The Neolithic period in our evolutionary history ushered in the development of agriculture, as tribes of Hunter gatherers increasingly converted their lifestyle from nomadic tribes to community oriented farmers who relied on the development of agriculture for their survival. Roughly 10,000 years before the Neolithic period, as they were gathering seeds in a meadow well populated with plants (that have since been developed into modern-day wheat), one or more of our ancestors apparently became inspired with the idea of planting some of the seeds from the most productive plants to see if the offspring would produce better than average yields. That simple act proved the benefits of a policy that has survived the test of time, and is still used today as the primary selective breeding technique used by plant breeders. In other words, when producing seed for next year's crop, foodgrains, such as corn, wheat, and rice, for example, are selected for high production potential, in order to feed a growing world population. Pre-Neolithic soils were rich with nutrients. Ever since the beginning of time, nothing had been taken out of the soil that hadn't been returned, as expired plants and animals decomposed so that their nutrients were returned to the soil. When rain fell, minerals (such as magnesium, potassium, and calcium, for example) leached from various rocks to enrich the soil and river and lake water. Nutrient content of the soil is critical for both plants and animals. Over time, intensive agriculture without adequate replenishment of nutrients can strip soils of essential minerals, which cascades through the entire food system, affecting plant health, animal nutrition, and ultimately, human health. When soils are depleted of essential minerals like magnesium, zinc, selenium, iron, and potassium, crops grown in those soils typically show a reduction in mineral density. This is well-documented in multiple studies showing declines in nutrient content in fruits, vegetables, and grains over the last 50–70 years. For example, wheat and spinach today have been shown to contain significantly less iron and magnesium than in the mid-20th century. Crops grown in mineral-poor soils also tend to be more vulnerable to pests and diseases, reducing yield and quality. Fertilizer practices often don't replace micronutrients. Modern industrial farming often relies heavily on N-P-K fertilizers (nitrogen, phosphorus, potassium), which encourage plant growth but don’t replenish trace elements. Over time, this creates an imbalance — high yields, but with reduced nutritional value. Animals raised for meat, milk, and eggs rely on either forage or grain crops for nutrition. If these crops are grown in depleted soil, the animals consuming them may also suffer from subclinical deficiencies of key minerals. Furthermore:
These mineral deficiencies often don't cause obvious disease but can reduce productivity and meat quality, which can then affect the nutrient density of the animal products humans consume. Ultimately, this affects human health. When the entire food chain is built on nutrient-depleted soils, the end result tends to be: Lower dietary intake of essential minerals (like magnesium, iron, zinc, iodine, and selenium). A higher risk of micronutrient deficiencies, especially in populations dependent on local food systems or in regions with poor soil health. Soil is not just a growth medium — it's a living system that directly influences the nutritional quality of our food. When it becomes depleted, the effects ripple across ecosystems and food webs, from plants to animals to humans. Long-term food security and nutrition depend not just on crop yields or animal growth rates, but on investing in soil health as a foundational pillar of agriculture. Selective breeding of grains such as corn, sorghum, wheat, and rice has historically emphasized enhancing yield and accelerating growth to meet the demands of a growing global population. While these efforts have successfully increased production, they have also led to notable changes in the nutritional composition of these crops. Prioritizing yield can result in the "dilution effect," where the concentrations of essential nutrients decrease as carbohydrate content increases. This phenomenon has been observed in various crops, including vegetables and grains. In wheat, for example, breeding for higher yields has been associated with reductions in protein content and essential micronutrients such as iron and zinc. Some plant breeders have attempted to enhance grain nutrition. To counteract nutrient reductions, biofortification strategies have been implemented. These involve breeding crops to enhance their nutritional profiles. A notable example is Quality Protein Maize (QPM), developed to contain increased levels of lysine and tryptophan, essential amino acids lacking in conventional maize. Note that the U.S. refers to maize as "corn", while most of the rest of the world uses the term "maize". Unfortunately, few farmers plant QPM. Despite