What Is the Immune System?

This complex interaction of organs, cells, and microbes keeps us alive, though few of us understand it
By Conan Milner
Conan Milner
Conan Milner
Conan Milner is a health reporter for the Epoch Times. He graduated from Wayne State University with a Bachelor of Fine Arts and is a member of the American Herbalist Guild.
January 16, 2020 Updated: February 9, 2022

Remember learning the systems of the body? The skeletal system describes our inner architecture. The circulatory system shows our heart and blood vessels. The digestive system traces the path of our food as it travels from assimilation to elimination.

Each system provides a basic lesson in anatomy and function. Together they reveal the body’s multi-layered complexity.

But where is your immune system? What parts are involved? How do they connect and communicate?

These questions can be difficult to answer, because you can’t get a good understanding of the immune system from just one angle. It’s also a bit of an enigma. The immune system is a relatively recent discovery, but the concept may be as old as medicine itself.

In fact, modern medicine has just begun to verify ancient notions about how the body protects itself from disease.

When doctors and scientists discuss immunity today, they typically speak at the microscopic level. They talk about things like leukocytes, lymphocytes, T-cells, B-cells, and several other specialized immune cells that protect the body against microscopic threats like viruses and bacteria.

But what does the immune system look like at the macro level? If we define immunity as the body’s ability to protect us from microbial threats, the first line of defense is the skin. It’s the places where the skin is open—like our mouth and nose—where our body becomes more vulnerable to infections.

Past the skin barrier, things get a lot more complicated. Orthopedic surgeon Dr. Erin Nance describes the immune system as a “complex network of physical, hormonal, and chemical defense mechanisms.”

All of this infrastructure is needed to deliver immune support to every cell of the body in a timely manner. However, the organs at the conceptual center of immune function are those that circulate lymph—a bodily fluid that contains high levels of immune cells.

“The primary lymph organs, the thymus and bone marrow, are responsible for generating white blood cells,” Nance said.

The thymus is a gland located in the upper chest, just above the heart. It produces and distributes immune cells in response to microbial threats. Marrow is spongy tissue found inside bones where more of these immune cells grow.

They are called primary lymph organs because these structures are essential for our immune development.

Our understanding of these vital organs is relatively new. That’s because modern medicine’s concept of immunity is only about a century old—and we’re still learning how it all works. For example, scientists didn’t know what the thymus did until the 1960s.

A more recent example of our ever-evolving immune understanding involves two small lymphatic organs found right behind your mouth and nose. For decades, doctors believed that tonsils and adenoids were little more than troublesome tissue. When these parts become chronically inflamed—often in children who get recurring sore throats and ear infections— they are routinely removed.

But this practice may be weakening our immunity. A 2018 study published in a JAMA journal found that kids who lose these organs saw “significantly increased relative risk of later respiratory, allergic, and infectious diseases.”

Tonsils and adenoids belong to the secondary lymphatic organs category, along with the lymph nodes (clusters of bean-shaped nodules located in your chest, neck, groin, and armpits), and the spleen—an abdominal organ that filters damaged blood cells, and releases immune cells when an infection is detected.

Secondary lymph organs contribute to our overall immune strength, but unlike the thymus and bone marrow, we can live without them if necessary. According to Nance, one of the great features of our immune system’s design is its built-in redundancy.

“There are multiple places where the white blood cells are produced, stored, matured, and activated,” she said.

Gut Immunity

So far, our picture of the immune system includes a physical barrier (skin), and the lymphatic organ network. But in the last few decades, we’ve discovered a whole new level to our immune system—the gut.

About 70 percent of our immune system is located in our digestive system. But why is it there? According to Stephen Wangen, a doctor who specializes in treating gut disorders, it’s because the digestive system needs extra protection.

“This is the place where we are most exposed and most vulnerable to the microbial world,” Wangen said.

That 70 percent figure refers to the mucosal lining that covers the gut wall. This is lymphatic tissue that acts as a surveillance system, constantly scanning for microbial invasion. Other parts of the body with a mucosal lining, such as your mouth, nose, and urethra, also have this detection feature.

Gut bacteria play a role in our immunity as well. A healthy microbiome—that three to five pounds of beneficial bacteria that lives in our intestines—can crowd out undesirable pathogens, preventing them from settling and thriving inside of us.

This new level of immune understanding has helped explain the purpose of another previously puzzling organ—the appendix. Like the tonsils and adenoids, surgeons routinely removed the appendix because it was thought to be a vestigial leftover that only caused problems. However, today we know the appendix is another appendage of the immune system. It helps mature white blood cells, produce antibodies, and stores healthy gut bacteria if the rest of the microbiome gets wiped out during a GI infection.

The microbiome concept has also helped explain previously puzzling malfunctions, such as why we now see so many people with food allergies.

“All the drugs, chemicals, and antibiotics we take in have impacted the microbiome,” Wangen said. “It’s changed how the immune system views the food.”

Inflammation: The Language of the Immune System

The more scientists study the immune system, the more complex it appears to be. However, such complexity also means that this system can malfunction in numerous ways.

So how do we take care of our immune system? And how can we recognize when things go wrong?

Wangen believes that modern medicine’s microscopic perspective may actually get in the way of real healing. He remembers learning about leukocytes, cytokines, and all the other immune cell lingo when he was in medical school. But he came to see it more as a business model, rather than good medicine.

“They’re just taking it down to this molecular level and then creating drugs that will change different factors,” Wangen said. “But what does that mean in the big picture?”

