MDPI’s “The International Journal of Environmental Research and Public Health” Does Not Publish Unbiased Research or Advances in Methodology


After 250,000 reads, the journal retracted our study, Relative Incidence of Office Visits and Cumulative Rates of Billed Diagnoses Along the Axis of Vaccination (2020 Nov 22;17(22):8674. doi: 10.3390/ijerph17228674) after one reader submitted a poorly written email (with typos and grammatical errors) about an imagined confounder they thought might explain the results.

We asked the Editor-in-Chief and the Editorial Board of the journal to publish the readers’ comments, and our reply. They did not respond to that request. Instead, they decided to retract it without further discussion of our reply.

We had published an Erratum, and wanted to publish a small Corrigendum for an error we had reported to the Editor-in-Chief. These issues were unrelated to the anonymous readers’ concerns.

Our concerns are not vainglorious. It is unfortunate that they allowed themselves to be duped by a ghoul. A ghoul is one who haunts journals working to retract only studies that include results they don’t want published). This imparts a ghouling bias, also known as retraction bias, into the literature, preventing unbiased meta-analyses. In our cases, it also prevents advances in the methodology of the analysis of data from vaccine safety studies from being adopted and tried out by other scientists.

We would have preferred rational discourse so the scientific community could make their own assessment of the issues at hand. Instead, we have to assess the journal’s integrity, or at least their ability to discern that they have been defrauded by the ghoul.

We are deeply disappointed to learn that the International Journal of Environmental Research and Public Health’s Editor-in-Chief and Editorial Board do not support the publication of unbiased research, that they do not support rational discourse, and that they will not publish clear advances in the statistical methodology of vaccine research. In response, Dr. Lyons-Weiler has cut all ties with this journal and publisher due to concerns over their objectivity, including an SPECIAL VOLUME of IJERPH where he was acting as Guest Editor on the effects of COVID-19 vaccines on human health.

Here is our response to the reader’s statements. We refer to the ghoul as as ANONYMOUS; part of their ploy is to pretend that they are afraid of reprisals from so-called “Anti-vaxxers” if their identity is known. We reproduce our response to the feigned concerns here, in full.

For and with Paul Thomas,

James Lyons-Weiler, PhD

Allison Park, PA 7/25/2021

— 2/26/2021Incl: Letter from Dr. Mawson, Dr. Lyons-Weiler’s NIH Biosketch, Board Letter page 1 image

Dear Editor-in-Chief and Editorial Board, ANONYMOUS has communicated a number of points critical of some aspects of our study, “Relative Incidence of Office Visits and Cumulative Rates of Billed Diagnoses Along the Axis of Vaccination” (Int. J. Environ. Res. Public Health 2020, 17, 8674). At the invitation of the Editor-in-Chief, we submit the following point-by-point retort.
“Paul Thomas runs the clinic (Integrative Pediatrics), where the unpublished data for the IJERPH­ article data has been collected. The conflict of interest has been expressed, but the strong connection between the data and the role of Paul Thomas has not been discussed in the article.”

Our access to the data was made possible by Dr. Thomas’ position at Integrative Pediatrics via adherence to regulatory compliant processes. Access to the data occurred under regulatory-compliant protocol with IRB supervision. Per the IRB-approved research proposal:

“All data and records generated during this study will be kept confidential in accordance with HIPAA on subject privacy. The Investigator and other study personnel will not use such data and records for any purpose other than completing this study. Monitors, auditors, the IRB, and other applicable regulatory authorities will have access to the study-related medical records as needed. Study records will be kept confidential, and, to the extent permitted by applicable laws and/or regulations, will not be made publicly available. Once the study results are published, the subject’s identity will remain confidential at all times. No identifiable data will be used for future analysis without first obtaining IRB approval. All sensitive data and data that contains HIPAA identifiers, when electronic, will be stored on a hard drive and thumb drive back-up that is encrypted by and accessible only by the Honest Broker at the Performance Site. To facilitate independent review of our results, the identifiers will be retained, encrypted, for seven years following publication. The other data will be retained for the duration of the study plus seven years. Supplementary data made available at the time of publication will not include any of the HIPAA identifiers but will contain the study-specific UID.”

US HIPAA requirements forbid the sharing of identified data without IRB oversight for the purpose of IRB-approved research of a study design and data analysis plan. Our HIPAA-compliant process of patient de-identification was, in fact, explained in detail in our study. How we could have conducted the study without access to the data is not explained by ANONYMOUS.

“As he has had a possibility to influence all the essential elements – recommendations for vaccination, information on who is vaccinated, diagnoses made and number of office visits – it is not obvious that the data can be treated as neutral. For example, the diagnosis of autism and ADHD are complex as well as culturally dependent. Unintentional positive bias can emerge for a GP that is known to associate vaccination with autism or ADHD.”