the fact that QPM varieties have been available for approximately 50 or 60 years, and new varieties with improved and enhanced features have been introduced within the last 30 or 35 years, less than 1% of the corn produced in the U.S. is from this category. Worldwide, precise statistics are not available, but probably less than 5% of the corn/maize produced has QPM genetics. It's most widely used (5–10%, depending on the country) in sub-Saharan Africa, where diets rely heavily on the use of maize. A recently posted online article with the title "Fruits and vegetables aren't as nutritious as they used to be. What happened?" describes many of the nutrition problems with today's food (Millerm, 2025, March 27).2 The article notes that fruits, vegetables, and grains today are less nutritious than they were 70+ years ago, with notable declines in six key nutrients:
And the author mentions that a him study cited found up to a 38% drop in riboflavin (vitamin B2) in commonly consumed vegetables since the 1950s. In addition to the problem of soil nutrient depletion, modern crops are bred for higher yield, pest resistance, and faster growth, and this typically occurs at the expense of nutritional value. In other words, fast-growing plants accumulate fewer nutrients per unit of weight. Even global warming negatively affects nutrition levels of plants. As the author points out, rising CO2 levels may increase carbohydrates (sugars and starches) in plants while diluting minerals such as zinc and iron, because increased CO2 levels increase photosynthesis rates. Can utilizing organically produced foods improve our nutrition? The author recommends choosing organically produced food because it's often more nutrient dense, and grown in healthier soils. While research shows that organically managed soils typically contain more nutrients than soils used in conventional commercial production, whether or not the food produced by organic methods actually contain more nutrients than conventionally produced foods depends on which nutrients are under consideration. It is under certain conditions, but the difference is not universal across all foods, and results vary, depending on the crop, farming practices, and environment. A major 2014 meta-analysis published in the British Journal of Nutrition analyzed 343 peer-reviewed studies and found that organically produced crops had 18–69% higher levels of antioxidants like flavonoids and phenolic acids. These compounds have been linked to lower risks of chronic diseases. And some studies showed higher levels of iron, magnesium, and phosphorus in organic vegetables and grains. Organically produced milk, meat, and eggs often contain higher omega-3 levels due to grass-based feeding and access to pasture. But that doesn't mean that organically produced foods are always better. The study showed that organically produced crops did not always show higher levels of certain macronutrients (such as protein, carbs, and fats). In the study, these levels were usually comparable between organic and conventional produce. Some studies showed slightly higher levels of vitamin C and calcium in organic produce, while others showed no significant difference. Comparing organic and conventional crops, the bottom line appears to be:
The researchers concluded that organic foods can be more nutrient-dense, especially in antioxidants and certain minerals, but the difference is not guaranteed across the board. Looking at a more recent study: A more recent comprehensive systematic review of 147 scientific articles, designed to evaluate whether organic foods are consistently more nutritious than conventional foods (based on 68 different food types, and the consideration of 22 nutritional properties) found that (Thaise de Oliveira Faoro, et al., 2024):2 1. 29.1% of comparisons showed significant nutritional differences between organic and conventional foods. In these cases, organic foods may have shown higher nutrient levels or lower levels of contaminants, but only in specific foods and nutrients. 2. 29.0% of comparisons showed inconsistent results across studies. Some studies found differences, and others did not, so there was no consensus. 2. 41.9% of comparisons showed no significant difference in nutritional content between organic and conventional foods. The researchers concluded that there was no generalizable nutritional superiority of organic over conventional foods. In other words, nutritional advantages of organic foods are specific to certain food types in certain nutrients. Therefore, the belief that organic is always more nutritious is not supported by this large-scale review. Feedlot animals and poultry: Selective breeding in feedlot animals and poultry has long focused on enhancing traits like rapid growth and improved feed conversion efficiency. While these advancements have bolstered production metrics, they have also introduced notable changes to the nutritional composition of meat, particularly concerning fat content and fatty acid