The science of enclosed ecosystems


Earlier today I did a guest post for fellow blogger, writer, and scientist, Dan Koboldt. I came across his blog about a month ago. He and I share the same mission, to promote the use of accurate science in sci-fi. But rather than do all the background research on his own, he wisely seeks out professionals in related fields and asks them to write about scientific misconceptions in sci-fi and how to get it right. Since my own lab work concerns cellular respiration, I offered to write a post for him on enclosed ecosystems, and he generously agreed. You can see the original post by clicking on the graphic below:


Enclosed ecosystem and life-support systems in sci-fi

A Closed Ecological System (CES) is a broad term that encompass any self-sustaining and closed system in which matter does not leave or enter. These artificial habitats can be built in space, underground, or underwater, but no matter where they are, chances are they are closed for a reason. Whether it is an underground bunker in a post-apocalyptic setting, a distant planet in the early stages of colonization, or a spacecraft carrying the last remnants of humanity, the environment outside is not hospitable. To ensure long-term survival, the occupants must maintain a well-balanced air and water system, a continuous food supply, and a reliable source of energy.

So far, no artificial enclosed ecosystem has successfully supported human life for long periods of time. Even the astronauts on the International Space Station get regular supply runs and have to exchange personnel. The largest CES was Biosphere 2, which sustained 8 crew for 2 years; however, they had to resort to some extreme measures to keep oxygen and carbon dioxide levels in normal ranges, and many of the plant, animal, and insect populations died off.

Creating and maintaining a CES is difficult, as many fluctuations or imbalances can cascade into environmental collapse without continuous monitoring and support. Here I will discuss a few of the misconceptions about Enclosed Ecosystems and Life Support systems and suggest ways to get it right in Sci-fi.

Myth: Waste is useless and should be disposed of.

You see this in many sci-fi stories set in space; the airlock door opens and a stream of garbage is ejected into the vacuum. This might be acceptable for short-term missions, where all the supplies needed are carried along, but for an ecosystem intended to last for a long time, being wasteful is not an option. It is a matter of mass balance. In most situations, it won’t be possible to obtain resources from outside the enclosed system, so if your characters are ejecting waste of any kind out the airlock, soon there won’t be anything left. By the same principle, if some waste product cannot be recycled, it will build up and eventually consume all of the precursor materials.

Getting it right

When creating a life-support system for a fictional crew, they must adhere to a strict recycling policy. Most solids, such as plastics and metals or glass, can be melted and recast into any number of shapes. Of greater importance is the conversion of gaseous, liquid, and solid wastes into breathable air, drinkable water, and edible food. Solid organic wastes such as material from dead plants, animals, or their excrement, contain large amounts of nitrites and nitrates, phosphates, and other inorganic compounds that serve as fertilizer for plants.

Having a ‘living soil’ or cultured hydroponic system is also necessary, as bacteria, like those found in the human gut, are great at breaking down complex organic molecules and making them assessable to the roots of plants. So far, there is no easy way to convert waste, carbon dioxide, and water into an edible food source, outside of a biological system, such as a plant. Such plants can be consumed as food, and the cycle is repeated.

Myth: Water evaporates and condenses, but the total amount doesn’t change.

You hear this often in terms of a large environment like the Earth, where water rises from the oceans and falls again as rain, and it is true for the most part. Only a few processes create or break down water, but in a small, highly balanced environment, they can make a huge difference. Water is made and destroyed in biological systems during condensation reactions and hydrolysis reactions, respectively.

But the most significant of these reactions occurs in the mitochondria, the ‘energy’ producing organelle in nearly every cell. In the mitochondria, oxygen receives 4 electrons from the Electron Transport Chain and is reduced to water. Yes, nearly all of the oxygen you absorb through your lungs is converted into water. The reverse happens in plants, where water is hydrolyzed into oxygen during the construction of carbohydrates during photosynthesis.

Getting it right

The balance between animal and plant life on the ship should ensure a stable supply of water, but water can be made and eliminated artificially if there is ever an imbalance. Electrolysis, breaking water into hydrogen and oxygen, can be accomplished with a little electricity. That processed can be reversed by burning hydrogen in the presence of oxygen. A means of storing oxygen and hydrogen or water should be in place to deal with small fluctuations. Humidity and condensation can cause severe damage to electrical systems, especially in zero gravity, where air currents can become stagnant. This also increases the risk of mold. Cold surfaces or specialized air filters can trap the water vapor and return it to storage.

