Laboratory Science Deception — An Important Reframe of Disease Causation
Simple Observation — Demolition Crew
I went to a naturopathic medical school which was located on a beautiful campus right on the long island sound. While on campus, you could look around at all the well-constructed buildings, but as soon as you stepped off campus, there were droves of abandoned, and semi-abandoned, buildings. These buildings had broken windows, boarded-up doors, trash everywhere and gangs of raccoons. It would be safe to say that the inside of these buildings was a ghastly sight. Although these buildings lost their functionality a while ago, there was still hope for a rejuvenation process.
While walking home one day, I discovered that a few of these buildings had fences around them and they were being demolished by specialized machinery. I wasn’t used to these types of machines being so close to my residence but I quickly understood their purpose: They were demolishing these buildings as a first step in the reconstruction process. I wasn’t worried that they would destroy my residence because that wasn’t their purpose. I also wasn’t worried about their destructive nature because I understood that the deconstruction process was the first step in rejuvenating this area.
Human Body Analogy — Internal Demolition Crew
Osteoclasts are specialized cells known for mainly doing one thing: Breaking down bone. They appear where there are holes/pits in bone — Their activity/number increases where there is more bone breakdown — They release acidic compounds which can break down mineral structures and collagen/connective tissue — Lastly, their inhibition leads to less bone breakdown and abnormally dense bone. This extra bone density is termed osteopetrosis and the consequences are severe. They include frequent fractures, chronic pain and bone infections — Also, nerve compression leading to vision and hearing loss, facial paralysis and nasal congestion — Don’t forget about bone marrow failure leading to anemia, abnormal bleeding and frequent infections.
Osteoclasts in the body are an analogous representation of the specialized machinery I saw which was demolishing the abandoned buildings. I like this analogy because osteoclasts are breaking down the structural support of the body which is similar to these machines. If you look in other places of the body, this analogy can be expanded upon because there are other types of cells with similar characteristics.
So-called immune cells fit this bill nicely. They are located everywhere throughout the body, with specialized cells residing in specific organs, and other cells travelling around the body as needed. The brain has microglia — The liver has Kupffer cells — The skin has Langerhans cells. Travelling immune cells are termed white blood cells and include neutrophils, macrophages, natural killer cells, dendritic cells, T-Cells and B-Cells. Comparing them to osteoclasts → These “immune” cells are located where degradation processes are occurring throughout the body, but not where osteoclasts reside. Their activity/number increases where there is more breakdown in specific areas of the body, except where osteoclasts reside. They utilize acidic compounds to break down certain materials in locations where osteoclasts are not located. Lastly, their inhibition leads to tissue breakdown around the body, a different negative outcome from osteoclasts, but still negative.
So osteoclasts break down bone and immune cells break down things in different organs and throughout the body where they can migrate. Together they can target a large portion of the body, but they still get help from another major group: Microbes.
Microbes share similar characteristics to osteoclasts and immune cells. They are located throughout the body with a large portion of them residing where food breakdown occurs: The intestines. Their activity/number increases when there is more stuff to break down, such as the large intestine. They secrete various digestive enzymes to break things down. Lastly, getting rid of groups of microbes causes severely negative complications to the digestive and “immune” systems.
To summarize this analogy → A major role of osteoclasts, “immune” cells and microbes in the body is breaking down substances which is similar to the demolition crew at the abandoned buildings. This role is vital for human physiology just like construction crews. Although this role is vital, you could interpret this breaking down characteristic as pathogenic to the body, or antithetical for a construction crew, if you choose to analyze this phenomenon in an isolated manner.
You Can’t See the Forest in the Trees
It’s important to remember that osteoclasts, immune cells and microbes don’t work in isolation, just like demolition crews. To judge them in an isolated scenario could lead to a greatly inaccurate understanding. Just as construction crews have people and machines for demolitions, they also have people and machines for reconstruction. When it relates to bone, these reconstructing cells are termed osteoblasts. At a construction site, nobody would call demolishers bad and reconstructors good. Similarly, we shouldn’t think of osteoclasts as bad and osteoblasts as good — They are both necessary parts of a complex response system whose goal is proper remodeling of bone. This better understanding of bone health is only elucidated by taking a step back and looking at how everything interacts in a complex, multicellular system.
