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Humans build big rockets and fly generation ships to extrasolar planets to settle. There’s already sentient alien life on that planet, but the humans has none of the immunizations and natural resistance to diseases that the aliens do. How am I going to prevent the humans from dying en masse and going extinct from diseases like the alien flu or small-reptile-who-can’t-fly-and-lays-eggs-pox?

Don’t worry about the aliens getting sick. After commandeering flight 19 and a few other groups of missing humans, they commenced immunization of their species against human diseases.

Edit: not similar to the linked question because the other question asks for bacteria, and I am asking for viruses.

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    $\begingroup$ Can this Q be answered? We know nothing about the alien environment, ecology, or pharmacology. The only solution to the problem is for the humans to bring an entire epidemiology and pathology lab with them and keep themselves sealed up while tests are run on atmosphere, insects, and animals from around the world to develop immunization. Do you have a specific problem? Because there's not really just one way this can be done. Given the tech level for meeting aliens, this is more of an issue of diplomacy than any kind of procedure. $\endgroup$
    – JBH
    Sep 20, 2022 at 21:36
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    $\begingroup$ BTW, you might have struck on an issue as difficult to answer as asking what climate a planet will have. There ought to be a badge for that. $\endgroup$
    – JBH
    Sep 20, 2022 at 21:38
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    $\begingroup$ @JBH, wouldn’t that be nice. Badge: Tough Stuff. Description: ask a question that sounds like it could be answered, but turns out you can’t actually answer it (yet). $\endgroup$ Sep 20, 2022 at 21:40
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    $\begingroup$ Infectious disease management is highly dependent on the specifics of the pathogen, and the population in question. Without knowing either of these this question is unanswerable in all but the most general sense without us building bits of your world for you. $\endgroup$
    – sphennings
    Sep 21, 2022 at 2:55
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    $\begingroup$ Going down the route of considering bacteria, you're still a step ahead of the actual, real problem for humans. Forget "hostile" bacteria - how do humans survive without their own benevolent microorganisms present? That's a problem right now on Earth. Disruptions in the gut biome can make you sick. Even travelling to another country or just irregular diet can cause that. And we're surrounded with native bacteria. Having none of that in space and/or another planet is going to exacerbate the problems $\endgroup$
    – VLAZ
    Sep 21, 2022 at 6:17

8 Answers 8

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I am going to frame challenge this question.

Why is this a problem? Are the aliens sexually compatible with humans? Can we see human/alien hybrids?

Or perhaps their alien-cows can breed with human cows.

No?

Life is hard, it requires very specific conditions for it to function and flourish. Give a virus/bacteria too much heat, or to little it will die2. Mixup the PH of the substrate: too low or too high, it will die.

Take a fish virus, and stick it into a human? The virus dies, the human doesn't notice it, human cells don't have the mechanisms that virus exploits to duplicate itself. Fish bacterial infection? Humans run too hot, it dies.

Then handwave the problem away with incompatible biology1.

If a cross over event did happen, it would probably be extremely lethal and kill a lot of humans, possible all of them. And human scientists without any past experience with the new diseases wouldn't have enough knowledge about the disease to make a cure/vaccination. Aliens wouldn't have any knowledge either, being unfamiliar with human biology...

So don't have it be a problem

The chance of a virus that infects a species completely unrelated to us is very low. Their cells just wouldn't have the right mechanisms for a virus to hijack, and alien bacteria wouldn't be adapted to their biochemistry. Just think how rare of an occurrence it is for a virus/bacteria to jump hosts with creatures that are pretty close to us (Cows, Rats, Dogs, Cats...)

[1] There might be a crossover event in the future as "Life, Uh, Finds a Way." There is a chance however slim that a virus/bacteria mutates something that allows it to survive in both Alien organism of some sort and Humans, but that is a problem for future humanity, not current humanity. It also might never happen, if humans/aliens are different enough biologically. I don't know of any instance where diseases jump from Alligators to Humans, and we come from the same common ancestor.

