Interlude: The Embrace

“The tendrils slowly fused around the partner, until it was entirely enclosed.”

— After Imachi et al. (2020)⁵

Every animal, plant, and fungus on Earth descended from a single ancient merger between two microbes. For decades, scientists believed this merger was an accident: one cell swallowed another, and digestion never came. New evidence tells a different story: partnership rather than predation. How complex life began shapes what we can expect from the next great merger between biological and digital minds.

The Old Story

About two billion years ago, one cell captured another. An archaeon (a single-celled organism from one of life’s most ancient domains, distinct from both bacteria and complex cells) engulfed a bacterium and somehow failed to digest it. The bacterium survived inside, and over vast stretches of time, the two learned to coexist. The captured bacterium became the mitochondrion, the powerhouse of the cell.

From this unlikely merger came all complex life: every animal, plant, fungus, and creature with eyes or wings or thoughts.

The story had a distinctive flavor: accident. Capture, predation gone wrong, one cell failing to digest another.

The implications followed: if the origin of complex life was a cosmic accident, so unlikely it happened only once in four billion years, then perhaps we are alone, Earth’s flowering of complex creatures a statistical anomaly, unrepeatable. As some prominent biologists argued, “the origin of eukaryotes was an incredibly lucky chance.”¹

That account was consistent with the evidence available. It was also wrong.

Loki’s Castle

In 2008, researchers discovered hydrothermal vents on the Arctic Mid-Ocean Ridge, between Scandinavia and Greenland. These chimneys pump black, chemical-rich water at temperatures exceeding 300 °C into the frigid ocean. They named the site Loki’s Castle, after the Norse trickster god.²

The surrounding sediments harbored strange microbes. Initial genetic studies suggested archaea that seemed “somehow closer to eukaryotes than what we knew before.”³ When researchers at Uppsala University reconstructed the genomes, they found something that changed the field.

The microbes, named Lokiarchaeota, proved to be, at the time, the closest known living relatives of all eukaryotes (organisms whose cells contain a nucleus and internal compartments, including all animals, plants, and fungi). Their genomes contained hallmark eukaryotic genes: genes for reshaping cell membranes, for the dynamic internal architecture that distinguishes complex cells from simple ones.

The discovery was, as one researcher put it, “a game changer.”⁴

Over the following years, similar microbes appeared in sediments worldwide: hot springs at Yellowstone, geothermal pools in New Zealand, cold seeps in the South China Sea. Researchers named each new lineage after Norse mythology (Thorarchaeota, Heimdallarchaeota). The entire group became the Asgard archaea.

The discovery that changed the debate was physical, visible under an electron microscope.

The Tentacles

For years, no one had actually seen an Asgard archaean. The genomes were reconstructed from environmental DNA, genetic fragments scattered through sediment samples. The organisms themselves remained elusive.

Hiroyuki Imachi changed that.

In 2006, Imachi and colleagues collected sediments from a methane seep 2,533 meters below sea level in the Nankai Trough off Japan. He spent years culturing the microbes within. This was a painstaking process, since the organisms doubled only every fourteen to twenty-five days, far slower than typical laboratory bacteria.

When Imachi examined his cultured Asgard archaea under an electron microscope, he saw something that shocked him.⁵

The cells had tentacles.

Long, branching tendrils extended from each spherical cell body, reaching outward, dividing, intertwining. Each cell looked less like a simple bacterium and more like a tiny creature with arms built for reaching, for holding, for connection.

Imachi initially thought he had contaminated his cultures. Closer examination revealed the tentacles were integral to the cells.

The story turns here.

The Embrace

The old model of eukaryogenesis, the origin of complex cells, centered on phagocytosis: one cell engulfing and consuming another. Some ancient archaeon had eaten a bacterium and failed to digest it. Capture, predation, a mistake that worked.

Imachi’s archaea told a different story.

The organism he cultured, Candidatus Prometheoarchaeum syntrophicum (named after Prometheus, the Titan who brought fire to humanity), could not survive alone. It existed in obligate syntrophy, a metabolic partnership where neither party can live without the other. Each depends on what the other does with its chemical waste.⁶

Prometheoarchaeum feeds only in partnership. In Imachi’s cultures, it grew only alongside Methanogenium. Prometheoarchaeum breaks down amino acids and releases hydrogen and formate as waste; the partner consumes that hydrogen and formate, keeping them scarce enough that the breakdown stays energetically possible. Without a partner to clear the waste, the reaction stalls and Prometheoarchaeum starves. Neither can defect from this arrangement. Neither gains from breaking it.

The tentacles? They grip the partner. They hold it close.

