Germ Theory Is Incomplete | Part 2
After a full year of ruminating on this topic, the time has come for Part 2 of this conversation.
For those who are new here and haven’t read Part 1 of this series, I would highly recommend you read it before proceeding.
In the first part, we discussed the origins and basic tenets of germ theory, insofar as it aims to prove that certain micro-organisms are the proximate cause of disease. We also discuss how and why this framework falls apart under the slightest scrutiny.
We also discussed Terrain theory, which has been historically presented as the competing model to germ theory. Evidently, a combination of research funding and sociocultural trends have favored a “germ” and “infectious” framework. This is likely why Germ Theory prevailed in the academy as the de facto model to inform Infectious Disease (the medical discipline).
As you may expect, the truth tends to lie somewhere in the middle.
In my opinion, Germ Theory is a special case of Terrain Theory. In other words, these are not mutually exclusive models. Rather, one (germ) is a subset of the other (terrain).
There are two important contentions that arise when I make this statement.
First, what does that even mean?
Second: “But, antibiotics!”
I think what people want to know is, once we understand the role of microorganisms in this new framework, how do we address states of “infection?”
Which are great questions. Let’s dig in.
Germ Theory Is The Special Case
The fundamental framework of germ theory is that disease in humans is caused by the presence/growth of a micro-organism. That is to say, a specific disease’s proximate cause is the presence of a specific microorganism.
For example, one alleged cause of community-acquired pneumonia is streptococcus pneumoniae.
Even with something as common as pneumonia, we immediately encounter a problem. As mentioned in Part 1, our lungs are filled with bacteria and bacterial genomes (important because we typically test for presence of genes when diagnosing these days; see PCR).
The bacteria which are supposed to be the cause of pneumonia (e.g. Haemophilus Influenzae or Strep Pneumoniae) are routinely found in the lungs of people who are healthy and without any clinical symptoms of respiratory dysfunction.
This is the case nearly everywhere you look:
The skin is covered in bacteria.
The GI tract is covered in bacteria, including Clostridium difficile in patients with no gastrointestinal symptoms.
The urinary tract has many bacteria, and is often inappropriately treated as a “urinary tract infection” despite the fact that the patient has no symptoms.
Typically, germ theory apologists will say something like “these are opportunistic infections” or “there are other risk factors for infection.”
But, what they don’t realize is that they are actively making a case for Terrain Theory.
How?
Let’s look at this from the perspective of a specific bacteria. Actually, the example of C. Difficile is very informative here.
If your host’s GI tract experiences a major disturbance, what does this mean from your (C. Diff’s) perspective?
Simple: the environment in which you reside (the colon) has changed. As a result of your environment changing, a new equilibrium develops by an interaction of the resources in the colon and the life-forms which exist in it.
A certain percentage of humans have detectable levels of C. Diff under normal conditions. Typically, a C. diff “infection” arises in people who have received antibiotics which destroy bacterial populations of the gut.
This event signifies a change in the environment (or terrain).
This drastic change in the gut allows bacteria which are more hardy and competitive to flourish. Like Clostridium difficile.
Now, in this example - tell me:
What is the proximate cause of gastroenteritis/diarrhea/toxic megacolon?
Is it the C. diff? Or, the antibiotic which created the conditions for C. diff to grow?
Is it the bacteria at fault? Or, whatever caused a change in the environment? Because, fundamentally the bacteria hasn’t changed.
The bacteria continues to act as it always has. But, the environment has changed.
This is the case with many infectious diseases. ‘Opportunistic infection’ and ‘risk factors’ all account for the same thing.
Something has changed in the host - which is indistinguishable from the environment, from the perspective of the microorganism.
Sometimes the change in the environment allows something that was always there to flourish.
Other times, a change in the environment introduces a new microorganism.
For example, if you cut your skin - you now have a defect in the boundary between the surface of the skin and the soft-tissue underneath. This allows bacteria to move from one environment into another, and initiate an inflammatory response we call cellulitis.
If a surgeon makes an incision, he runs the risk of moving skin-surface bacteria into a deeper cavity of the body. This is why they sterilize the surface before they start cutting.
From the perspective of the micro-organism, this is the same thing.
