Meditation: To Empty or Fill?

What a Huberman Podcast Got Me Thinking About Meditation and the Brain

I recently listened to a podcast hosted by Andrew Huberman, the Stanford neuroscientist, featuring Dr. Alok Kanojia — "Dr. K" — a Harvard-trained psychiatrist who spent seven years as a monk before going into medicine. It was a long, thoughtful conversation about how people actually change. And somewhere in the middle of it, as they talked about meditation, I found myself scribbling notes — because the practice they were describing and the practice the Bible describes are aiming at two very different destinations.

Dr. K described a practice he called shunya — the void. The idea is to strip away every label, every "I am," every role and comparison and fear, until what's left is the most fundamental part of you, underneath everything built on top. Empty the mind. Dissolve the ego. Reach the nothing underlying the noise.

It's a nice discipline, and there's wisdom in learning to stop being ruled by your own labels. But as a pastor, I kept thinking: the goal of Christian meditation is never emptiness. It is encounter.

Two kinds of meditation, two destinations

Eastern meditation, at its root, is subtraction — empty yourself, quiet the mind, detach from desire, move toward stillness. Christian meditation runs the opposite direction. The Hebrew word is hagah — to mutter, to chew on, to turn something over and over until it soaks in.

"Oh, the joys of those who… delight in the law of the Lord, meditating on it day and night" (Psalm 1:1–2 NLT).

Joshua is told to keep the book of instruction on his lips and meditate on it day and night (Joshua 1:8). That's not emptying. That's filling.

The difference matters more than it seems. One practice clears the thoughts. The other fills it with Someone. You're not trying to reach the empty place beneath the noise — you're trying to meet the God who is already present with you.

And here's what struck me: the neuroscience in that very same conversation actually explains why the filling version works.

What the brain requires to actually change

Huberman has spent years teaching how the adult brain rewires — a process called neuroplasticity. His framework comes down to three non-negotiables: you need alertness, you need focused attention, and then you need rest — real rest, especially sleep. Miss any one, and lasting change doesn't take. As he says flatly: no alertness, no neuroplasticity.

But the part that stopped me is this: the actual rewiring — the physical remodeling of the circuit — doesn't happen during the effort. It happens afterward, in deep rest and sleep. The striving only marks which circuits need to change. The change itself is consolidated when you stop striving.

Pause for a moment with that thought, because it dismantles the most popular self-help ritual on earth: the affirmation. Standing in front of a mirror and repeating "I am enough" for thirty days, and if underneath you have spent your whole life believing you don't matter, here is what happens — nothing. We all know who we are inside. All the positive affirmations won’t change that. But what if we began to believe about ourselves what God believes about us? What if we focused more on what God thinks about us rather than trying to inflate our own view of ourselves?

Why the verses you already know don't seem to reach you

If you've been in church any length of time, you already know the verses. Fearfully and wonderfully made. No condemnation. A child of God. You could recite them in your sleep. And still, on a hard day, they land like words on a page — true, but not yours.

I've come to say it this way: a braced nervous system can't embrace the truth it already knows. When your body is in alarm — guarding, bracing, half in fight-or-flight — truth cannot reach depth. It stays on the surface, which is exactly where the neuroscience says change cannot stick.

Scripture said this first, in its own language. "Be transformed by the renewing of your mind" (Romans 12:2). Transformed, not merely informed. Not more repetition — a renewing that reaches the root. And God is even more direct through Ezekiel: "I will give you a new heart… I will take out your stony heart" (Ezekiel 36:26 NLT). Not sand down the stone. Replace it.

The contrast worth naming

Here's where the science and the gospel gently part — not as enemies, but as two people describing different halves of the same scene.

The neuroscience tells you the conditions: the brain changes in a state of focus followed by rest, when truth enters at depth rather than at the surface. That's a genuine gift, and I'm grateful for it. But it cannot tell you what truth to plant, and it cannot give you the safety to receive it. It describes the soil. It can't hand you the seed.

That's the difference between emptying and filling. You can quiet your mind to the void and still walk away with a heart that doesn't believe it's loved. The gospel doesn't ask you to empty yourself into nothing, and it doesn't ask you to affirm what you don't believe. It fills you — it re-fathers you — until the true thing becomes felt, not just recited.

So what do you actually do?

Stop trying to override who you are by force, and start letting yourself be changed at the root. Three moves make that real.

First, get safe before you get to work — you can't receive truth in a hyper-protective state, so slow the nervous system down first; even a few minutes of slow breathing helps.

Second, truth is about depth, not volume — sit with one verse in a settled state until it's felt, instead of trying to read a whole chapter. My best practice is to read until something captures my attention.

Third, let it consolidate in rest — here the science and the Sabbath agree: the change takes root when you finally stop striving.

You are not broken. You have been trying to override a system that was designed to be healed — and no amount of effort, and no amount of striving for emptiness, can substitute for our being aware and met by the God who is already there.

If you're worn out from white-knuckling your way toward a peace that never sticks, my book No Longer Stuck is where the framework begins — and my forthcoming book, The Three Wounds, takes it all the way to the root. Visit our Store to check out all of the resources. Or, if you'd rather talk to a real person, book a Discovery Call at helpingothersheal.org.