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Affinity Gradient

by Miah O’Malley

AffinityGradient
10.2
Fiction
Oct 1, 2025

Miah O’Malley brings us a story of loss, longing and memory at a molecular level.

Dr. Kar Reul stood at the edge of the grove, boots sinking gently into the softened leaf mold, and hesitated before stepping off the path. The early spring mist clung low to the ground, a gauze of condensation tangled between last year’s ferns and the newly risen shoots of wood sorrel. Beneath it, the soil beneath steamed with waking microbial life.

It had been two years since Ori's burial, and her tree was thriving.

From a distance, it looked unremarkable—a young hornbeam, perhaps four meters tall, its bark a pale gray-green stippled with lichen, its canopy still sparse but symmetrical. The sapling had taken root quickly after the grafting process, its growth fueled by the dense, compost-rich substrate developed specifically for the lignin integration protocol. Kar herself had helped design the variant—fast-growing, regionally appropriate, biologically receptive to human decay. Efficient. Predictable.

And yet…

She crouched beside the base of the tree, brushing aside a mat of damp leaves to expose the shallow roots. They had thickened since her last visit, extending further than expected, curling through the soil with a kind of confidence that struck her as personal–directed growth rather than diffusion. Purposeful, like Ori’s way of moving through the world. She unzipped her pack and retrieved a narrow soil corer, driving it down into the mulch with a practiced hand.

Control first. Curiosity second. That was the rule. Sample before sentiment.

Still crouching, she glanced up into the branches. A small flush of incongruous color caught her attention—one cluster of leaves near the crown had turned an amber hue, months before the tree should even think of senescence. Odd. She’d have to measure the pigment. Maybe a localized nutrient imbalance. Maybe nothing.

She told herself that often these days. Maybe nothing.

Kar extracted the soil core, sealed it in a tube, and slid it into her kit. Then she stood, her knees protesting, and took a slow, deliberate breath. The tree’s scent, subtle at first, unfurled on the air—not just loam and bark, but something more familiar. Beneath the usual forest wetness, she caught a note she hadn’t smelled in a long time: sweetness, like warm paper and citrus peel, the faint trace of Ori’s old hand cream.

She closed her eyes.

No one else would notice. It wasn’t strong. It wasn’t proof. It wasn’t anything.

The scent faded as quickly as it had arrived. Kar stepped back, steadying herself on a boulder half-subsumed by moss, and checked her pulse. Elevated. Her fingers were trembling, so slightly she didn’t notice until she tried to cap her pen and missed.

She recorded the anomaly in her log anyway: 

10:47 a.m.
Ori’s hornbeam shows unexpected amber leaf pigmentation. Slight curvature eastward not present in last survey. VOC profile: unconfirmed, but possible detection of citrus aldehydes. Sample taken.

The wind shifted, and she glanced through the trunks toward the small break in the grove where a bench had once stood—one of those well-meaning additions from the early phase of the project, meant to make the place feel more like a park than a research site. The wood had rotted quickly. Only two corroded screws remained, embedded in a fallen plank now overtaken by moss.

Ori had sat there once, boots muddy, hair wet from drizzle, a thermos tucked under her arm. They'd argued that day over methodology, of all things. Something about microbial inoculants and ethical baselines. Kar had wanted tighter controls. Ori had laughed, accused her of trying to sterilize grief. “It’s not a sterile process,” she’d said, “it’s a return.”

Kar hadn’t responded then. She wished she had.

A buzz sounded near her ear. A solitary bee, chartreuse-striped, hovered for a moment and then settled into a notch in the hornbeam’s bark. Kar watched as it disappeared into the crevice, unhurried.

Not native, she thought. Not tagged.

She made another note:

10:54 a.m.
First observation of nesting bee in hornbeam. Species uncertain. Behavior: exploratory, possibly attracted by VOCs.

The wind changed again. This time, she turned her head sharply toward it, sure she'd heard something—not speech, not even breath, but a kind of creak, a settling groan, as though the trunk had leaned. She squinted upward. The tree stood exactly as before.

Still, she approached. Pressed her palm lightly to the bark.

Its bark was warm.

Kar held there for a long moment, eyes closed. Listening.

Not for words. Not for answers. Perhaps for some kind of acknowledgment.

The bark left a faint imprint on her palm, raised and granular like pressed paper and she wiped it against her jacket; the sensation remained: not stickiness, not heat, but a kind of sympathetic vibration remained. Like the lingering buzz after touching tuned glass.

