Functional Medicine

What is Functional Medicine?

Functional medicine is not an easy concept to define, but Dr. Mark Hyman of the Institute for Functional Medicine does an excellent job in the following video. Following the video there are excerpts from many of the world’s top experts in functional medicine, which I hope will help you to understand this progressive
approach to health and disease.

Stephen Smith, MD

Our story


  • Functional Medicine Definition from Wikipedia
  • Functional Medicine Definition.
  • Web-like Connections of Physiological Factors
  • The Processes
  • Nutritional Imbalances
  • Immunological Imbalances and Inflammatory Response
  • Gastro-intestinal Imbalance
  • Impaired Detoxification
  • Oxidative Stress
  • THE FOUNDATION SCIENCES — How to answer the question?
  • Metaphors of functional medicine
  • Summary
  • References

Functional Medicine Definition from Wikipedia

Functional medicine is an alternative medicine that focuses on improving physiological function as a primary method of improving the health of patients with chronic disease.

Functional Medicine Definition

Institute for Functional Medicine Website

Functional medicine is personalized medicine that deals with primary prevention and underlying causes instead of symptoms for serious chronic disease. It’s a science-based field of healthcare that’s grounded in the following principles:

Biochemical individuality describes the importance of individual variations in metabolic function that derive from genetic and environmental differences among individuals.

Patient-Centered medicine emphasizes “patient care” rather than “disease care,” following Sir William Osler’s admonition, “It is more important to know what patient has the disease than to know what disease the patient has.”

Dynamic Balance of internal and external factors.

Web-Like Interconnections of physiological factors. An abundance of research now supports the view that the human body functions as an orchestrated network of interconnected systems, rather than individual systems functioning autonomously and without any effect on each other. For example, we now know that immunological dysfunctions can lead to cardiovascular disease, that dietary imbalances can cause hormonal disturbances, and that environmental exposures can precipitate neurological syndromes such as Parkinson’s disease.

Health as Vitality, not merely the absence of disease.

Promotion of Organ Reserve as the means to enhance health span.

An examination of the core clinical imbalances that underlie various disease conditions anchor functional medicine. The body, mind, and spirit process those imbalances, which arise as environmental circumstances, such as diet, nutrients (including air and water), exercise, and trauma, through a unique set of genetic predispositions, attitudes, and beliefs. The fundamental physiological processes include communication, both outside and inside the cell; bioenergetics, or the transformation of food into energy; replication, repair, and maintenance of structural integrity, from the cellular to the whole body level; elimination of waste; protection and defense; and transport and circulation. The core clinical imbalances that arise from malfunctions within this complex system include:

1- Hormonal and neurotransmitter imbalances from cellular membrane function to the musculoskeletal system

2- Oxidation-reduction imbalances and mitochondriopathy

3- Detoxification and biotransformational imbalances Immune imbalances

4- Inflammatory imbalances 

5- Digestive, absorptive, and microbiological imbalances

6- Structural imbalances

Imbalances such as these are the precursors to the signs and symptoms, which we use to detect and label (diagnose) organ system disease. Improving balance in the patient’s environment and in the body’s fundamental physiological processes is the precursor to restoring health, and it involves much more than treating the symptoms. Functional medicine focuses on improving the management of complex, chronic diseases by intervening at multiple levels to address these core clinical imbalances and to restore each patient’s functionality and health. 

Functional medicine is not a unique and separate body of knowledge. It’s grounded in scientific principles and information widely available in medicine today, combining research from various disciplines into highly detailed yet medically relevant models of disease pathogenesis (origin of the disease) and effective clinical management. Functional medicine emphasizes a definable process of integrating multiple knowledge bases within a pragmatic matrix that focuses on functionality at many levels, rather than a single treatment for a single diagnosis. Functional medicine uses the patient’s story as a key tool for integrating diagnoses, signs and symptoms, and evidence of clinical imbalances into a comprehensive approach to improve both the patient’s environment and his or her physiological function. Functional medicine directly addresses the need to transform the practice of primary care.

