Ask most people what their muscles are for and they will say the obvious: moving around, lifting things, looking good at the beach. All true. But in more than thirty years of practice — I have been working with Autoimmune patients since 1996 — one of the most useful ideas I get to share is this: your muscle is not just a set of contracting ropes. It behaves like an organ. A living, chatty, metabolically busy organ, right up there with your liver in terms of how much it shapes your mood, your energy, your blood sugar, and your capacity to heal.
That reframe changes everything about how we approach movement in The Epigenetic Autoimmune Protocol (the Epi-AIP). So let me walk you through why your muscles deserve far more respect than we usually give them.
Are Your Muscles Really an Internal Organ?
It is a common misconception that muscle is just protein tissue that squeezes and relaxes. In reality, muscle is endocrine and metabolic tissue. It sends out signaling molecules, it regulates the rate at which you burn fuel, it influences how fast you age, and it has a great deal to say about how well you recover from illness.
When you train, muscle cells get hungry — genuinely hungry — for glucose. They pull sugar out of your bloodstream to rebuild and grow. That is why regular movement, especially resistance training, is one of the most powerful ways to steady your blood sugar and soften those late-afternoon energy crashes that turn us into the least friendly version of ourselves around three or four o’clock. This is the Second Pillar, Metabolic Adaptability, made flesh: a body that can flexibly reach for the right fuel at the right time.
Why Are Fit People So Often So Happy?
There is real physiology behind the cliché. As you exercise:
- Your muscles pull glucose out of the blood, helping regulate the swings that fray your mood.
- Your adrenal hormones get put to use, which is the honest version of “blowing off some steam” — you burn through the nervous, pent-up feeling that daily stress leaves behind.
- Your body secretes more Human Growth Hormone, which does not only build muscle. It tells the whole system to feel nourished, energized, and creative.
Regular resistance training has also long been associated with lower cholesterol (muscle membranes are literally built from cholesterol), lower blood pressure, better sleep, and improved libido. Being in good shape tends to ease depression and anxiety and supports immune and lymphatic function.
But the most profound benefit, in my experience, is the shift in attitude. Once you gain a little momentum and start seeing results, you become the more empowered version of yourself — the one with enough self-love and creative energy to move toward what you actually want, with confidence and a bit of ease.
The Car-Engine Metaphor (Forgive the Emissions)
Here is a picture I use with patients. If you rarely move, you are getting around on a small four-cylinder engine. Reasonably active, and you have a solid six-cylinder. Training three or more times a week — gym, pool, mountains, bike, whatever you love — and you are driving a powerful V8.
It is an imperfect metaphor environmentally, I know. But metabolically it holds: the bigger, better-tuned engine burns more fuel, keeps a healthier lean-mass-to-fat ratio, and tends to carry you further into a long life.
What Actually Makes the Engine Bigger
Two things set the size of your muscular “engine”: mitochondria and fiber type.
Mitochondria are the spark plugs. They take oxygen and fuel and combust it into energy. The more spark plugs each cell carries, the more fuel it burns all day long — not just during the workout. In fact, after a good session your body keeps burning glucose, protein, and fat for many hours afterward.
Your muscle fibers come in a few flavors:
- Slow-twitch — for long, steady effort like walking that can go on for hours.
- Fast-twitch — for more intense work.
- Very fast-twitch — for explosive efforts you can only sustain for a few seconds.
Picture their cross-sections like this: slow-twitch the size of your little finger, fast-twitch the size of two fingers together, and very fast-twitch as thick around as your wrist. Build those very fast-twitch fibers and your muscles get bigger fast — and building them burns a lot of energy in the process.
The training levers are simple:
- High-repetition resistance training increases the number of mitochondria per cell — more spark plugs, more daily fuel burn. A wonderful place to begin.
- High-intensity work that exhausts a muscle in under a minute builds those elusive very fast-twitch fibers.
Train to Good Form, Not to Collapse
If you go the heavier bodybuilding route, you work lower reps with heavier weight — heavy enough that you can only manage around ten before your posture starts to break down. Bodybuilders call staying inside that limit being “strict.”
I have watched too many people grind out extra reps with their backs arched, shoulders hiked, and breathing out of control. Here is why that matters: your nervous system remembers your last three repetitions as your true capacity as an athlete. Reinforce good form and that is what your body learns. Reinforce collapse and that is what it learns instead. Choose the failure of form over the failure of sheer willpower.
Start With the Core
Your core is essentially every muscle between your ribcage and your femur. It governs how much you can safely lift with your arms and legs, and it sets your posture and mechanics when you stand, walk, and run. A weak core lets the spine, pelvis, and legs drift out of alignment — the quiet setup for many chronic, painful problems. Strengthening your core is one of the most reliable ways to lower your risk of injury.
Movement Is Rebuilt, Not Rushed
Improving strength is honestly the least complicated way to improve your health. Pick things up, put them down. Simple — and, eventually, fun.
But we meet you where you are. This belongs to the Third Pillar of the Epi-AIP, Physical Fitness, Rest, and Sleep, and rest and sleep are named right alongside fitness on purpose. If you are in a flare, rest comes first — full stop. Movement is rebuilt gradually as your body signals it is ready. Across the Four Phases of the Epi-AIP, what movement looks like naturally changes: gentle and restorative early on, more robust as capacity returns.
Strength training also doubles as an honest read on your recovery. If you begin training and bounce back after a few days of ordinary soreness, that is a green light. If recovery is slow and torturous, that is worth a conversation with Dr. Michael Smith or your own provider about why — not a reason to blame yourself and push harder.
A few practical guardrails for getting started:
- Aim for roughly 20 to 40 minutes per session. Work until you feel a satisfying fatigue, never exhaustion.
- Start with something you already know you can do, then put your attention on breathing and coordination.
- Only add to the routine when you are genuinely not tired after a session.
- Interval Circuit Training is a friendly on-ramp: about 45 seconds of an exercise, then 15 seconds of rest, moving through a pre-planned circuit. A free interval timer on your phone saves you from watching the clock.
- Tabata training — 20 seconds hard, 10 seconds rest, eight rounds for four minutes — builds stamina and fast-twitch fibers with little risk of losing muscle. Rest a couple of minutes before the next exercise.
And watch for the “shakes” twenty minutes after a hard workout. That trembly feeling is excess adrenaline, and it can actually work against muscle gain and fat loss. If you feel it, simply do fewer sets next time. Your body is not failing you; it is giving you data.
Your muscles are amazing — not as decoration, but as a metabolic and endocrine organ that helps run your mood, your fuel, and your resilience. Treat them well, build them patiently, and they will help carry you through this healing journey.
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The information on this website is provided for general educational purposes. It is not a substitute for individualized medical advice, diagnosis, emergency assessment, or treatment from your physician or another qualified healthcare professional.
