An old saying goes that if you have an army, it will want to fight a war.

That seems to be true also for our personal army, our immune system: there seems to be various pieces of evidence that many of the allergies and/or autoimmune diseases some of us have to deal with arise from an under usage of the system, which then devotes its energies to fight the body hosting it.

Let's assume that the above is true, and consider the situation on a generation ship, ensuring a proper shielding from cosmic radiation and providing adequate gravity by the usually accepted means, aka rotating habitats.

The generation 0 will be a ground-raised one, thus with the possibility of interacting with a highly diverse environment. But all individuals starting from generation 1, though not exposed to a perfectly sterile environment, will be dealing with a fairly monotonous environment for the immune system and thus have greater chances of developing allergies or autoimmune diseases.

What is a suitable system to keep the immune system of the passengers at a fair usage level so that adverse effects can be prevented?

Considering that resources (space, energy, water, oxygen, ...) are scarce, preference will be given to those proposals which make a leaner usage of them.

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    $\begingroup$ One presumes that a generation ship will be a few years in the future. What level of bio-tech is available in, say, the year 2040? We are today sniffing around the edges of a much fuller control of such issues. By the time we are able to build a generation ship, are we able to tune our immune systems at will? Sort micro-organisms in real time? Use the bio-filter on the transporter? $\endgroup$
    – puppetsock
    Commented Dec 9, 2019 at 15:15
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    $\begingroup$ Is the evidence for this conclusive? I always thought that it was strong candidate for the explanation of allergies, but not yet proven - and most likely not the only cause. $\endgroup$
    – Vilx-
    Commented Dec 9, 2019 at 16:50
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    $\begingroup$ I actually once had an idea for this problem, a planetary colony with an AI that was designed to create mild diseases to keep the population's immune system healthy. The AI at some point accidentally creates something too strong that kills everyone. Yes, it was inspired by Fallout. $\endgroup$
    – GammaGames
    Commented Dec 10, 2019 at 23:16

6 Answers 6


Pets and other animals

While it seems wasteful to have live pets in the resource limited environment of a generation ship, their influence on mental wellbeing should not be underestimated. In this case however we're more interested in their tendency to be rather unhygienic by human standards. Walking in places you'd rather they didn't then climbing on the food surfaces without washing their paws. Licking their bottoms then licking your face. It all helps maintain a suitable level of bacterial transfer to keep a baseline immune system running in your population.

While you can leave things like polio and measles behind when you travel, so specific vaccinations may not be helpful, you'll probably manage to brew up a few good coughs and sniffles among your tightly packed population anyway. Some things will always find a way.

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    $\begingroup$ Yes, and exotic pets! Llamas. Hermit crabs. Terrestrial leeches. The more variety the better! TAlso: 45 million years later spacefarers can encounter a world colonized by the descendants of escaped pet hermit crabs, diverging to fill every ecological niche. $\endgroup$
    – Willk
    Commented Dec 9, 2019 at 13:27
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    $\begingroup$ @Willk, Cat? $\endgroup$
    – SeanC
    Commented Dec 9, 2019 at 15:55
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    $\begingroup$ I believe the line is "Life uh... finds a way." I'm not sure if saying it while wearing a black leather jacket partially unbuttoned black shirt is required, but I hear it helps. $\endgroup$
    – T.J.L.
    Commented Dec 9, 2019 at 18:22
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    $\begingroup$ Partially unbuttoned shirt is required, but only if it's Jeff Goldblum. $\endgroup$
    – Sach
    Commented Dec 9, 2019 at 19:02
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    $\begingroup$ @Cadence: Actually, dogs seem to be unusually good at reducing future allergies in infants; it's not just being filthy, it's providing support for bacteria humans don't naturally host. Babies are petri dishes, but not the right kind of petri dishes for this purpose. $\endgroup$ Commented Dec 10, 2019 at 3:36


While you're probably not at risk of several of the diseases that vaccines help against in such a controlled environment, you could still use vaccines to keep the immune system active. It would also be very controlled.

You might even be able to save some resources by not trying to engineer a docile version of the virus or bacteria. Most bacteria and viruses are easy enough to keep alive and will happily mutate to be a constant challenge for your immune system. Influenza changes so much year-to-year that previous vaccines won't be effective for instance.

