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Alternative Microbiology

A man of science rises ever, in seeking truth; and if he never finds it in its wholeness, he discovers nevertheless very significant fragments; and these fragments of universal truth are precisely what constitutes science.

~ Claude Bernard.

I almost never have to search for material for this blog. The Secret always seems to provide topics. Subject matter appears unbidden out of the ether. But not this week. I enjoy deconstructing the nonsense of SCAM papers or blog entries more than any other type of blog entry. Perhaps the glee that last week’s entry provided had to be countered by some kind of cosmic balancing mechanism. Although the rational part of my mind objects to the personification of random existence, I suppose the Universe just does not want me to have that much fun two entries in a row. Probably explains why I have a viral URI and my brain has slowed almost to the point of functional inactivity. There is no shortage of SCAMs to write about, they are just not created equal in their ability to generate a passionate rant.

I am, as you know if you are regular reader, an infectious disease (ID) doctor. I find the field endlessly fascinating as ID reaches into all aspects of the human condition. I remember when I was driving from Minneapolis to LA in 1986 for my fellowship, Petersdorf wrote his (in)famous article that ID was a dying profession and soon, thanks to antibiotics, vaccines and other advances, infections would become a problem of the past. Fortunately for me, and unfortunately for thousands of people, that prediction has not come to pass although we are sliding slowly into the post-antibiotic era where soon I will be able to diagnose but not treat disease.

Infections have always been a major cause of human morbidity and mortality. Through most of human history, infections, trauma and starvation were the primary ways by which humans died. Tremendous amounts of work by thousands of people have elucidated many of the factors that increase the risk of infection. There are 1,213,762 citations on the PubMeds if you search for ‘infection’. Medicine has pushed infectious diseases to the edge of society. Compared to the past, most outpatient infections are trivial or easily treated. TB, malaria yellow fever, smallpox, measles, typhoid fever etc. etc. no longer commonly plague those in the developed world.

With the understanding of the life cycle of diseases, how they are spread, good nutrition, vaccination, flush toilets and a reasonably safe food supply we do not get infected at the rates that occurred in the bad old days. Infections do happen, sometimes for good reasons, sometimes for no reason at all, and with just enough frequency to keep me gainfully employed, although as I have whined about in the past, my consult volumes have declined about 50% this century as we have learned how to prevent many infections that once made up much of my practice.

We have an incredible understanding of the microbial pathogens that try to kill us and that will, someday unless we are cremated, consume us all. There is so much we understand about the microbial world and its interactions with us that it always flabbers my gaster to run across alternative microbiology: the many realty-free and somewhat incoherent frameworks that deny germs, our understanding of microbiology or have discovered their own unique understanding of the pathogenicity of various organisms. Rather than my usual detailed deconstruction of a single idea or topic, today will be a birds-eye overview, a compendium of microbiologic weirdness as seen through the fog of interferon.

I came across a peculiar book, The Genesis of Germs by Dr. Alan Gillen (the doctorate, ironically enough, in science education; like last week’s computer science degree, evidently the ‘science’ part was thought superfluous) a professor of biology at Liberty University. From my understanding, life on earth is old, billions of years old, and germs result from slow evolution over time. I never really had a sense of that time until I read John McPhee’s Annals of the Former World. Dr. Gillen has an alternative explanation for germs and infectious diseases.

I knew of intelligent design mostly in the context of the battles over the teaching of evolution in the schools several years ago, but I never paid it much mind professionally. ID is often understood as applied evolution. It may be the bacterial resistance or the human response to disease, but evolution has left its footprints all over my subspecialty. I suspect there are more variations in the human genome as a response to infections than any other process.

What is odd from Gillen’s textbook is that he starts from the premise that the world is about 6,000 years old, that evolution is not true and that intelligent design explains the world, then Gillen creatively interprets microbiology to fit these preconceived ideas. Why do we have germs and infection? Original sin.

It was not until after sin entered the world that some micro-organisms became pathogenic, or harmful, to man. One explanation is that the good bacteria began to deteriorate or degenerate into pathogenic bacteria. Genomic decay is one of the most likely theories for explaining the origin of bacterial pathogenicity….When a bacterium degenerates it loses valuable information and must find other sources to survive. Bacteria generally are made as one cell; as they lose information from their genetic hardware they consequently can no longer produce their own needed materials to synthesize their cell parts. And so, as they lack information they have to gain that information from some other creature (an animal or a person) and in doing so they cause disease symptoms.

Somehow I do not think that is a conceptual framework that will result in a deeper understanding of disease pathogenesis and treatment. Solutions to the next pandemic are unlikely to be forthcoming from the biology graduates of Liberty University. As we slowly slide into the post antibiotic era I am not sanguine that his approach of belief in scripture and Jesus leading to an end of germs and infectious disease, is likely to help me treat the next patient with a multi-drug resistant E. coli infection.

I know we have been writing on this topic for years but it remains remarkable how huge amounts of information can be ignored or creatively interpreted if they do not fit pre-existing beliefs. Does refining ones facts lead to opinion or does opinion lead to your understanding of the facts? My career, now in its 30th year, has been one of constant reassessment of my understanding of infectious diseases as new information appears with a change in my practice as a result. The old saying is half of what you learn in medical school will be eventually proven wrong, but the problem is you don’t know which half. It must be nice not having to worry about pesky facts or having to change your mind.

