I am posting this Journal as a reference writing for those to whom I am recommending basic gene analysis to determine if one carries important gene mutations which are actionable by simple nutrigenomic treatments and lifestyle alterations. I have referenced such genomics testing in a number of past Journal writings.
This is a good time to devote a single Journal to some generalized comments about genes and genomic testing, and how you can easily go about the testing yourself. This Journal will explain some important information about what you were born with that makes you…you. And so, this is a sort of birthday Journal.
For the past several years I have been offering interpretations of complex genetic information to assist clients with their general health maintenance, anti-aging, and disease prevention, as well as helping clients who are consulting about their known disease states and pharmaceutical regimens.
A brief description of the genetic process may be helpful without going too deeply into the more complicated cellular events of how genes code for proteins via all of the intricate and miraculous mechanics of molecular biology.
After this brief description, I will write about how you can begin your own genetic testing with a simple saliva kit which can be sent to your home from 23andMe.
Some Genetics Basics
Our entire set of 23 human chromosomes is called a genome.
The human genome is composed of 3 billion base pair sequences formed by the nucleotide base molecules adenine, guanine, cytosine, and thymine. These 4 nucleotide bases pair up with one another in a particular manner to form connecting bridges between 2 strands of a coiling double helix of molecular blueprint information which we call DNA (deoxyribonucleic acid).
All of our DNA strands are arranged as 23 pairs of chromosomes which are super-coiled and packed inside of the cell nucleus. If these strands were to be uncoiled and stretched out they would measure almost 7 feet in length. This micro biology comprises an enormous amount of information, and inside of this long chain of information there is ample opportunity for coding errors to occur.
The research to elucidate and define the human genome was accomplished via the Human Genome Project, which was initiated in 1990, and was announced as “complete” in April, 2003. This international research project mapped out about 90% of the entire genome. Certain types of genetic information, such as telomere information, were not addressed in this study.
A mutation event is a variation from normal at a single base pair site, as compared to other members of the same species. If this mutation is present in more than 1% of the population it is called a single nucleotide polymorphism, or, a SNP.
Over 10 million SNPs have been identified in the human genome. SNPs account for our differences, how we develop diseases, how we deal with pharmaceutical drugs, and a lot about how we deal with everything in life.
SNPs have evolved over thousands of years, and at this point in our learning curve, it is estimated that we all have about 1000 important SNPs in our genetic coding for the enzymes and other specialized proteins which control vital chemical processes. Thus, we are all mutants from the normal wild type at various points in our chromosomal make-up.
An abnormal substitution of one nucleotide for another, or a deletion of a nucleotide in the normal ordering of the 4 base pairs, results in SNPs. If you want, you can substitute the words “one letter change” as a simple way to conceptualize the words “single nucleotide polymorphism.”
Most SNPs have little or no negative effects in our lives. SNPs are more likely to occur in larger enzymes, such as the MTHFR enzyme, which has a make-up of some 500 sequenced amino acids, and has a molecular weight of 77,000 (77 Daltons). In this enzyme a SNP in the genes which code for its function will alter just one amino acid in the enzyme’s structure, and that is enough to reduce its functionality.
As you can see from this Journal writing on methylation chemistry, a mutated MTHFR enzyme at just 2 different gene sites (the A1298C and the C677T sites) can contribute to a lot of significant biochemical and common disease processes.
A nice, simple, and short video explanation of these genetic molecular biology basics can be seen here.
Genes function to pass on inherited information from our parents to code for protein production inside of the cell. All genes do is code for proteins…the most common proteins made in the cell from the gene coding are enzyme proteins which carry out all of the functional biochemistry of our lives. Genes also code for receptor proteins, as well as all of the other specialized protein units in our bodies.
There are many different enzymes in our biochemistry which create life as we know it. Each of our enzymes requires biochemical cofactors, or coenzymes, for their efficient function. These life enhancing enzyme co-factors are vitamins, minerals, and a host of other natural internal biochemical molecules. This critical co-factor chemistry is part of the epigenetic process which will be covered in my concluding remarks.
