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Chemistry Protocols

The BUILD Phase

Feed the cell. Everything else is downstream.

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Why BUILD Comes First The Three BUILD Pillars Vitamin D Magnesium Vitamin B12 Omega-3 Fatty Acids Iron / Ferritin Diet Hydration Supplement Selection Dosing Principles When to Move to SUPPORT

Why BUILD Comes First

The Chemistry dimension has three phases: BUILD what the body needs, SUPPORT what is struggling, and CLEANSE what has accumulated. These phases are sequenced, not separate — and the sequence matters.

You cannot CLEANSE effectively if your body does not have the nutrients to run its detoxification systems. You cannot SUPPORT a struggling organ system if the foundational nutrients are missing. Every advanced protocol depends on a body that has the raw materials to do the work.

BUILD is the foundation. It is also where most patients see the most dramatic changes the fastest — because most chronic symptoms in modern life are downstream of foundational nutrient deficiency that has gone unrecognized for years.

This page is the practical guide to the BUILD phase: the foundational nutrients, the dietary framework, the hydration principles, and the supplement selection criteria that make the rest of the Chemistry work possible.

The Three BUILD Pillars

The Chemistry dimension's BUILD phase rests on three pillars:

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Foundational Nutrients

The five compounds almost everyone in modern life is short on

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Diet

What you actually eat day to day

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Hydration

Clean water in the right amounts

If you address only these three things — well — you will be in a different body within ninety days. Everything else in the Chemistry dimension builds from here.

Pillar 1 — Foundational Supplementation

Start With a Quality Multivitamin

Before targeting any single nutrient, the most foundational supplement decision most adults will make is a quality multivitamin. A well-formulated multi provides modest doses of the dozens of vitamins and minerals the body needs every day, catching what diet alone often misses. It is the broad foundation. The five targeted nutrients that follow get individual attention at therapeutic doses because they are the most commonly deficient — but the multivitamin is the foundation that covers everything else.

A note on whole-food forms. Wherever possible, look for a multivitamin built on a whole-food base — where the nutrients are derived from or paired with concentrated food extracts (organic fruits, vegetables, herbs, mushrooms, fermented foods) rather than synthesized in isolation. Whole-food-based multivitamins provide not just the named nutrients on the label but also the phytonutrients, polyphenols, enzymes, and trace compounds that naturally accompany them in food.

This matters for two reasons. First, the body absorbs and utilizes nutrients more efficiently when the co-factors that come with them in nature are present. Second — and more importantly — there are thousands of compounds in whole foods that science has not yet identified or named. With a synthetic isolated nutrient, you get only what was put in the bottle. With a whole-food-derived multivitamin, you get what we know about plus some of what we don't yet know about. The humility built into a whole-food approach is itself part of the medicine.

The real foundation, of course, is the whole-food diet itself (see Pillar 2 below). No multivitamin substitutes for actually eating real food — but a quality whole-food-based multi supports what your diet provides rather than working against it.

What to look for in a quality multivitamin:

  • A whole-food base — nutrients derived from or paired with concentrated food extracts, providing co-factors and phytonutrients alongside the named vitamins and minerals
  • Active (methylated) B vitamins — methylfolate (5-MTHF), methylcobalamin (B12), pyridoxal-5-phosphate (P5P / B6). These are the bioavailable forms; synthetic folic acid and cyanocobalamin should not be in a quality multi.
  • Chelated minerals — bisglycinate, citrate, malate, or picolinate forms. Avoid oxide forms, which are poorly absorbed.
  • D3 (cholecalciferol), not D2 — D3 is significantly more bioavailable
  • K2 paired with K1 — supports cardiovascular health and directs calcium appropriately
  • Adequate trace minerals — zinc, selenium, copper, manganese, molybdenum, chromium
  • Multiple capsules per day, not a "one-a-day" — adequate doses cannot fit in a single capsule
  • Iron only if you need it — most quality multivitamins come in both "with iron" and "iron-free" versions. Most adults (especially men and post-menopausal women) should not take iron without lab evidence of need.
  • Third-party tested — USP Verified, NSF Certified, or ConsumerLab tested

What to avoid in a multivitamin:

  • One-a-day formulations — almost always provide inadequate doses
  • Synthetic forms of B vitamins (folic acid, cyanocobalamin)
  • Sugar, artificial colors, and artificial sweeteners — common in gummy multivitamins
  • Proprietary blends — you cannot tell what dose you are actually getting

Take a quality multivitamin with a meal containing fat, since several of the vitamins (A, D, E, K) are fat-soluble.

