Afraid of Numbers Part 1: Assessing the risk of vaccination and infectious disease in America
What is the risk of vaccination vs non-vaccination?
A few months ago a bunch of kids caught measles at Disneyland.  Scary. But, do you know what else is scary? In the aftermath of the outbreak, concerned citizens, health practitioners, government officials, the media, and mothers alike hurled insults at one another, accused one another of ignorance and deceit, and, in some cases, accused one another of murder.
It is not surprising, really. The stakes are high. We are talking about the health of society, the health of our children, the risks of tinkering with the human immune system, the risks of life-threatening diseases, and the risk of death.
Perhaps you believe there are no risks. Perhaps you believe vaccines are 100% safe, 100% effective, and those who believe otherwise are gullible victims of faulty science and/or disillusioned conspiracy theorists. Or, perhaps you believe the risk of an otherwise healthy individual contracting a life-threatening disease in the developed world is but fear mongering propaganda in the hands of corrupt pharmaceuticals. Either way, the data suggests otherwise.
Vaccines are not without risk. So-called fraudulent claims of former anti-vaccine doctors aside,  there exist many non-recanted studies pointing both to the known statistical risks of vaccines and to the largely immeasurable and unknown potential side-effects of vaccination, both for the individual and for society at large. 
On the other hand, the risk of contracting a life-threatening disease in America is real. I know because I caught one: bacterial meningitis from haemophilus influenzae type b (Hib). And, I’m lucky to be alive.
It was an unusually sunny spring day in Eugene, Oregon with magnolias in early bloom. I woke up early, went for a run, and went to my Environmental Science class. By late afternoon I started feeling flu symptoms. Instead of going to a party as I had planned, I went with a small group of friends to the movie theater. We watched The Matrix. About halfway through, I felt my fever rise and started to see black spiders crawling across the screen. As the fabric of reality was cracking in the film, my fabric of reality was falling apart. Fully hallucinating, I got up to leave.
I barely remembered my friends bringing me back to our dorm. I collapsed on the stairs and woke up in my room. I told my friends to leave me alone and let me sleep this off. Luckily, I had a great friend who recognized that this was no ordinary flu. She had a few of the guys in the dorms carry me to a car and they drove me to the ER.
In the ER I woke up to find myself in a tub filled with ice. I also briefly woke up for the spinal tap. The next few days, I floated in and out of consciousness. I drifted between this world and the others. The matrix became very vivid for me. I nearly left. At some point, my dad arrived, but I couldn’t see or hear him; I was blind and deaf. Family and friends from around the world were praying for me to live.
When other cases showed up, the university quarantined the dorm hall I lived in and inoculated everyone I came into contact with: the entire dorm community and all my classmates. After a student died, everyone else lined-up for vaccines.
I spent a few weeks in the hospital, but suffered years of ongoing complications that included migraines, neuromuscular issues, vision problems, hearing problems, etcetera. I’m fine now, but the other students who contracted it weren’t so lucky. At least one died and others suffered permanent effects. As I was in and out of consciousness during that time, I only got snippets of the whole story in the months and years that followed. While meningitis is relatively rare, it is a common occurrence on college campuses, where students live in tight quarters and share bathrooms. Just this March (2015) another 18 year old died from meningitis at University of Oregon after six cases were reported. The parents of students who fell ill are urging parents to vaccinate their kids before sending them to college .
This is scary stuff. Personal stories have a way of being scary, often in a way that numbers and statistics are not. But I’m not the only one with a story.