If a gene is mutated, then the enzyme which is made from that mutation will not function correctly, or adequately. It is well known that the function of a down-regulated (insufficient) or an up-regulated (too active) enzyme can be modulated and improved in its function by supplying the enzyme with its specific cofactor nutritional components. This established biochemical fact is the basis for the new treatment paradigm known as nutrigenomics. Using food (vs. nutritional supplements) to address mutation concerns is now called culinary nutrigenomics.
Pharmacogenomics is a similar study which allows one to know if their unique chemistry can metabolize individual pharmaceuticals correctly. Because the pharmaceutical industry has been trying to take over natural human health since the early 1900’s, and because pharmaceuticals are suspected to cause over 100,000 deaths a year (Journal of the American Medical Association, 4-14-98), the advancement of pharmacogenomics is an important evolutionary consideration in the overall science of what is now known as personalized medicine. Furthermore, I suspect that 100,000 deaths per year due to pharmaceuticals is a very conservative estimate.
Personalized medicine considers both nutrigenomics and pharmacogenomics. Here is a more advanced and detailed description of personalized medicine.
I’ll now present what I consider to be the simplest and most utilitarian cost-effective way to obtain a large amount of very reliable personalized genetic information.
How to do a Simple Gene Testing
Step #1…Your first step is to order a saliva test kit from www.23andMe.com. This is a simple at-home saliva sample collection for the subsequent analysis, and it costs $199. This test assays 195 gene sites in the important biochemical categories of detoxification, neurotransmitters, methylation, cardiovascular chemistry, endocrine chemistry, digestion, vitamins, minerals, and antioxidants.
These biochemical categories and the particular enzymes and molecular receptors studied provide an enormous array of vital information about the biochemical tendencies of each individual. These categories of biochemical function cover a lot of very important data which can also be assimilated with other types of functional medicine testing to help your individual life style decision process.
The array of information is of great value, and so I am recommending to most clients that they order the simple test kit from the 23andMe website, and proceed with obtaining this information about some of the significant mutations in their foundational genetic blueprint.
Of the 195 gene sites which are assayed most clients have 50 to 70 mutations. The number and type of mutations tends to add up in the aggregate, and the information gained offers a very good composite snap shot of a client’s biochemical tendencies.
The mutations are reported as homozygous mutations (an abnormal copy of the gene was inherited from both parents) or as heterozygous mutations (an abnormal copy of the gene was inherited from one parent). Homozygous mutations are less common, but they result in a more deranged enzyme or receptor function.
In the kit is a plastic test tube with a unique bar code on the tube. Your saliva goes into this tube, and then you register the test tube bar code on the 23andMe website. This insures that the tube is not mishandled in the lab.
The kit provided is then returned to the lab by your normal postal carrier. The small test box kit is already post marked. It then takes about 6 to 8 weeks for the lab to work up your results.
These results which you receive back from 23andMe will be your raw genomic data represented as a collection of seemingly indecipherable coded numbers which are known as rsID#’s. There will be 4 to 10 digits in the coded number which stand for a gene mutation event at particular gene sites.
This rsID# nomenclature stands for “reference SNP ID number.”
Step #2…There are various web based apps which will interpret the 23andMe raw genomic collection of rsID#’s into a meaningful and useful document which can then be used to tailor and streamline nutritional co-factor recommendations for the more important mutations in enzyme and receptor molecule functions.
The website app which I prefer for the 23andMe raw genomic data interpretation is at www.NutraHacker.com.
Upon entering this site you will click on the button on the top of the home page which says “Connect with 23andMe.” On the next page you enter your 23andMe user name and password to get to the next page where you have to give NutraHacker and 23andMe permission to communicate about your raw genomic data.
You then have to pay NutraHacker $40 for the Complete Gene Mutation Report which is rendered for you in a few minutes minutes as a 10 to 12 page document of information about your rsID#, the protein coded for by that gene, the function of that gene, and the consequences of abnormal function. Recommendations are then given for the appropriate nutritional co-factors which assist in normalizing the gene function. This information is relatively complicated and requires consideration by someone who has understanding of biochemistry and pathophysiology.
Knowing which of the nutritional recommendations is appropriate for your life circumstances and mutation composite is how I am able to assist you.
