Breakthrough Study Shows Unvaccinated Children Are Healthier

Introduction

A study by renowned pediatrician Dr. Paul Thomas and research scientist Dr. James Lyons-Weiler published in a peer-reviewed journal in November 2020 found that, compared to unvaccinated children, the vaccinated children in Thomas’s practice had a higher incidence of diagnoses for a wide range of health conditions as well as a higher incidence of office visits for those conditions.

Days after that study was published, Dr. Thomas’s medical license was suspended by the Oregon Medical Board on the demonstrably false pretext that his approach of respecting parents’ right to informed consent instead of pressuring them to comply strictly with the CDC’s childhood vaccine schedule constituted an “emergency” threat to public health.

The study was also subsequently retracted by the journal editors without the editors specifying any flaws in the study that would warrant such a drastic action. Instead, the pretext for retraction was a hypothesized selection bias in the patient data, which is a highly unusual grounds for retracting a study, to say the least.

Now, Dr. Lyons-Weiler in collaboration with Dr. Russell Blaylock has published a second study utilizing Dr. Thomas’s patient data that directly falsifies the key allegation that led to the original study’s retraction, which was that their findings represented a lack of health care usage by parents of unvaccinated children, resulting in a failure to diagnose their equivalent health conditions, rather than a true effect of parents choosing not to vaccinate.

The newly published study tests the hypothesis that the original study’s findings are explainable by differences in healthcare-seeking behavior and demonstrates beyond any reasonable doubt that Thomas’s unvaccinated patients truly have had better overall health outcomes. This poses a direct challenge to the “public health” establishment, which helps to explain why the original study was retracted on such a flimsy pretext, now thoroughly refuted.

Dr. Thomas’s Vaccinated vs. Unvaccinated Study

Dr. Paul Thomas is a pediatrician who started out practicing medicine the way he was taught in medical school, which meant vaccinating pediatric patients according to the recommendations of the Centers for Disease Control and Prevention (CDC). In time, however, he started questioning the “one-size-fits-all” approach of the medical establishment and doing his own research into the medical literature on the safety and effectiveness of the various vaccines on the CDC’s routine childhood schedule.

After witnessing four of his own patients developmentally regress into autism after vaccination, Thomas decided that he could no longer in good conscience continue business as usual. Because the other doctors in his group practice felt that it would be unethical to not continue pushing the CDC’s schedule, Thomas left and in 2008 opened his own clinic in Portland, Oregon, founded on the principle that parents have a right to make their own informed choices about whether to vaccinate their children.

Along with coauthor Dr. Jennifer Margulis, he wrote the book The Vaccine-Friendly Plan to inform parents and help them navigate the difficult decision-making process about childhood vaccinations. Published in 2016, the book advocated this approach of informed choice based on an individualized risk-benefit analysis, which brought Thomas squarely into the crosshairs of the state government’s medical board.

Whereas Thomas aimed for a healthy childhood population, the government aimed for high vaccination rates, and those differing and opposing objectives led to the Oregon Medical Board persecuting Thomas for threating the government’s policy aim by advocating individualized medicine and respecting parents’ right to informed consent.

The board demanded that Thomas produce peer-reviewed evidence to support his alternative approach, which was thickly ironic since the board would be incapable of doing the same for the CDC’s schedule, given the absence of studies comparing long-term health outcomes between children vaccinated strictly according to the CDC’s schedule and children who remained completely unvaccinated.

Evidently, the board assumed that it had presented Thomas with an impossibly high hoop to jump through in demanding peer-reviewed evidence for his approach, but Thomas instead got institutional review board approval to conduct and publish research using the deidentified data from his own clinic, which he did with research scientist and data analyst Dr. James Lyons-Weiler.

Since few patients in his practice were vaccinated strictly according to the schedule and there was such a wide variety of individualized approaches, the study by Thomas and Lyons-Weiler examined health outcomes between unvaccinated versus variably vaccinated children, indicating that the most highly vaccinated had the worst health outcomes.

