The Framework That Makes Functional Medicine Actually Work

Functional medicine has a chaos problem.

Not a science problem. Not an effectiveness problem. A chaos problem.

A version of this walks into my office every couple of weeks — often patients who've driven from Temple, Killeen, Georgetown, and across Central Texas looking for answers. They've seen multiple practitioners. They've done elimination diets, detox protocols, hormone panels, food sensitivity tests. They've spent thousands of dollars and months of their life trying everything. And they feel exactly the same.

The supplements aren't bad. The labs are legitimate. But there's no framework. No sequence. No logic to what gets addressed first and why. They're taking adrenal support, gut healing, detox blends, and hormone support — all at the same time, with no baseline understanding of which problem is actually driving the others.

This is the single most common mistake in functional medicine: doing everything at once and solving nothing.

The difference between good functional medicine and expensive chaos is architecture. You need a system. A hierarchy. A framework that tells you where to start, when to go deeper, and which problems to fix first so the downstream ones resolve on their own.

Why a Framework Matters More Than Testing

Every functional medicine doctor says they "find the root cause." Most of them are guessing. I know because I see the aftermath. Patients walking in with hundred-panel lab results and no one who can tell them what it all means, or which problem to tackle first, or why fixing problem A before problem B actually matters.

You can test for everything. Food sensitivities, mycotoxins, heavy metals, genetic SNPs, organic acids, comprehensive stool analysis, comprehensive hormone testing. I could order $10,000 in labs on day one. But without a framework, you're just collecting data. And data without a hierarchy is noise.

The whole point is knowing what to look at first, what to fix first, and when to go deeper. That's what my tiered system does.

Tier One — The Foundation

​Gut health. Metabolic function. HPA axis.

Every single patient starts here. I don't care if you came in for hormone optimization, ADHD, chronic fatigue, or weight loss. We start at the foundation because if these three things are broken, nothing else we do is going to stick.

​Gut health — I've talked about this extensively, but the short version: roughly 70% of your immune system lives in your gut. Your neurotransmitter production happens largely in your gut. If you've got dysbiosis, intestinal permeability, or chronic GI inflammation, every other system in your body is affected. We look here first.

​Metabolic health — this is your blood sugar regulation, insulin sensitivity, and thyroid function. We start with baseline metabolic markers and an expanded thyroid panel — free T3, free T4, total T3, total T4, TSH. If those don't explain the symptoms, we go deeper. But we start here because metabolic dysfunction is wildly common and often the simplest explanation for fatigue, brain fog, weight gain, and mood changes.

​HPA axis — that's your hypothalamic-pituitary-adrenal axis, your stress response system. When this is dysregulated — and it is in most of my patients — your cortisol rhythm is off, your sleep suffers, your immune system weakens, and your body prioritizes survival over repair. We look at cortisol patterns and how they're affecting everything downstream.

The way I think about it: tier one is the foundation of a house. You can put in beautiful countertops and new windows, but if the foundation is cracked, the house is still falling apart.

And here's what surprises people — most of the time, tier one work resolves or dramatically improves the primary complaint. I'd estimate 60 to 70% of cases. Gut cleanup, metabolic optimization, stress response support, and the pillars of health. Sounds simple. It's not — but it works.

Tier Two — Going Deeper

​Hormones. Toxins. Infections.

If tier one doesn't fully resolve things — or if the initial labs show obvious problems in these areas — we move to tier two.

​Hormones — now we expand the picture. If the baseline thyroid didn't explain things, we add reverse T3, antibodies. We look at the full sex hormone panel — testosterone, estrogen, progesterone, DHEA. Here's the key insight: hormones are often downstream of tier one problems. Fix the gut and inflammation, and hormones frequently normalize on their own. That's why we don't start here. But when they need direct support, we provide it — bioidentical hormone replacement when indicated while we fix the foundation.

​Toxins — mold exposure, heavy metals, environmental chemicals. These are real and underdiagnosed, but they're also overhyped in some functional medicine circles. I test for them when the clinical picture suggests it — unexplained neurological symptoms, treatment resistance, known exposure history. I don't run mycotoxin panels on everyone.

