Class Assignment - Synthetic Biology Governance Engineering Heat Resistant Coral Reefs The Great Barrier Reef (GBR) is one of the most ecologically diverse places on the entire planet, with over 1,200 species of coral creating a complex three dimensional environment that nurtures a vast variety of unique life. The GBR is also estimated to contribute approximately $11.6 billion to the Australian economy each year as one of the largest tourism attractions of the continent, alongside the vast fisheries industries its biodiversity supports. The GBR is also a cornerstone of the Australian national identity, holding deep cultural value for both the Aboriginal and Torres Strait Islander peoples, with 85% of Australians proud of its heritage status.
Class Assignment - Lab Automation Opentrons Artwork Something
Post-Lab Questions Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications. Something
Subsections of Homework
Week 1 HW: Principles and Practices
Class Assignment - Synthetic Biology Governance
Engineering Heat Resistant Coral Reefs
The Great Barrier Reef (GBR) is one of the most ecologically diverse places on the entire planet, with over 1,200 species of coral creating a complex three dimensional environment that nurtures a vast variety of unique life. The GBR is also estimated to contribute approximately $11.6 billion to the Australian economy each year as one of the largest tourism attractions of the continent, alongside the vast fisheries industries its biodiversity supports. The GBR is also a cornerstone of the Australian national identity, holding deep cultural value for both the Aboriginal and Torres Strait Islander peoples, with 85% of Australians proud of its heritage status.
Despite holding the love and support of the nation, the GBR is currently existentially threatened with the onset of climate change. Warming waters, seawater acidity, an increasing prevalence of marine pests and the cumulative impacts of overfishing are simultaneously devastating this unique environment with some estimates now placing the reef at less than 10% of its original scale.
Synthetic biology may be able to mitigate the continued impacts of climate change through the identification and propagation of genes conveying heat resistance - a vital trait to support all coral species into the near future. Significant coral reseeding efforts (including extensive selective breeding efforts) are already underway, gene editing these coral polyps prior to their reintroduction to the environment may greatly bolster their chances of successfully reseeding reefs.
Governance & Policy Goals
All applied synthetic biology must be done with social permission of a majority of the Australian people and align with indigenous values. Representatives of the Aboriginal and Torres Strait Islander peoples should be represented at every stage of the project. The work must maintain social support and in no way undermine the heritage status of the GBR.
Any risk of ecological or economic harm that may arise through the release of genetically engineered coral must be assessed and mitigated as far as reasonably possible. Prior to release, all coral should be genomically assessed to minimise the risk of unintended editing and prevent any vector genes from being released into the wild coral genome. To the fullest extent possible, selective breeding should be applied over gene editing, and gene editing should be applied over any possible transgenic approaches. The risk of unintended ecological impacts or adverse cascades should be assessed in-depth prior to any coral releases. The release of genetically engineered coral must not undermine the reef’s role as an economic engine for tourism.
All experimental work must be conducted transparently and in alignment with best practice as defined by the international scientific community. International scientific perspectives must be included in the design of this work to ensure knowledge flow and cutting edge best practice is followed as much as possible. All data collection must be conducted transparently, with inclusive opportunities provided for international collaboration, to ensure the international community as a whole can leverage the novelty and scale of the work as much as possible as a case study.
Potential Actions
Pre-emptive collaboration with indigenous perspectives. Purpose: Actively releasing genetically engineered organisms into the environment, especially sacred species with vast cultural importance is complex in aspects well beyond synthetic biology. Hence, this work would need to seek out cultural and indigenous leadership from the very earliest stage, to ensure everything undertaken is conducted in a manner aligned with the heritage of the reef. Design: Cultural leaders of both the Aboriginal and Torres Strait Islander would be pivotal. Assumptions: These leaders are supportive of the ambition on a foundational level & are willing to invest their time into the work. Risks of Failure & “Success”: Without indigenous support, this work would run the rest of devastating social perception of the reef and undermining the protection of the very environment the work is designed to safeguard.