Titled “Relative Incidence of Office Visits and Cumulative Rates of Billed Diagnoses Along the Axis of Vaccination”, the study was published in the International Journal of Environmental Research and Public Health on November 22, 2020. The Oregon Medical Board responded on December 3 by completely ignoring Thomas’s fulfillment of their demand that he produce peer-reviewed data supporting his approach and issuing an “Order of Emergency Suspension” to strip Dr. Thomas of his medical license on the grounds that his refusal to push the CDC’s schedule on his pediatric patients constituted a threat to public health.

As I have shown in my book The War on Informed Consent, the medical board’s specific accusations against Thomas all revolve around his having committed the sin of heresy against the vaccine religion by respecting parents’ right to informed consent. The suspension order delivered the message to all physicians in the state that they had better coerce parents into strictly adhering to the CDC’s schedule, including by expelling patients whose parents declined to comply if necessary to maintain a sufficiently high vaccination rate in the practice, or else they would risk losing their license to practice medicine.

Thomas has legally fought back against the suspension of his license without due process, and on June 3, 2021, the board conditionally withdrew its suspension order. Dr. Thomas has since been able to practice medicine but remains prohibited from discussing vaccines with his patients’ parents and from participating in further research using his clinic’s patient data.

The Baseless Retraction of the Vaccinated vs. Unvaccinated Study

In late February 2021, Dr. Thomas and Dr. Lyons-Weiler were informed by the editors of the International Journal of Environmental Research and Public Health that an anonymous reader had written a letter to them to express concerns about the study. Thomas and Lyons-Weiler proposed that the editors bring the criticisms to light by publishing the anonymously written letter and allowing them an opportunity to publicly address those criticisms in a letter of their own.

The journal editors refused, however, and instead retracted the study on July 22, 2021. In doing so, the editors also refused to specify any problems with the study that would warrant this drastic measure.

The retraction was instead based on the vague grounds that “concerns were brought to the attention of the editorial office regarding the validity of the conclusions of the published research.” An editorial review concluded that there were “several methodological issues” and that “the conclusions were not supported by strong scientific data.”

The journal editors refused to specify which of the authors’ conclusions they were alleging to be unsupported, what the alleged methodological issues were, or how the scientific data presented in the paper were not strong—all of which explanations would be required for a truly scientific inquiry into the validity of the study’s findings and conclusions.

While the editors refused to explain their decision, the anonymously written complaints echo those of David Gorski, a cancer surgeon known for publishing hateful screeds against “anti-vaxxers” on his blog Respectful Insolence under the pen name “Orac”.

On November 25, 2020, just three days after publication of the study, Gorski published a blog post dismissing the study as “crappy” and “incompetent”, calling Thomas an “antivax pediatrician” despite the fact that he vaccinated children in his practice, and dismissing Lyons-Weiler as a “scientist turned antivax crank”. Gorski dismissed the study as “poorly designed and executed” and “singularly uninformative”, with conclusions that “are not supported by their data and design.”

He accused Thomas of “bias” in his care for unvaccinated versus vaccinated patients, suggesting that the appearance of a higher incidence of various diagnoses among vaccinated children was due to an alleged propensity for Thomas to ignore health conditions among the unvaccinated rather than to diagnose and provide ongoing care to those children for their conditions. Gorski naturally produced no evidence to support this attack on Thomas’s character and professional integrity, which ad hominem argumentation is characteristic of his screeds.

Gorski’s chief complaint, though, was the innovation by Thomas and Lyons-Weiler of measuring what they called the Relative Incidence of Office Visits (RIOV) in addition to using the more traditional method of calculating odds ratios for incidence of diagnoses.

As noted in the study, RIOV is more informative and statistically powerful. Whereas incidence of diagnoses looks at the binary “yes/no” question of whether a child has received a diagnosis for a given health condition, RIOV is more indicative of the severity of that health condition since it accounts for the incidence of office visits associated with that condition.

Gorski irrationally objected to this innovation on the grounds that no study had ever compared health outcomes between vaccinated and unvaccinated children that way before. He described it as “a new, unvalidated metric” and on that ground dismissed the study’s findings, suggesting that the unvaccinated children in Thomas’s practice weren’t really healthier; it just appeared that way because “parents who are more accepting of vaccines will have different health-seeking behavior than those who do not, being far more likely to bring their children in to be seen”, and hence more likely to receive a diagnosis.

While such a selection bias could be fairly seen as a theoretical possibility, Gorski provided no evidence to support his hypothesized explanation for the study’s findings and failed to identify any actual flaws in the study despite purporting to have debunked it.

