If we look at who is susceptible to the influenza virus that could lead into a potentially fatal situation it tends to be the elderly and the very young.  In between that, the folks that are well fed and rested, are reasonably able to handle their daily stress load and they tend to handle most colds, flus and diseases effectively.  They may catch it, but it is not a fatal occurrence.

One of the things that have confused doctors and scientists is the presence of microbes that we think are pathogenic.  Should we kill them?  An example is the systematic attack of H. Pylori, the bacteria that cause gastric ulcers.  Helicobacter Pylori is important bacteria that can be beneficial to our stomach.  Some H pylori can cause ulcers.  Over the last 25 years if they see H pylori they kill it with antibiotics.

Research now shows that systematic eradication of H. pylori increases the risk for gastroesophageal cancer.  It plays an important role in maintaining a homeostasis in our body.  So while some bacteria are bad, removing them can sometimes cause more serious problems down the road.  Clostridium bacteria are thought to be really bad.  They are discovering that high levels of Clostridium are associated with lower incidence of allergies and asthma, psoriasis, dermatitis and things of that nature.  It turns out that Clostridium play an important role in teaching our immune system how to function.

The moral of this story is we don’t know what we don’t know.  The ecology of our body is extremely complicated.  When we do precision attacks on microbes we tend to make more problems than solutions.  E. coli and Candida are not necessarily bad.  We have to look at the symbiotic relationship, the ecology of our body.  Just like farmers know that certain pests will keep other pests off their crops we need to rethink about our desire to kill the microbes that allow us to live.  Whether pathogenic bugs become disease causing or not is often determined by our internal ecologies’ health.

There are thousands of variables and a large proportion of those thousands of variables are our microbes that belong inside us and not run over by the dump truck of modern living.  One of the elements of our microbiome that are overlooked is the viome, which is the total set of viruses that are continually present as part of our giant organism known as us.  Bacteriophages are in the category of virus.  They oversee the bacterial population.  They have the ability to consume or kill other bacteria.  A good portion of our day is spent having our bacteria rejected by these bacteriophages.   Our viome is information.  They are a horizontal mechanism for gene transfer.  Genes are information.

The protein coding genes were once number at about 23,000 in the human genome.  The number keeps going down.  It is around 18,000 now.  About 7% of those genes are retroviruses in origin.  A retrovirus is defined as a virus that uses its own RNA genetic code to produce new DNA inside a human cell.  This new viral DNA then becomes part of the human genome and is incorporated into the human cell line.  The most horrific virus we can think of today is HIV.  That category of virus has been responsible for producing a large portion of what is considered to be important aspects of our genome such as the placenta.  The neuro- plasticity of our brain and the encephalization of our brain from 2 million years ago, that explosion of the size of our brain was helped along by the incorporation of these retroviruses.  They have become indispensable parts of why we have become the remarkable species that we are today.

As long as our immune system learns to live in harmony with these once classically labeled bad bacteria we do well.  When our gut microbiome goes out of balance it creates inflammatory responses and can predispose us to disease from germs that have always been in there and not bothering us.  When the inflammation process occurs in the gut and damages the lining, we can get leaky gut syndrome.  We can get microbes from our gut in other areas of the body where they don’t belong and disease can occur.  Chemicals can be produced by bacteria, viruses and fungi that can affect us.  One example of these compounds are short chain fatty acids such as butyrate.  We can use it for energy, but it is also a powerful anti-inflammatory and has in an amino regulatory affect.  People with autoimmune disease are often found to have low levels of butyrate.  This is one reason why I put my autoimmune patient’s on probiotics.  Butyrate has been shown to preserve the barrier in your intestine that would stop it from leaking even when damaged with antibiotics.  If the bacteria or the bacterial byproducts link across the intestine it becomes systemic and that leads to inflammation throughout your whole body.  That affects your immune system.  This ultimately leads to organ dysfunction.

Getting sick is confusing for many people.  They wonder what they should do.  Should I take anti-fever medication?  A fever is very uncomfortable, but it is increasing our body temperature because it makes a less optimal environment for bacteria and viruses to replicate and increases our metabolic rate so that our immune system can be more active.  That fever is valuable and instead of suppressing it, ancient cultures would cool the back.  It would allow the heat to leave your body, but not stop the process of the fever to kill the bugs.  That requires a lot of work and it is easier to pop a pill, but not smarter.  When you are mounting an immune response against a  cold, a bacterial or viral infection, your immune responses are up regulating.  That means it’s also looking for cancer cells.  It is looking for everything.  Unfortunately when our autoimmune system is not working correctly, it is also looking for the good stuff that makes us, but it doesn’t recognize it any longer as us and sees it as something it must attack.  Basically the only treatment for that in the medical world is anti-inflammatory medications such as prednisone, which blows you up to four times your size.  Natural anti-inflammatory diets and supplements are not considered.  Certainly probiotics are not prescribed even when you have been labeled with the autoimmune disease of Crohn’s.  Again, allowing us to get a fever from typical or routine illnesses not only allows our bodies to fight a cold or the flu, we are allowing our immune system to also fight future cancer.  We want that immune response even if the commercials on TV tell you they have something for your fever.

We are a very mobile society today.  Societies where people live in the same region for multiple generations have a stronger immune system to fight against the things they live among.  The bacteria in the soil and their plants work symbiotically to build their health.  By building a very solid relationship with their biome of the environment that they are in,  they developed the ability to be able to withstand a lot of foods that might make a stranger sick.  Geography will determine your gut biome.  As I typed that, I couldn’t help but think how fortunate I was to get food poisoning in so many Third World countries.  Different microbiota blend with local foods to ferment and byproducts of that fermentation are beneficial to the host.

