Biotechnology researcher focused on genetic engineering and synthetic biology applications for environmental sustainability. Currently enrolled in How to Grow (Almost) Anything (HTGAA) Spring 2026.

Research Interests: Synthetic biology, environmental biotechnology, bioremediation, genetic engineering, IoT-monitored bioreactors.

Location: Monterrey, Nuevo León, México

Proposed Application: An Engineered Living Biofilter for PFAS and PFOS Transformation

I propose to develop a genetically informed living biofilter designed to transform and partially defluorinate persistent per- and polyfluoroalkyl substances (PFAS), including PFOS, in contaminated water streams. The system integrates naturally occurring PFAS-transforming microorganisms as gene donors with safe, well-characterized microbial or algal chassis suitable for controlled bioreactor environments.

PFAS and PFOS are widely used industrial compounds often referred to as “forever chemicals” due to the exceptional stability of the carbon–fluorine bond. Conventional remediation approaches—such as activated carbon adsorption, ion exchange resins, or high-energy destruction methods—are costly, energy-intensive, and often shift contaminants rather than eliminate their hazard. Biological approaches, while historically limited, have recently demonstrated initial defluorination and molecular transformation of certain PFAS compounds, suggesting that biology can play a meaningful role when carefully engineered and governed.

This project aims to explore biological transformation rather than complete mineralization, focusing on:

• Identifying genes and enzymatic pathways associated with initial PFAS/PFOS defluorination or activation from environmentally relevant bacteria (e.g., Rhodococcus spp. and Acidimicrobium spp.).

• Transferring or functionally expressing these pathways in safe, genetically tractable chassis organisms (e.g., Bacillus subtilis or a model microalga) suitable for contained bioreactors.

• Conceptually integrating this biological system into an IoT-monitored bioreactor, enabling real-time control, containment, and performance assessment.

The broader motivation for this application is to reframe PFAS remediation as a hybrid biological–engineering challenge, where biology contributes selectivity, adaptability, and lower energy requirements, while engineering and governance provide containment, safety, and accountability. This approach could enable more sustainable remediation strategies while avoiding environmental release of engineered organisms.

References:

Wackett, L. P. (2022). Nothing lasts forever: understanding microbial biodegradation of polyfluorinated compounds and perfluorinated alkyl substances. Microbial Biotechnology.

Wackett, L. P. & Robinson, S. L. (2024). A prescription for engineering PFAS biodegradation. Biochemical Journal.

Khan, M. F. et al. (2025). Recent progress and challenges in microbial defluorination and degradation for sustainable remediation of fluorinated xenobiotics. Processes (MDPI).

Ochoa-Herrera, V. et al. (2016). Microbial toxicity and biodegradability of PFOS and shorter-chain PFAS. Environmental Science: Processes & Impacts.

Governance and Policy Goals for an Ethical Biological Future

Overarching Governance Goal

Ensure that engineered biological systems for PFAS and PFOS transformation contribute to environmental remediation without introducing new risks to human health, ecosystems, or global biosecurity, while supporting responsible innovation and equitable access to remediation technologies.

This project explicitly acknowledges that engineered organisms—especially those designed for environmental applications—raise ethical concerns related to containment, misuse, unintended ecological impact, and governance gaps between laboratory research and real-world deployment.

To address these concerns, the following governance goals and sub-goals are proposed.

Goal 1: Prevent Harm Through Strong Biosecurity and Containment (Non-malfeasance)

Rationale: Genetically engineered microorganisms capable of interacting with persistent pollutants must not become environmental liabilities themselves.

Sub-goals:

• Prevent unintended environmental release: Ensure that engineered organisms are restricted to closed, monitored bioreactor systems. Avoid open-environment deployment during early-stage research.

• Minimize misuse or dual-use risks: Limit genetic designs to narrowly scoped metabolic functions. Avoid transferable traits that could be repurposed outside remediation contexts.

• Enable traceability and accountability: Ensure engineered strains and systems are clearly attributable to responsible institutions.

Goal 2: Promote Laboratory Safety and Responsible Research Practices

Rationale: Even low-risk chassis organisms can pose safety challenges when engineered for novel metabolic functions.

Sub-goals:

• Align experimental design with appropriate biosafety levels (BSL-1/2): Prefer organisms with long histories of safe laboratory use. Avoid pathogens or environmentally invasive species.

• Encourage anticipatory risk assessment: Incorporate safety and failure-mode analysis early in the design process. Treat uncertainty as a governance issue, not only a technical one.

Goal 3: Protect the Environment Beyond Immediate Remediation Goals

Rationale: An ethical remediation technology should not shift risks across time, space, or species.

Sub-goals:

• Avoid ecological burden shifting: Ensure PFAS transformation does not generate equally persistent or toxic byproducts. Design systems that facilitate downstream treatment or capture of intermediates.

• Prevent biological persistence outside engineered systems: Favor organisms with limited survival outside controlled conditions. Design for dependency on reactor-specific nutrients or conditions.

