The Problem with Genomics

The Problem with Genomics

Interesting title from the man who co-created a clinical genetic interpretation web-app, PureGenomics, but there is a problem. It’s the same problem that our world suffers from in so many ways. Things are viewed as all good or all bad and no middle ground is being found. Whether this is politics, religion, science or the science that is medicine, everyone is trying to discredit everyone else. Where does the truth lie?

Somewhere in between.

So what is this middle ground when it comes to genetics and MTHFR? I think it comes down to viewing genetics as a tool that helps the clinician apply leverage. This leverage is understanding how these polymorphisms, (genetic variations which change the protein structure of enzymes, hormones, and their receptors) affect function, and how this possible change in function may affect clinical outcomes. It’s understanding that this change in function is hundreds of years in the making and is not a mutation, but a change, that in some cases, is beneficial, depending on the environment the organism finds itself in. Let’s use an illustration of the most famous reindeer of all, I mean the most famous genetic polymorphism of all, MTHFR, (got to love that name).

MTHFR is the most misunderstood SNP (Single Nucleotide Polymorphism), just like Rudolf. This is an enzyme, like a lot of other enzymes, that has more than one function. It has many changes in its code, and I think there are around 25 of these polymorphisms (one base pair is exchanged with another), and like so many other genes with mutations, most of these do not affect the function of said enzyme. Two polymorphisms do affect function, but in the literature, there is lots of confusion as many researchers do not seem to understand that enzymes have more than one function, and one SNP may affect an enzyme in one function it carries out but not in another function. For example, C677T seems to affect MTHFR as it goes about creating SAMe for methylation donation for neurotransmitter generation, DNA methylation, and detox.

The other mutation, MTHFR A1289C, does not affect homocysteine but appears to be affect the enzyme more in the pathway of dopamine and serotonin generation. It seems to escape so many peoples grasp that an enzyme is like a Swiss knife, and just because the corkscrew is broken, doesn’t mean the knife cannot open a box. As an example, we cannot say the A1298C mutation is not important because it does not affect homocysteine and the diseases that arises from poor methylation, because it affects another function of MTHFR enzyme.

This is where clinicians and researchers run into problems. We fail to comprehend the context of the polymorphism. This creates frustration when we are using the wrong tool for the job, and making claims that addressing a particular mutation does something, when in actuality it does not. This creates loss of validity in a field that is highly valid and transformational to a clinical practice.

Another problem with SNP’s, and if you ever had teenagers you will understand this, their impact/behavior often is dependent on the crowd they hang out with. Not understanding this complexity, and seeing nutrigenomics as a linear equation, takes away the validity of the field and the clinicians’ claims of what intervention of a mutation will accomplish.

One case is the MTHFR gene which in the presence of adequate riboflavin has almost completely normal function even with the polymorphism at the 677 location.  Often, polymorphisms/SNP’s have fail safe(s), if you will, or supporting genes, and vitamins, that help correct the decreased function of said gene, so that the organism can live, not thrive necessarily, but ultimately reproduce, which per Brian Hawkins brilliant book, “The Selfish Gene,” is what genetics is all about. If we just talk about the MTHFR gene as being the only instrument that matters, and do not see it as one instrument in an orchestra, then we are giving it too much credit. Likewise, if I were to be the violinist in said orchestra, one would also understand that an “aberration” can definitely have an effect on the overall sound, yikes! Now if said orchestra was playing for the hearing impaired, I’d be awesome! In some ways, that is what a gene like MTHFR does when looked at from a historical context.

MTHFR C677T polymorphism was a genetic advantage. That’s right, or it would not be so prevalent (At least 60-70% of us have at least one copy, of the two copies, for this mutation). Why would evolution allow such a thing? Advantage, and a big one if you live in an endemic malaria region. It helped our ancestors survive malaria. Where was this gene most common?  In the Mediterranean region. What is the local diet there composed of? Lots of folate rich foods, which compensated for this less effective methylating enzyme of folate. Sweet huh? The standard American diet does not have a lot of natural folate (lots of synthetic folic acid–another paper for a later date.). This is an issue that leads to problems with a genetic advantage being turned into a disadvantage as an organism’s environment changes from its original environment to the adaption. So, what does this mean for us as we navigate this gene which has generated so much controversy?

We have to understand that we do not have it all figured out. We do know that the data is conflicting in some cases because nuances are not understood by even the researchers doing the research. A lot of researchers believe folic acid is equivalent to methyl-tetrahydrofolate which is in a paper like this, https://www.ncbi.nlm.nih.gov/pubmed/21069462?dopt=Abstract, one has to question the validity of the findings. The actual polymorphism which led to the homocysteine is not directly addressed, but rather the biomarker, homocysteine. It also looked at this polymorphism in relation to people already with cardiovascular disease and did not look at outcomes if we address this gene in prevention (when MTHFR C677T is addressed in blood pressure we see very positive outcomes and decreased risk of stroke). Then we find studies like this, https://www.ncbi.nlm.nih.gov/pubmed/27973419, which seem to support the conclusion addressing methylation is quite beneficial.