When Dr. Thomas approached Dr. Lyons-Weiler with the request to help design the study, Dr. Lyons-Weiler informed Dr. Thomas that his participation in this design and execution of the study was conditional: that any result found would be published, whether the data indicated that exposure to vaccines were associated with increased, or decreased health. The data were drawn from the electronic medical records according to the reported inclusion/exclusion criteria (as reported in the study); no patients were included or excluded using any criteria beyond that were reported, meaning the sample was completely representative of the patients in Dr. Thomas’ practice.

This representativeness means that any concern over “bias” that the sample is not representative of patients in other practices are moot; we stated this clearly in the article.

The should be no confusion regarding potential bias related to adhering to informed consent, either. The universal adherence by all of the physicians in the practice to Oregon State Law to provide informed consent is, sadly, relatively unique. In spite of laws that protect informed consent, and Federal Regulations that forbid coercion for inclusion in clinical research, the American Academy of Pediatrics supports dismissal of patients from practices (AAP, Edwards, 2016). In so doing, the AAP sanctions coercion, including dismissal of entire families from pediatric practices in violation of state and Federal laws protecting patient rights to informed consent.

The AAP website (AAP, 2021) reads:

“The current AAP Clinical Report, Countering Vaccine Hesitancy, provides information about addressing parental concerns about vaccination. It can assist pediatricians with understanding vaccine development and safety monitoring processes, and it reviews the current state of vaccine exemptions, discusses communication strategies for responding to parental concerns and considers the option of dismissal from a practice of families which refuse vaccinations.”

And the page links directly to Edwards et al. (2016), who conclude

“Nevertheless, the individual pediatrician may consider dismissal of families who refuse vaccination as an acceptable option.”

Although strictly forbidden in matters of informed consent, coercion itself has been proposed as a necessary and useful means to increase overall vaccination rates (Edwards, 2016; Grzybowski et al., 2017). The use of coercion is in conflict with existing rights to free, prior and informed consent. In direct conflict with AAP’s position, the State Law of Oregon childhood vaccination includes the right to claim religious or philosophical exemptions are contained in ORS 433.267(1):

“(1) As a condition of attendance in any school or children’s facility in this state, every child through grade 12 shall submit to the administrator, unless the school or facility the child attends already has on file a record that indicates that the child has received immunizations against the restrictable diseases prescribed by rules of the Oregon Health Authority as provided in ORS 433.273 (Rules), one of the following:(a) A document signed by the parent, a practitioner of the healing arts who has within the scope of the practitioner’s license the authority to administer immunizations or a representative of the local health department certifying the immunizations the child has received;(b) A document signed by a physician or a representative of the local health department stating that the child should be exempted from receiving specified immunization because of indicated medical diagnosis; or(c) A document, on a form prescribed by the authority by rule and signed by the parent of the child, stating that the parent is declining one or more immunizations on behalf of the child. A document submitted under this paragraph:(A) May include the reason for declining the immunization, including whether the parent is declining the immunization because of a religious or philosophical belief; and(B) Must include either:(i) A signature from a health care practitioner verifying that the health care practitioner has reviewed with the parent information about the risks and benefits of immunization that is consistent with information published by the Centers for Disease Control and Prevention and the contents of the vaccine educational module approved by the authority pursuant to rules adopted under ORS 433.273 (Rules); or(ii) A certificate verifying that the parent has completed a vaccine educational module approved by the authority pursuant to rules adopted under ORS 433.273 (Rules).”

From this, it can be seen that the decision to not vaccinate is not undertaken by families without due consideration of stated risks and benefits. It also demonstrates that the parents’ decisions to accept or deny a specific vaccine are not, in the end, in the final control of the physicians of any practice in Oregon providing lawful pediatric medical care. To do otherwise would be unlawful.
The standard of care for the diagnoses of autism and ADHD involves referrals to physician specialists outside the practice, and the final diagnosis was not made by the physicians in Integrative Practice over the 10-year period from which the data were drawn.

As stated above, we acknowledged in our study that the data from this single performance site might not be non-representative of other practices and that the results may not generalize. This is especially true if other practices do not provide parents with the opportunity for free, prior and informed consent. But this does not invalidate the within-practice comparisons in any way.

“In December 2020 the Oregon Medical Board, State of Oregon, published an official declaration on Dr Thomas. The emergency suspension of Dr Thomas’ license to practice medicine disclosed data that strongly suggest Dr Thomas to have acted towards patients in a manner that seriously compromise (sic) the very basic principles of clinical research as well as confidence in gained results thereof.”

