Functional Medicine

What Is It? How Does It Work? Is It Right For Me?

Aaron Hartman MD
13 min readAug 1, 2023
Diagram using a tree metaphor to outline the primary components of the functional medicine model, including five stages of drilling down from syptoms to root causes: 1. Signs & Symptoms, 2. Organ System Diagnosis, 3. The Functional Medicine Matrix, 4. Antecedants, Triggers, & Mediators, and 5. The Foundations of Functional medicine.

I routinely receive questions about functional medicine:

What is Functional Medicine?
How does it work?
How long will it take to feel better?

Ultimately, what people are asking is: Is functional medicine right for me? Is this going to be a good fit?

These are important questions.

In a previous article, I untangled “conventional,” “integrative,” and “functional” medicine. All three models are useful in a holistic model of care. In this article, I want to dive deeper into functional medicine. Functional medicine isn’t a loosey-goosey, less-strict kind of medicine. Not at all. I advocate functional medicine because it’s really great science. Functional medicine actually goes further than the current standard of care. Don’t be fooled by the pictures of trees; the diagrams used here are designed to simplify something that is quite complex.

What Is Functional Medicine?

Functional medicine is a systems biology approach focused on identifying and addressing the root cause of disease. It’s not a disease-based approach or a symptom-based approach. Rather, functional medicine drills progressively down from your symptoms on the surface to the root causes disrupting your health.

The current standard of care in conventional medicine typically stops at signs & symptoms organized into organ systems diagnosis (e.g. cardiology, gastroenterology, urology) … then outsourced to specialists who typically don’t communicate with one another (and often don’t know how to communicate with one another because they only really understand their specialty). If you have a complex diagnosis or several separate diagnoses, then you probably have dealt with the frustration of trying to make sense of disconnected labs and prescriptions from independent specialists.

Functional Medicine goes further.

Together, we examine your past history, your family history, your health history, your genetics, your nutrition, your lifestyle, your physical health (past and present), your lab data, and even where you’ve lived — all the factors that make you … you. Then, we apply all of that data, along with the health information currently in the literature, to your individual situation.

If that sounds like a lot; you’re right. In order to drill deeper through all of that data, Functional Medicine utilizes three primary toolsets:

  • The Functional Medicine Matrix
  • Lifestory Blocks (Antecedents, Mediators, & Triggers)
  • Foundations of Functional Medicine

The Functional Medicine Matrix

Diagram of the Functional Medicine Matrix superimposed over an image of a young, healthy child skipping across the beach.

Functional Medicine views the body’s overall function in light of seven fundamental systems. The Functional Medicine Matrix guides FM practitioners in organizing and prioritizing a patient’s health issues.

Why does this matter?

As this graphic below illustrates, a diagnosis can be the result of more than one cause. For example, depression can be caused by many different factors, including inflammation. Likewise, a cause such as inflammation may lead to a number of different diagnoses, including depression. The specific manifestation of each cause depends on your individual genes, environment, and lifestyle.

The Functional Medicine Matrix acts like a web decoder, organizing your complex web of causes and conditions.

Body Systems in the Functional Medicine Matrix

The seven body systems in the functional medicine matrix are as follows:

1. Assimilation

Digestion, absorption, microbiota, respiration

This is how your body breaks down the foods you eat and the water you drink and then converts those broken-down products into energy and nutrition for your body. This process starts in the mouth and ends at the cell level where the final products are utilized. The nervous system interacts with the GI tract in controlling transit and digestion. The hormone system interacts with the GI tract in producing digestive hormones. Your blood and hematologic system carry the nutrition to all the parts of your body and finally your immune system evaluates the potential danger of all that enters your body and 99.9% of the time determines it is safe, if this interaction is overstimulated chronic inflammation can occur.