My current recommendation
Whole-Food Multi → Iron-Free Multi → Phyto-Multi Powder →

The Five Most Commonly Deficient Nutrients

Even with a quality multivitamin in place, these five nutrients typically need to be supplemented at higher doses than any multi provides — because they are the ones I find depleted in the majority of patients walking into my clinic, across age groups, diets, and demographics. They are not the only nutrients that matter. They are the ones most commonly missing at the levels the body actually needs.

Vitamin D

The single most important supplement decision most adults will make.

What it does

Vitamin D is not really a vitamin — it is a hormone with receptors in nearly every tissue in the body. It regulates immune function, bone health, mood, cardiovascular health, and gene expression. Low vitamin D is associated with autoimmune disease, depression, cancer risk, infection susceptibility, and chronic inflammation.

What to look for

  • D3 (cholecalciferol), not D2 — D3 is significantly more bioavailable
  • With K2 (preferably MK-7 form) — directs calcium to bones rather than soft tissue
  • Take with a meal containing fat — vitamin D is fat-soluble

Testing matters

Vitamin D dosing should be guided by your 25-OH vitamin D level. Optimal range is generally 50-80 ng/mL. Adults with deficient starting levels often need significantly higher doses than the RDA suggests, under practitioner guidance.

My current recommendation
Vitamin D + K2 5K IU → Vitamin D +K2 2K IU →

Magnesium

The mineral most adults are deficient in, even on a clean diet.

What it does

Magnesium is a cofactor in over 600 enzymatic reactions in the body. It is essential for energy production, nervous system regulation, muscle function, sleep quality, blood sugar regulation, and detoxification. Modern soil depletion plus high intake of processed food means that even people eating well are often deficient.

What to look for — the form matters significantly

  • Magnesium glycinate — well-absorbed, calming, excellent for sleep and anxiety. The most universally useful form.
  • Magnesium threonate — crosses the blood-brain barrier. Useful for cognitive support, brain fog, mood.
  • Magnesium malate — supports energy production. Often used in fatigue, fibromyalgia, muscle pain.
  • Magnesium citrate — useful when constipation is a concern (it has a laxative effect).
  • Magnesium oxide — common in cheap supplements, poorly absorbed. Avoid as a primary source.

Testing

Serum magnesium is unreliable. RBC magnesium reflects cellular status more accurately.

My current recommendation
Glycinate → Threonate → Malate →

Vitamin B12

Essential for energy, mood, neurological function, and methylation.

What it does

B12 is required for red blood cell production, neurological function, DNA synthesis, and the methylation reactions that support detoxification and neurotransmitter production. Deficiency is common — especially in people over 50, vegetarians, vegans, those on metformin or acid-blocking medications, and anyone with gut absorption issues.

What to look for — the form matters significantly

  • Methylcobalamin — the active form. Best for most people, especially those with MTHFR variants.
  • Adenosylcobalamin — the mitochondrial form. Useful for energy issues.
  • Hydroxocobalamin — converts to either active form. A reasonable middle option.
  • Cyanocobalamin — common in cheap supplements. Contains a cyanide molecule the body must clear. Avoid.

Often paired with methylfolate (5-MTHF) for full methylation support. Sublingual or injection forms are useful for patients with absorption issues.

Testing

Serum B12 misses functional deficiency. Pair with MMA (methylmalonic acid) or homocysteine to assess whether B12 is actually being used at the cellular level.

My current recommendation
Methyl B12-MTHF → Tri-Form B12 →

Omega-3 Fatty Acids

The anti-inflammatory foundation.

What it does

Omega-3 fatty acids (specifically EPA and DHA) are structural components of every cell membrane and the precursors to anti-inflammatory signaling molecules. The modern diet provides far too much omega-6 (from seed oils) and far too little omega-3, creating a chronic pro-inflammatory state that drives nearly every chronic disease.

What to look for

  • EPA + DHA content — what matters is the actual EPA and DHA dose, not the total fish oil capsule weight. Many cheap supplements have low concentrations.
  • Triglyceride form over ethyl ester form — better absorbed, more stable
  • Third-party tested for purity — look for IFOS (International Fish Oil Standards) certification or equivalent. Fish oil can be contaminated with heavy metals, PCBs, and rancidity.
  • Algae-based options for vegetarians/vegans — DHA-rich; some products now include EPA as well

Testing

The Omega-3 Index (a blood test) measures the percentage of EPA + DHA in red blood cell membranes. Optimal is above 8 percent. Most Americans test in the 2-4 percent range.

