The ACIP Case Gets Stranger

A troubling pattern emerges from the court record

By: Dr's Robert W. Malone and Jill Glasspool Malone

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Yesterday’s Court Hearing

Yesterday, October 6, the U.S. Court of Appeals for the First Circuit heard oral argument in American Academy of Pediatrics v. Kennedy. What was striking was how little of the forty-five-minute hearing was actually about vaccine science. The three judges kept returning instead to basic questions about standing, statutory authority, final agency action, and the extraordinary remedy imposed by U.S. District Judge Brian Murphy. Chief Judge David Barron, an Obama appointee, was particularly persistent. He asked AAP attorney Andrew Pincus to begin with what he called “the narrowest part of the case”: Murphy’s order suspending the thirteen ACIP appointments. Barron wanted to know what statutory authority permitted Murphy to do that and what injury to AAP required such a remedy. When Pincus argued that allowing an unlawfully constituted ACIP to meet would make no sense, Barron cut through the abstraction with six words: “Well, it may not make any sense, but who’s it hurt?” That is the standing problem in plain English. Federal courts do not exist to stop government conduct simply because a private organization objects to it. A plaintiff must show an actual injury caused by the action being challenged, and the court’s remedy must redress that injury [Transcript of Oral Argument, American Academy of Pediatrics v. Kennedy].

Judge William Kayatta Jr., also an Obama appointee, attacked the standing problem from another direction. He asked Pincus to imagine that ACIP met the next day with all thirteen of Kennedy’s stayed members and adopted exactly the recommendation AAP wanted. Would AAP still have been injured by the alleged FACA violation? Pincus said yes, because the committee itself would remain improperly balanced. That answer exposes how expansive AAP’s theory really is. The claimed injury is not necessarily an adverse vaccine recommendation. Under AAP’s theory, the organization can be injured by the composition and existence of the advisory committee itself, even if that committee produces precisely the policy AAP favors. Kayatta also pressed both sides on the causal chain between an ACIP recommendation and subsequent government action, including whether a recommendation has legal consequences before adoption by the CDC Director. AAP identified the Vaccines for Children program as a possible exception, but the broader question remained: is AAP injured by who sits in the room, or by what government officials ultimately do with the recommendations that come out of that room? [Transcript, 26:43–30:41.]

Judge Joshua Dunlap, the Trump appointee on the panel, concentrated on another basic requirement of Administrative Procedure Act litigation: what exactly was the “final agency action” that Murphy was reviewing when he suspended the appointments? AAP offered two answers. It argued that Kennedy had effectively announced and implemented a new policy for reshaping ACIP, and alternatively that the composition of the committee itself constituted final agency action. Dunlap also questioned whether Murphy had really confined himself to judging the overall balance of ACIP or had instead examined individual members and made judgments about their qualifications. But perhaps the most revealing exchange came between Barron and Pincus over the legal authority for Murphy’s remedy. Section 705 of the APA allows a court to “postpone the effective date” of agency action. These appointments, however, had already taken effect. Barron stated the problem directly: “There already was an appointment. There’s nothing to postpone. So how could it be relying on 705?” When Barron later asked Pincus what authority actually supported Murphy’s order, AAP’s own lawyer conceded that §705 was “a little hard” for precisely that reason and suggested the authority might instead come from §706 or ordinary preliminary-injunction powers. Barron then pointed out the underlying problem: Murphy’s order itself does not clearly identify which statutory authority he was using to suspend the appointments. [Transcript, 7:31–8:46; 14:43–17:56.]

There is a larger Supreme Court precedent hanging over all of this. In June 2025, the Supreme Court decided Trump v. CASA, a 6–3 decision restricting the power of individual federal district judges to issue universal injunctions that extend relief far beyond the plaintiffs actually before them. The central principle is straightforward: a federal court’s remedy generally should go no further than necessary to provide complete relief to the parties who established standing to sue.