2. Biotransformation & Elimination

Toxicity & detoxification

These processes account for the way your body interacts with your nutritional inputs and then converts the waste products of metabolism into non-threatening inert compounds that can be excreted from your body. If these don’t perform correctly toxic compounds and metabolites can slowly build up in your system over time. Your biochemical systems have to convert solid food, liquid drink, and gaseous air into the most basic elements that can nourish each cell in your body. Your body has multiple redundant biochemical systems to facilitate this. However in some individuals — due to nutritional deficiencies, toxin or toxicant exposures, genetic mutations, chronic stressors or chronic inflammation the cellular — systems won’t function properly resulting in a slow breakdown in function.

3. Defense & Repair

Immune system, inflammation, infections/microbiome

Your immune system has the task of identifying enemies from within and without; then, facilitating cellular repair when the inflammatory assault on the invader is finished. Every cell in your body has an immune system tag that tells it not to destroy that particular cell. When a cell dies, the immune system recognizes the changes in the tags of the dead or dying cells and goes in and cleans them up. Your cells are also preprogrammed with an ‘auto destruct’ program called apoptosis. If the cell becomes diseased or sick it will die and again your immune system will clean it up; then, assist in tissue repair. If this system becomes dysregulated, chronic inflammation becomes rampant; often resulting in autoimmune diseases or immune system and repair dysfunction.

4. Energy

Energy regulation/production, mitochondrial function

Mitochondria are the nuclear powerhouse of every cell in your body. Single-cell organisms, like bacteria, don’t have a fully developed mitochondrial system and so can only exist as single cells. Humans, however, have a complex biochemical system that acts like an atomic reactor, breaking down nutritional compounds and capturing the energy released from the breakdown. If the system works correctly, you can have a high-performance athlete; if it doesn’t work properly, you can have someone debilitated from Chronic Fatigue Syndrome. Because energy is the basis for life, this system’s interactions with all other systems is legend. Without an understanding of bioenergetics (the science of energy production in biologic systems) it is impossible to appreciate the interconnected web of mitochondrial energy affecting any particular disease.

5. Transport

Cardiovascular and lymphatic systems

The transport system involves the transport of nutrition, hormones, and enzymatic factors. Hormones are transported either paracrine (cells in close proximity to other cells like in GI tract) or endocrine (across multiple domains like thyroid hormones). Energy itself can be transported intracellularly via ATP or within the body via glucose and fatty acid molecules. Immune systems can function via transcellular migration (across cells walls) or through the blood to different parts of the body. Transport attempts to uncover disconnections in the body’s natural transport systems and then to either address these issues or enhance them based on the interactions within the web of all other interconnections in the body.

6. Communication

Endocrine system, neurotransmitters, immune messengers

Communication can be understood as your whole-body hormone system. It includes your thyroid system, the male or female hormone system, the hormone organs of origin (ie-adrenal and thyroid) and their connections with the nervous system. This also includes the hormones’ communication with cells at their cell walls and the nucleus of each cell. We are discovering the neuroendocrine system (the integrated nervous system with endocrine hormone system), neurohormonal system (the integrated nervous system with sex hormones like estrogen and testosterone) and also the neuroimmunological system (the integrated nervous system with its interactions with the immune system). This all falls under Communication.

7. Structural Integrity

From musculoskeletal system to subcellular membranes

While more complex, structural integrity can best be thought of as cellular integrity. Things need to stick together in order to function. If the bricks in your house fall out of place one by one, eventually the whole house collapses. Cellular integrity includes that of your arteries and veins as well as that of your tissues. However, tissue breakdown starts at the cellular and arteriolar level. So, we typically view cardiovascular disease as its own specialty and in Functional Medicine it is given a whole study module yet the same processes that cause heart attacks and strokes also decrease kidney function, brain perfusion and blood flow to the entire body. So the break down in vascular integrity that starts in the teen age years doesn’t result in heart disease for decades yet the same process is ongoing in the entire body, not just the heart. It’s best to view vascular disease as a whole body process and not merely limited to the heart and brain.

