Longevity & Healthspan: Why Functional Medicine is the Future of Health

20 min readSep 15, 2023

About Functional Medicine: A Clinical Model to Address Chronic Disease and Promote Healthspan

Functional medicine is an evolution in the practice of clinical medicine of shifting the aperture of focus from a traditional disease-centered model to a preventive and health-centered one. By taking a patient-centered perspective, functional medicine addresses the whole person, rather than treating an isolated set of symptoms.

What is Functional Medicine?

At its core, Functional Medicine is the science of creating health. When you create health, disease disappears as a side effect. It is the application of the latest advances in science combined with the philosophy of systems — or network — thinking to redefine healthcare and the understanding of disease and aging. Since the body is a biological ecosystem, a network of dynamically interacting, interconnected systems, Functional Medicine proposes that the focus of medicine should be on restoring health in the system, not just treating individual symptoms. Functional medicine may be described as the clinical application of systems biology.

Functional medicine asks how and why illnesses occur by addressing the root causes of disease or imbalance for each individual. It is an approach to patient care that views health and illness as part of a continuum in which all components of the human biological system interact continuously with their environment, producing patterns and effects that change over time. Chronic disease is usually preceded by a period of declining function in one or more of the body’s core systems. Indeed, it is often the case that the felt symptoms or pathological diagnoses common in complex chronic disease appear to arrive without warning, but on a cellular and systems level, these types of disease develop gradually over time due to an imbalance throughout the entire biological ecosystem. Restoration of health requires identifying and then improving the specific dysfunctions that have contributed to the disease state. Functional medicine provides tools and a reproducible method to enable clinicians to identify dysfunction and promote balance in physiology as the primary means of improving patient health.

Why do we need Functional Medicine?

Recent years have seen a dramatic increase in the number of people suffering from complex, chronic diseases, such as diabetes, heart disease, cancer, mental illness, dementia, autoimmune disorders like rheumatoid arthritis, along with an unprecedented increase in disabling yet catch-all conditions like irritable bowel syndrome. The question we need to ask ourselves is: why? Why the sudden uptick in chronic illness? What has changed in our bodies, our environments, our ecosystems — our broader lifestyles — that may be responsible for this change in health outcomes? The answer to this is multifaceted, and encompasses cultural developments which are beyond the scope of the clinician such as the relatively recent adoption of heavily processed diets ridden with chemicals, an increasingly sedentary lifestyle, a lack of relational consistency, and a striking increase in the environmental toxins that contaminate our ecosystems and air.

The good news is that many of the physiological and psychological assaults we encounter are (fairly) easily prevented, if only we had the right tools or frameworks to understand their impact on our bodies. The challenge for medicine now is to first broaden its perspective to look at the whole human system, and then to help inform the patient of the ways in which their lifestyle may be injurious, thereby enabling them to actuate a healthier, more restorative life. This is where allopathic medicine fails to provide patients with agency in their own health. Taking an almost nihilistic view on complete recovery, allopathic care emphasizes instead a primarily palliative care model.

The dominant paradigm of modern medicine is one of reactive and acute care. It is excellent for urgent and life-threatening events (you most certainly want to be treated in the ER following a car crash) but fails to appropriately diagnose and resolve conditions which are either chronic or systemic in nature. When it comes to these complex illnesses, the logic tree of Western medicine identifies clusters of symptoms, diagnoses a pathological condition through a rigid (and infrequently updated) ontology, and prescribes (most frequently) a pharmacological intervention. At no point are they tasked with uncovering the unique conditions that may have contributed to the identifiable systems, and are therefore not expected to challenge the epistemology behind the ontology — the why. But take this example as a thought experiment: how could heart disease possibly be a symptom of the body’s deficiency of statins, or depression, a deficiency of SSRIs, when both statins and SSRIs are artificially manufactured chemicals, neither of which are found in the natural environment in which we evolved? These pharmaceuticals, while effective in treating symptoms, are not in any way, resolving the underlying cause as to why either developed to begin with. Rather than endeavoring to understand the root cause of illness — the “why” did it appear to begin with — modern medicine frequently pacifies states of ill-health by muting the body’s symptoms through pharmacological shortcuts.

Clearly, there is a need for both acute and chronic care systems of medicine, but there is presently an outsized burden of cost (both economically and in terms of quality of life) on chronic illness. This is where our current medical infrastructure and paradigm falls short.

