3 Levels of the Brain

Level One: Autonomic Thinking – The Brain on Autopilot

Autonomic thinking is the most primal, automatic level of thought—so automatic, in fact, that we often don’t even realize it’s happening. Just like your brain keeps your heart beating and lungs breathing without conscious effort, it also follows emotional routines designed to keep you safe. From an evolutionary standpoint, sameness means survival. Change, on the other hand? It could mean danger.

At its most basic level, the brain is wired to resist the unfamiliar. New experiences require extra energy, attention, and—most importantly—pose unknown risks. So, the brain defaults to what it knows. It sticks with the predictable, the routine, and the habitual.

Take your typical morning. You wake up, make your coffee, check your emails, and drive to work. On the surface, it’s all routine. But under the surface, each of these actions is linked to a subtle, often unconscious emotional signature.

Now imagine that every morning on your commute, you hit traffic. And every morning, you get irritated, impatient, maybe even angry. Over time, your brain doesn’t just expect the traffic—it expects the frustration. That emotional reaction becomes part of the routine. Your brain, trying to stay efficient and “safe,” serves it up automatically, like clockwork.

This is autonomic thinking at work. It’s not thinking in the traditional sense. It’s predictive pattern-matching, built from your past. It’s not asking, “Is this reaction helping me?” It’s saying, “This is what we did yesterday, and we survived. Let’s do that again.”

The problem is, not all of these emotional routines are healthy—or helpful. Left unchecked, they can quietly dictate your entire mood, your decisions, and even your sense of identity. You’re not just someone who hits traffic. You start to believe you’re someone who’s always stressed, always reactive, always on edge.

Reprogramming Your Autonomic Brain

The good news? You’re not stuck with the emotional routines your brain has picked up over the years. Just like physical habits, mental and emotional habits can be unlearned—and replaced with ones that actually serve you.

Here’s a simple but powerful process to start reprogramming your autonomic thinking:

1. Decide what you want to feel.
   Take a moment to think about the kind of emotions or thoughts that would actually benefit your life. Calm? Confidence? Gratitude? Choose one or two that feel meaningful. These are your new defaults—but you have to train your brain to make the switch.
2. Become aware of the old patterns.
   Start observing your emotional routines like a detective. Notice when that familiar irritation creeps in during your commute. Pay attention to the self-talk that kicks in when you’re checking emails. This isn’t about judging yourself—it’s about seeing the program run so you can pause it.
3. Interrupt the loop.
   The moment you notice the old routine playing out, intentionally stop. Take a breath. And here’s the key: substitute the thought or emotion with the one you’ve chosen. If your go-to reaction is frustration in traffic, replace it with calm acceptance. If your inner monologue is self-doubt in the mirror, replace it with one word of self-encouragement.

This isn’t easy at first. The old routines are well-worn grooves. But with consistency, your brain begins to rewire. New neural pathways form. Eventually, what was once a conscious choice becomes the new automatic.

It’s like installing an emotional “update” into your operating system—one small shift at a time.

Level Two: Emotional Thinking – The Feeling Filter

While autonomic thinking runs in the background like a silent operating system, emotional thinking is more like the front-end interface—intensely felt, often loud, and deeply tied to our experiences. Emotions influence nearly everything: our reactions, our decisions, even our memories.

In fact, emotion is the biggest puzzle piece of a memory. If you want to dive deeper into that concept, check out my other post, The Pieces of Memories—it explores how emotion actually anchors a moment into our minds. We don’t just remember what happened; we remember how it felt.

Let’s go back to our driving example.

You’re heading to work, just like every other morning. But today, your mind drifts to something upsetting—maybe an argument you had recently, or even something from years ago. You find yourself thinking, “I wish I would have said…” and begin replaying the scene in your mind, this time with the perfect comeback or the response you wish you’d had.

Here’s what’s wild: your brain doesn’t know the difference between remembering the emotion and actually experiencing it again. When you mentally revisit that moment, your emotional brain kicks in, reactivating the feelings you had back then—frustration, shame, anger, sadness.

But it doesn’t stop there.

Your autonomic brain—always listening—picks up on those emotional cues and responds as if the threat is happening right now. Stress chemicals are released:

• Cortisol, your body’s primary stress hormone, prepares you to fight or flee.
• Adrenaline spikes your heart rate and sharpens focus.
• Norepinephrine amps up your alertness and reaction time.

Your grip on the steering wheel tightens. Your breathing becomes shallow. Your heart pounds. As far as your body is concerned, you’re under threat—even though you’re just driving to work.

This is emotional thinking pulling you into a physiological stress state, simply because your mind decided to revisit a past experience.

Emotions Can Heal, Too

But here’s the good news: the opposite is also true.

When you experience positive emotions, your brain releases an entirely different set of chemicals, each with powerful health benefits:

• Dopamine: The “motivation molecule” that boosts mood, focus, and drive.
• Serotonin: A mood stabilizer that contributes to feelings of happiness and well-being.
• Oxytocin: The “bonding hormone” that enhances trust, connection, and reduces fear.
• Endorphins: Natural painkillers that promote pleasure and relieve stress.

Think about a moment of genuine laughter, a hug from someone you love, or the quiet peace of watching a sunrise. These experiences flood your brain and body with feel-good chemicals that lower blood pressure, reduce inflammation, boost immunity, and even help you heal faster.

So yes—your emotional state literally impacts your physical health, every single day.

And the best part? You can intentionally create more of these moments. You don’t have to wait for happiness to randomly show up—you can practice emotional self-care like a skill. Curious how? Check out my post, Cultivating Emotion States, for some simple yet powerful ways to consciously shift into healthier, more supportive emotional patterns.

Level Three: Cognitive Thinking – The Power of Awareness

If autonomic thinking is unconscious and emotional thinking is reactive, cognitive thinking is where your awareness finally steps into the driver’s seat.

This is the level where you think about your thoughts. It’s where you pause, reflect, and make intentional choices instead of defaulting to old patterns or emotional impulses. Cognitive thinking is slower, more deliberate, and—most importantly—more powerful.

It’s the difference between reacting and responding. Between surviving the day and shaping your life.

Whereas autonomic and emotional thinking often run on past programming, cognitive thinking allows you to create new programming. It’s where logic, reason, creativity, and long-term vision live. It’s the space you enter when you ask questions like:

• Why do I keep reacting this way?
• Is this belief really true—or just familiar?
• What emotion would serve me better right now?
• How can I respond from intention instead of habit?

Let’s revisit that traffic scenario one more time.

This time, you’re aware that you’re gripping the wheel. You feel the tension in your jaw. You recognize the pattern. And instead of letting the loop take over, you pause.

You take a breath.

And then, instead of reacting from emotion or autopilot, you choose a different thought:
“I’ve been here before. Getting angry doesn’t help. I’ll use this time to practice patience.”

That’s cognitive thinking in action. You’re still experiencing the moment—but now, you’re not owned by it. You’re observing. You’re deciding. You’re growing.

This is the level where change becomes possible.

This is where we finally get to put into action the new thoughts and emotional responses we chose for ourselves back in the section Reprogramming Your Autonomic Brain.

Your cognitive mind is the tool that brings all the pieces together. It allows you to notice when the old routines show up, interrupt them with awareness, and intentionally replace them with the thoughts, beliefs, and emotional responses that support the life you actually want to live.

This is how you shift from being a passenger in your own mind to becoming the one behind the wheel.