Faith · Prayer · Charity
A note before we begin. What follows is not a collection of feel-good spiritual observations loosely dressed in scientific language. The neuroscience in this post is real, sourced, and documented – I will cite every claim so you can go deeper on your own. The theological framework is Catholic. The testimony is mine. I encountered the research while trying to make sense of my own experience of loss – and what I found was that the science and the theology were describing the same thing from opposite directions. That discovery felt too important to keep to myself.
I did not expect grief to make me a better person at prayer. I expected it to make me worse – angrier, more distant, more inclined to turn away from a God who had allowed something I could not explain. What happened instead was something the researchers have a name for and the mystics mapped centuries before the brain scans existed. The neuroscience of suffering and prayer turns out to be one of the most surprising intersections in all of human experience – and understanding it changed the way I understood everything that had happened to me.
We lost three babies. Three consecutive pregnancies, three losses, in a season of our lives when hope was the most costly thing we owned. I will not detail the clinical specifics here because the clinical specifics are not the point. The point is what happened in me during those years – and what the science now tells us was happening in my brain at the same time – and how those two things together point to something the Church has been saying all along.
Furthermore, this post is not only for women who have experienced pregnancy loss. It is for anyone who has been through a heavy season – grief, illness, injustice, prolonged stress of any kind – and emerged on the other side wondering what God was doing in the middle of it. The answer, it turns out, involves both your amygdala and your soul. And they are more connected than you might think.
What Suffering Does to Your Brain
The Prefrontal Cortex and the Illusion of Control
The prefrontal cortex is the part of your brain responsible for what neuroscientists call executive function – strategic planning, impulse control, and the management of complex decisions. Researchers describe it as the center of “top-down control” over behavior and emotion. In practical terms, this is the part of you that believes it can handle things – the seat of self-sufficiency, the part that makes plans and confidently tells the rest of you that everything is manageable.
Published research from the National Institutes of Health confirms that prolonged psychological stress and the cortisol that accompanies it cause measurable decreases in synaptic density in the prefrontal cortex. A 2018 review published in Pharmacology Biochemistry and Behavior established that uncontrollable stress specifically takes the prefrontal cortex “off-line,” switching the brain from what researchers call a reflective state to a reflexive one. In other words, serious and sustained suffering neurologically dismantles the part of you that thinks it is in charge.
Consequently, here is what that means in plain language: when you are in the middle of real grief – the kind that goes on for months, the kind that strips away the comfortable buffer of normal life – your brain loses its capacity to maintain the pretense of self-sufficiency. The stress itself structurally weakens the neurological architecture that supports the belief that you can manage this alone.
The mystics called this purgation. St. John of the Cross described the Dark Night of the Soul as God’s way of stripping away everything the soul has been using as a substitute for Him – including its reliance on its own competence, its own plans, its own sense of control. Neuroscience describes the same experience from the outside. The prefrontal cortex goes offline. The soul stops pretending it can do this alone. And in that stripping away, something opens that was closed before.
The Amygdala and the Rawness of Real Prayer
While the prefrontal cortex is losing its hold on control, the amygdala – the brain’s emotional processing and threat-detection center – becomes significantly more active under prolonged stress. The amygdala governs emotional sensitivity, the processing of fear and grief, and the depth of emotional response to experience. When it is hyperactivated by sustained suffering, the filter between what you feel and what you are aware of feeling becomes much thinner.
Most people who have been through serious grief report that their prayer in that season was rawer, more honest, more desperate, and in a strange way more intimate than prayer had ever been in comfortable seasons. The neuroscience explains why. In normal life, the prefrontal cortex filters and manages emotional expression – but suffering weakens it. The amygdala, meanwhile, processes the full weight of what is actually happening, and sustained grief heightens it significantly. The result is a person who arrives at prayer without the usual protective layer of composure – who cannot perform okayness before God because the neurological machinery that enables that performance has broken down.
