3 Giving Up Certainty to Embrace Mystery: Affliction

3

Giving Up Certainty to

Embrace Mystery

Affliction

Every good thing given and every perfect gift is from above, coming down from the Father of lights, with whom there is no variation or shifting shadow.

God, who is the source of all good things, is in no way responsible for evil. Evil is not a substance, but a deviation from the good, and it enters human life through the misuse of free will.

WATCHING THE DOCTOR examine my twenty-two-week pregnant wife was torture, and what she said next, death. “Your son’s foot is halfway out of your womb. Which means in all likelihood he will be born tonight—and there’s less than a 10 percent chance he’ll survive. If he does, he’ll be mentally impaired and physically disabled all his life.”

I’ve never felt fright so strong and solid in my body like I did in that hospital room.

Our son Smith wasn’t born that night. My wife fought to carry him for ten more days, giving him as much time as possible to develop and grow.

I’ll never forget watching him slide out of her womb.

He was so little; you could almost hold him in the palm of your hand, which is exactly what I wanted, but the neonatal nurses and doctors hurried him to an incubator to give him the optimal chance to survive.

I couldn’t hold him—we were separated by a piece of plastic and a breathing tube.

Day after day we waited and prayed and cried and forced smiles and hoped and believed and doubted and despaired. Some scenes from that time are unforgettable, like when the doctors and I raced the incubator from the labor and delivery wing of the hospital to the Neonatal Intensive Care Unit. There I was, a first-time father, and all I could feel was fear. I remember passing family members, I remember their faces, the strain in their smiles. I wanted to be strong but all I could manage was a pose.

As the days ticked by, Smith’s lungs got weaker.

Each time they lost strength, the doctors were forced to increase the pressure of his ventilator so he could breathe. On the eleventh day, our doctor pulled my wife and I aside and said, “If we increase the pressure any more his lungs will rupture; if that happens, not only will it be excruciating, but his lungs will fill with blood and he’ll drown. It’s time to let him go.” I’m not sure I can put down on paper the way that felt—the grief, the guilt, the relief, the terror.

We sat down beside his incubator and looked over him, stuck with so many wires and needles, a patchwork of tape and gauze, and a little chest racing up and down desperate for air.

Then the nurse took off every IV, wire, and bandage—everything but the breathing tube—and my wife and I gave him a little bath, gently scrubbing the dried blood and adhesive off his skin.

And then the doctor said it, the thing that we’d been longing to hear from the very beginning—“Would you like to hold him?”

The first time we held our son would be the last.

The nurse placed him in my wife’s arms and we got as close as we could, touching his toes, caressing his head, and kissing him. Then she carefully handed him to me. I remember feeling unsure of how to hold something so fragile. I placed my index finger in his palm, hoping his little fingers would curl around it but his hand was still, gently resting against mine. Then the nurse and I exchanged a silent nod, and with that she slowly pulled the breathing tube from his lungs and vanished behind a curtain.

We were all alone, my wife, myself, and my dying son—finally in my arms.

And I just held him and cried and whispered into his ear, over and over again, “Daddy’s got you . . . it’s okay . . . I’m here now . . . I’ve got you . . . Daddy’s here.”

And, of course, it wasn’t okay. He couldn’t breathe, he was in pain, and he was dying.

It only took a couple of minutes and he was gone.

Dark Days of Purgation

After the funeral, I found myself in dark purgative days, feeling my way through a wilderness I hadn’t known before.

Training with spiritual practices felt like a natural part of purgation, a part I wanted to play, a part I was ready for—this, I wasn’t.

When I was training, I felt like I was plowing the soil of my soul—which was good and right. But I soon discovered that there are transformational depths training can’t reach. Places where old illusions live, undisturbed, waiting for the kind of shattering only affliction can bring.

Yes, walking the purgative path was not just about doing; it was about being undone.

This recognition wasn’t instantaneous, though. It was a slow unraveling, an emptying that happened over time and in ways I didn’t even recognize until much later. If I was going to cross the purgative stage, I had to recognize that it wasn’t just about practicing spiritual disciplines—it was about learning to stay open in the face of affliction and let grace shape me.