Myth: Plants convert carbon dioxide into oxygen, while animals do the opposite.

Unfortunately, the biochemistry isn’t so simple. Oxygen is not converted into carbon dioxide in animals. As I already mentioned, nearly all of the oxygen you absorb is converted into water. Carbon dioxide is released from the breaking down of metabolites like sugar, proteins, and fats. This takes place in the mitochondria. In plants, oxygen is made when both carbon dioxide and water are converted into carbohydrates like glucose during photosynthesis. This occurs in the chloroplast in plants.


Another misconception is that producing oxygen is all plants do. In reality, plants have mitochondria too, and they consume oxygen and carbohydrates and produce carbon dioxide and water. When the lights are on, plants tend to produce more oxygen than they consume, but without light, they will suck up the oxygen as hungrily as we do.

Getting it right

Even as little as 1% concentrations of carbon dioxide can cause acute health effects such as fatigue and dizziness, but even higher concentrations (7-10%) can lead to unconsciousness, suffocation, and death within hours. To control fluctuations in carbon dioxide, CO2 scrubbers can be used. However, carbon dioxide is an intermediate step in oxygen and carbon cycles, so this artificial means to lower carbon dioxide may cause downstream effects on plant growth and lower oxygen concentration. This occurred accidentally in Biosphere 2 when carbon dioxide was converted into calcium carbonate in exposed concrete.

Materials like metal oxides and activated carbon can be used in CO2 scrubbers and then the carbon dioxide can be released at a later time. Large variations from the normal 21% oxygen is more easily tolerated than variations in carbon dioxide, but long-term exposure to greater or lower concentrations can lead to many acute and chronic health effects. Adjusting the amount of artificial or natural light available for photosynthesis is an effective means of controlling oxygen concentrations.

Myth: Energy must be produced within the ecosystem.

No closed ecological system is completely enclosed. If it were, it would soon succumb to the laws of entropy, making it a very cold and dark place. Something has to enter the system, and that thing is energy. The energy driving the weather, the currents, and the very life on this planet is coming from the sun.

Getting it right

Most common energy sources:

  • Solar
  • Wind
  • Water
  • Geothermal
  • Gas
  • Fusion/fission

The first four examples are the only types applicable in a completely closed ecological system, since energy can be moved into the system without any exchange of matter. A major drawback, however, is that the habitat can’t leave the source of the energy. A spaceship powered by the sun will have a hard time operating in interstellar space.

Any technology that requires the use of combustible fuels or fissionable (uranium 235 or plutonium 239) or fusible (Hydrogen 2 and 3, deuterium and tritium, and helium) materials will have to be resupplied on a regular basis, so they are not suited for long term ecosystems. By nature of their bi-products, they cannot be reused for more energy, but they have the benefit of being disposable and can be used as a form of thrust in spaceships without upsetting the mass balance.

Other Considerations for Environmental Control and Life Support.


My year old Ecosphere. Going strong except for a slight algae overgrowth (The lab decided to keep lights on around the clock this past month).

Size- Closed ecological systems can come in all shapes and sizes, but the larger the better. Larger ecosystems, like the Earth, can sustain much more life and complexity and take longer to collapse if poorly maintained.

Nutrition- The nutritional demands of a human are more than getting the right amount of calories. There are many essential trace elements, minerals, amino acids (9 of them), and fatty acids (omega 3 and omega 6) and nearly everything that is classified as a vitamin, that cannot be synthesized by the human body. Until these things can be synthesized by machines, a complex ecosystem of many different plant and animal life forms would be required to maintain optimum human health.

Temperature regulation- Heat will build up rapidly in most enclosed systems, even in the cold of space, especially when you have heat generating electronics around. Heat needs to be dumped back into space as thermal radiation, usually a high surface area radiator that circulates a fluid capable of picking up heat in the interior and then dispensing with it outside. The opposite may be true in the deep ocean or underground, where heat may be drawn out of the enclosed system, and insulation will be necessary.

