“Junk” DNA includes a whole subset of names such as introns, retrotransposable elements, and non-coding RNAs (ncRNAs). In fact, ncRNAs are often located near genes known to be important to both stem cells and cancer, to serve as enhancer elements which promote their gene expression. Stem cells are the cells that have the potential to turn into lots of other cells. So this junk DNA can influence how stem cells specifically differentiate into multiple cell types.
In fact, it is now estimated that 80% of our genome is biologically active with only 1% of our genome encoding for proteins:
A staggering batch of over 30 papers published in Nature, Science, and other journals this month, firmly rejects the idea that, apart from the 1% of the human genome that codes for proteins, most of our DNA is “junk” that has accumulated over time like some evolutionary flotsam and jetsam.The papers, representing 10 years of work of the ENCODE (“Encyclopedia of DNA Elements”) project, completed by hundreds of scientists from dozens of labs around the world, reveal that 80% of the human genome serves some purpose and is biochemically active, for example, in regulating the expression of genes situated nearby.
That was known for some time, but it is now official since September 2012 or so. Evolutionary speaking, it makes a lot of sense…
Viral “Junk” DNA
The greatest shock of genomic science was to find that the human genome contains more viral than “human” genes. That is, the human genome is made from thousands of viruses that infected our distant ancestors. They got there by infecting eggs or sperm, inserting their own DNA into ours.
Viruses are peculiar things that at a zoomed-in level may look very pretty or downright creepy depending on the virus. A virus may have DNA or RNA and the type of genetic material depends on the function and nature of the virus. Some are very infectious, others allowed us be alive since the gene that encodes for a protein that allows for babies to fuse to their mothers during pregnancy, is a virus gene.
Most of the genetic diversity can be found in virus genes. Scientists agree that there are some 1,000,000,000,000,000,000,000,000,000,000 viruses in the ocean and it matches almost nothing to any gene from any microbe, animal, plant or other organism, even from any other known virus.
All living things have hundreds or thousands of genes imported by viruses. There are a group of viral species known as retroviruses which insert their genetic material into the host cell’s DNA. When the host cell divides, it copies the virus’s DNA along with its own. Retroviruses have “on switches” that prompt their host cell to make proteins out of nearby genes. Sometimes their switches turn on host genes that ought to be kept shut off, and cancer can result. This is precisely what our junk DNA –ncRNA- seems to be doing “next” to genes that have to do with stem cells and cancer cells.
What is known as endogenous retrovirus – endogenous meaning generated within, are the viruses that lurk in the genomes of just about every major group of vertebrates, from fish to reptiles to mammals. Virologists have found retrovirus-like segments in our human genome and they were able to track its genetic code down to an original functioning virus. The virus was called Phoenix, for the mythical bird that rose from its own ashes.
It is known that part of our junk DNA, the retrotransposable elements, are viral in its origin. It includes the endogenous retroviruses. But it is now argued that ncRNA (non coding RNA) might be viral in its origin as well. This has interesting implications in the sense that epigenetic control of gene expression involves this junk DNA – ncRNAs. It would mean that our entire junk DNA (98%) might well be very functional epigenetically speaking (more info on epigenetics below), and active in the induction of regulatory genes that code for stem cells, or for reprogramming o modulating genes known to response to oxidative stress, DNA damage and p53 – a protein that regulates the cell cycle and is implicated in about half of all human cancers.
You might be wondering why we are reviewing all this viral genome potential. As it happens, the damage done by evil lectins – antinutrients – in our diet is through a lock and key mechanism, that is, a circulating lectin serves as a key that unlocks the cell to within it attaches. Evil lectins can initiate a cascade of events once they attach to the cell “mem-brain” that may lead to attraction of the immune system, cell death, production of chemicals, multiplication of the cell and so forth. It depends. And it might well depend on the adaptation response from the viral-like properties inside the cell, our “junk” DNA.
Harmful lectins – such as the ones found in gluten, soy, dairy, corn – cause inflammation and damage without a defense/immune response which end up being secondary to the initial damage. Some response in quite a drastic way (i.e. autoimmune diseases) others respond in a milder way, constituting thus the wide nature of symptoms among people.