Goal 4: Support Responsible Innovation and Public Trust

Rationale: Environmental biotechnology operates at the intersection of public concern, regulatory uncertainty, and scientific innovation.

Sub-goals:

• Promote transparency and explainability: Clearly communicate system capabilities and limitations. Avoid overpromising complete PFAS destruction.

• Enable equitable and constructive use: Design systems that could be adapted for communities disproportionately affected by PFAS contamination. Avoid remediation approaches accessible only to highly resourced actors.

Why These Goals Matter for This Project

Together, these governance goals ensure that the proposed living biofilter:

• Advances constructive environmental applications of synthetic biology
• Respects precaution in the face of uncertainty
• Aligns with emerging norms for responsible biotechnology governance
• Treats ethics as a design constraint, not an afterthought

These goals will later serve as the evaluation rubric for comparing concrete governance actions (technical, institutional, and regulatory) in subsequent sections of the project.

References:

National Academies of Sciences, Engineering, and Medicine (2018). Biodefense in the Age of Synthetic Biology. Washington, DC: National Academies Press.

Kelle, A. (2020). Synthetic biology and biosecurity: challenging the “myths”. Global Security Studies, 11(2).

Garfinkel, M. S., Endy, D., Epstein, G. L., & Friedman, R. M. (2007). Synthetic genomics: options for governance. Biosecurity and Bioterrorism, 5(4), 359–362.

Oye, K. A., et al. (2014). Regulating gene drives. Science, 345(6197), 626–628.

Proposed Governance Actions

Governance Action 1: Technical Containment and Genetic Safeguards in Closed Bioreactors

Purpose: Currently, many environmental biotechnology projects rely on physical containment and institutional oversight as primary safety measures. This action proposes strengthening harm prevention by embedding technical containment mechanisms directly into the biological and reactor design. The goal is to prevent unintended environmental release and persistence of engineered organisms used for PFAS/PFOS transformation.

Design: This action would require academic researchers and technology developers to:

• Use closed, instrumented bioreactor systems rather than open environmental deployment.
• Select well-characterized, low-risk chassis organisms suitable for BSL-1 or BSL-2 laboratories.
• Incorporate built-in biological dependency mechanisms, such as reliance on reactor-specific nutrients or environmental conditions not found outside the system.
• Integrate real-time monitoring (e.g., IoT-based sensors) for biomass levels, system integrity, and operational anomalies.

Implementation would require opt-in by research laboratories, approval by institutional biosafety committees (IBCs), and alignment with existing biosafety regulations rather than the creation of new high-burden rules.

Assumptions:

• Technical containment measures are sufficient to significantly reduce environmental escape risk.
• Researchers and institutions have the capacity and incentives to adopt enhanced containment designs.
• Monitoring data can be meaningfully interpreted and acted upon in real time.

Risks of Failure and “Success”:

• Failure could occur if containment systems create a false sense of security, leading to reduced human oversight.
• Successful implementation may increase project costs and technical complexity, potentially limiting participation by under-resourced laboratories.

Governance Action 2: Mandatory Pre-Deployment Ethical and Environmental Risk Assessment

Purpose: At present, many research projects undergo biosafety review but lack structured evaluation of environmental ethics, long-term ecological impact, and uncertainty. This action proposes a formal requirement for project-specific ethical and environmental risk assessments prior to advancing beyond laboratory-scale research.

Design: This action would be implemented through:

• Expansion of existing institutional review processes (e.g., IBCs or environmental health and safety offices) to include environmental and ethical risk review.
• A standardized assessment template addressing:
  • Intended and unintended environmental impacts
  • Potential byproducts of PFAS/PFOS transformation
  • Failure modes and uncertainty
  • Plans for monitoring, shutdown, and remediation
• Review by interdisciplinary committees including engineers, environmental scientists, and ethics or policy experts.

This approach leverages existing governance structures rather than introducing external regulatory oversight at early research stages.

Assumptions:

• Structured assessment improves decision-making and researcher awareness.
• Institutions are willing to broaden review criteria beyond immediate biosafety.
• Early-stage reflection can meaningfully influence project design choices.

Risks of Failure and “Success”:

• The process may become a procedural “checkbox” exercise rather than substantive engagement.
• Excessive review burdens could slow exploratory research if not carefully scoped.

Governance Action 3: Voluntary Transparency and Research Registry for Environmental Synthetic Biology

Purpose: Public trust in environmental biotechnology is often undermined by limited transparency and unclear accountability. This action proposes a voluntary research registry for engineered biological systems intended for environmental applications, promoting openness without mandating disclosure of sensitive intellectual property.

Design: Key elements include:

• A publicly accessible registry maintained by academic consortia, professional societies, or funding agencies.
• High-level project descriptions covering:
  • Intended application and organism type
  • Containment strategy
  • Stage of development
  • Responsible institution
• Participation incentivized through funding requirements, publication norms, or professional recognition rather than legal mandates.

Actors involved include academic researchers, funding bodies, journals, and professional societies.