Air circulation- This is particularly important in zero G space, where hot and cold air will no longer rise and fall, respectively. To prevent air stagnation, humidity fluctuation and condensation, air needs to be well circulated. Filters are also necessary to remove any particulate matter such as skin cells or microbes.

The human element- Most enclosed ecosystems designed to support human life have not lasted nearly as long as they were intended to. Why? Because they failed to factor the human element into the equation. People get lonely and fall in love, personalities clash and people fight. Close quarters and a limited food supply can cause even the most patient and respectful of people to lose their temper. In Biosphere 2, the eight crew were barely on speaking terms by the time they exited, and two of them got married soon after.

Writing Update-October

fall-in-seattleIt is Fall, a beautiful time of year in Seattle. All the leaves are changing color, and the days are either rainy, sunny, or a bit of both.  I wish I could blame the weather for the late writing update this month, but the truth is, I just forgot. I do have some fun blog posts planned, but you will have to wait till next week to see them.

My works-in-progress.

The thing I love most about this blog is that it allows me to research dozens of topics I would otherwise have no reason to research. In so doing, it has given me more ideas than I know what to do with. These ideas have found their way into my writing and into the outlines of several new works in progress.

In case you missed it in my last post, I am working on a new story called Grounded (working title). Quotidian is more dystopian than sci-fi, but Grounded is very sci-fi. You can read the blurb here. It will be set in the near future, just like Quotidian, but unlike Quotidian, it will be chock full of science and innovation. It has been fun learning all about orbital mechanics and buoyancy and speculating about what will change when gravity has been eliminated. I have even consulted with my uncle, who works for NASA. You will be hearing more about this project in the near future.


Quotidian is coming along slowly. In my August update, I had planned to make it through several rounds of edits and several drafts by the end of the year, but I am still wading through the current draft. The hardest part it deciding what stays and what goes. If a subplot doesn’t contribute much to the overall story, character development, or setting, I eliminate it. Unfortunately, this means I have to comb through the draft and remove all mentions of it. The earlier the subplot is introduced, the more there is to eradicate as the story progresses.

Typically writers fall into one of two categories: underwriters and overwriters. I think I am an overwriter, but not to the extreme. As I am editing, my word count is shrinking, but not by much. I think I outlined it well enough that there isn’t a whole lot of extraneous exposition or excessive subplots.

I usually write my entire story as one Word document. It is easier to keep track of the drafts that way verses having a Word document for each chapter. I regularly make new versions of the same document with a new save date to ensure, if I lose one copy or make a significant change, I can return to a previous version if necessary. This has resulted in a huge file of documents over the years. I love graphs, so I plotted the word count for each of my document versions over time to get an idea of my writing pace and speed:


Word count for Quotidian

The book started relatively high in word count, but this was mainly due to all the notes, outlines, and about a chapter or so of actual story. It was pretty slow to get started because I was finishing Book 2 of the Abyssian. I didn’t start making headway on Quotidian until the end of 2014. Of course, this didn’t last long. I had to graduate. The next several months were spent writing my dissertation and graduating. I started my postdoc about a week after my last day in grad school, and that week was spent packing my bags, leaving Alabama behind, and traveling across the country to Seattle. Once in Seattle, the setting for Quotidian, I felt much more inspired. During the day, I was in lab, but afterwards I would find a quiet place in some nearby café or bar and write, nearly every day, until I completed Quotidian. Now I am in the editing phase, and I am really missing the daily writing. I have since started Grounded, but juggling both is making editing and writing progress pretty slowly.

Thankfully, I get quite a lot of editing and feedback from members of Critique Circle. On this website, I post chapters to my private queue, and my queue members read and critique it. I only have 16 chapters posted so far, but will be putting all of them up by the end of the year. In addition to finding me some alpha readers, CC was able to generate some pretty cool stats for my posted chapters:


The readability stats indicate what grade level the reader needs to have in order to understand each chapter. Mine is pretty standard for a book targeting a broad audience, I think. The other stats give me assurance that my writing style isn’t dramatically changing throughout the story, and they show me where I am heavy on description or dialogue. I highly recommend CC to other aspiring writers. When I get into some other editing software, I will be sure to post my reviews and recommendations.