That matters enormously here. Murphy did not merely protect AAP and the other plaintiffs from particular vaccine decisions they challenged. He suspended the appointments of thirteen members of a federal advisory committee and effectively prevented that committee from functioning for anyone, anywhere. DOJ therefore argued on appeal that Murphy cannot escape CASA simply by calling what he did a statutory “stay” rather than an injunction. The Supreme Court left unresolved an important question about the separate statutory remedies available under the APA, so CASA does not automatically decide this case. But it puts the scope of Murphy’s remedy squarely in question: once the vaccine actions allegedly injuring AAP had themselves been stayed, what additional injury to these plaintiffs required a district judge to disable ACIP itself?

What was surprising yesterday was that the judges barely needed to reach CASA. DOJ devoted considerable attention to it in the briefs, but the Supreme Court’s universal-injunction ruling was not a major subject of oral argument. Instead, the panel found more elementary problems with Murphy’s order before ever reaching that larger question.

• What injury did AAP suffer merely because these thirteen people were appointed?

• What final agency action gave Murphy authority under the APA to review those appointments?

• What statutory provision allowed him to suspend appointments that had already taken effect?

• And why was disabling the committee itself necessary to redress whatever injury AAP claimed?

Chief Judge Barron eventually suggested that the First Circuit might not need to resolve the larger standing or FACA questions at all. It could conclude simply that Murphy failed to explain what statutory authority supported this extraordinary remedy and what specific harm the remedy was supposed to address. [Transcript, 34:10–35:07.]
That may be the most remarkable takeaway from yesterday’s hearing. CASA raises a serious question about whether Murphy’s remedy went far beyond the plaintiffs’ standing before him. But the First Circuit may never need to get that far, because Murphy’s order may fail on the more basic question of what gave him the authority to suspend the thirteen appointments in the first place.

The Original Case and Why It Matters

To understand why yesterday’s questions matter, it helps to remember just how far Judge Murphy went in the original case. The American Academy of Pediatrics is a private nonprofit professional association. ACIP does not regulate AAP, appoint its officers or direct its members’ medical practices. ACIP is an advisory committee within the federal government. Yet Murphy accepted AAP’s argument that it had sufficient interest in ACIP’s work to challenge not merely a particular recommendation, but the composition of the committee itself under the Federal Advisory Committee Act. FACA requires advisory committees to be “fairly balanced in terms of the points of view represented and the functions to be performed,” but Congress did not supply a formula for determining what “fairly balanced” means. There is no statutory allocation of seats among vaccinologists, epidemiologists, pediatricians, infectious-disease specialists, immunologists, statisticians or dissenting scientific viewpoints. Nevertheless, Murphy moved from reviewing whether HHS had complied with the law to deciding whether the people Kennedy appointed collectively represented an acceptable scientific balance.

That distinction is critical. The appointment of ACIP members belongs to the Executive Branch, with the HHS Secretary responsible for selecting the committee’s voting members. Murphy did not simply identify a procedural violation and send the matter back to HHS. He examined the qualifications of individual members, judged the expertise represented on the committee, concluded that Kennedy’s ACIP was not fairly balanced, and then suspended all thirteen appointments. The result was straightforward: ACIP could not meet. Nothing in FACA transfers the appointment power from the Executive Branch to the judiciary or provides a federal district judge with a formula for deciding which combination of scientists constitutes the proper balance. Judicial review of whether the Executive followed the law is one thing. A judge substituting his judgment about the acceptable composition of a federal scientific advisory committee for that of the official legally charged with appointing it is something considerably different.

There is also an important piece of history that makes the treatment of Kennedy’s ACIP difficult to view as some unprecedented problem created by this administration. Incoming administrations have removed and replaced members of FACA advisory committees before. In 2021, Biden EPA Administrator Michael Regan removed the existing members of two major federal scientific advisory committees, the Science Advisory Board and the Clean Air Scientific Advisory Committee, and reconstituted them. Former members sued, alleging among other things that the newly constituted committees violated FACA’s requirement that advisory committees be “fairly balanced.” The challenge failed. When Trump returned to office in 2025, his administration again removed Biden-era members of EPA scientific advisory committees and began rebuilding them. The circumstances and administrative records were not identical to ACIP, but the basic exercise of executive authority was hardly novel: new administrations have reconstituted inherited scientific advisory committees before, and courts have confronted FACA challenges arising from those decisions.