Web-like Connections of Physiological Factors

[This article was originally posted on The Institute for Functional Medicine website.]

Sidney Baker, M.D., explains that “people do not get sick from diseases, but rather diseases reflect a disruption in the dynamic balance between themselves and their environment.”(8) Fundamental to functional medicine is a profound awareness of web-like interactions among all systems – interactions that have been artificially singularized by disease taxonomy. Robert Heinlein [the science fiction author] describes the dilemma as follows: “The greatest crisis facing us is…a crisis in the organization and accessibility of human knowledge. We own an enormous ‘encyclopedia’ which isn’t even arranged alphabetically. Our ‘file cards’ are spilled on the floor. The answers we want may be buried in the heap.” Three key notions, first articulated by Leo Galland, M.D., help illustrate and organize the web-like thinking that is essential to the success of the functional medicine practitioner.

The antecedents of our patients’ dysfunction nest within their biological terrain and genetic susceptibilities. The patient’s dynamic balance has constant perturbations that require adaptation. However, sometimes a force of change such as allergens, xenobiotics, drugs, endotoxins, and emotional stress are strong enough to create a dysfunctional response; Dr. Galland labels these forces triggers. The patient’s response to a trigger consists of complex, web-like effects on the biologic system known as mediators. For example, cytokines, prostanoids, leukotrienes, and lipid peroxides are mediators that cause an inflammatory response.

 As futuristic as it may seem, the next step in diagnosis and treatment protocols can incorporate an assessment of the unique risk factors present by virtue of the patient’s DNA interacting with the end-products of his or her lifestyle, diet, environment, and thoughts. For example, we know that the byproducts of tobacco smoke interact with cellular gene structures in the lungs to induce translational molecules.

The presence or absence of these molecules affects the detoxifying function of patients’ liver cells. In turn, these cells arbitrate the development of breast cancer. This research regarding the polymorphic expression of inherited detoxification capabilities helps explain contradictions regarding the connection between smoking and breast cancer. The phenotypic expression of breast cancer is controlled by the genetic susceptibility of the patient experiencing the tobacco smoke, which helps define this susceptibility.

 This genetotrophic disease and susceptibility model dates back to Roger Williams, PhD,(9) who discovered many of the B vitamins. The year prior, Linus Pauling published pivotal research demonstrating that genetically controlled translational molecules control form and function in sickle cell disease. Today we see clinical applications that decrease sickle cell crisis flowing from the understandings evolved from this model. (10) Rich literature exists on the genetics and epidemiology of aging and chronic illness as well. (11) A model allowing for modifiable factors for achieving healthy aging has been reported by Evans and Rosenberg from their Tufts Medical School study on aging. (12)

Health as a Positive Vitality – Not Merely the Absence of Disease

Today medicine is at a crossroads. Although medicine has successfully contributed to the evolution of the science of disease diagnosis and treatment during the past four decades, it has not been as successful in promoting healthy aging. A majority of the aging baby boomer population expects that they will never retire and will continue to engage in multiple activities, travel the world, be physically active, meet exciting new challenges, and be available as catalysts for social change as they grow into their 70’s and 80’s. This is not a health as the absence of disease model, but rather health as a positive, achievable vitality model.

Fries (Stanford University Medical School researcher in the processes of aging) explains that much of the loss of function associated with disease among older individuals is a consequence of the progressive loss of “organ reserve.”(13) When we are young, there is a reserve of organ function beyond that which is necessary for the baseline requirements of most organ systems.

