The Architecture of Agony

How Games Make 'Stones Within' Compelling and What Scientists Can Learn

I cut open a kidney stone under the microscope and immediately reached for my pearls.

The rings were unmistakable similar. Perfect concentric bands radiating from a central nucleus, each layer distinct, each boundary sharp. The kind of precise geometric growth that makes you stop and stare because your brain recognizes pattern even before it understands what it’s seeing.

I pulled out stromatolite thin sections next—3.5-billion-year-old fossils, some of Earth’s earliest evidence of life. Same pattern. Same patient layering. Same chemical response to gradients creating structure over time.

Here’s what struck me: I was looking at kidney stone, pearl, and ancient bacterial reef under the same magnification, and I genuinely could not tell which was which without checking my labels.

The process happening inside a human kidney isn’t fundamentally different from what happens in an oyster, in ancient oceans, or even in cave systems across our planet. We’re all part of the same natural processes, using the same chemical principles that have built structures for billions of years.

Nature creates strikingly similar layered patterns across completely different systems. Whether built by daily cycles, tides, seasons, or disease processes, these structures grow in rings that record each episode of mineral deposition—like tree rings made of crystals. The layered appearance follows the same basic rules of how crystals form and grow in water, regardless of what's driving the process: bacteria, living organisms, or mineral-rich body fluids. These patterns show how similar physical limitations—like how fast materials can move through water—create nearly identical structures whether they form over hours, years, or millennia, and whether they're microscopic or hand-sized. Kidney stone, horse pearl, stromatolite.

Then I started noticing something stranger: video games have been telling stories about internal crystallization for decades. They just disguised them as alien plagues, magical curses, and divine transformations. And hundreds of millions of people find these stories compelling enough to spend thousands of hours engaging with them.

“Why do people enthusiastically explore geological processes in games but show little interest in the actual geology happening in their own bodies?”

The $200 Billion Question

Before we go further, let me explain why a mineralogist and museum curator is spending time analyzing video games.

The numbers tell a stark story:

• Video games: $200+ billion industry

• Active players worldwide: Hundreds of millions

• University geology programs: Declining enrollment

• Mineralogy courses: Shrinking numbers

Here’s what strikes me: games are FULL of geology. Crystals, minerals, stone formation, geological processes—they’re everywhere. Players spend hundreds of hours mining, collecting gems, understanding mineral properties, exploring cave systems. They’re deeply engaged with geological concepts.

Meanwhile, we struggle to get students into geology programs.

I want to understand why. Why are video games so successful at drawing people in and keeping them interested in geological concepts, while the actual scientific processes they’re emulating struggle to attract students?

This isn’t about “games are better than science.” It’s about learning from a medium that’s clearly doing something right. What narratives are they using? How do they make minerals feel important? Why does game geology resonate when real geology doesn’t?

And here’s the deeper question I keep coming back to: Is real life just too difficult or depressing to want to know more about? When you can explore crystallization in a fantasy world where it means divine transformation, why would you want to know about the kidney stone forming in your actual body?

This article explores one specific pattern: internal crystallization—the formation of layered mineral structures inside biological systems. I’ve catalogued 41+ games that explore this concept, from literal kidney stones in medical simulators to metaphorical crystallization that transforms entire worlds.

Nature’s Favorite Building Method

At the Natural History Museum of Los Angeles County, I’m investigating how bacteria contribute to calcium oxalate kidney stone formation using high-resolution imaging. The research aims to understand these microbiological factors for developing prevention strategies and improving patient outcomes.

What I found under the microscope was surprisingly beautiful: layer-by-layer crystallization around a nucleus, responding to chemical gradients, building outward from a center, creating perfectly banded structures.

This isn’t unique to kidney stones. It’s a pattern that appears across nature:

Stromatolites, formed 3.5 billion years ago by photosynthetic bacteria building limestone reefs, layer by layer. These bacterial communities precipitated calcium carbonate in response to their environment, creating structures that eventually helped change Earth’s atmosphere, making it breathable for complex life.

Pearls, created when oysters secrete nacre (layers of aragonite) around an irritant. The mollusk responds to a foreign particle by coating it, layer by layer, in lustrous mineral deposits.

