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Childhood vaccinations are so controversial because untruths and myths about vaccines have been circulated for hundreds of years. Complaints and concerns range from invasion of privacy and "bodily integrity" to concerns about safety, the use of animals to prepare and test vaccines, and religious issues.
Some parents refuse to vaccinate their children. The most recent controversy around vaccines stems from suspicion of a possible link to the rising rates of autism of either the preservative thimerosal, which contains mercury, or the measles component of the MMR (measles/mumps/rubella) vaccine. Parental concern led to numerous scientific investigations regarding such links, with study after study finding no connections. Nonetheless, thimerosal was phased out of most vaccines in 2001.
In a nutshell, here's the conflict: There's surely enough data to show that vaccines do save lives and protect against illness (the size of that benefit may be debatable, but I consider it significant). There are also safety concerns (as is the case with any medication), in that there's not - and never can be - enough data to guarantee the safety of vaccines in any given individual, especially as they interact with other vaccines, drugs, foods, and that person's specific environment.
So what are we left with? In one corner, we have a group of people who examine the data and believe the advice of the majority of pediatricians and the government. These "support" people conclude that vaccines are much more likely to benefit their children than harm them and are helpful to the long-term health not only of children, but of the population at large. They cite data that show how many infant deaths are prevented every year by immunization and studies that show non-immunized children report more disease events that are categorized as "side effects of vaccine" occurring in immunized children (such as epilepsy; delayed development; communication difficulties).
In the other corner, we have a group of "against" people who believe that vaccines are detrimental to the long-term health of their children, that no studies effectively show that vaccines are safe, and that the full range of serious consequences being caused by vaccines is being minimized and ignored.
The great news is that there is some common ground: Both sides acknowledge that the debate has forced vaccines to become safer, and that's a good thing. Beyond that, your decision may ultimately come down to a) what kind of person you are at heart (trusting of the medical profession or skeptical of it), b) how tolerant you are of risk, and c) what kind of family history of disease you have (whether you're relatively healthy or have genetic dispositions for things like allergies and autism).
I think you are smart enough to digest the arguments and make rational decisions for your children. Most people will follow the official guidelines, which offer the least chance of missing important vaccinations. Others will follow alternative schedules to reduce to the smallest degree possible the potential perceived complications.
Individuals need to customize their own programs with willing physicians as advisors. The one-size-fits-all schedule is dangerous for too many kids.
Important: This content reflects information from various individuals and organizations and may offer alternative or opposing points of view. It should not be used for medical advice, diagnosis or treatment. As always, you should consult with your healthcare provider about your specific health needs.