“My son had MMR shots when he was 2 1/2. I put it off a little bit for some reason or another. He received them at the Bear Run Clinic in Orange Park, Florida. He screamed and cried the whole ride home and that night he started banging his head into the floor!!!! He was a totally different kid and stopped everything he had learned. He never was unaffectionate towards me though but immediately developed autistic like behaviours, especially echolalia and adhd. He ran a high fever and developed some kind of rash looking thing on part of his chin! Years later I learned he had a major allergic reaction to the toxins in the vaccines. I wrote Tallahassee Vaccination whatever they’re called and they wrote back saying basically ‘we’re sorry but the vaccinations help more kids than they hurt.’ He went most of his life being misdiagnosed because Dr’s didn’t have a clue about autism. Finally at age 13 he was diagnosed with PDDNOS, tourettes, echolalia, adhd, and sleep disorder. It doesn’t take a rocket scientist to know you DON’T GIVE SO MANY SHOTS IN ONE DAY TO A TODDLER.”
The above is one of several such stories taken from the website: followingvaccinations.com.  And, here is another story, this one taken from thinktwice.com. 
“My fiance recently took our son Christian for his 2-month checkup on March 4. He received three vaccines that day: DTaP, IPV (inactivated polio) and Hib. (Actually, he received 5 vaccines that day because DTaP is 3-in-one.) That night he was very fussy, wouldn’t take his bottle and cried all night. Christian usually would go back to sleep in the middle of the night after he ate, but this night was different. It was so bad, I stayed home from work to be with him. I didn’t think anything of it due to the fact he was colic.
March 7th, I took him to his doctor because he had conjunctivitis and they gave him a routine checkup. The next two nights he wouldn’t sleep much and was a little fussy, but not as bad as when he first got the vaccines. Saturday night, March 8th, I put my baby down to sleep around 12:45am. Christian woke up around 6am. His daddy tried to feed him but he wouldn’t take his bottle; all he did was cry. Finally, Christian fell asleep from exhaustion.
Around 9:30am I woke up and grabbed my baby — he was all blue. He died in his sleep. He was rushed to the hospital in a matter of minutes. They worked on him for about a half hour and there was nothing they could do. My angel was gone. The doctors said they believed it was a case of SIDS. His tissues are still under investigation for the next 6 weeks. I really believe his death had something to do with the vaccines.”
As a parent, reading these stories make me want to vomit. Stories are scary because they are tangible and emotional. They invoke fear, and from this fear we make decisions — often irrational ones. I know many people are so terrified of flying that they choose to drive long distances, failing to realize that they are more than 100 times more likely to die in an auto accident than in an airplane crash. 
This is why talking about fear is so important. The conversation we need to be having is not about who is right and who is wrong; it is about how we weigh the risks. Understanding the statistical data is critical because we are irrational creatures, us humans. If we consider the personal stories within the context of the bigger picture, hopefully we can make better decisions.
The Bigger Picture
I am writing this post to follow up on a particular online conversation where a number of friends asked for my “analysis of the data.” I agreed to do the analysis and walk my readers through my process. In addition to providing the analysis, I hope this post serves as a guide or a “how to” for doing this type of analysis for other topics.
First of all, how do we acquire knowledge and how does this affect our decisions? Psychologist Daniel Kahneman breaks ‘knowing’ down into two systems. The first is fast, emotional, and intuitive, and the second is slower and more logical. According to his book, Thinking Fast and Slow, the first system is mostly unconscious, often emotionally driven and can cause us to make huge errors in judgement. 
Personal stories like the ones above fall largely within the first (fast and emotional) system of acquiring knowledge — which is not to say that they are invalid and shouldn’t play a role in our decision making, but if we are not careful to pause and consider the knowledge acquired through emotional anecdotes within the context of knowledge acquired through the second more analytical system, we risk making irrational decisions.
So, how do we acquire knowledge through the second system?
How to Analyze Data
I’m a visual person. I would wager that everyone who can see is also “a visual person” in that it is helpful to see data to understand it. Hence presenting data in a visual format is very helpful in data analysis. In his book, Beautiful Evidence, Edward Tufte describes a set of principles for data analysis and presentation. For the purposes of this analysis, we will look at the first five: 
3. Analysis of the Variables [Multivariate Analysis]
4. Integration of Evidence
5. Documentation and Authorship
Over the next five blog posts, I will take you through these five principles of data analysis and conclude with my assessment of the risk of vaccination vs not vaccinating. I do not claim to be an expert. I am not an immunologist, so I can’t speak to the mechanisms of vaccines, but thanks to my education and work history (spending a lot of time analyzing massive amounts of data), I am highly skilled in cost or risk/benefit analysis. My data sources include CDC data, vital statistics, vaccine injury database, and other credible sources.