Interwoven Systems

As an example of how these systems work together (and contribute to dysfunction), someone diagnosed with Chronic Fatigue Syndrome may not only have loss of energy and decreased exercise tolerance (Energy) — but also abnormal hormone levels and sleep/wake cycles (Communication) as well as digestive issues/gas/bloating (Assimilation) and recurrent injuries (Structural Integrity). Their brain fog, lack of ability to concentrate and quick mental fatigability (Energy + Communication) limits their ability to handle their everyday life.

From a Functional Medicine approach, I would attempt to see how all these systems are interrelated and in what order they became dysregulated. Only then can we attempt to ‘unwind’ these tangled systems.

Lifestory Blocks:

ATMs: Antecedents, Triggers, & Mediators

In addition to the the Functional Medicine Matrix, I also take into account the your medical trajectory viewed through the lens of ATMs (Antecedents, Triggers & Mediators).

Antecedents

What preceded the development of my patient’s thyroid disease leading up to her diagnosis?
This could be poor diet, lifestyle, birth history, or even environmental factors.

Triggers

Then, I attempt to discover the triggers that pushed her over the edge into autoimmunity. Was it an acute infection, one last bout of bronchitis/pneumonia, or even the car accident resulting in a concussion?

Mediators

Finally, what event(s) are keeping the fire going? This could be poor sleep, chronic stress, work environment or even current/ongoing mold/lyme exposure.

As you can see in this model, the complexity continues to develop as we weave web upon web to help uncover the root cause of an individual’s current health condition.

Foundations of Functional Medicine

As the word foundations implies, these five elements are critical (foundational) to understanding functional medicine. The foundations are used both to understand your condition(s) and to prescribe the treatment.

After uncovering the antecedents, triggers, & mediators resulting in the current dysfunction — a combination of lifestyle & environmental factors interacting with a patient’s specific genetic predispositions — I work with my patient to progressively unwind specific lifestyle & environmental factors:

Nutrition

It’s true: You are what you eat. I’m not going to delve into this much further here. this is a recurrent theme throughout this website and medical practice.

Exercise & Movement

What is exercise and why is it important? Exercise is like a superfood, supplement, and mood enhancer all in one. It is a general performance enhancer, improving your hormone production and utilization. It improves digestion by increasing bowel motility and digestive enzyme production. It is the most effective antidepressant improving mood by 68%, beating the best medications currently on the market. It improves sleep, boosts your immune system, and helps with weight control. The better question to ask is, What does it not do or improve? Honestly, I do not know.

Sleep & Relaxation

Sleep is a complex biologic process that we are just beginning to understand. In many ways, we still do not understand it, but at a minimum, we are learning all the bad things associated with disrupted sleep.

Stress

Stress is the elephant in the room that people aren’t talking much about in the medical world today. We now know about so many ways that stress can affect our health. Unmanaged stress is associated with an increased incidence of cancer and heart disease. And did you also know that stress makes some medications less effective? It’s associated with anxiety, depression, and even severe episodes of COVID and long COVID. In our world today, it’s imperative that we manage our stress in order to reduce the risk of disease, improve our health span, and live longer and healthier lives.

Relationships

We are social beings. As individuals, we find our greatest sense of worth and value in the context of community founded on relationships. Solitary confinement has long been a powerful tool used for punishment, and during the COVID-19 pandemic, we have seen a whole myriad of detrimental effects from social isolation. We were made to know and be known. Yet rarely is this topic brought up within health care.

If you’re interested in learning more about the foundations of functional medicine, I recorded a podcast series: Foundations of Functional Medicine.

Functional Medicine Takes Time

Functional medicine takes a lot of cognitive and investigative work — not just by your doctor but by you as well. At times, it may feel like your FM practitioner is Sherlock Holmes or Dr. House. At other times, however, you are Sherlock Holmes and I merely play the role of Dr. Watson. I am a guide and support as you uncover your own health story.