As a side note, I was thinking about starting up a scientific consultant service to cater to writers’ specific story needs. I would probably do this service for free, unless demand rises rapidly. So if you are having trouble figuring out the science involved in your story’s unique context, or if you simply want someone to help you brainstorm, please feel free to contact me. I will likely not be an expert in the topic you need help with, but I do enjoy researching new things.

I am also happy to take suggestions for future blog posts. Any topic related to improving the accuracy and believability of science in science fiction is preferred.

That’s all for today. Back to writing… and editing, I guess.

The science of the presentation

presentationI am posting much later in the week than usual. It was a busy week. Most of my time was dedicated to analyzing data and preparing a research presentation for a group at the university. It was in preparing the presentation that I came up with the topic for this blog post. I realized that the mechanics of giving a presentation were very similar to the mechanics of writing a book. The goal is to make it sell.

I was lucky enough to be trained in how to give presentations by my first mentor, who was passionate about the mechanics of delivering presentations (he even gave a yearly presentation on how to give presentations). These were some of the main points he stressed:

Control the flow of information-

Don’t give any more background than the audience needs to be able to understand and appreciate the rest of the presentation. This is especially important when it comes to the content of individual slides. If you overload the audience with too much information at one time, they will become distracted from the heart of your message. Begin a presentation with a complicated scheme or figure and the audience’s eyes will wander to every part of it except for the area you want them to focus on. Worse, the audiences’ eyes might glaze over entirely when confronted with what appears to be a lecture. In a book, they call this an info dump, and it is a sure way to slow down a story and make people lose interest. In short, deliver the information only when they need it, and never more information than they need.

It is also important to deliver the information in a direct and logical fashion. If you are too vague and ramble, your audience won’t have gained anything in the time they spent listening. You want to anticipate their thoughts, giving them an answer right before they realized they had a question. This will keep them interested and give them confidence that you are an expert in the subject on which you are presenting. It follows that you should never bring up something you will not address or hope people won’t ask about. If you have a curious artifact in a piece of data, don’t draw attention to it, especially if you have no idea why it’s there or what could be causing it. You will be asked questions you can’t answer and the audience will get the impression you are ignoring something important, or just too dense to figure it out.

It is best to assume your audience is intelligent. Having a slide titled What is DNA? will be sure to offend all the geneticists in the room. By the same token, your sci-fi readers will not be pleased with a detailed description of why earth orbits the sun.

Which brings us to our next point.

Know your audience-

Delivering a presentation on muscle physiology and contraction kinetics to a group of geneticists is difficult. Trust me. So it’s important to deliver the information in a way that makes sense to them and gives them a bit of what they are expecting. You can judge your audiences’ reaction to a presentation by how many have fallen asleep in their chairs. On amazon, you can get an idea of your book’s success by number of reviews. At this point, it is too late to go back and fix things. Running these things past your lab or beta-readers will help you narrow down your audience.

If you are struggling to find a way to make your product (research or novel) interesting to the audience, it’s probably not your target audience, and you should not spend your time and effort on them. Selling a horror novel at a Romance Readers Conference is the definition of futile.

Be enthusiastic and confident-

Projecting enthusiasm and confidence is the best way to draw your audience in. But like all things, it is best in moderation. You can litter your presentation with animations and colors and media, just as thoroughly as you can fill your novel with flowery language, imagery, and description. But too much of it will be distracting and off-putting, and make it seem like you’re trying too hard, or compensating for a poorly plotted story or lack of data. Keeping things too colorless and dry, however, will come across as boring. If you sound bored, your audience will be bored too.

It’s okay to be a little nervous. When we put our stuff out there, whether it is in front of a lecture hall or on the virtual bookshelves of Amazon, anxiety is to be expected. I find that I am far more confident in my presentation if I have done a lot of preparation. This includes significant edits and revisions of my slides, and many practice runs with people willing to give me critiques. It is the same with my writing. I am far less nervous about my audience’s impression of my work if I know it is well thought-out and heavily edited for grammar, style, and structure.


Research presentations are a lot like books. The major difference is that your data shouldn’t be fiction (theorizing that your data is the result of ‘magic’ is frowned upon in most scientific circles). But no matter how much you prepare and polish, there will always be those who don’t care for your work and will criticize it. Don’t lose heart. You can’t please everyone… unless there’s free food involved. Nobody complains about free food.