On December 10, the website Health Feedback—a member of the Poynter Institute’s “International Fact-Checking Network”, which is partnered with social media companies to suppress information that does not align with the government’s policy aim of achieving high vaccine uptake—published an article that relied on Gorski’s unsubstantiated opinions and accusations in order to similarly dismiss the findings of the peer-reviewed study.

The “claim” that Health Feedback dismissed as “unsupported” was the partially quoted conclusion from the study that “vaccinated children appear to be significantly less healthy than the unvaccinated”. (The full statement read, “We can conclude that the unvaccinated children in this practice are not, overall, less healthy than the vaccinated and that indeed the vaccinated children appear to be significantly less healthy than the unvaccinated.”)

Of course, it is a simple point of fact from the data that the vaccinated children appeared to be significantly less healthy, which Health Feedback acknowledges by arguing that this was only an appearance. On its face, that statement was absolutely supported by the study findings, and it is nonsensical to declare a logical truism to be “unsupported”.

To support its claim that the data only appeared to show that the unvaccinated children were generally healthier, Health Feedback cited Gorski to similarly dismiss the findings of the peer-reviewed study. The article leveled the same baseless personal attack against Dr. Thomas’s professional integrity that he may have cared prejudicially for vaccinated patients.

Mainly, however, Health Feedback dismissed the quoted conclusion as “unsupported” on the grounds that the study “used a dubious metric for comparing disease incidence in both groups”. The argument was that ROIV was “not validated”, which simply meant that this methodology had never been used before to compare health outcomes between vaccinated and unvaccinated children. Of course, by the absurd reasoning that a methodology is invalid simply because it is new, no methodological innovations in science could ever possibly occur.

In an effort to support its claim that it was somehow invalid to measure incidence of office visits as opposed to incidence of diagnoses, Health Feedback also parroted Gorski’s claim that “vaccinated children are much more likely to be diagnosed with medical conditions, even though they are not necessarily more likely to develop such conditions compared to unvaccinated children.”

Health Feedback notably failed to disclose to its readers that, in addition to RIOV, the study also included analysis of the data using the traditional measurement of incidence of diagnoses, which still showed a higher incidence of numerous health conditions among vaccinated patients. By Health Feedback’s own reasoning, this was a valid methodology that did support the conclusion, which helps to explain the deceptive omission by the faux “fact checker”.

Having thus dismissed the study by Thomas and Lyons-Weiler, Health Feedback insisted that “Vaccines are safe and effective. The U.S. Institute of Medicine concluded in a 2013 review that the childhood immunization schedule is safe.”

In fact, the Institute of Medicine (IOM) in that review acknowledged that “No studies have compared the differences in health outcomes that some stakeholders questioned between entire unimmunized populations of children and fully immunized children.” The IOM reiterated that “existing research has not been designed to test the entire immunization schedule”, and again that “studies designed to examine the long-term effects of the cumulative number of vaccines or other aspects of the immunization schedule have not been conducted.”

Thus, far from contradicting the findings of Dr. Thomas’s study, the findings of the IOM review support the urgent need for this type of research to be done.

In sum, Health Feedback dishonestly dismissed the findings of a peer-reviewed study based on the groundless accusations and unsupported opinions expressed in Gorski’s blog.

The anonymously written letter that resulted in the retraction of the study—which Lyons-Weiler published on his blog on July 25, 2021, because the journal editors had refused to do so—parrots those exact same substanceless criticisms and the hypothesized selection bias.

It is of course not a standard practice among journals to retract studies simply due to concerns about a theoretically possible selection bias. Were that to be the case, practically no observational study could ever remain published since the possibility of selection bias is an inherent weakness of observational study design, which is why randomized controlled trials are rather considered the gold standard of evidence.

The Anonymous Letter

Like Gorski, the anonymous letter author baselessly accused Dr. Thomas of applying different standards for diagnosis and care depending on whether the patient was vaccinated or unvaccinated, implying, for example, that no cases of attention deficit hyperactivity disorder (ADHD) were found among the unvaccinated not because none of these children had ADHD but because Thomas simply refused to diagnose it; or conversely that he diagnosed vaccinated children with various conditions not because they really had presented with the symptoms of this condition but because they were vaccinated.

