|
Citizen Science: A Guide to Starting a Do it Yourself (DIY) Synthetic Biology Laboratory
5 Essential Ingredients
Since the late 1970s engineers and computer programmers have pioneered citizen science. From rudimentary garage and basement based operations, innovators named Jobs, Noise, and Horowitz “hacked” computer networking technology into more applicable, socially relevant forms. These original DIY scientists took technology developed by more established organizations like the US government and CERN and made it more productive and useful than anyone could have imagined.
Today a similar DIY movement is taking shape in the biological sciences. The emerging field of Synthetic Biology has inspired a growing contingent of professional and amateur scientists to create neighborhood laboratories in hopes of making meaningful contributions in this exciting area. Synthetic Biology is designing new, or redesigning existing, life forms using a combination of synthetic and natural molecules . Due to the rapidly declining cost of genetic sequencing and genome synthesis, the field has exploded over the past decade. Just like garage hacking of computer technology decades earlier, synthetic biology has the same potential for immeasurable social and economic progress.
Engineering a ubiquitous life form, like bacteria to cure cancer or manufacture ethanol has its own self-evident miraculous quality that anyone could find compelling. In addition to a life changing idea, there are four other essential ingredients for a successful DIY Synthetic Biology laboratory: people, workspace and equipment, funding, and regulatory compliance.
The Idea
Within the broad field of synthetic biology there are innumerable ideas worthy of further investigation. Initially, most DIY synthetic biology labs have focused on developing genetically engineered biological machines to perform socially beneficial functions. Some organisms, including certain species of bacteria, are ready made for this type of modification because of their ability to readily uptake plasmids (small bits of genetic information) from the environment & recombine it into their natural DNA structure through cell division. This unique property allows synthetic biologists to code plasmids for the production of certain desirable proteins and easily incorporate them into the organism's existing structure. Once incorporated, these plasmids convert the host organism into a functioning bio-machine with the ability to produce the target protein. These target proteins can then be mass produced, combined or otherwise modified using similarly engineered bio-machines.
Once the technology is developed at the DIY level, it can be expanded and optimized in more established and strictly regulated commercial and university laboratories to produce remarkable results. Synthetic biology allows for the expansion of conventional uses of bio-machines, like breaking down organic matter at your local water treatment plant, to encompass a multitude of other specific functions. Biochemical processes like molecular sensing to detect toxins/disease, selectively delivering drugs/nutrients, metabolizing oil, or producing ethanol from excess plant matter are just a few of the potential applications.
The People
DIY organizations can utilize people across the entire spectrum of skill and experience. High school students, weekend hobbyists, and retired persons all have a place in DIY science. As a result, these laboratories function as arenas of interpersonal education and community development in addition to their primary scientific initiatives. DIY laboratories are also a useful educational vehicle for giving volunteers access to basic safety training, professional laboratory equipment and reagents, and hands on experience performing lab techniques commonly used in biotechnology. In short, in exchange for their time and attention, volunteers given a new skill set and the opportunity to work on a project with tremendously beneficial social implications.
Despite these incentives, finding an ample volunteer time is often a challenge. In light of the fact a critical mass of scientifically minded people is required to operate a DIY synthetic biology laboratory, these projects are most likely to succeed in large metropolitan areas or specialized academic settings (Ann Arbor, MI or Charlottesville, VA for example).
Some synthetic biology labs like Seattle DIYbio group, a start up in Seattle, have the required critical mass and the initial spark to get off the ground. Like many start up organizations, however, some of these ventures struggle to maintain their existence due to a leadership vacuum. Unlike their established counterparts start up organizations categorically lack structure. In fact, this is a large part of their appeal. Someone, however, needs to ultimately be responsible for the organization for it to be sustainable. Whether it be a charismatic champion like Robert Carlson, author of Biology is
Technology & founder of Biodesic, Corey Tobin, founder of LA Biohackers, or a board of directors, some entity needs to be in place to make decisions. This kind of effective leadership ensures lab resources are efficiently allocated towards a common direction. Good leaders are also instrumental in maintaining a productive working environment by promoting a culture of accountability and encouraging supportive, colloquial interactions between staff members.