As we age, however, we lose organ reserve; stresses that we could have once accommodated now exceed our resilience, which results in health crises. Fries emphasizes that organ reserve is related to biological age. As we lose organ reserve, our biological age increases, making us more susceptible to disease. We can modify how quickly we lose organ reserve and undergo biological aging through changes in lifestyle, environment, and nutrition. It is now recognized that 75 percent of our health and life expectancy after age 40 is modifiable on the basis of such choices. (14),(15)

The Process

To add organization and accessibility to this large body of scientific knowledge, we’ve separated the evaluation phase into six interwoven processes that can cause imbalances. You’ll find these six processes or categories echoed throughout the training course. These categories also serve as the framework for the Functional Medicine Research Center’s Adjunctive Nutritional Clinical Practice Protocols. In truth, these categories are simply facets of the same dysfunction, intimately and insolvably interwoven. However, we separated these imbalanced functional processes into categories to start rethinking and reprocessing our assumptions about diseases.

1- Nutritional Imbalances
2- Immunological Imbalances and Inflammatory
3- Response Gastro-intestinal Imbalance
4- Impaired Detoxification
5-Oxidative Stress
6- Endocrine Imbalances


Molecular Medicine, Nutritional Biochemistry, and Preventive Medicine

Molecular medicine is to functional medicine what physics is to chemistry: the very underpinning. The amount of basic science that begs for clinical application is truly daunting and requires a rigorous sifting and assimilating.

Dr. J. Baker explains, “For example, the discussion of immunodeficiency diseases is no longer a clinical description of arcane disorders but the definition of immune dysfunction based on genetic defects at specific points in the immune response.” (45) The fundamental paradigm of molecular biology is succinct: “one gene-one enzyme.”

The details of how the genetic message specifies the synthesis of proteins and how proteins in turn regulate cell function (46) is core to the functional medicine paradigm. This genetotrophic disease and susceptibility model dates back to 1909. Amplifying findings from his study of an inborn error in metabolism, black urine, Archibald Garrod (47) developed the concept of chemical individuality. In 1931, he outlined this concept in greater detail: “In the case of every malady there are two sets of factors at work in the formation of the morbid picture, namely, internal and constitutional factors inherent in the sufferer and usually inherited from his forbearers, and the external ones which fire the train.”

(48) In his 1950’s landmark discussion of genetotrophic diseases, Roger Williams broadened Garrod’s concept of chemical individuality. Williams (49) defined genetotrophic disease as the faulty expression of genes resulting from a diet failing to meet an individual’s inherited nutritional requirements. The year prior to Dr. Williams’ publication, “The Concept of Genetotrophic Disease,” Linus Pauling (50) published pivotal research that argued that genetically controlled translational molecules control form and function in sickle cell disease. Recently, researchers have successfully applied high-dose nutrient interventions (cf. butyrate administration) to decrease sickle cell crisis. (51) However, it should be remembered that preventive medicine and risk factor analysis was the safe harbor within which the vessel of functional medicine first anchored.

Primary prevention, or risk analysis and early intervention based on biochemical individuality, are the sine qua non of functional medicine. Secondary prevention or reversal and/or stabilization of disease or dysfunction is another way of conceptualizing functional medicine. Along similar lines, rich literature exists on the genetics and epidemiology of aging, organ reserve, and chronic illness. (52) [William] Evans and [Irwin] Rosenberg (53) offer a model predicated on modifying biomarkers with lifestyle interventions for achieving healthy aging by maintaining organ reserve. Their work is based on research from Tufts University Medical School and the U.S. Department of Agriculture Human Nutrition Center on Aging.

Cognitive Sciences

Information mapping, information dissemination, and making the unconscious conscious are the techniques wrestled from the research in the cognitive sciences (what we know and how we know what we know). Raising the level of awareness, increasing the amount of information available, and thus improving the likelihood of making intelligent decisions together is the primary goal between the functional medicine practitioner and patient.

Healthy Changes is an awareness program for patient-centered choices of lifestyle changes with mental, emotional, and cognitive tools for awareness and change. (54) Healthy Changes formalizes the steps in this evolving paradigm: Tools for empowering patients to participate in their unique process of recovering health. Included in this process are tenets that have been gathered from research in cognitive science, behavioral psychology, philosophy, and the neurosciences.

