Update: The final version is live at SiMF as of 7/23/2012!
This is the first draft of an article I'm working on for Science in My Fiction, a speculative science fiction blog. I'm not quite satisfied with it and would appreciate any constructive comments. I think I need to re-write some bits to emphasize how accurately portraying the immune system, or at least acknowledging it more directly, opens up new and exciting ways to tell a story.
Immunology is a rapidly developing science, but it still isn't well-known or well-understood. And it shows, especially in science fiction. Time travelers and aliens easily adjust to life on present-day Earth without the need for vaccinations. Humans explore unknown planets with breathable atmospheres without any protection from the millions of potentially disease-causing microbes all around them. Or they willingly remove what protection they have...*cough*Prometheus*cough*. It's practically a tautology; an atmosphere that can support life is a safe atmosphere for humanoids to breathe. H. G. Wells more accurately portrayed the consequences of making this assumption in War of the Worlds. When the invading aliens were exposed to Earth's atmosphere, they were eventually killed off by microbial infections.
This glaring oversight is sort of understandable, though. Immunology,
the study of the immune system, is a relatively new field of science.
The germ theory of disease wasn't even validated until the late 19th
century. Antibodies, complex proteins that enable the immune system to
adapt to and remember past infections so that you generally don't get
sick again from the same thing, weren't fully characterized until the 1960s. Gerald Edelman, Joseph Gally and Rodney Porter won a Nobel prize for finally putting the pieces together. It was sort of a big deal.
If there is any life in an alien environment, there will be microbes. Higher forms of life may show up as well, but microbes are a guarantee if we are assuming that life is involved. If these microbes are from an alien environment, then every single one of them could be completely foreign to your immune system. There are a couple of different ways this could play out.
Microbes that cause disease generally do so entirely by accident. A survival mechanism of the invading organism just happens to interact with your bodily systems in such a way as to cause sickness or death. This is why our ability to recognize something as 'foreign' and get rid of it quickly is so important. Immune cells 'see' microbes by recognizing proteins or structures that are microbe-specific, either through specialized receptors, antibodies or other immune proteins. Given that your immune system is being exposed to something it has never
encountered before, it may be entirely unable to recognize these new
microbes as microbes. This would basically mean that you would be defenseless
against any incidentally lethal effects they might have on your cells.
Some of the mechanisms humans have evolved for dealing with foreign microbes are particularly unpleasant. The symptoms you experience when you have a cold or the flu, for example, are actually caused by your immune system trying to rid your body of the virus. The additional mucus protects your vulnerable membranes. The increase in body temperature makes for an inhospitable environment to viral replication. Your cells that are already infected are targeted and destroyed to prevent the spread of infection. The immune response, if activated strongly enough, has the potential to kill you outright...as those with severe allergies are well aware. The prospect that your immune system would respond to foreign microbes on an alien world is at least as terrifying as it not responding at all.
This problem applies even more strongly to human time travelers, who are already susceptible to human diseases but simply do not have the immunity or the vaccinations to protect them against the latest strain of measles or influenza. They could also introduce diseases from their own time, like smallpox or a multi-drug resistant bacteria, that present-day Earth is poorly equipped to deal with. The results could be devastating.
Humans are bacteria factories. Our mouths, guts and skin are absolutely coated with microbes. Our immune systems has been adapting to all of these microbes since we were born and recognizes them as 'normal' rather than foreign. They generally don't cause disease unless something goes wrong. In fact, we would quite literally die without them. But introducing our normal bacteria into a foreign environment could have disastrous consequences, and I'm pretty sure that accidentally causing a plague or wiping out the local population would violate the prime directive as well as significantly alter the course of history.
You can't remove microbes from the picture. They are part of us, and they will be a part of any ecosystem that supports life. So step it up, science fiction! This is fertile ground to be explored.