08–12/2023 Issue: What Has Been Going on in Microbial Instincts

A newsletter providing a short account of the articles published in the previous months.

Shin Jie Yong, MSc (Res)
Microbial Instincts


Hello everyone! It has been a while since I last sent a newsletter from Microbial Instincts, an independent publication about infectious diseases and vaccines. The last one was sent in August 2023.

Since then, I must admit I lost track. Other priorities started taking over, and I wasn’t seeing satisfactory growth in this publication from the newsletters I had been sending since June 2020. That said, I keep this publication close to my heart; after all, it was the first publication I created in February 2020. I can’t believe it has been over 4 years.

That said, it’s time for me to send out newsletters again, although they may not be monthly, but every 2–3 months or so, depending on the volume of articles Microbial Instincts publish. For August to December 2023, here is an overview of the articles (friend-linked) published in Microbial Instincts, which I hope you will find interesting.

Dr. René F. Najera

I recently invited Dr. René Najera, an epidemiologist at Johns Hopkins Bloomberg School of Public Health, to contribute to this publication. I’ve added several of his prior interesting articles into Microbial Instincts. Some of them include (1) Why the novel coronavirus causing the COVID-19 pandemic will never be eradicated, (2) The next pandemic pathogen will surprise us, but it won’t be a surprise, and (3) ChatGPT Gets a B+ in an Essay on Germ Theory From an Epidemiology Professor.

In the first article, Dr. Najera explains the key aspects of successful pathogen eradication based on historical examples of smallpox and rinderpest. One such aspect is the widespread public acceptance of vaccination. But because of the growing anti-vaccine movement, eradicating Covid-19 or other pathogens seems impossible.

The second article describes the potential microbial candidates with the potential to trigger the next pandemic. Dr. Najera puts his top choice on the influenza virus, but he also acknowledges tuberculosis and even the deliberate release of smallpox as a biological weapon as possible scenarios. But whatever pathogen it may be, Dr. Najera stressed that current public health is just not ready to face another pandemic.

In the third article, Dr. Najera shared his reluctance to assign take-home essays to his students due to the advent of ChatGPT technology. He did a little experiment and found that ChatGPT could produce an essay on germ theory that he graded as a B, which is actually not bad.

Dr. Najera graded an essay on germ theory written by ChatGPT.

Milton Kambarami

In “Why You Need Omicron XBB Booster to Protect Yourself from Fast-rising Omicron EG.5.1 (Eris),” Bioinformatician Milton Kambarami looked at the evolution profile of the latest Omicron subvariant at that time. He deduced that because of its close evolutionary distance to the parent XBB variant, the current XBB-based vaccine boosters will still be effective against the newer subvariants. Subsequent data supported his insights.

Milton also wrote 3 other insightful articles on Pirola, known as the most mutated Covid-19 variant: (1) As of now, omicron BA.2.86 isn’t on the verge of taking over the world; (2) Pirola (BA.2.86): The Silent Threat That Lurks Within Its Descendants, and (3) Pirola Covid Variant Has Evolved Again, Showing Enhanced Immune Escape.” The first one describes its emergence, while the latter two describe how Pirola has evolved further in immune evasiveness and how its descendants could pose a bigger threat.

Another two articles by Milton were (1) Exploring the 4 Menacing COVID-19 Variants of 2023 and (2) Why We Nickname COVID-19 Variants After Asteroids, Mythical Creatures, and Stars. I believe these titles are self-explanatory.

Gil Pires

Gil Pires, a biotech consultant, contributed two articles about tuberculosis: (1) Affordable Tuberculosis Drugs At Last, After Johnson & Johnson Loses Its Patent, and (2) Tuberculosis: An Old Enemy, A New Fight.

The former article describes the controversy surrounding Johnson & Johnson’s cunning attempt to extend the patent of its tuberculosis drug, which didn’t end well for the company. The latter details the disease process of tuberculosis, a disease as ancient as humankind itself yet which prevails to this day as a threat to public health.


I wrote four articles during this period across diverse topics in Covid-19 vaccines (When Someone Died Suddenly, What Could Be the Cause? Hint: It’s Not the Vaccine), long-Covid (The Problem with Long-COVID Research No One Talks About), gut microbiota (Why I Stopped Pursuing Gut Microbiota Research As An Academic), and multiple sclerosis (How a Single Study Proved the Cause of Multiple Sclerosis Is a Virus).

The first article touches on the contentious topic of sudden deaths among young adults, which have gained popularity thanks to anti-vaxxers wrongly attributing the cause to Covid-19 vaccines.

The second article describes how current long-Covid research falls into the common fallacy, post hoc, ergo propter hoc, Latin for “after this, therefore because of this.” But this doesn't mean the condition isn’t real; rather, it’s tricky to determine the precise cause of long-Covid.

The third article explains several reasons why the promise of gut microbiota being the holy grail of health has fallen short of expectations.

The fourth article describes a ground-breaking study that single-handedly and elegantly proves the Epstein-Barr virus (EBV) as the causative agent of multiple sclerosis, a type of neurodegenerative disorder.

Prevalence of fatigue and chronic fatigue before the pandemic. Many cases of chronic fatigue have no clear cause. If Covid-19 existed back then, chances are these people were believed to have long-Covid as well. But this doesn’t mean current cases of long-Covid are not real; it’s just that it’s tricky to attribute causation. Consequently, with unclear causation, designing and finding effective treatments may prove to be challenging.

Other authors

In “The pandemic is over but I still got Covid,” Peter Miller, a writer and winner of the $100,000 debate on Covid-19 origin, tells his story of catching Covid for the first time after 3.5 years. Contrary to popular belief that Covid is milder now, it didn’t feel mild at all to Peter. He then discussed how labeling the pandemic as over could do more harm than good at tackling the public health issues that Covid and long-Covid bring.

Dr. Agustín Muñoz-Sanz, an infectious disease specialist, describes how lice and humans have co-evolved over millenniums in “On Bedbugs and Lice.” As a result, studying lice epidemiology can infer interesting revelations about the history of humankind.

In “Three Common Viral Infections That Can Imitate, Trigger, or Worsen Systemic Lupus Erythematosus,” Stephanie Loo, a biotech graduate, writes a highly researched overview of how some everyday viruses are linked to lupus, a common autoimmune disease. But Stephanie highlights that current research in this area brings more questions than answers.

Joe Duncan, founder of Science of Sex, previously wrote “Keeping Up with COVID-19: A Closer Look at the Accuracy of Tests in 2023.” He discusses the varying accuracy of different COVID tests, sharing his experience using them and highlighting the underappreciated problem of false results.

Thank you for reading! Subscribe to Microbial Instincts here and support the contributing authors if you’d like. Feel free to reach out to me for any questions or feedback by email or commenting here.



Shin Jie Yong, MSc (Res)
Microbial Instincts

Named Standford's world top 1% scientists | Independent science writer and researcher | Medium boost program's nominator | Powerlifter with national records