The first step in this patient empowering process requires a reversal of the traditional relationship between practitioner and patient. Yes, we do have expertise in creating clarity of the functional processes that has brought illness into our patients lives. But unless we create a safe environment for this information to be owned and used uniquely by the patient, we have again been trapped within the “victim-expert” relationship that burdens us as practitioners and disempowers our patients.

The Healthy Changes process addresses this dilemma directly. From the beginning of the patient-practitioner relationship, a trust can develop from the belief that humans are not machines: when provided tools for self-nurturing, they can self-organize and heal. Healthy Changes provides these tools. Essential to this process of self-nurturing are tools of self-awareness, a product of the cognitive sciences. In a stepwise process inherent in the Healthy Changes process, patients learn about non-judgmental self-observation.

They learn how to create a state of mindfulness. The creation of mindfulness is the simple, but often forgotten, state of being aware of what is going on with one’s feelings, body, and perceptions without immediately judging and acting on these observations. Understanding about and compassion towards oneself can grow in a soil emptied of judgments. Once this non-judgmental state exists, patients can organize their personal context and begin the journey that reveals to them their present state of un-wellness as well as how they reached that state. This process involves two steps.

First we need to understand the “functional pathogenesis” of their present physiological state so that patients can begin their journeys with a clear foundation for recovery. Secondly, they need to learn how their present context of un-wellness grew out of their life choices through the technique of telling their personal story through exercises of self-awareness. Their journey of personal clarity and understanding includes exploring their “rules of living” that unconsciously drive their behaviors with their family, friends, at work, society and culture, personal eating and exercise patterns, as well as their priorities of self-care and love. As part of this journey, the patient learns structured information about food.

By learning what is in food that nourishes them, patients can make food choices based on scientifically validated information rather than fad, hearsay, and marketing misinformation. There is also an “Exercise and Health” section that guides the patient to explore the role physical activity can play in the transformation of their metabolism and, even more importantly, the pleasure that physical activity can bring to their lives. As a partner rather than an expert, we can travel with our patients through this functional process of re-empowerment and genuine self-care where patients again become “Rulers of their own Lives” and configure their activities from their inner curiosity, love, acceptance, and compassion – the most powerful forces we can invoke for our patients’ healing and reintegration.


The time I have spent in clinical practice and with thousands of patients has taught me principles that have become axiomatic in my medical practice. Foremost among these truths is the awareness that each patient is unique. Each person whom I see has distinct qualities and traits. In daily interaction we become most aware of this uniqueness, but it is mirrored throughout their being.

The science behind each person’s uniqueness is no longer controversial. At the heart of each cell in our body rests strands of DNA ready to respond and translate our uniqueness throughout our environment. We cannot change the genetic heritage (the gift of life from our parents) transmitted through these strands of nuclear DNA. However, our daily choices of what food we eat, water we drink, rest and sleep we achieve, and emotional responses we sustain have a powerful influence on our cells. These factors induce a vast, pluripotential variety of responses. How we choose to live these unique experiences profoundly affects the biochemical, electromagnetic flux that permeates and prompts direct gene responses.

 For example, in 1995 I was shown how researchers in Russia (at the Pavlov Institute in St. Petersburg) have experimentally configured different, artificial, and emotional contexts (e.g., fear, calm, anger). In the lab, they have traced the biochemical cascade of mediators that cause immediate differences in brain chemistry that then have downstream effects, some immediate and other longer acting responses, through gene expression. We are well aware of the vast varieties of lifestyle interventions (nutritional, pharmacological, exercise, etc.) that have been shown to alter basic biochemistry, many of which are now understood to be translated through gene expression. We identify the integration of these genetic responses as our unique lives. This integration defines our own, as well as our patients’, overall sense of health or illness.

