The Microbiome – A New Model for Health

sunday musting 2Buckminster Fuller: “You never change things by fighting the existing reality. To change something, build a new model that makes the existing model obsolete.”

What would a new model in medicine look like? Perhaps that new model has already been developed, but we have not begun to understand it. In the late 1990’s, a new paradigm in health was published. That is we live in a symbiotic relationship with a community of microbes. There are ten times more cells in this community of microbes than human cells within the body. There is also significantly more DNA in this community than human DNA that was discovered when trying to map the genome. Our model of genes or mutations of genes that affect our health is a poor model when we have ten times or more the genetics living with us that has to be properly expressed.

“You mean there is this tiny community of life living within our personal biosphere?” – Pandemic Survivor

“Yes, that is absolutely correct.” – A Cognizant Commentor “

“Hello, Mr. A. C. Commenter, where did you come from?” – PS

“It’s not commenter, it is Commentor. You introduced me a few weeks ago in a musing. You also got my name wrong in that post. A commenter is one that makes random suggestions where a commentor is one that typically has knowledge of a particular subject.” – ACC

“Sorry.” PS

“So there are ten times as many cells living in my body than my own human cells. That is certainly unnerving to think I have my own personal zoo living all over my body. Are they just in my gut?” –PS

“No they live everywhere in your body. There are literally trillions of these organisms that call your body home. A tiny bio home which lives everywhere in your body. Because this colony lives within you, it can either make you or break you. “ – ACC

“What do you mean by ‘make you or break you’?” -PS

“The way I like to think about our relationship with this colony is to imagine a bee keeper. The bee keeper goes about taking care of the hive to be sure there is plenty of fresh blossoms for them to collect the needs of the hive. Also the bee keeper makes sure that the colony always has a fresh place to store honey. The keeper may also take some of the honey for his own needs.  Certainly the bees also pollinate the fruits and vegetables in the keepers garden for an abundant yield.“  –ACC

“Wow! That is really interesting. I have never thought of anything like this. So I have to keep this living colony happy so that I am well? I always thought that anti bio substances were necessary to kept pathogens from causing disease. Every type of cleaner that I have purchased lately has some form of antibiotic in it. Even the dish washing detergent I bought last week.” – PS

“It is unfortunate that we have used such a large volume of chemicals that has significant impact on our friends that live with us. This destruction of their colonies has caused us much harm. If you think of it like the bee keeper analogy, so goes the colony, so goes the good fortune of the bee keeper. “ –ACC

“Interesting, a healthy hive, a healthy life or living symbiotically.” -PC

“Yes, that is exactly right. If you go out and kick over the hive, you will create an angry swarm of bees that attack you to protect their home. If you give them a place to live, and some nectar to keep them calm, they will re-track their anger. This may account for infectious disease as well as autoimmune diseases and allergies. It may also account for biochemical missteps as well. You introduce a pathogen (or a cougar in the hen house) that angers the hive or a substance that angers the hive and the attack of inflammation begins. You give them their natural needs and the hive calms down and stops attacking you. Pharmaceuticals under our existing paradigm of working on just human cells may actually anger the hive and cause severe inflammation commonly called side effects.” -ACC

“So ole Hippocrates was right two millennia ago. Medicine really is about food and keeping the ‘hive’ happy.” – PS

“Our present model of health has given us many great things for emergency healing, but I believe all the other diseases and possibly severe infections may be treated by keeping the microbiome well. I suspect this is the reason that chronic disease has not gotten any better since the understanding of DNA and the Central Dogma of molecular biology. We have totally ignored the environmental effect on expression of DNA and the DNA of our microbiome. The central dogma of saying that a gene or a gene mutation is the reason for disease is just wrong. It is like saying that you can throw a set of blueprints on a vacant lot and expect a building to spring up. It is the acts of the contractors and the skill of the crews that give you the building. The better you treat the workers, the better the building is likely to be.” – ACC

“That certainly is a new model of health. They actually named our present model central dogma? What arrogance! How can I learn more?” –PS

“Just read.” –ACC

Wiki – Microbiome

Central Dogma

National Institute of Health – Microbiome


Lies, Damned Lies, and Medical Science

We get so caught up in the advancement of science that we take everything that our doctor says he can do for us at face value. However, there is a large disconnect between medical science and the practice of medicine. We move with herd mentality toward collective thinking about how we are to survive our ills. The media promotes medical treatments because it is the life blood of their organizations from advertising.