For kids to be healthy and happy they need to connect with the natural world through eating it.  Golden arches do not exist in healthy primitive societies.  Kids used to be allowed to ingest and incorporate their environment into their bodies.  Today parents want to hermetically seal their children in a bubble.  I was fortunate enough to have plenty of forests to hike through as a young child.  There was a farm up the street and we chased the animals.  Today I’m sure my face would have wound up on a milk carton.  That farm later became my elementary school.  We did half of our learning outside under the trees laying in the grass playing with bugs and worms.  It will be okay if your kids play in dirt.  As a kid we all walked barefoot quite often.  More ancient cultures know that walking barefoot builds their immunity.  I was fortunate to be able to go to the Long Island sound on our North Shore and the Atlantic on our South shore.  We walked the beach and swam in rivers and streams weekly if not daily.

That was 1960 and none of the children had any of the diseases that they face now.  Ironically, my area where I grew up is a major breast cancer cluster of the universe.  All the pesticide runoff from the farms ran into our water supply and the estrogenic mimicking poisons attacked the women’s breasts.  Trying to forget that breast cancer part of the story for a moment and realize that modern city living does not provide a lot of the benefits that we require.  We do not get the flow of life living in a city.  Animals have a certain rhythm.  They get up early.  The humans that live with them have to get up early and take care of them.  That is not so bad if you want to live to be a healthy 100 years.

If we look back at evolution and examine what our ancestors did to support their microbiome that led us to this phase where we are right now, which is at the top of the food chain, we see that they played in the dirt, ate a diverse diet, they didn’t have chemicals that harm us, they went to bed when it got dark, and they had a strong social network because that was required to survive that harsh life.  Well harsh compared to having 500 channels of crap to choose from on the television set.  When we change our environment and our diets we change a genome just as surely as toxic chemicals do.

We are constantly doing things all day that alter our gene expression.  This is normal physiology.  It is not just genes alone, it is how they are influenced by our environment, which of course includes our thoughts.  There are many factors that have been discussed here that gives rise to our mitochondrial function.  Mitochondria are in constant communication with our genes.  This communication is necessary because our genes need to know what is happening in the outside world of the cell and the inside of the cell as well, since our genes are walled off in a nucleus.  It is our microbiota that control how much ATP production occurs.  All this communication determines how much food we are going to eat.  We have to be able to get food from our environment.  Our microbiota which comes from our environment is able to signal the mitochondria to let them know that food is coming.  Not only that it is coming but how much of it is coming.

When we talk about our genetics we need to realize that there is a crosstalk between our DNA and our mitochondrial function.  That crosstalk is directly tied to how your cell will methylate.  How these methyl compounds will come in and out of the mitochondria at a certain rate.  This helps determine mitochondrial defense mechanisms.  DNA divides and is translated and it makes protein.  This is the classic pathway of my seventh grade science project in 1966.  We now know that the messenger RNA can break off in vesicles and latch on to cell membranes of other cells that they want to communicate with.  There are two sources of DNA in a cell one from the nucleus and the other is from the mitochondria.  Both of these DNA can be controlled by epigenetic mechanisms.  This is how we can alter gene expression without actually altering the DNA itself.  This how we can get mitochondria to increase their production of ATP.  Both of these DNA systems can respond to epigenetic signals.  It turns out that this micro RNA can exist in foods that we eat.

Grapes or rice for example contain little nano particles that can be absorbed into our bloodstream and they can alter our gene expression.  Over the course of evolution we have outsourced gene regulation to the plants in our environment and they helped orchestrate our complexity of being human.  There is interspecies communication occurring through the mechanism of micro RNA such that the biosphere is actually all one on some basic molecular level.

One of the dogmas of molecular biology was a unidirectional flow of information.  A protein coding gene went out and created a protein in the ribosomes.  There was no accountability for information that came into the system.  Because of retroviruses that were discovered in the 70s we know that the opposite is true.  These viruses are able to insert genetic matter backwards so that they become a permanent part of the human genome.  That kinda kills my joke that we are all unique just like everyone else.

This means that some kids are going to be more susceptible to poisons injected into them than others.  If we look at the slow pace of change that occurs within the protein coding genes in the human genome and compare that to what viruses can do in real time we have to acknowledge that our moment to moment exposures in our environment to viruses as one example will affect our genome in an inheritable way.

This puts a profound responsibility on our choices if were going to reproduce.  We have the ability to affect all future generations by how we live our life.  If we collapse the timescale from billions of years ago to micro seconds, which is all the time it takes for a micro RNA molecule to change an egg or sperm cell you have to wonder what we’re going to look like in the near future.  A mere chance encounter with some micro RNA can forever change the phenotype of your offspring and their offspring.  If you think about what I just wrote science has disproved fatalism.  In most cases you were not dealt a lousy set of genes.  It is not the cards in life that we are dealt, it is how we play them.  We create our destinies on a biological level every moment.  We are doing this based on simple lifestyle choices.

What food should I eat, what exercise should I do, what am I my thinking and feeling, am I getting enough rest?  This is the new biology that is incredibly empowering.  I wish they would have taught me that in school for what we knew when I graduated postgraduate school in 1993 is nothing compared to what we know now.  This is completely mind blowing.  The quad trillions of microbes that we let in and on our body are in two-way communication with both our mitochondria and DNA.  We have the genetic information from our food communicating with our cells.  Our food is determining our genetic expression.  While this is boggling my mind we kinda always knew this way back in the 60s when our mothers told us we are what we eat.  Well my mother would say that.




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