Boundaries: Self and Nonself

Strict divisions between categories like nature and nurture, heredity and environment, and genetics and experience have little meaning in a functional perspective. Instead, a functional approach encourages exploring the anatomy of functional processes—the connections between “self” and “nonself”—to better recognize the limited division between the “inside” and “outside” factors that influence our health. But where do most of the processes relevant to functional medicine occur? In his lectures at the Second International Symposium on Functional Medicine (1995; Rancho Mirage, CA), Dr. Baker explained that four key interfaces act as settings for the interaction between inside and outside factors. Considering what qualifies as self and nonself among these interfaces helps us understand the action and reactions that trigger essential processes of survival such as active/passive transport, the inflammatory/immunologic cascade, etc. Asking how is each interface working leads to fruitful information about key functional processes.

The Environmental Interface

Where does the outside world (non-self) meet the anatomy and physiology of the inside world (self)? Three main tissues link us to the physical environment: 1) the digestive mucous membrane (the size of a tennis court and thickness of an eyelid), 2) the respiratory epithelium, and 3) the brain (psychoneuroimmunoendocrinological interface). The six processes we have been discussing adjudicate the success at these three tissue boundaries. Without their success, no life exists. With limited success, there are maladaptive processes set in motion. For example, short bowel syndrome in which the digestive mucous membrane of the small intestine stops digesting, transporting, and controlling permeability efficaciously results in debilitating symptoms of fatigue, cognitive dysfunction, and often upregulated inflammatory processes. These symptoms have consequences that affect many organ systems.

The Cellular Interface

Molecular medicine begins at the cellular interface—the cell membrane and its extensions throughout the cellular organelles to the molecular level. Each cell is a world within itself, but each cell is affected by the integrated successes and failures of the first interface of outside/inside. For example, the cellular interface includes the membranes of the organelles, where electrons are at risk of being ripped off by oxidative stresses that challenge dynamic balance within the cell.

The Perceptual Interface

The perceptual interface is a free-flowing anatomical systemic interface. This interface describes our sensory apparatus for perceiving and interpreting the world at-large. Immune recognition for the microscopic and molecular world literally requires the intimate processes connected to the outside world (e.g., ingestion, sampling, and processing by macrocytic white cells of molecules originating from outside).

The Memory Interface

The cellular basis for memory resides exclusively in the central nervous and immune systems, which act as a collective system.


The metaphor of dynamic balance is especially powerful and intuitive to both practitioners and patients. Illness results from imbalance in individuals who bring particular genetic strengths and weakness to their environments. Asked simply, what key functional process(es) were working well approximately one year ago, yet today manifest themselves as broken or dysfunctional? Taking the metaphor to another level, the questioning continues: Which of the six interwoven processes most likely has gone awry as this system and has lumbered to a new eccentric dysfunctional state? The same reasoning can be applied to the six functional processes. For example, the joint processes of nutritional and detoxification balance prompts the following two questions: 1) Could this person be failing to get something from his or her environment for which he or she has a special need or deficiency? and 2) Could this person be failing to avoid something from his or her environment for which he or she has a special need to avoid or an inability to detoxify and remove?(55) As you ask yourself these questions, keep in mind Dr. Baker’s Tack Laws: 1) if you are sitting on a tack, it takes a lot of aspirin to make it feel good (suppress symptoms), and 2) if you are sitting on two tacks, removing just one does not result in a 50 percent improvement (web-like relationships).(56)

Naming and Blaming

Old medical maps and guides indicated that sickness happens because “disease entities” attack “victims.” Along this line of argument, Dr. Baker has noted: Those of you who are relatively new to the concepts of functional medicine may be bewildered at first by the need to let go of naming and blaming. Name the illness and then blame the illness for the symptoms. Then look up “the treatment of choice“ for the illness and offer it to the patient with confidence that your peers stand with you. The basic error of the map we were given in our professional matriculation is the failure to distinguish between names, notions, and things.(57) What happens when the functional medicine practitioner abandons the comfort of naming a patient’s disease so that the patient has a group membership (the diagnosis) and has been prescribed the group treatment?