Kidney stones, where the kidney precipitates calcium oxalate in response to chemical supersaturation. Same layer-by-layer technique, same response to chemical gradients, same concentric banding.

You see this pattern in cave formations, tree rings, agates, and geodes. It’s one of nature’s most elegant solutions—a self-organizing response to chemical conditions that creates stable, layered structures.

High-resolution microscopy image of kidney stone cross-section showing concentric banding. Each band represents a chemical response—the same technique that built Earth’s earliest reefs 3.5 billion years ago.

Here’s the question I started asking: Can you tell which is which? If I show you a cross-section of a kidney stone, a pearl, and a stromatolite under the microscope, most people cannot distinguish them. The structures are remarkably similar.

Same process. Same layer-by-layer crystallization. Same chemical response.

What changes is the story we tell about it. The location where it happens. The meaning we assign.

Stromatolites are scientific wonders—”Earth’s memory,” evidence of early life. Pearls are precious, romantic, symbols of beauty from irritation. Kidney stones are medical problems, sources of pain, things to be removed and discarded.

But the process? Nearly identical albeit different chemistry.

Games Know Something About Internal Crystallization

Once I started looking, I found this pattern everywhere in games. Not just as background detail—as central metaphors, game mechanics, and narrative drivers.

Let me start with the literal examples, then move to the metaphorical.

The Medical Reality

Some games actually include kidney stones directly. The Binding of Isaac lets you shoot kidney stones as tears. SULFUR, a gritty action-adventure game, includes kidney stones as items you find in sewers—biological waste hardened into something you can pick up. Medical simulation games like Surgeon Simulator and Two Point Hospital include kidney stone procedures.

Genshin Impact, surprisingly, has the main character (the Traveler) explicitly discuss kidney stone formation in voice lines, complete with scientific accuracy. This confirms that the protagonist has traveled to worlds where modern urology exists. The Witcher 3 includes medical texts that mention “calculi”—the Latin term for stones—describing the “unbearable humors” and “grit of the kidneys” that plague commoners in a medieval fantasy world.

These aren’t central to gameplay, but they show something important: even in fantasy and sci-fi contexts, game designers recognize kidney stones as a real biological phenomenon worth including.

The Horror Metaphor

But where games really explore internal crystallization is through metaphor. They instinctively understand that crystals growing inside bodies = existential horror.

Arknights features “Oripathy,” where black crystals progressively grow in organs, blood, and eventually erupt from the skin. It’s described as causing “terminal sharp chronic pain” and is literally called “Magic Rock Cancer” by the community. Those infected face discrimination. The game captures something visceral about internal crystallization: the slow, inevitable transformation, the loss of bodily autonomy, the sharp geometric forms invading soft tissue.

Command & Conquer‘s Tiberium is an alien crystal that doesn’t just poison—it leeches minerals from your body and replaces your organic chemistry with rigid crystalline structures. Your tissues literally become jagged green mineral deposits.

BioShock Infinite made this unforgettable with its Vigors—superpowers that visibly transform your flesh. Shock Jockey causes electricity-conducting crystals to burst from under your skin. Bucking Bronco shows bloody cracks forming as flesh drops off in petrified clumps. Return to Sender peels away skin to reveal finger bones coated in black metallic substance. The game’s cut content included “Vigor Junkies”—enemies with crystals growing from their skulls due to excessive use. The message is clear: power costs your flesh.

Darkest Dungeon features a crystalline curse where blue jagged crystals erupt from your skin. Heroes clutch their sides in sharp stabbing discomfort, progressively becoming “shards” of their former selves.

Sea of Thieves has the Gold Hoarder’s Curse, where gold and gems literally replace your organs and bones. Players describe the “heavy, cold internal hardening”—greed consuming you from within.

Blasphemous presents The Miracle, a religious manifestation where glass, thorns, and gold grow from characters’ midsections and chests. Internal guilt becomes physical crystal growth—penance made visible as geometric agony.

The pattern across all these games: sharp, geometric forms in soft tissue. Slow, inevitable transformation. Something beautiful (crystals! gold!) becoming horrifying through location. Loss of bodily autonomy. The chronic, stabbing sensation.

