Chapter 14D: The Proton Code: How Minerals Keep Acid in Check
Rethinking “acid–alkaline” through the lens of proton flow, mineral charge, and the hidden physics of proton-mineral balancing.
Not that I want you to do this, but if you are uninterested or unknowledgeable in the biochemical and metabolic pathways that I will elucidate in the following, again, I suggest skimming, or just outright skipping to Chapter 15 - “Minerals Made Simple: How Nature’s Elements Keep Water, Plants, and People Alive” This way you won’t get annoyed with me or complain that I am being too “scienc-ey.”
Sorry, guys, but the chemistry lesson isn’t over. If you thought that simply having enough iron and sulfur to make enough OH- ions to neutralize ROS would solve everything, you’d still be thinking within the old, “traditional paradigm” of illness and wellness.
What follows is a new framework—one that proposes that “proton-mineral disequilibrium” may be as great (or even greater) a driver of oxidative imbalance as iron-sulfate deficiency itself. To grasp this novel concept, we’ll need to wade into some slightly “headier” waters (as if we haven’t already).
How the Proton Mineral Balance Concept Originated
While digging through every study I could find on trace minerals, I relied heavily on a Google Doc my wife, Lisa, helpfully compiled for me—an enormous archive of research and insights shared by Bakos and Postawski.
No offense to them, but it was a total hodgepodge—rich in insights, data, and research, but lacking a clear, conceptual flow (which is probably why this chapter went through dozens of rewrites and at least a hundred AI consultations).
The Google doc ballooned quickly, and although I came across this short paper early on, I didn’t get back to it until much later in my research and writing.
I am actually glad that happened, because when I did come back around to it, I was able to see it for what it was - a novel scientific insight. Yet, it isn’t peer-reviewed or formally published—at least not yet. It’s simply a concise, two-page distillation of scientific insights that Bakos began formulating nearly eighteen years ago.
Since that time, he’s spent years immersed in studying minerals and human health, refining his understanding of how they interact. During one period of deep thought, he began shaping what he would eventually call ”proton-mineral balance.”
As a non-biochemist, I could follow the concepts in broad terms, but I wasn’t sure how firmly grounded they were in established scientific precepts. To really know, I would have had to dig deep into the four references he cited at the end—something that would’ve required a lot more brainpower and time than I had to spare.
So, instead, I turned to AI to help me analyze the ways in which Bakos had applied the mechanisms detailed in those references and whether they truly supported his conclusion. That’s when I first began to even more strongly sense that his two page paper might represent something truly original—perhaps even a groundbreaking scientific insight regarding a critical aspect of mineral health.
So, I went back to AI, and asked it this question:
“Given that the citations support the paper’s core arguments, would you also consider its conclusions a genuinely novel contribution to human health—particularly regarding the role of minerals?”
AI’s answer:
Yes, the attached paper does provide an entirely unique insight into human health and mineral importance, and it is grounded in scientifically supported concepts.
Oh boy. What’s going on here? The very individual trusted by Shimanishi’s company to import and distribute his minerals—someone who never finished high school because his immense intelligence and depth of insight left him intolerably bored by it—may have stumbled onto an entirely new way to understand how the body sustains balance—and possibly a solution for ensuring it does so? What?
Disclaimer: since the paper has not been peer-reviewed and published, the above and the following should be considered as a proposed theory and not an established fact.
Beyond the Mineral Story: Toward a Proton-Driven Model of Health
Maybe I should take a moment here and reflect on my own mineral journey — the one I’ve been on (or perhaps led to) for many weeks now. Every minute I’ve had outside of seeing patients, writing their notes and plans, or spending time with my wife, I’ve been thinking about, researching, and writing this “story of the minerals.”
Bakos’s unique perspective grew from observing that “acid” is only problematic when the body lacks sufficient minerals to buffer and harness its excess positive charge. Blood, tissues, and cellular environments rely on minerals to keep pH and charge balanced. He understood that alkalinity isn’t simply about being “basic,” but rather about having the mineral capacity to buffer and regulate acids.
In Matt’s paper, “Proton–Mineral Balance and Oxidative Stress: A Working Model,” he argues that the health industry traditionally views acid (protons) as dangerous “waste,” when in reality protons act as essential charge facilitators — the very drivers of all bioelectric life.
So wait, acid isn’t bad? Not what I heard.
OK, let’s slow down. Before we go any further into trying to understand this novel conceptual (albeit unvalidated) framework, you (and I) need a little primer on high school chemistry.
The Chemistry of Proton–Mineral Balance
I promise to keep it simple (yeah, right):
An acid is a chemical compound that can donate a proton (H⁺ ion) to another molecule or ion. When that happens the compound that remains is called its conjugate base — the part left behind, which now holds an extra electron compared to when it was an acid.
What happens is that the positive charge (H+) is accepted by a different base than the one the proton left behind. In other words, the positive charge moves from one molecule to another— a process called proton transfer.
Are we good? Good. Let’s go backward for a moment and break it down again so it really sinks in.
Most acids are neutral molecules before they dissociate. When they do, they release a proton (H+), leaving behind a base with an extra pair of electrons. When that base uses its lone pair of electrons to bind a new proton from somewhere else, the electrons from the bond to the “old” hydrogen molecule that left now shifts—either forming a new bond in the base or remaining as a lone pair.