Of course, the same reasoning could be used to speculate that pediatricians who push the CDC schedule on parents prejudicially diagnose unvaccinated children while ignoring equivalent health conditions among the children of compliant parents. Presumably, the letter author would reject this speculation and so by the same standard must reject the equivalent accusation of prejudicial care on the part of Dr. Thomas.

Like Gorski, the anonymous letter author focused on Thomas and Lyons-Weiler having “invented a non-standard measure” with Relative Incidence of Office Visits, which the person dismissed nonsensically as being “more easily manipulated” than the typical measurement of the incidence of diagnoses, with no explanation for what that was supposed to mean or how this was so.

The person further criticized the study on the absurd grounds that it didn’t present individual patient data for each diagnosis, by which reasoning the published clinical trial results for mRNA COVID‑19 vaccines should all be retracted since the manufacturers have to date refused to release individual level data for independent analysis.

The anonymous critic also nonsensically argued that the analysis was inapplicable to the data because the study was not a randomized controlled trial, which is a curiously perverse argument in light of the IOM’s acknowledgment of the complete absence of studies examining the safety of the CDC’s schedule as a whole and the CDC’s adamant refusal to conduct randomized controlled trials—or even observational studies—to compare long-term health outcomes between children vaccinated according to its schedule and completely unvaccinated children. It is, of course, this lack of scientific data that gives rise to the need for observational studies such as Dr. Thomas’s.

Setting aside those nonsensical criticisms, “the most serious flaw” in the study according to the anonymous critic was that the data were “very likely” to simply indicate that “parents who are more sensitive to the health of their children and who can afford the payments of the private clinic visit the clinic more often both for vaccination and for health problems.” (Emphasis added.)

Thus, the alleged fatal “flaw” in the study was that its results “have no scientific value” because parents of unvaccinated children either don’t care as much about their children’s health or cannot afford to get their children health care. Naturally, the person provided no evidence to support either the absurd defamation of non-vaccinating parents or the alternative claim that these parents did care just as much about their children’s health but were too poor to take their kids in to see Dr. Thomas (and evidently uninsured).

In fact, as the journal editors were perfectly well aware, Thomas and Lyons-Weiler included in their study an analysis specifically designed to test the hypothesis that differences in the incidence of diagnoses or office visits were attributable to parents of unvaccinated children utilizing health care less than parents of vaccinated children.

To do this, they looked at incidence of fever, a known consequence of vaccination, and well-child visits, which are obviously not a consequence of vaccination. It was to be expected that more highly vaccinated children would have a higher incidence of visits for fever, which was indeed what the data showed. If the hypothesis were true, a similar result would be expected for incidence of well-child visits, which was not the case. Instead, compared to incidence of fever, there was a stable trend for relative incidence of well-child visits, indicating that the parents of the least vaccinated children tended to bring their children in for well-child visits the same as the parents of the most highly vaccinated children.

Thus, the data supported the conclusion that the differences in health outcomes observed were not attributable to differences in healthcare-seeking behavior. Neither Gorski nor Health Feedback nor the anonymous letter writer substantively addressed the fact that the study already included this analysis.

Nevertheless, Dr. Lyons-Weiler has now published further analyses of Dr. Thomas’s patient data specifically to address the criticism that the differences in health outcomes reflect differences in healthcare-seeking behavior rather than a true effect of different choices regarding routine childhood vaccinations. This new study thoroughly refutes the purely hypothetical basis for the original study’s retraction.

The New Study Falsifying the Ostensible Grounds for Retraction

Since Dr. Thomas remains prohibited by the medical board from conducting further research, Dr. Lyons-Weiler teamed up for this research with retired neurosurgeon Dr. Russell Blaylock. They published their findings in the International Journal of Vaccine Theory, Practice, and Research, a journal for which they are both associate editors, in a study titled “Revisiting Excess Diagnoses of Illnesses and Conditions in Children Whose Parents Provided Informed Permission to Vaccinate Them”.

This new study thoroughly refutes the claim that the findings of the retracted study were spurious due to parents of unvaccinated parents somehow caring less about their children’s health or otherwise failing to get their children’s equivalent health problems diagnosed and treated.

