Applying the Scientific Method to Vaccination

Joy: “All these facts and opinions look the same. I can’t tell them apart. “

Bing Bong: “Happens to me all the time. Don’t worry about it”.- Pixar’s Inside Out

Ah, the scientific method. People love to bring up the scientific method when talking about vaccination. Most will tell you that the scientific method supports vaccination. Actually it doesn’t.

What is the scientific method? Some people seem to struggle with what exactly it is, so here’s the definition: “...the process by which scientists, collectively and over time, endeavor to construct an accurate (that is, reliable, consistent and non-arbitrary) representation of the world.” So we’re talking about a method for testing hypotheses to see if our ideas translate to what actually goes on in the natural world. It’s based on observation, not popularity.

The Scientific Method has four steps:

“1. Observation and description of a phenomenon or group of phenomena.

2. Formulation of an hypothesis to explain the phenomena. In physics, the hypothesis often takes the form of a causal mechanism or a mathematical relation.

3. Use of the hypothesis to predict the existence of other phenomena, or to predict quantitatively the results of new observations.

4. Performance of experimental tests of the predictions by several independent experimenters and properly performed experiments.

If the experiments bear out the hypothesis it may come to be regarded as a theory or law of nature.”

So let’s apply the Scientific Method to the idea that vaccines stop the spread of illnesses.

1. Observation and description of a phenomenon or group of phenomena.

People are not severely disabled or dying in large numbers from infectious diseases. The spread of these diseases appears to be uncommon amongst vaccinated populations.

2. Formulation of an hypothesis to explain the phenomena. In physics, the hypothesis often takes the form of a causal mechanism or a mathematical relation.

The hypothesis is that vaccines create immunity in the vaccinated individual by getting the immune system to recognize and then fight off infectious agents without the individual actually developing the disease. If enough individuals are vaccinated, the disease will be eliminated or eradicated in a particular area or even across the whole world.

3. Use of the hypothesis to predict the existence of other phenomena, or to predict quantitatively the results of new observations.

So based on our hypothesis we think that vaccines could be formulated for all kinds of diseases and that they could lead to a disease free world. We would expect that vaccines would eliminate most incidences of disease (maybe 80-99% if we’re going to put a number on it).

4. Performance of experimental tests of the predictions by several independent experimenters and properly performed experiments.

…And here is where we start running into problems. Studies on large populations of vaccinated and unvaccinated populations have not been carried out. We have many studies for the approval of individual vaccines, but  we do not have tests run by several independent experimenters. Even the approval tests of vaccines do not fulfill this requirement because they are tests on specific vaccines for release onto the market and they are carried out by the pharmaceutical companies who have developed them- not independent experimenters who have no stake in the outcome.

In fact, media darling Dr. Paul Offit said in his interview to PBS that such experiments comparing the health of large numbers of vaccinated and unvaccinated individuals would be impossible because people who choose not to vaccinate are so mentally incompetent that the results can’t be accurately assessed. But if we can’t run such experiments, then we’re not dealing with a scientific fact, law or even hypothesis, we’re dealing with a  matter of belief or opinion. And the government certainly has no constitutional right to force opinions, beliefs and preferences on us.

Other problems with applying the scientific method to vaccination is that arguments in favor of vaccination have been subject to a number of biases related to the scientific method. They overlook information that does not support the use of vaccination (such as lack of efficacy and modified illnesses in vaccinated individuals that are still communicable, but lack classic symptoms.) They also overlook information pointing to other improvements in health that could explain a decrease in morbidity and mortality such as nutrition and sanitation. Another common one is the idea that vaccination is so safe and so essential and so established that we don’t need to run tests and experiments comparing the health of individuals or disease occurrence in populations- especially accounting for non-classical symptoms. And everyone I have met who supports the use of vaccination seems to be falling error to the most fundamental mistake of the scientific method: assuming that the hypothesis is an explanation for the phenomenon observed.

Also problematic with the concept of disease eradication is the concept of reproducibility.

