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Molecular Biology of Oxygen, Basics

Majid Ali, M.D.

A question people ask me is: Who do I trust for information about nutrition? A concern often expressed is: information about the effects of environments on health is controversial, often completely contradictory. The doubt and uncertainty about how stress causes dis-ease and disease is equally common. There are two reasons for it:

.  The sciences of nutrition, environments, and stress is widely misunderstood.

.  People commonly doubt information provided by news media, drug companies, and doctors.

Scientific knowledge concerning health and disease is misunderstood because the basics of life, energy, nutrition, metabolism, and detoxification are not duly studied. I address this problem in the 42 tutorials in this course on the basic molecular biology of oxygen and follow these tutorials with another 40 for advanced readers in the course entitled "Molecular Biology of Oxygen, Advanced." I hope the readers will find this material valuable in becoming familiar with the outline and content of the whole course.

As for the second point, news media, drug companies, and doctors have lost the trust of their patients because they are seen—rightfully, in my view—as promoting their business goals at the expense of truth and authenticity. I founded Wiki-Medical to address this serious problem. It is my commitment that no commercial concerns will be permitted to pervert scientific information at this site. Following is the list of tutorials in this course:

Tutorial FF.0 Simple Things

Tutorial FF.1 What Is Oxygen?

Tutorial FF.2 Oxygen Is the Primary Information Molecule of the Body

Tutorial FF.3 What Is Oxidosis?

Tutorial FF.4 What Is Oxidation?

Tutorial FF.5 What Is An Oxidant?

Tutorial FF.6 What Is An Antioxidant?

Tutorial FF.7 What Is Redox?

Tutorial FF.8 What Is A Free Radical? What Is An Oxyradical?

Tutorial FF.9 What Is Oxidative Coagulopathy?

Tutorial FF.10 What Is Cellular Grease? The Grease and Detergent Model of Cellular Injury

TutorialFF.11 What Is Oxidative Lymphopathy?

Tutorial FF.12 What Is An Oxy-detergent?

Tutorial FF.13 What Is Dysox?

Tutorial FF.14 How Do Acids Affect Axidant-antioxidant Reactions in the body?

Tutorial FF.15 What Is Acidosis

Tutorial FF.16 What Is Oxygen Signaling?

Tutorial FF.17 Oxygen’s Three-Legged Throne

Tutorial FF.18 The Oxygen Model of Disease

Tutorial FF.19 The Oxygen Model of Healing

Tutorial FF.20 Oxygen and Disowning Disease

Tutorial FF.21 What Is Oxygen Homeostasis?

Tutorial FF.22 Oxygen and Healing by Any Name

Tutorial FF.23 Oxygen, Enzymes, and Healing

Tutorial FF.24 Oxygen and Biofilms

Tutorial FF.25 The Oxygen Model of Fibromyalgia

Tutorial FF.26 The Oxygen Model of Chronic Fatigue Syndrome

Tutorial FF.27 Air Travel Dysox

Tutorial FF.28 Oxygen, the Bowel, and Inflammation

Tutorial FF.29 Oxygen Model of Polymyalgia

Tutorial FF. 30 Oxygen in the Dental Chair

Tutorial FF. 31 Oxy-pause for Low Testosterone

Tutorial FF. 32 Fewer Breaths, More Energy

Tutorial FF. 33 Oxygen-Depletion and Ocean Fatigue

Tutorial FF.34. Oxygen, Hydrogen, and Health

Tutorial FF. 35 Oxygen and Early African Medicine

Tutorial FF.36 The Oxygen Model of Adrenal Dysfunction

Tutorial FF.37 Oxygen, Compassion, and Spirituality

Tutorial FF.38 Oxygen, Cholesterol, and Lapdog Joes

Tutorial FF.39 Oxygen, the Liver, and Inflammation

Tutorial FF.40 Oxygen, the Thyroid, and Inflammation

Tutorial FF.41 Oygen, the Lung, and Inflammation

Tutorial FF.42 What Is Oxyology?

Tutorial FF.43 What Are Oxygen's Love-Hate Relationships with Other Molecular Species?


Seven Scientific Terms

Majid Ali, M.D.