The practitioner is left with what first feels like an unprotected open space, a foggy landscape, where the patient exists alone among her or his inconvenient individuality, a bewildering assortment of “natural” remedies, and the practitioner. Deprived of the convenience of placing individuals in groups (that have all been attacked by the same entity) and applying the same group treatment, the physician is left blinded by the variety of treatments at hand and doubly blinded if he or she tries to travel this land using the old maps. How does one find the way to becoming a happy doctor with establishing resonance among the patient, treatment, and doctor? The message to remember is that we are treating individuals not diseases. Diseases are not entities. They are ideas that we form about groups of people who have similar health problems. We do not treat conditions, and we do not prescribe for symptoms. The reason we listen to our patients’ stories is that those stories give us the best clues about what they may need to get or avoid to achieve better health.

Useful Maps

Logic: Get what is needed; avoid what causes disruption.
Anatomy: Understand the functional interfaces and processes that occur at the interfaces.

Determinants: Investigate the antecedents, triggers, and mediators.

Information: Together with your patient, create a full and rich story of his or her health.

Expectations: List the options based on the information; don’t waste effort on labels. Share with patients the maps and the logic of the maps as the information develops.

Short cuts: Understand the common processes of dysfunction in the medical landscape of the patient’s life (e.g., the epidemic in our culture of EFA and magnesium deficiency).


While retaining much of the approach to the diagnosis and treatment model that characterizes main stream medicine, functional medicine focuses more on understanding the individual biochemical, immunological, and psychological quirks that influence how illness becomes expressed in each person. It is similar to tailoring in that it requires some measuring and some trying it on to see how each treatment fits.

Detoxification as a Metaphor of Empowerment

John Furlong, ND, explains how detoxification is a useful metaphor of empowerment in the following passage:(58) The tenets of naturopathic medicine include prevention of disease and stimulation of the healing power of natural processes…

There are multiple syndromes, pathologies and diagnoses with which a person may be labeled…We can be seduced by our capacity for gnosis…(which) can lead to the patient identifying with a pathological persona… Detoxification represents the potential (for patient empowerment) as powerful as the news of a devastating diagnosis. (The process of detoxification) holds out to the patient the possibility of changing the current process their body (and mind) is immersed in. It allows them to paint their own picture of just what exactly they need “detoxified,” whether that be an organ system, attitude, relationships with other people or society at large. Detoxification is a term sufficiently general to afford unlimited potential and one that does not prevent physicians from pursing specific–even aggressive–treatments at the same time.   


If, as Dr. Baker suggests, “Illness is a signal to change,” then we must help our patients find purposeful and efficacious methods to change. This requires attention to individual peculiarities and searching for the clues to the disharmonies that produce the illness. We need to explore these functional/dysfunctional processes that underlie the many-faceted expressions we have learned to name diseases. Our hope is to separate these functional disharmonies into functional categories or processes to facilitate rethinking and reprocessing our assumptions about diseases.

As Dr. David Deutsch describes these changing priorities: The science of medicine is perhaps the most frequently cited case of increasing specialization seeming to follow inevitably from increasing knowledge, as new cures and better treatments for more diseases are discovered…. But as medical and biochemical research comes up with deeper explanations of disease processes (and healthy processes) in the body, understanding is also on the increase. More general concepts are replacing more specific ones as common, underlying molecular mechanisms are found for dissimilar diseases in different parts of the body. Once a disease can be understood as fitting into a general framework, the role of the specialist diminishes.

Physicians can look up such facts as are known. But (more importantly) they may be able to apply a general theory to work out the required treatments, and expect it to be effective even if it has never been used before.(59) As functional medicine providers, we can look forward to a simplified presentation of dysfunction and disease. We can begin to organize our thoughts along core functional processes, understanding why functional medicine views disease not as an enemy (not even as independent realities) with which to grapple, but as a manifestation of the breakdown of mechanisms which maintain control, resilience, and balance.(60)

Learn more about: Autonomic Response Testing (ART), Energetic Supplement Testing, Integrative vs Allopathic Medicine.


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