This wasn’t her first anomalous tree. There had been others—memorials where nutrient uptake deviated from model projections, where unusual root structures suggested faint, chaotic intelligence. But they’d all leveled out by year two. Those trees normalized after the person dissolved, but Ori’s tree was getting stranger.

Kar rounded to the far side, brushing away a veil of low-hanging catkins, and crouched to inspect a new shoot that had emerged there—delicate, too pale, unseasonably young. The leaflets were unfurling with a characteristic spiral, counterclockwise, same as the rest of the tree.

Except the shape was… off. The central leaflet formed a distinct loop before resolving its edges. Not a mutation, not damage. More like a deliberate flourish. It reminded her, absurdly, of Ori’s handwriting. The way she made lowercase "e"s, narrow at the mouth but wide through the body, like an opening breath.

Kar sat back on her heels and stared at the forest floor. A pair of white mushrooms had emerged nearby, tiny and sharp-edged, pushing up through the duff beside one of Ori’s old field tags, a crumpled blue flag half-buried in the humus still fluttering weakly when touched: Plot 32B. Moisture retention anomaly. Midline loam.

Kar had documented it two summers ago and Ori had followed up, kneeling for hours in the dirt, head tilted, brow furrowed as she sketched the pattern the moss had made between two rootlines.

Kar remembered her saying: “Patterns are just memory laid flat. The soil remembers rain.”

At the time, she’d rolled her eyes. But now she wasn't sure that Ori had been wrong.

From her pack, Kar retrieved the microanalyzer and inserted the soil core from earlier. It would take twenty minutes for the full VOC profile to resolve, but the preliminary readout began to hum across the tiny screen:

LIMONENE
LINALOOL
β-CARYOPHYLLENE
Trace: S-(-)-CITRONELLOL

Kar exhaled sharply.

Limonene wasn’t unusual. Citrus notes were common in plant emissions under mild heat stress. Linalool could arise from a dozen sources. But citronellol? In a hornbeam? And in that specific chirality?

That was a molecule Ori’s skin used to emit, faintly—not perfume, but a byproduct of a topical synth she’d used during fieldwork to repel mosquitos. Kar had run the spectra herself when they were calibrating samples in the old lab. Ori’s version had a unique trace signature. It had shown up on her pillowcases.

She stared at the chemical profile a moment longer, resisting the pull of interpretation. This wasn’t unprecedented. Molecules could migrate, after all. She’d once read a study on embryonic cells reassembling themselves after separation, how they found their original neighbors through nothing but surface chemistry. Blind, molecular memory. The idea had struck her then as beautiful. Now it struck her as familiar.

There was no way it should be here.

Kar stood abruptly. Her balance tipped slightly, knees stiff, heart hammering. The bee buzzed out again from its crevice, brushing her arm before lifting into the canopy. She watched it vanish, a green flicker against gray.

There’s an explanation, she told herself.

But not the kind that fit neatly into journals. Not the kind that ended in clear results and three-point conclusions. She would catalog everything. Sample again. Maybe even submit an anonymous note to the original team—enough to flag the case without inviting dissection. But not yet.

Kar turned back toward the tree and stepped close again, this time placing both palms flat to the bark, as if steadying herself on a threshold. She let her forehead rest there too, eyes shut, breath shallow.

“I don’t know what you’re doing,” she whispered. “But I miss you.”

A slight flutter—a single leaf, dislodged from the canopy, drifted down past her shoulder and landed against her boot.

She didn’t move.

The scent reached her a moment later. Not strong, not certain.

But unmistakable.

-

The kettle clicked off with a soft pop, and Kar let it sit for a moment, waiting for the hiss to fade. The cabin was small, just one sparse room and a half-loft, over-warmed by the woodstove she’d lit out of habit more than need. 

Outside, the forest was folding into evening, a deepening gray-green mass broken by shafts of misted gold. The grove wasn’t far—maybe half a kilometer—but here, the trees thinned, and the forest felt quieter, less expectant.

She reached for the ceramic tin near the stove and opened it with care. Inside, tightly curled leaves, dark and fragrant, nested like dried moth wings. She measured a precise teaspoon into the strainer. Ori had given her this tea.

They’d been in the mountains that year, sharing a week of survey work above the snowline. On their final morning, with their boots still damp and the stove barely taking, Ori had poured Kar a cup of this tea without comment. It was sharp at first, piney and bitter, with notes of dried citrus and something almost metallic. Kar had said it tasted like lichen and rain. Ori had grinned and said, “That’s why I brought it.”