So we know that osteoclasts aren’t inherently bad because they support vital functions in the body and work in concert with osteoblasts to properly remodel bone. Given this knowledge, when osteoclasts are found on diseased tissue, possibly osteoporotic bones, and they are discovered to have increased their destructive actions, it’s logical to conclude that something in the environment is altering their function. Humans are literally created and maintained with the help of osteoclasts so the actual cause of the imbalanced state has to be upstream from them. Osteoclasts and osteoblasts are similar to construction workers in that they are provided instructions about how to do their jobs. Based on these inputs, they perform specific functions. Blaming the osteoclast or the construction worker who is only carrying out orders is simply pointing the finger at the wrong problem.
Similarly, “immune” cells and microbes can be found in higher numbers on diseased tissue, and their destructive activity can be increased. Just like osteoclasts and construction workers, blaming them for the imbalanced state is inappropriate because they are simply following orders based on the inputs of the microenvironment. If there is more stuff to break down, it’s only logical for “immune” cells and microbes to increase their degradation activities. If these cells and microbes are responding to environmental changes, one must look at what changed in the environment to be able to understand what caused this type of response.
This relates to the idea of “autoimmunity” and “pathogenicity.” When immune cells are found associated with degraded tissue, sometimes very degraded tissue, they are incorrectly termed autoimmune cells because they are designated as bad for the body. Similarly, when microbes are found associated with degraded tissue, sometimes very degraded tissue, they are incorrectly termed pathogenic because they are also designated as bad for the body. Both the immune cells and microbes are performing their roles in the specific microenvironment. The “really bad” types of immune cells and microbes are simply associated with “really toxic” microenvironments. Designating them as adversaries only functions to create protocols which work against your body’s response to its state of toxicity.
There is a major fundamental issue that arises when we try to understand diseased states by hyper focusing on microscopic organisms/cells in isolation. We can fall into the trap of thinking that these organisms/cells are imposing their will upon us, and whenever they get angry, they turn on us by starting a destruction crusade. We simply have to remember to appreciate the complexities of the environment before coming to conclusions about specific components in the environment. These organisms/cells are literally a part of us throughout our whole life. When they are discovered on diseased tissue, we should support them rather than trying to suppress and eliminate them.
The same flawed interpretation can happen when we hyperfocus on molecules which are essential for human physiology. We can inappropriately start blaming them for imposing their will on us →
How could a hormone that supports your sexual development throughout puberty, like estrogen or testosterone, be the cause of a tumor?
How could stomach acid be the cause of an ulcer, when it has been used throughout your entire life to support digestion?
How could a gene be the cause of cancer in a middle-aged person when he/she has had the gene all along?
We are eager to ascribe blame to molecules which don’t have a will, yet we can be oblivious to the environmental factors which are right in front of us pulling all the strings.
Interpreting the Imperceptible
It’s important to remember that we can directly observe constructive crews but we can’t directly observe cells, microbes and molecules in their natural environment very well at all. We can use our senses to observe a constructive site and with enough time, awareness and logic, you can get a good idea of what’s going on. Cells, microbes and molecules are too small for direct observation so we need to use tools and techniques to try to understand what’s going on in these microenvironments. Due to this reliance on tools and techniques, these types of indirect observations can be inherently disconnected from reality and become problematic when it comes to accurate interpretation.
Let’s explore how microbes are studied to elucidate this issue.
The Culture Problem
Microbes are ubiquitous in nature and their form and functions are dictated by microenvironments. To study these microbes, the first step is to culture them, also known as isolation (which is an incorrect usage of the word). The process of bacterial “isolation” involves taking a sample of a microenvironment and then adding that to a growth medium, which is essentially another specific, controlled microenvironment meant to represent the ideal conditions to grow out a specific set of bacteria. It’s understood that the growth medium will select for certain bacteria and select against other bacteria based on the composition of the medium. Specific microbes can live in microenvironments with many microvariations, however, microbiologists have their standardized cultures for the microbes that they are planning on working with.
