July 12, 2022 | Jerry Bergman

Thymus Cells Train in Boot Camp

New findings about the thymus gland
reveal how it learns friend from foe


by Jerry Bergman, PhD

I have taught anatomy and physiology (A&P) at a medical school and other colleges for over 20 years. Most areas of A&P are straightforward and easy to teach. One area is not—the human immune system. It is so complex and convoluted that it tends to be confusing to students and, sometimes, even to the professor as well. It reminds me of a maze where you enter at one end and exit somewhere along the one path, except that with the immune system, all paths lead to an exit somewhere.

The main function of the immune system is simple: to detect a foe and kill it, or to discern a friend and ignore it. This is vital because if the immune system does not accurately discern a foe and kill it, the person will often get very sick and eventually die. Likewise, if it does not accurately discern self as friend, then the person may eventually die of an autoimmune disorder or, at the least, may suffer for years.

The Immune System is Irreducibly Complex

David Vetter, the “Bubble Boy,” in his sterile enclosure. From Wikimedia Commons.

The immune system is an excellent example of an irreducibly complex system. Without a working immune system, no eukaryotic life form can survive for very long. And the immune system must function at a high level of perfection, or disease and eventually death will result.

Persons born without an immune system, such as the famous “Bubble Boy,” David Vetter, illustrate this. David was born with Severe Combined Immune Deficiency (SCID) and had to live in a sterile germ-free environment, called a bubble.

Everything brought into the bubble had to be sterile: the water, the food, and even the air. In 1984, four months after receiving a bone marrow transplant at age 12, David died from lymphoma. Today, children with SCID, if diagnosed early, receive bone marrow transplants to allow them to develop a normal immune system. Most of them lead productive, healthy lives. David was reported as being physically and psychologically advanced for his age, developing an intelligence above average and a maturity beyond his years.

In a Harvard Medical School press release on June 27, reporter Ekaterina Pesheva begins with praise for the immune system.

The human immune system is a nearly perfect defense mechanism. It protects the body from disease-causing bacteria, viruses, and other pathogens. It detects nascent tumors and eradicates them. It cleans up cellular debris at the site of injury or infection. To perform its myriad functions, the immune system must, above all, differentiate between self and non-self—a remarkable selective ability that allows it to detect and disable harmful agents while sparing the body’s own tissues.[1]

It is ironic that she would say this now, given the fact that evolutionists thought the opposite for a century. The primary organ required to do this task, the thymus gland, was thought to be a vestigial organ without function. I included a chapter about it in my book on vestigial organs where I wrote the following in Chapter 17:

The thymus gland is an example of an important organ long judged not only vestigial, but harmful if it became enlarged.  Maisel reported that for generations, physicians regarded it “as a useless, vestigial organ which has lost its original purpose if indeed it ever had one.”[2]  Clayton noted an oversized thymus was once routinely irradiated in order to shrink it.[3] It was later found from follow-up studies that instead of helping the patient, such radiation treatment resulted in abnormal growth and a higher level of infectious diseases persisting longer than normally.[4]

The research I noted in Maisel’s 1966 article quoted above spelled the beginning of the end of the claim that the thymus gland was a vestigial relic of evolution. Immunologist Daniel Michelson correctly observed, “Until the mid-1900s, the thymus provoked little scientific interest because it was deemed vestigial.”[5] That attitude strongly discouraged research. Now, Michelson is part of a Harvard team that has brought more recognition to the importance of this highly functional and important organ.

Description of the Thymus

The Thymus Gland. From Wikimedia Commons.

The thymus is a small pinkish-gray organ located below the larynx in-between the lungs and behind the mediastinum in the chest.[6] The thymus lympho-epithelial organ consists of two pyramidal-shaped lobes connected by an isthmus. A capsule called the septae (septa) as shown in the figure below, from which trabeculae extend inward, surrounds it. This structure divides it into a large number of lobules, each of which contains the functional units called follicles.

The follicles are the workhorse of the thymus. The details of its function were not understood for decades, but the new research at Harvard Medical School has greatly clarified how it works.[7]

Thymus Boot Camp

In the 1960s, it was proven that the thymus gland is the organ where T cells are trained to distinguish “friend” from “foe.” T cells were named after the thymus gland in which they mature. Now we understand that the thymus educates nascent immune cells by exposing them to proteins made by thymus cells that mimic various tissues, such as muscle, intestine, and others. This includes all of the 200 basic tissue types used throughout the body.

The thymus showing the two lobes. From Wikimedia Commons.

Diane Mathis (the leader of the research reviewed below) demonstrated how this works like a boot camp. By assuming different cell identities, these specialized thymus cells train the T cells about the “self proteins” they will encounter when they leave the thymus gland.