Moreover, wheat’s evil lectin (WGA) and viruses share similar properties. For instance, when the influenza virus incorporates its own genetic material into our cells, the defense/immune system must attack its own virally transformed cell in order to fight the infection. WGA has access to our bodies and to our cells’ “mem-brain’s” through viral ports. Then they influence gene expression and trigger autoimmune attacks like viruses do. As John B. Symes, D.V.M. pointed out back in 2007:
Viruses are the principle, proven cause of cancer (e.g. retroviruses). Carcinogens simply incite the virus into causing that cancer. [...] After all, it is what some viruses do, incorporating their DNA into that of the host only to have that cell reproduce out of control at a later date. It is those ugly chemicals and pollutants we call carcinogens that trigger those viruses into turning the DNA into a cell factory.
But, viruses and carcinogens alone are not sufficient for the individual to develop cancer. The host must also experience some degree of immune failure in order to get the “big C”. So, it is this triad of factors…viruses, carcinogens, and immune failure…that come together to yield the resulting cancer. That is what we call a “syndrome”.[...]
The “big 4″ (gluten, dairy, soy and corn) are the “who’s who” of what is wrong with foods, as they damage our gut’s ability to absorb nutrients (e.g. celiac disease), shower our body with damaging proteins (lectins), load us up with staggering levels of “excitotoxins” (glutamate and aspartate) and pound us with estrogens. As a result, tissue health suffers, immunity fails, enzyme systems go down, and the Pandora’s Box of viruses is opened wide. [...]
The bottom line is that viruses don’t like certain things hurled at them (e.g. lectins, chemicals, and pollution). Their first reaction is one of adaptation, enabling the target cell to function in the presence of the offending agent. [...]
However, when viruses are called upon to repeatedly react to these noxious stimuli, a more involved form of adaptation is employed and one that draws the attention of the immune system. At this point, the individual had better hope that there is a competent immune system present to put down this “rebellion”. If not, that candidate may suffer the full blown syndrome, whether it be “refractory” epilepsy, cancer, or that myriad of things researchers love to call “autoimmune disorders”. These things are not as “idiopathic” as we have all been led to believe.
Our medical histories all line up with this once the role (and ultimate purpose) of viruses in nature and our bodies is grasped. They are not the malicious entities that we have labeled them to be. They are simply doing their job. The noxious stimuli being thrown at them is the real issue. We are literally forcing them into becoming pathogens. In addition to the plethora of obvious offending agents being imbibed, most individuals are compounding matters through poor nutrition, polluted environments, fast-paced lifestyles, and lack of sleep. All of these things add up to self-induced misery. [...]
I have suggested many times that, when reading a paper of genetics, the word “gene” be replaced with the word “virus” to see if that treatise makes more sense. Suddenly, answers to the above questions start coming. Coupled with the knowledge of viral stimulants (e.g. carcinogens, lectins, and other viruses), we can start to see what…or who…the real culprit is.
Not that outrageous at all considering that mutations in ncRNA are associated with cancer, autism, and Alzheimer’s disease AND that ncRNA can sense a viral infection within the cell, giving off signals that indicate the pathogenic virus presence.
An endogenous retrovirus has also been associated with multiple sclerosis, meaning that viral genes that are part of our genome can be “woken up”. As the authors of this study say, “retroviral infections often develop into running battles between the immune system and virus, with the virus mutating repeatedly to avoid the immune system, and the immune system repeatedly catching up. One can see the episodic nature of multiple sclerosis as such a running battle.”
It is crucial to understand that what we eat is information that effects epigenetic changes that regulate gene expression, and that can be passed from generation to generation.
Also, latent viral infections such as the ones of the herpes family is one thing that may be contributing to mitochondrial dysfunction. That plus our toxic food and environment makes a very bad combination.
