On the face of it, suspicion of the new H1N1 vaccine is incomprehensible. Vaccination has been one of the biggest lifesavers of the past 200 years. It is the cornerstone of public health, directly responsible for the dramatic drop in infant and child mortality and the dramatic extension of lifespan we have enjoyed over the last century. Despite countless conspiracy theories advanced by vaccine rejectionists in the past 200 years, not a single one has turned out to be true.

True, there are side effects, some serious. However, serious vaccine side effects like brain damage or death are so rare as to be measured per 100,000 people or per 1,000,000 people. There has been no effort to hide these serious side effects. Indeed parents are required to sign consent forms acknowledging the risk of serious side effects before their children can be vaccinated.

So why are people suspicious of vaccines? There are many reasons including the American love for conspiracy theories, the public campaigns led by prominent celebrities, and the desire to assign causes to diseases like autism where the cause remains unknown. The most important cause of the suspicions, though, is one that is very easy to address. Most people don’t know how vaccines work.

To understand how vaccines work, you need to understand how the body defends itself from bacteria and viruses. Just like the body has a dedicated system to digest food (the gastrointestinal tract) or to remove waste products (the kidneys and urinary tract0, the body also has a dedicated system to fend off bacteria and viruses; it’s called the immune system.

The body actually has three layers of defense against bacteria and viruses. The first is the physical barrier presented by the skin or the lining (mucous membranes) of interior passages like the mouth and nose. Although we are surrounded at all times by bacteria and viruses, most of them never make it beyond the skin. Of course the integrity of the skin and mucous membranes can be disrupted by a cut or puncture, allowing bacteria or viruses to be introduced directly into the body.

The second line of defense is a non-specific immune response. If bacteria colonize a cut on your hand, your body reacts in a predictable way. There will be swelling, redness, and pain, a response that does not depend on the identity of the threat. Special immune cells will race to the site and engulf the offending bacteria. When they die in the attempt, they accumulate as pus.

Even primitive animals have non-specific immune responses, but higher animals and human beings have an additional, more powerful response. We can produce antibodies. Antibodies are proteins that recognize specific bacteria or viruses and bind to them, thereby signaling to other immune cells that they are targets for swift neutralization. Each antibody binds to a specific site on a specific bacteria or virus.

We’re not born with those antibodies, though. We make them in response to a threat. For example, we are not born with antibodies to the chickenpox (varicella) virus. When exposed to the varicella virus, though, we can learn to make antibodies to it. It takes time, but gradually we can produce enough antibodies to fend off the disease.

Unfortunately, we don’t always get the time we need. We can make antibodies to smallpox, for example, but many individuals are overwhelmed and killed by the virus long before they could make enough antibodies to fend it off. Those who do win the race and manage to produce enough antibodies to survive are now permanently protected. That’s because the immune system retains the ability to make the specific antibodies against the smallpox virus. Whereas it may take days to produce smallpox antibody when first exposed, a second exposure will be met with rapid and massive production of antibody, generally preventing the individual from getting sick at all.

So in order to be protected from the disease, you had to get the disease, and you might die before you were able to make enough antibody to protect yourself. Imagine, though, if you could learn to make the protective antibodies without actually getting sick. That’s the theory behind vaccines.

In order to make antibodies to a virus (or bacterium) the body need to “see” the virus. In other words, it needs to have direct exposure to the virus, but that virus doesn’t have to be functional, and it doesn’t even have to be whole. A virus can be inactivated (live attenuated) or killed and still produce an immune response. It can also be broken down into its constituent parts and the parts can produce an immune response. Any future exposure to the live virus (though contact with others who have the disease) will be met with rapid and massive production of antibody, preventing the individual from getting sick at all. A vaccine is merely and inactivated or dead form of the virus, letting you learn to make antibody without getting sick in the process.

Vaccines do not produce perfect immunity. The dangerous part of the virus might be the part that evokes the most powerful immune response. Rendering the virus harmless by inactivating it, killing it or breaking it up, may remove that part and the immune response to the less dangerous parts might be weaker. So actually getting the disease may produce a better immune response than the vaccine … but only if you survive the disease.

Successfully fighting off a disease depends on being able to produce enough antibody before the disease kills you. Until vaccines, the only way you could learn to produce antibody was to actually get the disease. Now, instead, you can learn to make antibody by being exposed to a harmless form of the virus or bacterium.