This isn’t about creating or losing electrons — it’s about redistributing them. That process, called electron transfer, works hand-in-hand with proton transfer to create something called “charge shuttling.”
In this process, acids are proton donors and bases are proton acceptors (or, if you prefer to look at it the other way, bases are electron donors). Many biological and chemical reactions depend on this back-and-forth movement of both protons and electrons—(i.e. “charge shuttling,”) either simultaneously (concerted) or in a specific sequence (stepwise). This dual movement powers some of the most fundamental processes in existence: photosynthesis, respiration, energy metabolism, and chemical catalysis.
Why Minerals Matter for Charge Shuttling
Here’s the catch though — remember, this is a story about minerals. Minerals are absolutely essential for this “charge shuttling,” because they exist primarily as ions (charged particles like Na⁺, K⁺, Ca²⁺, Mg²⁺, Fe²⁺). Their movements and interactions enable ion flow—including proton gradients—across membranes, and electron transfer within protein complexes.
Many minerals, such as iron, copper, and zinc, are also integral to metalloproteins—specialized proteins that “shuttle” electrons during energy metabolism (like in the mitochondrial electron transport chain). Within these systems, the metals act as reversible electron acceptors and donors, driving chemical reactions and energy transfer.
Remember from Chapter 2, when I stated that without minerals, life could never have originated? Well, now you know why.
Current scientific consensus (ugh) posits that minerals found in soils, sediments, and rocks once acted as natural “batteries” or catalysts, enabling primitive electron transfer and charge storage long before biological cells existed.
The most dramatic aspect of “earth-origin science” is that minerals didn’t just sit there passively. They catalyzed the formation and storage of key biomolecules, concentrated these compounds, and provided the structural organization needed for early metabolic activity.
To wit, engineered “nanoscale mineral clusters,” such as metal-sulfide nanoparticles—have atomic arrangements of metal and sulfur atoms that closely resemble the catalytic centers (“active sites”) in many modern metabolic enzymes. These similarities suggest that mineral surfaces may have served as primitive enzyme catalysts on early Earth, possibly leading to the structure and function of biological enzyme active sites.
Even more amazing: modern experiments show that parts of the electron transport chain — the foundation of metabolism and energy creation — can partially be replicated by minerals alone, without any proteins at all. That means minerals were the original “engines” of life itself — a literal bridge between geochemistry and biology.
Still with me? Good — because I have to apologize. I took you down the rabbit hole of early life science when we are supposed to be talking about acidity and acid-base balance — the central point of Matt’s paper. So let’s get back to it.
The Proton–Mineral Hypothesis
The proposed, but as yet unvalidated construct of Bakos’s paper is simple but profound: minerals appear to influence acid–base (pH) balance within biological systems.. His idea rests on several key conceptual building blocks:
Protons provide positive charge to energize electrons, moving them to higher energy states due to changes in the local electric field (i.e. the presence of positive charges).
In aqueous or biological systems, this facilitates the activity of charged (ionic) minerals
Sulfated iron, among others, stabilize OH⁻ states by “buffering” these protons.
When there isn’t enough sulfated iron, it exists in its free form, Fe²⁺, which catalyzes “Fenton” reactions that generate acid.
Lets unpack that : Fenton reactions occur when the free Fe²⁺ reacts with hydrogen peroxide (H₂O₂) to generate highly reactive hydroxyl radicals (- OH) and protons (H⁺).
These hydroxyl radicals — a type of reactive oxygen species (ROS) — can damage proteins, lipids, and DNA.
In short, insufficient iron sulfate = more free Fe²⁺ = more acid generation and more ROS = cellular or tissue damage.
Balanced mineral composition, on the other hand, allows electrons to move in a more orderly fashion, maintaining stable OH⁻ states that facilitate natural redox balance and electron transport.
Implications for Life — From Cells to Soil
The same principle applies beyond the human body. In soils and sediments, minerals act as natural “batteries,” storing and transferring charge between microorganisms and the environment. Microbes depend on these minerals as enzyme cofactors — and when that mineral-based charge exchange breaks down, so does their ability to handle environmental stress.
Unlike the traditional model that focuses solely on fighting ROS with antioxidants, Bakos’s model reframes the problem entirely. It suggests that long-term health depends on maintaining mineral–proton balance. Minerals don’t just buffer acids — they orchestrate proton and electron flow, enabling living systems to convert energy, regulate charge, and sustain equilibrium even under oxidative conditions.
Bottom line:
Minerals are not just structural building blocks — they are the essential regulators that allow our cells to safely use charge and energy, prevent damage, and keep all tissues functioning. Without them, the most basic processes in the body break down,
This shift—from viewing acid and minerals as antagonists to understanding them as cooperative partners—is the novel perspective of Bakos’s proposed theory.
Next: Chapter 14E: The Cell’s Battery: Proton Gradients, Leaks, and Modern Stressors
P.S. If you’re curious about the volcanic-mineral water purification product that this book led me to help develop, you can find it at Aurmina.com. Think of it as a quiet act of restoration — starting with your water. And yes, I know — I’ve become the guy who includes links at the end. But this one just might change your water (and your mind)
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© 2025 Pierre Kory. All rights reserved.
This chapter is original material and protected under international copyright law. No part of this publication may be reproduced, distributed, or transmitted in any form or by any means, including photocopying, recording, or other electronic or mechanical methods, without the prior written permission of the author.