Notes on indoor food production, life support for space colonies, “refuges”, “biobox”, and related

Epistemic status: initial stab from a non-expert

Thanks to Shannon Nangle and Max Schubert for helpful discussions. 


There are a variety of potential scenarios where a self-sustaining, biologically isolated Refuge would be needed towards existential risk reduction. 

Currently, there is very little work going on towards technical common denominators required for all such approaches, e.g., highly efficient and compact indoor food production. 

Shallow overview of prior writings related to the BioBox/Refuge concept:

There are a number of concepts floating around about Refuge or “Bio Box” that gesture at different design criteria.

There is the abstract concept around bio-risk

There is the Carl Shulman blog version

Shulman envisions greatly increased wealth or cost-benefit calculus motivating society to equip many standard living and working spaces with BSL-4 level biosafety precautions, e.g., “large BSL-4 greenhouses”. This does not address the issue of radical improvements in the density or autonomy of food production or waste management, but rather proposes the use of advanced filtering and sterilization procedures in the context of more conventional infrastructure.  

There are old BioSphere 2 projects, which include a lot of extraneous stuff up front, like goats and waterfalls — these are arguably not technically focused enough to drive the core capability advancements needed for a Refuge

There is the notion of a regenerative life-support system for space, e.g., for future space stations. This bleeds into the notion of a bio-regenerative life-support system where a large number of essential regenerative functions, e.g., waste recycling or gas balance functions are done by biological organisms, e.g., MELISSA, BIOS-3

MELISSA stands for micro-ecological life support system ALTERNATIVE, where “alternative” means it is using biology for some aspects where, for example, the International Space Station would use more conventional chemical engineering methods. See:

There is the notion of a food production and waste recycling system roadmap for early Mars colonies

See Except below.

While optimized for the Martian setting, they point to core technology problems that may be relevant for Earth-based refuges, including efficient indoor food production, and have led to some roadmapping work taxonomizing where biological versus non-biological solutions could be most useful in a simplified, minimal closed habitat.

There is simply the idea of highly efficient indoor food production to protect against risks to the food supply.

There is the idea of nuclear submarines being able to operate and hide ~indefinitely as a deterrent to attacks, by having a Refuge on board.

There is the notion of using Refuges as a way of maintaining other defensive or counter-offensive biotech capabilities in a safe space, e.g., if a Refuge is where we keep our vaccine/countermeasure synthesis capacity.

Within all this there are parameters including whether it is totally sealed, size, number of people supported, comfort level supported, and so on. 

There is the George Church version of BioBox which is closest to a modern idea for fully closed bio-regenerative life support system on Earth, building on MELISSA, but with an emphasis on photosynthesis and certain unconventional applications in mind. This proposes to use photosynthetic microbes as a food source, in contrast to the Nagle et al first stage Mars plan which proposes to use methanol-using heterotrophic and CO2-using lithoautotrophic fermentation.

Finally there is the idea of pushing relevant (e.g., compact indoor food production) technologies by first developing economically viable products (such as niche food products for consumers).

Then there is the “hydrogen oxidizing bacteria” (HOB) approach — see these papers:

Alvarado, Kyle A., et al. “Food in space from hydrogen-oxidizing bacteria.” Acta Astronautica 180 (2021): 260-265.

Martínez, Juan B. García, et al. “Potential of microbial protein from hydrogen for preventing mass starvation in catastrophic scenarios.” Sustainable production and consumption 25 (2021): 234-247.

Nangle, Shannon N., et al. “Valorization of CO2 through lithoautotrophic production of sustainable chemicals in Cupriavidus necator.” Metabolic Engineering 62 (2020): 207-220.

Liu, Chong, et al. “Water splitting–biosynthetic system with CO2 reduction efficiencies exceeding photosynthesis.” Science 352.6290 (2016): 1210-1213.

Chen, Janice S., et al. “Production of fatty acids in Ralstonia eutropha H16 by engineering β-oxidation and carbon storage.” PeerJ 3 (2015): e1468.