In the mid-1800s, long before science knew what the thymus does—or even that the adaptive immune system existed—biologists noticed cells in the thymus that looked to be skin cells and other cells. They seemed way out of place. These cells were called mimetic cells because they looked like they came from muscle, intestine, skin, or other body cells. Scientists at the time were puzzled. Why were these foreign cells in the thymus, and how did they get there? It turns out that the thymus produces them as part of its teaching role to instruct the immune cells what cells are “self” so they will ignore them.

The thymus does not need to produce the entire cell; it only needs to produce the part that the immune system uses to determine a cell type, called the epitope. The epitope is the part of an antigen molecule to which an antibody attaches. The antibody-epitope bind is what triggers the immune response required to destroy an invading bacteria cell or organism. The thymus does not need to produce an entire skin epidermis cell, just the protein identification tag.

The antibody antigen binding site called the epitope. From Wikimedia Commons

The mimetic cells effectively adopt the identities of approximately 200 types of tissues, including skin, lung, liver, and intestine. These mimetic cells interact with immature T cells in the thymus. An auto-reaction results which causes the clone line to self-destruct or become repurposed into other T cell types that restrain other immune cells from attacking. As Pesheva explains,

the thymus gland—the organ where T cells are born and trained—educates nascent immune cells by exposing them to proteins made by thymus cells that mimic various tissues throughout the body. Specifically, the research demonstrates that by assuming different identities, these specialized thymus cells preview for the maturing T cells self-proteins they would encounter once they leave their native thymus gland.[8]

Pesheva summarized the importance of the once “useless” thymus organ—a central part of the immune system—as follows:

Our immune system is super-powerful. It can kill any cell in our body, it can control any pathogen we encounter, but with that power comes great responsibility… If that power is left unchecked, it can be lethal. In some autoimmune diseases, it is lethal… the immune system’s elite forces are charged with multiple functions. They recognize and eliminate pathogens and cancer cells; they form long-term memory of viruses and bacteria encountered in the past; they regulate inflammation and tamp down hyperactive immunity.[9]

Defects in this epitope protein can lead to a serious immune syndrome characterized by the development of multiple types of autoimmune disorders. This may open up a new understanding of why certain types of autoimmune diseases develop.


The thymus is another example of how the ‘vestigial organ’ idea impeded research. This idea was begun by Charles Darwin, who called these parts of the body ‘rudimentary organs.’ His notion of rudimentary organs was no small impediment to science. At one time fully 100 organs and structures were claimed to be vestigial; now, there are exactly zero on the list. All 100 were determined by scientific research to have a function.[10] In contrast to the vestigial organ dogma, research has been encouraged by the belief that the body was designed by God. A logical implication of that belief is that each part most likely has a purpose. Following that motivation, scientists would likely have discovered the functions of these organs far sooner.

Source paper: Diane Mathis, Daniel A. Michelson, Koji Hase of Keio University, Tsuneyasu Kaisho of Wakayama Medical University, and Christophe Benoist of HMS (Harvard Medical School). “Thymic epithelial cells co-opt lineage-defining transcription factors to eliminate autoreactive T cells.” Cell; https://www.cell.com/cell/fulltext/S0092-8674(22)00649-3, 16 June 2022.


[1] Pesheva, Ekaterina. Boot camp for the immune system: How immune cells learn to discern friend from foe. Harvard Medical School News & Research, 28 June 2022.

[2] Maisel, Albert. “The useless glands that guard our health.” Reader’s Digest, p. 229, November 1966.

[3] Clayton, John. “Vestigial Organs Continue to Diminish.” Focus on Truth 6(6):6-7, 1983.

[4] Bergman, Jerry. Useless Organs: The Rise and Fall of a Central Claim of Evolution. Bartlett Publishing: Tulsa, Oklahoma, 2019.

[5] Pesheva, 2022.

[6] Seeley, Rod R., Trent D. Stephens, and Philip Tate. Anatomy and Physiology. McGraw-Hill: Boston, MA, p. 778, 2003.

[7] Pesheva, 2022.

[8] Pesheva, 2022.

[9] Pesheva, 2022.

[10] Bergman, Jerry. 2019.

Dr. Jerry Bergman has taught biology, genetics, chemistry, biochemistry, anthropology, geology, and microbiology for over 40 years at several colleges and universities including Bowling Green State University, Medical College of Ohio where he was a research associate in experimental pathology, and The University of Toledo. He is a graduate of the Medical College of Ohio, Wayne State University in Detroit, the University of Toledo, and Bowling Green State University. He has over 1,300 publications in 12 languages and 40 books and monographs. His books and textbooks that include chapters that he authored are in over 1,500 college libraries in 27 countries. So far over 80,000 copies of the 40 books and monographs that he has authored or co-authored are in print. For more articles by Dr Bergman, see his Author Profile.

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