NutraHacker will also give you free reports about your Detoxification and Methylation mutations and your Celiac disease carrier status, but these are contained in the more complete full report, and so I suggest buying the full report so that you can receive all of the other associated biochemical and biological systems mutation information.
The interactive nutritional tool which they provide is confusing for most clients who are not highly knowledgeable about nutritional biochemistry. I don’t recommend that clients try to figure out this free report by themselves, as there is often a presentation of seemingly conflicting information.
One other very helpful free report which can be obtained from NutraHacker is called the Drug Carrier Response report. It details one’s genetic tendencies to various uncommon diseases, and it also details some pharmacogenomic data about which classes of pharmaceuticals that one should not be exposed to. This information is quite valuable.
Considerations for the Conscious Health Care Consumer
I offer the service of genomics interpretation which is proving valuable for all who do it. At this point in my practice, after conducting dozens of these interpretations, the clients have come away empowered and revitalized by the information.
No one has contracted into any kind of fear or dread response, or proceeded to shrink away from embracing the information. The information is enlivening and helps clients with a broadening and deepening of their self accountability life practices.
Gene analysis interpretations and epigenetic lifestyle recommendations should be embraced and practiced in a whole life process which includes epigenetic considerations and evolution in body, mind, emotion, and spirit. Gene analysis should not be thought of as a quick-fix type of remedy for one’s problems. The practice of good lifestyle epigenetics unfolds over a lifetime when one becomes aware of how to engage in this process.
Such a lifestyle approach should reduce one’s need for encounters with the conventional medical industry which I consider to be rather hazardous.
There are a number of good quick-fixes which the conventional medical system offers as a life or limb saving interventions and in its arsenal of emergency or urgent crisis interventions. After practicing in this realm of medicine and surgery for over 20 years, and while still interfacing with it as a present-day patient advocate, I am very familiar with medicine and surgery’s strengths and good aspects, and also with its burgeoning and awkward problems.
I left this way of treating patients because of inherent inadequacies in treating most chronic illnesses, and because of the many different types of life threatening complication considerations which always seem to arise at some point in this type of treatment paradigm.
Natural biochemistry and its healing power is usually dismissed by conventional medical industry practitioners. Pharmaceuticals are used in an attempt to outsmart our divinely ordered healing intelligence. This can become a grave mistake for many. Such a dismissiveness of our natural healing abilities represents a massive shortcoming of the type of broad holistic care which we really need to be considering in our evolving culture.
Treat the Whole Patient
I commonly encounter patients whose cases have been managed by physicians who seem intent and content to vigorously treat the patient’s laboratory abnormalities with pharmaceutical regimens, while seemingly ignoring the actual individual who is in their office. Injurious polypharmacy regimens tend to pile up in the patient’s life. This pattern is all too common, and I deal with it’s aftermath more often than not.
From this statistical chart you can surmise that an average American, aged 19 to 64, may be taking up to a dozen, or more, prescription drugs. This is in line with what I often encounter in many patients. As you can see from the chart, no age group is spared from the perils of such polypharmacy. This type of medical practice is simply a mild form of madness, or worse. It is an indictment and condemnation of a medical industry which does not know how to help people heal their lives.
The profit driven pharmaceutical industry has absolutely no intention to assist humanity and health evolution. Drug companies revolve around monetary profit, and the propaganda which is needed to create their profit, and make their massive shareholder base happy.
Physicians who practice polypharmacy are usually compressed by various forces within their own practice model. They may be overly focused on avoiding malpractice, peer, or medical review board scrutiny. Likewise, it seems as if the average doctor is working hard to tend to the electronic medical record (EMR) and lab values rather than dealing directly with the human being who has sought their care.
I have been told by many patients that their time-compressed physician appears to be too busy typing information into their computer to have any significant eye contact or deeper human exchange. Furthermore, I have never read an EMR which was without inaccuracies.
The whole-patient treatment philosophy is commonly dismissed and ignored by many physicians.
Likewise, when considering genetic mutations, it is important to treat the whole patient and not the SNP.