What is there to make of this confusion? Should we just throw up our hands and say let’s not look at it or try to make decisions because it’s not clear? I don’t think so. Let’s agree that literature is not completely clear on the benefit of using 5-MTHF in all diseases, but it’s clearly helpful in many diseases. We also know it is much more effective in cellular uptake and this fact is very beneficial in many preventative strategies compared to its synthetic precursor, folic acid. Is it going to be the panacea that so many people have made it out to be? No, because we are giving it to much credit, and when it is not the magic hammer people claim it to be, it allows the faulty logic by the uninitiated, that since it cannot do all things, then all the polymorphisms that can be used in clinical practice are ineffective as well. This could not be further from the truth.

We have a saying where I come from, “Don’t throw the baby out with the bath water” and this is really saying, don’t get rid of the good waiting on the perfect. We as clinicians, who so desperately want to heal, get in trouble when we create the magic hammer where everything becomes a nail. We lose credibility because we a looking for something that works on everything.

Nutrigenetics is a tool. It is incredibly effective as such, and the research supports this. Clinically, ask any psychiatrist if dosing with higher doses of Methyl-folate has not turned around a large number of refractory depressed patients. You would be hard pressed to find one not using this as a clinical tool. Is it where they start? No, nor should it be. The same goes with the functional medicine practitioner. We need to focus on what we know to be the foundations of functional medicine first. Heal the gut, address sleep, decrease stress and eliminate toxins. Then, and only then, should we be then looking at nutrigenetics to help us apply leverage in assisting the above-mentioned areas of focus. It works brilliantly when we understand its benefits, but also embrace its limitations.

Dr. Nathan Morris, MD

Surviving or Thriving the Holidays?

Surviving or Thriving the Holidays?

“Surviving Holidays and Social Outings” is always a large concern for patients working to place symptoms of Autism and chronic conditions into remission. But is that all we want to do? Merely survive? With a little planning and some modified expectations, the holidays, and social outings can be enjoyable for every member of the family, including those with the diagnosis.

It’s important to discuss what is important to each family member, and make a plan. A plan will help replace traditional ingredients that later will cause symptoms to flare. A plan will help extended family members understand how much this mean to you, which will reduce their feelings of being hurt or offended.

The internet is flooded with recipes that provide satisfying substitutions for most traditional foods. Google Search words such as: Paleo Auto Immune Thanksgiving, Paleo Thanksgiving, SCD Thanksgiving, provide ample ideas. Starting the planning process now will not only provide food you can eat, but also reduce “holiday stress.”

Here are some suggestions to have the best Holiday Season yet:

Prepare in advance.
Talk with your extended family or friends and identify what is being served for the holiday. Feel confident to ask permission to bring your own version or something different to share with family and friends. When you are kind and Matter of Fact about living this lifestyle, more people will be intrigued than insulted. Chances are they or someone they know are struggling with digestion issues and poor health.

Desserts
Sugar is a large villain, which compromises your efforts. Bring some dark chocolate to satiate your sweet tooth and help you feel satisfied in order to by-pass the dessert table. Another great way to reduce the carbohydrates is with crust-less pies or with pumpkin mouse. There are many dairy free versions of mousse, which use ingredients such as: avocado, cacao powder, maple syrup or honey, and coconut milk.

Helpful Supplements
In the event you do eat food which creates a flare, talk with Dr. Morris ahead of time about which supplements are best for you to help break down and digest the high allergen proteins more quickly such as Gluten/Dairy Digest Enzyme, L-Glutamine, or Inositol powder.

Magnesium
Talk with Dr. Morris about taking extra magnesium to make up for any that alcohol indulgence will deplete further from your body.

Abundance vs. Scarcity
A large piece to healing is to train the mind to look for abundance rather than scarcity. To look at what we can do rather than staring all the seemingly insurmountable obstacles. To look at what our condition is teaching us rather than what it is taking away. To look at all the foods we can eat rather than perseverating on the foods which will cause us to react/regress. Read more about Mindful Eating, and our Mind Concept Piece to include in your Care Plan.

Cook ahead of time
Try the recipes, found on the internet or in a cookbook, ahead of time. Print out the recipes and take notes. Make your own binder of recipes to use for future holidays. A little bit of planning goes a long way to feeling pleased with your food options. Againstallgrain.com has a fantastic library of recipes.

