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Joe Rogan

#2534 - Annie Jacobsen

Friday, 31 July 2026 · 4 min read · Listen to the episode ↗

Annie Jacobsen joins the podcast to discuss her research into biological and nuclear warfare, gain of function research, and the government's continuity of operations planning. She argues that gain of function research is effectively biological weapons engineering, that virtually every expert she interviewed believes COVID originated from a lab leak, and that Fauci's private emails contradict both his public statements and sworn congressional testimony.

Annie Jacobsen's book uses a Pneumonic Plague scenario because plague sits at the top of the government's tier one select agent list of dangerous pathogens. Her first six books covered historical subjects, but her nuclear and biological war books are written in the future tense as scenarios modeled on Pentagon war games, with access granted to officials who actually run those exercises.

Jacobsen describes gain of function research as a euphemism for biological weapons engineering, a characterization offered by most subject matter experts she interviewed. Much of that research is funded by the military, and despite being publicly justified as a path to developing cures, no cures have resulted. Every expert she spoke to encouraged her to state that COVID's origin was almost certainly a lab leak. Fauci consulted roughly a dozen scientists on the question, ten of whom leaned toward a lab leak and only two toward natural origin, yet he preferred the natural spillover explanation and the group worked to shift the public narrative accordingly. Jacobsen says his emails contradict both his public statements and his sworn congressional testimony. He has since taken the fifth during congressional testimony and holds a blanket pardon covering ten years. The CIA, ODNI, and DOD have not brought their Wuhan lab information into the public domain.

Jacobsen argues biological war may be grimmer than nuclear war because biological weapons are living munitions that self-replicate and carry incubation periods. Defense Department documents she reviewed identify fear of infection, not the pathogen itself, as the primary driver of anarchy and insurrection. In her Pneumonic Plague scenario the chaos point arrives at day six, at which stage the Insurrection Act is declared, Posse Comitatus is lifted, and the military takes over civilian governance. A declassified Defense Department document ranks biological weapons as the greatest overall threat on the WMD spectrum, above nuclear weapons in terms of broad danger. No nation has ever deployed biological weapons on a wide scale, and the 1972 Biological Weapons Convention has no enforcement mechanism, unlike nuclear treaties which allow facility inspections and create back-channel dialogue that subject matter experts identify as their most important function.

Before September 11 the United States had two BSL4 labs. Dick Cheney was personally terrified of bioweapons and spearheaded a large biological military industrial complex after the attacks, causing the number of BSL4 labs to grow from two to fifteen. There are now 110 BSL4 labs worldwide, including in countries currently at war, along with 1,500 BSL3 labs in the United States and 3,500 globally, with 90 percent of those global BSL3 labs operating under no safety guidelines. BSL3 labs can work with plague, anthrax, and hantavirus. Subject matter experts Jacobsen interviewed expressed serious concern that AI-enabled biotechnology has lowered the barrier to bioweapon development so much that a high school student with limited biology knowledge could now make one at home. Six AI CEOs are in discussion about pulling the plug on AI-enabled bio threats but must all agree before acting, meaning private company executives currently hold more decision-making power over certain technologies than the Department of Defense.

Aafia Siddiqui was an MIT-trained biologist related by marriage to Khalid Sheikh Mohammed who led an al-Qaeda biological weapons program. Her handbag contained plans to engineer a genetically modified pathogen combining rabies with chickenpox to produce an airborne variant. Rabies carries a 100 percent fatality rate without countermeasures. David Relman, a presidential advisor on biodefense, confirmed the plans were found and caused serious concern. How far she progressed on the airborne rabies pathogen is classified. Siddiqui also had a separate project aimed at modifying America's poultry supply to allow chickens to pass salmonella to humans more easily.

The government maintains a classified continuity structure called COG CON with four readiness levels. At COG CON 1, pre-designated officials deploy to underground facilities around the United States. Raven Rock, the Pentagon's alternate underground command center roughly 51 miles from DC, has at least seven levels. Jacobsen notes Russia would target it with approximately five nuclear bombs, that nuclear fires alone would incinerate everyone inside, and that air supplies would be contaminated by fallout, making the bunkers effectively useless against a serious nuclear strike. The FEMA director told her there is no population protection planning after a nuclear strike because everyone would be dead. The Pentagon has issued 1.7 million gas masks to personnel tasked with protecting critical infrastructure, not the general population, and Colonel Tom Earhart, who ran catastrophic war games under Andy Marshall's Office of Net Assessment, concluded that in a catastrophic biological incident the realistic goal is only to mitigate extermination.

Jacobsen used ChatGPT to locate the classified position of the strategic national stockpile nearest to her in Los Angeles by surfacing it from an earthquake emergency manual where a bureaucrat had accidentally listed the location. She confirmed the site physically and reported the finding to colleagues connected to Sam Altman, who wanted to discuss it, after which the information was removed from the system's accessible outputs. Altman did not know his product could surface classified information until she told him. Her broader concern is that bad actors outside those corrective feedback loops have access to the same systems and face no equivalent accountability.

This summary was generated from the episode transcript and can contain mistakes.