As Lyons-Weiler and Blaylock comment:

Such post-publication anonymous attacks permitting a single reader’s guesswork to overrule the recommendations of the original peer-reviewers is not consistent with any reasonable ethical standard for publishers. Journals should instead publish statements of concern following peer-review, allowing the authors to either defend their research or withdraw their study if the concerns expressed are true and bring valid issues to light that have been overlooked or misunderstood. Such rational discourse is part of the staid and honored practice in genuine science, allowing individual scientists and the community to engage in a transparent manner consistent with honor and integrity.

As they note:

The original study in question was retracted after an anonymous reader communicated the unsubstantiated opinion, evidently a personal suspicion, that the results were due entirely to variation in the health-seeking behavior of parents who provide informed permission for their children to be vaccinated compared to those who refuse to provide informed permission.

The anonymous critic “provided no data to support such an idea, which had already been addressed during peer-review”. This concern about the possibility of a selection bias resulted in the inclusion in the original study of the analysis “showing that the reader’s supposition was likely to be false.”

Nevertheless, to more thoroughly test the hypothesis of a selection bias arising from differing healthcare-seeking behaviors, Lyons-Weiler and Blaylock did several additional analyses.

For one set of analyses, they defined three groups or “blocks” of patients based on routine health care visits, classified into high, intermediate, or low attendance.

For another, they matched vaccinated patients to unvaccinated patients who were the most similar both in age and in keeping up with routinely scheduled health care visits.

Additionally, they took the third approach of adjusting the data using multiple linear regression, which is “classically used to help those studying the relationships among independent variables via model comparison”, to study “the effect of variation that might be attributed to healthcare utilization, age, and ‘natural’ lifestyle choice.”

In this set of analyses, the variable of “Health Care Visits per Day of Care” was used as an independent measure to study “the effects of vaccination exposure (number of vaccines) on requiring an office visit for any condition other than vaccination.”

Breastfeeding was also used as a correlate of lifestyle choice to further study the effects of adjusting for the “natural” lifestyle hypothesized to explain the apparent differences in health outcomes between vaccinated and unvaccinated children.

Using the “blocking” approach, the “high” visitation group naturally correlated to older age since younger patients had fewer opportunities to attend routine office visits. The average age of patients with between eight and nine health care visits, however, was the same whether they were vaccinated or unvaccinated. Matched to “days of care”, which correlates with age since the study only included patients born into Dr. Thomas’s practice, the unvaccinated patients had overall higher attendance at routine health care visits.

As Lyons-Weiler and Blaylock remarked, that result rules out the possibility that the original findings could be explained by the parents of unvaccinated children simply failing to bring them in for routine checkups.

They also looked at non-routine health care visits for a broad range of conditions. Conditions for which the highest number of office visits were from the most highly vaccinated children included fever, gastroenteritis, allergic rhinitis, anemia, otitis media, eczema, diarrhea, Coxsackie virus infection (hand, foot, and mouth disease), breathing issues, and asthma. It also included conditions for which there were zero unvaccinated patients, which were edema, digestive tract issues, nausea/vomiting, food allergy, pain, and seizure.

As the authors noted, “Some of the rarer conditions were difficult to study due to small sample sizes (e.g., no cases of autism were found among the matched sample of 561 vaccinated persons due to its overall rarity).”

(Indeed, a remarkable finding of the original study was that only 0.36 percent of patients born into Dr. Thomas’s practice had autism compared to the CDC’s estimate of the national rate of 1.85 percent. Therefore, without insinuating anything about causality, we can fairly say that being born into Dr. Paul’s practice is associated with a fivefold decreased risk of being diagnosed with autism compared to the general population of highly vaccinated children. Just as remarkably, there were zero unvaccinated patients in the study population with ADHD compared to 5.3 percent among the variably vaccinated, which in turn compared with the US national rate, according to the CDC, of 9.4 percent.)

Lyons-Weiler and Blaylock calculated odds ratios for each condition. Least controversially, vaccinated patients had a three times higher odds of a non-routine office visit for fever. That was to be expected. Other conditions for which vaccinated patients had a significantly higher odds of office visit were gastroenteritis, eczema, anemia, otitis media, and food allergy. Additionally, vaccinated patients had an at least 50 percent higher odds of having office visits for allergic rhinitis, breathing issues, and diarrhea.