Transparent work conduct and open access. Purpose: Given the sensitivity of re-engineering coral on a genetic level, operating with an exceptionally high degree of transparency and ensuring all data and conclusions are published in such a manner as to be accessible to all potential stakeholders seeking to safeguard the reef will be vital. Design: All funding and contractual obligations of the project must align with open access principles and capacity must be allocated to public outreach across every stage of research and release. Assumptions: Stakeholders will be open to engaging directly with the scientists. Risks of Failure & “Success”: Transparency may backfire with misrepresentation and well meaning but destructive activism.
Ensure genetic change is minimised. Purpose: When assessing potential genetic mechanisms to develop heat resistance in coral, minimising the genetic change implemented must be a foundational requirement. Additionally genetic screening must be conducted on all coral prior to wild release to minimise the risk of leaking vector DNA. Wherever possible, applied selecting breeding to deliver the same heat resistant outcome will also be preferentially used. Genetically editing the coral directly shall only be conducted on the coral species that truly require it. Design: This requirement may increase the technical difficulty of the undertaking and so it must be asserted as a guiding principle upfront for all funding stakeholders. Assumptions: This guidance assumes that selective breeding will be insufficient to convey heat resistance to coral varieties at large. Risks of Failure & “Success”: This guidance may result in sub-optimal coral strains being selected that ultimately have not obtained heat resistance to a high enough degree to survive future summers, undermining long term success and overall reef survival.
Pre-emptive ecological modeling must be prioritized. Purpose: Ecosystem engineering infamously coincides with unintended consequences and runaway cascading impacts. Computational modeling to assess likely impacts on the coral reef ecosystem at large from the spontaneous re-introduction of a significant pass of heat resistant coral must be conducted prior to any coral release. Ensuring ecological impacts are considered and contingency plans are in place for any risks identified will lower the overall risk of unintended impacts on the reef’s overall ecosystem. Design: Seeking dedicated reef ecosystem expertise will be a foundational requirement of this undertaking. Assumptions: The project as a whole acts on the assumption that reseeding coral reefs is an effective mechanism for regenerating these habits. Risks of Failure & “Success”: Ecological modeling may highlight potential adverse impacts of large scale coral release, which may necessitate novel approaches to introducing any engineered corals back into their environment, may undermine the potential positive impacts of the work, or may even reject the feasibility of the project as a whole.
Critical Analysis of Potential Actions
Does the option:
Pre-emptive collaboration with indigenous perspectives.
Transparent work conduct and open access.
Ensure genetic change is minimised.
Pre-emptive ecological modeling must be prioritized.
Align with social & indigenous values.
• Align with indigenous values
3
3
2
2
• Maintain social trust
3
3
3
3
Prevent ecological or economic harm
• Coral Assessment
3
n/a
3
3
• Minimise Genetic Change
3
n/a
3
3
• Ecological Alignment
3
n/a
3
3
• Economic Alignment
2
2
3
3
Transparent Conduct
• International Collaboration
2
3
n/a
n/a
• Accessable data
3
3
n/a
3
Other considerations
• Minimizing costs and burdens to stakeholders
2
2
1
1
• Feasibility?
3
3
1
1
• Not impede research
1
2
1
3
• Promote constructive applications
3
3
n/a
2
Conclusions
Given the diversity of stakeholders that will bear direct consequences of this work, the complexity of the interactions between the various disciplines involved and the scale of resourcing required, it is likely that all of the actions listed above would be considered foundational requirements if attempting to conduct this project in any capacity beyond foundational research.
Pre-emptively gathering the full breadth of expereince and perspectives from both the local and scientific community to deeply consider the approach alongside potential impacts and trade offs would be essential. Even in the writing of this high level overview, assumptions had to be made concerning what indigenous leaders would value when considering work such as this, which only highlights how essential their early engagement would be in designing foundational governance for this project. The true threshold of this work sits at the release of genetically modified coral back into their native environment, however this is also the turning point where the benefits of the work could potentially be realised. As such moving quickly will also be pivotal, coral bleaching is an ongoing problem that is rapidly decimating the remaining reefs every summer - the sooner all parties involved unify their vision on how to apply synthetic biology, the greater the chance we can salvage the reef into the future.