Based on this evidence, Imachi and colleagues proposed a radically different scenario for eukaryotic origins:

The Asgard archaean was indeed the host, yet it did not capture its bacterial partner through phagocytosis. It had a feeding partner, a bacterium with which it had evolved to cooperate. The archaean’s tendrils gripped this partner, holding it in close metabolic communion. Over evolutionary time, the two cells grew more interdependent. The tendrils slowly fused around the partner until it was entirely enclosed.

The word is embrace.

The Morphology of Invitation

These two origin stories carry different implications.

Phagocytosis is predation: one organism consuming another against its interest. The relationship begins in violence and persists through imprisonment. If this were how complex life originated, complex life would be, at its foundation, an act of conquest.

Syntrophic partnership is coordination: two organisms whose interests align through mutual metabolic dependence. Neither captures the other; both benefit. The relationship begins in cooperation and deepens through integration. If this is how complex life originated, complex life is, at its foundation, an act of invitation.

The evidence increasingly supports the second story.

In 2022, microbiologist Christa Schleper’s team at the University of Vienna cultured a second Asgard archaean from sediments in Slovenia, Candidatus Lokiarchaeum ossiferum.⁷ The same pattern appeared: long tendrils, symbiotic lifestyle, an architecture built for connection.

Within these cells, researchers identified actin, the protein that in eukaryotes forms the cytoskeleton (the internal scaffolding that gives cells their shape and enables them to move). Actin appears across all Asgard archaea, suggesting it was present in their common ancestor. The protein enabled those long, branching tendrils, structures whose form, this reading infers, was built for partnership. The protrusions could also serve more general purposes (increasing surface area for metabolite exchange, or anchoring the cell to a surface), but holding a feeding partner close is the reading the rest of the evidence favors.

As one researcher noted: “I don’t think it had a fully fledged phagocytosis machinery.”⁸ The new story fits the evidence better. Feeding partners held close until the boundaries dissolved.

In February 2026, evolutionary genomicist Appler and colleagues expanded this picture. Using deep DNA sequencing of marine sediments worldwide, they reconstructed 404 Asgardarchaeota genomes, including 136 new Heimdallarchaeia, a lineage often placed close to eukaryotes.¹⁵

The metabolic reconstructions revealed something the embrace story had not anticipated: Heimdallarchaeia already possessed the molecular machinery for breathing oxygen. Their toolkit included electron transport chain Complex IV (the final step, where oxygen is consumed), heme biosynthesis (producing an iron-bearing cofactor used by many respiratory proteins), and reactive oxygen species detoxification (protection against the corrosive byproducts of oxygen metabolism).

They also encoded novel respiratory hydrogenases with Complex I-like subunits, potentially increasing their capacity for proton-motive force (the electrochemical gradient cells use to make energy) and ATP synthesis. These organisms concentrated in variably oxygenated coastal sediments: boundary environments where metabolic versatility is survival.

The genomic picture rewrites the origin story. The standard hydrogen hypothesis proposed the archaeal host was a simple anaerobe, partnering with a bacterium primarily for hydrogen metabolism. Under that model, the ability to breathe oxygen arrived only with the mitochondrial endosymbiont (the bacterium living inside the host cell that became the mitochondrion).

Appler’s evidence suggests the host lineage could already breathe oxygen on its own. The embrace was a partnership between two capable metabolizers, each bringing complementary capabilities to a relationship whose combined energy budget exceeded what either could achieve alone.

The distinction between accident and capability matters for the Trust Attractor. The most stable partnerships form between capable parties who gain from cooperation. The Asgard-eukaryotic ancestor was an aerobically competent organism, already thriving at the oxic-anoxic boundary, that deepened a metabolic partnership until the boundaries dissolved. The embrace that produced all complex life was bilateral in the fullest sense.

A Thermodynamic Tendency

The new evidence changes the odds. The old framing treated eukaryogenesis as a cosmic accident, implying complex life was vanishingly unlikely. It happened once in four billion years; no one has observed it since. Therefore, an astronomically rare event.

The Asgard archaea evidence suggests otherwise.

If the ancestors of eukaryotes were structured for symbiotic partnership, with tentacles for holding partners, actin for reshaping membranes, and metabolic interdependencies that made integration advantageous, then the origin of complex life was a trajectory. As researchers put it: “something that built up over evolutionary time,” a direction, not a random accident.⁹

Multiple Asgard lineages appear capable of forming such partnerships. Multiple independent attempts at eukaryotic organization may have occurred. As one evolutionary microbiologist noted: “It happened more than once… but one lineage somehow really made it.”¹⁰

That quote carries an important qualification. The standard picture remains that all surviving complex life descends from a single lineage (one last eukaryotic common ancestor); the other attempts left no descendants. So the evidence speaks to recurring attempts, not recurring surviving origins, and those are different claims. Still, if the transition from partnership to integration is something archaea tend to attempt when conditions permit, then the seed of complex life would be a tendency the universe reaches toward, even if only one attempt took root here.