Divine Transformation

Final Fantasy XIII centers its entire plot on crystallization as divine curse. The l’Cie are branded by gods and given a “Focus”—a mission they must complete. Success means crystal stasis: you become a beautiful crystal statue, preserved in eternal sleep. Failure means Cie’th transformation: your body mutates into a monstrous crystal-flesh hybrid, losing all humanity to wander mindlessly forever.

Your brand progresses like a ticking clock. Emotional trauma accelerates the transformation. Both outcomes are crystallization—neither is really winning. The game understands that even “reward” crystallization traps you.

Sekiro: Shadows Die Twice has something even more striking: the Shelter Stone, described explicitly as a “stone found in the womb of a bride,” formed through years of drinking Sacred Water. It’s a calcified mass—a direct reference to lithopedions (stone babies) or bladder stones—transformed into a holy relic required to reach the Divine Realm. Function becomes myth: calcification becomes sacred.

Corruption and Crystallization

Dragon Age: Inquisition‘s Red Lyrium is more explicitly crystalline—a corrupted, living mineral. When consumed or stabbed into the body, it begins growing through living tissue. Victims describe a sharp burning sensation as the crystal “sings” inside them, progressively turning them into statues from within.

Hollow Knight‘s Infection manifests as orange crystalline growths spreading like plague. Miners continue mining crystals even after infection overtakes them. The forgotten deity’s revenge appears as literal crystallization consuming the kingdom.

Sci-Fi Abstraction

Games take this further in science fiction contexts.

Dead Space‘s Necromorphs feature skeletal systems reshaped by Marker signals so bone shards erupt through palms as calcified blades. It’s kidney stones as cosmic horror weapons.

Deus Ex‘s Gray Death involves failed nano-augmentation where self-replicating nanites multiply uncontrollably. Victims describe “agonizing internal stiffness” as biological systems are replaced by rigid microscopic machines—the gray goo scenario as internal calcification.

Control shows bodies reorganized by The Hiss into brutalist geometric shapes—”loss of soft biology to hard mathematical logic.” Floating corpses sprout jagged crystalline clusters.

Top Left: Arknights Oripathy crystals. Top Right: Final Fantasy XIII crystal stasis. Bottom Left: Sekiro Shelter Stone item. Bottom Right: BioShock Infinite Vigor transformation. Games instinctively treat internal crystallization as profound transformation.

Why Does This Disturb Us?

After cataloguing 41+ examples, I started asking: why does internal crystallization appear so consistently as horror, transformation, and profound change?

The False Boundary

We’ve created an artificial division: minerals are “geology,” bodies are “biology.” But crystallization doesn’t respect these categories. The same chemical processes occur everywhere—in caves, in organs, in oysters, in ancient oceans.

The discomfort comes from our categories, not from the process itself. Nature doesn’t distinguish between “inside” and “outside”—we do.

Games like Control and BioShock Infinite make this explicit by showing the transformation visually. Crystals bursting from skin, geometric structures replacing curves—these violate our imposed categories. We expect bodies to be organic, soft, warm. Crystals are geometric, hard, cold. But bodies make geometry all the time. We make bone, we precipitate minerals, we form crystal structures.

The juxtaposition only creates wrongness because we expect separation.

The Control Factor

There’s another layer: we choose to collect minerals, wear them, display them. We don’t choose when our bodies make them. This loss of agency appears consistently in games. In Final Fantasy XIII, your brand progresses regardless of your wishes. In Arknights, Oripathy is terminal. In Warframe, given enough time, you become fossil.

Games understand that internal crystallization represents loss of control over your own chemistry. The Overlord series includes a torture device designed by someone who had kidney stones—they modeled it specifically to replicate that pain, complete with 5mm spikes. Everyone who’s had kidney stones instinctively recognizes it as a weapon.

The Hidden Frequency

Here’s what makes this especially interesting: internal crystallization isn’t rare.

Kidney stones affect approximately 1 in 10 people. Gallstones affect 10-15% of adults. Dental calculus (tartar) affects nearly everyone. Atherosclerotic plaques—arterial calcification—become increasingly common with age. Lithopedions (calcified fetuses) are rare but documented.

We’re all participating in these natural processes. Games tap into something universal: the visceral understanding that mineral formation can happen inside us, and it’s simultaneously natural, painful, and profound.