profiles. Selective breeding has led to leaner meat in certain livestock breeds. For instance, the Large White pig (a British breed) is renowned for its efficient feed conversion and high slaughter value, resulting in a significant proportion of lean meat. The emphasis on rapid growth and leanness can affect the balance of fatty acids in meat. While leaner cuts may have reduced total fat, the composition of essential fatty acids, such as omega-3 and omega-6, may also shift, potentially altering the nutritional quality of the meat. Beyond nutritional changes, intensive selection for growth traits has been linked to meat quality issues. In poultry, conditions like woody breast, white striping, and spaghetti meat have emerged, affecting texture and consumer acceptance. No easy solution exists. The healthier soil, environmental practices, and reduced chemical exposure often associated with organic farming are real benefits, but do not guarantee better nutrition in every crop. Decisions about organic vs. conventional foods should consider specific goals (for example, reducing exposure to pesticides, supporting sustainability, or seeking higher antioxidant content), not just perceived nutritional superiority. References 1. Millerm, K. (2025, March 27). Fruits and vegetables aren’t as nutritious as they used to be. What happened? Yahoo!Life, Retrieved from https://www.yahoo.com/lifestyle/fruits-vegetables-aren-t-nutritious-090004954.html 2. Thaise de Oliveira Faoro, D., Artuzo F.D., Rossi Borges J. A., Foguesatto, C. R., Dewes, H., and Talamini, E. (2024). Are organics more nutritious than conventional foods? A comprehensive systematic review. Heliyon, 10(7), e28288. Retrieved from https://pmc.ncbi.nlm.nih.gov/articles/PMC10987935/
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Autoimmune diseases such as IBDs, rheumatoid arthritis, and multiple sclerosis have long been treated with powerful immune system-suppressing drugs. These medications, while effective, can be expensive, and come with significant side effects, including an increased risk of infections. A possible groundbreaking approach, using vagus nerve stimulation (VNS) may be a promising alternative (Hanilton, 2025, February 3).1 The vagus nerve runs from the brainstem through the body, connecting to major organs like the heart, lungs, liver, gut, and spleen. This nerve is a key component of the autonomic nervous system, helping to regulate inflammation and immune responses. Vagus nerve stimulation involves the use of implanted devices that deliver tiny electrical pulses to the vagus nerve. The idea that the vagus nerve could control inflammation was discovered over 20 years ago when researchers observed that an experimental drug given to rats not only prevented brain inflammation but also reduced systemic inflammation. Further investigation revealed that the vagus nerve acted as a brake system for inflammation, sending signals that instructed immune cells to reduce cytokine production, thereby preventing excessive immune responses. SetPoint Medical, a company specializing in bioelectronic medicine, has developed an implantable VNS device that is currently under review by the U.S. Food and Drug Administration (FDA). The agency is expected to make a decision by late 2025. A pivotal study involving 242 rheumatoid arthritis patients demonstrated that after 12 weeks of vagus nerve stimulation:
This treatment would provide many advantages over traditional treatments.
SetPoint Medical is now assessing VNS effectiveness in:
VNS provides a way to utilize the body’s own electrical signals to heal itself. If approved, this technology could revolutionize how autoimmune diseases are treated, offering a non-pharmacological option that harnesses the body's own regulatory systems. Much of the modern research into VNS and inflammation is being conducted at the Feinstein Institutes for Medical Research. Scientists are mapping the vagus nerve’s pathways and even converting its electrical activity into real-time audio signals, providing unprecedented insights into its role in immune regulation. While vagus nerve stimulation is not yet a mainstream treatment, its potential is undeniable. With ongoing research and FDA approval on the horizon, VNS may soon provide a revolutionary step in the management of autoimmune diseases — offering patients an innovative, non-drug-based method to control chronic inflammation and improve their quality of life. Reference 1. Hanilton, J. (2025, February 3). Vagus nerve stimulation may tame autoimmune diseases. NPR, Retrieved from https://www.npr.org/sections/shots-health-news/2025/02/03/nx-s1-5272748/vagus-nerve-stimulation-may-tame-autoimmune-diseases