To push it further, you can "overdo" vaccines, with the intention of making your population resistant to diseases or toxins that we are currently vulnerable to. Micro dosage of poisons in order to build up resistance to it for example.

Poor Hygiene

The body has a bunch of essential bacteria that cause problems if they end up in the wrong places. If your ship in general have poor hygiene, then some of them are bound to end up in the wrong places.

For example, if nobody washes their hands because water is a limited resource.

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    $\begingroup$ That last section reminds me of some play throughs of the video game "Oxygen not included" where you can end up with a sick crew because someone decided to skip washing their hands just before touching the food supply. $\endgroup$
    – Muuski
    Commented Dec 9, 2019 at 15:38
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    $\begingroup$ Isn't the whole "micro dosage of poisons in order to build up resistance" thing a myth perpetuated (or perpetrated?) by the Count of Monte Cristo? $\endgroup$
    – Martha
    Commented Dec 10, 2019 at 19:42
  • $\begingroup$ 'You can "overdo" vaccines' anti-vax terrorist detected! Red alert! #include std_provax_lecture $\endgroup$ Commented Dec 10, 2019 at 23:22
  • $\begingroup$ @Martha I suppose that depends on the poison. It's fairly well known that addicts build up resistance to the substance they consume, but it doesn't necessarily apply to everything. $\endgroup$ Commented Dec 11, 2019 at 9:58
  • $\begingroup$ @Harper-ReinstateMonica See what happens if you take a couple hundred vaccines in a day.That's overdoing vaccines, and I doubt you'll find any serious medical professional recommending that. $\endgroup$ Commented Dec 11, 2019 at 10:07


Tapeworms seem to have some ability to partially supress the human immune system. This obviously benefits the tapeworms, because it means they don't get attacked as much.

But tapeworms appear to have been extremely common -- that is, normal -- during our evolutionary history. So, the argument is that our immune systems evolved to be adequate when partially supressed by tapeworms. We moderns, with no tapeworms, have immune systems that are more active (in some ways) than they are evolved to be.

So says at least one researcher, anyway. His hypothesis is that the increase in auto-immune problems in the past century is largely due to our lack of this specific class of parasite.



Dirt (as in soil)

Just as with pets, growing food in real soil may be less efficient than hydroponics, but the act of growing it has significant mental benefits. It also tastes better. In addition, if that soil starts with a representative sample of Earth soil microbiota, eating things grown in it, raw, with traces of those microbes still attached, is likely to be beneficial for health.

I remember somewhere reading that if you have to raise children in an ultrahygenic tower block with infrequent access to a park or suchlike for the kids to play in the dirt, then it's actually a good idea to sprinkle a few grains of dirt from soil used for growing crops for human consumption, onto their salad. It reduces the chance of the kids developing severe allergies and other autoimmune disorders.

I have a hunch that if we ever get to the details of generation ships, we will find that the secret to maintaining a liveable environment will lie in a certain minimum area of "park" and "lake". Or perhaps I've just been convinced by "A Deepness in the Sky".


Assuming you have the biotech to engineer the microbiome needed to make the soil at the destination usable the ship could introduce asymptomatic diseases at suitable intervals. Once you have a small seed the self replicating nature of the infection will take care of widespread distribution.

Data gathered from regular health checks would be ideal for fine tuning the next sparring partners for the crews immune systems.

It might be wise to introduce multiple shutoff switches or apoptosis triggers in case a mutation threatens to push the project to gar off the intended course.


Selective breeding, this could seem brutal, but our immune system works pretty well because we evolved/adapted to live on our planet.

On a generation ship, the environment will change and it will be hard to reproduce the same conditions on the earth.

Bacteria will change and adapt to live on the ship, humans should too.

People with a better immune system will give birth to children and the others will be sterilized.

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    $\begingroup$ I would argue that in the enclosed environment of a generation ship you won't have enough data to make that judgement as to superior individuals. Vastly sub-par individuals, perhaps, but there would be little enough immune stress that anyone not obviously deficient is fungible with any other not obviously-deficient individual. And given that you don't know what you are headed to keeping as wide a population as possible is likely a good idea. $\endgroup$ Commented Dec 9, 2019 at 17:49
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    $\begingroup$ The last thing you want to do on a generation ship is reduce genetic diversity. $\endgroup$
    – Martha
    Commented Dec 10, 2019 at 19:43

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