Herpes simplex virus is a widespread human pathogen and it goes right after our mitochondrial DNA. A latent viral infection might be driving the brain cell loss in neurodegenerative diseases such as Alzheimer’s disease. Members of the herpes virus family, including cytomegalovirus and Epstein-Barr virus which most have, can go after our mitochondrial DNA, causing neurodegenerative diseases by mitochondrial dysfunction. But a ketogenic diet – a diet based on animal fats- is the one thing that would help stabilize mitochondrial DNA since mitochondria runs the best on fat fuel. As it happens, Alzheimer’s disease is the one condition where a ketogenic diet has a profound positive effect (For more information on the ketogenic diet, check out the threads in Sott.net‘s forum “Life Without Bread” and “Ketogenic Diet“.)
Our mitochondrial energetic sources are essential if we are to heal from chronic ailments and we need to stabilize our “viral” genome so that epigenetic changes can be unlocked in a beneficial way.
It is our mitochondria the one that lies at the interface between the fuel from foods that come from our environment and our bodies’ energetic demands. And it is a metabolism based on fat fuel, a ketone metabolism, the one which signals epigenetic changes that maximizes energetic output within our mitochondria and help us heal.
A ketogenic diet promotes the die-off of pathogenic viruses through autophagy. It seems to be the key to stabilize our junk DNA (“viral” DNA) and activate it in a positive way.
In the book When the Body Says No, Dr. Gabor Maté says the following:
The actual results of the genome project are bound to be disappointing. Although the scientific information uncovered is important for its own sake, very little can be expected from the genome program that will lead to broad health benefits in the near future, if ever.
First, there are many technical problems still to be solved. Our current state of knowledge about the genetic makeup of human beings may be likened to using a copy of The Concise Oxford English Dictionary as “the model” from which the plays of William Shakespeare or the novels of Charles Dickens were created. “All” that remains to duplicate their work now is to find the prepositions, grammatical rules and phonetic indications, then to figure out how the two authors arrived at their storylines, dialogues and sublime literary devices. “The genome is the biological programming,” one of the more thoughtful science reporters wrote, “but evolution has neglected to provide even the punctuation to show where genes stop and start, let alone any helpful notes as to what each gene is meant to do.”
Second, contrary to the genetic fundamentalism that currently informs medical thinking and public awareness, genes alone cannot possibly account for the complex psychological characteristics, the behaviors, health or illness of human beings. Genes are merely codes. They act as a set of rules and as a biological template for the synthesis of the proteins that give each particular cell its characteristic structure and functions. They are, as it were, alive and dynamic architectural and mechanical plans. Whether the plan becomes realized depends on far more than the gene itself. Genes exist and function in the context of living organisms. The activities of cells are defined not simply by the genes in their nuclei but by the requirements of the entire organism-and by the interaction of that organism with the environment in which it must survive. Genes are turned on or off by the environment. For this reason, the greatest influences on human development, health and behavior are those of the nurturing environment .
It is a marvelous way to put it. Puts the whole genetic profiling at a back stage!
The genetic code contains only the hardware for life, it is the epigenetic code who has the software determining how the hardware behaves. This is what you want to focus on since genes are codes that are turned on and off by the environment which includes the foods we eat, nurturing or the lack of it, our toxic world, and so forth.
It is the epigenome which consists of chemical compounds that modify, or mark the genome in a way that tells it what to do, where to do it and when to do it. The marks, which are not part of the DNA itself, can be passed on from cell to cell as cells divide, and from one generation to the next.
Epigenetic control is basically how environment signals control the activity of your genes. The information that your environment signals goes on to a regulatory protein, and only then does it go to the DNA which will end up coding a protein. The contribution of nature (genes) and the contribution of nurture (epigenetic mechanisms) have to be considered if we are to make sense of ourselves.
The most important tool you have to change your health is the food you eat. It doesn’t rely in the latest stem cell study or genetic tweaking in mad scientist lab. Food is information that talks to your genes and that are capable of turning them on or off, telling them what not to do or do. The food you eat has the information needed to affect your health in the fastest way.