The Oregon Medical Board’s emergency meeting took place five days after our study was published; the suspension of his license is therefore clearly a retaliatory move designed to discredit Dr. Thomas, and thereby, the study. The IJPERH Editors and the Editorial Board should be advised that in 2019, the Oregon Medical Board had requested that Dr. Thomas show that the unvaccinated patients in the practice were not less healthy than those whose parents choose to accept the CDC offered vaccinations. This board letter is attached. The Medical Board’s allegations, which Dr. Thomas intends to vigorously rebut at an upcoming hearing, had existed for quite a long time prior to our published study. Thus, the timing of the Board’s “emergency suspension” is circumspect.

The retrospective analysis we conducted was objective and reflects the medical records of unbiased samples of two populations: patients whose parents chose to accept some or all of the offered vaccines, and patients whose parents declined to accept the offered vaccines. The results clearly threaten orthodox messaging on vaccine safety, but that cannot be helped: the data show what the data show. The Medical Board’s and ANONYMOUS’s apparent attempts (via ad hominem) to discredit Dr. Thomas necessarily requires a discrediting of our study. Given the rigor with which the study was designed and the analysis was executed we see that outcome as unlikely.

“The data is (sic) collected from one clinic only, which means that the health data for the patients is inadequate and can be biased. It is well known that in (the) U.S.A. the health care (sic) system is relatively scattered, and patients use several health care providers. Comprehensive data sets that enable negative conclusions (i.e., claims, such as patients lacking certain symptoms, concluded from data encompassing only one single service provider) are very difficult to obtain.”

The data analyses we conducted addressed the issue that patients might vary in their enrollment in Integrative Pediatrics. Specifically, the Days of Care (DOC) matched analysis involved a comparison of 561 vs. 561 matched on the range (in days) between first and last electronic record. The matching was conducted by Dr. Lyons-Weiler, using only Study Patient IDs and the DOC data element. No other datapoint was viewed at the time of matching. Thus, the DOC results are included for due consideration of any concerns related to variation in healthcare seeking behavior.

We also explicitly noted that the results of the study may only be applicable to the population under study. We reported that the data are from a single practice that is unusual in practicing informed consent, and that the results may therefore not be generalizable to the general childhood population, and we called, therefore, for further research to be done using data from a larger number of practices. The fact that the results of a study is limited to populations from which the sample is representative is universal to all studies that use samples from populations; our study at least specifically acknowledged the uniqueness of the characteristics of the population under study and this fact was given due consideration by the authors in their conclusions.

“Our family history of autoimmune conditions analysis points to numerous conditions likelycarrying a genetic risk of vaccine-related adverse health effects. This, however, is only one study from data from a single practice, so any absence of a pattern consistent with a genetic risk of adverse health effects should not be taken as evidence of absence of a role of genetic risk. Larger studies able to estimate the interaction term between family history and vaccine exposure should be undertaken.”
The criticism is redundant and unwarranted.

“The authors have invented a non-standard measure (Relative Incidence of Office Visit (RIOV)) for the health problems. The measure has several weaknesses compared to the diagnoses (sic) data. For example, it is more easily manipulated, the visit can take place because of false expectations of the parent, the link between the reason of the visit and the health problem is vaguer(sic) and at one visit several health problems can be assessed, which complicates the classification of the reason for the visit.”

The history of science, including genetics, and biomedical research is filled with the development of “non-standard measures” that go on to become adopted due their increased utility compared to the “standard” methods of the time. In 1908, William Sealy Gosset invented a non-standard measure (Student’s test statistic) for the analysis of parametric data (Ziliak, 2008).

In 1934, Sir Ronald Fisher invented a non-standard approach to analysis called null hypothesis testing (Fisher, 1935) In 1973, Nei invented the non-standard method for studying genetic differentiation in populations (Nei, 1973). In 2020, Lyons-Weiler and Thomas invented the non-standard measure RIOV. Science progresses by the introduction of “non-standard methods”.
ANONYMOUS claims that the RIOV test has several “weaknesses”; however, they fail to provide any explicit theoretical derivation of “weakness” in the method, nor any data or evidence of any kind to support that these supposed weaknesses are indeed correctly surmised, nor that they apply to the implementation of the RIOV measure in our study.

We consider the supposed “weaknesses” in turn.

First, ANONYMOUS claims that (relative to odds ratio of incidence):

“It (RIOV) is more easily manipulated”.

If by “manipulated”, ANONYMOUS means “executed”, the RIOV involves a few more, not fewer steps than the calculation of the odds ratio of incidence. If, by “manipulated”, ANONYMOUS is implying that the results of RIOV can be made fraudulent, we agree in principle that it can be done, but have no idea why or even if data manipulation is being implied. In the wrong hands,, any data can be manipulated and can be made to mislead any method of analysis. We have no frame of reference as to the “ease” with RIOV could be manipulated by fraudsters relative to the incidence-only based methods. The execution of the method was conducted without preference to the outcome of the analysis.

“the visit can take place because of false expectations of the parent”
We have no reply to this statement because we do not know what is being implied and would not care to guess.

