
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Try to think outside the box, what is the absolut worst case scenario for human health or the environment, that you could imagine?
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Risks need to be seen in conjunction with the benefits. Although we would like to decrease the risk to absolute zero, this is hardly possible. So the question is not so much if something is safe or not, but rather if it is safe enough! Deciding whether a risk is acceptable or safe enough is no easy task and people may have different opinions. A whole professional field, so called risk management deals with that issue.
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<h3>2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,
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did you document these issues in the Registry? </h3>
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how did you manage to handle the safety issue?
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How could other teams learn from your experience?
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Datasheets on registered biobricks already contain some but few information on safety. For example, reliability of parts is be included, distinguishing genetic reliability and performance reliability that describe the number of generations it takes to cripple 50% of the circuits in the cells. This is a first step towards a more comprehensive safety characterization of biological circuits, but more detailed safety characterizations will be necessary to do a proper risk assessment to decide whether or not a device is safe enough for your particular application. Your contributions to documenting safety issues in parts, devices and systems are therefore greatly appreciated!
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Here are some examples how you could document your work:
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Parts: Most bioparts will not pose any safety problems, but some can. The simplest example would be a part that encodes for a toxic protein (e.g. Botox, botulinum toxin, or ricin WIKI link). Other parts may produce milder toxins or anaphylatoxins (causing allergic reactions in some people). The fact that a protein can be toxic doesn't automatically mean that you cannot use it, some proteins are helpful pharmaceuticals in lower doses but become toxic in higher doses. In general the safety categorization of parts would best be based on the conventional BSL 1 to 4 levels and Select Agents and Toxins list (see e.g. the HHS AND USDA Select Agents AND TOXINS list http://www.selectagents.gov/Select%20Agents%20and%20Toxins%20List.html).
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Devices and systems: a genetic circuit could exhibit different safety characteristics than the parts it is based upon. Thus different safety categories should also be used for devices and systems.
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Cell chassis enhancement: Parts that extend the environmental range of a cell chassis, by increasing for example the tolerance of relevant biotic and abiotic conditions, should be documented as well.
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Other questions are: How can a safety issue be reported that was discovered in a certain bio-circuit and that was not foreseen (emergent) so other people can learn from that experience? How can safety and security aspects be integrated into the design process so the design software automatically informs the designer in case the newly designed circuit exhibits certain safety problems?
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<h3>3. Is there a local biosafety group, committee, or review board at your institution? </h3>
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If yes, what does your local biosafety group think about your project?
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If no, which specific biosafety rules or guidelines do you have to consider in your country?
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There is already a number of international and national guidelines, laws and professional associations that you have to consider. Here is an overview of some of them:
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<h3>4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h3>
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4.1. Biosafety engineering
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Synthetic biology holds the potential to make biology not only easier to engineer but also safer to engineer. In many established engineering disciplines (e.g. mechanical engineering, aviation, space flight, electronics, software) safety engineering is already an established subset of systems engineering. (System) safety engineering is an engineering discipline that employs specialized professional knowledge and skills in applying scientific and engineering principles, criteria, and techniques to identify and eliminate hazards, in order to reduce the associated risks. Safety engineering assures that a system doesn't pose a risk even when parts of it fail. This is more than needed in synthetic biology due to the evolutionary forces of biological systems. If synthetic biology is going to become the new systems engineering of biology, then it needs to establish an equivalent subset in safety engineering: biosafety engineering (Schmidt 2009).
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Biosafety engineering could be practiced by designing robust genetic circuits that account for possible failure of single parts or subsystems, but still keep working or at least don't cause any harm to human health or the environment. Safety engineering has many techniques to design safer circuits (systems), for example
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Event Tree Analysis and  
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Fault Tree Analysis
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Both methods are normally used in assessing the safety of engineering systems (e.g. aircraft, space travel, mechanical engineering, nuclear energy) based on standardized parts and true engineering designs.