As an example, let’s take for instance the agouti mice experiment where scientists found that an enriched environment with nutrients (that are typically in animal foods) can override genetic mutations in mice. Agouti mice are yellow and extremely obese, and are predisposed to diabetes, cardiovascular disease and cancer: our modern age maladies. In the study, scientists used B-complex vitamins including choline found in high amounts in animal foods, and betaine found in high amounts in spinach. These nutrients are very rich in methyl groups which are involved in epigenetic modifications. Methyl groups attach to a gene’s DNA, changing the way regulatory proteins bind to the DNA molecule. If the proteins bind too tightly to the gene, the gene cannot be read. Methylating DNA can silence or modify gene activity. In the experiment, scientists gave these nutrients to pregnant yellow mice with the abnormal “agouti” gene that were obese, and they ended up giving birth to the brown lean mice, even though the offspring had the yellow agouti gene. The agouti mothers, who didn’t receive B vitamins, had yellow pups, which ate much more than the brown ones. A grain-based diet will lead you to a deficit of B-vitamins which leads to hyperhomocysteinemia: a risk factor for strokes and heart disease. It can be treated with a diet rich in animal foods!
Babies that were undernourished during pregnancy are more likely to be obese and experience metabolic problems later in life. It makes their metabolism thrifty, readily converting the overabundance of carbs into fat and leading to insulin resistance and obesity. But it would have made them survive much easily periods of famine and scarcity. It was handy for our Paleolithic ancestors, who never had carb rich foods foods like the ones we have today.
Another story that should give us all pause is Francis Pottenger’s cat experiments. In the 1930s, this scientist conducted a series of feeding experiments and which spanned more than 10 years and several feline generations. From the 2nd generation onwards, the cats that were fed processed foods showed vulnerability to disease, more structural deformities, allergies, reduced learning abilities, reproductive problems and stress-driven behaviors. It took around 4 generations of healthy food feeding in order for the cats to return to normal. If we are too many unhealthy generations of “Pottenger’s cats” into the Big Agra Revolution, the odds are against us and we can no longer afford to ignore this. It is catastrophic to see that we no longer have the same strength and resilience some cultures enjoyed before the industrial era.
Despite the extent of the damage, it is equally important to give ourselves the chance to effect epigenetic changes through a diet in which humanity thrived for most of its history. We can “control” our genome through our food rather than being controlled by it. There is indeed hope!
As outstanding as the genetic profile stored in the nucleus of the cells is, it is actually our fatty cell membranes which happen to be the interface between the cell and the environment. As biologist Bruce Lipton explains, information from the environment is transferred to the cell via the cell membrane. The cell membrane (“mem-brain”) monitors the condition of the environment and then sends signals to the genes inside the cell so they can engage cellular mechanisms, which in turn, provide for its survival. 
Another important aspect to consider is that our genes live inside the cells, and the nutrients that best protect them from undesirable effects are those who are able to cross the fatty cell membrane that encloses the cell, that is, fat soluble nutrients in animal foods.
Ditch the Carbs!
In Art and Science of Low Carb Living it is explained how the genome consists of 3 billion base pairs on the 23 chromosomes. The DNA length that contains a typical gene extends about 50,000 base pairs, of which only a fraction (i.e. 3,000) encodes a protein. Each of us has around 22,000 genes scattered around the genome. What all of this means, is that the majority of the genome (98%) consists of DNA which was considered to be junk because it didn’t encoded protein. In fact, it is called non-coding DNA. But as we already reviewed, functions for this “junk” are starting to be elucidated. Some are like genetic switches that regulate when and where genes are expressed.
We are told that a person’s DNA is about 99%-99.5% identical to any other person’s DNA and our differences relies on what is called copy number variants – places in the DNA where the number of copies of a gene can vary from one to many hundreds. Copy number variations took place over a million years ago, others a few thousand years ago. Another way in which we can differ to each other is what is called single nucleotide polymorphisms (SNPs) – a location on the DNA where one of the four nucleotides (whose pairing constitute DNA’s base pairs) has been replaced by another. Two people can differ for about 3 million SNPs, which is about 0.1% of their total DNA.