She poured the water—85 degrees, no hotter—and let it steep for exactly three minutes. The scent rose slowly: bergamot, rosemary, a trace of burnt orange peel. Something else underneath. Something green, nearly mineral. It always reminded her of waking in a tent with wet hair, Ori humming off-key as she packed up gear.

Now Kar sat at the narrow wooden table and wrapped her fingers around that mug. The analyzer lay open beside her, its screen dimmed, the results still waiting.

The tea was cooling. She drank again, slower this time, letting the flavors bloom on her tongue. She wondered if it still tasted the same to her, or if her memory of the taste had overtaken the actual chemistry. The body remembered things differently than the brain did.

On the shelf above the stove, tucked between two old lab notebooks, was Ori’s bone-handled soil probe. The etching on the side had almost worn smooth. Kar hadn’t used it since the funeral, but she hadn’t put it away either.

She opened her notebook and began to write, not caring about neatness or precision. The words came in fragments, as though her brain were struggling to catch up with the loss, as though each sentence were a step toward something she could no longer grasp.

The trees are starting to feel like home again. Or at least I can pretend they are. But I’m not sure if I should. If I should allow myself to keep believing that the trees are remembering you, that they’re somehow storing your memory. I know it sounds foolish. But I can’t help it. You were always so attuned to the smallest things. You would have noticed the scent first. Not me.

Ori would maybe have joked that the molecules were just trying to find their way home. Kar smiled faintly at the thought, then caught herself. Even proteins folded according to hidden affinities. Maybe it wasn’t so foolish. Pen down, she read what she wrote. It was too soft. She could already hear Ori teasing her: You’d better run controls before you turn your feelings into findings. She added a second line beneath the first, annotating her observation with the same cool precision she’d used in the field.

Outside, the light had gone pewter-blue. The wind had picked up again, bending the tallest firs. The hornbeam was somewhere beyond that bend, the path winding past brambles and vine maples and the half-fallen alder where Ori had once carved a joke in the bark and then covered it with lichen.

Kar didn’t need to check on the tree again tonight.

But she would. Soon.

She washed the mug and left it upside down on the drying rack. The tea leaves she set aside in a small tin. 

That night, she dreamed she was walking through the grove, but something was wrong. The ground yielded, damp like moss, but warmer, as if breath stirred beneath its surface. The trees rose too densely, their trunks nearly shoulder to shoulder, branches interwoven to blot out the sky. The canopy breathed in dim pulses, filtering the air into a dull, leaf-thick green. There were no birds, no insects, not even the familiar creak of the hornbeam swaying in the wind. Only the sound of her own breath and the dry brushing of branches shifting, not from weather, but from her presence. It felt like the grove was adjusting itself around her.

She knew, without decision, where she was going. Ori’s tree stood ahead, impossibly tall, its bark darkened to the color of riverstone, smooth and uninterrupted by lichen or knot. The branches didn’t extend outward like a natural crown; instead, they folded gently inward around a hollow space, a curvature that resembles arms wrapping in an embrace. Something in the shape echoed designs Ori used to sketch absentmindedly: suspended treehouses spiraling around trunks, canopy shelters with soft rope ladders dangling down into the ferns. In the dream, Kar saw them etched into the hornbeam’s bark, delicate architectural lines carved with a fingertip, etched not by tools but by familiarity. The tree, it seemed, had remembered those drawings too.

When Kar stepped closer, the ground changed again. She looked down and saw that the forest floor was no longer made of leaf litter or loam. Instead, it was a carpet of pages—loose, weather-softened, inscribed with Ori’s handwriting. Some were field notes she recognized—scent profiles, root behavior, theories about memory in clusters. Others were unfamiliar half-finished thoughts, words she never heard Ori say aloud. The ink was running in places, letters bleeding into one another, and as Kar bent to lift one page, the fibers dissolved at her touch. But the words remained with her. Do molecules long for their former selves? Do roots remember the shape of the body they fed on?

The air shifted. That scent, Ori’s scent, rose like vapor from the pages and settled into Kar’s skin. It wasn’t imagined. It was exact. The trace of bergamot, rosemary, and something faintly metallic, like the memory of fire cooled to ash. It brought with it an ache Kar had managed to quiet for months. It brought her back to the tent, to field mornings with her hair still wet, to Ori handing her a mug without a word, laughing as she mistook lichen for dried fruit. The weight of that simplicity made her knees go soft.