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In a device or system, for example, a mutation in one of the bioparts could cause the part to become dysfunctional. The Event Tree Analysis (ETA) would look at the way the whole system is going to be affected by the failed part. It will answer the questions: Will the device or system still be able to fulfill its tasks? Will it behave in a different way, and if yes in which way? Or will it shut down completely? Based on this analysis additional safety systems could be installed, such as redundant sub-circuits.  
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The Fault Tree Analysis (FTA), on the other hand, looks at defined unwanted failures of the systems and then traces backward to the necessary and sufficient causes. For example, a genetic circuit should not fail in a way that leads to the overproduction of a particular protein that is regulated by the network. The FTA can show which basic events could cause such an overproduction, and thus help to improve the circuit to avoid these unwanted failure, for example in designing the circuit in a way that all basic events would cause the expression of the protein to diminish but never to increase.  
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The full range of possibilities to include safety considerations in designing biological circuits has not yet been explored in great detail but will be extremely helpful. How could you contribute to make it happen?
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4.2. Designing and using a safer host organims/chassis
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4.3. Public perception of risks and safety issues
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As we work with a technology that is in the public eye, we need to understand that besides scientific risk ''assessment'', as described before, there is also a public risk ''perception'' of what we do. It is useful to understand the "soft facts" of risk perception that, especially in case of lay people, outdo the "hard facts" such as technical or medical expertise. Experts typically define risk strictly in terms of the probability of a certain damage (e.g. mortalities, life years lost, financial loss). Lay people, however, almost always include other factors in their definition of risk, such as catastrophic potential, equity, effects on future generations, controllability, involuntariness and trust in the people responsible. These differing conceptions often result in lay people assigning relatively little weight to risk assessments conducted by technical experts or government officials, instead they use these other factors to form an opinion. See table for some of the most relevant factors affecting risk perception:
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How do you think synthetic biology, and especially the iGEM competition, is perceived by the public? What could you do to influence that?
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There is already heaps of articles on risk perception, for an introduction see:
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<center><img src="https://static.igem.org/mediawiki/2010/2/2d/Ubcs3.jpg"></src>
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<h3>2. Do the new BioBrick parts that you made this year raise safety issues? </h3></center>
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<p>
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Our new BioBrick part, DspB is a biofilm matrix-degrading enzyme and does not raise any significant safety issues. It has been sequenced and assayed for its enzymatic activity and found to be reliable. In the circumstance that a safety incident occurs, users will be able to contact us and we will update the Registry with their report.</p><br></br>
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<center><img src="https://static.igem.org/mediawiki/2010/8/84/Ubcs2.jpg"></src>
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<h3>3. Is there a local biosafety group at your institution?</h3></center>
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<p>
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The local biosafety group for our project is the Department of Health Safety and Environment (HSE) of UBC. Our laboratory space and equipment meets all safety requirements as per Canadian regulations and the regulations of the HSE. All members of our team have also taken the required Laboratory health safety course from our local biosafety group. Presently, our team has not embarked on research using pathogenic bacterial strains or phages. Our research also does not involve the transference of toxins or drug resistance that could compromise the use of the drug to control disease agents in humans, veterinary medicine, or agriculture.</p><br></br>
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<center><img src="https://static.igem.org/mediawiki/2010/5/54/Ubcs6.jpg"></src>
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<h3>4. Do you have ideas to deal with safety issues that could be useful for future iGEM competitions? </h3></center>
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<p><b>4.1. Biosafety engineering and design of a safer chassis</b>
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<br/>
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Current safety engineering tools such as Event Tree Analysis (ETA) and Fault Tree Analysis (FTA) have yet to be extensively incorporated into synthetic biology models. One large obstacle is the fact that organisms are complex and not everything is known about their inner processes and community interactions. So while synthetic biologists are able to make logical predictions regarding their designed part or system, the sphere of knowledge of the chassis is greatly limited. This reason also motivates the current search for a safer chassis-one that is understood inside and out. In order to engineer safety into our synthetic biology parts or systems, it is necessary to attain a good understanding of what it does in its natural setting, design safety elements based on this knowledge and its extrapolation, and then collect experimental data on its behavior and mutability in synthetic settings. Just as conventional safety engineering utilizes real engineering data and designs, biosafety engineering has to become a whole and unique field unto itself. Research in controlled system-destruction is growing, and there will probably be research in the mutability of different types of synthetic biological circuits. One field of research that is instrumental to biosafety engineering is that of the intelligent synthesis of whole genomes from scratch. This will no doubt provide valuable insights as to the workings of the organism in study and also lead to the production of synthetic chassis and systems that are much more manipulable, controllable and predictable.