Workspace and Equipment
Due to the US manufacturing decline over the past several decades obtaining a physical laboratory workspace is not terribly difficult or expensive. Most synthetic biology DIY labs rent raw, warehouse, or industrial space. This is commonplace because most reagent providers will not ship to home addresses due to federal regulations imposed on their operations. Obtaining a workspace divorced from residential areas is also a good idea because DIY synthetic biology takes up a significant amount of space. Bacteria must have counter space to grow in a petri dish, plants time to germinate and grow in a greenhouse, and lab bench space is needed to mix reagents and perform extracting and inserting procedures.
In addition to the requisite space, synthetic biology also requires substantial analytical equipment. The immense expense associated with instruments like a PCR thermocycler (DNA amplifier), autoclave sterilizer, electrophoresis seporatory gel, optical devices, and microscopes were some of the greatest initial barriers to DIY synthetic biology projects. Over the last decade, prices of these machines have fallen dramatically while existing machines have become more rapidly outdated.
These effects mean outfitting a lab is much cheaper and less time consuming than in previous years.
Today, obtaining basis biology lab equipment costs a few thousand dollars on eBay and can be assembled in a short time.1 Additionally, online shopping gives DIY synthetic biologists access to a global marketplace of enzyme and chemical reagent suppliers.
Alternatively, Corey Tobin's group, LA Biohackers, equipped through more conventional methods. The group collected donations to purchase old equipment at auction from local universities. These acquisitions were bolstered by successful dumpster diving ventures which produced two thermal cyclers from a dumpster at the University of California, Los Angeles, and DNA sequencer cast aside by the University of California, Santa Cruz. Furthermore, people readily build their own equipment using specification and fabrication instructions posted online. BioCurious a DIY Biology Lab based in Sunnyvale, CA exemplified this approach by engineering a bio-printer from scratch.2 The group transformed an old inkjet printer and motors scavenged from CD drives into a printer that can extrude bacteria into any desirable configuration.
Funding
In addition to information the internet is its own virtual gold mine. Crowd sourced funding organizations like Kickstarter and Indiegogo have already enabled numerous DIY type technology developments. Along these lines, more conventional solicitation of donations from the community could be more successful when coupled with a web presence. A good website which displays the lab's initiatives and results gives potential donors a better idea of the cause they are supporting. Additionally, the virtual nature of online transactions enables DIY laboratories to communicate with and accept donations from interested parties anywhere in the world.
Monetizing the educational component of a synthetic Biology DIY laboratory is another proven successful funding model. BOSSLAB5 Boston's open source science center, exemplifies this approach by charging a $200 class fee for the safety & techniques training class it administers to potential volunteers.2 The group also offers weekend workshops for unaffiliated members of the community for a fee. Alternatively, the membership model similar to a gym service or professional organization has also proven effective. BUGSS (Baltimore Underground Science Space) charges a membership fee of $85 a month to keep its operations running.2
Regulatory Compliance
The lack of DIY specific legislation is sensible in light of the fact amateur scientists lack the resources to be capable of harming to the public or the environment. A 2010 report from the Presidential Commission for the Study of Bioethical Issues summarized the limitations of amateur science by recognizing costs are too high to develop a new organism in a home–based lab1. Even if capable, possessing the desire to harm society at large is an exceedingly rare characteristic possessed by members of a generally good natured community.
