by James Lyons-Weiler, PhD, Popular Rationalism, ©2025
(Mar. 30, 2025) — Dr. Peter Marks, former director of the FDA’s Center for Biologics Evaluation and Research (CBER), resigned on March 28, 2025, with an overly dramatic letter (see below) citing conflicts with Health and Human Services Secretary Robert F. Kennedy Jr. over vaccine misinformation. His tenure was marked by significant controversies, particularly concerning the approval and oversight of COVID-19 diagnostics and vaccines.
The PCR Catastrophe: False Positives, Fear, and Fatal Protocols
Under Dr. Marks’ leadership, the FDA authorized the widespread use of RT-PCR tests for COVID-19 diagnosis. Concerns arose regarding their specificity and the potential for false-positive results, especially in low-prevalence settings. Marks oversaw the deployment of high-cycle RT-PCR testing without adequate controls or interpretive guidance.
To this day, the public largely confuses False Positive Rate (FPR) with False Discovery Rate (FDR)—a distinction crucial to understanding the magnitude of harm. While the FPR is the proportion of truly negative tested samples that test positive (usually low), the FDR is the proportion of positive results that are false. In low-prevalence settings, even a highly specific test with low FPR can yield an FDR exceeding 50%, meaning that most positive test results are wrong.
And that’s exactly what happened.
By spring 2020, when COVID-19 prevalence was low in most of the country, mass PCR testing at 35–40 cycle thresholds (Ct) created an illusion of widespread infection. The consequence? Entire hospitals locked down, patients were isolated unnecessarily, and fear permeated every layer of society. People died alone. Cancer screenings were missed. Suicides climbed. Lockdowns shattered lives and economies—fueled by a case count inflated by PCR artifacts.
There has been no accountability for the FDA’s failure to issue clear guidance on Ct thresholds, viral culture correlation, or proper confirmatory testing. The FDA continued to green-light high-Ct PCR tests under Emergency Use Authorization (EUA), even after peer-reviewed studies showed the test was detecting non-viable viral fragments long after infectiousness ended. At no point did the FDA publicly quantify the FDR in specific population contexts or mandate transparent Ct reporting.
Furthermore, FDA never issued warnings to doctors implementing an untested, unproven protocol that restricted options for patients seeking to reduce the severity of their symptoms. Patients were told to go home and stay home for ten days, and then seek care if they were sick enough to required emergent care. Where were the randomized clinical trials backing that decision? Where was Marks’ outrage when promising repurposed drugs and over-the-counter treatments were being bashed, including by his own agency? Remember Ivermectin? We do.
Fauci’s Henry Ford Hospital Study Debacle
When Dr. Anthony Fauci publicly mischaracterized the results of a July 2020 observational study from Henry Ford Hospital—claiming it showed a “clear-cut, significant” one-quarter drop in COVID-19 mortality—Dr. Peter Marks said nothing. The study, published in the International Journal of Infectious Diseases, examined the use of hydroxychloroquine in hospitalized patients but lacked randomization and failed to control for confounding variables such as timing, comorbidities, and concurrent steroid use. The authors themselves cautioned against drawing firm conclusions, noting that the study design was retrospective and observational.
Yet Fauci, speaking as the face of U.S. public health policy, selectively amplified the results to suggest hydroxychloroquine was definitively ineffective—while quietly ignoring other studies that showed benefit when used early and in outpatient settings. Dr. Marks, as head of the FDA’s biologics division, had the scientific and ethical responsibility to step in and clarify the limitations of the evidence, especially given the politicization and polarization surrounding treatment protocols.
Read the rest here.
There’s no discussion of false negatives. False negatives (Type II error) are worse and for obvious reasons. Risk management should focus on the acceptable frequency of false negatives, i.e., a percentage of the time something is measured judged not present when, in fact, it is.
We were all glued to the news in 2020 and 2021. I don’t recall a single instance of a discussion of false negatives.
There are several drawbacks, however, to false and not harmless positives. One is indiscriminate application of curatives. Another is related: how far can the money go when $ is spent on those not sick or infected? Third: unnecessary patient distress. Fourth: poor treatment outcome statistics, as snake oil IS effective after all!
It is no wonder the resistance movement found a home in an unanticipated relative position: against the medical and scientific establishment. Rightly so, as the contrarians were right and the Karens and Marks were not.
Another awesome, informative, richly detailed, explanation of the failings of the FDA and the CDC. There is an additional story to be told about the choice of PCR primers. It is at least as damning.