The overwhelming result is inadequate care of chronic conditions, due in part to:

Focus on acute or sick-care. The system of medicine taught in Western medical schools and therefore practiced by most physicians, is oriented toward acute care — the diagnosis and treatment of trauma or illness that is of short duration and in need of urgent care, such as appendicitis or a broken leg. This model does not educate physicians on how to act like a detective and uncover the culprit in a chronic condition.
Naming and blaming: The fundamental concept in Functional Medicine is that conventional diagnosis is flawed because our naming conventions — for example, cancer or dementia — are based on a cluster of symptoms or geography in the body, not based on causes. Identifying the name of an illness provides no meaningful insight as to why the illness developed to begin with. Two people with the same disease diagnosis and symptoms may have very different causes and require entirely different treatment approaches.
One-size-fits-all: Allopathic medicine treats all disease as fundamentally the same, and offers the same treatment irrespective of what the underlying cause might be. But we know that no two patients are genetically the same even if they have the same diagnosis. So why do we treat them as such?
Downstream Symptomology Treatment: Once diagnosed, the standard clinical response is to treat the downstream symptoms instead of the upstream causes. And many of the treatments for these symptoms result in a cascade of consequences that interrupt or interfere with other biological processes, often causing additional and unnecessary complications. Wouldn’t a better approach be to find the cause and just remove that?
Infrequent Monitoring: As a result of the cost structure of clinical medicine, the majority of individuals undergo infrequent or inconsistent monitoring of their whole body health, preventing the possibility of monitoring data points over a period of time to establish trendlines. If your body were a company, you would never be able to measure performance year-over-year to fully evaluate the true picture of health.
Clinical Labs “Normals” are not healthy: The biomarker numbers reflected on clinical lab data performed by a standard General Practitioner are measured against “normal” clinical ranges rather than optimal health numbers to determine health or disease. The problem with this, is that “normal” is defined as two standard deviations from the average of all labs conducted. This does not anchor “normal” in an objective metric, but rather a sliding scale that reflects the health of the general population — a population that, certainly in the US, is almost entirely sick. Does it make sense to be comparing your health to your neighbor and calling yourself healthy, just because your neighbor is sicker? No — you might also be sick, just not quite as sick.
Gaps between research and practice: The way many doctors practice isn’t up-to-date with new research. The gap between emerging research in the basic sciences and its use in medical practice is enormous — a few decades or more — particularly in the area of complex, chronic illness. Additionally, the prevailing model of clinical and academic studies is predicated upon systems like double-blind trials, which requires controlled conditions across multiple participants. The reality is that each human is a distinct system with distinct genetic and environmental expressions, making each person an N-of-1. This recognition does not fit conveniently into the legacy model of “science-based medicine” which requires substantial clinical trial results to consider adopting a change in perspective. This approach is too parochial for complex systems biology.
Shortfalls in training: Most physicians are not adequately trained to assess the underlying causes of complex, chronic disease and to act as detectives to uncover the true cause of the imbalance or pathology. Strategies such as evaluating nutritional status, lifestyle, exercise and environment to diagnose the culprit of imbalance and treat and prevent these illnesses are not yet broadly adopted in medical academia. In fact, most medical schools require graduates to take at most, one class in their four year curriculum on nutrition science. This results in complex illness that is either inappropriately diagnosed, or superficially treated.

How Is Functional Medicine Different?

A Functional Medicine practitioner is a Medical Doctor (MD) who has undergone supplemental training in applying the practice of systems thinking to their evaluation of illness and imbalance. Functional medicine suggests that all diseases have a root cause, or an etiology. Functional medicine involves understanding the origins, prevention, and treatment of complex, chronic disease, and therefore asks a different series of questions than traditional medicine does. It is concerned with deep questions around how we create health? What conditions can we apply that either enable or inhibit health? How can we optimize function? How do we reverse dysfunction caused by the insults of modern lifestyles (nutritional deficits, toxins, immobility, etc)? How do we reframe our perspectives such that we align with our body’s essential needs, and build forward from there?