Additionally, independent innovation and inventing are part of the fabric of America. A multitude of Constitutional (Free Speech, Freedom of Expression & Freedom of Association) issues and practical barriers discourage regulating a dispersed industry that’s akin to home woodworking and gardening1. In lieu of regulation, governments have taken an outreach and education approach. Lawmakers realize aggressive policing would push even legitimate, well intentioned DIY scientists underground. Alternatively, maintaining a dialogue with scientists promotes disclosure and puts the government in the best position to respond just in case a benign research project takes a serious turn. The National Science Advisory Board for Biosecurity (NSABB), a subsidiary of the National Institutes of Health’s Office of Biotechnology Activities is federally administering the issue. In their 2011 report, the board promoted this culture of responsibility over regulation. Either way there are numerous protections already on the books which could potentially ensure the nation’s safety and security. Everyone, however is not convinced communication offers enough protection.
Critics of DIY Synthetic Biology worry about three primary forms of risk: lab safety, environmental safety, and bioterrorism. Lab safety is governed internally through the scientific community and insures against accidental harmful exposures of research staff. Uniform codes of laboratory safety and best practices are promulgated by research organizations like the American Chemical Society, ACS. To prevent carelessness and ensure lab efficiency and efficacy, this basic code of laboratory conduct is universally embraced and followed within the scientific community.
Additionally, scientific specializations, even relatively new ones like synthetic biology, are built upon a strong ethical foundation that practitioners take very seriously. This ethical code is an essential component of lab safety while and an integral part of accurate data collection and reporting.
This system of ethics and professional standards has been largely successful in policing internal lab activities. As a result, local, state, and federal regulations focus on guarding against bioterrorism and protecting the environment. Local zoning codes stand as the first line of defense against environmental exposure. These local ordinances partition potentially harmful research from residential and high traffic commercial areas by designating zones for special land uses like scientific research.
In Los Angeles for example, Title 22 of the Los Angeles County Code specifies zone SR-D for scientific research and development. In order to comply with this zoning code, laboratory space is required to maintain permitted use, structure size, required parking, building set back, and maximum lot coverage. Los Angeles County Department of Regional Planning enforces these provisions my monitoring land usage and ensuring land owners comply with the requirements of the code.
In addition to zoning laws, state and federal agencies regulate hazardous waste disposal to prevent DIY laboratories from contaminating their surrounding environment. Federally, hazardous disposal is regulated under the Resource Conservation & Recovery Act (RCRA). In California, the California Environmental Protection Agency administers this federal statute in addition to provisions of the California health and safety code through is child agency the California Department of Toxic Substances Control (DTSC). DTSC has more than one thousand employees, and is headquartered in Sacramento. The agency also maintains regional offices across the state including two environmental chemistry laboratories, and field offices in Sacramento, Berkeley, Los Angeles, Chatsworth, Cypress, Clovis (Fresno), San Diego and Calexico.
Under the RCRA, disposal without a permit is permitted in most states9. The law, however, augments this freedom by specifies three acceptable avenues of disposal: elementary neutralization, treatment in accumulation containers, and treatment as part of a disposal process or treatability study. 9 Elementary neutralization is appropriate for handling chemicals that are hazardous only because they are corrosive (pH < 2; pH > 12.5). Upon neutralization, these substances are safe to put down the drain to any publicly owned water utility as long as the waste complies with their localized standards. Alternatively, small quantity generators (< 100kg a month) may store waste in accumulation containers. These entities have no time limit on how long they may collect waste but are required to dispose of their waste at an approved disposal site after accumulating more than 1000kg of waste. DIY and other laboratories are also permitted to experiment w/ novel ways to reduce waste without facing legal liability by conducting in house disposal studies. Since products not considered waste until producer declares them as such, green thinking laboratories are encouraged to develop effective methods for reducing the overall environmental impact of their operations.
Bioterrorism is the most controversial, serious, and difficult to regulate of three aforementioned concerns. Doomsdayers are alarmed about the possibility of a catastrophic biological attack through release of some deadly disease or virus. Recent publications in Nature and Science detailing ways to create new variants of H5N1 influenza that are transmissible between mammals through the air exacerbate these fears. Similarly, reports of DIY scientists conducting dangerous experiments, like atom splitting in a microwave or vaccine synthesis in facilities akin to “your mother’s spare bedroom” do not inspire much confidence.