“Independent confirmation of a scientific hypothesis through reproduction by an independent researcher/lab is at the core of the scientific method.” So when we start talking about eradicating measles, polio, etc. just like we eradicated smallpox, we’re not dealing with a fact. There is no fact or law that a disease can be completely eradicated from the planet, because the declaration of eradication has only happened once. (And there are significant problems with it that are rarely discussed.) Assuming that all of the ideas eradication is based on hold true, it’s only been done once and has not yet been reproduced by anyone. Yet a great deal of public health policy is based on the hypothesis of eradication and simply assumes that it is true.

Vaccination may be popular, yes, but its current use in not based on systematic observations and experimentation.




What Does It Mean When A Disease Is Declared Eliminated/Eradicated?

“This announcement might be premature in view of the unreliability of statistics in underdeveloped countries.”Noted medical historian Erwin H. Ackerknecht on the announcement of the eradication of smallpox (See page 507 of cited document.)

We’ve heard the claim before: “Vaccines have eradicated smallpox from the whole world and diseases like polio and measles from many developed nations.” But do you know what eradication or elimination of a disease really entails?

Most people think that when a disease is declared eliminated or eradicated that the virus or bacteria has become extinct in that area or the entire world- like the dodo bird or quagga. What it usually means is simply that the disease has been declared eradicated or eliminated. Allow me to explain in further detail…

The concept of disease elimination is rooted in the theory of community (herd) immunity- that a disease won’t be able to take hold in a population with high immunity- especially highly vaccinated populations. This sounds like a great idea “on paper”, but real world applications pose numerous problems. Efficacy is often far less than health organizations would like to admit. I’ve listed these well-documented cases from medical and scientific literature before, so if you would like to see them, read this post here for a good collection of cases of vaccine failure. Generally, the assumption that is made with elimination of a disease is that almost all individuals who have received the vaccine are immune to the disease and that immunity will last for very long periods of time. However, the reality of vaccine efficacy is much different.

A great example is the flu vaccine. The CDC has released a statement saying that the 2014 flu vaccine was only about 14% effective. They say it is usually more like 50-60% effective. Since herd immunity generally requires anywhere from 75-95% of a population to be immune, there is simply no way herd immunity could ever be achieved through the current influenza vaccination. Even if 100% of  eligible population were to be vaccinated, the maximum immunity would only be about 60%.

Yet another example is pertussis. A survey of nine counties in California showed that between 44 and 83 percent of individuals with pertussis had been immunized. Again, at those rates of failure even a fully vaccinated population will not result in herd immunity- especially when the threshold for community immunity for pertussis has been set at 92-95%.

And yet another example lies in measles. The Huffington Post reported on this here. Renowned vaccinologist Dr. Gregory Poland states that the MMR shot is not effective at preventing measles. He says that it is both far less effective than anticipated and that immunity from it quickly wanes. Despite all this, he also condemns in no uncertain terms those who refuse vaccination. (So you’ve told me that your solution doesn’t work, but I must still get it or I will be hurting others by not getting the ineffective solution? And yet I am dismissed as the emotional, unscientific one?) In a situation where immunity is conferred but quickly wanes, even if you had that “community-immunity-dream-come-true” where 100% of the eligible population has been vaccinated, because immunity is very brief, widespread immunity will be achieved only for short periods of time if at all.

(Penn and Teller, would you care to do a video where you explain how the above examples factor into community immunity?)

Moving on to the next issue with elimination and eradication, let’s talk about vaccines spreading disease. Yes, I can see the eye rolls now. Most dismiss this as fear mongering from people who where foil hats on their heads to prevent the government or the Illuminati or aliens from reading their minds. However, it is actually medically documented and is one of the prime reasons that we no longer vaccinate for smallpox. Page 501 of an article in the 1983 Microbiolocial Review details several cases of individuals who were vaccinated for smallpox after the disease was declared eradicated and subsequently became reservoirs for the vaccinia virus and passed it to others. Many of these cases came from military personnel who were vaccinated for smallpox and then passed the virus to other military personnel or family members such as children who then passed it to others.