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<b>4.2. Public perception of risks and safety issues</b>
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Through our human practices project, we are exploring different perspectives of synthetic biology by asking members of the public, as well as iGEM participants, to create art in the form of visual arts or stories conveying their perception of synthetic biology and its potential impact on the world. We hope that by stimulating the public to learn more about synthetic biology and hopefully engaging in a meaningful exchange of ideas, the public will gain a deeper and sounder understanding of what synthetic biology is and how synthetic biologists also seek to install the necessary safety infrastructure. By asking for public opinion, synthetic biologists also have the opportunity to address public concerns and lay a firmer foundation for future synthetic biology ventures and applications in the real world. Since the benefits and consequences of synthetic biology research are shared by both researchers and the public, the two must actively seek to listen, inform and negotiate. Scientific risk assessment may produce quantitative measures of potential damage, but this is only a model of what may happen in reality. In order to validate the assumptions, applicability and foresight of these risk assessment estimates, we need to receive the input of the public, who are representative of real-life data. As the term “human practices” suggests, synthetic biologists who endeavour to develop the human practices aspect of their research must consider the same things that society considers. Will the fruits of our research be accessible to the poor? Are people in charge trustworthy? Will there be potential consequences for future generations? Are there ways for us to control the applications of our research? In other words, our synthetic biology parts and systems are like children born into the world. Scientific risk assessment is careful planning. Engaging with society is the actual raising of synthetic biology children. There has to be an increase in public awareness of what synthetic biology is and what it can do. There also has to be an increase in dialogue (whether through public forums or through art and entertainment) not just within the scientific community but also with the public.
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<h3>Biosafety Quick Links</h3>
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<p>Biosafety deals with the containment principles, technologies and practices that are intended to prevent exposure to pathogens and toxins, and their accidental release.
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</p>
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<a href="https://2010.igem.org/Safety">2010 iGEM Safety Questions</a><br></br>
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<a href="http://www.who.int/csr/delibepidemics/WHO_CDS_CSR_LYO_2004_11/en/">WHO Biosafety Manual</a><br></br>
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<a href="http://oba.od.nih.gov/rdna_ibc/ibc.html">NIH Institutional Biosafety Committees</a><br></br>
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<a href="http://www.cdc.gov/biosafety/">CDC Office of Health and Safety</a><br></br>
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<a href="http://www.hse.ubc.ca/welcome.html">Health Safety and Environment, UBC</a><br></br>
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<br></br><br></br>
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<img src="https://static.igem.org/mediawiki/2010/4/46/Ubcs5.jpg"></src>
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<h3>Risk Perception Quick Links</h3>
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<p>Risk perception is the subjective judgment that people make about the characteristics and severity of a risk.</p>
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<a href="http://www.synbiosafe.eu/">Synbiosafe</a><br></br>
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<a href="http://www.markusschmidt.eu/pdf/Intro_risk_perception_Schmidt.pdf">An Introduction</a><br></br>
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<a href="http://www.cepis.ops-oms.org/tutorial6/i/pdf/topic_04.pdf">Risk Perception</a><br></br>
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<a href="http://www.markusschmidt.eu/pdf/slovic_risk-perception.pdf">Placing Risks in Perspective</a><br></br>
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<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2759424/pdf/11693_2009_Article_9031.pdf">Communicating Synthetic Biology</a><br></br>
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<a href="http://syntheticbiology.org/Press.html">Synthetic biology Press</a><br></br>
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<a href="http://ec.europa.eu/european_group_ethics/publications/docs/round_table_ethical_aspects_of_synthetic_biology.pdf">Ethical Aspects of Synthetic Biology</a><br></br>
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<a href="http://www.springerlink.com/content/h81458455710n37n/fulltext.html">Synthetic Biology and Society</a><br></br>
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<a href="http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1264804">Culture and Synthetic Biology</a><br></br>
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Latest revision as of 23:35, 27 October 2010