“,,,the link between the reason of (sic) the visit and the health problem is vaguer(sic) and at one visit several health problems can be assessed, which complicates the classification of the reason for the visit.”

ANONYMOUS has evidently confused the process of providing medical care with the conduct of the design and execution of retrospective studies on the resulting data. Patient care in the practice was provided in accordance with the tenets of individualized care; each patient appearing in the examination rooms was either there for a well-child visit, or due to a health complaint.

Naturally, under the ethics of medicine, any concern reported or discovered during any office visit will have been recorded, and, if allowed, reported as a billable service. The data we analyzed were for billed services and RIOV reflects the number (count) of office visits at which those services were rendered, regardless of other conditions also addressed at each visit. Each and every condition addressed in any office visit led to an increase of 1 office visit for that condition, for that patient. Each office visit “related to” any billed condition was captured by the billing data as related to the health outcome, and therefore ANONYMOUS is incorrect; addressing multiple concerns at a single office visit does not “complicate” anything in our calculations.

RIOV allows the study of variation in the number of office visits related to diagnosed conditions. Patients with recurring office visits related to a particular health condition (due to more severe asthma, for example) of course will naturally have more office visits related to the specific health outcome of interest, as is appropriate for the measure RIOV. The criticism by ANONYMOUS of ROIV is unfounded. We also demonstrated that RIOV has advantages, including higher intrinsic power compared to diagnosis-only based analysis. We also conducted and included the results from odds ratio on incidence of diagnosis.

“The authors claim to have proven that this measure is superior compared to the diagnosis­-based measurement. The data for the diagnoses has not been described and the power analysis used do not apply to the data, as it is not from (a) randomized controlled trial.”

Statistical power is a measure of the probability that a given test statistic will reject the null hypothesis Ho when Ho is, in fact, false. The relative power of a test is determined by its possible distributions both when the null hypothesis is correct and when then alternative hypothesis HA is correct. The more powerful the test, the less likely a true association will be missed; i.e., more powerful tests have lower false negative rates (Type II error). Factors that influence power beyond the intrinsic power of each type of test includes sample size (N), the effect size, and the stringency of how the test is applied, i.e., researcher tolerance for risk Type I errors.

The simulation we conducted shows that, given the same sample size, the same a(alpha), and the exact same data, RIOV is more powerful than odds ratios on incidence of diagnosis.

We did not publish a formal proof that RIOV is a more powerful test. Instead, we have provided an elegant and straightforward simulation demonstration that it appears to be a more powerful test. We also explain why: a diagnosis-only count is a special case of the office-visit-based count, and as such the diagnosis-only count has lower dynamic range. Contrary to the claim made by ANONYMOUS, the “diagnosis-based measurement” to which ANONYMOUS is referencing is, in fact, described in detail, with equations in our study.

Power is always a concern when null hypothesis testing is undertaken in science, and the claim that power considerations only apply to randomized controlled trials is utterly incorrect; see examples of analyses decrying underpowered observational studies across a wide diversity of disciplines, including cancer studies (e.g., Stocken et al., 2008), studies in nutrition science (Allan et al., 2016), treatment of respiratory illnesses (e.g., Fallagas et al., 2010), psychiatry (Farrell et al., 2015).

“…the most serious flaw in the article is that the obvious problem of selection has not been assessed. It is very likely 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. The ‘Well Child’ Visits per child is 34 % higher in the Vaxxed group, see Table 2. Analysing days of care (DOC) related to the treatment episode does not remove the selection problem, since children of sensitive parents are likely to have longer episodes. Therefore, the results provided have no scientific value.”

Regarding unvaccinated patients being somehow less “sensitive to the health of their children”, this spurious, unfounded and paternalistic supposition is counter to the physicians in the practice and is not based on any published data. In fact, if anything, the opposite trend exists: direct experience by the physicians and staff in the practice in consultations with parents in families joining the practice informs us that they have sought out care specifically at Integrative Pediatrics because they have learned that the physicians provide lawful pediatric care by which the physicians abide by the state and Federal requirements of informed consent. Regarding cost of care, the practice accepted insurance from most insurers, providing a broad number of options for access to healthcare.

ANONYMOUS has also conflated the higher incidence of Well-Child visit in the vaccinated vs. unvaccinated (which we reported as 1.3 in Table 2) with the RIOV analysis, which compares the incidence of office visits related to health outcome at varying levels of vaccine uptake to the same measure in the unvaccinated. Our study had both an internal positive (fever) and negative (well-child visit) control. Fever being an outcome known to be causally related to vaccination, was found to have increased RIOV with increased vaccine uptake. By contrast, the negative control variable “well-child visits” did not have increased RIOV with increased vaccine uptake (our Fig 3). This falsifies the hyperbolic claim made by ANONYMOUS that “the results have no scientific value”.