And herein lies yet another problem with campaigns for eradication of a disease. The chances of any one person becoming a reservoir for pathogen is probably relatively small. But when you start having mass vaccination campaigns where many vaccines are being administered, the chances increase that someone is going to become a reservoir and start passing the disease. If there is a relatively high failure rate of the vaccine, the potential exists for several individuals to become infected even in a highly vaccinated population. This probably explains why during the smallpox eradication campaign areas that had very high levels of vaccination were still seeing cases of smallpox. (See page 491.)

But even with all these problems with eradication, smallpox was still declared eradicated. How did they do it? Well let’s take a look at the criteria for declaring smallpox eradicated. Going back to the 1983 Microbiological Review, the criteria for declaring eradication of smallpox required that no cases of smallpox had been reported within the last two years and that the country’s epidemiological surveillance system be evaluated and declared adequate by the World Health Organization (pg. 498).

Now surveillance and reporting bring up a number of interesting problems. The United States has a great surveillance system for diseases and yet not every disease is reported. (I never let the authorities know when my kids had chickenpox. There’s absolutely no incentive for me to do so since I would be met with persecution.) I know of other people who have “flown under the wire” with pertussis, chickenpox, the flu and even measles.

We have also seen that even in countries whose reporting and surveillance systems are adequate that breakdowns- or abuses can occur. Initially, rewards were offered for reporting cases of smallpox, but there came a point when a country’s health authorities didn’t want to report smallpox cases because it would interfere with gaining eradication status. Health officials in Somalia suppressed information about smallpox cases in the final months of that eradication campaign, not wanting their country to bear the stigma of being the last to harbor the virus. In a more recent occurrence, China kept information about its SARS outbreak secret.

The other problem with surveillance is that especially in vaccinated populations, diseases can frequently be asymptomatic. Modified measles is a medically documented phenomenon in which individuals who have been vaccinated for measles still contract the virus but because of the vaccine don’t display the typical the symptoms of the disease. The characteristic spots associated with measles are very frequently absent in modified measles. Most doctors aren’t very familiar with this so they won’t consider it a possibility in vaccinated individuals or test for it. A similar phenomenon called atypical measles was noted when the killed strain measles vaccine was in use. Pertussis is notorious for this. It is a medically documented fact that individuals who have been vaccinated for pertussis and contract the disease often don’t display any symptoms.

Furthermore, declaring measles eliminated is in many ways like a “self-graded” test. The WHO Regional Office for the Western Pacific (WPRO) has a set of criteria for the definition of elimination of  measles. However, their definitions have changed over the years. Originally the definition for measles elimination required zero incidence of infection within a defined geographic area. Now, measles elimination is defined as “the absence of endemic measles transmission and the lack of sustained transmission following an importation of measles virus in a large and well populated geographical area.”

Now here is where things get interesting. A report from the World Health Organization on the elimination of measles in Australia states: “Australia, like many other countries that have declared elimination, would have difficulty meeting the WPRO elimination criteria based on currently available reporting of the investigation of presumptive measles cases (Table 2, available at: However we believe multiple lines of evidence conclusively demonstrate the elimination of endemic measles transmission from Australia since 2005 at the latest.” OK, so Australia and most other countries that have declared measles eliminated haven’t actually met the WPRO’s definition of elimination, but these countries feel they have done a good job, so they can declare measles eliminated? This is the scientific basis for the elimination of measles? In fact, there is a nice little chart on the WHO’s site showing all the ways that countries that have declared elimination of measles have met and not met the WPRO’s definition for measles elimination. If you take a look at this chart, it shows that Australia has neither a low incidence of measles nor a high quality surveillance system, however, they can still declare measles eliminated within their borders.

And on top of all this are disease associated side effects with vaccination. Provocative polio is a well-documented example of this. In 1998, Drs. Matthias Gromeier and  Eckard Wimmer found that injury to tissue to during certain types of injections allowed the polio virus easy access to nerve channels, thereby increasing the likelihood of paralysis. The more recent HV Wyatt study from 2003 found that three-quarters of children with paralytic polio receive injections just before the onset of paralysis. Then there is Vaccine Acquired Paralytic Polio. According to the CDC, between 1980 and 1999 162 cases of paralytic polio were confirmed in the United States,  154 of which were VAPP.