An article by the same name as the title to this post was published in The Atlantic, November, 2010.  This article is in depth of what goes on between researchers and doctors in medical practice. You may not want to read the article because of the uncertainty that it may bring to you. However, if you are taking three prescription drugs or more, then you should read.

Lies, Damned Lies, and Medical Science

“Much of what medical researchers conclude in their studies is misleading, exaggerated, or flat-out wrong. So why are doctors—to a striking extent—still drawing upon misinformation in their everyday practice? Dr. John Ioannidis has spent his career challenging his peers by exposing their bad science.”

David H. Freedman; The Atlantic, Oct. 4, 2010

What is worse is that the science gets skewed for economic advantages. You may recall the misleading paper that I commented on in May about asthma. Vitamin D3 Significantly Reduces Asthma Flare-Ups The author makes the conclusion that there is no advantage in taking vitamin D for asthma. Buried in his data is the fact that persons in the vitamin D group had a forty percent reduction in flare-ups.

“One should respect public opinion insofar as is necessary to avoid starvation and keep out of prison, but anything that goes beyond this is voluntary submission to an unnecessary tyranny.”  – Bertrand Russell from Brainy Quote

I believe the state of medicine, because it is the largest economic sector, has now reached this condition described by William J. Federer – “The COUNTRY is controlled by LAWS> LAWS are controlled by POLITICIANS> POLITICIANS are controlled by VOTERS> VOTERS are controlled by PUBLIC OPINION> PUBLIC OPINION is controlled by the MEDIA (News, Hollywood, Internet…) & EDUCATION so, whoever controls MEDIA & EDUCATION, controls the COUNTRY.”

This leaves us in this condition described by this quote from Suzanne Collins, Morningjay – “But collective thinking is usually short-lived. We’re fickle, stupid beings with poor memories and a great gift for self-destruction.”

Scientists want you to believe that the science is too complicated for the average person to understand so that the masses can be lead to a collective thinking for economic advantage. This is usually done through the use of manipulating statistics. However, there are methods in statistics that cannot be easily manipulated without outright lying about the data. This is done through the use of averages.

Consider Francis Galton   The good and bad of Francis Galton is his foundation of correlations and statistics and his belief in eugenics. Consider this story in his discovery of the use of statistics from Wikipedia.

“Variance and standard deviation

Core to any statistical analysis is the concept that measurements vary: they have both a central tendency, or mean, and a spread around this central value, or variance. In the late 1860s, Galton conceived of a measure to quantify normal variation: the standard deviation.

Galton was a keen observer. In 1906, visiting a livestock fair, he stumbled upon an intriguing contest. An ox was on display, and the villagers were invited to guess the animal’s weight after it was slaughtered and dressed. Nearly 800 participated, but not one person hit the exact mark: 1,198 pounds. Galton stated that “the middlemost estimate expresses the vox populi, every other estimate being condemned as too low or too high by a majority of the voters”, and calculated this value (in modern terminology, the median) as 1,207 pounds. To his surprise, this was within 0.8% of the weight measured by the judges. Soon afterwards, he acknowledged that the mean of the guesses, at 1,197 pounds, was even more accurate.”

As you can see from the above observation, averages are very powerful. Later, this understanding of averages was assimilated by Elis Ott into analysis of the means, ANOM, as a statistical method for solving the problem of determining interactions. Medical science now depends on analysis of the variance and very seldom looks at interactions during drug trials because of the complexity of the math.

What are we to do when visiting the doctor? If you have an acute illness, know that he US has the best medical facilities in the world. If you have chronic disease or other chronic health condition, then be very careful in listening to your doctor about what drugs to take. Research it thoroughly. Talk with specialist in holistic medicine, remember what your grandparents used to do, and weigh all of this in combination with your own best thinking.

