I’m a biology student who’s curious about how science shapes the world around us—and how people shape science in return.
I enjoy learning, reflecting, and asking questions that don’t always have simple answers. I’m especially interested in how technology, biology, and ethics intersect, and how scientific ideas move from the lab into real life. Outside of classes, I like observing everyday things, turning small moments into thoughts, and learning through conversations and experiences.
I joined HTGAA because I wanted to better understand how science, responsibility, and society connect—not just what we can do with technology, but how and why we should use it. I’m excited to learn, listen, and grow through this space.
Project Interest I am interested in the application of synthetic biology to help address waste problems, particularly plastic and organic waste. I envision the use of microorganisms that can help decompose waste in a more environmentally friendly way. This topic interests me because waste is a real issue that we often encounter, yet it remains difficult to address effectively. Using a biological approach, I hope this technology can provide a more sustainable solution than conventional methods.
Professor Jacobson Question 1 DNA polymerase is the enzyme responsible for copying DNA during cell division. It does not work perfectly and has an error rate of about one mistake per 10⁷ to 10⁹ nucleotides. When this is compared to the size of the human genome, which is around 3 billion base pairs, it means that errors could potentially happen every time DNA is replicated. Biology deals with this problem by using several layers of correction. DNA polymerase can proofread its own work and fix mistakes as replication happens. In addition, cells have DNA repair systems that detect and correct remaining errors. Because of these mechanisms, most mistakes are fixed before they can cause serious problems, allowing genetic information to remain stable.
Subsections of Homework
Week 1 HW: Principles and Practices
Project Interest
I am interested in the application of synthetic biology to help address waste problems, particularly plastic and organic waste. I envision the use of microorganisms that can help decompose waste in a more environmentally friendly way.
This topic interests me because waste is a real issue that we often encounter, yet it remains difficult to address effectively. Using a biological approach, I hope this technology can provide a more sustainable solution than conventional methods.
Governance Goals
Main governance goal:
Ensuring the use of microorganisms for waste treatment is carried out safely and without negative impacts.
Sub-goals:
Preventing the uncontrolled spread of microorganisms into the environment.
Ensuring safety for humans and ecosystems.
Ensuring this technology is used for the public good, not for misuse.
Governance Options
Option 1: Regulatory Control on Engineered Microorganisms
Purpose :
Currently, the use of genetically engineered microorganisms still poses risks if released into the environment without controls. This option aims to ensure that microorganisms used for waste treatment do not cause harmful impacts.
Design :
Government regulators and academic institutions need to establish licensing regulations, conduct risk assessments, and oversee the use of microorganisms in open environments.
Assumptions :
It is assumed that all parties will comply with regulations and that regulators have the capacity to conduct oversight.
Risks of Failure & Success :
If regulations are too strict, research can be hampered. However, if successful, the use of microorganisms becomes safer and more controlled.
Option 2: Mandatory Biosafety Training for Researchers
Purpose :
To reduce the risk of human error in the use of engineered microorganisms.
Design :
Educational institutions and laboratories should require biosafety training for students and researchers before engaging in synthetic biology projects.
Assumptions :
It is assumed that training can increase awareness and compliance with safety procedures.
Risks of Failure & “Success” :
Training can become a mere formality if not supervised. However, if effective, the risk of laboratory accidents can be reduced.
Option 3: Technical Safeguards (Biological Kill-Switch)
Purpose :
Untuk mencegah mikroorganisme bertahan hidup di luar lingkungan yang dirancang.
Design :
Peneliti mengembangkan sistem biologis seperti kill-switch yang membuat mikroorganisme mati jika berada di kondisi tertentu di luar laboratorium atau sistem pengolahan limbah.
Assumptions :
Diasumsikan bahwa sistem kill-switch bekerja sesuai desain dan tidak mudah gagal.
Risks of Failure & “Success” :
Jika sistem gagal, mikroorganisme bisa menyebar. Namun jika berhasil, teknologi ini memberikan lapisan keamanan tambahan.
Scoring
Does the option:
Option 1
Option 2
Option 3
Enhance Biosecurity
• By preventing incidents
1
2
1
• By helping respond
2
2
3
Foster Lab Safety
• By preventing incident
2
1
2
• By helping respond
2
1
3
Protect the environment
• By preventing incidents
1
2
1
• By helping respond
2
2
3
Other considerations
• Minimizing costs and burdens to stakeholders
3
1
2
• Feasibility?