We have pro-SCAM commenters who come and go at the blog, but they all have a common characteristic: they do not change their mind because of facts. The pattern is consistent: they make errors of fact and those errors are corrected, but the pro-SCAM commenter never admits they were in error, nor do they have a change of opinion as a result of new information; they move on to other errors in fact. I suspect all the information about germs that contradict Dr. Gillen’s understanding of infection as a fall from grace 6,000 years ago cannot and will not be incorporated into a better understanding of infectious diseases. And I am glad the Dr. Gillen’s of the world, who advocate for a “biblical or creation perspective on disease”, are not in charge of the CDC.

The first cases of AIDS were reported when I was in medical school. AIDS has gone from a curiosity of unknown cause to a plague that filled my hospitals with sick and dying young men to an often-manageable chronic illness. It has been rare to see a death due to HIV this century; so much better compared to the 6 months from diagnosis to dead we used to see. It is amazing what has been learned about HIV and its complications and I would point out that none of the increase in survival we have seen has been due in any way to alternative medicines of any kind, for HIV or any disease. Science-based medicine delivers.

Germs don’t cause disease: if they did, we’d all be dead.

Yet there are those that still deny that HIV leads to AIDS. Last year I heard Peter H. Duesberg deliver a Gish Gallop on this opinion, contrary to a positively enormous scientific literature, that HIV does not cause AIDS but instead is due to drugs and sexual promiscuity. He may be the most prominent of the AIDS deniers. As I mentioned in the past, reality is a honey badger, it don’t care what your opinion is. You can deny the importance of HIV and convene a panel, as did the President of South Africa with Dr. Duesberg a member and support policies that HIV is not responsible for AIDS and promote alternative therapies. The result? Death.

Once that battle was lost in the courts and in the political arena, the Health Minister, Tshabalala-Msimang, continued to portray ARVs as ‘poison’ and to support alternative untested therapies. Demographic modelling suggests that if the national government had used ARVs for prevention and treatment at the same rate as the Western Cape (which defied national policy on ARVs), then about 171,000 HIV infections and 343,000 deaths could have been prevented between 1999 and 2007.

That is a remarkable record and a depressing result of denying reality. Not just HIV, there is still a contingent of people who deny germs cause disease, which to my mind is akin to denying that water is wet.

We do not catch diseases. We build them. We have to eat, drink, think, and feel them into existence. We work hard at developing our diseases. We must work just as hard at restoring health. The presence of germs does not constitute the presence of a disease. Bacteria are scavengers of nature…they reduce dead tissue to its smallest element. Germs or bacteria have no influence, whatsoever, on live cells. Germs or microbes flourish as scavengers at the site of disease. They are just living on the unprocessed metabolic waste and diseased, malnourished, nonresistant tissue in the first place. They are not the cause of the disease, any more than flies and maggots cause garbage.

You can always tell a germ denier as they spread the lie that Pasteur recanted on his death bed that bacteria cause disease. He actual final words were “I cannot” in response to being offer a glass of milk, although I suspect he spoke in French. He was right when he said “Messieurs, c’est les microbes qui auront le dernier mot (Gentlemen, it is the microbes who will have the last word)”. I hope my last words will be directed at my brother: “touched you last”. Like he will let me even on my death bed.

The real mystery—one that deeply intrigued me 25 years ago—is that so many therapies that totally disagree with one another manage to bring results. Ayurveda isn’t qigong; yoga isn’t Reiki; none of them is a placebo. Yet somehow healing exists, and the channel it takes can be quite unexpected and inexplicable.

~ D. Chopra

It is no mystery to me; they are all nonsense. But for every SCAM there is an equal and opposite SCAM. For every homeopathic nostrum there is a megadose therapy. And for every germ denier there is a proponent that all diseases or symptoms are due to infections. It is true of all interesting diseases, however.

Hulda Clark was of the opinion that all cancers and other diseases were due to Fasciolopsis buski, the liver fluke, and that HIV was due to the same pathogen.

If (Fasciolopsis) establishes itself in the thymus, it causes HIV/AIDS!

There is Candida and Lyme, both allegedly causing the same list of symptoms. How to tell the difference between the two? I have Lyme, given that only Lyme has the symptom of “Decreased ability to spell correctly.” Or the imaginary infection of Morgellons. Or the Marshall Protocol, which hypothesizes, among other things, that autoimmune illnesses are perpetuated by bacterial colonies in biofilms and that promoting vitamin D deficiency is the treatment. You know there is something wrong with an alternative treatment if even Dr. Mercola finds fault with it.

So many different ways to ignore the real, complex, and interesting fields of microbiology and infectious diseases. New microbiology, ignoring microbiology, new diseases and life cycles for existing organisms. A rich fantasy world.

Despisers of their fellows: They make poor observations, because they choose among the results of their experiments only what suits their object, neglecting whatever is unrelated to it and carefully setting aside everything which might tend toward the idea they wish to combat.

~Claude Bernard.

Posted in: Epidemiology, Evolution, Science and Medicine

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