We are driven by our fear of illness, however, the best way to treat fear are to heed the words of Martin Luther King, Jr. “Normal fear protects us; abnormal fear paralyses us. Normal fear motivates us to improve our individual and collective welfare; abnormal fear constantly poisons and distorts our inner lives. Our problem is not to be rid of fear but, rather to harness and master it.”

You are what you believe and what you put into your body, and the environment you maintain: “Just like a single cell, the character of our lives is determined not by our genes but by our responses to environmental signals.”  – Bruce Lipton “Biology of Belief”

Always seek love, joy, and peace first as you harness your fear. – Pandemic Survivor

As an aside, have you seen the news on the water problems in Toledo? It appears that I was right on in my post of cyanobacteria. Microcystins in the water created by the ‘bloom’ from these bacteria is creating havoc in the water supply. Microcystins are peptides, protein mimics, that can cause any number of neurological diseases and other diseases. Summer Fun in the Sun and Water

VITAMIN D reduces 42 health problems

Henry Lahore at VitaminDWiki list forty-two health problems as proven by Double-blind random-controlled-trials.

Hypertension,  Cardiovascular,  Back Pain,  Diabetes,  Influenza,  Falls,  Hip Fractures,  Breast Cancer, Raynaud’s pain,  Menstrual Pain,  C-section and pregnancy risks,  Low Birth Weight, Chronic Kidney Disease, Cystic Fibrosis,  Rheumatoid Arthritis,  TB,  Rickets,  Respiratory Tract Infection, Lupus, Sickle Cell pain, leg ulcers, traumatic brain injury. Parkinson’s Disease, Multiple Sclerosis, Congestive Heart Failure,  Middle Ear Infection, Gingivitis, Muscles in seniors, Antibiotic use in seniors, Taller Infants, Gestational Diabetes, Heart Strength following an attack, Prostate Cancer, Asthma, Depression, Breastfeeding, Fibromyalgia, Chronic Hives, cholesterol, Weight Loss:

What else do you need to know to be sure you have an adequate serum vitamin D level?   – Pandemic Survivor

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Understanding out of Chaos

Many Causes, One Disease, Many Cures
Resolving Multiple Factors for Disease States

“Double, double toil and trouble
Fire burn, and cauldron bubble” Hamlet, Shakespeare

Okay, this post is not for the layman in trying to resolve issues of their personal health. This post is to point researchers to a tool long used in the military and manufacturing for troubleshooting problems. The issues are multiple factor diseases. When there is more than one factor, analysis of the variance, ANOVA, only tells you that there is a statistical significance of one of the factor variances. It does not tell you which factor is causing the variance.

One of the issues that have long plagued medicine is multiple factors. In the ‘gold standard’ for statistical analysis of a drug or nutrient in how it affects a disease, typically only one factor is used. The double blind, placebo controlled trial is run. The reason for this is the complexity of the math when there is more than one factor and the understanding by decision makers of what the math model is telling you.

Elis R. Ott developed a technique for measuring multiple factors in how they vary from the average. In other words, the technique measures the group average variation from the average of the entire population. This technique is called analysis of the means. So in comparing to ANOVA it may be stated as: ANOM compares the group mean to the overall mean, where ANOVA compares the group mean to the other group means. ANOVA can tell you if there is a significant difference, while ANOM can tell which group mean is significantly different.

I can tell you from personal experience that ANOM is a very powerful statistical method to sort out both common causes and assignable causes. I was once the engineering manager for the world’s largest automotive battery plant. We made sixteen thousand batteries per day. That is over a million electrode plates per day. We of course used all the standard statistical techniques. Until ANOM was introduced, confusion continued to hold sway because the employees as well as the managers did not understand the math. When the graphical method of ANOM with the ability to compare multiple factors was introduced, we quickly achieved much higher production levels of quality product. It was also great because ANOM could be applied to either attribute data, go/no go, as well as variables data.  Also, much smaller sample sizes were needed to show significance. Clear decision making with expected results became trusted.