All of this understanding began with that one-word question, the question that could hold both pain and promise, the question I found myself repeating after Smith’s death: Why?

Where Was God in My Tragedy?

If God is all-loving, wouldn’t he want to act? If he is all-powerful, wouldn’t he be able to? I wrestled with those questions, trying to understand why God didn’t step in to help Smith survive—why God wouldn’t grant us the grace of a few more days, a little more time for his lungs to grow?

I dug into those questions, reading everything I could, trying to find a way to resolve the tension inside me. Even now, after all my searching, the struggle remains. It’s not just that God didn’t answer our prayers—it’s that his silence felt so hard to reconcile with his goodness.

Why not just answer our prayers?

Did he want Smith to die?

Did he cause it?

“God whispers to us in our pleasures,” I remember reading from C. S. Lewis, “speaks in our conscience, but shouts in our pain: it is His megaphone to rouse a deaf world.”

And then there was this from A. W. Tozer, “If we understand that everything happening to us is to make us more Christlike, it will solve a great deal of anxiety in our lives.”

Quotes like these raised more questions than answers: I remember wanting to know what kind of God I was dealing with. Is he the God that orchestrates every action and decision I make? Is he the secret architect of evil, layering it into our world to teach lessons and grow characters? In other words:

At the time I was recommended books that suggested those very things. As I wrestled through my own struggles, many seemed to imply that suffering was good in itself, a kind of blessing, and that enduring pain without complaint was virtuous. These perspectives confounded me. And so, all at once, I was caught at the meeting of two rushing rivers: The desperate need for answers after a tragedy, and the deep hunger for theological certainty.

I’ll never forget the people who suggested that there was a kind of comfort in Smith’s death, likening it to a puzzle piece in God’s grand design—a picture we couldn’t yet see, but would make sense in time.

Ultimately, I found their logic cold and unconvincing. And yet, for many, such an allure remains. As Sarah Clarkson, a contemporary writer of immense skill, wrote,

We would rather God be neatly culpable for the evil that comes upon us, would rather believe that cancer and infant death and abuse and tornadoes are explainable as necessary to the overarching story of the world, than face the kind of ancient, true drama in which God himself weeps at the sight of what he has made, now defiled and destroyed.

All of this is a topic for a much longer and detailed book. But eventually, I came to agree with Saint John, “God is light, and in him is no darkness at all” (1 John 1:5 ESV).

In other words, I don’t believe that God causes tragedies to transform us.

I do not believe God willed Smith’s death. Instead, I believe it was the result of living in an unpredictable world, with what philosophers call “contingencies” or The Book of Common Prayer calls the “changes and chances” of this life.

I do not believe that God willed what happened to Smith, but I do believe that he was present in it.

How? Who can say?

Surely God was present with my wife—enduring night after night, pumping breast milk for a child she could not hold, hoping each drop would somehow matter. Surely he was present in the gloved hands of the nurses who never left Smith’s side, the singing voices of grandparents keeping vigil over the incubator, and maybe even in my own trembling legs—legs that were not as strong and steady as a son deserves from his father.

I don’t know—maybe that’s where he was.

I guess if I’m honest, I wanted more. I was hoping for rescue. I was hoping for a miracle. God’s unwillingness to save Smith remains a painful mystery for me. I don’t know many people who wouldn’t help a struggling infant if they had the power to do so.

“You arrive at enough certainty to be able to make your way,” Flannery O’Connor once wrote to someone who was experiencing a similar tragedy, “but it is making it in darkness. Don’t expect faith to clear things up for you. It is trust, not certainty . . .”

And maybe that’s where I’ve landed.

I’m learning to let go of my need for certainty, that part of my old transactional mindset that had to explain every tragedy with a clear purpose, as though my spiritual life worked like some kind of equation or formula.

But letting go hasn’t been easy.