[2] Extremophile bacteria exist that can survive in both really hot/really cold places, However those extremophiles do not survive in places where other bacteria live, they only seem to survive/thrive in environments hostile to everything else.

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    $\begingroup$ This. Viruses are very custom tailored. Bacteria require a fitting environment to defeat our immune system. Our immune system attacks anything that is not ours. Also, we could still be able eat those alien plants and livestock. Sugars are sugars, some we will not be able to process to dump out (like cellulose). You could even have deficiency problems for humans dining on alien food. It could also be poisonous for us if you wish. There are many alkaloids that are poisonous to us which could be metabolized or even required by the aliens. $\endgroup$ Sep 21, 2022 at 7:19
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    $\begingroup$ Yeah: "War of the Worlds" gave everyone the idea that aliens would be defenseless against human diseases but it's more like the opposite of that. Human diseases would not have an attack vector against alien biology or vice versa. I'm sure the idea stems from European settlers infecting Western hemisphere natives but that was humans infecting humans. This is more like "can you catch the flu from alligators". There are cross-species diseases but they are notable for their rarity. $\endgroup$
    – JamieB
    Sep 21, 2022 at 14:45
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    $\begingroup$ Even when a microorganism jumps between species, it is because it exploits a common chemical receptor that probably was inherited by both species thorugh a common ancestor. ncbi.nlm.nih.gov/pmc/articles/PMC7087625 $\endgroup$
    – Mindwin
    Sep 21, 2022 at 16:08
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    $\begingroup$ @CemKalyoncu: Note that our ability to eat alien food assumes its chirality matches ours. See also mirror life. $\endgroup$
    – Brian
    Sep 21, 2022 at 16:41
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    $\begingroup$ And unless you have panspermia from same origin, any compatibility in biology is extremely unlikely. Cross species jumps are possible cause some building blocks and DNA is shared. But with aliens there is near zero of this. $\endgroup$
    – Ekaros
    Sep 22, 2022 at 5:29
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Some introductory biology could be helpful for you if you want this to be believable.

For example, your edit details don't make any sense in terms of biological function:

Assume in all applicable cases that the pathology for the aliens would be mirrored of our diseases. (E.g. if the flu DNA is ACCGTTG, the alien flu is TGGCAAC)

That's not how functional biological information works.

Living things store information in DNA/RNA, and use that information to make proteins, regulate their states, and replicate that information, among other things.

The central dogma of biology, describes how information is transcribed from DNA to RNA, and then translated from RNA to proteins. Proteins are the workhorses of biological systems--they're quite literally little machines that catalyze reactions, move things around, error-correct, and more.

So a few things:

  1. If you just flip the bases, assuming the alien codon system was the same, chances are exceedingly high that you just get some useless information that doesn't make anything functional.
  2. You could get around this by assuming that the aliens used the same nucleotides, but have a different codon chart (groups of those nucleotides correspond to different amino acids, and therefore different proteins). BUT if they entered our cells, with our cellular machinery, they would again be useless because their information wouldn't correspond to how we translate information. (an analogy would be going to Spain and speaking english--in England what you're saying means something, but in Spain no one can do anything with your information because it's decoded differently.

Bacteria would be a different story, because they don't have to hijack our information processing systems.

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Soften them up first.

Before the humans come

1: Rockets with neutron bombs. Get rid of as much of that pesky alien life as you can. Then right behind the bombs-

2: Rockets full of poop and dirt. A bunch of good home planet micro-organisms. WHatever aliens are left will still be reeling from the bombs. Earth bacteria, fungi and micro-organisms can make the alien planet good and earthy.