Therefore, what suffering produces in prayer is not distraction and distance – though it can feel that way. Rather, it produces the conditions for the most unguarded conversation with God most people ever have. The Psalms are almost entirely written from this place. “My God, my God, why have you forsaken me?” (Psalm 22:1) is not composed prayer. It is amygdala prayer – raw, unfiltered, honest in a way that polished devotion rarely achieves.
The Default Mode Network and the Gift of Surrender
The default mode network – often called the brain’s narrator – is the system of interconnected brain regions that activates when we are not focused on external tasks. It governs rumination, self-referential thinking, and the constant internal monologue that most of us live inside without noticing. Research published in the Proceedings of the National Academy of Sciences found that overactivity in the default mode network drives unhappiness, anxiety, and psychological stuckness.
Here is what is remarkable: serious suffering disrupts the default mode network in ways that closely parallel what years of contemplative prayer practice try to achieve deliberately. The brain that is overwhelmed by grief cannot sustain the usual narrative about itself – the story it tells about who it is, what it controls, where it is going. That narrative requires cognitive resources the suffering brain does not have. As a result, the internal narrator goes quiet. What remains is something closer to presence – a raw, unmediated awareness of what is actually real.
Contemplatives across every tradition have described this state as the fruit of years of disciplined prayer. Suffering can produce it involuntarily – not as a reward, but as a byproduct of the stripping. The person who has been through serious loss often reports a quality of presence, a clarity about what actually matters, and an inability to be distracted by what used to consume them. The neuroscience names what the mystics experienced: the narrator has been interrupted, and what lies beneath it is closer to God than the narrator ever was.
Post-Traumatic Growth Is Not a Metaphor
In the mid-1990s, psychologists Richard Tedeschi and Lawrence Calhoun introduced the term post-traumatic growth to describe a phenomenon they had been observing in trauma survivors for years: not merely recovery from trauma, but actual transformation beyond previous levels of functioning. Their research – now supported by decades of follow-up studies – identified five specific domains in which growth consistently occurs following serious trauma.
Post-traumatic growth is the experience of positive change that occurs as a result of the struggle with highly challenging life crises. It is manifested in a variety of ways, including an increased appreciation for life in general, more meaningful interpersonal relationships, an increased sense of personal strength, changed priorities, and a richer existential and spiritual life.
That last domain – a richer existential and spiritual life – appears consistently across cultures, trauma types, and belief systems. Furthermore, many trauma survivors move through a period of questioning their beliefs because suffering makes existential and spiritual issues feel immediate rather than abstract. Grappling with these questions often produces a deeper satisfaction – a sense of experiencing life at a level of awareness that comfort never reached.
What Growth Actually Looks Like
In other words, the research confirms what the Church has always taught: suffering, when moved through rather than around, does not diminish the soul. It enlarges it. Consequently, the person who has been through serious loss and come out the other side often carries something the comfortable cannot access – a depth of faith that the storm alone could build.
What the Church Has Always Known
The Three Stages and the Brain That Lives Them
The classical Catholic mystical tradition describes the spiritual life in three stages: purgation, illumination, and union. Purgation is the stripping away – the losses, the suffering, the dismantling of what you thought you were and what you thought you controlled. Illumination is the clarity that comes after – the changed priorities, the deepened prayer, the raw honesty with God that suffering makes possible. Union is the destination – not the absence of future suffering, but the settled knowledge that God is present in all of it and that His presence is enough.
The neuroscience maps onto this framework with striking precision. Purgation is the prefrontal cortex going offline – the stripping of the illusion of self-sufficiency. Illumination is the amygdala-driven rawness of honest prayer and the default mode network’s narrator going quiet. Union is post-traumatic growth – the transformed person who has been through the fire and emerged carrying something that was forged there.
St. John of the Cross did not have access to fMRI scans. Nevertheless, what he described in the Dark Night of the Soul is recognizable in the neuroscience literature with almost no translation required. The soul that has been stripped of its consolations, its self-sufficiency, and its comfortable distance from God – that soul is, in neurological terms, a brain whose prefrontal cortex has been weakened, whose amygdala has been opened, and whose default mode network has been interrupted. The mystic and the neuroscientist are pointing at the same thing.
