Human Practices

To ensure that our iGEM project remained mindful and engaged with the broader world, we began our Human Practices as soon as we started project ideation. In fact, our project topic was inspired by the challenges faced by Dr. Bartelle, one of our faculty mentors, when trying to utilize PACE in his research. Through subsequent meetings with other scientists in the protein engineering space, we came to realize just how inaccessible and resource-intensive PACE was and embarked on a journey to develop more accessible tools for protein engineering. Given the upstream nature of our research, we knew it would be easy to overlook assessing the true effects of our work on the wider community. As such, we prioritized making Human Practices the most important consideration of our project.

To achieve this, we referred to the iGEM guidelines to identify the questions we needed to address to ensure that we did not miss anything.


To learn more about the different questions we address, click on the headers!

1. What values—environmental, social, moral, scientific, or other—did you have in mind when designing your project?

One of our biggest priorities for this project was to reduce the cost of protein engineering research to make it more available to the general scientific community. Although PACE removes many of the greatest barriers to entry shared amongst DE methods, the biggest hurdle that still remains is cost - whether that be the cost of chemical inducers, chemo or turbidostats, or computational work. As such, one of our core values is accessibility. We hope to democratize protein engineering research and spark greater interest in its applications and usage.


Given our work on upstream protein engineering tools, we were particularly interested in developing an ethical framework to evaluate the downstream effects of projects like ours: where the end user is unclear and the potential applications of the technology are too numerous to list. This led us to approach the project with a strong focus on responsibility from the start.


Finally, because of how abstracted protein engineering research can be, we also prioritized connecting researchers to their local community through educational initiatives, showcasing another one of our core values: community. While working on our project, it was important to us to remember that research is just a means to an end: it has a real human impact.


2. Which resources or communities did you consult to ensure those are appropriate values in the context of your project?

We established our core values of accessibility, responsibility, and community after extensive dialogue with various stakeholders in our project.

  • Accessibility: Through ongoing discussions with protein engineering experts like Dr. Ahmed Badran and Dr. Jeremy Mills, we were able to explore their research experience with PACE. Their challenges in breaking into the field, combined with the fact that we were also new to the space, strongly motivated us to create accessible tools to lower the barrier to entry in protein engineering.
  • Responsibility: We consulted with ethical experts, including Dr. Gary Marchant, Dr. Karin Ellison, and Dr. James Wetmore, who emphasized the importance of responsible research practices. Their guidance helped us commit to continuous efforts to foster ethical conduct.
  • Community: As students who learned about synthetic biology from past iGEM team members, we were driven to pass on that knowledge by teaching other students. Our motivation to grow and sustain the synthetic biology community deepened after recognizing the need to stay connected to the real-world impact of our work given its upstream nature. Our discussions with bioethicists led us to create an ethical framework to enable others in the scientific community to thoughtfully and responsibly consider the broader impact of their research.
1. What evidence do you have to show that your project is responsible and good for the world?

Given how far removed our project is from a direct consumer product, our team found it challenging to quantify the societal impact of our work. However, this difficulty only strengthened our resolve to ensure that our research is responsible and good for the world. Evidence of this commitment includes:

  • Responsiveness to the needs of protein engineering experts during the ideation and throughout the development of our project
  • Engagement with bioethicists and the creation of an ethical framework to promote responsible research
  • Promotion of synthetic biology education and a strong undergraduate scientific community through the development of an Open Lab manual and fun, cross-disciplinary educational initiatives

2. What impact will your project have?
a. Who are your proposed end users? How do you envision others using your project?

Our project's primary end users are individuals already involved in or interested in getting involved in protein engineering research. For newcomers, our open-source hardware design and user-friendly software will help ease the learning curve and cost barrier of setting up and implementing a PACE system. For established researchers, our optogenetic tools for DE offer a more efficient and cost-effective alternative to the chemical inducers they are currently using. Our tools are designed for everyone in the protein engineering community, from novices to experienced scientists.
Educationally, we have developed a manual to teach synthetic biology in an easy and accessible manner. We hope that other iGEM teams or anyone interested in growing the synthetic biology community will find these materials as beneficial as our team has. Our ethical framework is intended to encourage other researchers to engage with the public and consider how their projects can maximize positive outcomes for all.


b. How would you implement your project in the real world?

We have made all parts of our project open-source and easily accessible from our Wiki:


  • Optogenetic controls: All of our parts have been uploaded to the iGEM Registry of Standard Biological Parts, which can be found here
  • Hardware: A complete description of our hardware design and step-by-step instructions to implement it can be found here
  • Software: A complete overview of our software design and steps for implementation can be found here
  • Open Lab Manual: All materials, including presentation slides and worksheets, can be found here

Our Journey

This section is inspired by the format used by the 2023 Exullose Vilnius-Lithuania iGEM team


All of our integrated human practices meetings have been summarized in the timeline below. To ensure that our meetings were actually informing our project development, we organized each one based on three key aspects:


Our meetings can be divided into four main categories: Wet Lab, Hardware, Software, and Engagement.


