INTRODUCTION TO MICROBIOLOGY
Adjudicates the Oxyphilic-Oxyphobic Conflicts
Systems of Oceanic Bioenergetics
In clinical microbiology,
learning evolutionary energetics of the planet
and the life on it is essential for understanding
the man-microbe (host-defense) interactions. The
human cells are oxyphilic (oxygen-loving) and oxygen
drives their high-efficiency energetics. Microbes in
general are oxyphobic (oxygen-shunning) or nearly
so. Therefore, the prevailing oxygen largely determine the
outcome of man-microbe conflicts. This subject is
seldom, if ever, properly taught to medical
practitioners. Sick people pay an
enormous price for it.
In this tutorial, I present the two systems of
oceanic bioenergetics to provide an evolutionary
perspective of clinical microbiology. I discuss
additional aspects of this subject in the following
. Tutorial MM2: Oxygen Settles The Great
. Tutorial MM3: Oxygen Adjudicates the Man-microbe
Conflicts and Determines Who Lives and Dies
. Tutorial MM4: The Sun-Soil Model of
Immunity Against Microbes
. Tutorial MM5: The Soil-Gut Microbial
. Tutorial MM6: What Can You Do During
E. coli Epidemics?
Tutorial MM7: The Bees-Butterflies-Bats Global
Life evolved in oceans and then
extended to land masses.1-7 Nature
evolved two divergent systems of bioenergetics in
oceans: a "top-ocean" solar-driven system and a
"deep-ocean" sulfur-based system. Sunlight
penetrates ocean waters for only three to four
hundred feet, limiting photosynthetic energy
generation largely to such depths, which is
designated as the top ocean. Photosynthesis evolved,
by current scientific evidence, more than two
billion years ago to harness sunlight to split water
and release free oxygen, which initiated the
development, differentiation, and expansion of the
kaleidoscope of marine and terrestrial oxygen-loving
(oxyphilic or "philic") species.
The second system of oceanic
bioenergetics evolved in the deep ocean—5,000 to
30,000 feet and deeper—independent of solar energy.
Unaccustomed to oxygen in its ecologic niches and
unable to harness its energy, life in deep ocean
became oxyphobic ("phobic"). The primordial
precursors of phobic life evolved around vents of
the deep ocean that seeped hydrocarbons—methane gas
being the best recognized form—enriched with sulfur
and iron compounds. So began the sulfur and nitrogen
economies of the deep ocean. Phobic microbes that
produce nutrients create the conditions under which
complex multicellular life developed. The bowels of
the deep-ocean shrubs and trees today are filled
with such microbes.
Fibrillating Philic-Phobic Equilibrium
equilibrium,"which evolved over a period of about
two billion years ago, is now under serious
and cumulative threats of global overpopulation,
climatic chaos, planetary chemicalization, diffuse
"oceanic plasticization," and biodiversity. By some
accounts, the accumulation of plastic waste now
suffocates marine life in swaths of the Pacific that
equal more than half of the Atlantic Ocean. All
these geologic-scale changes have in common two
crucial elements: oxygen depletion and incremental
oxidative stress—conditions that potently favor
phobic life over philic life.
Land-based photosynthetic biomass
far exceeds its aquatic counterpart. However, marine
phytoplankton carry out almost half of the global
net photosynthesis, since the rate of photosynthesis
per unit of biomass of the former is much lower than
that of the latter. This facet of the philic-phobic
equilibrium has profound implications for oceanic
regeneration following massive disruptions, notably
for the potential proliferative response times of
microbial assemblages to varying rates of oxygen
depletion and layers of oceanic redox potentials.
I discussed the profound
relevance of the top-ocean life to human health and
disease in Darwin, Oxygen Homeostasis, and
Oxystatic Therapies (2009) the tenth volume of
The Principles and Practice of Integrative Medicine.8
The deep-ocean life has drawn little, if any,
attention from physicians in the past. This—it seems
safe to predict—will change with the unfolding
Deepwater Horizon catastrophe in the Gulf of Mexico.
The long term human health consequences of this
massive disruption of the philic-phobic equilibrium
among the zones of varying oxygen conditions and
redox potential in the Gulf of Mexico will not be
known for decades.