My current recommendation
Multi-Form Omega → Omega-3 w/ D →

Iron / Ferritin

The most underrecognized deficiency in conventional medicine.

What it does

Iron is required for hemoglobin (oxygen transport), energy production, thyroid function, immune function, and neurotransmitter production. Functional iron deficiency — where ferritin is low but conventional anemia markers are still "in range" — is widespread and undertreated. It drives fatigue, hair loss, mood symptoms, restless legs, and exercise intolerance.

Important caveat

Iron is the only foundational nutrient on this list that you should not supplement without testing first. Iron overload is also possible and harmful, especially in men and post-menopausal women.

What to look for if supplementation is needed

  • Iron bisglycinate — gentle and well-absorbed. Significantly less GI side effects than ferrous sulfate.
  • Avoid ferrous sulfate as a primary form — constipating, often poorly tolerated
  • Take with vitamin C — significantly improves absorption
  • Take away from coffee, tea, calcium, and dairy — all inhibit absorption
  • Take every other day in many cases — new research suggests this improves absorption and reduces side effects

Testing

Ferritin is the most useful single marker. Functional iron deficiency exists below ferritin of about 50 ng/mL even when hemoglobin is normal. A full iron panel (ferritin, serum iron, TIBC, transferrin saturation) gives the complete picture.

My current recommendation (when supplementation is indicated)
Iron Bisglycinate → Iron BisGlyc w/ C →

Pillar 2 — Diet

What you eat becomes what you are made of.

The Principle

Most of what you put in your mouth should have either walked, swam, or grown. This is the simplest framework for evaluating a meal:

  • Walked — meat from animals raised on appropriate diets (grass-fed beef, pasture-raised poultry, eggs, etc.)
  • Swam — fish, especially wild-caught and lower on the food chain (smaller fish accumulate fewer heavy metals)
  • Grew — vegetables, fruits, herbs, spices, nuts, seeds, legumes

If most of what you eat fits one of these categories, you are doing well — regardless of which specific diet you follow.

What to eliminate (or significantly reduce)

The biggest gains in dietary work usually come from removing the worst inputs rather than adding the best:

  • Ultra-processed foods — anything with an ingredient list you cannot pronounce or that contains more than a handful of components
  • Industrial seed oils — soybean, corn, canola, sunflower, safflower, cottonseed. These are pro-inflammatory and have replaced healthier fats in most processed food.
  • Added sugars and high-fructose corn syrup — the average American consumes 70+ pounds per year
  • Artificial sweeteners — most disrupt the gut microbiome
  • Conventional dairy — if reactive (many patients improve significantly by removing it)
  • Gluten — if reactive, especially in autoimmune patterns

What to prioritize adding

  • Protein at every meal — most adults are under-protein, which drives muscle loss, blood sugar instability, and unhealthy cravings. Aim for 0.7-1.0g per pound of body weight daily.
  • Vegetables — variety and color — the variety of plant compounds matters more than the specific vegetables. Aim for several colors per day.
  • Healthy fats — olive oil, avocado, nuts, seeds, fatty fish, pasture-raised animal fats
  • Fermented foods — sauerkraut, kimchi, yogurt, kefir, kombucha — for microbiome support

Practical implementation

  • Cook at home most nights. Restaurants and packaged foods almost universally use industrial seed oils and excess sodium.
  • Shop the perimeter of the grocery store. Most of what you need is there.
  • Make one or two diet upgrades at a time, not everything at once. Sustainable change beats perfection.

Pillar 3 — Hydration

The medium every cell lives in.

How much

The basic guideline: half your body weight in ounces of clean water daily. A 150-pound person needs roughly 75 ounces (about 2.2 liters). Adjust upward for hot weather, exercise, sweating, or higher-protein diets.

Water quality

Tap water in most regions contains chlorine, fluoride, heavy metals, pharmaceutical residues, PFAS, and other compounds you do not want to drink chronically. See the Environmental Recommendations page for the full guide to water filtration. Briefly:

  • At minimum, a quality carbon filter (Berkey, Brita Elite, etc.)
  • Ideally, an under-sink reverse osmosis system with remineralization
  • For most patients, this is one of the highest-leverage upgrades they can make

Electrolytes

Plain water alone, in large quantities, can deplete electrolytes — especially for patients who sweat heavily, exercise, eat low-carb, or have adrenal issues. Adding small amounts of high-quality salt (Redmond, Celtic, Himalayan) or a clean electrolyte product to your water can be useful.