I remember liking how certainty felt, how it gave me a sense of control when everything felt chaotic. But the more I let go, the more I’ve found myself drawn into a world of mystery—a kind of wondrous darkness. Not a machine-like universe bound purely by cause and effect, but a deeper, more ancient drama unfolding beneath the surface, as Clarkson suggests. Surprisingly, it hasn’t filled me with fear, but faith. Yes, the more I’ve jettisoned certainty, the more trust has emerged, the more the unknown has invited me to believe—truly believe.

And by believe, I don’t mean agreeing that something is true but trusting that someone will be true.

In other words, my faith has become less about a set of beliefs to agree with, and more about a relationship to count on.

And this, I think, is what purgation is all about; it’s about stripping us of the illusions we live with about God, ourselves, and our world. It’s about pruning, so that trust and love can deepen and strengthen within us. The further I walk this threefold path, the more this keeps happening—the more my old transactional approach to faith keeps crumbling. It’s too juvenile, too black-and-white, too either-or.

Tragedies shouldn’t be rationalized.

They’re just there—raw and unresolved. They’re nothing more than a distortion of God’s good creation, something that was never part of his original intent. He has allowed it, yes, and I don’t know why he doesn’t always intervene. This is what it means to live a mystery, I think. Each time tragedy strikes, we’re simply left with “Why?”

Come to think of it, Jesus had his “why” question too.

The Afflicted God

“My God, my God, why have you forsaken me?” (Mark 15:34, emphasis added).

Yes, I had forgotten about Jesus’ “Why?”

And the more I thought about it, the more I realized that in Christ, God suffered too.

This was hard to see at the beginning. I think it was all of those sanitized storybook Bibles and Sunday school lessons I encountered growing up. What I remember back then, what really registered was the triumph of the cross, the victory of Christ crucified. I was always singing and celebrating it, making colorful paper crosses, decorating them with glitter and glue.

Yet, if I would have been there on that afternoon, with the sun bearing down on my shoulders, I would not have been singing. If I was there on that day, the world I so hoped was coming true would have been smashed. If I was there on that day, I would have seen a man in pieces, weeping, gasping for breath, and asking why.

I only need to substitute Jesus’ body for my wife’s, and the horror comes alive. It was not glorious, it was gruesome. It was not beautiful, it was barbarous. It was not heaven, it was hell.

Could I see the God who suffered?

I needed to.

I needed to see Jesus this way. I needed to feel his mother’s misery. I needed to feel his friend’s terror—when I saw the horror, then, and only then, did I begin to perceive its significance.

God has chosen not to eliminate suffering but to suffer with us.

His submission to suffering, his participation in pain, his embrace of affliction is his way of telling us who he is, who he’s always been, and who he always will be—God with us.

His decision to be with us in affliction is his way of identifying with us. It’s his way of showing solidarity. It’s his way of communicating to us in the most striking and graphic way imaginable: “I am with you.”

“I made this world seed-like,” I can almost hear him saying, “knowing it would crack, but I made it anyway, because I’ve seen the eternal-infinite-forever-end. It is more radiant than a thousand suns, more beautiful than the richest imaginations can conceive. I’ve seen it all—the sprout, the shoot, the tree—and it’s worth it. I can’t explain it to you now. Trust me. Trust me because I entered the cracking-seed myself. I entered affliction. I will not ask you to do anything that I am not also willing to do myself. For I have been sick, I have lost friends, I have died—I know tragedy.”

The Other Side of the Coin

It was a relief to realize that God wasn’t the source of my suffering—but none of this made my pain disappear.

And I still had to wrestle with other kinds of affliction. I still had to encounter its persistent presence in my life, and in the lives of those I loved. And if I had any sense of compassion, I had to face it when it struck others across town or across the world. I couldn’t dismiss it.

Dallas Willard’s “Golden Triangle of Transformation” placed “trials and tribulations” as one of the three essential elements for spiritual transformation.

Clearly, I couldn’t throw affliction out; it’s an essential part of the purgative stage. Just because God didn’t cause it, didn’t mean it was something I could avoid or escape. The saints and spiritual masters knew this well. Their lives were filled with suffering, not because they sought it, but because they recognized that avoiding it was actually a hindrance to love. They understood what I was starting to learn—affliction, when faced honestly, has a strange way of enlarging the heart.