1. Would any of your project ideas raise safety issues?

Our project idea is to engineer a Staphylococcus aureus-specific phage that contains DspB, a biofilm matrix-degrading enzyme and is controlled by a S. aureus quorum-sensing system. In terms of human or animal safety, this engineered phage should not pose any biohazardous risk since it is specific to bacteria and can already be found in nature albeit without DspB. DspB is also found in nature and not harmful to organisms since it serves only to degrade extracellular carbohydrate polymer bonds in the biofilm matrix. Furthermore, the phage and DspB are expressed/triggered by elements of the S. aureus quorum-sensing system when a notable concentration or biofilm of S. aureus is present. Our project ideas should also not have any severe impact on the environment since the phage targets S. aureus biofilms.

The phage standard which we are introducing to the iGEM competition allows basic modification of bacteriophage genomes and must be treated with care. Due to a bacteriophage's higher potential for mutation (as high as 10^-6 mutations per base pair compared to eukaryotes at 10^-8 mutations per base pair) there is a greater chance of catastrophic mutations occurring. It should also be considered that if phage DNA mutates to be harmful in some way, the potential spread is greater because every phage is capable of up to 200 progeny. However, since phage genomes generally range from 15 to 150 kilo base pairs so that the genome can fit inside the capsid, the genomes are highly refined and do not contain much redundant DNA available for novel gain-of-function mutations. In summary, the phage standard does not introduce any inherent risk that is not already present when dealing with phages.

If our phage does mutate to become more promiscuous, there are still many barriers in place to prevent it from effectively eliminating other species' biofilms. The phage will still be under the control of the S. aureus quorum-sensing system, and it will unlikely be expressed/triggered in its new infected host. DspB is also only known to degrade S. aureus and Escherichia coli biofilms. Conversely, if the phage mutates to become unable to infect S. aureus, then that phage will fail to infect or replicate. The probability of this happening is moderate considering the great number of phages produced during each infection, but the results are not hazardous as explained.

If DspB mutates and gains the ability to degrade a greater variety of biofilms, the mutation may not be uncommon in nature although the fact that it is propagated by phage may increase the mutation frequency. Nonetheless, it will still be contained within a phage specific to and only expressed in S. aureus. On the other hand, if DspB loses its function, then the phage will just have to work alone, but there will not be catastrophic consequences. The probability of this happening is moderate based on the rate of mutation in phages and the numbers of phages produced per infection.

If the quorum-sensing promoters that control the expression of the phage and DspB mutate to become constitutive or incorrectly activated without the presence of a biofilm, then the phage will simply lyse its host prematurely. If the promoters mutate to become inactivated, then the system will cease to function, but once again there will not be catastrophic consequences. The probability of this happening is moderate as before.

If we had to imagine the worst case scenario ever... if the phage manages to target various bacteria AND DspB also degrades various biofilms AND the quorum-sensing promoter becomes appropriate to various bacteria, resulting in widespread degradation of all types of biofilms without control, THEN this would have some environmental ramifications since biofilms are found on most natural surfaces. But the probability of this happening is vanishingly small considering that most bacteria don't even recognize each other's promoters and have internal guard mechanisms to shut down expression of DNA from foreign species.

If we had to break through the bounds of imagination to imagine the absolute worst case apocalyptic scenario ever, maybe our phage will mutate into a human-specific virus AND DspB will become able to degrade various polymers in humans AND the quorum-sensing promoter will become a constitutive promoter so that our phage will wipe out the human race. There is no chance of this occuring.



2. Do the new BioBrick parts that you made this year raise safety issues?

Our new BioBrick part, DspB is a biofilm matrix-degrading enzyme and does not raise any significant safety issues. It has been sequenced and assayed for its enzymatic activity and found to be reliable. In the circumstance that a safety incident occurs, users will be able to contact us and we will update the Registry with their report.