From a Denkenberger paper: “The main companies currently pioneering mass production of H₂ SCP are: SolarFoods, NovoNutrients, Avecom, Deep Branch Biotechnology [looks like they are making animal feed], Kiverdi [“air protein”] and LanzaTech [making Omega3 fatty acids from CO2, for one thing]…”. See also, notably, Circe

Other more mature aspects of life support systems outside food production

Note: the ISS imports food and some water from Earth but recycles other things like oxygen, as I understand it

Relevant excerpt from The Case for Biotechnology on Mars (Nangle et al):

“Recent advances in fermentative production of flavors, textures and foods can form the basis for new Mars-directed engineering efforts. Successful deployment will require the in-tandem development of organisms and fermenters for Martian conditions; the system must use CO2 and CH3OH as its sole carbon sources, accommodate unreliable solar irradiance and tolerate the potential presence of contaminants in water and regolith. To support this development, we propose scaling Martian food production in three stages: Stage I involves lithoautotrophic and heterotrophic fermentation; Stage II involves photoautotrophic fermentation and small-scale crop growth; and Stage III involves large-scale crop cultivation. 

Stage I. Both methanol-using heterotrophic and CO2-using lithoautotrophic fermentation will be used to complement the crew’s diet and serve as an initial demonstration of Martian food production. 

Fermentation technologies also have the added benefit of shorter boot-up and production timelines (days to weeks) compared with the production of staple plant crops (weeks to months). Fermentation can be carried out in simple stir tanks or airlift reactors that use engineered organisms to produce complex carbohydrates and proteins40,41. Several suitable methylotrophic organisms, such as Methylophilus methylotrophus and Pichia pastoris, are already genetically characterized, industrially optimized and extensively deployed for large-scale production. Methylotrophic genes have also been heterologously expressed in model organisms such as Escherichia coli and Bacillus subtilis41. Such organisms can be engineered to produce a wealth of ingredients, including flavors, protein, organic acids, vitamins, fatty acids, gums, textures and polysaccharides41. Bioreactors with these organisms have very high process

intensities, with a single 50-m3 reactor able to produce as much protein as 25 acres of soybeans, with only a few days to the first harvest42–44. CO2-using lithoautotrophs could similarly be engineered to couple their hydrogen oxidation and CO2 fixation into oligosaccharides, protein and fatty acid production. 

Maximizing yields in these microbial chassis and adapting the above organisms to Martian minimal medium remain key challenges. Initial applications can focus on small-scale sources of backup calories and on establishing benchmarks for subsequent larger-scale implementation. Demonstration of aero- and hydroponic systems to grow spices, herbs and greens would be explored in this stage45.

Stage II. The second stage focuses on introducing photoautotrophs to synthesize food. With increasing investment in Martian infrastructure, more complex bioreactors can be deployed to grow green algae rich in carbohydrates, fatty acids and protein46. Several well-developed terrestrial examples of algal industrialization exist, such as Arthrospira platensis for food or commercial algal biofuels47. On Earth, the high capital costs of building reactors and supplying high concentrations of CO2 for optimal production are commercially challenging. On Mars, however, this challenge becomes an advantage: the CO2-rich atmosphere can be enclosed and pressurized for algal growth.

As photoautotrophic growth is scaled to meet more nutritional requirements of the crew, maintaining reliable production despite the weaker Martian sunlight and planet-engulfing dust storms will be a key challenge, requiring surface testing of several reactor designs. We do not anticipate using natural sunlight as an energy source for photoautotrophs at these stages because it alone is insufficient for growth: once solar photons have passed through greenhouse materials, photoautotrophs would receive around 17 mol m–2sol–1—up to fourfold less than their typical minimal requirements35,48.

Thus, at this stage, photosynthetic organisms would be grown in photobioreactors or growth chambers with optimized artificial lighting. For longer habitation, the psychological benefits of having living plants and familiar foods are substantial49….”