The Deep Metaphors

Some games take internal crystallization beyond direct body horror into landscape-scale metaphor.

Dear Esther features a narrator whose letters include feverish descriptions of an island’s caves. Community theory, backed by dialogue clues, suggests he suffers from syphilis and recurring kidney stones. His cave descriptions blur the line between geological formations and his internal structure—stalactites become his stones. His body becomes the landscape. Physical pain transforms his perception of the entire world.

Pathologic 2 is even more explicit. This medical horror game has a surgeon protagonist who sees the plague-ridden town as a diseased body. The town itself is described as “a jagged, hard, unyielding thing inside the body of the steppe”—something that needs to be “cut out” like an internal obstruction. The entire town is a kidney stone in the landscape’s body.

Star Wars lore includes Krayt Dragon Pearls—giant pearls formed inside the dragon’s body through high-pressure formation and creature suffering. These internal deposits become lightsaber crystals, sources of immense power. Pain stone becomes power source—the folklore transformation complete.

The Loot Economy

Games also treat internal stones as treasure.

Bezoars—stones formed in animal digestive systems—appear across multiple games. Historically, people believed these cured poisons (the Persian word “pâdzahr” means antidote). Diablo 3, Terraria, Kingdom Come: Deliverance, and RLCraft all include bezoars dropped from monsters that grant poison immunity. The Elder Scrolls features bezoars from rare animals used to create poison cures.

Monster Hunter builds entire progression systems around harvesting internal monster gems. Rathalos Rubies, Wyvern Gems, Firecell Stones—these rare internal deposits make monsters more valuable. You’re literally farming creatures for their kidney stones, gallstones, and internal calcifications.

The pattern mirrors historical beliefs: painful internal stones must be valuable and magical. Games perpetuate this folklore cycle while making it central to gameplay.

The Escapism Question: Why Game Geology Instead of Real Geology?

But here’s where it gets psychologically interesting. We have a choice:

Option A: Learn about the actual crystallization happening in your body right now. Your arterial walls calcifying. Your kidneys potentially forming stones. The minerals precipitating in your teeth. Real processes, real chemistry, real consequences for your health and aging.

Option B: Play a game where crystallization means you’re gaining magical powers, or being cursed by gods, or transforming into something mythic.

Hundreds of millions of people choose Option B.

Why?

Is Reality Too Difficult?

Real internal crystallization comes with uncomfortable truths:

• You can’t fully control it

• It’s associated with pain, aging, disease

• It reminds you of mortality

• The solutions are often medical: procedures, lifestyle changes, medication

• There’s no “winning”—just management

Game crystallization comes with dramatic stakes:

• You’re the hero of the story

• You can defeat it, control it, or be transformed by it heroically

• It’s connected to power, destiny, transformation

• There are clear win conditions

• Even “tragic” crystallization (Final Fantasy XIII) feels mythic, not mundane

Real geology is happening to you whether you want it or not. Game geology is something you choose to engage with, and it makes you feel powerful even when your character is threatened.

Is Reality Too Depressing?

There’s something profoundly depressing about the medical framing of internal crystallization. Kidney stones are “nephrolithiasis”—a condition to prevent, treat, manage. Arterial calcification is cardiovascular disease. Gallstones require surgery.

“Medical framing says: your body is doing something wrong. Games say: your body is doing something profound.”

When you learn about kidney stones in a medical context, you’re learning about pain, procedures, prevention. When you encounter crystallization in Sekiro, you’re learning about sacred stones in wombs that unlock divine realms. Same chemical process, completely different emotional register.

Which would you rather think about?

The Narrative Protection

Here’s what games provide that real geology doesn’t: narrative distance.

When Tiberium consumes bodies in Command & Conquer, you’re not the one being consumed—you’re watching it happen, or fighting against it, or managing its spread. When crystals erupt from Arknights characters, you’re sympathizing with them, but it’s happening to someone else.

When it’s your actual kidney forming an actual stone, there’s no distance. It’s happening TO YOU, and the narrative is: “This is painful, expensive to treat, and might happen again.”

Games let you explore the horror and fascination of internal crystallization without actually experiencing it. They provide the psychological safety of fiction while still engaging with the profound weirdness of bodies making minerals.

