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Oxygen Adjudicates the Oxyphilic-Oxyphobic Conflicts Two Systems of Oceanic Bioenergetics

Majid Ali, M.D.

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 three tutorials:

.  Tutorial MM2: Oxygen Settles The Great Pasteur-Beschamp Debate

.  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 Equilibrium

.  Tutorial MM6: What Can You Do During E. coli Epidemics?

Tutorial MM7: The Bees-Butterflies-Bats Global Who-done-it


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

The "philic-phobic 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.

Planet’s Oil-Eaters

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.

Physicians and Eco-sensitivity

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.

Fermenting 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 effects. 9,10

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 this time.

Treatment 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 future.

The Gulf 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!


1.Bowler C, Karl DM, Colwell RR. Microbial oceanography in a sea of opportunity. Nature. 2009;459:180-184.

2.Curtin TB. Belcher EO. Innovation in oceanographic instrumentation. Oceanography. 2008; 21, 44-53.

3.Dawson MN., Gupta S, England MH. Coupled biophysical global ocean model and molecular genetic analyses identify multiple introductions of cryptogenic species. Proc. Natl Acad. Sci. USA. 2005;102:11968-11973.

4.Follows MJ, Dutkiewicz S, Grant S. Et al. Emergent biogeography of microbial communities in a model ocean. Science. 2007;315:1843-1846.

5. Falkowski PG, Fenchel T, Delong EF. The microbial engines that drive Earth's biogeochemical cycles. Science. 2008;320:1034-1039.

6. Field CB, Behrenfeld MJ, Randerson JT, Falkowski P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science; 1998; 281:237-240.

7. Kolber Z. Energy cycle in the ocean: powering the microbial world. Oceanography. 2007; 20:79-87.

8. Ali M. The Principles and Practice of Integrative Medicine Volume III: Darwin, Oxygen Homeostasis, and Oxystatic Therapies. 3 rd. Edi. (2009) New York. Institute of Integrative Medicine Press.

9. Ali M. The Principles and Practice of Integrative Medicine Volume XI: Darwin, Dysox, and Disease. 2000. 3rd. Edi. 2008. New York. (2009) Institute of Integrative Medicine Press.

10. Ali M. The Principles and Practice of Integrative Medicine Volume XI: Darwin, Dysox, and Integrative Protocols. New York (2009). Institute of Integrative Medicine Press.

11. Etkin DS, Han J. Twelve (Imperfect) Ways to Clean the Gulf. The New York Times. June 6, 2010.

Dr. Ali's Course on Microbiology


* Introduction to Inflammation, Infections, and Immunity

* What Is Inflammation?

* Infectious Diseases

* Fungi and Molds

* Oxygen Adjudicates Oxyphillic-Oxyphobic Conflicts

* What 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

Anti-Inflammatory Topical Oil Therapies for Arthritis

* LAPs and TAPs Determine the Outcome in Infections Everywhere in the Body

* Viruses and Virology


* Chronic Lyme Disease is Mismanaged Acute Lyme Infection



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