The other major assumption with the WHO’s eradication criteria is that if no new cases are reported after two years that the disease must be gone. A similar assumption has been made with polio eradication, and yet has proved faulty.  For example, in 2004 a case of wild type 3 poliovirus in Sudan was discovered when the last case in Sudan was detected in 1999. The criterion for certification of eradication is the failure to discover wild poliovirus for at least three years in countries with certification-quality surveillance- very similar to that of smallpox eradication. Genetic sequencing of the wild virus found in 2004 showed that it may have been circulating undetected in Sudan for more than three years—a time when surveillance in Sudan was thought to be satisfactory. Barrett points out that while surveillance probably was satisfactory at the national level, it must also be of an acceptable standard within every local district. As Sudan has been a high conflict zone, it is very possible that local surveillance may not have been adequate.

And to be realistic, during the smallpox eradication effort there were a number of countries embroiled in conflicts, such as the Vietnam War, the Cambodian civi war and subsequent “Killing Fields”, and the Soviet invasion of Afghanistan. Even the practice of apartheid in South Africa, for example, could have led to inequalities in surveillance and reporting. Not to mention the number of localized areas that were poverty stricken or remote that could lead to inadequate surveillance and reporting on a local or regional level.

Furthermore, another big weakness with the system is that once eradication status was granted to a country, surveillance for smallpox was not quite as careful. In fact, in 1987 it was recommended that smallpox be removed from the National Notifiable Diseases Surveillance System. However, surveillance began again after the September 11 attacks in 2001 because of the possibility of a bioterrorism attacks.

When assessed from a realistic perspective, the WHO’s criteria for eradication is based on the assumption that all components of a country’s reporting and surveillance for diseases are working perfectly- not well or adequately- but perfectly. That’s a pretty big assumption. (It brings to mind something I heard in a podcast interview with General Stanley McChrystal where Gen. McChrystal talked about the importance of a “red team” to do an outside assessment of a plan. He said that something can sound like the most brilliant plan when it’s your own head, but when you get other people to look at it, they can bring out the weak points and pretty soon you see that you aren’t dealing with a strategy, but rather a set of miracles based on everything working perfectly.)

But even with all of these very significant challenges in disease eradication/elimination, let’s for the moment assume that a disease in particular can or has been eliminated. When we talk about eliminating/eradicating a disease, it is because we believe it has very detrimental effects and that if eliminated/eradicated, that people will no longer suffer those effects. But are we really free from the detrimental effects of a disease just because it has been declared eliminated or eradicated? Let’s take a look at the data…

Smallpox: We’ve already established that cases of smallpox have been documented to spread from vaccinated individuals. However, even if smallpox is no longer a threat to humans, there are a number of other animal pox viruses that can cause similar symptoms and even death. Monkeypox is one of the more well studied examples of this as detailed in pages 503-506 of the Microbiological Review. However, there are a variety of other possible pox viruses that could take hold in humans including cowpox, camel pox, tanapox, rat pox, gerbil pox and raccoon pox.

Polio: Because of polio, no one has to worry about their child coming home sick and being paralyzed, right? Wrong. One interesting newspaper article from India asserts that while polio has been eliminated in India, Acute Flaccid Paralysis (AFP) is on the rise.  According to the Johns Hopkins School of Medicine, AFP encompasses all cases of poliomyelitis. And guess what? AFP can get you here in the United States too. Several cases of paralysis from non-polio enteroviruses have been reported in the United States.

Measles: Sure, it is possible to get encephalitis from measles. But guess what else can cause encephalitis? According to the Mayo Clinic, encephalitis can occur as a result of vaccination with a live virus vaccine– like MMR.