Groups like the LA Biohackers use the “hacker” moniker fondly as a reference to “someone who enjoys solving problems, taking things apart, building things from scratch and prioritizes technical competence and aptitude over appearances or hubris.”12 In an effort to quell concerns about bioterrorism, however, the DIY synthetic biology community has divorced itself from the term “hacker” due to its malevolent public perception. The Federal Government has responded too. In 2011, the NSABB identified dual use material getting into the wrong hands as the most probable source of bioterrorism. Dual use materials can be used for both constructive and nefarious purposes1 and are ubiquitous in biological research. Everything from influenza strains to drug delivery devices to engineered microbes has dual use potential. The board recommended engaging the DIY community on this issue by educating it about the hazards that dual use materials might pose to the nation’s biosecurity. Consensus between the government and the scientific community has established education and communication as the best way to avoid accidental exposure. Other agencies like the FBI, NSA, CIA, and DOD bolster this collaborative atmosphere by aggressively policing and monitoring biochemical weapons. This dual front solution seems like the most reasonable balance between maintaining national security and promoting innovation.
In some ways, concerns about bioterrorism are analogous to copyright owners’ objections to computer copying and distribution technologies. Both DIY critics and copyright owners publicize dooms day scenarios in which new technology used in the wrong way by the wrong people causes vast economic damage. So far copyright owners have found other ways to successfully monetize their copyrights as tightening regulation on online copyright infringement is chilled by political unpopularity. New technology is always disruptive, but rarely are such disruptions catastrophic. As more and more labs responsibly enter and thrive in the DIY synthetic biology space, those more fearful and less supportive of this technology may soon have to find a different tune as well.
At the federal level, there are a number of administrative agencies and guidelines relevant to the community laboratory that hopes to practice synthetic biology. Although many of these are aimed at the traditional lab setting, the aspiring community laboratory should abide by all pertinent regulations for the number of reasons stated above. Most importantly, the community laboratory should follow relevant guidelines to ensure the safety of lab its members. Additionally, the lab should strive to ensure they do not adversely affect the environment around them.10
For example, the National Institute of Health (NIH) has compiled a set of guidelines for the regulation of research involving recombinant and synthetic nucleic molecules. The Center for Disease Control and Prevention (CDC) has cited the NIH Guidelines as the key reference in assessing risk and establishing an appropriate biosafety level for work involving recombinant DNA molecules. Any group that seeks funding from the NIH must comply by these guidelines. Often, other funding sources require compliance with these guidelines. Generally, the NIH Guidelines provide a sensible backdrop for any DIY organization.Here, the NIH defines recombinant and synthetic nucleic molecules as molecules that a) are constructed by joining nucleic acid molecules, and b) can replicate in a living cell (i.e. recombinant nucleic acids); nucleic acid molecules that are chemically or by other means synthesized or amplified, including those that are chemically or otherwise modified but can base pair with naturally occurring nucleic acid molecules, i.e., synthetic nucleic acids, or molecules that result from the replication of those described in (i) or (ii) above.13
Six different categories of experiments involving recombinant or synthetic nucleic acid molecules are recognized by the NIH Guidelines.13 These categories encompass experiments that: a) require Institutional Biosafety Committee (IBC) approval, RAC review, and NIH Director approval before initiation; b) require NIH/OBA and Institutional Biosafety Committee approval before initiation; c) require Institutional Biosafety Committee and Institutional Review Board approvals and RAC review before research participant enrollment; d) require Institutional Biosafety Committee approval before initiation; e) require Institutional Biosafety Committee notification simultaneous with initiation; and those that are exempt from the NIH Guidelines.13 Again, while compliance with these guidelines is mandatory only if the group receives NIH funding, these guidelines are often seen as the best current practice. Additionally, and more relevant to the aspiring community laboratory, four risk groups are recognized by the NIH Guidelines.13 These risk groups then determine the appropriate biosafety level applied to the specific experiment. The biosafety level and risk assessment help determine the appropriate containment conditions and how organisms should be handled.