That history makes Murphy’s remedy more consequential, not less. Kennedy did not invent the practice of replacing the membership of a federal advisory committee. What is unusual here is that a private professional association successfully persuaded a district judge to evaluate the scientific balance of the replacement committee, examine the qualifications of its individual members, and then suspend every appointment so the committee could no longer function. If that becomes an accepted application of FACA, the implications extend far beyond vaccines or ACIP. Every incoming administration that changes the composition of an advisory committee potentially invites private organizations that dislike the new membership to litigate what “fairly balanced” should mean and ask a federal judge to referee the scientific composition of the committee. Congress required balance. It did not appoint federal judges to choose the balance.

The Defense That Wasn’t Made

Which brings us to the strangest part of this case: the government’s own defense of ACIP. AAP put the qualifications and scientific balance of Kennedy’s appointees directly at issue. If HHS intended to defend that committee on the merits, the obvious response was to build a factual record showing exactly who these thirteen people were, what expertise each brought to the table, and why their combined backgrounds satisfied FACA’s requirement of a “fairly balanced” committee. Yet we have found no evidence that DOJ submitted the complete CVs of the thirteen members or constructed a comprehensive evidentiary defense of their collective qualifications. Instead, the government concentrated heavily on the legal argument that the Secretary had discretion over appointments and that courts should not be second-guessing those choices. Once Murphy rejected that argument and began judging the qualifications of the members himself, the factual record needed to prove him wrong appears not to have been there.

Robert Malone’s case makes the problem concrete. CDC itself publicly described him as a “Vaccinologist, Scientist, Biochemist, Contributor to mRNA Vaccine Technology.” Yet neither HHS nor DOJ asked him for his complete CV for submission in this litigation (CV attached here). Murphy subsequently reduced his relevant vaccine expertise largely to his early work on mRNA technology and discounted that experience because it occurred decades ago. A complete CV would have documented the work that followed, including subsequent vaccine development, clinical research, medical countermeasures and biodefense. Whether Murphy ultimately would have found that record persuasive is unknowable. What matters is that the government apparently never put the complete record in front of him. And now, after Murphy used the record before him to make factual judgments about the qualifications and balance of ACIP, DOJ has told the First Circuit something equally remarkable: “we’re not challenging any factual findings on appeal.”

The omissions do not stop there. The government did not make the previous reconstitution of major scientific FACA committees a centerpiece of its defense, even though the Biden administration had removed and replaced members of EPA scientific advisory committees and successfully defended the resulting litigation. DOJ anticipated that Murphy might interfere with ACIP’s membership, because it proposed as alternative relief that he stay only enough appointments to address whatever imbalance he believed existed while leaving the committee capable of functioning. Yet despite anticipating that possibility, the government apparently did not build the strongest factual record defending the appointments themselves. Murphy rejected the alternative and suspended all thirteen.

What happened next is harder still to understand. After Murphy disabled ACIP, proposed intervenors tried to obtain a stay of his preliminary injunction. The federal government apparently did not seek its own stay of the injunction that was preventing its advisory committee from functioning. DOJ instead sought to stay the underlying district-court proceedings while pursuing its appeal. Later, the government asked for expedited appellate consideration on the grounds that ACIP urgently needed to get back to work. Now, before the First Circuit, DOJ has deliberately confined its appeal largely to Murphy’s treatment of the appointments, while leaving other portions of his vaccine-policy relief unchallenged. The contradiction was obvious enough that Chief Judge Barron asked government counsel Matthew Zorn directly: “How come you’re not challenging the rest of the order then?”

Put the pieces together. No complete CVs. No comprehensive defense of the committee’s collective qualifications. No major reliance on the obvious historical precedent of other administrations reconstituting scientific FACA committees. No government motion that we can find seeking an immediate stay of the order disabling ACIP. An appeal that expressly declines to challenge Murphy’s factual findings. And now a deliberately narrow request for relief that would restore the Secretary’s ability to constitute ACIP while leaving significant portions of Murphy’s underlying vaccine rulings alone.