I think at this point we should be asking ourselves if it is really realistic or prudent to eliminate a disease causing pathogen. We talk a lot about the importance of the ecosystem and that if a species like a plant or insect goes extinct, it could upset the entire ecological balance of an area. Yet, our scientists feel that these laws do not apply to bacteria and viruses. Instead of trying to eliminate viruses and bacteria, perhaps it would be more practical and lifesaving to focus on efforts to help people avoid them through clean water and fight them off through better nutrition and healthcare.

Slaughtering the Sacred Cow Part Two: Smallpox Eradication

The eradication of smallpox has been heralded as one of the greatest scientific achievements in history. However, it is possible that the story we have been presented is not entirely accurate.

The eradication of smallpox seems to be based on how many people received the smallpox vaccine, and this of course, is based on the assumption that the smallpox vaccine is extremely effective. However, there are a number of problems with this idea, the first being that the smallpox vaccine has had a troubled history plagued by failures. (No pun intended…)

There were high hopes for smallpox vaccination and variolation and these led to mandatory vaccination laws in England in 1853. In fact, compulsory vaccination with penalties for not vaccinating was not able to stop another outbreak from occurring in 1877 and another 1881. (I find it ironic that this webpage condemns objectors to vaccination while acknowledging that outbreaks continued to despite smallpox vaccination laws and affirmations from the government and health board that vaccination was effective. They offer up comments of objectors stating that they were concerned about their children’s lives and health and the infringement of their liberties as some sort of proof that opposition to vaccination is dangerous. All it proves is that these people were concerned about their freedom and their children’s health. But I digress…)

Even in the 20th century, problems with smallpox persisted despite high rates of immunization for the eradication program instituted by the World Health Organization. A quote from a scholarly paper on the history of smallpox reads: “The concept of mass immunization, originally proposed to include 80% of the population in each country to achieve herd immunity proved ineffective as herd immunity did not cease and smallpox persisted in such immunized or ostensibly over-immunized populations.” (pg.491 of document.)  So while smallpox vaccination rates were high, the disease continued to persist. This does not constitute eradication.

Can a disease be eradicated? I think it worth questioning since despite all the money and pharmaceutical technology, no other diseases have been eradicated altogether. There are reports that certain diseases have been eradicated in certain areas of the world, but these have problems as well. I think polio is the perfect comparison.

Despite a massive campaign to eradicate polio, the disease has persisted. Even in countries where it has been declared eradicated, cases of Acute Flaccid Paralysis have remained high. For example, India has been declared polio-free but now has some of the highest rates of Acute Flaccid Paralysis in the world. So even if you get a disease doctors do not classify as polio, you can still suffer the same consequences. In fact, MD’s like Suzanne Humphries who have talked openly about the misconceptions surrounding vaccination point out that polio itself was merely a diagnosis for a number of different conditions that could result in paralysis. So it’s quite possible that instead of being “eradicated”, polio simply got a name change. Doctors can call a disease resulting in paralysis Acute Flaccid Paralysis and continue to laud the eradication of polio, even though the threat of death and paralysis is still there.

And India is hardly alone. Americans have had a brutal wake-up call as paralysis from so-called non-polio enteroviruses has gotten more attention. Isn’t it possible that smallpox could still be going around, but the diagnosis is just different now? We have never seen any other disease be eradicated. We are dealing with an occurrence that has not been replicated.

I think we also need to consider the historical and political context of the “eradication” of smallpox as well. At a time when vaccines seemed to be under great suspicion from lawsuits over Vaccine Acquired Paralytic Polio, deaths from the 1976 flu vaccine, and settlements for deaths from the DTP shot, the World Health Organization announced that vaccines had given mankind its greatest epidemiological achievement: defeat of a disease. In 1979, smallpox was declared eradicated from the planet. The medical and public health communities must have breathed a sigh of relief. The “eradication” of smallpox could not have happened at a more convenient time.

Update: This interview with Dr. Suzanne Humphries MD about vaccines and what really happened to polio and smallpox is excellent if you would like more information. It’s an hour and a half long, but it is well worth listening to.

Update: I have written a post about what disease eradication/elimination actually means and how it is “achieved”. It can be found here.