Synergizing Germ Theory


Germ theory has been the major guiding force behind today’s biomedical research, practice and ambition. Germ theory evolved over centuries of philosophical exploration of the nature of human character and the origins of life. Humans have an inherent inquisitive longing to know and explain the source of their existence. At some point in the history of Western civilization and for many possible reasons, our collective paradigm adopted a reductionist perspective with which to examine the workings of the universe. Esteemed French philosopher, René Descartes (1596–1650), contributed the initial thoughts and writings on the philosophy of dualism. This binary system dissected the human organism into separated parts leading to the concept of the mind/body split and identifying the mind and body as contrary aspects; henceforth, ‘the dual’.  Scientific exploration began to utilize this mechanistic structure of reduction to observe the fundamental operating systems of life as individual pieces, zooming in and dividing physiological functions to study them. This paradigm continues to govern our cultural endeavors toward all aspects of human life, and in the words of author and herbalist Stephen Buhner, we are all living inside Descartes psychosis.

Two centuries after Descartes, Charles Darwin’s theory of natural selection and “survival of the fittest” arose out of a cultural milieu that was heavily indoctrinated by the “universe as a machine” perspective. There is significant controversy surrounding the interpretation of Darwin’s work, but it is true that his concepts have been applied as a hierarchical structure to reduce, classify, and divide all of the Earth’s living systems and organisms to separate parts functioning in relative isolation.  “Survival of the fittest” has been delineated as survival of the most vicious and brutal, or the survival of those that can out-compete their fellow beings for the acquisition of resources. Natural selection is dog-eat-dog by this treatise, and life is perceived as a battlefield where it’s kill or be killed. This is our good old fashioned ‘I win, you lose’ model of making sure you have enough to eat and that your DNA will survive and continue to proliferate. Humans, of course, have classified themselves as the most highly evolved and, it’s clear, that we appear to have been the most ‘red in tooth and claw’ of all organisms in our capacity to eliminate any and all perceived competitors.


Competition and cooperation have succumbed to this dichotomous split as if there are only two choices with which we may stand in relationship to the living world; as if the road comes to a T paved with blacktop instead of a trail winding through a diverse geography. Nature, life, and the Universe are complex, dynamic systems that contain a multiplicity of qualities and it would be a form of denial to say that competition does not exist. Not only does it exist, but it is at times a necessary force that can bring balance to a pattern or cycle that has gone awry, and nature expresses both competitive and cooperative qualities among others. Competition for resources leads to struggle that then leads to a truce as defined by leading evolutionist, the late Lynn Margulis (1938-2011). This is the win-win method of survival in an ever dynamic universe where life depends on the ability to adapt well. Competition may have an appropriate purpose in the balanced context of life, but it has become the dominant method of action in modern society, economics, environmental policy, public education, medicine, public health policy and scientific methodology. Cooperation and all other symbiotic life systems, being seen as a maladaptation to survival, have been sequestered to the shadows of all that is considered weak, foolish, and unrealistic.  Fortunately, there have been many scientists, philosophers, naturalists, and others who have bravely questioned and studied the logic of Darwinian doctrine.  These modern explorers of the symbiotic universe are rediscovering what primitive people knew intimately. Our ancestral roots didn’t arise from the instruction of modern science or any empirical knowledge of the microscopic collective of nature, but were sustained by intelligent collaboration and intentional resonance with the balanced and dynamic forces of nature.  Our most popular current hypothesis is called Gaia theory and was developed by James Lovelock and Lynn Margulis.  Stephen Buhner, a recent contributor, has written and spoken extensively on this topic and Gaia theory has been the foundation for much of his work with current health issues related to bacteria and viruses.

Traditional biologists generally view all species as isolated units unconnected to the larger ecosystem within which they live or the large system of Earth itself. This perspective-that we or any life-form can be viewed in isolation from all other life-forms-has been encoded in our present cultural epistemology. It is a far from accurate view and has had tremendously negative impacts on Earth and human ecosystems.” ~Stephen Buhner

Lynn Margulis pioneered the scientific exploration of the symbiotic origins of life and conceived Serial Endosymbiosis theory which contends that the very cells that we are all composed of were created by the merger of different species of bacteria. These bacteria were initially in competition for food and nourishment leading to a struggle, which eventually forced them to give in by either innovating or ceasing to exist; they innovated. This innovation or, as I like to call it, creative solution, called for them to join forces, share genetic information , enlarge, expand and re-invent themselves into a new life form.  As evolution continued, more and more complex forms evolved creating a multitude of communities inside communities all related to one another and living in mutuality and symbiosis, ultimately emerging into a myriad of forms of first protocists(one celled organisms with a nucleus), then fungi, plants and animals(that means us). When any particular species grew beyond the limits of its own capacity to obtain nourishment , the ecological imbalance of this situation would create either a natural die off or force a functional innovation often involving the exchange and integration of genetic information.  From this perspective, survival of the fittest becomes survival of the most able to adapt and communicate genetic information effectively.