Assumptions:

• Transparency reduces suspicion and supports responsible norms.
• High-level disclosure does not meaningfully increase misuse risk.
• Incentives are sufficient to encourage participation.

Risks of Failure and “Success”:

• Low participation could limit the registry’s value.
• Over-disclosure could raise concerns about intellectual property or dual-use risks if poorly designed.

Summary

Together, these governance actions form a layered approach:

• Technical safeguards reduce physical and biological risk.
• Institutional review embeds ethical reflection early in the research process.
• Transparency mechanisms support accountability and public trust.

This combination balances safety, feasibility, and innovation, aligning governance with the realities of early-stage environmental biotechnology research rather than imposing rigid, one-size-fits-all regulation.

Governance Actions Scoring Table

Prioritized Governance Strategy and Rationale

Drawing upon the scoring across biosecurity, laboratory safety, environmental protection, feasibility, and research enablement, the governance strategy I would prioritize is a combination of Option 1 (Technical containment and genetic safeguards) and Option 2 (Mandatory pre-deployment ethical and environmental risk assessment), with Option 3 (Voluntary transparency and research registry) serving as a complementary, secondary measure.

Option 1 consistently scored highest in categories related to preventing incidents, including biosecurity breaches, laboratory accidents, and environmental harm. For an engineered biological system designed to interact with persistent pollutants such as PFAS and PFOS, prevention is ethically preferable to post hoc response. Embedding containment directly into both the biological design and the reactor architecture aligns with the principle of non-malfeasance and reduces reliance on perfect human behavior or institutional oversight alone.

Option 2 complements this technical approach by addressing a different but equally important dimension: uncertainty. While Option 1 reduces the likelihood of physical or biological escape, Option 2 improves preparedness for unforeseen consequences by requiring structured ethical and environmental reflection before scaling or deployment. This option scored particularly well in helping response, fostering lab safety culture, and protecting the environment through anticipatory governance rather than reactive regulation.

Option 3, while scoring lower in direct prevention, offers significant benefits in terms of feasibility, cost, and public trust. However, transparency alone does not sufficiently mitigate the risks associated with engineered organisms in environmental contexts. As such, it is best positioned as a supporting action that reinforces accountability and legitimacy once strong technical and institutional safeguards are already in place.

Trade-offs, Assumptions, and Uncertainties

This prioritization involves several trade-offs. Technical containment strategies increase system complexity and cost, potentially limiting accessibility for smaller or under-resourced laboratories. Mandatory ethical and environmental assessments may slow early-stage research and risk becoming procedural if poorly designed. However, these burdens are justified by the high potential costs of failure in environmental biotechnology, where unintended consequences may be irreversible.

Key assumptions underlying this strategy include the belief that:

• Closed bioreactor systems can meaningfully reduce environmental exposure risks.
• Early ethical and environmental reflection improves design decisions rather than merely documenting them.
• Existing institutional governance structures can be adapted without creating excessive regulatory friction.

Uncertainties remain, particularly regarding the long-term fate of PFAS transformation byproducts and the behavior of engineered organisms under non-ideal conditions. These uncertainties further support a governance approach that emphasizes containment and reflection rather than premature deployment.

Target Audience for the Recommendation

This combined governance strategy is primarily directed at academic research institutions and funding agencies, such as MIT leadership, U.S. federal research funders, and international research consortia in environmental biotechnology. These actors are well positioned to:

• Set norms for responsible design before commercialization pressures emerge.
• Integrate governance expectations into funding and institutional review processes.
• Influence downstream industrial and regulatory practices through precedent.

By acting at this early stage, these institutions can shape the ethical trajectory of environmental synthetic biology rather than reacting to failures after deployment.

Ethical Reflections from This Week’s Class

One ethical concern that emerged strongly during this week of class was the tension between urgency and precaution. PFAS contamination represents a pressing environmental and public health problem, creating pressure to deploy solutions rapidly. However, the history of environmental interventions demonstrates that well-intentioned technologies can produce new harms when uncertainty is underestimated.

A second concern was the risk of responsibility diffusion in complex technological systems. When harm occurs, accountability can become fragmented across designers, operators, institutions, and regulators. This reinforces the need for governance mechanisms that assign responsibility clearly and early.

Finally, the class highlighted how ethical considerations are often treated as external constraints, rather than as design inputs. In this project, ethical governance is treated as an integral part of system architecture, shaping choices about organisms, reactors, and deployment pathways.

Additional Governance Actions to Address These Concerns

To address these ethical issues, two additional governance actions are appropriate:

1. Embedding ethical reflection into technical milestones, such that progression from laboratory proof-of-concept to pilot-scale systems requires explicit justification of risk reduction and uncertainty management.

2. Clear assignment of institutional responsibility, ensuring that specific actors remain accountable for system performance, monitoring, and shutdown even after research transitions to applied settings.

Together, these measures reinforce a vision of environmental biotechnology that is not only innovative, but also cautious, accountable, and ethically grounded.