  1. Now land the humans! They will feel right at home.
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    $\begingroup$ You beat me to it. (And expressed it better). $\endgroup$ Sep 20, 2022 at 21:51
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    $\begingroup$ Speaking of new badges, we need one for answers that are perfectly reasonable despite not being helpful for the OP at all. :-) I'd call it the "Dr. Strangelove or How I Learned to Love the Bomb" badge. $\endgroup$
    – JBH
    Sep 20, 2022 at 21:54
  • $\begingroup$ "Earth bacteria, fungi and micro-organisms can make the alien planet good and earthy." or entirely uninhabitable by either the native species or Earth species. You're talking about introducing random microorganisms and leaving them unchecked which will somehow recreate Earth conditions. Maybe one microorganism species thrives and suppresses all others. This can be disastrous for all species. You may get "the slime mould planet". Or if only some species can survive, it might be "the cockroach planet". $\endgroup$
    – VLAZ
    Sep 21, 2022 at 6:26
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    $\begingroup$ @VLAZ If that happens, start again from step 1. Repeat until satisfied with the result. ;) $\endgroup$
    – ooak
    Sep 21, 2022 at 10:06
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    $\begingroup$ The Galactic HOA is not going to approve of this behavior. :) $\endgroup$ Sep 23, 2022 at 3:19
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Send an advanced party.

If you're gonna start a colony you're gonna want to do a few tests first. Send down a few UAVs to survey the area and grab samples, and then send down a few scientist colonists with some equipment to test the common local wildlife for diseases. They can stick their blood in a petri dish with human cells and see if anything reproduces well. If they find anything bad they can fast track a vaccine.

Quarantine the people

At the early stages you're gonna want to be very careful with your people. Anyone who goes out and interacts a lot with alien wildlife will need to be quarantined for a while and have some medical tests done.

Fast track antibody treatments

If you can cross the stars, your biotech is probably advanced enough to cheaply make antibodies. If someone gets infected and produces an antibody which can damage the alien pathogen you can mass produce that antibody and give it to everyone.

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  • $\begingroup$ Yep, with our current tech in 2020 we managed to churn out a decent enough Covid vaccine in under two years. A civilization capable of interplanetary travel and colonization would very likely be able to do it in mere hours (they probably have to with different immunothreats developing on distant worlds), so they can likely just plop down and heal + vaccinate against anything that crops up. $\endgroup$
    – Hobbamok
    Sep 23, 2022 at 11:22
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2 options: Burn the entire planet then settle, or cooperate.

Humans need to exist in sealed and controlled communities until they develop immunity to the new world diseases.

First you must establish good relations with the locals. A cynical man might point out to the colonization of the Americas. But this is the opposite. They are the ones with the ability to kill humans with nothing more than common diseases.

With a sentient life form on the planet. them weaponizing diseases is a recipe for disaster. They don't need to invent nukes. They just need to cough in our general direction.

And if they are capable of engineering viruses or such things. This it's better to either destroy them or coexist.

So. Either completely burn all life on the planet, burning everything including bacteria and viruses.

Or just go in and get them to give you a big piece of land that nobody is using and would make a good colony.

Exchanging knowledge and resources would be a great way to benefit everyone.

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Don't Land:

Until the people identified the threats on the planet, there's simply no way they would go to the surface of the planet. They wouldn't even allow direct contact with the aliens.

Humans are already working out the protocols for this, and have dealt with lots of diseases. There are plenty of cases on Earth of local populations (or sometimes crews of ships) being wiped out by a surprise disease.

The aliens already possess an advanced industrial base and technology if they have traveled to Earth and back before humans even could, and have advanced biotechnology. If they don't want us there, odds are we don't stand a chance. Landing would be exceedingly foolish even if there weren't diseases. Once the colonists learned the aliens were familiar with humans, the colonists should really crank down and be on their best behavior. Ask nicely to get an out-of-the-way corner to build habitats. Make friends with the aliens to learn their capabilities. Copy any available technologies and broadcast the information back to Earth.

Ideally, the aliens will overlook the human history they may have seen and be friendly. If so, the biology sounds close enough that if the humans themselves can't develop medications and vaccines, the aliens may help them. After all, they've already studied our biology.

  • Biology is messy, and while the aliens may have studied diseases that affect humans, there are a lot of other diseases and invasive species that could spread back and forth. Wiping out the green pig-oid farm population of animals might be almost as devastating to the aliens as if they got anthrax. Similarly, terrestrial animals and plants could suffer from molds and growths that will destroy food supplies, melt plastics or rapidly oxidize metals.
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There are couple facets to the biological hazards that you need to consider.