This teensy percentage may account for a lot of differences between each one of us, including the way we tolerate carbohydrates. But experiments which severely restrict carbs point to a consistent shift in our metabolism with little variability. That is, we are hardwired to respond to carbohydrate restriction in a reliable and healthy way. From a genetic point of view, our ability to thrive under a low carb diet is highly conserved as opposed to our ability to tolerate a high carb diet intake. Low carb eating seems to be the normal metabolic state associated with health, which is consistent with the view that throughout most of our human evolution, we thrived under a low carb diet.
There is no such thing as an essential carbohydrate. According to Dr. Eades, author of The Protein Power, “the actual amount of carbohydrates required by humans for health is zero.” Our bodies are perfectly capable of making sugar to sustain our bodies without no carbs from our diet.
This non-essentiality of carbs to our bodies is related to our ancestral past and the medium in which our brains and bodies thrived where carbs were really a dispensable food.
It is recognized that the change in diet since the Agricultural Revolution, Industrial Revolution and the Modern Age has systemically destroyed our health and that the mismatch between our ancient physiology and current diet is at the root of many so-called diseases of civilization: coronary heart disease, obesity, hypertension, type-2 diabetes, cancer, autoimmune disease, osteoporosis, etc. which are virtually absent in hunter-gatherers and non-westernized populations. Most of the human genome has ancestral genes that adapted for over millions of years to a caveman diet.
Basic human physiology goes back hundreds of thousands of years, if not a million or two. Our physiology did not changed with the consumption of vast amounts of sugar in the span of a few thousand years.
We are here today because our ancestors survived prolonged periods of fasting while they hunted for foods and they were able to thrive on animal foods under very interesting conditions.
As Nora Gedgaudas puts it in Primal Body Primal Mind (a highly recommended reading!), we are children of the Ice Age, that is, our ancestors survived major cooling and glacial ice sheets which began and ended roughly every 11,500 years. This had a major impact on our human physiology; it is what made us human. We have spent a significant amount of time on an Ice Age. Only those who adapted under such frigid and difficult conditions survived. It is certainly food for thought as we approach the next ice age.
Animal fat was our primal energy, as it was – and still is – the most efficient, dense and long-burning fuel. It is agreed by experts that our extended dependence on meat and animal fats (i.e. fish fat) throughout these continual freezing periods of time actually encouraged our brains to enlarge and develop so that we became human. We became smart because we ate animal fat and meat. Thus, it is not surprising to note that evidence is growing that vegetarians and members of agrarian societies have smaller brains.
The case for our evolutionary history is a strong one and it is made by evolutionary biologists which have been researching and writing about this for a long time with no agenda to support the food industry as the medical profession researchers have.
Essentially, we are much more alike physiologically than not and even though we all have our own genetic susceptibility and biochemical individuality, we all still have the same fundamental anatomic and physiological landmarks and laws. Genetically speaking, we are essentially the same with respect to genetic expression to those humans living over 40 thousand years ago. Our physiology is the one of those people who lived during the Paleolithic Era, which refers to the human evolutionary time spanning from around 2.6 million to 10 thousand years ago right before the Agricultural Revolution. We are not alien bodies from a different planet meant to be eating processed foods for astronauts; we are simply the direct descendants of our paleo ancestors eating something aberrant until very recently.
We are highly optimized and geared by nature to be hunter gatherers from a biological, genetic, physiological point of view. As for human evolution, we have been mostly skilled hunters eating high-quality animal foods that were hormone, antibiotic and pesticide free with no genetic alteration. It was very high in fat which was hold very dearly and low in carb. The little carb ingested, if any, was eaten as seasonally available.
For most of us, from an evolutionary perspective, a high sugar diet is a metabolic challenge that some find difficult as early as they are born and many fail to meet as early as adolescence. It is evident that these negative consequences can be dealt with avoidance of carbs, intermittent fasting, resistance training and stress reduction through meditation and play. Arguably how our ancestors lived.
I think nutrition plays an essential role and I’m learning again and again how those in an evolutionary diet which is best suited for our biology, fare much better. We evolved with sea food rich in selenium among others and it seems that a ketogenic diet or paleolithic diet along with liposomal vitamin C is the best to counteract dangerous viruses. A ketogenic state promotes autophagy which is essential for the innate immune system to destroy problematical intracellular microbes.