Forty tutorials listed below are included in this course on the basics of the molecular biology of oxygen. A clear understanding of these materials is essential for learning the sciences of nutrition, environment, and self-regulation. Forty additional tutorials are included in the course on of the course on advanced molecular biology of oxygen (see the hyperlink on the side panel).

Seven scientific terms appear repeatedly in my writings at Wiki-Medical. It is essential to understand the meanings of those words. In this article, I give brief descriptions of these terms. Some readers without medical background may find the terms tedious in the beginning. I urge them to read the following pages slowly and take the time to grasp the full meanings of those terms. If necessary, the readers should re-read these pages to become familiar with the terms. Once that is done, I am confident the scientific knowledge presented in this book will become easily understandable. There are other rewards for that effort. I can promise the readers that with that knowledge they will be able to separate good from bad medical writings.


Oxidosis (oxi-do-sis) is excessive loss of energy through rapid loss of electrons. In the context of aging, oxidosis causes disease and premature aging. Oxidation is loss of electrons. In chemical reactions, electrons are transferred from one atom or molecule to the other. The donor substance loses electrons and is so oxidized. The recipient gains electrons and so is reduced. The gainer becoming reduced seems strange but that is the awkwardness of the scientific terminology.

People see electrons every day. There is a spark when the plug on an electric appliance is pulled without first turning the unit off. That spark is a storm of electrons. In this example, a running appliance gains electrons from the source in the power company and uses it to produce energy for its function. That is exactly what happens in oxygen-driven oxidative reactions in the body. Oxygen first gains (steals) electrons from other substances and so begins the process of generation of energy. Those substances, in turn, are oxidized. Light is produced by a light bulb in a similar way. A high-energy beam of electrons loses some energy as light particles called photons and turns into a low energy beam of electrons.

Butter turns rancid, a flower wilts, meat decomposes—that is oxidation. A person develops a cataract and loses his eyesight. That happens when the proteins in the lens become oxidized. When a heart fails after a heart attack, that is because oxidosis in the heart muscle cells interferes with their function. In all tissues, excessive oxidation means a rapid breakdown in tissues. Thus, I see the hand of oxidosis at autopsy in each and every case, regardless of whether the death was caused by cancer or by chemotherapy, by coronary artery spasm or by a cardiologist's stent, by hepatitis or by pneumonia.2

Oxidosis leads to dysfunctional oxygen metabolism, which is the basis of all symptoms of fibromyalgia and chronic fatigue syndrome.2 It is the molecular basis of pain, fatigue, and brain fog in those syndromes.


Dysoxygenosis (dys-oxy-gen-o-sis) is my term for dysfunctional oxygen metabolism.2 It is not merely lack of oxygen due to heart disease or asthma, nor poor transport of oxygen due to anemia. The scientific term for that is anoxia. Dysoxygenosis is the failure of cellular oxygen metabolism due to damage to the enzymes of oxygen metabolism. Thus, dysoxygenosis threatens the health of every cell, every tissue, every body organ.

Dysoxygenosis in muscle cells causes severe fatigue. In brain cells, it causes problems of mood, memory, and mentation. In the skin and eyes, it causes advanced dryness. In the cell membrane, it causes leaky membrane dysfunction, so that what is inside the cell hemorrhages out and what is outside floods the cell innards. Thus, the cell becomes dehydrated, shrunken, and loaded with toxins. Such a cell cannot function well.


Acidosis (acid-o-sis) is excess acidity. Acidosis slows or blocks the enzyme systems of the body, including those involved with energy, digestion and absorption, detoxification, muscle function, and neurotransmitters. Enzymes are catalysts that facilitate life processes. Acidosis fans the flames of both oxidosis and dysoxygenosis which, in turn, cause more acidosis. As in the case of dysoxygenosis, acidosis in muscle cells causes severe fatigue.3 In brain cells, it causes problems of mood, memory, and mentation. In the skin and eyes, it causes advanced dryness. And so on.


Oxidative coagulopathy (co-ag-u-lop-athy) is the process by which clean blood turns into "dirty" blood.

In health, the red blood cells are rounded, smooth in outline, and do not stick to each other. The hunter immune cells have irregular but sharp boundaries and move around like amoebae, searching for microbes to kill and digest. The antibody-forming immune cells are also smooth, rounded, and free of debris stuck to their surfaces. The plasma (fluid part of the blood) is clear and without any areas of congealing. There is no microclot or microplaque formations.