What we often fail to appreciate is how powerful the innate healing system is within our body. When you truly understand the mechanics of your body’s natural defense and repair system, you’ll think it’s a work of magic. How does your body know to deploy inflammation to drive white blood cells to a cut and stimulate tissue repair? How does it know to trigger a fever when a toxin enters your system, knowing that hyperthermia is one of the soundest methods to kill pathogens? Our bodies are smart, unbelievably honed machines. So to enable health, we simply need to get out of our own way, and activate our innate healing system by removing or avoiding the inputs that negatively impact our core seven systems (defined below) and provide it with what it needs to function optimally. Put simply: take out the bad stuff, put in the good stuff.

The latest in scientific understanding is that human biology (and health or illness) is far more complex than the fixed human genome. In fact, most diseases — especially chronic illnesses — are not genetically determined. It is gene expression rather than genetic inheritance that is essential in the emergence of disease. Gene expression, known scientifically as the Epigenome, is like toggling between on and off switches of each of your genes. Altered by myriad influences, including environment, lifestyle, diet, activity patterns, psycho-social-spiritual factors, and stress, your epigenome is surprisingly adaptable. Insults from environmental triggers (toxins, pathogens, microbes, allergens, poor diet and stress, etc), combined with inadequate or insufficient ingredients for health (micro-and-macro nutrients, phytochemicals in plants, healthy hormones, strong relationships, etc) interact with genes to create the phenotype expression of health or disease. All of these influences render disease more or less likely by quite literally, turning on — or off — certain genes, all the time. Everything you interact with everyday influences this system. Every bite of food, every night of sleep, is either a signal for health or disease. Functional medicine directly addresses modulators of gene expression and other underlying causes of disease through a systems-oriented approach.

Functional medicine also recognizes that a patient’s “environment” is not limited to physical and biochemical exposures, but also to societal conditions and what is now being labeled the “human interactome.” Advanced brain scans and hormonal testing has evidenced the influence of social determinants like trauma and relationships — both to others and to self — on health outcomes. Functional medicine provides a roadmap to assess the comprehensive set of inputs like environment, lifestyle, social history, as well as predisposing factors — genes, stress, toxins, trauma, microbes, diet, allergens, and so on, that cause imbalance in the whole biological system.

Functional Medicine attempts to remove the impediments to health, and provide the ingredients for health, to restore balance an optimal function in these biological networks. The functional medicine clinical model provides practitioners with the method and the means to thoroughly evaluate the thousands of interactions among genetic, environmental, diet, and lifestyle factors that influence health and may manifest as complex chronic disease.

Principles of Functional Medicine

The knowledge base of Functional Medicine has been shaped by seven core principles, as documented by the Institute of Functional Medicine (IFM):

Acknowledging the biochemical individuality of each human being, based on concepts of genetic and environmental uniqueness.
Incorporating a patient-centered rather than a disease-centered approach to treatment.
Seeking a dynamic balance among the internal and external factors in a patient’s body, mind, and spirit.
Addressing the web-like interconnections of internal physiological factors.
Identifying health as a positive vitality — not merely the absence of disease — and emphasizing those factors that encourage a vigorous physiology.
Promoting organ reserve as a means of enhancing the health-span, not just the life-span, of each patient.
Functional Medicine is a science-using profession, practicing science-based medicine.

The hallmarks of a functional medicine approach include:

Whole Systems Thinking: Functional medicine addresses the whole person, not just an isolated set of symptoms. Functional medicine practitioners spend more time with their patients, listening to their histories and evaluating the interactions between environmental, lifestyle, and genetic factors that influence health. This allows functional medicine practitioners to look upstream, considering the complex web of interactions in the patient’s history, physiology, and lifestyle that can lead to expressions of illness. It embraces the complexity of multifactorial influences on disease.
Ecosystem Medicine: Your body is not a set of independent organs performing functions autonomously. It is a weblike ecosystem. The same root cause can result in multiple different symptoms and conditions. As we address the causes and provide the conditions for health, diseases go away as a side effect. Rather than an organ-based approach, functional medicine utilizes a Matrix model to address core physiological processes that cross anatomical boundaries. This approach provides the basis for the design of effective multimodal treatment strategies.
Health-focused Care: The focus of functional medicine is on identifying and promoting health in the body’s ecosystem, beyond merely the absence of disease. The distinction between “health” and “disease” is not binary but is instead a long continuum that gets modulated constantly. The tools of Functional Medicine allow for the early identification of potential risks that help patients implement corrective behaviors that allow for agency in disease prevention.
An integrative, science-based approach: The functional medicine practitioner examines a multitude of available interventions and customizes a treatment plan specific to each patient. Leveraging a combination of allopathic examination practices including advanced laboratory testing and diagnostics, and more traditional holistic practices like lifestyle and environmental analysis, a functional medicine practitioner applies a complex system of testing to evaluate the patient’s whole system. Treatments equally incorporate both modern medicine and integrative therapeutics, including a combination of pharmaceuticals and surgical intervention (where necessary), and nutritional supplementation, botanical medicines, therapeutic diets, detoxification programs, or stress-management techniques, resulting in a truly tailored approach for each unique individual.
Personalized and Precision Medicine: Functional Medicine is a personalized approach to diagnosis and treatment. Functional medicine is based on understanding the metabolic processes of each individual at the cellular level. By recognizing how each person’s genes and environment interact to create their unique biochemical phenotype, it is possible to design targeted interventions that modulate gene expression to correct physiological dysfunction.