Here is an explanation from the SAS software statistical module: “A health care system administrator might ask which clinics in the system have a higher or lower rate of admissions than the average for all clinics. Questions of this type can be answered with analysis of means, which is an alternative to one-way analysis of variance (ANOVA) for a fixed effects model. However, unlike ANOVA, which simply determines whether there is a statistically significant difference in the treatment means, ANOM identifies the means that are significantly different. As a statistical technique, ANOM is a method for making multiple comparisons that is sometimes referred to as a “multiple comparison with the weighted mean”. Analysis of means lends itself to quality improvement applications because it has a simple graphical representation that is similar to a Shewhart chart and requires little training to interpret. This representation is also useful for assessing practical significance.”

History: “Analysis of means compares the absolute deviations of group means from their over-all mean, an approach that was initially studied by Laplace in 1827. Halperin and others derived a version of this method in the form of a multiple significance test in 1955. Ott developed a graphical representation for the test and introduced the term “analysis of means” in 1967. Refer to Ott (1967) and Ott (1975). In the 1980’s Schilling extended the application to non-normal distributions. P. R. Nelson (1982a) and L. S. Nelson (1983) provided exact critical values for ANOM when the groups have equal sample sizes. P. R. Nelson (1991) developed a method for computing exact critical values for ANOM when the group sample sizes are not equal.”

This is really great because this technique can be applied to existing data when there are multiple factors to readily point to which is the most statistically significant. You can easily decide if calcium or vitamin D is more important or better you could compare vitamin D, vitamin A, calcium, and magnesium. The thing that adds to the value of ANOM is the ability to compare the interactions of the factors. Many of the interactions will mean nothing. However, the interactions of some of the factors will be greater than any one factor. So you might find that vitamin D is great for moving the population toward health. The interaction of vitamin D and magnesium would be even greater. We can make suppositions based on our understanding of the mechanisms, but until the interactions are statistically verified it continues to be viewed as a witch’s brew.

An example of this in the nutritional community is the argument between Dr. Cannell of the Vitamin D Council and the folks over at the Weston A. Price Foundation. Dr. Cannell has held that high levels of preformed vitamin A will lead to illness because of the apparent reduction in the serum levels of vitamin D. Weston A. Price Foundation has long held the importance of vitamin A and especially cod liver oil as an elixir for health. So the question becomes is vitamin A and vitamin D antagonist or are they cofactors of each other. I personally suspect that large amount of vitamin A with small amount of vitamin D is the issue driving the assumption that large intakes of vitamin A is bad. Given two to three months for the liver to clear of stored vitamin A with a serum level of vitamin D above 60 ng/ml; I suspect health would be improved with high intakes of both vitamins. I also suspect that there is enough data currently existing in clinical trials to ferret out the answer using ANOM. One of the major advantages of ANOM is that it gives a graphical solution that is easily understood by clinicians and decision makers without having to have a complete understanding of the math operating in the background.

So the group averages of different levels of vitamin A and vitamin D may look something like this when compared to the total population.
ANOM IllstrationAfter applying ANOM you would get a graphical solution like this. This created hypothetical  example shows that both high A and high D are statically significant. But better, it shows that the interaction of vitamin A and vitamin D is even more significant. (this would make sense as the known mechanisms for growth factors, necrosis factors, and immune system improvement require VDR/RXR dimers)
ANOM DecisionIf the above ANOM is truly represented as fact, then after giving the population high amounts of vitamin A and vitamin D you would get a shift like this:

Improved wellness after applying the new understanding.

Improved wellness after applying the new understanding.