3. Is there a local biosafety group at your institution?

The local biosafety group for our project is the Department of Health Safety and Environment (HSE) of UBC. Our laboratory space and equipment meets all safety requirements as per Canadian regulations and the regulations of the HSE. All members of our team have also taken the required Laboratory health safety course from our local biosafety group. Presently, our team has not embarked on research using pathogenic bacterial strains or phages. Our research also does not involve the transference of toxins or drug resistance that could compromise the use of the drug to control disease agents in humans, veterinary medicine, or agriculture.



4. Do you have ideas to deal with safety issues that could be useful for future iGEM competitions?

4.1. Biosafety engineering and design of a safer chassis
Current safety engineering tools such as Event Tree Analysis (ETA) and Fault Tree Analysis (FTA) have yet to be extensively incorporated into synthetic biology models. One large obstacle is the fact that organisms are complex and not everything is known about their inner processes and community interactions. So while synthetic biologists are able to make logical predictions regarding their designed part or system, the sphere of knowledge of the chassis is greatly limited. This reason also motivates the current search for a safer chassis-one that is understood inside and out. In order to engineer safety into our synthetic biology parts or systems, it is necessary to attain a good understanding of what it does in its natural setting, design safety elements based on this knowledge and its extrapolation, and then collect experimental data on its behavior and mutability in synthetic settings. Just as conventional safety engineering utilizes real engineering data and designs, biosafety engineering has to become a whole and unique field unto itself. Research in controlled system-destruction is growing, and there will probably be research in the mutability of different types of synthetic biological circuits. One field of research that is instrumental to biosafety engineering is that of the intelligent synthesis of whole genomes from scratch. This will no doubt provide valuable insights as to the workings of the organism in study and also lead to the production of synthetic chassis and systems that are much more manipulable, controllable and predictable.

4.2. Public perception of risks and safety issues
Through our human practices project, we are exploring different perspectives of synthetic biology by asking members of the public, as well as iGEM participants, to create art in the form of visual arts or stories conveying their perception of synthetic biology and its potential impact on the world. We hope that by stimulating the public to learn more about synthetic biology and hopefully engaging in a meaningful exchange of ideas, the public will gain a deeper and sounder understanding of what synthetic biology is and how synthetic biologists also seek to install the necessary safety infrastructure. By asking for public opinion, synthetic biologists also have the opportunity to address public concerns and lay a firmer foundation for future synthetic biology ventures and applications in the real world. Since the benefits and consequences of synthetic biology research are shared by both researchers and the public, the two must actively seek to listen, inform and negotiate. Scientific risk assessment may produce quantitative measures of potential damage, but this is only a model of what may happen in reality. In order to validate the assumptions, applicability and foresight of these risk assessment estimates, we need to receive the input of the public, who are representative of real-life data. As the term “human practices” suggests, synthetic biologists who endeavour to develop the human practices aspect of their research must consider the same things that society considers. Will the fruits of our research be accessible to the poor? Are people in charge trustworthy? Will there be potential consequences for future generations? Are there ways for us to control the applications of our research? In other words, our synthetic biology parts and systems are like children born into the world. Scientific risk assessment is careful planning. Engaging with society is the actual raising of synthetic biology children. There has to be an increase in public awareness of what synthetic biology is and what it can do. There also has to be an increase in dialogue (whether through public forums or through art and entertainment) not just within the scientific community but also with the public.




Biosafety Quick Links

Biosafety deals with the containment principles, technologies and practices that are intended to prevent exposure to pathogens and toxins, and their accidental release.

2010 iGEM Safety Questions

WHO Biosafety Manual

NIH Institutional Biosafety Committees

CDC Office of Health and Safety

Health Safety and Environment, UBC





Risk Perception Quick Links

Risk perception is the subjective judgment that people make about the characteristics and severity of a risk.

Synbiosafe

An Introduction

Risk Perception

Placing Risks in Perspective

Communicating Synthetic Biology

Synthetic biology Press

Ethical Aspects of Synthetic Biology

Synthetic Biology and Society

Culture and Synthetic Biology