For this reason, instead of typical 10–12 minute office visit, my intake visit is two hours. The follow-up is 45–60 minutes, and additional follow-ups after that are generally 30–45 minutes.

While using pharmaceuticals to address symptoms can sometimes be a quick solution, true healing usually takes much more time. My patients have to practice patience, trust the process, and take each step in turn. My most successful patients change their mindset from one of symptom resolution to that of addressing root causes and supporting the body in its natural ability to heal.

Is Functional Medicine Right for You?

If you’re looking for a whole-person approach, this is for you. If you’re trying to get to the root cause of your health issues, functional medicine is for you. If you’re willing to make hard changes to alter your health trajectory, this is for you. If you’re willing to change your diet, lifestyle, sleep patterns, stress management, even some toxic relationships, then this kind of medicine is for you.

The fact that this kind of medicine takes more time and skill also usually means that it comes at a higher financial cost to the patient. This is largely because functional medicine is not recognized by the current healthcare insurance model that is focused on symptoms and diagnoses with surgical procedures and medication treatments. The current insurance-based model is not a root-cause approach, but a symptom and disease-based approach, which sometimes are complimentary but many times are diametrically opposed.

Who is NOT a Good Fit for Functional Medicine?

  • If you’re looking for a quick fix to your underlying symptoms and illness, functional medicine is not a good fit for you. There are no quick fixes in personalized medicine.
  • If you’re someone who needs to be in control, you may find functional medicine challenging. You will have to move through uncertainty before arriving at clarity.
  • If you feel the need to be in the driver’s seat, making medication decisions or higher treatment determinations, functional medicine is likely not a good fit. FM works best with a true doctor-patient relationship, where we come together and make decisions in a cooperative way. This key functional medicine doctor-patient relationship can’t be patriarchal on the side of the doctor, and it also can’t be dominated by the patient. Both sides need to listen to each other and work together to get to real health change.

Functional medicine includes environmental medicine, toxicology, nutritional medicine, as well as the typical medical specialties all combined into one field of practice. A typical functional medicine physician, like myself, in addition to four years of college, four years of medical school, and three years of residency training, has an additional two years of certification training, and another 2–3 of fellowship training. There’s really no way to reproduce this kind of learning without actually going through the training.

This kind of medicine is likely not for you if you’re not willing to move on from your past healthcare experiences. It takes work to move on from negative doctor experiences in the past, bad diagnoses, and difficult outcomes. Those patients who are willing to make the hard changes to move forward with a new health team have the best outcomes.

Facing Medical Trauma

One of the things I commonly see is a certain degree of medical trauma or other health-based trauma. About a quarter to a third of all patients that functional medicine practitioners see will have some kind of trauma, whether it is their own personal past trauma, the trauma from an illness, or the trauma from just dealing with the healthcare system. This is real, and I see it every day. Someone who is going to work with a functional medicine practitioner needs to be willing to work through this difficult, messy, dirty work and move forward. This is the route to true change in your health and your personal wellness.

I covered a lot of ground in this article, but I noted at the outset that I routinely answer many of these questions. Chances are you had at least some of them. I hope this has been helpful and you are armed with more knowledge as you pursue the best standard of care to address your health.

Always remember: You were made for health.

Aaron Hartman, MD is board certified in Functional Medicine, Integrative & Holistic Medicine, Family Medicine, as well as Anti-Aging & Regenerative Medicine. Dr. Hartman started Virginia Research Center in 2010 and RIFM in 2016. He is a Key Opinion Leader for Novum Nordisk in diabetes research; an assistant clinical professor of Family Medicine at VCU and a physician with RIFM.

Originally published at https://richmondfunctionalmedicine.com on August 1, 2023.

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Aaron Hartman MD

Dr. Aaron Hartman specializes in addressing chronic health issues through holistic care, including conventional, integrative, & functional medicine.