When Wangen wants the big picture to immune problems he sees in his practice, his primary focus is inflammation: symptoms of redness, heat, and swelling.

“One of the fascinating things that we tend to neglect, and I don’t think the average person would have any idea about it, is that the immune system is what creates inflammation,” he said.

We typically see inflammation as something bad, and it definitely can be. But it also has a positive aspect that is vital to our health.

We need some inflammation for healthy immune function. It is a weapon our body uses to fend off infection, as well as an appropriate reaction to an injury. If you sprain your ankle or bump your head, swelling and redness results. This inflammatory response allows immune cells to get to the site quickly, clear out the damage, and rebuild healthy tissue.

However, inflammation is supposed to be a temporary state, because it can also be hard on the body if it rages for too long. Once the infection is defeated and the wound healing is underway, the swelling and redness are supposed to fade.

But when inflammation fires up at the wrong time, or your body becomes chronically inflamed—these are immune malfunction signals that demand attention. Otherwise, it will turn into disease.

“Almost everything is inflammatory, from dementia to cancer,” Wangen said. “If you dig deep, you start to find that all disease has an inflammatory foundation. I was surprised a few years ago hearing about decreased bone density in osteoporosis turns out to be an inflammatory process as well. Everything might be inflammatory at some level.”

The conventional treatment for excess inflammation is anti-inflammatory drugs. But Wangen urges his patients to think instead about what might be behind their inappropriate inflammatory response. It could be something we know to promote inflammation, like unrelenting stress or excess sugar consumption, or it could be something unexpected—like a food that most of us would consider healthy.

“People can react to just about anything—dairy, eggs, almonds—you name it. It just depends on the person and how their immune system is responding to that food,” Wangen said. “When we figure it out, their digestive tract gets better. Their chronic sinusitis, headaches, or what have you, all get better.”

So why do some people suffer from numerous food allergies, and others seem to be able to eat anything without consequence? According to integrative physician Dr. Terry Wahls, we may all have the same basic parts, but the factors we’ve been exposed to are often drastically different.

“We all have a different set of microbial exposures, antibiotic exposures, and polluting chemical exposures. We have had a different set of lifestyle factors (sleep deprivation, physical and emotional stress),” Wahls said. “All those factors influence how readily my immune cells can protect me, and how readily they can repair and maintain me. If I can’t be repaired and maintained, then I go down the path of rapid aging, early cancers, and dying from infections. I have a shortened life span.”

In her practice, Wahls looks at a patient’s past to understand why their immune cells got over activated. She then determines what can be done to get immune cells back to normal healing function. Often, all the patient needs are diet lifestyle changes.

“We’ve been very successful with that,” Wahls said.

Old-Fashioned Immune Health

The immune system, as we understand it today, is a relatively recent construct. However, the idea that our body has the power to heal and protect itself from disease has been observed for millennia.

Compared to modern medicine’s increasingly complex picture of the immune system, the ancient ideas were very simple. Interestingly, these old concepts are starting to make a comeback.

If you look at ancient Chinese medicine, you won’t find mention of cytokines and T-cells, but you will find time-tested techniques on how to keep the body well.

The oldest known book of traditional Chinese medicine—The Yellow Emperor’s Classic of Internal Medicine—explains that the way to defend against seasonal illness is with abundant internal energy, known as qi. The book says that if you’re full of good qi, “no evils can invade.”

In this paradigm, in which the aim of good health is to embody the balance of nature, disease is merely evidence of living out of balance. One chapter in the Yellow Emperor book states, “Whenever the evils are gathered inside, a deficiency of healthy energy must be present.”

Gathering good qi simply means living in balance with nature, and practicing the basic tenets of good health: exercise, a healthy diet, reduce stress, etc. Chinese medicine includes very clear prescriptions for diet and lifestyle, including an emphasis on moderation, something that was also commonly proposed by health practitioners of other ancient traditions.

A few decades ago, modern medicine scoffed at the diet and lifestyle prescriptions of the past. But as new science validates old ideas, more doctors can see their value.

In her clinical research, Wahls has been able to show that lifestyle factors can have a profound effect on immune health. The four most significant factors she has found are eating vegetables, emotional connection, getting outside (the immune system needs ample vitamin D), and sufficient sleep.

“When we don’t get enough sleep, our immune cells are nowhere near as effective at protecting us against the various viruses that lay dormant in our brain and our body,” Wahls said. “That’s when these latent viruses can turn on and lead to chronic health problems.”

Wahls knows firsthand how valuable diet and lifestyle can be. It’s how she was able to resolve her multiple sclerosis—a debilitating disease where the immune system attacks and destroys the body’s own cells. The experience changed how she practiced medicine and clinical research. And the evidence is beginning to change the minds of other doctors.

“My conventional rheumatology, dermatology, and neurology colleagues are starting to realize that diet and lifestyle can be very effective in cooling off disease,” Wahls said. “But it takes a lot of patient education to help people understand, and take some effort to change their diet, to begin meditating, to pay attention to sleep, to give up foods that increase leaky gut, to eat more deeply colored vegetables, like carrots, beets, berries, and leave out the sugar.”

Wahls’ work helps bridge the divide between the simple lifestyle instructions of the ancient medical model with the proof we demand in modern times. She struggled for years to get her papers published, but she says now the tide is turning.

“This is the nature of human existence,” she said. “When we all have the understanding of our current constructs, it’s really hard to see something other than what you expect to see. It can be frustrating to the innovators on the cutting edge. But this is how life is.”