My approach to genetic interpretations and recommendations is to consider several aspects of the patient’s life:
- the past medical history
- the current health, life, and medical process
- the vision which the client wishes to manifest in a future time
- the quaternary of body-mind-emotion-spirit of this individual person
I would like to help you by working with you to help you understand important mutations in your gene carrier status, and how you can mitigate any possible negative effects of such.The information you will come away with is biochemical in nature, and it is highly tailored and streamlined to your individual biochemistry.
Except at the level of medical school academia where genetic research is very active, the conventional medical industry at the community level is not very open to embracing this very foundational and strongly established science at this time. This disparity will change as more types of genomics testings become widely accepted and are demanded by conscious health care consumers, and as community physicians become more open-minded about aligning their practice philosophy with natural molecular biology instead of rote pharmaceutical prescriptives.
DNA’s Early History, the Epigenome, and the Exposome
In 1968 I read James Watson’s autobiographical account of the discovery and elucidation of the structure of the DNA double helix in his bestselling book The Double Helix: A Personal Account of the Discovery of the Structure of DNA. I recall the book reading like an adventurous treasure hunt.
Watson and his co-discoverer colleague Francis Crick made the discovery of the structure of DNA in 1953 based on a series of findings, most notably the X-ray diffraction discoveries of Rosalind Franklin and her colleagues at King’s College, whose major contribution to the work was down-played by Watson in his original account. He attempted to make up for what seems to be his purposeful oversight in later editions of this book.
Linus Pauling was also a major contributor in the discovery process, as were many other researchers since the time when DNA was first discovered in 1869. Controversy about Watson’s scientific research ethics still remain, and is considered by many to be an example of sexism and self referential bias in scientific research.
Watson, Crick, and Maurice Wilkins were awarded the 1962 Nobel Prize in Physiology or Medicine “for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material.”
Rosalind Franklin’s contributions to the discovery process were of tremendous significance. She died at age 37, in 1958, and was not allowed to be considered as a co-recipient of the prestigious award because the Nobel Committee did not allow for posthumous awards at that time. Among her noteworthy contributions was the intriguing Photograph 51, an X-ray diffraction picture which provided important clues about the structuring of the DNA double helix. This image was produced by Franklin and her research colleague Raymond Gosling, in 1953. You can read more about her life and Photo 51.
James Watson went on to write a major textbook on genetics and molecular biology entitled Molecular Biology of the Gene which was first published in 1965, and is now in its 7th edition. This was the text I used in molecular biology courses in my college years. It is still the gold standard text used in most educational institutions for the instruction courses about the complexities of molecular biology. It is an excellent text.
Watson is still alive at age 87, and he stills holds forth with some lectures and teaching. Watson’s latest scientific contributions have been centered on the role of antioxidants in human health. He has also evolved his thinking on the cellular biology of the cancer process, a subject I hope to address in a future Journal.
This brings me to the subject of the epigenome.
In the early days of the development of molecular biology it was a common assumption that genes were somehow autonomous, and expressed for proteins by way of some unknown code which was hidden within their own matrix. We now know that this is not the case at all. Genes are not autonomous. All genes require molecular biochemical or electromagnetic signaling from outside of the nucleus in order to trigger or suppress their expression.
The term which has been ascribed to the mechanisms of DNA signaling is called epigenetics. The etymology of the Greek prefix “epi” relates to all biochemical and electromagnetic events which occur above or around the gene and influence its function.
Although the term has been with us since 1942, epigenetics is the relatively new science of all of the factors which influence genetic expression at the level of the molecular biology of the cell. Epigenetic considerations encompass all influences which affect the transcriptional potential of our DNA to express itself without changing the native nucleotide sequencing of the DNA itself.
Epigenetic biology alters other dynamics of DNA through processes which includes DNA methylation and acetylation, histone coiling and uncoiling, transcription of DNA into RNA, translation of messenger RNA subunits into protein in the cellular ribosome, replication of DNA for cell division, repair of DNA mutations, and a variety of other DNA activities.
As it is the study of external or environmental factors which affect how cells read genes and how genes are turned on and off, epigenetics refers to the host of very important external forces such as environmental exposures, nutritional exposures, drug exposures, oxidative load, inflammatory chemistry, sleep health, stress, electromagnetic exposures, and emotional processes.