Risk Group 1 (RG1) agents are not associated with disease in healthy adult humans and correlate to a Biosafety Level of 1 (BSL-1). This group can include Escherichia coli and baculovirus. BSL-1 follows standard microbiological practices allows work to be done on open bench tops, suggests that standard microbiological practices are followed and suggests the posting of biohazard signs. Risk Group 2 (RG2) agents are associated with human disease which is rarely serious and for which preventive or therapeutic interventions are often available. Agents in this group fall under a Biosafety Level of 2 (BSL-2), and may include adenovirus, all human and non-human primate blood contaminated specimens, and herpes simplex virus. BSL-2 suggests restricted lab access during experimental work, biological safety cabinets, biohazard signs, specific training in handling of agents and personnel protective equipment. Risk Group 3 (RG3) agents are associated with serious or lethal human disease for which preventive or therapeutic interventions may be available. RG3 agents fall under a Biosafety Level of 3 (BSL-3), and may include M. tuberculosis and concentrated Lentivirus. Risk Group 4 (RG4) agents are likely to cause serious or lethal human disease for which preventive or therapeutic interventions are not usually available. The latter two groups stipulate much more strenuous safety guidelines, but most aspiring community laboratories will be unlikely to work with agents falling under RG3 or RG4. 13
In the context of the LA Biohackers’ experiment, the primary types of experimental agent, Bacillus subtilis or Eschericia coli, fall under RG1 and BSL-1. The aim of the experiment, however, is to use these agents as hosts for the DNA of agents that are more difficult to modify either due to the complexities of their growth requirements or lack of transformational tools, such as Mycoplasm genetalium. According to the NIH Guidelines, experiments involving the DNA of agents from RG2, RG3 within a nonpathogenic host may be performed under BSL-2 containment guidelines. Additionally, experiments involving the DNA of agents from RG4 within a nonpathogenic host may be performed under BSL-2 containment guidelines after demonstrating that only a totally and irreversibly defective fraction of the agent’s genome is present in the given recombinant.13 Thus, should any group choose to apply the method demonstrated by the LA Biohackers, BSL-2 adherence will likely be required.
Aspiring community laboratories should also be wary of their impact on the environment. Thus, the laboratory should take great care to abide by the relevant Environmental Protection Agency (EPA) regulations as well as regulations promulgated by the Food and Drug Administration (FDA). FDA regulations, however, would likely only apply if the group sought commercial application of their experiments. EPA regulations that will likely apply to the aspiring community laboratory deal mainly with the disposal of hazardous waste. For example, the LA Biohackers sought and received the appropriate permit to allow for the disposal of their hazardous waste products.The EPA has written detailed regulations to make sure that TSDFs operate safely and protect people and the environment. The EPA wrote these regulations to implement the Resource Conservation and Recovery Act (RCRA) of 1976 and the Hazardous and Solid Waste Amendments of 1984. The U.S. Congress passed these laws to address public concerns about the management of hazardous waste.14,
Compounding the general risk of hazardous waste to the environment is the generally unpredictable nature of synthetic agents as compared to natural agents. For example, the inherent pathogenicity of a microorganism greatly depends on the regulation of its virulence genes. Even the smallest of nucleotide changes may have a dramatic effect on the pathogenesis or the viability of the organism. Additionally, many pathogenic bacteria contain clusters of genes called pathogenicity islands (PAI). These are not present in related non-pathogenic bacteria. Thus, in experiments such as the one conducted by the LA Biohackers, the transfer of the DNA of a pathogenic agent into a non-pathogenic agent may have wholly unexpected results when released into a set environment.18 Specifically, until we know how a partially or wholly synthetic agent’s sequence, structure, and biological context contribute to its biological properties it will be difficult to predict how it will exert its influence on the environment. Adding to this uncertainty is the fact that the synthetic biology field is progressing at a lightning-fast pace. New techniques are being developed every day that may enable the ability to generate novel organisms with unknown properties, such as enhanced virulence. These developments pose novel risks to biosafety, and present a multitude of ethical considerations, and only reinforce the need to practice synthetic biology under stringent biosafety guidelines.19
Community laboratories should also be mindful of the type of organization they seek to create at the federal level. A larger group, such as the LA Biohackers, with its rental fees, membership fees, and public outreach and teaching may be more concerned with this aspect than the fledgling community laboratory in a neighbor’s garage, for example. In the case of the LA Biohackers, they sought and received approval from the IRS to incorporate as a Section 501(c)(3) tax exempt entity.