You can either change the environment the bacteria is already in, or you can move the bacteria into a new environment.
In both cases, the living organisms and resources of this new environment have to arrive at a new equilibrium.
Sometimes, this process results in a strong inflammatory response which threatens the host (human).
How Do We Handle Infections?
This brings us squarely into the conundrum people seem to face with this new perspective.
If we accept this new framework, how do we deal with bacteria?
There have been a handful of times where I have had very strong bouts of bronchitis/pneumonia. As I am sure many people have had.
Personally, I do not resort to antibiotics. Because, as we already discussed, antibiotics tend to result in environmental disruptions elsewhere in the body.
My first and second line of treatment is to support my body:
Rest. Nutrition. Hydration. Sleep. Supplements.
All of the typical things your grandmother told you to do.
Almost always, the body takes care of itself if you provide it with the appropriate support. In fact, I haven’t taken any antibiotics in several years.
Now, of course there are people who are already at such a disastrous baseline health (chronically ill) that they may need more support than others, and in some cases need antibiotics in addition to all of the other supportive measures.
In my opinion, antibiotics alone are rarely the answer.
One More Critical Consideration
I find the assumption that microbes are intent on hurting us unconvincing.
I am not referring to the fact that viruses are not alive, and therefore can have no biological drive. This is a separate issue.
As far as I can tell, higher lifeforms (like mammals) have intention to kill or harm other lifeforms. But, it is a stretch to think that a single-celled organism can have intent to harm on the basis of something like territory.
This implicit assumption may just be a case of anthropomorphizing.
But, the question remains: how do microbes hurt us?
For the most part, harm from microbes arises from competition for resources. These resources can be as basic as nutrients, water, or oxygen. Or, as complex as hijacking cellular machinery for the needs of the microbe. An example would be of viral information taking up the genetic and protein expressing bandwidth of a cell.
There is one more way that microbes can to hurt us. This is by toxins. Toxins that microbes can release, or toxins that our own cells can release under times of distress. Important to note, not all microbes make equally harmful toxins.
In the early phases of microbial proliferation (or “infection”), this toxin load can be negligible. Usually, a healthy person will handle both the microbe and toxin without need for any additional intervention beyond support of the body.
However, conditions in which microbial proliferation is prolonged, the body is under greater distress. Or, in a person who is severely unhealthy…this toxin load can be overwhelming.
Which brings us to the final consideration, “anti-toxins.”
I use quotation marks here, because I am not referring to substances that are strictly marketed as anti-toxins. Anything can be a toxin, depending on which substance is present in your body at toxic levels. For example, if for some reason you have an overload of Fluorine in your body…you can consider use of Iodine to displace Fluorine, as they have similar hydration shells and interactions in the body.
In Summary
The best way to fortify your body against abnormal microbial proliferation, or dysbiosis, or “infection” is to fortify your body.
For someone in good metabolic health, it is rare to be critically and chronically affected by short-term fluctuations in microbe population.
It is almost always those who are chronically ill who suffer the most.
Secondly, if you do find yourself quite stressed by this dysbiosis…then, the ideal first-line approach is to support the body. Rest, nutrition, hydration (includes electrolytes and minerals), and natural remedies when possible.
Antibiotics are to be reserved for severe situations, unless you want to pay the price of dysbiosis that is caused by the antibiotic as well.
Finally, in the most severe cases, it may be worthwhile to address accumulation of toxins.
Anecdotal but certainly fits the idea of Terrain....
About six years ago I stopped getting my teeth cleaned regularly, after the dentist had referred me to an oral surgeon for an unnecessary and botched biopsy. And then the "virus" holocaust closed down the dentist for a couple years. I've been suffering from the neglect in obvious ways, plus one non-obvious way. Two years ago I had a UTI for the first time ever, which turned out to be caused by Klebsiella, not E coli. Klebsiella is typically a mouth bacterium.
Migrant got into the wrong terrain where the border patrols weren't authorized to deport it.
I finally got back to the dentist last year, and after many months of waiting because they're overworked and understaffed after the "virus" holocaust, I'm getting a deep cleaning. The first part is done, and the second half will be done on Friday. The difference between sides makes a dramatic controlled experiment. No more pain or swelling on the cleaned side. I've learned my lesson!