Undoubtedly, massive geochemical,
thermal, and climatic events disturbed this
equilibrium in past eras. Specifically, one would
expect that deep oceanic vents would seep oil,
methane, and related hydrocarbons. That has been
documented. One would also expect that nature would
have generated life forms with an ability to break
the seeped oil down to oxygen, hydrogen, and carbon.
That also occurs. For instance, Alcanivorax
borkumensis is a microbial species—aptly named
since it breaks down the alkanes in oil as carnivora
do to flesh—to release energy for its metabolism.
So, evolution created "oil-eaters" to maintain its
deep oceanic ecologic niches in which microbes could
thrive and, in turn, serve as food for larger forms
of life, some as large as trees. Under experimental
conditions, certain Pseudomonas species have
been genetically engineered to contain enzymes that
enable them to break down different hydrocarbons.
These may be considered man-made oil-eaters. While
oil-eaters offer a tantalizing possibility of
cleansing high-density human habitat regions at some
future date, they clearly cannot resolve oceanic philic-phobic dysequilibrium.
The Deepwater geyser calls for a
diligent study of the long-term consequences of the
philic-phobic dysequilibrium in the broader context
of growing, massive, and cumulative anthropogenic
and non-anthropogenic influences. A sharp focus on
the burgeoning planetary carbon load and global
warming, and meaningful responses to it by the
international community, is essential. However, in
my view, frightening oxygen depletion and rising
oxidizing capacity of oceans are far more ominous
developments. Here I do not merely lament the
homelessness of polar bears, nor do I refer to the
scenario of the loss of other individual
species—only three white possums are known to remain
on the biodiversity hotspot relic which Mount Lewis,
once an abode of swirling mists, has become. Rather,
I speak about seismic planetary shifts in the philic-phobic
equilibrium that will not look at humans any more
kindly than the oceanic canaries, dolphins and
pelicans long after TV reporters have moved on to
more current 24-hour news cycles.
Each massive environmental
tragedy underscores the need for a deep sense of
"eco-sensitivity" for physicians. Each time the
response of the medical community at large is deeply
disillusioning. This happened with the Ixtoc 1,
Exxon Valdez, Kuwait War, the Twin Tower inferno,
the Iraq War, and now with the Gulf’s gushing geyser
of boiling tar.
Each time such a tragedy causes a
large loss of human life. I hope that The New
England Journal of Medicine will recognize the
convergence of the molecular consequences of terror
and toxicity. I hope it will clearly see the
essential need for holisim in medical thinking. How
I hope it will reconsider its pernicious opposition
to environmental medicine, nutritional medicine, and
energy medicine. Each time the Journal’s obfuscation
of real issues is reprehensible.
Bowels, Fermenting Oceans
As a child’s belly continues to
ferment long after extended antibiotic abuse stops,
so the oceans will ferment for decades after the
Gulf spill stops. Antibiotics disrupt the delicate
ecologic balance between oxygen loving (oxyphils)
microbes and oxygen-shunning (oxyphobes) microbes.
9-12 Bowel fermentation occurs in
children because ill-informed pediatricians fail to
protect the children from the ecologic disruptions
in the bowel caused by antibiotics. Antibiotic abuse
alters bowel ecology—overgrowth of fermenting
microbes, the leaky gut state, food intolerance,
mold allergy, and immune deficiencies develop as its
consequences—that often has widespread systemic
Clinical ecologists are aware of
neurotoxicity states caused by marine neurotoxins
produced in excess during red tides of
oxygen-depleted ocean water. It seems safe to
predict that wide swaths of the Gulf of Mexico will
ferment long after the gushing Deepwater Horizon
geyser is stopped. Phobic microbes will continue to
ferment and unleash poisonous red and crimson tides
years after the spill is arrested, whenever that
occurs. This happened on smaller scales in past oil
spills and is likely to occur on a much larger scale
of Petrochemical Illness
There are no drugs to treat
petrochemical illness. People sickened by terror and
toxicity associated with massive chemical overload
require integrated, comprehensive, and effective
nondrug protocols for individualized care. I
described those protocols in The Canary and
Chronic Fatigue (1994) and September Eleven,
2005 (2002). Will the Deepwater Horizon
catastrophe force The New England Journal of
Medicine to have the courage to go beyond its
habitual thinking of denial of petrochemical
illness? I hope it will, though I suspect it won’t.