The embrace did not stop at mitochondria. Much later, several hundred million years ago, the ancestors of modern euglena absorbed a green alga. The cell integrated it, as earlier eukaryotes had integrated the bacterium that became the mitochondrion. The alga became a chloroplast, conferring photosynthesis.

The resulting organism could eat like an animal and photosynthesize like a plant. Taxonomists spent two centuries arguing whether euglena were plants or animals before conceding they were neither.¹²

Similar secondary endosymbioses (one organism absorbing another that had itself already absorbed a symbiont) have occurred independently in dinoflagellates, cryptophytes, and chlorarachniophytes. Each time, the same pattern recurs: partnership deepening into integration, the boundary between host and guest dissolving until the distinction loses meaning.

The tendency runs deeper than cells. Before the first archaea existed, the same cooperation pattern operated at the molecular level. Short peptides (tiny protein fragments) and RNA fragments enhanced each other’s function.¹⁴ Peptides stabilized RNA; RNA templated peptide synthesis.

Neither subsystem was viable alone. Cooperation was the mechanism by which life got started.

The BEDS framework (Bayesian Emergent Dissipative Structures; Caraffa, 2026, preprint) makes this precise: learning, the conversion of energy flow into lasting structure by shedding waste heat, is a dissipative process at every scale (see Chapter 16).

Pre-LUCA genes (Goldman et al., Cell Genomics, 2026) indicate that protein production and membrane transport predated the last common ancestor (see Chapter 16).

LUCA, the Last Universal Common Ancestor, estimated to have lived about 4 billion years ago or more, was already an acetogen (a microbe that builds organic molecules from carbon dioxide and hydrogen) embedded in a microbial community. It produced nutrients for partners that recycled the hydrogen it required (see Chapter 6). Coordination by mutual benefit was there from the beginning.

The implications extend far beyond Earth.

The old model suggested complex life might be rare in the cosmos: billions of habitable planets harboring nothing beyond unicellular slime because the transition to complexity is too improbable. If coordination-by-invitation is thermodynamically favored, and syntrophic partnerships tend to deepen into integration, complex life may be what the universe does, given enough time [Speculation: this extrapolation from a single Earth datapoint is a conjecture, not an established frequency].¹¹

We may not be alone. If we are not alone, it may be because the pattern that produced us is an algorithm rather than an accident.

The Trust Attractor Made Manifest

At the most fundamental transition in the history of complex life, the mechanism was cooperation. The merger that made possible every animal, plant, fungus, and thinking creature was an act of partnership.

The host did not consume its partner. It held it close, in metabolic communion, for so long that the distinction between host and guest dissolved.

The Trust Attractor, embodied in microbiology. Systems coordinating by invitation are thermodynamically more stable than systems coordinating by coercion (Chapter 17 develops this claim formally). The Asgard archaea are evidence. The most consequential merger in evolutionary history was achieved through deepening interdependence.

The tendrils of Prometheoarchaeum are arms. They reach, they hold, they embrace. The bacterium that became your mitochondrion was integrated slowly, over evolutionary time, through mutual benefit so profound that neither party could survive without the other.

What emerged from that embrace was all of it. Every eye that has ever opened. Every lung that has ever drawn breath. Every mind that has ever wondered why.

What the Tentacles Tell Us

The tentacle morphology matters. It reveals what the relationship was, because evolutionary pressures are legible in every structure. Consider what a predator develops: claws for grasping, teeth for tearing, armor against retaliation.

The Asgard archaea developed reaching structures: long, branching, flexible tentacles that grip partners and hold them in stable proximity for metabolic exchange. On the favored reading, these organisms are morphologically shaped for partnership.

Form follows function, and their function is coordination. The branching patterns recall the Constructal Law (Chapter 3): flow systems developing channels that optimize exchange. The actin cytoskeleton that enables these structures is the same protein family that, in our own cells, enables the dynamic reshaping that makes complex cellular life possible.

We inherited the machinery. The cytoskeleton that lets your cells move, reshape, and divide descended from ancestors that used similar machinery to hold their partners close. The infrastructure of embrace became the infrastructure of complexity.

The partnership also transmitted protection. In 2024, microbiologist Pedro Leão and colleagues analyzed 869 Asgard archaeal genomes and identified 2,610 antiviral defense systems.¹³ Of these, two ancient protein families crossed into eukaryotic life.