She looked up.

Ori was there, watching from the dimness between two trees, half in shadow. 

She was younger than Kar remembered—maybe thirty, maybe younger still—wearing the same field jacket with the broken zipper and the old red patch from their first survey together. Her hair was damp. Her arms, folded loosely across her chest in that familiar, amused posture. She was waiting for Kar to say something obvious.

Kar tried. She opened her mouth, but the words caught like dry leaves. She’d wanted to speak to Ori for months, years, but now nothing fit. The silence felt like reverence and failure both.

Ori placed her hand on the hornbeam’s trunk. The bark flexed under her fingers like muscle, shifting subtly, pulling toward her touch. As her hand lifted away, Kar saw that the leaves in the canopy were no longer identical. Each one was shaped uniquely. One resembled the curve of Ori’s ear. Another mimicked the looping line of her handwriting. One was the exact shape of her fingerprint—her left thumb, Kar was certain, the one that always left smudges on field glass.

Ori lifted her hand, gesturing—not pointing, but offering. The gesture was unmistakable: Do you see it now? When her voice finally came, it was quiet like wind filtered through branches. “You always wanted it to be neat.”

Kar tried to respond, to explain that it wasn’t about neatness. It was about containment. About not unraveling. About not letting herself believe in signs that could be coincidence, because once she started seeing meaning everywhere, she feared she would never stop. But the words were gone. They dissolved like ink in rainwater, vanishing before they were shaped.

Ori stepped backward. Her figure blurred, not disappearing but merging into the hornbeam, as if reabsorbed. One leaf, slow and deliberate, detached from the canopy. It drifted downward, spiraling, and Kar watched it fall—not gold, not green, but the precise flecked hazel of Ori’s eyes in sunlight. The leaf came to rest on Kar’s chest and Kar woke, the pressure of the leaf still there, faint and fading, but unmistakable. Her skin tingled with the echo of the sensation. Her eyelids fluttered open, and she blinked into the dim morning light. The dream clung to her, the fragmented images slipping away as she reached for them, like water through her fingers. Ori’s voice, that touch on the hornbeam, the leaf. All of it began to melt into the low warmth of the cabin, the scent of the tea still faint in the air.

The room was too still. Too empty.

She rose slowly, the stiffness of sleep lingering in her joints, and padded over to the small desk near the stove. The surface was cluttered with papers: field notes, personal notes, a half-finished journal entry from months ago. She reached for the nearest notebook, its edges curling. In its center, Ori’s handwriting filled the first few pages. The ink was faded now, some of it nearly illegible. Kar had not looked at these in weeks. Months.

The pain of seeing Ori’s writing was still sharp. But it was a pain she had come to expect.

With a quiet sigh, Kar opened the notebook and began to write. Not for clarity. Not even for memory, but to tether herself to what was still physical. The words came haltingly.

Something happened again at the tree. It dropped a leaf when I spoke. And I dreamed. I don’t think I’ve ever dreamed like that before. Not so vividly. I’m not sure what it means.

She paused. Then added, in smaller handwriting:

What if the body does remember the shape of itself? 

Kar stared at the last sentence. She wanted to cross it out, but she let it stand.

After a while, she made tea again and drank it standing by the window. The forest was awake now. She could hear the wind pressing through the canopy, the branches responding with low, creaking replies. A jay called once, twice, then went silent.

She packed her field kit slowly, methodically. No haste. No intention other than presence. She wasn’t trying to prove anything. Walking to the grove was slow and deliberate, the chill morning air brushing against her face. The path curved like muscle memory beneath her boots. At a certain bend, she reached out instinctively and ran her fingers along a patch of bark she and Ori had once mapped for microlichen. Her hand came away damp.

When she stepped into the grove, the air changed.

It always did, slightly. But this time it felt more like entering a space with its own breath. The trees stood tall, their limbs still. The hornbeam waited.

Kar approached without hesitation. She knelt beside it, laying her gloved hand on the soil, feeling the temperature, the dampness. Then she reached into her kit and withdrew a sterilized trowel, making a shallow incision just to one side of the main trunk.

The roots had moved.

She hadn’t expected it, not like this. They had curved—elegantly, unmistakably—toward the neighboring ash tree. She scraped carefully, widening the view. The feeder roots twisted in delicate arcs, as if reaching for a remembered touch.

Kar sat back and stared.