The multivariate study further showed that the number of vaccines received was associated with an increase in the number of office visits required for health issues in a manner that is “independent of any effect of the covariates” of “health care visits per days of care” or breastfeeding.

Additionally, a comparison of the most highly and least highly vaccinated patients suggested that “vaccine cessation leads to a reduction in many conditions”.

“The original publishing journal”, Lyons-Weiler and Blaylock noted, “had received one letter of complaint that alleged (without providing any data or evidence) that the results of the published study must have resulted due to differences between the vaccinated and unvaccinated populations with respect to adherence to ‘well-child’ visits.”

However, the fact is that it was Dr. Thomas’s unvaccinated pediatric patients who overall kept their health check visits “with a higher regularity and higher frequency than the vaccinated”, regardless of age.

Therefore, differences in healthcare-seeking behavior cannot explain the increased incidence among the vaccinated of non-routine office visits for various health conditions. As Lyons-Weiler and Blaylock rightly conclude, “The sole reader’s imagined concerns were unfounded, and the Lyons-Weiler and Thomas study should not have been retracted.”

They further concluded that “There is no way to interpret the data as showing that, overall, the unvaccinated are less healthy than the vaccinated. This addresses the [Oregon] medical board’s request to answer this question.”

On the contrary, “For most of the conditions, the vaccinated have a higher disease burden even when patients are matched for age, days of care, and healthcare utilization behavioral differences.”

In closing, the authors summarized:

The method developed by Lyons-Weiler and Thomas (RIOV; 2020) was new and was shown to have more intrinsic statistical power than odds ratios [OR] or relative risk [RR] estimates. This is because the use of rates of a given diagnosis, which is how the data are usually presented to odds and relative risk ratio analyses, are lossy transforms of the rates of office visits required to address health issues related to the diagnoses. . . .

We have shown, using a variety of exhaustive methods, that the anonymous reader’s concerns that led to the retraction of Lyons-Weiler and Thomas (2020) were unfounded. Given the insensitivity of the evidence to methodological differences, we conclude that the paper was wrongfully retracted and for other reasons than the alleged problem originating from a single reader using unscientific reasoning. At this point, unless the journal in question reinstates the study, the journal’s reputation as an objective publication outlet will remain forever suspect.

The medically important findings in these data should not be ignored. These include the possibility of developmental effects of vaccine aluminum-induced anemia, gastrointestinal disorders, and increased risks of these medical conditions secondary to vaccine-induced dysfunctions of various elements of the immune system.

Indeed, it was apparent from the start that the journal editors retracted Dr. Thomas’s study not for containing egregious flaws that warranted a retraction but for political reasons. Specifically, the study was retracted because its valid findings and the valid conclusions drawn therein challenged the unevidenced assumption of policymakers that achieving strict compliance with the CDC’s routine childhood vaccine schedule results in better health outcomes.

Conclusion

Dr. Paul Thomas and Dr. James Lyons-Weiler had already addressed the objection raised during the peer-review process that the association between vaccination and higher incidences of diagnoses and office visits for various health conditions could be simply due to different healthcare-seeking choices of parents of unvaccinated children. Their study included a positive and negative control indicating that their findings were not explainable by those parents choosing not to bring their children in for routine checkups.

Now, Dr. Lyons-Weiler, in collaboration with Dr. Blaylock, has gone even further, utilizing a variety of different methodological approaches to further test that hypothesis. The result of these additional analyses is the falsification of that hypothesis.

It is simply not true that the unvaccinated children in Dr. Thomas’s practice had parents who chose not to bring them in for routine well-child visits. It is simply not true that they are just as unhealthy as vaccinated children but were just never diagnosed because their parents care less about their health or cannot afford the cost of routine checkups, or for any other reason. The whole basis for the study’s retraction is simply false.

The findings and conclusions of Dr. Thomas’s study stand. His patient data do in fact show an association between vaccination and a higher incidence of office visits for various health conditions that cannot be explained by difference in healthcare-seeking behaviors. Both the journal and the media’s “fact checkers” have done a disservice to science and to our children by wrongly dismissing the possibility that the evidently superior health of unvaccinated children is precisely because they were never vaccinated.