Cyanobacterial food

But is the cyanobacterial path the right one? To compare the hydrogen oxidizing bacteria (HOB) approach with a photosynthetic microalgae or cyanobacteria approach, consider this quote from one of the Denkenberger papers: “Electricity to biomass efficiencies were calculated for space to be 18% and 4.0% for HOB [hydrogen oxidizing bacteria] and microalgae, respectively. This study indicates that growing HOB is the least expensive alternative. The [equivalent system mass] of the HOB is on average a factor of 2.8 and 5.5 less than prepackaged food and microalgae, respectively.” So HOB is significantly more efficient, per this analysis. 

The supplemental materials of the Metabolic Engineering paper includes this comparison with cyanobacterial food production:

“Comparison to cyanobacterial co-culture systems

As bioproduction technologies have expanded, co-culture and cross-feeding has been explored as a possible solution to lower feedstock costs while supporting the existing infrastructure of engineered heterotrophs. Efforts towards autotrophic-heterotrophic co-cultures have primarily focused on cyanobacteria as the autotroph 1,2 . Cyanobacteria are an obvious choice as they natively produce sucrose as an osmoprotectant—rather than a carbon

source—to high concentrations without toxicity, making it an attractive feedstock-producer for heterotrophs. Engineered cyanobacterial strains able to convert and export up to 80% of their fixed carbon successfully fed three phylogenetically distinct heterotrophic microbes (E. coli, B.

subtilis, and S. cerevisiae) 3 . However, cyanobacteria produce reactive oxygen species through photosynthesis and protective cyanotoxins, which are ultimately toxic to the heterotrophs. While cyanobacteria have higher solar-to-biomass conversion efficiencies than plants, efficiency remains 5-7% and is thermodynamically limited to ~12%—several fold lower than photovoltaics 4. In addition to their biological limitations, there are a variety of implementation constraints that hinder industrial scale-up. Because cyanobacteria grown at scale require sunlight, two common culturing methods allow for optimal sunlight penetration: pools and photobioreactors. The large shallow pools can only be used in certain regions, are susceptible to environmental changes and contamination—and so it is difficult to maintain consistent batch-to-batch cultivation. In an effort to mitigate some of these issues, these pools can be modified to grow the cyanobacteria in small diameter tubing, but this kind of containment often deteriorates from radiation exposure as well as generates substantial plastic waste 5 . Because these issues4 are all challenges for cyanobacteria monoculture, it is not clear how a co-culture system would be successfully implemented at scale.”

See here for more on comparison with using cyanobacteria:

I am not an expert here but this seems to basically be saying photosynthesis is not actually that great compared to what can be done with other kinds of conversion. 

Note: other comparisons could be made to other food from gas and food from woody biomass approaches. 

A counter-argument against this kind of industrial instrumentation and bioengineering heavy approach is that in some catastrophic scenarios on Earth, e.g., post nuclear, one might have very limited infrastructure capacity and one could perhaps instead be focusing on producing sufficient food from woody biomass with sufficient net gain to the human workers doing a lot of stuff by hand in that scenario (no power grid, no chemical manufacturing whatsoever, no good temperature control systems, etc)? 

This addresses a scenario relevant to post-apocalyptic (nuclear winter) food production but not necessarily the Refuge/BioBox scenario per se.

Some questions:

Q: Is efficient indoor food production from simple feedstocks indeed the “long pole in the tent”, technically, for a Refuge/BioBox/closed life support system in general?

Other parts of life support do seem more solved, e.g., from work done by the International Space Station teams:

Q: What about doing natural gas to food biologically as a means of producing food

or coal to food chemically (See:

Q: Is there value in pushing conventional indoor vertical farming instead? See:

Much less efficient than using microbes? 

Q: Would we really do direct air (or ocean) capture of CO2 for a refuge on Earth?

One of the Denkenberger papers states: “Electrolysis based H₂ SCP production requires an external carbon source. This study conservatively uses direct air capture (DAC) of CO₂ as the basis of our calculations; however, CO₂ capture from industrial emitters is in most cases less expensive and in some cases can already contain some amount of hydrogen that can be used.”

“​​The nitrogen requirements can be satisfied by using ammonia from the fertilizer industry….”

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