But Here’s What We’re Missing

The real process is MORE interesting than the game versions.

Your body IS doing something profound. It’s using 3.5-billion-year-old chemical techniques. The same processes that built early life, that create precious gems, that form cave systems. You’re not separate from planetary geology—you’re participating in it.

“The real process is MORE interesting than the game versions. We’ve just communicated it so poorly that people would rather engage with metaphorical crystallization in games than learn about actual crystallization in their bodies.”

That’s not because reality is boring. It’s because we’ve made reality FEEL boring, clinical, and depressing. We’ve stripped the wonder out of it and left only the medical management.

Games prove that people WILL engage with complex geological concepts. They’ll spend thousands of hours thinking about mineralization, crystallization, and the boundary between organic and inorganic. They just need it framed in a way that feels meaningful, not merely medical.

Natural Processes Connect Everything

Here’s what this research revealed: games instinctively understand that internal crystallization is profound. They’ve been exploring it through metaphor for decades—treating it as curse, disease, divine punishment, alien invasion, and cosmic transformation.

What they’re actually exploring is our discomfort with recognizing continuity. The processes in kidneys aren’t separate from the processes that built early life or create gems.

Look at the pattern again:

Stromatolites: Bacterial biofilm precipitating calcium carbonate—natural process responding to chemical gradients over time.

Pearls: Mollusk secreting nacre around irritant—natural process responding to chemical gradients over time.

Kidney stones: Kidney precipitating minerals in response to supersaturation—natural process responding to chemical gradients over time.

Same physics. Same layered structure. Different narrative.

Games understand something medicine sometimes forgets: these processes feel mythic and transformative because they ARE. There’s something profound about recognizing these connections, about understanding that the boundary between “life” and “mineral” is more permeable than we think.

Sekiro got it right: these natural processes CAN be sacred.

What Are We Doing Wrong?

When stromatolites did this 3.5 billion years ago, they changed Earth’s atmosphere. Layer by layer, bacterial communities built structures that made the planet breathable—using the same chemical principles.

When an oyster does this, we call it precious and pay thousands of dollars—same chemistry, different context.

When a human kidney does this, we have medical interventions—same layer-by-layer crystallization, different narrative.

There isn’t much difference between what’s happening in your body and what’s happening elsewhere on our planet, or even our solar system. Crystallization occurs in Martian caves, in Earth’s deep oceans, in living tissues, in ancient reefs.

But here’s the uncomfortable question: if these connections are so profound, why don’t more people want to know about the actual world they live in?

The Communication Gap

Here’s what I want to be clear about: geology has excellent pedagogy. It’s a mature science with strong teaching methods. The problem isn’t what happens in classrooms once students arrive.

The problem is that most people never arrive at all.

By the time someone walks into a geology classroom, they’re already interested. The challenge is reaching everyone else—the hundreds of millions of people who play games with geological content but would never think to take a geology course, read a geology article, or visit a natural history museum’s mineral hall.

That’s a science communication problem, not a teaching problem.

Where We Lose People

Think about how geology appears in public discourse—news, radio, video, social media, popular culture:

Geology appears when things go wrong: Earthquakes. Volcanic eruptions. Landslides. Floods. We’re the disaster science in the public imagination.

Geology appears as scenery: Beautiful landscapes, national parks, pretty rocks. Aesthetic but passive. Something to look at, not participate in.

Geology appears as ancient history: Dinosaurs (which aren’t even geology), deep time too vast to grasp, things that happened millions of years ago to rocks far away.

What geology rarely appears as: Something happening in you, to you, around you, right now.

Games do something different. They don’t wait for you to be interested in geology—they make geology relevant to what you’re already doing. Surviving. Building. Exploring. Fighting. Transforming.

What Games Do That We Don’t

Games put geology in contexts people already care about:

Identity: Arknights and BioShock Infinite make crystallization about who you are and who you’re becoming. Your body changing. Your choices about transformation.

Power: Monster Hunter and bezoar-harvesting games make minerals the source of advancement. You need these stones to get stronger, build better equipment, progress.

Survival: Hollow Knight and Elden Ring make geological processes environmental threats you must navigate. The Infection spreading. The Scarlet Rot consuming landscapes.