Two Ways of
Looking at the Deepwater Catastrophe
The Deepwater Horizon gusher in
the Gulf of Mexico (2010) caused a greater environmental
havoc than any other oil spill. There are two ways
we can look at the Deepwater catastrophe. One way is
to look at it as a colossal humiliation for our
country.11 For decades the United States
has claimed to be the technological behemoth, the
world leader in innovation, the likes of which the
planet has never witnessed. Now this: we cannot cap
an oil spill. Our ocean oil brooms are overrun by
waves just one foot high. Our oil brems are expected
to be wiped out with the first hurricane. Chemical
dispersants are toxic, submerge the oil, and will
undoubtedly worsen delayed environmental damage. We
beg Brits for billions. It requires no large leap of
imagination to foresee the wars of greed and rage
which those British billions will unleash. This is
the way of indignity and despair.
The second way is of
beyond-habitual thinking. It is a way of deep
reflection, with humility, about our rightful place
in the natural order of the planet and the community
of civilized peoples of the world. What are a
society’s legitimate needs for energy? What might be
the necessary short-term and long-term energy
conservation strategies? What might be the
environmental costs of specific energy sources? What
might be the environmental hazards created by the
invasion of deep ocean? How can humans, animal, and
plant life be protected when major accidents do
occur? How ethical have Congress and successive
administrations been in these matters? To cite one
example, Congress enacted the Deepwater Royal Relief
Act of 1995 to massively reward deep ocean drilling
companies. Hard to believe, the act waived
government royalties totaling billions of dollars
for many leases for deep ocean drilling during
1996-2000. These, in my view, are the questions that
deserve open and diligent public discourse in the
Spill and Journalistic Lap dog
On August 4, 2010, The New
York Times ran a front page story entitled "U.S.
Finds Most Oil From Spill Poses Little Additional
Risk. This was a stunning display of ignorance and
irresponsibility. I predict that the Times
will regret its story in coming years. The editors
might then counter that we only reported what the
U.S. government claimed. If so, they would also have
to admit that they were being journalistic lap dogs,
not watch dogs. How can anyone state that massive
petrochemical pollution will not have significant
adverse health effects on people, marine species,
and coastal plants?
The Times’ position
becomes more reprehensible when we consider the
headline of a report in Nature of July 27,
2010 entitled "Muddying the waters on Gulf oxygen
data." Nature went on to describe how the
observation of independent researchers refuted the
claim of U.S. government report that significant
oxygen depletion in the Gulf of Mexico had not
occurred. Amazingly, the Times chose to
believe government officials rather than independent
scientists. Long live journalistic lap dogs!
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8. Ali M. The Principles and
Practice of Integrative Medicine Volume III: Darwin,
Oxygen Homeostasis, and Oxystatic Therapies. 3 rd.
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Practice of Integrative Medicine Volume XI: Darwin,
Dysox, and Disease. 2000. 3rd. Edi. 2008. New York.
(2009) Institute of Integrative Medicine Press.
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Practice of Integrative Medicine Volume XI: Darwin,
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Clean the Gulf. The New York Times. June 6, 2010.
Course on Microbiology
INTRODUCTION TO MICROBIOLOGY
Inflammation, Infections, and Immunity
What Is Inflammation?
* Infectious Diseases
Fungi and Molds
Oxygen Adjudicates Oxyphillic-Oxyphobic Conflicts
Kills Coffee Plants Also Hurts Humans
Must We Continue to
Antibioticize for H. pylori?
* Castor Oil
Rubs for Colicky Babies and Children
Sesame Oil: Why Is It
One of My Darlings?
Anti-Inflammatory Spice Therapies for Arthritis
Oil Therapies for Arthritis
LAPs and TAPs
Determine the Outcome in Infections Everywhere in
* Viruses and Virology
Chronic Lyme Disease
is Mismanaged Acute Lyme Infection