In identifying a diagnosis and therapeutic recovery plan, a functional medicine practitioner will consider multiple factors like those identified in Figure 2, including:

Biological Status: Testing includes a combination of traditional clinical laboratory data, as well as supplemental functional medicine labs which seek to identify the core biochemical and metabolic imbalances that may be at the root of a disease process. Such imbalances can include: digestive, absorptive, microbiological imbalances, detoxification and biotransformation imbalances, among others. Practitioners review these results through a new lens that addresses the fundamental biological networks that comprise human biology, as well as from the perspective of an “optimal health range” for biomarkers, rather than the standard “average health range”.
Physiological Signs & Symptomatology: A highly detailed patient intake form including history back to birth evaluates the patient’s objective medical signs like a rash or high blood pressure, and their subjective felt symptoms like a headache or brain fog. These help inform the relationship with the biological status along with the below inputs in establishing a personalized therapeutic plan.
Environmental Inputs: Toxins (both internal and external such as pesticides, herbicides, plastics, heavy metals and more), allergens (environmental and food), microbes (bacteria, viruses, parasites, worms, ticks, including imbalances in the microbiome), poor diet and stress (physical or psychological) all act as triggers influencing the expression of the Epigenome. A practitioner will thoroughly analyze lifestyle habits, environmental history and current events that may contribute to these inputs.
Mind-body connections: Psychological, spiritual, and social factors have been clinically proven to have a profound influence on health expression. In addition to the triggers of disease, there are necessary ingredients for health — real food, nutrients, hormones, light, water, air, rest, rhythm, sleep, movement, love, connection, meaning and purpose. These “lifestyle” ingredients are responsible for nutritional and hormonal cascades that influence health directly. These are the raw materials, each needed in proper balance, and different for each individual, to create a healthy human. Disease occurs when you have too many triggers and not enough of the right ingredients.
Genetic makeup: Although an individual’s ~22,000 genes are fixed and may make them more susceptible to some diseases, the health outcome is determined by the activation of them. In this way, DNA is not an unchanging blueprint for life. Informed by the emerging research of the ‘OMICS’ revolution which considers the gene-environment phenotype through the expression of proteomics, metabolomics, and metagenomics, genes appear to be influenced by environment, experiences and even internal attitudes and beliefs. That means it is possible to change the way genes are activated and expressed, whether for health or disease.
Too little / too much: Imbalance in a system is usually a result of “too much” of something, or “too little” of something. Functional Medicine investigates these imbalances and provides recommendations to help restore the body to its natural equilibrium — a health state. Food is the biggest lever to impact all these systems. The wrong food harms each system and the right food helps optimize each system. The right food regulates the health of your microbiome, your immune system and reduces levels of inflammation and oxidative stress and improves your energy systems. Food balances your hormones and brain chemistry, supports detoxification and improves the function and health of our circulatory and lymphatic systems and even provides the raw materials for every cell, muscle, tissue, organ and bone in your body.
Multimodal Treatment Plans: The functional medicine approach uses a broad range of interventions in concert to achieve optimal health, including diet & nutrition, exercise & movement, stress management, sleep & rest, and targeted nutraceutical & pharmaceutical therapies. These interventions are tailored to address the antecedents, triggers, and mediators of disease and dysfunction in each individual patient.