Click through the dropdowns to access the information about each of our meetings and see how each of these interactions changed the trajectory of our project direction.


February


  • Description: As part of our recruitment process and to kickstart ideas for this year’s project, we hosted an Idea Bowl. Over the course of three weeks, our team members formed small groups, each brainstorming a project proposal to present to a panel of advisors and past iGEM members. We invited various ASU faculty members and our advisors to be a part of the panel, including Dr. Benjamin Bartelle, Dr. Christopher Plaisier, Dr. Emma Frow, and Dr. Jong Seto.
  • Contribution: Our advisors suggested that given that the majority of our team was new to research, we could turn this into a strength by focusing on accessibility and education.
  • Our Next Steps: The Idea Bowl helped us identify potential challenges and limitations in our initial ideas. Advisor feedback helped us narrow our many ideas down to OptoPACE. They also strongly emphasized that we reach out to our stakeholders to refine our approach.

March



  • Description: The purpose of this interview was for our team to begin gaining insight about PACE from Dr. Bartelle because it was his experience that inspired our project. We specifically aimed to understand the pitfalls he had faced to help us identify areas where PACE could be improved.
  • Contribution: Dr. Bartelle highlighted the difficulty of balancing simplicity and functionality in hardware design. He noted that students in his lab often lose sight of accessibility by prioritizing adding new functions to the hardware. However, certain functionalities are essential, so the challenge is to create a simple, accessible design that can be adapted by others for their specific experimental needs.
  • Our Next Steps: To achieve accessibility, our hardware design should function in a basic lab environment and have clear documentation and instructions. We will ensure that the design is affordable and easily adaptable.


  • Description: Given the similarity between our de novo design project and Dr. Woodbury’s work, we sought his guidance on refining our project goals and experimental validation methods.
  • Contribution: Drawing from his experience in designing therapeutic peptides, Dr. Woodbury emphasized the importance of demonstrable success and recommended simultaneously performing assays that align with the simulated conditions of our machine learning models. He specifically recommended fluorescence polarization and biolayer interferometry.
  • Our Next Steps: We will assess the feasibility of the binding assays Dr. Woodbury recommended and implement them into our experimental validation process if possible.

April



  • Description: In the early stages of our project planning, our team had many questions about PACE. To answer them, we reached out to Dr. Costello, a postdoctoral associate at the Scripps Research Institute, to discuss our project design and gather input on our initial ideas.
  • Contribution: Dr. Costello advised us to focus on the foundational work of PACE. The key takeaways include:
    • Optogenetic tools offer greater tunability than chemical inducers due to the absence of “wash out” time.
    • Reducing the lagoon volume can help save costs.
  • Our Next Steps: We will research optogenetic switches to incorporate into our genetic circuit and test their tunability under different wavelengths. Additionally, we will design our hardware with a smaller lagoon size to reduce costs.


  • Description: In their research, Dr. Marchant and Dr. Ellison have explored the discrepancies between technological advancements and ethical oversight. We wanted to get their perspective on how to ensure clear ethical considerations for our project.
  • Contribution:Since the technology that we are developing is so upstream, Dr. Marchant and Dr. Ellison recommended reaching out to Dr. Jameson Wetmore, who previously worked at ASU’s Center for Nanotechnology. There, he faced similar challenges in anticipating the outcomes of upstream, emerging technologies. As such, they believed that he could offer valuable guidance for our ethical considerations. They also suggested engaging in public discourse on our project’s potential ethical issues through venues like the Arizona Bioethics Conference or synthetic biology forums.
  • Our Next Steps: We will email Dr. Wetmore to schedule an interview and attend the Arizona Bioethics Conference in late April to gather feedback on the ethics of our project.


  • Description: Our goal is to create a turbidostat that is accessible to first-time users. To achieve this, we reached out to Dr. Takahashi, a professor at the University of Washington, to learn about his process for developing an affordable, open-source turbidostat.
  • Contribution: Dr. Takashi provided valuable feedback regarding the logistics of designing a turbidostat. In particular, he noted that peristaltic pumps can introduce air bubbles through the waste line and that our proposed pressure-based system might create inconsistencies between different media bottles.
  • Our Next Steps: To mitigate air bubble inconsistencies, we will add a priming button that runs the pump to flush media through the tubes. We will also elongate the pipette that dispenses media to ensure that it remains fully submerged, preventing the intake of air bubbles.


  • Description: Following our meeting with Dr. Costello earlier this month, he connected us with his PI, Dr. Badran, at the Scripps Research Institute.
  • Contribution: Dr. Badran provided insights on optogenetic controls, noting that LOV domains, which regulate at the transcriptional level, are likely to be less tunable than regulatory methods that act at the translational level.
  • Our Next Steps: We will develop an assay to assess the tunability of protein expression using both less and more optimal wavelengths of light with our LOV domains.