Over the past five months, I have learned more about vaccines than I ever thought to question. In doing this deep dive with the motivation to prove myself right in my pro-vaccine stance, I have been very surprised to learn that there are some highly credentialed and reputable scientists who are speaking out against a select few vaccines and the CDC pediatric recommendations.
I assumed that “the scientific consensus was clearly in favor of all vaccination” and that any rational and intelligent person would be pro-vaccine, but I have learned that there is a small and growing group of scientists and doctors who are speaking out about vaccine safety and effectiveness for a select few vaccines. They are not “quacks” by anyone’s definition and are speaking out for reasons I hadn’t expected – primarily because of the lack of research!
While vaccines have been important for public health, unfortunately the CDC has a communications problem. For years, they have been saying that vaccines are 100% safe, but they are not: Vaccines are relatively safe. This means that they are safer than a lot of other things we participate in regularly (such as driving a car), but they aren’t entirely safe and sadly vaccine injury does happen. Unfortunately the public relations strategy of declaring vaccines “safe” has backfired by destroying trust with the public. The CDC communications strategy has actually caused the problem they have been trying to prevent and it has spiraled out of control. They should have given the general public more credit, by acknowledging that vaccines are “relatively safe,” but not completely safe and helping the public to understand the risks and benefits.
My goal to help illuminate the vaccine risks and benefits by walking you through data analysis in a fun and approachable way. If any of this comes across as confusing, please comment and I will try to clarify. If there are errors in my data, please comment with ways to make it more accurate, such as finding a more valid or more recent source. I hope this brings about a healthy conversation about how we understand risk and benefits, as this applies to topics beyond vaccination. I hope you enjoy this series.
 National Vaccine Information Center (NVIC),. ‘Measles In Disneyland – Vaccine Exemption Ban – National Vaccine Information Center Newsletter’. N.p., 2015. Web. 2 June 2015.
 NaturalNews,. ‘Media Parades Dead Children As Victims Of Anti-Vaxxers Despite Medical Facts Contradicting The Narrative’. N.p., 2015. Web. 2 June 2015.
 Ageofautism.com,. ‘The Lancet Should Reinstate The Andrew Wakefield Paper – AGE OF AUTISM’. N.p., 2015. Web. 2 June 2015.
 Greenmedinfo.com,. ‘200 Evidence-Based Reasons NOT To Vaccinate – FREE Research PDF Download’. N.p., 2015. Web. 2 June 2015.
 Hanrahan, Mark O. (2015). 6th student in Oregon infected with meningitis bacteria. USA TODAY. Retrieved 18 June 2015, from: https://www.usatoday.com/story/news/nation/2015/03/19/meningitis-outbreak-oregon/25049737/
 Followingvaccinations.com,. ‘Redrockcloud’. N.p., 2015. Web. 11 June 2015.
 Thinktwice.com,. ‘Vaccines And Sudden Infant Death Syndrome (SIDS): A Link Thinktwice!’. N.p., 2015. Web. 11 June 2015.
 SSD, A. (2015). Motor Vehicle Accidents and Fatalities – The 2012 Statistical Abstract – U.S. Census Bureau.Census.gov. Retrieved 18 June 2015, from https://www.census.gov/compendia/statab/cats/transportation/motor_vehicle_accidents_and_fatalities.html
 Kahneman, Daniel. Thinking, Fast And Slow. New York: Farrar, Straus and Giroux, 2011. Print.
 Tufte, Edward R. Beautiful Evidence. Cheshire, Conn.: Graphics Press, 2006. Print.