Homework Questions from Professor Jacobson
What is the error rate of polymerase & how does this compare to the length of the human genome?
Error correcting polymerase has an error rate of approximately 1:10^6. In the context of the 3.2 billion bp human genome, this would equate to ~1000 errors over the course of a full replication
How does biology deal with this discrepancy?
DNA Polymerase activity is accompanied by a wide variety of error correcting proteins that act to support the DNA replication process, significantly reducing the error rate - though ultimately this process has never been perfect and some degree of mutation is inevitable. Genetic redundancy mitigates the potential for adverse functional outcomes for a significant portion of the errors that do occur regardless. Additionally there is always the potential for a mutation to convey a functional advantage as well!
How many different ways are there to code (DNA nucleotide code) for an average human protein? In practice what are some of the reasons that all of these different codes don’t work to code for the protein of interest?
Given the average human protein is encoded by ~1036 bp, equating to ~345 amino acids in the resulting protein chain, and that the average amino acid is encoded for 3 possible codons, there would be around 3^345 unique DNA sequences to encode for it. Despite this extreme redundancy in the genetic code, these DNA sequences would not be functionally identical. Codon variation will potentially impact the stability of the resulting mRNA, which may prevent translation from occurring outright. If the mRNA is indeed translated, the synonymous codons may also impact the speed of the translation process (tRNA availability is a bottleneck for some codons more than others, due to a bias in which codons are preferentially used) potentially resulting in a reduced protein yield or outright misfolding.
Homework Questions from Dr. LeProust
What’s the most commonly used method for oligo synthesis currently?
Phosphoramidite oligonucleotide synthesis
Why is it difficult to make oligos longer than 200nt via direct synthesis?
200nt is often cited as the upper limit of phosphoramidite oligonucleotide synthesis due to the cumulative effects of incomplete sequence truncation. As the length of the complete chain grows, so to does the ratio of incomplete chains present within the mixture. Even with exceptionally high-efficiency coupling, by ~200nt the ratio of incomplete waste chains to the complete end product will have reached a point of extreme diminishing returns.
Why can’t you make a 2000bp gene via direct oligo synthesis?
Alongside the aforementioned issue of cumulative sequence truncation, seeking to scale the process towards thousands of base pairs will also see issues arise through sequence mutation with the potential for deletions, insertions, and substitutions all potentially resulting in incorrect end products. This will be further compounded when purifying the final product as the molecular weights between the complete final product and the contaminating incomplete products will now be separated by a very narrow margin, making product purification another challenge in of itself.
Homework Question from George Church
What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?
The 10 essential amino acids for all animals are: Arginine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, and Valine. These amino acids are unique in that animals are incapable of synthesizing them independently, necessitating their presence in the animals diet.
The Lysine Contingency refers to a fictional fail-safe mechanism in Jurassic Park, where all of the dinosaurs had their ability to produce Lysine knocked out - forcing a reliance on artifical Lysine dietary supplements. The logical failing of this plan is two-fold, firstly as stated above all known animals are already incapable of producing Lysine rendering it unlikely the dinosaurs were the sole exception. Secondly, even if an innate ability to produce their own Lysine had indeed been knocked out, Lysine’s presence in natural plants would completely negate any proposed reliance on an artificial Lysine supplement to maintain healthy metabolism.
Week 2 HW: DNA Read, Write & Edit
Benchling & In-silico Gel Art
The Great Barrier Reef (GBR) is one of the most
Week 3 HW: Lab Automation
Class Assignment - Lab Automation
Opentrons Artwork
Something
Post-Lab Questions
Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.
Something
Write a description about what you intend to do with automation tools for your final project.