The major problem here is that there is a huge assumption being made→ The isolation/culturing procedure of the microbe doesn’t change the microbe at all. If microbial function is dictated by microenvironments, and in order to study these microbes, they are taken out of their respective microenvironments and placed into artificial cultures, then we are studying artificial situations which are detached from reality to varying unknown degrees. Any conclusions that are drawn about these microbes can only apply to these artificial conditions, not reality. Just because microbes can be taken out of their respective biological systems and kept alive in other artificial cultures, doesn’t mean that their functions have remained the same. Based on the varying interactions between microbial content and growth medium components, molecular lab testing will be able to discover different sets of genetic material and biomarkers in the medium. This shows how microbes will change their characteristics based on the microenvironments that they are placed in. To put it plainly, microbiologists are changing the very things that they are working with BEFORE they try to figure out what they are working with.
The Infection Issue
This manipulation of microbes before working with them has serious consequences, such as the perpetuation of the false idea that germs cause disease, termed “Germ Theory.”
When lab scientists claim to “infect” organisms with microbes to cause disease, they routinely use these artificial cultures as their starting point (they also use other artificial conditions and unnatural administration routes). If they actually used isolated microbes, they would be working with dead or dying microbes because they would have to remove these microbes from their natural microenvironment which is sustaining them. This is why when isolated microbes are used in experiments, effects are minimal. Even if scientists produced effects using isolated microbes, this would be detached from reality because isolated microbes don’t exist in nature, they are always integrated into a microenvironment — Microbes are too small to travel long distances so a sustainable environment is a necessity. When artificial cultures are used, these types of studies are also detached from nature because of the artificial manipulation. Even worse, when these lab scientists use artificial cultures to produce disease, they attribute the entire effect of these artificial microenvironments to one component of it, the microbe. All in all, lab scientists can’t cause disease with isolated microbes, they resort to using artificial concoctions and procedures for causing disease, and then they claim that nature’s biological responders, microbes, are the sole cause of disease.
Look at the challenge/transmission studies below and see how scientists are resorting to artificial cultures and procedures to produce the desired effects. They are not testing natural processes — They are artificially creating diseases which unfortunately is hiding the true causes that we should be discovering.
“Mouse models for the study of Borrelia burgdorferi infection” — Kimberly J Olsen, Shilpa Sachan, Nicole Baumgarth — PMID: 39193882
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Basic Infection Protocol 1: “Intradermal infection of mice via inoculation of CULTURE-GROWN bacteria…”
- Artificial Culture → “B. burgdorferi … was grown in BSK media with 6% rabbit serum at 37°C with 5% CO…” — BSK II media: 6g HEPES (Millipore Sigma H3375), 0.7g Sodium Citrate (Fisher S279–500), 5g D+ Glucose (Millipore Sigma G8270), 0.8g Sodium Pyruvate, stored in a desiccator at 4°C (Millipore Sigma P2256), 0.4g N-acetyl-D-glucosamine, stored in a desiccator at −20°C (Millipore Sigma A8625), 0.3g Magnesium Chloride, stored in a desiccator at room temperature (Sigma-Aldrich M2393), 2.2g Sodium Bicarbonate (Millipore Sigma S8875–500), 5g Neopeptone (Fisher Scientific DF0119–17–9), 1g Tryptone (Fisher Scientific DF0123–17–3), 1g TC Yeastolate (Fisher Scientific DF5577–15–5), IL CMRL Media (Thermo Fisher 11530037), 100ml Rabbit Serum (Thermo Fisher 16120099), 143ml 35% BSA (Millipore Sigma A7979) — “The gene expression profile of tissue grown B. burgdorferi, however, is likely neither representative of that seen in the ticks, nor that expressed in the mammalian host.”
- Artificial Administration → “Anesthetize mice with a short-acting anaesthetic like isoflurane…”
Basic Infection Protocol 2: “Infecting mice with B. burgdorferi through the feeding of live ticks…”
- Artificial Organisms: “Borrelia-infected immunodeficient mice (e.g., B6-SCID_Jackson)” — Created by housing mice in artificial lab conditions, selecting mice with a severe propensity to illness and then excessively inbreeding them over many generations.