Eventually I recognized that there were two sides of the affliction coin: uninvited and self-inflicted. Sometimes affliction struck unexpectedly, like the death of Smith. And other times, it was rooted in my own misguided choices and illusions, for example:

And maybe that’s what C. S. Lewis was getting at when he said, God “shouts in our pain.” Perhaps what he meant was that when I experience the affliction of my own making, it is God shouting at me, lovingly trying to get my attention, breaking through my illusions, inviting me into deeper experiences of purgation. Yes, God’s love was calling me to see the truth I’d been running from, waking me up to the reality of the destructive path I was on.

“Jon! Slow down. Pay attention. Life’s precious, yours and others. Don’t waste it. Choose love.”

“Jon! Why are you accumulating so much? Stuff won’t fill you up. Only love does. Choose love.”

“Jon! You can’t run from hard things. Love means stepping into them, facing them. You can’t bury your anger. You have to speak it. Choose love.”

Yes, these afflictions were the natural consequences of my own deluded actions, but that didn’t mean I had to face them alone. God was there, always in the midst, using them to guide me deeper into purgation. Again, none of this was about punishment; it was about coming to terms with my own illusions and limitations, my own need for control, and my craving for invulnerability.

But could I really listen? Could I recognize his voice in affliction?

Holding My Hurt

When my children were young and would bruise their shins after crashing their bicycles or scrape their knees after tripping on a slab of sidewalk, they’d huddle into a little ball and place their hands over their wound. I remember how they’d sit still, tears trickling down their cheeks, holding their hurt. What’s interesting was their instinct to draw near to the pain, to hold it, to sit with it.

And maybe that’s the key.

Can I sit with affliction? Can I hold it? Can I stay with it long enough to listen to hear what’s behind it? Just like my kids reached for their wounds, I’m learning to reach for mine—not so much to fix them, but to hear them.

Even when something as small as irritation strikes, I try to pause and sit with the discomfort. Not to search for God’s hand in it—but mine. What’s my role in this? What do I need to own? This sitting often turns into a conversation with Jesus, where he, as he so often does, asks questions:

Why are you irritated, Jon?

Because the car in front of me is barely driving the speed limit.

Why is that annoying you?

Because I’m late to my kid’s basketball practice.

Why are you running late?

Because I wanted to finish reading my book.

Why did you prioritize reading over leaving on time?

Because I was feeling overwhelmed and needed a moment.

Why have you been feeling overwhelmed?

Because I’ve said yes to too many things and haven’t created enough margin.

Why have you overcommitted?

Because I want to meet everyone’s expectations, even if it’s at the expense of my own well-being.

Why do you feel the need to meet everyone’s expectations?

Because deep down, there’s a fear that if I don’t, I’ll let someone down and not just confirm their suspicion, but my own—that I’m not enough.

It’s strange how something as small as getting stuck behind a slow driver can unearth a web of deeper issues. If I can just sit with the pain long enough, if I can let Jesus ask me those probing questions, they eventually reveal the parts of myself that still need healing, that need purifying.

This is where genuine transformation begins.

Layers of Affliction

As I’ve learned to sit and listen to my own affliction, I’ve come to realize that it’s not a one-size-fits-all kind of thing. It has many degrees of intensity, each revealing something different. Just as a bruise differs from a break, affliction presents itself in different depths, each one asking something unique of me.

There are those small, almost laughable irritations; and then the kind of hardship that settles in for a season; and sometimes tragedy strikes. This realization led me to create a more nuanced way of thinking about affliction, eventually dividing it into three layers or degrees—maybe naming them could help me hold them:

Recognizing these degrees of affliction has given me a framework to better understand my experience of purgation and how to respond to it. Because affliction, in and of itself, doesn’t transform us, as Anne Morrow Lindbergh wisely wrote: “I do not believe that sheer suffering teaches. If suffering alone taught, all the world would be wise, since everyone suffers. To suffering must be added mourning, understanding, patience, love, openness and the willingness to remain vulnerable.”