As it happens, a paper just came into my attention just recently. I think it is very relevant in the sense that the fragments of hemorrhagic viruses that were speculated to be the cause of the Black Death (for more information see New Light on the Black Death: The Viral and Cosmic Connection), are listed as part of our genome, indicating that life on Earth has been exposed to rather dangerous viruses through our evolutionary history which then effected changes in our DNA:
Vladimir A. Belyi, Arnold J. Levine, and Anna Marie Skalka. PLoS Pathog. 2010 July; 6(7): e1001030.
Vertebrate genomes contain numerous copies of retroviral sequences, acquired over the course of evolution. Until recently they were thought to be the only type of RNA viruses to be so represented, because integration of a DNA copy of their genome is required for their replication. In this study, an extensive sequence comparison was conducted in which 5,666 viral genes from all known non-retroviral families with single-stranded RNA genomes were matched against the germline genomes of 48 vertebrate species, to determine if such viruses could also contribute to the vertebrate genetic heritage. In 19 of the tested vertebrate species, we discovered as many as 80 high-confidence examples of genomic DNA sequences that appear to be derived, as long ago as 40 million years, from ancestral members of 4 currently circulating virus families with single strand RNA genomes. Surprisingly, almost all of the sequences are related to only two families in the Order Mononegavirales: the Bornaviruses and the Filoviruses, which cause lethal neurological disease and hemorrhagic fevers, respectively. Based on signature landmarks some, and perhaps all, of the endogenous virus-like DNA sequences appear to be LINE element-facilitated integrations derived from viral mRNAs. The integrations represent genes that encode viral nucleocapsid, RNA-dependent-RNA-polymerase, matrix and, possibly, glycoproteins. Integrations are generally limited to one or very few copies of a related viral gene per species, suggesting that once the initial germline integration was obtained (or selected), later integrations failed or provided little advantage to the host. The conservation of relatively long open reading frames for several of the endogenous sequences, the virus-like protein regions represented, and a potential correlation between their presence and a species’ resistance to the diseases caused by these pathogens, are consistent with the notion that their products provide some important biological advantage to the species.[full text available here]
This second paper was linked in the first one and is even more interesting. It expands and backs up Bryant M. Shiller’s explanations on Origin of Life: The 5th Option. Keeping in mind that “transposable elements” (TE) – which was once considered “junk” DNA – is viral in its origin, it would explain why humanity benefits from periodic plague diseases to give a kick-start or “reformation” to our genetic makeup and accelerate evolution or change through cometary impacts:
Keith R Oliver and Wayne K Greene. Ecol Evol. 2012 November; 2(11): 2912–2933.
In addition to the strong divergent evolution and significant and episodic evolutionary transitions and speciation we previously attributed to TE-Thrust, we have expanded the hypothesis to more fully account for the contribution of viruses to TE-Thrust and evolution. The concept of symbiosis and holobiontic genomes is acknowledged, with particular emphasis placed on the creativity potential of the union of retroviral genomes with vertebrate genomes. Further expansions of the TE-Thrust hypothesis are proposed regarding a fuller account of horizontal transfer of TEs, the life cycle of TEs, and also, in the case of a mammalian innovation, the contributions of retroviruses to the functions of the placenta. The possibility of drift by TE families within isolated demes or disjunct populations, is acknowledged, and in addition, we suggest the possibility of horizontal transposon transfer into such subpopulations. “Adaptive potential” and “evolutionary potential” are proposed as the extremes of a continuum of “intra-genomic potential” due to TE-Thrust. Specific data is given, indicating “adaptive potential” being realized with regard to insecticide resistance, and other insect adaptations. In this regard, there is agreement between TE-Thrust and the concept of adaptation by a change in allele frequencies. Evidence on the realization of “evolutionary potential” is also presented, which is compatible with the known differential survivals, and radiations of lineages. Collectively, these data further suggest the possibility, or likelihood, of punctuated episodes of speciation events and evolutionary transitions, coinciding with, and heavily underpinned by, intermittent bursts of TE activity.[full article available here].
We are living in interesting times indeed!
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