Molecular Biology of Oxygen, Basics
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
sciences of nutrition, environments, and stress is
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.1 What Is Oxygen?
Tutorial FF.2 Oxygen Is the
Primary Information Molecule of the Body
Tutorial FF.3 What Is
What Is Oxidation?
Tutorial FF.5 What Is An Oxidant?
Tutorial FF.6 What Is An
Tutorial FF.7 What Is Redox?
Tutorial FF.8 What Is A Free
Radical? What Is An Oxyradical?
Tutorial FF.9 What Is
Tutorial FF.10 What Is Cellular
Grease? The Grease and
Detergent Model of Cellular Injury
TutorialFF.11 What Is
Tutorial FF.12 What Is An
Tutorial FF.13 What Is Dysox?
Tutorial FF.14 How Do Acids
Affect Axidant-antioxidant Reactions in the body?
Tutorial FF.15 What Is
Tutorial FF.16 What Is Oxygen
Tutorial FF.17 Oxygen’s
Tutorial FF.18 The Oxygen Model
Tutorial FF.19 The Oxygen Model
Tutorial FF.20 Oxygen and
Tutorial FF.21 What Is Oxygen
Tutorial FF.22 Oxygen and Healing
by Any Name
Tutorial FF.23 Oxygen, Enzymes,
Tutorial FF.24 Oxygen and
Tutorial FF.25 The Oxygen Model
Tutorial FF.26 The Oxygen Model
of Chronic Fatigue Syndrome
Tutorial FF.27 Air Travel Dysox
Tutorial FF.28 Oxygen, the Bowel,
Tutorial FF.29 Oxygen Model of
Tutorial FF. 30 Oxygen in the
Tutorial FF. 31 Oxy-pause for Low
Tutorial FF. 32 Fewer Breaths,
Tutorial FF. 33 Oxygen-Depletion
and Ocean Fatigue
Tutorial FF.34. Oxygen, Hydrogen,
Tutorial FF. 35 Oxygen and Early
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,
Tutorial FF.40 Oxygen, the
Thyroid, and Inflammation
Tutorial FF.41 Oygen, the Lung,
Tutorial FF.42 What Is Oxyology?
Tutorial FF.43 What Are Oxygen's
Love-Hate Relationships with Other Molecular
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
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
4. OXIDATIVE COAGULOPATHY
Oxidative coagulopathy (co-ag-u-lop-athy) is the
process by which clean blood turns into "dirty"
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
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
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
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.
Ali M. Oxidative regression to primordial cellular
ecology (ORPEC): evidence for the hypothesis and its
clinical significance. J Integrative Medicine
4. Ali M, Ali O. AA oxidopathy: the core
pathogenetic mechanism of ischemic heart disease. J
Integrative Medicine 1997;1:1-112.
Ali M. Amenorrhea, oligomenorrhea, and polymenorrhea
in CFS and fibromyalgia are caused by oxidative
menstrual dysfunction. J Integrative Medicine
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