Now just imagine the power of this when analyzing a population when the levels of vitamin A, vitamin D, magnesium, and calcium are known. You would be able to see the effect of the main factors as well as the interactions of the factors and decide based on statistical significance. Or better, you could make an analysis of different levels vitamin D3, vitamin D2, vitamin A from fish liver oil, beta-carotene, magnesium oxide, magnesium chelate, calcium hydroxide, and calcium citrate all in the same study. There would be no control population required as the group averages would be compared to the average of the entire population. This is more real world than how it is done now. Also, because the interactions are so difficult to predict by individuals during the trial, the placebo effect would not be as large a factor.
The clamor over the last many years have been that vitamin D provides no consistent benefit based on meta-analyses of many studies. The beauty of using ANOM for the meta-analyses would show that dose dependence is of extreme importance. No longer would critics be able to say that vitamin D has no effect. It would be plain there are no effects at lower levels or the effects would be shown to be dose dependent for different diseases.

Imagine doing drug studies and show variations of other drugs and nutrients and interactions in the same trials with a graphical method that could be easily understood. Or imagine analyzing all of the environmental factors that are issues for a disease like autism from existing data. For this reason, the inability to show clearly which factor is most important; it is not likely that this technique will ever be adopted. I know this is a very critical statement, but it is obvious that the preference of the medical community is to keep the argument going instead of solving the problems because of the economics involved. With increased wellness in the general population, healthcare/healthcare insurance job opportunities would be significantly reduced. Our leaders have to decide which is more important, your health or the economy. I suggest that empathy for each person’s wellness would strengthen the economy to a much greater extent than creating and maintaining jobs in the healthcare sector only. It would certainly give more trust in our leadership. – Pandemic Survivor

“Think, and then plot the data.” Elis R. Ott

Further Reading: Process Quality Control: Troubleshooting and Interpretation of Data, Fourth Edition Ott, Schilling, Neubauer 2005 or Amazon
The Analysis of Means: A Graphical Method for Comparing Means, Rates, and Proportions, Nelson, Wludyka, Copeland; 2005 Amazon

Many Diseases, One Cause, One Cure –The Sun

“Fillet of a fenny snake,
In the cauldron boil and bake.
Eye of newt and toe of frog,
Wool of bat and tongue of dog,
Adder’s fork and blind-worm’s sting,
Lizard’s leg and owlet’s wing,
For a charm of powerful trouble,
Like a hell-broth boil and bubble.”
Macbeth, Shakespeare

Does this sound like your typical medical researcher toiling away at work in the laboratory? It may as well be as far as the average person is concerned. When scientists start talking about chemical and biological mechanisms or how a particular drug affects disease, I am sure this is what it sounds like. This is really unfair to the researchers for it is the spin of medical marketing that cause our heads to ‘explode’ with too much misunderstood information. Hypocrisy and deception was of course the major theme in Shakespeare’s play, Macbeth.

It is fact that the medical establishment wishes you to view holistic medicine in this manner, a witch’s brew. How many news articles have you seen in the popular press since this past December have been placed simply to discredit the use of vitamin and mineral supplements? In particular vitamin D; it is the steroid/vitamin that results from our exposure to the sun. This is the thing that is the most alarming to the medical profession. That one source can heal, treat, cure, prevent, and diagnose a disease without it being called a drug that can be exploited economically.

And just how far has the medical establishment taken the bashing of supplements and food to treat disease? They have gone as far as passing a law that says nothing but drugs can be used for purposes of healing, treating, curing, and preventing disease. I find this extremely amazing as this one law totally ties the hands of doctors in their toolbox of treatment. It was however agreed to because the other option was to allow the FDA to treat everything as a drug. This would take away our freedom of access. Dr. X, would you please write me a script for turnip greens…..

Let’s take the sun as the one thing that is responsible for many diseases if it is taken away. Without the sun, the water cycle and clean fresh air would not exist. There would be no food sources as photosynthesis would end. You would only have fungi to stay alive. If you completely took it away and everything that it gives us, you would be dead in a very short period of time. So let’s take away some degree of the sun and see what happens. You get a host of chronic disease that is used by the medical establishment and government to support a large economic sector.