Researchers at the University of California, San Francisco, recently published a study about using the ketogenic (keto) diet to help reduce inflammation in autoimmune disorders based on its effects on gut microbiota and immune modulation (Alexander, et al., 2024).1 For IBD patients, including microscopic colitis (MC) patients, this should be a topic of interest, since their clinical symptoms are the direct result of chronic inflammation. And a comparison of the ketogenic diet with the elimination diet recommended by the Microscopic Colitis Foundation (and discussed in detail on their discussion and support forum) for the past couple of decades, shows that the elimination diet is indeed, a specialized form of the ketogenic diet designed to minimize carbohydrates, and eliminate the food sensitivities so common with MC. The research article points out how the ketogenic diet could be a promising approach to manage inflammation, with a few key considerations based on the study's findings. Ketone bodies act as anti-inflammation agents. The ketogenic diet leads to the production of ketone bodies, especially β-hydroxybutyrate (βHB), which has been shown to have anti-inflammatory effects. For patients with autoimmune diseases like MC, this is significant because βHB can reduce immune activation. Specifically, βHB was found to help mitigate the activation of pro-inflammatory T helper 17 (Th17) cells in mice with multiple sclerosis (MS), suggesting a similar benefit might be possible for MC patients, whose inflammation also involves immune system overactivity. By reducing the activity of Th17 cells, which are involved in many autoimmune processes, βHB could help reduce the chronic inflammation seen in MC. Gut microbiome modulation: The study discovered that βHB influenced the gut microbiome by promoting the growth of specific beneficial bacteria, such as *Lactobacillus murinus*. This bacterium, when enriched in the gut, produces indole lactic acid (ILA), a metabolite that further reduces immune activation. For MC patients, fostering a gut environment that promotes anti-inflammatory bacteria like *L. murinus* could be valuable for reducing colonic inflammation. A ketogenic diet that supports the production of βHB and, in turn, encourages beneficial bacterial activity might create a less inflammatory gut environment, reducing symptom severity for MC. βHB supplementation may be beneficial. One of the significant findings of the study was that βHB supplementation alone provided benefits similar to the keto diet in reducing inflammation. This research was done based on a mouse model, but if research on humans supports this approach, MC patients might be able to consider βHB supplements as a way to reduce their inflammation (and their clinical symptoms). For MC patients who have difficulty following a strict ketogenic diet, βHB supplements might offer a more practical alternative. Or, more importantly, for those who are unable to attain remission despite following a strict elimination diet for an extended period, βHB supplementation might provide a way to gain relief from symptoms. This approach reduces the need for powerful medications. MC is often managed with anti-inflammatory medications, immunosuppressants, and corticosteroids. Incorporating the ketogenic diet or βHB supplementation may help reduce dependence on these drugs, and minimize the risk of the possible side effects that are sometimes associated with them. Given that many medications can have side effects that exacerbate digestive symptoms or further disrupt the gut microbiome, βHB supplements could serve as a complementary approach to conventional treatments. By reducing inflammation through dietary intervention, patients are typically able to experience improved outcomes with fewer medications and, subsequently, fewer side effects. This research at least partially validates our MC diet recommendations. For almost 20 years (since the creation of our MC Discussion and Support Forum) we've recommended using a a modified version of a ketogenic diet especially modified to avoid the common food sensitivities associated with MC as a way to control the symptoms of MC, and put the disease into remission. According to this research, our recommended treatment has been correct all along. And if future research is published showing that the human response to the ketogenic diet is similar to the response demonstrated by the mouse model used in existing research (in other words, if the human response to the keto diet is shown to result in βHB production), then maybe we will be able to add a recommendation of βHB supplementation to our treatment guidelines. Reference 1. Alexander, M., Upadhyay, V., Rock, R., Ramirez, L., Trepkam K., Puchalska, P., . . . Turnbaugh, P, J. (2024). A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity. Cell Reports, 114891. Retrieved from https://www.cell.com/cell-reports/fulltext/S2211-1247(24)01242-7