- Artificial Conditions: “Use freshly prepared solution of ketamine/xylazine (10:1 mg/kg administered i. p. in a volume of 100ml) or inhalation of isoflurane…”
Challenge model for Helicobacter pylori infection in human volunteers — D Y Graham, A R Opekun, M S Osato, H M T El-Zimaity, C K Lee, Y Yamaoka, W A Qureshi, M Cadoz, T P Monath — PMID: 15306577
- Artificial Culture: “On primary isolation (of H.pylori) from the donor, individual colonies… were picked, suspended in 100 μl of Brucella broth (Difco Laboratories, Detroit, Michigan, USA) with 5% heat inactivated calf serum (derived from certified US herds, HyClone Laboratories, Logan, Utah, USA), and plated onto Mueller Hinton agar (Difco) plates containing 5% heat inactivated calf serum. All plates were incubated for five days in a restricted use CO incubator at 37°C under 12% CO2. … (Samples were placed) into individual tubes of 1 ml Brucella broth containing 20% glycerol (Fisher Scientific, Houston, Texas, USA) and frozen at −70°C. — “The inoculum was prepared by seeding 100 μl of frozen stock to 8–10 Mueller-Hinton agar plates containing 10% heat inactivated calf serum. Plates were incubated for five days at 37°C in a gas pak jar containing a CampyPak Plus (Becton Dickenson BBL, Cockeysville, Maryland, USA) gas generating envelope. Growth was harvested in Brucella broth… Seed inoculum was added to 50 ml of Brucella broth supplemented with 10% calf serum… The inoculated flasks (150 cm tissue culture flasks; Corning Costar Corp., Cambridge, Massachusetts, USA) were loosely capped, then placed in a gas pak jar containing gas generating envelopes, and incubated overnight at 37°C.” — “The contents of the flasks were distributed in sterile 50 ml centrifuge tubes (Fisher) and centrifuged for 20 minutes at 3000 rpm. The bacterial pellet was gently resuspended in sterile saline and recentrifuged. The washed bacterial pellet was resuspended in College Inn Beef Broth (Nabisco Inc., East Hanover, New Jersey, USA)… The beef broth containing the bacterial inoculum (10 ml/challenge) remained on ice until used for the challenge (within 20–30 minutes of preparation).”
- Artificial Conditions: “Subjects… received the… strain of H pylori orally. On the evening prior to challenge, each subject received 40 mg of famotidine to suppress gastric acidity.”
Airborne Transmission of Bordetella pertussis — Jason M Warfel, Joel Beren, Tod J Merkel — PMID: 22807521
- Artificial Culture: “B. pertussis strain D420 was provided by the Centers for Disease Control. Bordet-Gengou (BG) agar plates were prepared with Bordet-Gengou agar (Becton-Dickinson, Sparks, MD) containing 1% proteose peptone (Becton-Dickinson) and 15% defibrinated sheep blood. Regan-Lowe plates were prepared from Regan-Lowe Charcoal Agar Base (Becton-Dickinson) with 10% defibrinated sheep blood and 40 µg/mL cephalexin.”
- Artificial Conditions: “Baboons were anesthetized with 10–15 mg/kg ketamine administered intramuscularly. For directly inoculated (index) animals, the pharynx was swabbed with 2% lidocaine solution and animals were intubated using a 2–3 mm endotracheal tube to deliver 1 mL inoculum to the top of the trachea. A 24-gauge, 3.2 cm intravenous (IV) catheter (Abbocath) was used to deliver 0.5 mL inoculum to the back of each naris.”
A Controlled Human Infection Model of Group A Streptococcus Pharyngitis: Which Strain and Why? — Joshua Osowicki, Kristy I. Azzopardi, Liam McIntyre, Tania Rivera-Hernandez, Cheryl-lynn Y. Ong, Ciara Baker, Christine M. Gillen, Mark J. Walker, Pierre R. Smeesters, Mark R. Davies, Andrew C. Steer
- Artificial Culture: “A chemically defined medium was developed (VR broth) consisting of RPMI 1640 (Gibco) and 2% (wt/vol) Veggietone genetically modified organism-free soya-peptone (Oxoid). Eight-hour growth assays were done comparing growth of M75 in this medium to that in Todd-Hewitt broth (Oxoid) with 1% (wt/vol) yeast extract (Bacto) (THY). Bacteria were grown in 125-ml Erlenmeyer flasks containing 25 ml of VR or THY broth and agitated gently at 75 rpm.”
- Artificial Conditions: “We used Detroit 562 (D562) human pharyngeal cells and skin HaCaT cells, simulating natural sites of infection.” — “Strain virulence was compared in a humanized plasminogen transgenic AlbPLG1 mouse model (36). In separate experiments, groups (n = 10) of AlbPLG1+/− mice were administered subcutaneous doses…” — These mice were specifically altered and bred to be sensitive to certain Strep species by expressing human plasminogen under the control of a mouse albumin promoter.