Yes, it’s not tragedy, hardship, or irritation that shapes us; it’s the opportunities they present and the grace that meets us right in the middle of them. Affliction provides an opportunity—not a guarantee—for transformation. By choosing to mourn, to wait, and to stay open, grace finds room to work within us, bringing about the change we long for in ways we could never engineer on our own.

Hate Evil, Trust Good

And now my thoughts return to Smith, lying there surrounded by wires, tubes, and bandages. At the time, I didn’t know what to do with the grief that was quietly growing inside me. I tried ignoring it, I tried staying strong for my wife, not letting my own pain add to hers. But what I didn’t realize then was that true strength doesn’t come from protecting others from my pain, from keeping it together, from hiding it.

Real strength is yielding to the pain and letting it have its way.

Looking back, I see that I held too much in, when perhaps I should’ve followed the words of the psalmist: “Hate evil, you who love the LORD” (Psalm 97:10 NASB). Or as Saint Paul said: “Hate what is evil; cling to what is good” (Romans 12:9 NIV). Or as David Bentley Hart wrote, in his brilliant little book, The Doors of the Sea, after a devastating tsunami:

We are permitted to hate these things [tragedy] with a perfect hatred. And we are not only permitted but required to believe that cosmic time as we know it … is only a shadow of true time, and this world only a shadow of the fuller, richer, more substantial, more glorious creation that God intends; and to believe also that all of nature is a shattered mirror of divine beauty, still full of light, but riven by darkness.

And so, I’ve stopped lying to myself and I just admit it: I hate the death of my son. I don’t look for God’s hand in it—I simply see the evil of it and hate it intensely. I still do. Just as I hate when I read of a drone bomb incinerating a young Middle Eastern family. Or a car smashing into a crowded patio of people. Or a toddler drowning in his swimming pool.

I hate these things. I hate that I live in a world where they are possible. And yes, I hate that God created a world where they are even permissible.

My old mindset would’ve tried to sanitize that previous sentence, hiding my anger from God. But the more I venture into purgation, the more I recognize that that won’t do. Hiding only distances me from the very relationship that has the power to make me whole. The figments I present to God—those cleaned-up versions of myself—aren’t really me. And because they aren’t really me, they can’t be healed. Healing requires substance, not shadows; reality, not a reflection.

The real me—angry, broken, and unfinished—is the very person Christ has come to love and transform.

I remember finally feeling safe to express my hatred; surprisingly, it didn’t lead me astray. It actually led me to something deeper, something more original, something more fundamental within me. For it is only when I expressed my hatred with tragedy that I came to recognize the gravity and greatness of the thing beneath it: Love.

Love was there.

We don’t hate what doesn’t matter to us. We hate when love is threatened, broken, or lost. My hatred didn’t represent the absence of love but its undeniable presence. It pointed to the gravity of what had been violated or taken away, and in a strange way it led me back to the love that was there all along, hidden beneath my hurt.

And so on our journey, if tragedy strikes, we are allowed to hate it, acknowledging it as a pure deprivation of the good—a cavity, a radical distortion of what life was meant to be. We need not look for God’s hand in tragedy. We do not need it in order to become more transformed.

To live this way requires trust, which I realize is so easy to write about and so hard to do.

Do I wish God would have answered my prayers and rescued Smith? Yes.

Why didn’t he intervene? I don’t know.

Did he cause it? No.

Was he present in it? Yes.

How? I don’t really know.

That’s the tension. I’m learning to release certainty and live the mystery of affliction—all while recognizing that suffering and love are bound one to another. I am trusting in God’s ultimate goodness. I am trusting that the last thing is never the worst thing. I am trusting that good is coming to me—a great good is coming to us all—too big for this world to hold, as George MacDonald would often say.

I am trusting that the God of love created a world where tragedy is possible but not final. And that he will one day, to quote Hart again,

strike off the fetters in which creation languishes; and that, rather than showing us how the tears of a small girl suffering in the dark were necessary for the building of the Kingdom [or her transformation], he will instead raise her up and wipe away all tears from her eyes—and there shall be no more death, nor sorrow, nor crying, nor any more pain, for the former things will have passed away, and he that sits upon the throne will say, “Behold, I make all things new.”

In Sum

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