Any one of those decisions can be explained as litigation strategy. Lawyers make tactical choices. They narrow appeals, abandon arguments, preserve others for remand, and sometimes decide that the quickest route to a favorable judgment is not the broadest one. But taken together, these choices are much harder to explain.

The Hypothesis

There is one fact we have deliberately kept separate from the legal analysis until now. Before this litigation played out, we had been told that senior administration officials did not want ACIP meeting again until after the midterm elections because of the political problems its decisions might create. We have no document showing that the White House or HHS instructed DOJ to lose this lawsuit. We have no email directing government lawyers to mount a weak defense, and no evidence establishing that DOJ attorneys deliberately withheld arguments in order to produce an adverse ruling. Those are serious allegations, and the evidence does not presently establish them.

What we do know firsthand is that keeping ACIP sidelined until after the midterms had been communicated to us as an administration objective. And to that point, the late-winter ACIP meeting on the vaccine-injured was canceled because of the political ramifications, although the government never publicly admitted as much.

So what happens when that fact is placed alongside the litigation record? AAP attacked the qualifications and balance of the new ACIP, but the government apparently failed to build the strongest factual record defending those qualifications. It did not submit the members' CVs; it did not even ask for them for the record. It did not make the previous reconstitution of scientific FACA committees a centerpiece of its defense. Murphy then suspended all thirteen appointments, accomplishing precisely what we had been told some within the administration wanted: ACIP stopped meeting.

Other parties tried to stay Murphy’s injunction, while the government apparently did not seek its own emergency stay restoring the committee. DOJ instead sought to freeze the underlying litigation. It later argued that ACIP urgently needed to get back to work, yet it now declines to challenge Murphy’s factual findings and has deliberately narrowed its appeal. None of this proves intent. But viewed through the lens of what we had already been told, a series of otherwise puzzling litigation choices begins to look considerably less random.

There is an even more uncomfortable possibility. Was sidelining ACIP the only objective? Or were some within the administration also content to let Judge Murphy’s stays of particular vaccine decisions remain in place? Chief Judge Barron put his finger directly on this problem when he asked DOJ at oral argument: “How come you’re not challenging the rest of the order then?” The government’s answer confirmed that it is not seeking to undo significant portions of Murphy’s other relief in this appeal. That does not prove that HHS wanted those vaccine decisions stayed. But it raises a question that HHS and DOJ should be able to answer plainly: which parts of Murphy’s order does the administration actually oppose, and which parts is it willing to leave in place?

This matters because there are two very different stories here. The public story is that the government lost an important case, Judge Murphy disabled ACIP, and DOJ is now fighting to restore the committee. The alternative hypothesis is more troubling: the court delivered an outcome that some within the administration already wanted, and the government’s litigation strategy was never designed to reverse all of it. That hypothesis remains unproven. But after reconstructing the original defense, following the government’s decisions after Murphy’s ruling, and listening carefully to yesterday’s oral argument, it can no longer simply be dismissed as implausible.

Perhaps there is an innocent explanation for all of this. If there is, HHS and DOJ should provide it. Why were the full qualifications of the ACIP members not put before the court? Why was the historical precedent for reconstituting FACA committees not aggressively developed? Why did the government apparently fail to seek immediate relief from the order that disabled ACIP? Why is DOJ leaving Murphy’s factual findings unchallenged? And why, when Chief Judge Barron asked why the government was not challenging the rest of Murphy’s order, was the answer essentially that it had chosen not to? These are no longer questions about vaccine policy. They are questions about what the government was actually trying to accomplish in this litigation.

After reading the briefs, reconstructing the original defense, and listening to the First Circuit argument, the government’s litigation strategy does not look like the strategy of an administration determined to defend every aspect of its own ACIP and overturn every adverse vaccine ruling.

It looks like something considerably narrower. The question is why.

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