​Infections — chronic viral reactivation like EBV, tick-borne illness, parasites. This is where targeted antiviral and immune-modulating protocols come in. If someone isn't responding to tier one work and their labs show active viral reactivation, we address it.

Tier Three — The Complex Cases

​Mitochondria. Genetics. Structural.

This is for patients who've been through tiers one and two and still aren't where they need to be.

​Mitochondrial function — are the energy factories in your cells actually working? We look at cellular energy markers and sometimes use direct mitochondrial support.

​Genetics — variants that affect how you methylate, detoxify, and process neurotransmitters. I don't lead with genetics because a genetic variant is just a tendency — it doesn't mean much without context. But in complex cases, it can be the missing piece.

​Structural — sometimes the problem is physical. Cervical instability affecting vagal tone. Jaw alignment affecting breathing and sleep. These aren't my primary domain, but I know when to refer.

The Pillars of Health

Running through every tier is what I call the pillars of health. These are non-negotiable regardless of your diagnosis, and they're not soft lifestyle suggestions. They're biochemical inputs.

​Sleep. If you're not sleeping 7 to 8 hours of quality sleep, nothing else I do will work as well as it should. Sleep is when your body repairs, detoxifies, and consolidates immune function. I address sleep problems aggressively and early — and I mean actually investigating why you can't sleep, not just handing you melatonin.

​Nutrition. Not a diet — a way of eating that reduces inflammation, supports gut health, and provides the raw materials your body needs. For most of my patients, this means something in the range of anti-inflammatory to ketogenic, depending on their specific situation. I use evidence-based dietary frameworks as a starting point — straightforward, research-backed approaches that work.

​Movement. Exercise is medicine. But the right kind matters. Overtraining with chronic fatigue is counterproductive. Under-moving with metabolic syndrome is equally bad. I think about exercise like a prescription — specific type, duration, and intensity matched to where you are.

​Stress management. Not platitudes about yoga and meditation — actual nervous system regulation. If your sympathetic nervous system is stuck in overdrive, your body can't heal. Period, end of story.

​Environment. What are you being exposed to? Mold, chemicals, endocrine disruptors in your home, your water, your personal care products. This matters more than most people realize.

​Community and purpose. This one might sound soft, but loneliness and lack of meaning are independent risk factors for chronic disease. Elevated cortisol, systemic inflammation, impaired immune function — the research is clear. I ask about this and take it seriously.

But — and this is important — some patients are so depleted by the time they get to me that telling them to "fix their sleep" and "eat better" is almost insulting. They can barely get through the day. So sometimes we have to jump above the pillars. We intervene medically first — address the thyroid, the insulin resistance, the gut dysfunction — and get them functional enough that they can actually make lifestyle changes. You have to meet people where they are.

Why This Prevents the Two Biggest Mistakes

​Mistake one: doing everything at once. Twenty supplements, three dietary changes, and a detox program starting Monday. The patient feels overwhelmed, nothing gets properly assessed, and when they improve — or don't — you have no idea what actually moved the needle.

​Mistake two: going too deep too fast. Running a mycotoxin panel before checking if the patient is actually sleeping. Prescribing bioidentical hormones before fixing the gut inflammation that's disrupting hormone metabolism. You end up chasing problems upstream when the real driver is downstream.

The tiers force discipline. Start simple. Fix the foundation. Only go deeper when you need to. And always come back to the pillars. This is never a straight line — there are hiccups, adjustments, course corrections. But the framework keeps you moving in the right direction instead of spinning in circles.

The Bottom Line

If you've been to a functional medicine doctor and felt like they were throwing spaghetti at the wall, you weren't wrong. Good medicine requires a system, not just good intentions.

My system is the tiered framework plus the pillars of health. It's how I treat every patient, from straightforward hormone optimization to the most complex chronic illness cases. And it works — not because it's magic, but because it forces us to answer questions in the right order.

If you're looking for a doctor who actually has a plan — not just a lab order — that's exactly what we do at Rooted Health.

Give us a call at 254-780-0023 or visit rootedhealthclinic.com to schedule a consultation.

Rooted Health Clinic — Salado, Texas