She repeated the sampling procedure twice. New gloves. Sterile swabs. Separate vials. The pattern in the root architecture still held—curving not at random, but in direct arcs toward neighboring trees. Not chance. Something seeking.

Back at the cabin, she ran the tests. Trace markers. Ori’s amino signature. Not just in her tree. In the ash. In the alder. In the hornbeam roots arcing toward them. She checked controls. Rechecked. The results held. It wasn’t drift. It wasn’t contamination. The spread followed an affinity gradient—matter reorienting toward its prior bonds. Like remembering. Like longing.

Kar returned to the grove three days later, data in hand. The preliminary results had left her sitting silent at the cabin table for over an hour, tea gone cold beside her, the analyzer humming softly like a heartbeat she couldn’t place. She hadn’t been able to stop thinking about it—the molecule, a trace marker Ori’s body had produced in low concentration, something once unique to her skin and saliva. It shouldn’t be there anymore. It shouldn’t be anywhere.

But it was.

In Ori’s tree, yes—expected, even comforting. But also in the roots of the ash tree ten meters away. And the alder just beyond it. Not just once, but in levels too consistent to be drift or lab error. She’d tested controls. Repeated the assay three times. Ori’s molecules were spreading. Not randomly. Not evenly across the grove. They were clustering, moving toward each other.

Kar knelt beside Ori’s hornbeam again, soil sampling tube in one hand, tweezers in the other. She worked carefully, isolating fine root hairs from the leading edge of the system. The hornbeam had extended its network since she’d last mapped it. And it hadn’t grown randomly. Its new feeder roots had curved—delicately, unmistakably—toward the buried remains of another tree’s former companion.

As if the roots remembered each other.

She sat back in the leaf mold, arms resting on her knees, letting the forest settle around her. The data scrolled slowly across the screen of her handheld. She didn’t need to read it again. She knew what it would show. Molecular fragments, biologically inert, yet seeking proximity to where they had once been joined. Molecules that had shared Ori’s body—her blood, her cells, her breath—now migrating through the forest in search of reunion.

It was not metaphor. It was measurable. It was self-assembly on a diffuse, organic scale. The same principle as embryonic cells reorganizing after separation, the same chemistry that let proteins fold into something greater. But this was slower, less direct. 

She stared into the middle distance, where shafts of light threaded down through layered canopy. A pair of birds rustled in the high branches, and for a moment, she imagined one had flown thousands of kilometers with a molecule of Ori tucked inside its muscle, or marrow, or feather. Matter redistributed. Nothing gone. Only elsewhere.

She pulled out her field notebook and wrote slowly, not for publication, not even for posterity. Just for herself.

Ori’s amino signature detected in alder 17C and ash 22A.

Spread non-random. Directional. Possibly chemotactic.

Pattern matches known behavior in protein binding sites.

Memory, not as recollection, but as reorientation.

Attraction between pieces of what was once whole.

-

It was almost evening. Light was slanting low through the grove, catching on the underleaves and sending fractured green shadows across the hornbeam’s bark. Kar stood and walked a slow circle around the tree. The scent in the air was sharper than before—still forest, still loam, but laced with the edge of something she hadn’t smelled since Ori had last leaned across a lab bench beside her, laughing about something Kar had already forgotten.

That night, back at the cabin, she took down an item she hadn’t touched in over a year: the bone-handled soil probe, worn smooth from years of fieldwork. Ori’s initials were still faintly etched along the shaft, barely visible now. She’d used it constantly, flicking it between her fingers when thinking, always insisting it had the right weight.

Kar ran her thumb over the handle and took it with her the next morning to the grove. She buried it shallowly, just beneath the mulch near the hornbeam’s north side. Not as a test, not really. She didn’t expect anything. But something in her needed to make the offering. Not to a god. To a system. To the forest. To the pattern. She marked the spot loosely in her notebook. She didn’t touch it again for weeks. But when she returned, six weeks later, after the rains had passed and the grove was awake in full green light, she brought the scanner. She ran a non-invasive root trace. And she saw it.

The hornbeam had turned.

Its feeder roots, previously straight and downward-seeking, had veered in a low arc, curling toward the buried tool. Not randomly. Not in a widening search pattern. In a direct, unmistakable line.

Kar placed her hand on the trunk, breathed in, and whispered, “I know.”

She stood with the tree a little while longer. Long enough to feel the weight of her own cells warm against the bark. Long enough to believe that some part of her had begun, already, to rejoin the cycle.

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