How to Grow Almost Anything 2021
Principles & Practices Assignments
Class Recording
Recitation Recording
Ethics, safety and security are essential considerations throughout (and beyond!) this class. We have therefore designed an assignment this week to give you a strong foundation, and then will ask you to reflect each week and in the design of your final project.
Principles & Practices - Class 1 Assignment
- First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about.
- Next, describe one or more governance/policy goals related to ensuring that this application or tool contributes to an "ethical" future, like ensuring non-malfeasance (preventing harm). Break big goals down into two or more specific sub-goals. Below is one example framework (developed in the context of synthetic genomics) you can choose to use or adapt, or you can develop your own. The example was developed to consider policy goals of ensuring safety and security, alongside other goals, like promoting constructive uses, but you could propose other goals for example, those relating to equity or autonomy.
- Next describe at least three different potential governance "actions", each presented in four sections. Try to outline a mix of actions (e.g. a new requirement/rule, or incentive, or technical strategy) pursued by different "actors" (e.g. academic researchers, companies, federal regulators, law enforcement etc). Draw upon your existing knowledge, with a little digging, and feel free to use analogies to other domains (e.g. 3D printing, drones, financial systems, etc.).
- Goal: What is done now and what changes are you proposing?
- Design: What is needed to make it “work”? (including the actor(s) involved - who must opt in, fund, approve, or implement, etc)
- Assumptions: What could you have wrong (incorrect assumptions, uncertainties)?
- Risks of Failure & “Success”: How might this fail, including any unintended consequences of “success” of your proposed actions?
- Next score (from 1-3 with, 1 as the best, or n/a) each of your governance actions against your rubric of governance goals.
This is one framework but feel free to make your own
Your context:
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Enhance Biosecurity |
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Foster Lab Safety |
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Protect the environment |
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Other considerations |
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- Minimizing costs and burdens to stakeholders
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- Promote constructive applications
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- Last, drawing upon this scoring, describe which governance option, or combination of options, you would prioritize, and why. Outline any trade-offs you considered as well as assumptions and uncertainties. For this you can choose one or more relevant audience for your recommendation, which could range from from the very local (e.g. to MIT leadership or Cambridge Mayoral Office) to the national (e.g. to President Biden or the head of a Federal Agency) to the international (e.g. to the United Nations Office of the Secretary General, or the leadership of a multinational firm or industry consortia). These could also be one of the “actor” groups in your matrix.
Principles & Practices - Weekly Homework
- Reflecting on what you learnt and did in class this week, outline any ethical concerns that arose, especially any that were new to you. Then propose any governance actions you think might be appropriate to address those issues. This should be included on your class page for that week.
Principles & Practices - Final Project Homework
- As part of your final project, design one or more strategies to ensure that your project, and what it enables, contributes to growing an ethical biological future.
Related Readings and Resources (Palmer)
Related Readings and Resources (Church, Jacobson, Kong)
Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design (Ogden, Kelsic, 2019)
Next-Generation Digital Information Storage in DNA (Church, Gao, Kosuri, 2012)
Rapidly evolving homing CRISPR barcodes (Kalhor, Mali, Church 2016)
Developmental barcoding of whole mouse via homing CRISPR (Kalhor, Mali, Church 2018)
Toward eliminating HLA class I expression to generate universal cells from allogeneic donors | Blood (ZFN: Torikai 2013)
A Multidrug-resistant Engineered CAR T Cell for Allogeneic Combination Immunotherapy (TALEN: Valton ... Poirot 2015- Cellectis)
CRISPR-Cas9-mediated multiplex gene editing in CAR-T cells (CRISPR: Yang, et al 2015)
Genome-wide inactivation of porcine endogenous retroviruses (PERVs) (CRISPR: Yang, et al 2015)
Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9 (Niu, et al. 2017)
Full article: Harnessing gene drive (Min, Smidler, Najjar, Esvelt 2017)
Review The Hallmarks of Aging (Carlos López-Otín, et al. 2013)
A single combination gene therapy treats multiple age-related diseases (Noah Davidsohn et al. 2019)