Romans 5 and the Mechanism of Formation
Paul’s letter to the Romans contains one of the most precise descriptions of spiritual formation through suffering in all of Scripture: “We also boast in our afflictions, knowing that affliction produces endurance, and endurance produces character, and character produces hope, and hope does not disappoint, because the love of God has been poured into our hearts through the Holy Spirit that has been given to us.” (Romans 5:3-5)
The sequence Paul describes is not metaphorical. It is a formation process – each stage producing the conditions for the next. Affliction does not directly produce hope. It produces endurance first. Endurance then produces character. Character finally produces hope. The process takes time, and God does not waste a moment of it.
The Brain That Is Ready to Receive
Furthermore, the mechanism Paul identifies at the end – the love of God poured into our hearts through the Holy Spirit – is precisely what the neuroscience describes in different language. The brain that suffering has stripped of self-sufficiency, that grief has opened, and that silence has quieted – that brain is most available to receive what God pours. Suffering does not block the love of God. It clears the channel for it.
God does not waste suffering. He uses the neurological changes it produces to create the conditions for the deepest prayer, the most honest encounter with Him, and the most durable formation of the soul. Therefore, what feels like damage is often the preparation.
The Rainbow Is Not an Accident
Three Losses and What They Built
I told you we lost three babies. What I did not tell you is what those years built in me – not immediately, not without cost, but over time and in ways I am still discovering.
The losses stripped away my comfortable relationship with prayer. Before them, prayer was something I did well – structured, consistent, theologically informed. After the first loss, it became something rawer. After the second, it became something I could barely sustain. And after the third, it became the only thing I had left – not because I had nothing else, but because everything else had proven insufficient to hold what I was carrying. Consequently, I arrived at God without the protective layer of my own competence, and what I found there was not what I expected. It was more.
The prefrontal cortex had gone offline. My amygdala had opened wide. Into the quiet that followed, God spoke in ways He had not been able to speak into the noise of my sufficient, managing, planning self.
Furthermore, I want to be careful here about what I am saying and what I am not saying. I am not saying the losses were good. I am not saying God caused them to teach me a lesson and I am not saying the babies I did not get to hold were instruments of my formation rather than persons I loved and grieved. What I am saying is that God did not abandon me in the flood – and that what He built in me during those years was something I could not have become without them.
The Covenant Sign and the Two Who Came After
After the three losses, we had two more daughters – our two youngest. They are the covenant sign in our story. Not the replacement for what was lost – nothing and no one is replaced – but the bow God set in the clouds after the flood. Genesis 9:13: “I have set my bow in the clouds, and it shall be a sign of the covenant between me and the earth.” The promise is not that the waters will never come again. The promise is that God will not abandon His people to them.
I can say with conviction – not performance, not toxic positivity, not the kind of faith that has never been tested – that all will be ok. I can say it because I have proof. Not proof that nothing bad will happen. Proof that God is present in the bad when it comes, that He uses it for something real, and that the person who comes out the other side of serious suffering is carrying something the person who never went in could not have.
The neuroscience confirms it. The theology names it. The testimony lives it. And the two youngest daughters, who are here because we kept going through seasons that gave us every reason to stop, are the bow in the clouds that I point to when I need to remember.
What This Means for Your Prayer Life Right Now
If you are in a heavy season – if grief or loss or sustained stress has stripped away the composure you usually bring to prayer – the research and the tradition are both telling you the same thing: you are not further from God right now. You are closer. The neurological conditions that suffering produces are precisely the conditions under which the deepest prayer becomes possible.
Your rawness is not a problem to solve before you come to Him. It is the offering itself. The amygdala wide open, the narrator gone quiet, the prefrontal cortex no longer pretending it can manage this alone – these are not failures of faith. They are the conditions St. John of the Cross described as the beginning of the soul’s deepest work.