Our current relationship with bacteria and other pathogens is not based on an understanding of the multitude of forces that define nature synergistically. The competitive interpretation of Darwin’s precepts deeply informed the development of future biological research and scientific doctrine. Germ theory developed through the 1800’s and was scientifically substantiated by Louis Pasteur as he sought a solution to the many serious and life threatening illnesses of his time. He introduced the world to the reality of the many microbes that were prolific in Europe at the time and his theory simply states that germs from the outside environment infect humans and cause disease.  Pasteur was the first scientist acknowledged for his work identifying the previously indeterminate germ as being an ultimate presence in the disease process. This concept is the foundations of our contemporary medical model and it guided Pasteur’s successors to the development of antibiotics and vaccines. This theory led to great advancements in the understanding of how hygiene and cleanliness in medicine and in communities was an imperative to reducing the spread of disease, although:

Bacterial presence is correlated with disease and food contamination. Pasteur’s brilliant experiments enjoy a great legacy. He established the prevalent view: infectious, indeed near-diabolical, bacteria are “germs” that need to be destroyed. The great successes of modern medicine reinforce the idea of microbes as enemy. Cleanliness, sterilization of surgical instruments, and especially antibiotics are all described as weapons of war against microbial aggressors.

 The more balanced view of microbe as colleague and ancestor remains almost unexpressed. Our culture ignores the hard-won fact that these disease “agents”, these “germs”, also germinated all life…..Bacteria, seen only as causes of disease, were then and are now nearly always branded as “enemy agents”. Note how they are “waiting to be conquered” by the “weapons” of modern medicine. It is ridiculous, of course, to describe them primarily in military, adversarial terms: most bacteria are no more harmful than air, nor can they, like air, ever be removed from our bodies and our environment.” Lynn Margulis, Symbiotic Planet


There is no doubt that Pasteur’s contribution has been an important element in our understanding of the nature of microbes and their relationship to all of life. Antibiotics have been undeniably life-saving and we, as a species, have learned a great deal about healing and the influence of microbes on human physiology. It’s not to say that germ theory has not been a significant tool to understand sickness, but it is only a portion of the cycle of human disease and our complete faith and reliance on this slice of life has led us now to a precipice of epic proportion.

Germ theory has contributed to an ontology that would retain humans as victims in a hostile world where we are a separate species living in isolation from others, including the many beings we call ‘pathogens’.  Our western imperial hard wiring has set the stage for our “battle” against these “invaders” that cause disease in the human body at random with no respect to any other contributing factors. Disease has been reduced to simply an interaction between host and germ. Hence, substantiates our obsession with sterilization and weapons of mass destruction towards microbes everywhere.  With the discovery of antibiotics and vaccines our society has been in a marathon race to end all human malady, including death (not really a malady).  We seem to believe that we can amass enough technological artillery to potentially sever ourselves from the ignoble Earth bound forces of nature that are the source of every living cell that constitutes the ‘us’ we think we are.  The discovery of antibiotics seemed, at first glance, to be a miracle and whatever affliction antibiotics couldn’t cure, vaccinations could.

Vaccines were developed for many of the most devastating plagues of humanity and they have been purported as solely responsible for the great reduction and all out near extinction of many a threatening contagious virus and bacteria despite much evidence to the contrary:

“Apparently this war on germs has been a great success, as all of the feared epidemic killers of the 19th century have been conquered. Actually, the ideology of the germ has greatly exaggerated the role of the two great weapons of modern medicine, the vaccine and the antibiotic, in the demise of infectious disease. According to Ivan Illich, "The combined death rate from scarlet fever, diphtheria, whooping cough, and measles among children up to fifteen shows that nearly 90 percent of the total decline in mortality between 1860 and 1965 had occurred before the introduction of antibiotics and widespread immunization."i Adult diseases such as cholera, tuberculosis, polio, and typhoid fever show a similar pattern, which can be attributed more to an improvement in living conditions than to medical advances. Nonetheless, medical propaganda would have us believe that the noble cause of "modern medicine" is to extend it to those backward parts of the globe still in thrall to such diseases. Meanwhile in developed countries, we believe we can be even healthier by extending our vigilance with anti-bacterial soaps, flu vaccines, frequent medical check-ups and earlier screenings.” ~Ascent of Humanity by Charles Eisenstein

Vaccinations have been the source of intense controversy between vaccine advocates and the general public, parent led organizations, and national and international advocacy groups who have been bringing awareness, policy, and attempts at legislation to compensate for the known and unknown consequences of mass vaccination. A discussion of the numerous elements of the vaccination debate is beyond the breadth of this post, but it is obvious that there is enough contrary information to make anyone question vaccine certitude. There is tenuous evidence supporting vaccine efficacy in certain situations but not without risk to an undetermined percentage of people.

Vaccination seeks to instigate our immune system to a state of heightened responsiveness to potentially pathogenic organisms while bypassing certain aspects of natural exposure to disease. While this can indeed be a critical factor in disease prevention, the long-term costs to the optimal functioning of the human organism may be greater than previously expected.” Aviva Romm, Vaccinations

Antibiotics in all their glory have been extensively overused in the hopes of completely eliminating bacterial disease and has, paradoxically, only served to procreate vast resistance in many strains of bacteria that are immune to our most advanced antibiotics. Even when used appropriately, if we take antibiotics to ‘fight’ infection they indiscriminately kill all of the bacteria in our bodies, not just the pathogenic germs. They destroy our own microbial flora that is necessary for many of our physiological processes including healthy immune function. A well-established microflora prevents infection because they provide a spatial barrier to our cells, consume all of the available nutrients(outcompete), and create a chemical barrier of substances that are inhospitable to the growth of pathogenic bacteria. Killing these important bacterial partners makes us more susceptible to future illness and less able to provide ourselves with the appropriate immune response.