Key Tools of Functional Medicine

Functional medicine tools (including the IFM’s Timeline and the Matrix model detailed below) are integral to organizing clinical data and promoting clinical insights. This approach ensures that the patient’s whole picture is understood, the therapeutic relationship is fostered, therapeutic options are expanded, and patient activation is improved.

Functional Imbalances: Form Follows Function, Function Follows Environment

The diagram in Figure 3 represents some of the Key Systems responsible for health or illness, along with external lifestyle factors. Imbalance in any or all of these 7 Systems is the underlying driver of almost all disease. Nearly every one one of the 155,000 diseases listed in the disease classification system known as ICD-10 are caused by imbalances in seven interconnected systems. Fix those systems and you don’t have to treat the actual disease.

What are the 7 key systems?

Transportation (circulation and lymphatic system)
Defense and repair (immune and inflammatory system, infections, pathogens)
Hormonal Communication System (endocrine system, neurotransmitters, etc.)
Gut and Digestive Health: how we assimilate nutrients, digestion, and the microbiome (the gut flora including its resident microbiota like fungi, yeast, bacteria, etc)
Detoxification (toxicity elimination, biotransformation, detoxification)
Energy production (energy regulation, oxidative stress, mitochondrial function)
Structural integrity (from subcellular structures to the musculoskeletal system)

The Functional Medicine Matrix (Figure 4) is a tool produced by the Institute for Functional Medicine (IFM) that organizes and integrates the biological systems in which core clinical imbalances reside. This helps translate the rich basic scientific literature concerning physiological mechanisms of disease into the clinical studies, clinical diagnoses, and clinical experience acquired during medical training. These core functional imbalances serve to bridge the mechanisms of illness with the clinical manifestations (and diagnoses) of disease.

Using this construct, it is possible to see that one disease or condition may have multiple causes (i.e., multiple clinical imbalances), just as one fundamental imbalance may be at the root of many seemingly disparate conditions. The IFM has developed concepts and tools that help to collect, organize, and make sense of the data gathered from an expanded history, physical exam, and laboratory tests, including the Functional Medicine Matrix (Figure 4), the Functional Medicine Timeline (Figure 5 ) and the GO TO IT model (Figure 6), among others.

The Matrix is useful in producing a blueprint or map of the patient’s complete history. It qualifies the patient’s lifestyle influences, antecedents, triggers, and mediators of disease/dysfunction are entered in the upper left corner. Using this information architecture, the clinician can create a comprehensive snapshot of the patient’s story and visualize the most important clinical elements of Functional Medicine:

Identifying each patient’s antecedents, triggers, and mediators of disease and dysfunction;
Discovering the factors in the patient’s lifestyle and environment that influence the expression of health or disease;
Applying all the data collected about a patient to a matrix of biological systems, within which disturbances in function originate and are expressed; and
Integrating all this information to create a comprehensive picture of what is causing the patient’s problems, where they are originating, what has influenced their development, and — as a result of this critical analysis — where to intervene to begin reversing the disease process.

Use of the Matrix and Timeline tools helps map imbalances and key events. These illuminate potential root causes of illness and uncover a pattern of dysfunction. The Functional Medicine Timeline (Figure 4), helps to connect key events in the patient’s life with the onset of symptoms of dysfunction. Integration of this information provides the clinician with a comprehensive perspective on the origins and influences that may have contributed to the patient’s problems. The process of critical analysis and synthesis leads the clinician to arrive at recommendations personalized for each patient that help reverse the disease process and improve health.

The Functional Medicine Treatment Plan

A functional medicine treatment plan may involve one or more of a broad range of therapeutic modalities, including many different dietary interventions (elimination diet, anti-inflammation diet, low glycemic-index diet), nutraceuticals (vitamins, minerals, essential fatty acids, botanicals), and lifestyle changes (improving sleep quality or quantity, increasing physical activity, decreasing stress and learning stress management techniques, quitting smoking, etc.). It takes a ‘Food First’ approach, emphasizing nutrition is essential to the practice of functional medicine. In fact, so vital is nutrition to the practice of Functional Medicine that IFM has established a core emphasis on Functional Nutrition and has funded the development of a set of unique, innovative tools for developing and applying dietary recommendations.