Lab scientists have essentially been cheating to cause the diseases they are looking for. This serves to perpetuate the idea that germs are the sole cause of disease. When you consider this necessity to cheat, or lower the standards, it actually provides solid evidence to refute the Germ Theory. Despite this evidence against their hypothesis, they continue to hyperfocus on microbes while the discussion of the natural disease-causing microenvironments gets lost in translation.
Disease-Causing Microenvironments
Let’s examine an acute disease that everyone is familiar with: Food poisoning. Many people understand that foods can be health-promoting in certain instances, and unfortunately many people also know that foods can cause acute problems, such as nausea, vomiting and diarrhea. The same health-promoting food can turn into a disease-promoting food if the environmental conditions allow/promote it to do so. Both types of foods contain specific sets of microbial life and they will differ according to the specific environmental conditions. When people “get food poisoning,” they can get tested for the presence of a microbe which leads people to think that the microbe is the cause of their illness. In reality, the microbe is simply the biomarker that can be tested to analyze the microenvironment that led to the illness. Since nobody eats microbes in isolation, it’s logical to conclude that the cause of food poisoning is the consumption of spoiled, contaminated food.
Another example to consider is the process associated with producing milk. A farmer could milk a cow, collect the fresh milk in a jar and drink it for health-promoting effects. On another occasion, that farmer could milk a cow without proper sanitary conditions and get feces in the milk. He could store that milk in a humid, hot and moldy basement for a few months. He could then subsequently drink that milk and “get food poisoning” because the milk was contaminated and spoiled. You could blame the microbes in the spoiled milk but they weren’t responsible for milking the cow and storing the milk. Certain microbes existed naturally in the properly produced milk and other microbes flourished in the altered conditions associated with the spoiled milk. The conditions dictated the microbial content and the spoiled milk caused the food poisoning, not simply the isolated microbe.
Taking this information into account, we can predictably estimate which microbes will inhabit a certain location in an organism based on the characteristics and composition of the microenvironment. We can take a biological sample from the human body, perhaps a stool sample, and identify specific sets of microbes that relate to the diet and digestive function of the individual. Heavy meat eaters will have a specific set of microbes, vegans will have a different set and people with acute/chronic digestive issues will have yet another set. In these examples, the foods and digestive function provide varying microenvironments which cause shifts in the microbial content of the bowels. The foods and digestive function are the cause; the microbial content is the effect. The microbes will then produce genetic material and other biomarkers based on the specifics of the microenvironment.
This is the important point → Microbes exist within complex microenvironments and solely blaming them for any problem is denying their interconnected and responsive roles within microenvironments (similar to inappropriately blaming osteoclasts and “immune” cells). When we talk about “bad” and “good” bacteria, we are really talking about microenvironments which are associated with poor health and cause disease vs associated with good health and promote optimal function. Finding genetic material and biomarkers in a human body simply illustrates the metabolic capacity and current metabolic characteristics of the microenvironment — These markers are associated with “bad” or “good” bacteria, but they are once again pointing to a disease-causing or health-promoting microenvironment as the real issue.
When microbes produce “toxic” compounds which can generate physiological problems, it’s important to remember the story about osteoclasts → Analyzing an isolated phenomenon, such as osteoclasts breaking down bone, can lead to an inaccurate understanding, mainly that osteoclasts are bad for human health. Appreciating the causative influence of the environment can lead to a better understanding → Microbes, osteoclasts and immune cells are part of a complex response system and their actions are dictated by the environmental inputs. If microbial byproducts are considered bad for human health, such as bacterial endotoxins, then the complete microenvironment which led to these byproducts needs to be addressed and eliminated from the body.
Just as microbes can produce toxic compounds, they can create vital compounds for the human body. They can create vitamins, neurotransmitters and short-chain fatty acids (good fuel source) to name a few. The inputs available to the microbes, the microbes themselves and the products they create are all important to understand. This is why many supplement companies started selling probiotics (microbes), then they added prebiotics (inputs) and then they finally added post-biotics (microbial products). To make things easier, you could simply consume a fermented/cultured food because it will contain all the inputs, microbes and products in a natural mixture. The beneficial health effects of these cultured foods, which are essentially specifically designed microenvironments, has been known for a long time.