Consider that B cells are like the "memory keepers" and "weapon-makers" of our immune system. They're a type of white blood cell that plays a vital role in defending our body against harmful invaders like bacteria, viruses, and toxins. When a pathogenic bacteria or virus enters our body, B cells can recognize specific parts of it, called antigens. Think of antigens as the unique "name tags" on the invaders. Once a B cell recognizes an infectious agent, it gets to work making antibodies, which are like custom-designed weapons that specifically target the invader. These antibodies latch onto the invader's antigens and help neutralize it or mark it for destruction by other immune cells. After the infection is dealt with, some B cells become "memory B cells." These cells stick around and remember the pathogen for a long time. If the same pathogen tries to invade again, these memory B cells can produce antibodies much faster, stopping the infection before it can make us sick. This is why we often don't get the same illness twice and how vaccines work. B cells don't work alone; they get help from other immune cells, like T cells, to become activated and know which invaders to target. B Cells are vital for the proper functioning of our immune system because:
Without properly functioning B cells, our body would struggle to recognize and fight off infections, leaving us vulnerable to illnesses. They're a key part of keeping us healthy and protected over the long term. Compromised kidney function can interfere with the production of B cells. Research shows that chronic kidney disease (CKD) reduces the survival and function of B cells (Peroumal, et al., 2024).1 Uremic toxins (molecules that accumulate in the bloodstream due to inadequate kidney functioning), particularly hippuric acid (N-benzoylglycine, an amino acid derivative found in the urine of humans after the consumption of fruits and juices), accumulate due to kidney dysfunction and induce B cell apoptosis (programmed cell death and replacement) by impairing mitochondrial function through the G protein-coupled receptor 109A pathway. So what does this actually mean? Mitochondria are tiny structures inside our cells that act like power plants, producing the energy our cells need to work properly. If something impairs mitochondrial function, it means the energy factories are not working well. When mitochondria are damaged or disrupted, cells can’t produce enough energy to survive or function normally. A "pathway" in this case is like a series of signals inside the cell that help regulate certain processes. The G protein-coupled receptor 109A is a kind of sensor on the cell’s surface. It receives signals (like from molecules in the body) and passes them along, triggering changes inside the cell. In the context of this issue, harmful molecules (like toxins in kidney disease) activate this receptor, leading to disruptions in how the mitochondria work. This disrupts the normal functioning of the cell. When the G protein-coupled receptor 109A pathway is activated in a harmful way, it can cause the mitochondria to malfunction. This can lead to the cell not getting enough energy, becoming stressed, or even dying. In simple terms, this means that certain harmful signals in the body can compromise the cell's ability to create the energy it needs to function normally, by interfering with the communication system (the G protein-coupled receptor 109A pathway). This can lead to serious problems, especially in cells like B cells in the immune system, which need energy to fight infections. This leads to weakened immune system responses. In mouse models with influenza infections or immunizations, CKD leads to weaker antibody production against pathogens. Patients with CKD exhibit poor responses to both natural infections and vaccines, putting them at heightened risk of severe infections and poor recovery outcomes. Infections are the second-leading cause of death in CKD patients, with mortality rates as much as 10 times higher during the COVID-19 pandemic compared to individuals with normal kidney function. The reduced immune response correlates with elevated serum blood urea nitrogen (BUN) levels and the degree of kidney dysfunction. The uremic toxins that result from CKD cause most of the damage. Uremic toxins, particularly hippuric acid, cause B cell death, reducing the ability of CKD patients to mount effective immune defenses. Hippuric acid disrupts mitochondrial membrane electric potential, further leading to compromised B cell viability and function. It behooves us to keep a close eye on our kidney function test results. If any of our routine kidney function test results are out of range, and our Doctor doesn't follow up with additional tests, or explain why these particular results don't matter, we need to point out and discuss the issue, because by the time our next tests are normally scheduled, the problem might be completely out of hand, with serious consequences. Especially note the eGFR level, and make sure it's in the normal range. Reference: 1. Peroumal, D., Jawale, C.V., Choi, W., Rahimi, H., Antos, D., Li, D-d., . . . Biswas, P. S. (2024). The survival of B cells is compromised in kidney disease. Nature Communications, 15, 10842, Retrieved from https://www.nature.com/articles/s41467-024-55187-w
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November 2025
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