  • Description: The Arizona Bioethics Network (ABN) is an organization dedicated to increasing awareness of bioethical issues. We attended the 12th annual conference to connect with individuals who could provide insight into ethical issues surrounding PACE.
  • Contribution: Unfortunately, this year's conference was focused on the ethics of AI, which was not relevant to our project, and the attending ethicists were unable to offer any feedback. However, we learned of a venue called Venture Cafe that could help us connect with individuals interested in discussing the ethics of PACE.
  • Our Next Steps: We plan to attend the upcoming “Intersection of Art and Science” event hosted by Venture Cafe at the Phoenix Bioscience Core on May 9, 2024.

May



  • Description: We attended Venture Cafe's ART X SCIENCE event, which showcased new art installations developed through the PBC Arts Committee's Student Grant Program. We heard experts explain how the artist-scientist pairs were selected and then each of the pairs discussed how the artwork represented the scientist's research. We also participated in a guided tour to view the installations.
  • Contribution: We observed how the integration of art and science can spark curiosity about unfamiliar topics. We were also able to learn unique methods and processes through these artist-scientist collaborations, giving us a new perspective on both art and science.
  • Our Next Steps: Inspired by the potential of art as a tool for engagement and learning, we will incorporate art into our planned education events through DIYbio.

June



  • Description: We were able to come up with our initial optogenetic circuit designs by just reviewing the literature review, but we were unable to figure out how to characterize the system and finalize the plasmid design. To address this, we consulted Dr. Jang, a postdoc at Princeton specializing in engineering optogenetic circuits using cyanobacteria chromes.
  • Contribution: Dr. Jang advised us to use sfGFP to characterize promoter activity and measure it with a plate reader instead of flow cytometry. He also pointed out a missing component in our design: a chromophore, which is required for all photosensitive proteins. Specifically, cyanobacteriochromes need phycocyanobilin (PCB). He suggested two options: expressing PCB via enzymes in the plasmid or adding PCB molecules directly to the media.
  • Our Next Steps: We will replace luciferase in our plasmids with sfGFP for activity characterization, using a constitutive promoter as a positive control, and will measure fluorescence with a plate reader. To reduce costs, we will integrate PCB into our plasmid design. Following Dr. Jang's advice, our next steps are to find compatible PCB enzymes and begin planning plate reader experiments.

July



  • Description: We interviewed Dr. Wetmore to gain insights on upstream ethical analysis, drawing from his experience with the Center for Nanotechnology.
  • Contribution:Since our parts are open-source, we can't prevent misuse by bad actors. Instead of focusing our attention on issues we cannot solve, we should instead work on helping people who have good intentions but unintentionally do bad things. To accomplish this, we should encourage researchers to conduct an ethical analysis of their project by developing an ethical framework that addresses the questions they might have.
  • Our Next Steps: Rather than creating an ethical framework specifically for our project we will develop a general one that includes case studies applicable to all researchers. To ensure that it addresses real concerns, we will interview ASU graduate students about the broader implications of research, including their own. We will also incorporate case studies to help researchers better understand ethical considerations.


  • Description: We had an insightful conversation with Stephanie Tong from the Queen's University iGEM team to establish a collaboration for the development of an ethics handbook for future iGEM teams.
  • Contribution: While working with the Queen's iGEM team on the ethics handbook, we gained valuable insights into international ethical frameworks, including CityU's perspective on global health disparities
  • Our Next Steps: When developing our ethical framework and considering different case studies to assess, we will make sure that our approach is internationally inclusive. We will analyze the studies from a philosophical and deontological perspective rather than using regulatory legal frameworks.


  • Description: We completed a survey sent by the McGill iGEM team to showcase our cyanobacteriochrome system, Ccar and Ccas, in their 2024 BIOME Book.
  • Contribution: The protein illustrations in the BIOME Book beautifully captured the essence of molecular biology, emphasizing the connection between protein structure and function and demonstrating how art and science can converge to enhance our understanding of complex scientific processes.
  • Our Next Steps: This collaboration further reinforced our plan to integrate art and science in our upcoming DIYbio educational initiatives to introduce students to synthetic biology in an engaging and creative way.


  • Description: Patrick was interviewed by the UW iGEM team regarding our project topic to be included on the YouTube Educational Series they were developing.
  • Contribution: This interview helped broaden our insights into different perspectives regarding protein structural analysis. Furthermore, the emphasis on adapting university-level materials for publicly available sources helped motivate and inspire our own education efforts.
  • Our Next Steps: This collaboration further reinforced our plan to work with larger-scale educational outreach and public engagement.

August



  • Description: For the validation of our de novo design project, we consulted Dr. Mills on protein extraction and characterization methods, as well as the pitfalls in predicted tertiary structures versus actual conformational states.
  • Contribution: During our meeting, we gained valuable insights into protein purification workflows. Dr. Mills offered nuanced perspectives on various ways to express the proteins we wished to purify.
  • Our Next Steps: We will design an HIV-RT protein expression construct using a pCDF-Duet system and determine an appropriate kit and protocol for the purification process.

September



  • Description: We met with JPT Technologies to learn more about their peptide synthesis services.
  • Contribution: We reached an agreement about what the best assay to experimentally validate OpenBind was.
  • Our Next Steps: Unfortunately, the quote for their services was too high for us to proceed.