You Are in the Formation Process
Furthermore, the post-traumatic growth research tells us that the richer spiritual life that suffering builds does not appear immediately. Growth takes time and moves through the struggle, not around it. Therefore, if you are still in the middle of the flood – if the rainbow is not yet visible – you are in the formation process, not outside of it. The growth is happening even when you cannot see it. Consequently, the question is not whether God is using this. The question is whether you will let Him.
The bow will appear in the clouds. It has before. It will again. And the person who sees it will be someone the storm made capable of understanding what it means.
Reflection Questions
Use these for personal prayer, journaling, or small group discussion.
1. When you have been in seasons of serious suffering, how did your prayer change? Did it become rawer, more honest, more desperate – or did it become more distant? What does the neuroscience suggest about why that happened?
2. The prefrontal cortex is the seat of the brain’s illusion of self-sufficiency. Where in your spiritual life are you still relying on that illusion – and what would it look like to let God dismantle it before suffering forces the issue?
3. The default mode network – the brain’s narrator – goes quiet under serious stress. What does your internal narrator usually say that gets in the way of honest prayer? What happens when it goes silent?
4. Tedeschi and Calhoun identified five domains of post-traumatic growth. Which of those domains – deeper relationships, personal strength, changed priorities, appreciation for life, or richer spiritual life – do you most recognize in yourself after a hard season? Which is still being formed?
5. St. John of the Cross described purgation, illumination, and union. Where are you in that sequence right now? What does it mean that the stage you are in is not the final one?
6. Romans 5:3-5 maps the sequence from affliction to hope. What stage of that sequence are you in – and what would it mean to trust the mechanism even when you cannot yet see the outcome?
7. What is the rainbow in your story – the covenant sign that God was present in the flood and kept His promise? If you cannot see it yet, what would it take to trust that it is coming?
8. God does not waste suffering. Looking back at the hardest seasons of your life, what did they build in you that comfort could not have? What would you say to the person you were in the middle of them?
Citations and Sources
Neuroscience Research
- Shansky RM, Lipps J. “Stress-induced cognitive dysfunction: hormone-neurotransmitter interactions in the prefrontal cortex.” Frontiers in Human Neuroscience, 2013 – PMC
- Arnsten AF. “Stress signalling pathways that impair prefrontal cortex structure and function.” Nature Reviews Neuroscience, 2009 – NIH/PMC
- Brewer JA, et al. “Meditation experience is associated with differences in default mode network activity and connectivity.” PNAS, 2011 – PMC
- Tedeschi RG, Calhoun LG. “Posttraumatic growth: Conceptual foundations and empirical evidence.” Psychological Inquiry, 2004 – PTGI/UNCC
- Tedeschi RG. “The post-traumatic growth approach to psychological trauma.” World Psychiatry, 2023 – PMC
Scripture
- Romans 5:3-5 – Affliction produces endurance, character, and hope – USCCB NABRE
- Psalm 22:1 – My God, my God, why have you forsaken me
- Genesis 9:13 – The rainbow as covenant sign
Catholic Spiritual Theology
- St. John of the Cross, Dark Night of the Soul – New Advent
- Catechism of the Catholic Church, 1508 – On suffering united to Christ’s passion – Vatican
- USCCB – Catholic Teaching on Suffering and Hope – USCCB
Further Reading
- Tedeschi RG, Moore BA. Posttraumatic Growth Workbook (New Harbinger, 2016) – the foundational clinical resource on PTG
- St. John of the Cross, The Ascent of Mount Carmel – companion volume to the Dark Night, covers the active night of the soul
- Fr. Jacques Philippe, Searching for and Maintaining Peace (Alba House) – the most accessible Catholic treatment of interior peace through suffering – Alba House
If this post spoke to you, share it with a woman who is in the middle of the flood right now. She may not be able to see the rainbow yet. But she needs to know it comes.
— M.