  1. Viruses.
    This one is actually the least threatening of them all. Notice how rare it is for a virus to jump between earth species. A flu virus that can be transferred from pigs to humans? That was a huge deal!
    But from humans to entirely different species? Unless they use the same kind of DNA and are actually our crypto-ancestors (or humans are theirs), it is not happening. The inner workings are just too different.

  2. Bacteria.
    These ones are an obvious contenders. They don't need to be compatible with host organism, they just need acceptable environment. If they find that human blood is edible, and find a way in, then you have a real problem (TM). Or any part of human body really - if they can live and thrive in there, and produce harmful byproducts, or use up some valuable resource, you have an alien disease.
    On the plus side, bacterium are usually large, complicated things. If your humans have an access to good electron microscope imaging and can synthesize molecules and proteins in lab, they should be able to quickly manufacture substances that damage the bacteria outer shell, or their inner workings. That's what some antibiotics do - they just "disassemble" the outer shell and whole bacteria rips open. Given the alien disease will be strikingly different to human cells, it might be possible to use "strong" substances that affect the intruders, but are otherwise neutral to human biology. A bacterium susceptible to ethanol? Colonists are going to love the treatment (and hate the hangover).

But we're not done yet. Enter

  1. The fungi. Shrooms and all that weird stuff. They vary in size from single cell to complicated multicellular organisms. If the local fungi can process anything found on human body, you will have a problem. A spores that like wet conditions, total dark, and feed from airborne particles? They are going to love human lungs. [The gross description of having something growing in person lungs is left to the writer].
    Or maybe they like to go after human shed skin? Or toenails? There is a lot of inspiration in nature.
    There are also fungi that love some organic or inorganic compounds. Imagine one that loves eating polyester. Human clothes just falling apart [totally not a setup for adult movie or comic].
    Fungi are often tough bastards, but we managed to find substances to fight them, so the human colonists should be able to do the same. Air filtration, containment control, frequent checkups.

  2. Parasites.
    You could also consider some small animals that can feed on something human produces, or just want a "safe" nesting spot. Standard safeties apply - a macro scale problems like this can be treated by direct intervention. Anyone say "space ticks"?

And finally, consider basic non-biology hazards:

  • does the air contain enough oxygen to be viable?
  • any other gasses or airborne compounds that are harmful?
  • is that pool water or sulphuric acid?
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Just plop down and deal with it

We are talking about a spacefaring civilization that is colonizing foreign worlds. Aka they have likely already colonized some dead worlds and have an interplanetary civilization.

Distant, separated human communities (be it full planets or "small" 2000 people outposts) are already a perfect condition for something far worse than alien diseases* : Evolved, novel diseases adapted to infecting humans.

If you let the common Flu evolve in a separate group from most of earth and after just 10 years introduce that specimen to earth, we would likely have something far worse than the current Covid pandemic.

Since your civilization still exists however (and even flourishes, given they want to expand), they must have mastered time-critical vaccination campaigns long ago. Something that is not that unrealistic either: We, with our 2020 tech managed to develop a decent enough vaccine in under 2 years. And we struggle hard to just get to the moon. So even if your human's medical science evolve at just a fraction of their spacefaring skills, developing a disease (and likely even in-vitro antibodies for those already infected) within a day seems very plausible, if not just logical.

Also: yes, some diseases could be too foreign for these methods to work. But then they would also be too foreign to abuse human biology (like viruses or most problematic bacteria). If the bacteria (because it won't be an alien virus) is only after "digesting" us like mould then we could have a problematic case, but one where the disease would progress slowly enough for a cure to be found anyway. [If that diseasy is problematic by producing toxins, then those would be picked up as present in pre-colonization planetary scans already and airlock- or sterilization-based colonization would have been chosen anyway]

*which, as shown in the other answers are very likely simply irrelevant to human biology

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