Transformation: Final Fantasy XIII and Warframe make mineralization about fundamental change—divine curse or evolutionary endpoint.

Horror: Dead Space and Command & Conquer make internal crystallization viscerally disturbing. Your bones becoming weapons. Your flesh becoming Tiberium.

Meanwhile, our science communication says: “Geologists discover new mineral.” “Study finds ancient rocks reveal climate history.” “National Park features stunning geological formations.”

All true. All important. All... distant.

The Narrative Problem

Games understand something crucial: The facts are only interesting when they connect to something that matters to your audience.

A game doesn’t say “Learn about layer-by-layer precipitation.” It says “You’re slowly turning to crystal and you have limited time to complete your mission before the transformation is permanent. What do you do?”

The player learns about crystallization through caring about the character. The geological process becomes meaningful because it has stakes.

Our science communication rarely creates those stakes for general audiences. We present geology as:

• Things that happened long ago

• Processes occurring far away

• Phenomena studied by specialists

• Knowledge valuable for its own sake

Games present geology as:

• Happening NOW

• Affecting YOU

• Mattering to YOUR goals

• Connected to everything else you care about

The Boundary Problem

Here’s something games do unapologetically that we shy away from: They cross the boundary between organic and inorganic constantly.

Tiberium in your blood. Crystals growing from your organs. Your skeleton reshaped into weapons. Gold replacing your bones. Divine stones forming in wombs.

Games embrace the discomfort of bodies doing geology. They don’t apologize for it. They explore it, make it central, force you to grapple with it.

Our science communication tends to keep biology over here, geology over there. We talk about minerals in rocks, not minerals in bodies. We discuss crystal formation in caves, not crystal formation in kidneys.

When we do discuss body mineralization, it’s usually medical—kidney stones as pathology, arterial calcification as disease, dental calculus as hygiene problem. We don’t connect it to the broader pattern. We don’t say “your body is using the same precipitation technique as ancient stromatolites.”

That connection feels weird, uncomfortable, boundary-crossing. So we don’t make it.

Games make it. And hundreds of millions of people find it compelling.

What We Could Do Differently

I’m not suggesting geology news should become horror stories. But we could:

Make it relatable. These aren't just ancient geological curiosities—mineralization is an active process in living systems. Bone formation, tooth enamel development, and kidney stone formation all follow these same fundamental crystallization principles. Understanding these patterns helps us recognize the deep connections between Earth's history and human physiology.

Cross boundaries unapologetically. Stop keeping “life” and “minerals” in separate boxes. Show the connections. Make people uncomfortable with how blurry that line actually is.

Create stakes. Not disaster stakes, but personal stakes. “This process affects how you age. This chemistry determines what you can eat. This mineralization shapes your options.”

Connect to what people already care about. Games don’t make you care about geology first—they make you care about survival, power, identity, then show you geology matters to those things. We could do that with health, technology, food, energy.

Use narrative. Games prove people will engage with complex geological concepts if they’re embedded in stories with stakes. Science communication can tell stories too.

The Real Question

Why doesn’t everyone want to know more about the actual world they live in?

Maybe because we’ve made that world feel distant, academic, and separate from their lives. We present geology as something specialists study, not something everyone participates in.

Games make geology feel immediate, personal, and consequential. They show—not tell—that mineralogy matters to survival, identity, and power.

They’re doing science communication, whether they intend to or not. And they’re doing it successfully for audiences we struggle to reach.

What This Research Shows

Games have found ways to make internal crystallization compelling to hundreds of millions of people. They make kidney stones into alien invasions, divine transformations, and cosmic horror because they recognize—correctly—that there’s something profound about bodies participating in planetary chemistry.

They don’t apologize for crossing boundaries. They don’t isolate geology from life. They don’t present mineralogy as something distant and academic.

They make it matter.

As I look at my kidney stone microscopy images, with their perfect concentric rings identical to pearls and stromatolites, I keep thinking: the process is beautiful. The process is ancient. The process connects everything.

We know this. We study this. We teach this in classrooms.

But are we communicating it to the people who never make it to those classrooms? The people playing games with rich geological content who don’t realize the real world is even more interesting?

That’s the challenge. That’s what games are showing us is possible.

We just need to learn from their success.