The fact that RIOV itself shows no increase in well-child visits with increasing vaccine update (ergo, “the axis of vaccination) in fact has immense scientific merit, as it allowed us to show that patients with low vaccine uptake attend their well-child visits at the same rate as patients with higher vaccine update, relative to the unvaccinated rate.

The logical flaw made by ANONYMOUS is to generalize the increase in well-child visits under the incidence analysis to the RIOV analysis, ignoring the added dimensions of office visits and the fact that RIOV is office visits in the vaccinated relative to the unvaccinated. Had we restricted our consideration to “incidence only” as ANONYMOUS has implied we should have, the concern might be somewhat more valid in that we may have missed association of vaccination with adverse events. Our findings demonstrate the advance made by the introduction of our analysis.

There is no evidence of selection bias in the data from our study. The in-practice experience is that families who choose to not vaccinate feel as welcome in the practice as vaccinating families; they trust their physicians likely because they know they will not have to meet with physicians who are hostile to informed consent. Nevertheless, we indeed did address selection bias by presenting clinical and demographic indicators that support the comparability of the vaccinated and unvaccinated patients in our Table 1, including breastfeeding and birth weight.

The non-vaccinating families did, however, have a higher rate of family history of autoimmunity, used by the families and by the physicians as a potential indicator for a modified vaccination strategy (31% in the unvaccinated compared to 25.6% in the vaccinated). We are not the first to propose that indicators of adverse health outcomes from vaccination might be predictable (e.g., Soriano et al., 2015). In fact, a massive analysis of the published biomedical literature found clear evidence of biologically plausible pathways to adverse autoimmune events of vaccine-related autoimmune disease (McGarvey et al., 2014).

The results of our study are not due to selection bias; rather, the variable “family history of autoimmunity” explains the differences because there is a known functional relationship between the physician/patient dyad using evidence of family history or prior evidence of autoimmunity and patients’ decisions on vaccine acceptance. We specifically contrasted this situation to “healthy user bias”, but the critique did not acknowledge that important distinction.
For the concern over the assumed bias to be valid there should be evidence in support of the existence of such a bias; there is none. In contrast, we are concerned over the bias in the published literature over an ongoing, consistent effort to have studies that report evidence of risk of vaccines retracted from journals. This activity often involves a single individual, writing to the journals, arguing for anonymity over feigned concern for retaliation. This destructive effort has been researched recently (Elisha et al., 2020). Open rational discourse, not study assassination by retractions solicited by anonymous persons, should become the new norm, unless evidence of outright fraud is uncovered. Errors in articles can be productively addressed by Errata and Corrigenda, leading to progress in science instead of leaving gaping holes where otherwise valid studies were once published.

The net effects of focused effort to target published studies that have already survived the double, or triple jeopardy of peer review would obviously cause a bias in the published literature that would prevent systematic reviews and meta-analyses from reporting on a balanced literature. Further, the scientific literature would be relatively deplete of studies with results supporting evidence of specific mechanisms of vaccine injury. For example, our own finding of anemia related to vaccination may further clarify the highly plausible mechanisms of potential vaccine sensitivity of individuals with mitochondrial dysfunction previously outlined by Rose et al. (2018).

Targeted, focused retraction effort, if successful then biases the outcome of adjudication of vaccine injury cases of the injured, and families of the injured, in the US National Vaccine Injury Compensation Program, a program that prefers to offer settlements instead of findings of harm caused, consistent with the programmatic bias enforced by the actions and inactions of the US Department of Health and Human Services, who, while being the defendant in vaccine injury cases, administers the program in a breach of the separation of executive and judicial powers.
Another source of bias is codified into CDC’s preferred approach to assume that covariates are confounders, instead of potentially useful risk factors. Many past studies have shown that ‘adjusting for’ covariates has a substantial impact on the role of vaccines in adverse health outcomes. Unfortunately, this has been interpreted as “vaccines play no role” in risk; in reality, the interpretation should be “the role of vaccines in health outcomes is modified by” whatever factors those studies have shown to impact the significance of vaccine as a correlative or associative factor. We already addressed the paradigm adopted by the US CDC and others in post-market surveillance studies which leads to over-adjustment bias in an apparent bid to indemnify vaccines as a potential factor in poor health. Had all the patients in the study been fully vaccinated, and then had we “adjusted for” family history of autoimmunity and treated it as a competing hypothesis, the result would likely have been the further, false exoneration of a causal contribution from vaccines. Our favored approach of direct comparisons of vaccinated to unvaccinated patients is more in line with individualized medicine because it allowed the determination of an easily identifiable risk factor. Our study supports and provides impetus for the use of family history of autoimmunity and other covariates as potential risk factors in further studies. Factors such as family history of autoimmunity should not be treated as competing hypotheses but instead as potential risk factors for vaccine-associated adverse health conditions.
In 1986, when Congress passed the National Childhood Vaccine Injury Act, the law required the Secretary of Health and Human Services to not only do a broad study of vaccine risks, but to find those who are most susceptible (US CONGRESS, 1986, emphasis ours): “STUDY OF OTHER VACCINE RISKS Pub. L. 99–660, title III, §313, Nov. 14, 1986, 100 Stat. 3781, provided that:‘‘(a) STUDY.—‘‘(1) Not later than 3 years after the effective date of this title [see Effective Date note above], the Secretary shall, after consultation with the Advisory Commission on Childhood Vaccines established under section 2119 of the Public Health Service Act [42 U.S.C. 300aa–19]—‘‘(A) arrange for a broad study of the risks (other than the risks considered under section 102 [21 U.S.C. 382]) to children associated with each vaccine set forth in the Vaccine Injury Table under section 2114 of such Act [42 U.S.C. 300aa–14], and‘‘(B) establish guidelines, after notice and opportunity for public hearing and consideration of all relevant medical and scientific information, respecting the administration of such vaccines which shall include—‘‘(i) the circumstances under which any such vaccine should not be administered,‘‘(ii) the circumstances under which administration of any such vaccine should be delayed beyond its usual time of administration, and‘‘(iii) the groups, categories, or characteristics of potential recipients of such vaccine who may be at significantly higher risk of major adverse reactions to such vaccine than the general population of potential recipients.