Many people mistakenly assume that the presence of a certain SNP means they are destined to experience an associated disease. However, most genes have flexible expressions as well as complex interactions among multiple genes. The external forces and the environment, as referenced in the preceding paragraph also affect gene expression.
The plot deepens when we consider the new science of the exposome, which was postulated in 2005. Exposomal influences predate our birth and go back into our intrauterine existence and back even further into our ancestral bloodline. Major scientific research on the exposome is now being conducted all over the globe.
You can type in the words “genetics” or “genes” or “SNPs” into the search engine in the upper right hand corner of this page and you will be directed to other Journal entries which reference some of this information.
The consideration that nutritional epigenetics is the most important practical and useful information presented in this Journal writing. Food is epigenetic information which directs cellular life and growth.
It is one thing to know about some part of your unique palette of possible mutations. It is another thing to enter into the learning of all of the epigenetic factors which influence your normal gene and mutated gene functions.
All life events have an epigenetic influence on how our genes express our biology.
This consideration includes negative epigenetics such as toxic xenobiotic chemistry, food industry toxicities, electromagnetic toxicities such as cell phones, the whole array and spectrum of other manifold unnatural electromagnetic forces, toxicities from water and our atmosphere, and toxicities in our home environment. These types of toxicities are the obvious culprits of the biochemical and electromagnetic varieties which are currently known about and are considered as negative epigenetics.
I also consider these types of biochemical epigenetic factors to be the literal tip of the iceberg in terms of the entire array of epigenetic forces.
Around the globe, many teams are now pursuing lines of epigenetic research. In just one example of such research, a team of researchers at UCLA recently showed that people with a deep sense of happiness and well-being had lower levels of inflammatory gene expression and stronger antiviral and antibody responses.
The Halean LifeStream model was created to address all of the possible epigenetic factors which make up and influence our lives at the body-mind-emotion-spirit interface. This quaternary of our being is a singularity in process and action. It is only reduced into its 4 component elements in this model for the sake of formulating a health and a life manifestation plan by way of considering the 4 life force dynamics as common-sense and separately manageable components. The quaternary reunifies around the physiology of Heart electromagnetics and the mysteries of Heart multidimensionality.
In summary, if one were to just do the 23andMe study and the NutraHacker interpretation, much good would be forthcoming in terms of just the information of the nutrigenomic epigenetics alone. This kind of epigenetic consideration would fall into the “body” aspect of the quaternary.
If one journeys deeper into the realm of Heart electromagnetics, subconscious belief processes, and one’s emotional process, then these more life enhancing epigenetic influences can be understood and practiced at a larger life fulfilling spiritual level.
There is no conceivable place, time, or dimension where the conscious Intelligence of all is absent. Thus, the Divinity that you are is also encoded into your genes, and it expresses Itself as your life and all that is in your life.
It is true that God comes to us disguised as our life.
Thank you for reading.
Signing off from Crestone and Beyond.
- The following article was sent to me by colleague Ron L. Martin, Founder and President, Nutrigenetics Unlimited, in Fullerton, California. Ron presents generalized considerations about this growing field of biology, and addresses some helpful insights about some of the disparities mentioned above. Please see “Gene-Environment Interactions: Emergence of Knowledge, and Its Successful Translation into Practical Applications” which was published on December 24, 2015.
- Medical Errors are No. 3 Cause of US Deaths, Researchers Say
- Pharmaceuticals Kill 100,000 Hospital Patients per Year
- OP/ED: How 23andMe Will Affect Your Medical Practice…an opinion registered by my genomics friends down in Santa Fe, on May 15, 2017. Physicians are not trained or experienced in this valuable new modality of care.
- How Soil Microbes and Intercellular Communication Affects Human Health...important new information on the interrelationship and affects of “junk DNA,” micro-RNA, and soil microbial influence on intercellular communication.
- Deep Nutrition: Why Your Genes Need Traditional Food, by Catherine Shanahan, M.D. …A biochemist and physician explains four nutritional strategies—fresh food, fermented and sprouted foods, meat cooked on the bone, and organ meats—that form the basis of “The Human Diet.” Food is epigenetic information that directs our cellular growth.