My current recommendations
Counter Filter $ → Electrolytes → Electrolytes #2 →

Supplement Selection Principles

Once you know what nutrients you need, the next question is which products to buy. The supplement market is enormous, largely unregulated, and full of products that are either ineffective or contaminated.

Quality Markers to Look For

Third-party testing

USP Verified, NSF Certified, ConsumerLab tested. These are independent verifications of purity and potency.

GMP certified

The manufacturer follows Good Manufacturing Practices quality standards.

Transparent ingredients

Every ingredient disclosed at full dose, no "proprietary blends" that hide what you're actually getting.

No unnecessary fillers

Avoid magnesium stearate, titanium dioxide, artificial colors, sweeteners.

Brands and Platforms

Two general approaches:

Retail supplement brands — available at health food stores, online retailers, sometimes amazon. Quality varies widely. Stick to brands with strong third-party testing and clean ingredient profiles.

Practitioner-grade brands — typically available only through licensed healthcare practitioners or through platforms like Fullscript, Wellevate, or Emerson Ecologics. Generally higher quality and stronger third-party testing standards. Examples include Designs for Health, Thorne, Orthomolecular, Quicksilver Scientific, and Standard Process.

My current preferred brands and platforms
Top Preferred Brands → Multi-Brand Platform →

What to Avoid

  • Products with proprietary blends (you don't know what you're actually taking)
  • Products with cyanocobalamin (cheap B12 form)
  • Products with ferrous sulfate as the primary iron source
  • Products with significant amounts of magnesium oxide
  • Multivitamins that do not use whole food sourcing or doesnt contain phytonutrient co-factors
  • Bargain-bin omega-3s without IFOS certification
  • Anything making specific disease claims (legally not allowed; quality red flag)

Dosing Principles

This is the area where practitioner guidance matters most. A few general principles I follow:

Start with foundational nutrients before targeted ones. Get your D, magnesium, B12, omega-3, and iron status right before layering in more specific supplements.

Test before dosing when possible. Especially for vitamin D, B12, iron, and other measurable nutrients. Generic dosing leaves significant value on the table.

Dose to response, then retest. Most patients should retest key nutrients at 3-6 months to confirm replenishment, then again at 12 months to confirm maintenance.

Less is often more. Many patients walk into my clinic on twenty supplements that are not working. A focused, smaller stack — built on accurate testing — almost always outperforms a larger generic protocol.

Take fat-soluble nutrients with fat-containing meals. Vitamin D, K, A, E.

Take iron and calcium separately from each other and from coffee/tea. Absorption competition is real.

Magnesium, glycine, and other calming nutrients are usually best at night. B vitamins and CoQ10 are usually best in the morning.

When to Move From BUILD to SUPPORT

The BUILD phase is foundational, but it is not the whole picture. You should continue maintaining the BUILD pillars indefinitely — but at some point, you will be ready to move into SUPPORT (Chemistry Pillars 4-9), where the work targets specific organ systems and physiology that need attention beyond the foundations.

Signs that you are ready to move into SUPPORT:

  • Your foundational nutrient labs are in optimal ranges
  • Your basic diet and hydration are sustainable
  • You feel meaningfully better than when you started — but you have remaining specific concerns
  • You have data (from testing) suggesting specific organ systems need targeted attention

The SUPPORT phase is covered in detail in Chapters 9 and 10 of the book. Specific protocols and recommendations will be added to this site as they develop.

Related Resources

3D Healing Starter Workbook

Assess whether Chemistry is your Weak Link

Explore →

Lab Testing

Testing the foundational nutrients before and after intervention

Explore →

Environmental Recommendations

Water quality and broader chemical input reduction

Explore →

Practitioner Interview Guide

Finding a practitioner who can guide testing, dosing, and ongoing protocol management

Explore →

Cleanse Resources

For the CLEANSE phase that follows SUPPORT

Explore →

The 3 Dimensions

Understand the complete 3D Healing framework

Explore →

Stay Updated

This page is updated periodically as my recommendations refine. Sign up to be notified when new resources release:

Medical Disclaimer: The information provided on this page is for educational purposes only and is not intended as medical advice, diagnosis, or treatment. Always consult with a qualified healthcare practitioner before making changes to your supplement or nutrition protocol. Dr. James Macie is a Doctor of Chiropractic (DC), not a medical doctor (MD), and this content does not establish a doctor-patient relationship. Individual results may vary, and supplement recommendations should be tailored to your specific health status and needs through appropriate testing and professional guidance.

Dr. James Macie, DC

3dhealing.com

Last updated: 2026-06-17