Unfortunately, the Office of the Secretary has failed in this duty. In fact, close examination of past and current ACIP “General Best Practice Guidelines for Immunization” reveals a habit and preference of eliminating evidence of risk factors without any scientific basis for doing so, and in recommending vaccination in situations for which no safety studies exist. These situations include vaccinating individuals who are mildly ill, on antibiotics, hospitalized, or recently under anesthesia and that have prior evidence of autoimmunity. With the US federal government shirking its duty to attend to and complete the 1986 Congressional mandates, pediatricians across the nation are misinformed on the existence of evidence in support of risk factors. Practitioners such as Dr. Paul Thomas, who provide lawful informed consent and pay heed to their empirical experience of adverse outcomes following vaccination are performing the duties required under the 1986 mandates. When current practices are no longer supported by current science, it is the duty of physicians to update the science because they are best equipped to advise the parents of their patients on vaccination risk factors.

The Advisory Practice for Immunization Practices has supported physician decisions on lawful vaccination, e.g. from Ezeanolue et al., (2021),’

“ACIP recommends that physicians and other health-care providers comply with local or state vaccination requirements when scheduling and administering vaccines.”“The degree of altered immunocompetence in a patient should be determined by a physician.”

ANONYMOUS misunderstands the “Days of Care” (DOC) measure; given that patients in the practice are scheduled for each well-child visit regardless of vaccination preferences, the DOC measure matches for the time each patient has been in the practice. It correlates strongly with age. The motivation of the DOC matching analysis was to protect against any potential confounding because DOC measure did vary between vaccinated and unvaccinated. Thus, DOC matching protects against both age, whatever extent to which people started or stopped being seen at Integrative Pediatrics for any reason, including health-care seeking preference, limiting the concern over selection bias. This only then leaves the difference in interpretation of why people who only have a 1.3 increase rate of well child visit (the vaccinated) would have such massive increases in the adverse health outcomes associated with vaccination that require billed medical care. Vaccine activists have claimed in such conditions to know causality – that the result must be due to families who do not vaccinate eschewing visits to the doctor. The problem is that the results of our study are over a range of vaccine uptake and not restricted to “vaccinated vs. unvaccinated”. We did, nevertheless, address this concern in the study and point out that whatever additional, mysterious unreported lifestyle factors non-vaccinating parents adopt that explains the large difference in measures of health in their children, all of pediatric science should be shifted to focus on what those lifestyle factors are – because, for the population under study at least, for example, these families must have all – independently – found a highly effective prophylactic that prevents ADHD. Anemia is a standard-of-care screen; all patients in the practice are screened at 9 months, and we observed much higher future office visits related to anemia associated with vaccine uptake.

“The variation in the number of the vaccinations/child (0-39) is statistically enormous and raises a question of the medical practices of the clinic and the recommendations given. It should be stated, e.g., how much of the variation is due to children evaluated at different stages of an active vaccination scheme, and how much is a result of parents deciding to discontinue the vaccination scheme for their children. Based on such data, the results should be controlled for statistical errors possibly caused by two very different reasons for the variation.”

We do not know what ANONYMOUS means by a “vaccination scheme”. However, because the physicians provided, as required by Oregon Law, informed consent, and respected, in each case, the parent’s decision to accept or decline each vaccine. These decisions were made on a child-by-child basis, and, importantly, on a vaccine-by-vaccine basis. One-hundred percent of the variation unrelated to age is due to parental choice. We conducted and provided the age-blocked analysis as part of the original analysis to address variation in outcome of the analysis based on variation in patient age (Result 3.9; our study’s Supplementary File 1).