A Better Understanding
Due to the overmanipulation of microbes in science labs before experimentation, modern-day scientists are missing the boat when it comes to understanding microbes in the human body. Many scientists in the past, across different continents, had discovered tiny little organisms called somatids, microzymas, etc. with microscopes they were able to build themselves. They built high-quality microscopes but they couldn’t magnify samples beyond the capabilities of modern-day microscopes. The special designs weren’t just focused on providing the highest intensity of magnification, but on examining the microscopic world in its most natural form. The “trick” that they used was to not stain the biological sample before viewing it and to try to observe the tissue samples in their most biologically reminiscent state, as fresh as possible (the longer the sample is detached from the body, the less it will resemble its natural characteristics). By viewing fresh, unadulterated tissue/blood samples, the pleomorphic cycle became observable, where the mobile microzymas could morph into various forms of microbes and back, depending on the environmental conditions. From this perspective, bacteria, fungi and other microscopic life forms are not foreign entities — They are derived from an internal precursor.
With the right microscope and an unadulterated, fresh blood sample, you can see microzymas traverse the landscape and enter and exit cells. This basic observation indicates that they have both intra and extracellular effects. Extracellularly, they can be seen to pleomorphize into various microbial forms — Intracellularly, they could be stimulating the function of the specific tissue/cell. So-called intracellular vesicles, such as peroxisomes/lysosomes and endosomes, could simply be derivatives of these microzymas.
These tiny life forms could actually be the orchestrators of our consciousness on a microscopic level → They can change into different microbial forms in certain environments which require more breakdown and they can go inside cells/tissues to orchestrate the construction of products which can be used by the body in some capacity. In part, they are responding to the environment — In another capacity, they are invoking their will upon the environment with the capabilities allowed via the blueprint of the body.
If the will of the organism is to live and it’s challenged by a perturbation of the terrain, these microzymas could utilize the blueprints of the tissues to produce various proteins, signalling molecules, etc. to bring the terrain back to homeostasis, while concurrently creating the necessary microbial life forms to aid in the same mission. From this perspective, there exists a blueprint of the body which is a static item brought into existence by these microzymas. These tiny organisms could be the precursors to all the internal mobile parts of the body and provide the necessary spark of microscopic life within complex organisms. It’s as if microzymas can put on various hats, like construction or chef hats, and then change their form and function to carry out all these necessary microscopic activities.
When taking this new model of microscopic life into account, it becomes rather obvious that there is always a good reason for all the specific microorganisms and activities which are occurring at specific locations. You wouldn’t think that a degradation process carried out by a cell or microbe, such as an osteoclast/immune cell or bacteria, is caused by an invading pathogen bent on your destruction. You would understand the complex requirements of the body in different terrains, and know that the microscopic life forms are working with you, not against you. You would understand the best way to solve a problem is working through the problem, such as a remodelling process, not simply stopping early because it’s easier. From a medical perspective, you would understand that concentrated antibiotic formulations are working against the microbial forms of your microzymas, and taking them could provide certain beneficial short-term effects, but they will increase issues long-term.
Optimize Health
To truly understand how to support ourselves in the most natural, optimal ways, we must truly understand ourselves. The microbial environment is a reflection of our own consciousness. How we interact with the macroscopic world will dictate our microscopic selves. A beneficial relationship with our surroundings will then translate into beneficial microterrains. This is why things like good nourishment, movement, relationships and lifestyle are so important for our total existence, including our microenvironments.
Although we can gain insight from analyzing microenvironments, we have to be careful about the techniques and tools that are used because they can distort our understanding. Being too reductionistic, we can greatly misunderstand the goals of our own cells and microbes throughout our bodies and treat them as enemies. The good news is that we actually don’t need to have any microscopic knowledge to understand how to live a healthy life. There aren’t any secrets to health that are hidden within research labs. We can live by principles which have been derived from our macroscopic experiences. We can use our five senses, reasoning capabilities and passed down wisdom to reach our full health potential. We can cultivate our passion to create flourishing environments, big and small, which are teeming with vitality. We can use our human potential to shape a beautiful world. This is the path towards healing for you, me and the world.
Written by Derek Reilly ND — 8/19/2026




