Ethics & policy: Interplanetary synbio

Synthetic biology in space

Promising applications of synthetic biology for long duration space travel include a variety of biologically engineered products and biologically aided processes and technologies. While these applications would aid human space exploration, they could result in several unintended consequences in the long run. Therefore, it’s critical that we discuss and set up protocol frameworks in the context of ethical, legal and social realms.

Ongoing R&D for near future applications of synthetic biology in space points to genetically modified plants and microorganisms designed to produce food and medicine. Other applications include bio-mining, carbon capture and air purification, personalized diagnostic tools, biomaterial etc. However, in the future, these application could expand to other GM organisms, including humans, that are more suited to endure multiple stressors. Long term effects of GM organisms in the context of multiplanetary expansion of terrestrial life and interplanetary interactions should therefore be considered.

image: thetimes.co.uk

Governance and policy

In contrast to earth-based synbio, space applications have additional challenges such as those raised by space microbiology and environmental factors, legal complications, planetary protection, lack of decision-making infrastructure(s), long duration human missions, terraforming and the possible discovery of extraterrestrial (ET) life. Until recently, the main actors of space exploration included politicians, scientists, and engineers. However, with privatized companies, such as SpaceX, entering this industry and turning space exploration into a for-profit economy, it’s important that we set up transparent and more robust governance/policy systems. The desired ecosystem should include more diverse disciplines, such as evolutionary biology, ecology research as well as social sciences to define “long-term” goals of the space programs and ensure an ethical future of synbio in space.“This perspective requires subscribing to a new paradigm that no longer sees ‘long-term’ as months or years but rather as time in an evolutionary context”.

Long-term goals could include, but are not limited to:

• Non-malfeasance

• Access

• Planetary environmental protection

potential governance "actions", each presented in four sections. (TBD)

• 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?

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References

Race, M., Moses, J., McKay, C., & Venkateswaran, K. (2012). Synthetic biology in space: Considering the broad societal and ethical implications. International Journal of Astrobiology, 11(2), 133-139. doi:10.1017/S1473550412000018

Criscuolo F, Sueur C, Bergouignan A. Human Adaptation to Deep Space Environment: An Evolutionary Perspective of the Foreseen Interplanetary Exploration. Front Public Health. 2020;8:119. Published 2020 Apr 24. doi:10.3389/fpubh.2020.00119

Design: Radiation resistance

1.)  Overview and rationale:

Humans and most organisms, except for some microbial extremophiles, aren’t fit to survive the host of stressors in deep space or on other planets. To survive long duration space exploration or to inhabit planets other than Earth, we need to make organisms that are more suited to endure multiple stressors. Genetic engineering could help us to build the ultimate astronaut. One that is resistant to high radiation(CTNNB1), and bone loss(SOST) due to altered gravity; but also more mentally resilient with genes that make them less prone to anxiety, and cognitively more agile(PDE4B, FOXP2, CCR5, GRIN2B). We could even augment their physical capabilities by adding a gene that gives them six-fingered hands(HOXA11).

High cosmic radiation is one of the most detrimental stressor in deep space, as well as on a planet like Mars that lacks a magnetic field or a thick atmosphere to shield humans and most organisms that have evolved on earth from radiation. Long duration space exploration will require radiation protection measures. Designing radiation resistant organisms could be a method to ensure long term radiation protection in space.

CTNNBI is a gene with radiation resistance properties. This mutation could be applied to humans to make them more fit to survive and thrive in space.

2.)  Genomic sequence: 

3.)  Genome editor design:

CRISPR/Cas9-based

delivery: TBD

screening: TBD

Protein Design: Structural Colors

I’ve always been intrigued by vibrant iridescent colors. In nature, iridescence is caused by structural coloration, which is the production of color by nanostructure surfaces that interfere with visible light, sometimes in combination with pigments.

Another fascinating phenomenon is dynamic coloring in some animals including cephalopods such as squid are able to vary their colors rapidly for both camouflage and signaling. The mechanisms include reversible proteins which can be switched between two configurations. The configuration of reflectin proteins in chromatophore cells in the skin of the Doryteuthis pealeii squid is controlled by electric charge. When charge is absent, the proteins stack together tightly, forming a thin, more reflective layer; when charge is present, the molecules stack more loosely, forming a thicker layer. Since chromatophores contain multiple reflectin layers, the switch changes the layer spacing and hence the color of light that is reflected. Additionally, within the chromatocytes, where the pigment resides in nanostructured granules, we find the lens protein Ω- crystallin interfacing tightly with pigment molecules.

Protein Analysis

Pick any protein (from any organism) of your interest that has a 3D structure

Briefly describe the protein you selected and why you selected it.

• Identity the amino acid sequence of your protein.

  • How long is it? What is the most frequent amino acid?

  • How many protein sequence homologs are there for your protein?

    Hint: Use the pBLAST tool to search for homologs and ClustalOmega to align and visualize them.

  • Does your protein belong to any protein family?

• Identify the structure page of your protein in RCSB

  • When was the structure solved? Is it a good quality structure?

  • Are there any other molecules in the solved structure apart from protein?

  • Does your protein belong to any structure classification family?

• Open the structure of your protein in any 3D molecule visualization software

  • Visualize the protein as "cartoon", "ribbon" and "ball and stick".

  • Color the protein by secondary structure. Does it have more helices or sheets?

  • Color the protein by residue type. What can you tell about the distribution of hydrophobic vs hydrophilic residues?

  • Visualize the surface of the protein. Does it have any "holes" (aka binding pockets)?

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References

Williams, T.L., Senft, S.L., Yeo, J. et al. Dynamic pigmentary and structural coloration within cephalopod chromatophore organs. Nat Commun 10, 1004 (2019). https://doi.org/10.1038/s41467-019-08891-x

Measurement and Imaging: Mycelium

Part 1: Imaging

For part 1, I chose to examine mycelium. I had been experimenting with growing mycelium for my biomaterial exploration research, and wanted to see the structures on a microscopic scale, using a scientific microscope with 40x-100x magnification.

I collected small samples using tweezers, which was quite challenging given how delicate mycelium is. I assume the sample was still corrupted during this process. A better way to observe mycelium under the microscope would be to grow it directly on slides to preserve the delicate structure of the root system.

I succeeded to observe chunks of the root structure and also small pieces of the substrate on which the mycelium had grown.

Part 2: Design of smFISH / Spatial Sequencing Assay (Computational)

Part 3: smFISH Image Analysis (Computational)