‘The overall probability (risk) of a vaccine-targeted diagnosis in the unvaccinated, however, was only 0.0123, among 13 conditions.’ p. 16. It is obvious that the reason for this is community immunity, but the text does not mention it.

ANONYMOUS is referencing the result showing the differences between the vaccinated patients and unvaccinated patients with respect to vaccine-targeted diagnosis. Unfortunately, ANONYMOUS seems misinformed or holds an outdated view of the effects of vaccines on human health. Some of the results may be due to actual immunity, defined as patients not experiencing any infection; others may be due to patients not receiving any diagnosis due to subclinical infections. It it has been recognized for some time that pertussis vaccines, for example, fail to protect individuals from subclinical infections, and do not prevent the spread of such infections (Cherry, 2015); the same now appears to be true for the MMR vaccine’s ability to suppress symptoms of viable, transmissible mumps infections (Wei et al., 2018). Two of the cases of Rotavirus were twins whose parents report had contracted the virus from a vaccinated neighbor. We chose our wording carefully; herd immunity is not possible if vaccines only mask symptoms and fail to prevent transmission. Even if the reason for the low incidence were due to herd immunity, it would not affect the findings or conclusions of the study in any manner.“The authors use expressions such as ‘Parents are almost universally told by their child’s health care provider that the health issue was not due to the vaccine in spite of growing evidence in the scientific literature that supports both plausible mechanisms of action for chronic illnesses including epidemiological associations’ pp. 21-22. Referring to evidence that is growing requires that the studies have scientific value, and their number is increasing. Both should be verified by referring to studies that have (sic) published in high-quality journals.”

The putative link between vaccines and autoimmunity motivating the advances in clinical care at Integrative Pediatrics has indeed been noted by many researchers, in high-profile journals (e.g., Salemi & D’Amelio, 2010); Segal & Shoenfeld, 2018)), a growing number of studies have also indeed reported association of other adverse health with exposure to vaccines. Mogensen et al. (2017) found a 10-fold increase in all-cause mortality in children receiving the DTP vaccine in a vaccine-naive urban African community following the introduction of the DTP vaccine; background differences between the vaccinated and unvaccinated could not explain the differences. Children who had received both the DTP and the oral polio vaccine had a 2.12-fold increased risk of death from all causes compared to the unvaccinated. We of course already had cited the study by Hooker and Miller (2020), who found increased risk of developmental delays, asthma, ear infections and gastrointestinal disorders.

Kiraly et al. 2016 found that when DTaP administration was delayed, children had reduced odds of being diagnosed with eczema compared to those vaccinated on time. Another study found that males given the hepatitis B vaccine within the first few days of life had a three-fold increased risk of later being diagnosed with autism compared to males who were vaccinated after 30 days old 21.

In another example, in a study 11,531 children, those who delayed vaccination had a much lower risk of asthma (McDonald et al., 2008). According to the authors, “Early childhood immunizations have been viewed as promoters of asthma development by stimulating a T(H)2-type immune response or decreasing microbial pressure, which shifts the balance between T(H)1 and T(H)2 immunity.” Reversibility of effect is key in determination of causation and while this study does not demonstrate reversibility, it demonstrates dose effect. The authors concluded: “We found a negative association between delay in administration of the first dose of whole-cell DPT immunization in childhood and the development of asthma; the association was greater with delays in all of the first 3 doses. The mechanism for this phenomenon requires further research.” Aluminum has been fingered as a causal factor in Crohn’s disease (Lerner, 2012). Leslie et al., (2017) found that subjects with newly diagnosed anorexia nervosa (AN) were more likely than controls to have had any vaccination in the previous 3 months [hazard ratio (HR) 1.80, 95% confidence interval 1.21–2.68]. Incidence diagnoses of AN, obsessive compulsive disorder, and anxiety disorder were also associated with Influenza vaccinations during the prior 3, 6, and 12 months. They reported that several other associations were also significant with HRs greater than 1.40 (hepatitis A with OCD and AN; hepatitis B with AN; and meningitis with AN and chronic tic disorder).Regarding risk of autism with exposure to vaccines, Young et al. (2008) examined the available data in the Vaccine Adverse Events Reporting System and found and association of exposure to Thimerosal-containing vaccines with “[c]onsistent significantly increased rate ratios were observed for autism, autism spectrum disorders, tics, attention deficit disorder and emotional disturbances with Hg (mercury) exposure from TCVs (thimerosal-containing vaccines).” Others have found increased risk, noting a potential additional factor (exposure to acetaminophen, indicative of high fever. Schultz et al. (2008), for example, found an increased risk of autism in a survey study of parents following MMR vaccination and acetaminophen use. In 2010, Shoffner et al., (2010) found that 71% of kids with regressive autism had an episode of fever > 101°F In 33% of these cases, the fever occurred right after vaccination – and none showed regression unless fever had occurred. Zerbo, et al. determined that first-trimester influenza vaccine was associated with an increased risk of Autism Spectrum Disorder (ASD) (adjusted HR 1.20)23.” This was their result before adjusting for risk factors as competing hypotheses, a common methodological flaw in past studies. Receipt of the pH1N1 vaccine two years in a row has been associated with a two-fold increased risk in spontaneous abortion within 28 days of receiving the vaccine (Donahue et al., 2017).