Scientific support for the modifiable lifestyle factors embedded in the functional medicine approach is found in the extensive and rapidly expanding evidence base supporting the therapeutic effects of nutrition, exercise and movement, sleep, and stress management.

As we consider physiology and pathophysiology from a systems-biology perspective, we assess and treat the interrelated functions of metabolism, biotransformation, energy production, immune modulation, and hormonal regulation. Treatment approaches incorporate other integrative modalities demonstrated to be of benefit in the peer-reviewed clinical literature, including acupuncture, botanical medicine, manual medicine like physical therapy and therapeutic massage, and mind/body therapies.

Steps to Recovery

The treatment plan almost always requires moderate-to-drastic lifestyle adjustments. This means potentially significant behavior change is required for the desired results. So while the medical review and clinical recommendations are conducted by the physician, it is essential that the practicalities of the treatment plan are designed within the context of a therapeutic partnership. The practitioner engages the patient in a collaborative relationship, respecting the patient’s role and knowledge of self, and ensuring that the patient learns to take responsibility for his/her own choices and for complying with the recommended interventions. Learning to assess a patient’s readiness to change and then providing the necessary guidance, training, and support are just as important as ordering the right lab tests and prescribing the right therapies.

The GOTOIT system developed by the IFM and outlined in Figure 5 below, presents a logical process for eliciting the patient’s whole story and ensuring that assessment and treatment are in accord with that story:

G = Gather Information

O = Organization Information

T = Tell the Complete Story Back to the Patient

O = Order and Prioritize

I = Initiate Treatment

T = Track Outcomes

How Functional Medicine Sees Ageing and Longevity

Advances in our understanding of our physiology are changing everything we know about the practice of medicine. Some of the most exciting advancements being thoroughly researched right now are:

The “OMICS” revolution — the mapping of the human genome, transcriptome, proteome, metabolome, microbiome, sociogenome, and so on, are providing a much more sophisticated roadmap for how our biology interacts with our environment.
Quantified-self measurement tools, including Function Health whole body lab testing, the Oura Ring, Levels Health continuous glucose monitoring, the Whoop, Apple Watch, Eight Sleep, and, soon, more advanced implantable biosensors that measure your biochemistry in real time.
Advances in artificial intelligence and machine learning that will analyze billions of personal data points, identify patterns and imbalances, and help create a personalized map for enhancing every aspect of your biology.
Quantum computing, which can process enormous amounts of biological information.

All of these are contributing to a greater understanding of “aging” as a disease rather than as a predetermined given. Of course, we still haven’t cracked the code for infinite life, but we are quickly discovering the cellular dysfunctions (or root causes) of the factors that broadly contribute to aging. These are being clinically referred to as the “Hallmarks of Aging”. They are types of biochemical changes that occur in all organisms that experience biological aging leading to a progressive loss of function, structural integrity and eventually, death. They were first listed as recently as 2013 in a landmark paper to conceptualize the essence of biological aging and its underlying mechanisms.

These hallmarks are essentially cellular or metabolic-level markers that indicate or contribute to, aging. There is not yet scientific consensus on which hallmarks are most essential, or even exactly how many there are (the number recently jumped from 9 to 12 and keeps growing as science progresses), but there is a general acceptance that they are important.

As a result of hallmarks of aging, changes in our biology that are upstream to the diseases they cause:

Disrupted hormone and nutrient signaling — food and aging
DNA damage and mutations — problems with our genetic blueprint
Telomere shortening — becoming unraveled
Damaged proteins — malformed, misshapen, dysfunctional molecules
Epigenetic damage — a dysfunctional environment or lifestyle
Senescent cells — the attack of the zombies
Depleted energy — the decline of our mitochondria
Microbiome dysregulation — the link between gut health and longevity
Stem cell exhaustion — the decline of our body’s rejuvenation system
Inflammaging — the fire that drives chronic disease and shortens life

As Dr. Mark Hyman writes in his latest book on longevity — Young Forever — the information theory of aging suggests that disease occurs because of corrupted information in our biological networks, like damaged software code that results in altered signals that prevent our innate healing and repair systems from doing their job. Functional medicine addresses the causes and repairs the corrupted software code.

Like the rest of functional medicine, each hallmark is affected by various imbalances — too much or too little of certain inputs that can negatively impact the expression and progression of the hallmark.

Basically, we have more agency than we think we do.