All of our modern medical treatments for infectious disease disregard the other variables that create the disease state and, even more importantly, the prospect of disease being a necessity in the evolution of a healthy immune system.  Our very contact with microbial pathogens is necessary for our cellular immune system to instill memory of the process and to differentiate the specific immune cells it needs to protect our bodies in the case of subsequent contact with germs of the same or similar species.  The immune system must exercise itself as any other biological system or else it will atrophy.

The conditions that cause disease cannot be attributed to the all-powerful, ubiquitous germ that invades for no reason and chooses it’s victims at will. There must be hospitable conditions to create a disease state. Healthy physiology is inextricably connected to many variables. A diverse microbial flora is imperative and is the front line of our immune system. Bacteria and other infectious organisms require a medium that will provide the fertile necessities of their existence. An infectious agent doesn’t so much invade, but discovers the appropriate tissue state that will be a supportive breeding ground. Other factors are nutrition, immune function, healthy living conditions and stress level. Bacteria exist everywhere but only become problematic when there are specific given elements that allow them to bombard and overcome a host. This is not a new or speculative theory:

"Pasteur's germ theory was not the only one; there were many competing schools of thought at the time. Researchers such as Max von Pettinkofer and Elie Metchinkoff insisted that it was not the bacteria that caused disease, but an interruption in the normal healthy ecology of the body that allowed pathogenic bacteria to infect it. To prove their point Pettinkofer in Bavaria, Mechtinikoff in Russia, and a number of others around the world ingested liquids filled with millions of cholera bacilli. Other than experiencing a mild diarrhea none became ill. Their point was that human beings live in a sea of bacteria all the time, and the human body has learned throughout its long development to deal with them. Something must be upsetting the body's normal ability to respond to such bacilli and that is what allows them to grow unimpeded. That is the source of disease."  ~ Stephen Buhner, The Lost Language of the Plants

Pasteur had other contemporaries who were also working on a deeper understanding of the nature of disease. French scientist Claude Bernard(1813-1878) was renowned for his work exploring the importance of homeostasis  in an organism’s internal environment as related to the resistance of disease states. He exalted the body’s innate ability to self-regulate and investigated how the presence of disease occurred only when this mechanism was thrown off. Bernard’s precepts were further expressed by Pierre Jacques Antoine Bechamp who, it is believed by some researchers, Pasteur plagiarized in the development of his doctrine. Bechamp postulated that germs did not cause illness on their own but in collusion with a weakened state of disequilibrium in the host. Germs were not perceived as indiscriminate invaders of healthy individuals. The disease state arose from an internal susceptibility and the microbe only an opportunistic collaborator.

It is not entirely clear why Pasteur’s germ theory was accepted while Bechamp and Bernard’s work was disregarded, except perhaps that Pasteur was more adept at self-promotion.  He accordingly had gained a great deal of support from a burgeoning pharmaceutical industry that may have been eager to begin producing vaccines. Both of these theories, germ vs. terrain, are invariably polarized and, as I always contend, dualistic thinking is inherently flawed. I suspect, based on these ideologies and my own understanding and direct observation of the cycles and processes of nature that, with further exploration both scientifically and philosophically, it will become known that illness itself is a dynamic transaction between the underlying conditions of the host organism and its contact with a pathogenic microbe. It is not hard to accept and experimentally validate that the spread of infectious disease is a more than a one-sided mechanistic process of invasion by a foreign organism and this is surely a positive prospect in the face of our now widespread juncture with antibiotic resistant infections. This is precisely the type of impetus that will offer an opportunity for innovation and the formation of a more cooperative, symbiotic, and mutual discourse between humans and the microbial world of which we inhabit and are inhabited.

It is important to acknowledge that perfect health is an ideal and that health and physiological equilibrium are not static states. In fact, nature itself is never static, but always dynamic.  By seeking perfect health, we are again attempting to gain control over natural forces and cycles. By aspiring for some unilateral condition of absolute health we miss out on the experience of being present and alive with the ebb and flow, rise and fall, and cyclical biorhythms of all that is considered life. The goal of healing instead, is to acquire the most resilient qualities of homeodynamasis  that are possible using the wisdom and gifts from a holistic mandala of modalities including all that modern medicine has to offer.


Symbiotic Planet, Lynn Margulis

Vaccinations-A Thoughtful Parent's Guide, Aviva Jill Romm

Herbal Antiobiotics, Stephen Buhner

The Lost Language of the Plants, Stephen Buhner

The Ascent of Humanity: Civilization and the Human Sense of Self, Charles Eisenstein



Louis Pastuer photo credit: Euclid vanderKroew via photopin cc

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