2
1
3
• Not impede research
2
1
2
• Promote constructive applications
1
2
2
Prioritization of Governance Options
Based on the scoring above, I would prioritize Option 2 (mandatory biosafety training), supported by Option 1 (regulatory control). Option 2 is prioritized because it is relatively feasible, low-cost, and can be implemented early, especially for students and early-career researchers.
One trade-off of this approach is that training alone may not fully prevent misuse or unintended consequences without clear regulatory oversight. Therefore, regulation remains important as a complementary measure.
This prioritization assumes that participants will actively apply biosafety knowledge in practice. However, there is uncertainty regarding the long-term effectiveness of training without continuous evaluation and enforcement.
Ethical Reflection
Reflecting on my understanding of synthetic biology and its application in waste management, I realized that biological technologies can offer powerful solutions while also posing risks if not properly governed.
One ethical concern that stood out to me is the potential environmental impact if engineered microorganisms are released unintentionally. There is also the issue of responsibility and accountability if such technologies cause harm.
To address these concerns, governance actions such as mandatory biosafety training, regulatory oversight, and technical safeguards should be considered to ensure responsible and ethical use of synthetic biology.
Week 2 Lecture Preparation
Professor Jacobson
Question 1
DNA polymerase is the enzyme responsible for copying DNA during cell division. It does not work perfectly and has an error rate of about one mistake per 10⁷ to 10⁹ nucleotides. When this is compared to the size of the human genome, which is around 3 billion base pairs, it means that errors could potentially happen every time DNA is replicated.
Biology deals with this problem by using several layers of correction. DNA polymerase can proofread its own work and fix mistakes as replication happens. In addition, cells have DNA repair systems that detect and correct remaining errors. Because of these mechanisms, most mistakes are fixed before they can cause serious problems, allowing genetic information to remain stable.
Question 2
The genetic code is described as degenerate because most amino acids can be encoded by more than one codon. This means that a protein consisting of 100 amino acids could theoretically be encoded in an extremely large number of different DNA sequences, due to the many possible codon combinations for each amino acid.
However, biology does not take advantage of all this degeneracy. In practice, organisms show strong codon preferences, often referred to as codon bias. This is because certain codons are translated more efficiently or accurately, depending on the availability of tRNAs and the cellular machinery. Using preferred codons helps reduce translation errors, improve efficiency, and maintain proper protein folding. As a result, biological systems favor reliability and efficiency over using all possible coding options.
Dr. LeProust
Question 1
The most common method used for oligonucleotide synthesis is phosphoramidite chemistry. In this approach, DNA is synthesized step by step by adding one nucleotide at a time to a growing chain that is attached to a solid support. This method is widely used because it is reliable, efficient, and well suited for producing short DNA sequences with high precision.
Question 2
One of the main limitations of current DNA synthesis methods is the accumulation of errors as the DNA sequence becomes longer. Since nucleotides are added step by step, small inefficiencies at each step can lead to deletions or incorrect bases in the final sequence. As a result, synthesizing long DNA sequences becomes more challenging and often requires additional purification and verification steps. These limitations also increase the cost and time needed for DNA synthesis.
Question 3
Future improvements in DNA synthesis may focus on increasing accuracy and enabling the synthesis of longer DNA sequences. One promising direction is the development of enzymatic DNA synthesis, which may reduce error rates compared to traditional chemical methods. In addition, automation and computational tools, including AI-based design and quality control, could help optimize synthesis processes and detect errors more efficiently. Together, these advances could make DNA synthesis faster, cheaper, and more reliable.
George Church
Cells as Computers and Logic
The idea of cells as computers suggests that biological systems can process information in ways similar to electronic computers. In synthetic biology, genes and regulatory elements can be designed to function like logic gates, allowing cells to respond to specific inputs and produce predictable outputs. For example, a cell might produce a certain protein only when multiple conditions are met.
This concept is exciting because it opens possibilities for smarter therapies, environmental sensing, and more precise biological control systems. However, cells are living systems and are much more complex and unpredictable than electronic computers. Small changes in the environment or mutations could lead to unexpected behavior.
From an ethical and governance perspective, it is important to ensure that such technologies are developed responsibly. There should be safeguards to prevent misuse, unintended environmental release, or harmful applications. Transparency, regulation, and continuous monitoring are important to balance innovation with safety.
Note: AI tools were used to help clarify concepts and structure this response.
Note: AI tools were used to help clarify concepts and structure this response.