Flour Alternatives
With so many patients becoming sensitive to Coconut and Almond there is the option of Cassava Flour. Cassava is gluten, grain and nut-free, as well as vegan, vegetarian and Paleo. Since cassava is a high in starch it could mean an insulin spike for you! This means use in moderation particularly if you’re following a low carbohydrate, low-sugar or Paleo-based diet. To reduce the amount of grains, a perfect place to skip the carbohydrates is the stuffing. Try a ground pork, mushrooms, green peppers, apples or pears or another version that does not require GF bread.

Translation: don’t eat cassava flour recipes at every meal! As always, moderation is key.

A Well-Stocked Baking Cabinet
Having a well-stocked baking cabinet helps to organize the ingredients, in one cabinet, to minimize the amount of time to bake your deserts/rolls for the holidays.

Fat
Use Ghee or Duck Fat or Avocado Oil to rub on the bird rather than butter. Melt Coconut Oil and Ghee together. Place in glass container and use on your GF rolls rather than butter. Use Ghee or Duck Fat for your gravy.

Kids
If your kids are the ones recovering from a chronic condition/developmental delay, it’s best if all family members adhere to the nutritional recommendations of his/her care plan. Parents are the role models and lead the family toward healing through their actions more than by their words. If you need to eat high allergen foods, then do so once the kids are in bed and there is no way for them to see you ‘sneaking’.

Restaurants/Catering
Eating out this holiday season? Feel confident to phone ahead and review the menu with the staff. Restaurants are becoming more accommodating to whole food nutrition and substituting out high allergen ingredients such as gluten and dairy. Taking a few minutes to explore what you can eat off the menu will eliminate the awkward feeling of asking a million questions at the celebration.

Ultimately, the holidays are for celebrating our relationships with the loved ones in our lives. Being together, communicating and sharing our experiences in life, even the burdens such as having to watch what we eat, allows those people we don’t see often to know us better.

We should never have to be ashamed that we are doing the best we can to take care of ourselves. Being matter of fact and kind enough to offer to bring safe food allows us to partake in the fun without the worries of exposure and subsequent reactions.

Wishing you a Happy Holiday Season from the Staff at Good Medicine!!

Kara Ware is Good Medicine’s Clinical Coordinator and Functional Medicine Health Coach. She also provides online courses and coaching for families living with Autism.

Sleeping on ADD and ADHD

Sleeping on ADD and ADHD

The diagnosis’ of Attention Deficit Disorder (ADD) and Attention Deficit Hyperactivity Disorder (ADHD) is skyrocketing among primary care physicians.
Although I am not the first one to get on my soapbox and holler about dietary modifications, supplementing for deficiencies, and lifestyle changes, I have discovered, through more research and even self experimentation, yet another common thread among these wonderful, complex children: Sleep disorders.
According to the data, 25-50% of Attention Deficit Disorder is sleep related. When I ask a parent, “How does he/she sleep?” I will usually get an immediate response because they have been dealing with these issues for years.

  • The child sleeps 12 hours per night, yet they are fatigued all day.
  • The child wakes up constantly.
  • The child has problems falling asleep.
  • The child wets the bed.
  • The child does not dream regularly, and if he does, he has night terrors.

These are the typical things I hear in the office, and as I’ve learned, they are many times a result of sleep and airway problems. These kids cannot get enough oxygen because many of them have mouths/airways that are not allowing them to breathe properly, therefore, both the quantity and the quality of their sleep suffers.
It is easy to see things like dark circles and drowsiness in these kids, but there are multiple things that can produce those symptoms, so I’ve had some training recently from dentists and orthodontists who are concentrating on airway problems and sleep apnea to identify some physical factors that will allow for proper diagnosis.

These physical characteristics include:

  • The child has poor posture with rounded shoulders.
  • When looking at the child in profile, their head will jut forward so that the ears are in front of the shoulder instead of being lined up on top of of the shoulder.
  • The child may have crowded teeth, indicating narrowed facial structure, which does not allow the tongue to fit correctly in the mouth.

Problems with concentration, inability to settle down and relax, feeling the need for stressful physical activities in order to keep a higher heart rate, and snoring are all considered for objective diagnosis.

Sleep studies are helpful and seeing a dental sleep specialist is a good place to start.

I can say that almost all of the kids I see, whether they are on the autistic spectrum, have depression, or diagnoses such as oppositional defiant disorder, have a sleep issue plaguing them as well.

From what I’ve seen in my office, and judging from all of the research I’ve done, ADD and ADHD have never been caused by a Ritalin deficiency. If you are concerned on any level about your child’s sleep and/or sleep patterns, consider having them evaluated properly. You too can rest easier with more knowledge on your side. With that in mind I have included a link to look at another major cause of attention issues. Best 5 minute presentation I have seen on this subject
Another Hidden Cause of Attention issues