In 1997, my colleague, Omar Ali, M.D., and I introduced the term oxidative coagulopathy to describe a range of abnormalities in the blood of patients with coronary heart disease.4 We observed the following changes in blood slides: deformities and clustering of red blood cells, death of immune cells, zones of congealed plasma, and microclot and microplaque formation. The blood clots and unclots all the time. However, in oxidative coagulopathy, microclot formation occurs at a rapid rate and unclotting cannot keep pace with clotting. Thus, microclots and microplaques accumulate in the blood and get stuck to the inside of small arteries in the heart and brain, causing heart attacks and strokes.

Later I described similar changes in fibromyalgia and chronic fatigue syndrome.5 Adding bacterial culture to milk turns it into yogurt. Lemon juice squeezed into milk curdles it. That happens because microbes and certain acids solidify the proteins in milk, the same way microbes and certain acids entering the circulating blood curdle it. In health, such curdles (microclots) are readily dissolved by clot-busting enzymes. In fibromyalgia, a large number of microbes and large quantities of toxic oxidants enter the blood from the bowel, causing excessive microclot formation.


Oxidative lymphopathy (lym-phop-athy) is my term for a process by which lymph becomes oxidized, rancid, thick and gluey. Lymph is the pale fluid that drains toxins from tissues. Such fluid stagnates in muscles and other tissues, preventing the free flow of oxygen-rich blood, causing soreness in tissues, and producing trigger points in muscles. I introduced this term in 1998 to focus on issues of stagnant lymph in tissues4 and described its clinical significance in fibromyalgia in 1999.6

Blood and lymph channels exist in all body organs. Thus, damage caused by oxidative coagulopathy and oxidative lymphopathy quickly spreads to all cells of the body. 3M oxidopathy is my term for oxidative damage to cell membranes, matrix, and mitochondria. Matrix is the cement that holds cells together. Membranes are coverings of cells and their inner structures. Mitochondria are tiny power batteries of the cells. Since all three are continuously exposed to oxidized (rancid) blood and lymph, it should not surprise us that the oxidative coals in the blood and lymph (microclots) will also sear the 3M (matrix, membranes, and mitochondria).5



ODD is a state in which: (1) oxidosis is caused by oxidants of all three types (metabolic, microbial, and man-made) that threaten health; (2) oxidosis leads to dysoxygenosis (abnormal oxygen metabolism), which slows or blocks all life processes; (3) oxidosis and dysoxygenosis together cause acidosis; (4) all three elements (oxidosis, dysoxygenosis, and acidosis) feed upon each other and together fan the flames of oxidative injury. In fibromyalgia, an oxidative-dysoxygenative (OD) state leads to injury to every microecologic cellular and macroecologic tissue-organ ecosystem of the body.6


Oxyology (oxy-olo-gy) is the study of oxygen, just as pathology is the study of diseases.7 A sound knowledge of oxygen metabolism in health and of dysfunctional oxygen metabolism in dis-ease and premature aging is of fundamental importance. Indeed, I believe neither health nor the aging process can be understood without such knowledge. In this volume, I present many aspects of oxygen that seldom, if ever, are discussed in medical textbooks.


1. Ali M. Spontaneity of Oxidation in Nature and Aging. Monograph. Teaneck, New Jersey, 1983.

2 Ali M. Darwin, oxidosis, dysoxygenosis, and integration. J Integrative Medicine 1999;1:11-16.

3. Ali M. Oxidative regression to primordial cellular ecology (ORPEC): evidence for the hypothesis and its clinical significance. J Integrative Medicine 1988;2:4-55.

4. Ali M, Ali O. AA oxidopathy: the core pathogenetic mechanism of ischemic heart disease. J Integrative Medicine 1997;1:1-112.

5. Ali M. Amenorrhea, oligomenorrhea, and polymenorrhea in CFS and fibromyalgia are caused by oxidative menstrual dysfunction. J Integrative Medicine 1998;3:101-124.

6. Ali M. Fibromyalgia: an oxidative-dysoxygenative disorder (ODD). J Integrative Medicine 1999;3:17-37.

7. Ali M. Oxyology: the need for a new discipline in clinical medicine. J Integrative Medicine 2000;4:1-2.


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