To be exempt under Section 501(c)(3) of the Internal Revenue Code an organization’s purpose must be charitable, religious, educational, scientific, literary, testing for public safety, fostering national or international amateur sports competition, and preventing cruelty to children or animals. Here, charitable includes the advancement of education or science.
Thus, a group that seeks to follow the model of the LA Biohackers, which prides itself in serving its community as a learning tool, may do well to aspire to these purposes. Groups that do not want or are unable to function in this manner are just as relevant, but are likely unable to achieve tax exempt status. These groups should still be mindful of the various organizational entity classifications promulgated by their state.
Typically, a community laboratory will not need to give much thought to potential international regulatory issues. There are, however, certain research subjects that would warrant international concern. For example, the World Medical Association (WMA) has developed the Declaration of Helsinki as a statement of ethical principles for medical research involving human subjects, including research on identifiable human material and data. Most aspiring community laboratories will be unlikely to venture into this research area as it is mostly aimed at clinical application of medical research.
Arguably more relevant, however, are the international implications under the Convention on Biological Diversity (CBD) and the Nagoya Protocol (NP), which the United States has yet to ratify.
The CBD aims to conserve biological diversity, promote sustainable use, and provide fair access to any benefits that may arise from genetic sources. Biological diversity is represented by the multitude of plants, animals, microorganisms, genetic differences between species and the wide variety of ecosystems that occur on Earth. The combinations of these factors has made the planet uniquely suitable to flourishing life.
The Nagoya Protocol servers to further develop the third main goal of the CBD: fair access to any benefits that may arise from genetic sources. It is an international agreement which aims at sharing the benefits arising from the utilization of genetic resources in a fair and equitable way, including by appropriate access to genetic resources and by appropriate transfer of relevant technologies, taking into account all rights over those resources and to technologies, and by appropriate funding, thereby contributing to the conservation of biological diversity and the sustainable use of its components. In the international context, the CBD and NP provide meaningful progress for third-world countries who would greatly benefit from new and innovative genetic research and would generally lack the resources on their own to conduct the same research.
In the context of synthetic biology, the CBD and NP apply to the genetic material often used by researchers. Synthetic biology research and experimentation necessarily utilize significant quantities of tangible genetic material. Thus, a fledgling community laboratory should strive to meet the admirable standards set forth by the CBD and NP. The extent of this application, however, is unclear, as synthetic biology is not specifically addressed by the CBD or NP. Specifically, although the NP does note the term “derivative” and defines it as a gene segment produced or isolated by human manipulation, synthetic gene segment produced by human manipulation, or a synthetic analogue chemicals or gene segments, it does not extensively address the impact of synthetic biology. Nevertheless, the CBD an NP provide meaningful goals that a community laboratory should strive towards.
The model of a community laboratory set forth by organizations such as the LA Biohackers is well on its way to promoting these goals, as exemplified by their mission statement: The mission of the Los Angeles Biohackers is to make science accessible to people of all ages and educational backgrounds.
|
|
|
"