“The authors suggest that the studies that has (sic) created the current scientific consensus are not independent:
‘Our results give agency to calls for research conducted by individuals who are independent of any funding sources related to the vaccine industry.’ p.1.Thomas gains obvious economic benefits from the results, which are in line with the recommendations of his book that was published a few years earlier and that can arguably also increase patient flow to the private clinic he is leading and from where the research data are exclusively collected from.”

To the contrary, Thomas’s clinic has suffered greatly from the resulting emergency suspension of his license by the Oregon Medical Board. The economics of honoring informed consent will soon be addressed in an upcoming publication that makes it totally clear that honoring parents desires not to follow the CDC vaccine schedule is economically devastating to a pediatric practice. In reality it requires incredible ethics to stand for parents rights when the option selected by most Pediatricians is to discharge those families who do not follow the CDC vaccine schedule and just keep the comparatively lucrative vaccinating families. Dr. Thomas has lost over $1 million a year just in administrative fees that he would have been paid had his patients all followed the CDC vaccine schedule.

Lyons-Weiler (Ph.D. in ecology) is CEO of the Institute for Pure and Applied Knowledge (IPAK), a nonprofit which have (SIC) funded the study. The funding of IPAK benefits from the results, as it is based on donations from those that agree with the vaccine critical strategy of IPAK. Moreover, IPAK is asking donations for Phase 2 of their vaccine study, using the published IJERPH article as a reference for the Phase 1.

Dr. Lyons-Weiler’s credentials are: BA in Biology, MS in Zoology, PhD in Ecology, Evolution and Conservation Biology; AP Sloan/DOE Fellow in Computational Molecular Biology. He entered biomedical research in the year 2000 and has an extensive publication record in biomedical research. His contribution on each publication as author required full engagement in study design and most often data analysis and interpretation – which requires a comprehension of the biological and clinical implications of variation in each study. All of the various research studies funded using public donations to IPAK are independent of and have no direct involvement, oversight or influence of any of the donors. This is in stark contrast to the vaccine studies conducted by other entities, including the US Centers for Disease Control, which is partly funded via pharmaceutical and vaccine manufacturers via the CDC Foundation. Vaccine safety studies are also usually conducted directly by vaccine manufacturers leading to short-term randomized clinical trials. Long-term vaccine safety is assessed via post-licensure retrospective studies conducted following licensure. Our study represents an independent post-market surveillance study from a single practice. We cautioned against making generalizations beyond the study population, unlike other vaccine safety studies which routinely exclude, for example, individuals with prior evidence of autoimmunity (as we have recently witnessed in COVID-19 studies) or which suffer from over-adjustment bias for variables that may actually serve well as predictors of individuals or families who might have better overall health outcomes without exposure to some or all vaccines.

Industry-sponsored research affects the outcome of research that then determines public health, which in turn determines the success of the pediatric vaccine market, estimated annually to exceed $35 billion (Li, 2020). Pharmaceutical industry direct-to-consumer marketing in the US enforces specific permitted coverage by mainstream media, biasing the public’s perception of vaccine risk and benefits. At the same time, the US population has high rates of chronic illnesses that have no other explanation. Custody battles across the country have pitted parents of children against each over the question of whether autoimmune conditions might be a risk factor. There is much at stake, and objective science is needed. It is time for a new era in vaccine safety science that moves beyond the goal of indemnifying vaccines and addresses the issues of vaccine risk head-on, with objectivity, as we have done in our study.

Neither Dr. Lyons-Weiler nor Dr. Thomas has affiliation with the vaccine industry. Dr. Lyons-Weiler has exited the National Vaccine Injury Compensation Program after learning or discovering anomalies consistent with questionable legal practices by participants and employees of the program, including the selective use of only part of testimony offered by experts; use of precedent from other cases dismissing new scientific research aluminum as a potential harm to infant and child health, when the program participants are not allow to cite other case ruling as precedent, and, most egregiously, the use of conditional compensation offered as leverage in return for testimony that would favor the defendant. Dr. Lyons-Weiler, therefore, has no conflict of interest with respect to involvement in the NVICP.

We are withholding further comment on the spurious and contrived allegations of the medical board against Dr. Thomas pending the resolution of their proceedings the outcome of other options available to us in Dr. Thomas’ defense.


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