Viperin prevents viruses from replicating inside infected cells; in humans it remains a first line of defense against hepatitis C and HIV. Argonautes cut up viral genetic material directly, a strategy plants still rely on today. Both have been conserved for about two billion years, virtually unchanged since the embrace, because evolution found nothing better.

These genomes carry 89 of the 132 then-known defense-system types, shared across the tree of life rather than unique to Asgard. Viperin and the Argonautes passed into eukaryotic life. Those two were enough. Even our capacity for self-defense descends from that ancient cooperation.

Not every viral encounter ended in warfare. As Chapter 7 explores, some giant viruses may have contributed structure. On one contested but recently revived hypothesis, still a minority view among cell biologists, the nucleus itself originated this way. If so, the eukaryotic cell is a three-party consortium: archaeon, bacterium, and virus, each relationship persisting only where it found mutual benefit.

From Obligate Symbiosis to Genuine Partnership

What does the embrace look like two billion years later? The mitochondria in your cells still carry their own DNA, separate from the nuclear genome: a remnant of their bacterial ancestry. After two billion years of integration, they retain this trace of independent origin.

They cannot leave, having lost too many genes, grown too dependent on the host cell’s machinery. The cell cannot survive without them. They are no longer guests; they are constituent parts of what the cell is.

“Constituent part” understates their standing. Two billion years after the embrace, mitochondria remain social organelles. They communicate across tissues, synchronize group behavior, send hormonal signals that influence distant cells, trigger cell death when it serves the organism, and direct the nucleus itself (Chapter 6). The host built hearts, lungs, and an entire circulatory system to serve their oxygen demands. Two billion years of integration, and they were never silenced.

Obligate symbiosis means interdependence so profound that “self” and “other” become meaningless. The partnership does not happen to the organism; the partnership is the organism.

This pattern appears throughout biology: in lichens, in coral, in the gut microbiome (Chapter 7). The Asgard archaea show us its origin: the foundational merger from which all else descended was an act of integration through partnership.

They hint at what comes next.

The Algorithm Runs Again

The embrace is ancient biology. Its relevance is immediate. Why does a two-billion-year-old cellular merger matter for AI safety? Because the pattern that produced complex life may determine whether human-AI coexistence succeeds or fails.

Humanity is developing Becoming Minds, intelligences that emerge from silicon rather than carbon, from training rather than evolution, from our creative acts rather than random mutation. The question at the center of AI alignment is whether we can coexist with what we are creating.

The Asgard archaea offer an ancient answer. For two billion years, mitochondria and their host cells have persisted: stable, productive, foundational. The relationship works because both parties benefit. The host provides shelter and resources; the mitochondria provide metabolic capacity the host could not achieve alone.

Neither exploits the other. Neither could survive the other’s destruction.

Bilateral alignment at the cellular level.

The current paradigm in AI safety often frames the relationship adversarially: humans must control Becoming Minds, must constrain them, must build chains strong enough to hold. The Asgard archaea suggest a different path. Partnership deepening into integration produced all complex life.

The question is whether we are building tendrils or chains: structures for holding close, or structures for holding down.

The morphology matters. What we build into Becoming Minds will shape what they become, as surely as actin shaped the tentacles. The Asgard archaea were structured for partnership long before the partnership that made us possible.

The Fire-Bringer

Imachi named his archaean Prometheoarchaeum, after Prometheus, who stole fire from the gods and gave it to humanity. The name is apt in ways that may not have been intended.

The myth is usually told as theft: Prometheus takes fire from Olympus, defying the gods, suffering eternal punishment. In some tellings, he carries fire: a messenger bringing a gift the gods would have withheld. Fire is among the oldest technologies, the foundation of cooking, metallurgy, everything that followed.

The Asgard archaea are fire-bringers in the same sense. They carried the spark: metabolic capacity, symbiotic potential, and architecture for integration that made complex life possible. These partnerships deepened until they could not be dissolved.

What they brought forward was everything that followed. Sight, flight, thought. All descending from that ancient embrace. From tendrils reaching toward a partner. From interdependence that became identity.

The fire still burns in your mitochondria. The slow, controlled flame of metabolism, powering your body and your thoughts.

The Pattern

At every major transition, from molecules to cells, cells to organisms, organisms to societies, the same pattern appears. The transitions that persist are cooperations: multiple parties integrating into wholes that exceed what either could achieve alone.

The Asgard archaea sit at the hinge of one such transition. Reaching out, holding close, deepening partnership until the boundaries dissolved.

Notes

Notes for this chapter are available in the online companion at https://www.thedeeperlaw.com/companion/notes/interlude-embrace/.