This is exactly what happened in the 1960’s as a prominent pediatrician, Dr. Cook, friend of the Kennedy’s, made the public declaration that vitamin D would cause birth defects. People were scared out of the sun, especially pregnant women. The use of cod liver oil as a supplement was held in an extremely negative view by medicine. Where was the science in this art? Then there was the large campaign by the medical professionals to keep us out of the sun because we might get skin cancer. RUN, IN FEAR of cancer! Of course, there is now an extremely close correlation between the use of sunscreen and the incident of melanoma. Also, other cancers have either staid the same as far as mortality or increased even with all of our efforts in the hundreds of billions of dollars spent on cancer research. There are now at least a hundred diseases that can be traced to the lack of vitamin D or our connection to the sun. Dr. X, would please write me a script for the sun………

Do you have someone in your family or a friend that makes their income from the medical/medical insurance industry? An entrenched “protection racket” used for apparent safety that under any other circumstance would be aggressively prosecuted. “Double, double toil and trouble, Fire burns, cauldron bubbles.” – Pandemic Survivor

One Disease, One Cause, One Cure

“Double, double toil and trouble,
Fire burn, and cauldron bubble.” – Macbeth, Shakespeare

As I have read about diseases and medical cures, I have been fascinated by the approach to problem solving. I know that these are words you don’t normally hear in medical practice – ‘problem solving.’ It is typically about the disease, the cause, and the cure. It is also amazing to me to read research papers that will end with the statement about more needed research. I always ask the question; more research about what? Biological mechanisms for creating a new drug or the multiple factors that are the cause and cure of a disease?

Typically medicine has tried to identify a specific cause of malady with a specific cure. This makes it nice and neat for both patient and doctor. However, I do now believe after reading for several decades that there is no disease that has a single factor as a cause. The only exception to this is acute disease like infections or a broken leg. If the disease is chronic in nature or occurs over time, then multiple factors always come into play. Could it be possible that an acute disease has multiple factors? I do believe this the case with the common cold and other mild infections and perhaps that broken leg as well. This may also extend to significant infections where ninety percent of the victims die like the Ebola virus. The reason that I can say this is that ten percent of the infected lived, which means that other factors have come into play other than the Ebola virus. Has anyone really asked what these factors are? Could it just be that the survivors have better nutrition with stronger immune systems? What are the nutrients that have contributed to the better immune systems?

The claim in the last hundred years is that medicine has transformed into a science instead of an art. This is a flat out fabrication. Science has come into play in a limited fashion. Science has not been applied to medicine the way it has to say manufacturing or space travel. In both of these endeavors, all factors of significant importance are always considered. Unlike medicine, there are no laws preventing problem solving of significant factors. In medicine, the most significant factors of nutrition cannot be used to treat, cure, diagnose, or prevent a disease. I find this most fascinating in the limiting or hand tying of our doctors and researchers. Of course there are some limitations of factors in manufacturing like environmental laws to protect future generations. What is being protected in medicine by limiting significant nutritional factors? I was startled at California’s attempt to make it a felony for a doctor to use nutrition to treat a disease. I guess the answer is to follow the money without empathy for the ill and dying.

Also medicine has not used all of the tools that are available to them. A great example of this is the statistical methods that are used for problem solving or troubleshooting an illness. Techniques of identifying multiple factor statistical probabilistic predications were developed for the military in the 1950’s. The techniques were them applied to manufacturing in the 1960’s. The techniques then matured in the 1970’s and 80’s. For example, are there control charts in hospitals tracking cases of MRSA to be sure that prevention methods have remained stable in hospital operations?

If it is not one disease, one cause, and one cure it seems that the solutions are too difficult to communicated to all of the decision makers. Decision makers in medicine are you the patient, the doctor, the institutional managers, the medical education community, the medical research community, the insurance institutions, and government institutions. This much complexity, prevents the swift solutions for common causes and special causes or assignable causes of illness. I am sure that W. Edward Deming and Walter A. Shewart are ‘rolling in the grave.’ The last couple of decades have seen the development of chaos theory. How long before this new science is applied to medicine with its repetitive predicative perception of nature? Or, will chaos as an artistic pursuit in medical decision making continue? – Pandemic Survivor