What is Bio-Ontology?

What is bio-ontology? Well, on one level it is pretty straightforward. It is the study of how living systems organize information, how they come to understand themselves, and how they make sense of the worlds they inhabit. On another level, none of that is straightforward. More than 200 theories of consciousness have been proposed.[1] We do not really know how minds come to be. A great deal of work has been done on how neural systems store information, but even that account remains incomplete and contested. The essays on this site investigate different parts of the problem: how living systems evolved awareness and self-awareness; how they acquired the ability to communicate; how communication then changed the systems doing the communicating; and what happens when many such systems live and act together. Each of those questions opens onto some of the deepest mysteries of human experience.

Much of human history—and prehistory—has been occupied by the search for meaning and for our place in the cosmos. That search is a bio-ontological phenomenon: biological organisms organizing experience into a world in which things mean something and in which they themselves have a place. We take that ability for granted because it comes so naturally. But it is an astonishing thing.

The essays in this collection often begin with an ordinary experience and then peel it apart in search of insights into what we are and how we came to be that way. They do not all concern humans. I learned a great deal about the difference between intelligence and civilization by thinking about everyone’s favorite five-legged interstellar rock spider, for example. Elsewhere I look at trade, the way assets acquire value, how language might have arisen, and how knowledge accumulates. These subjects are not instances of one thing, but the essays share at least one commitment: identifying the mechanics beneath the observation. The observation is where the essay begins; the mechanism is what it is looking for.

Some of the essays in this collection respond to ideas about what our future might look like in space and whom we might or might not encounter there. I use principles from economics, psychology, history, anthropology, sociology, and occasionally a little physics to challenge those ideas, see what survives, and ask what they can tell us about ourselves. That has produced several essays involving the Fermi paradox and its adjacent questions.

Consider Rocky. His home world, Erid, has a surface temperature of about 400°F and an atmosphere composed mostly of ammonia. Project Hail Mary gives Rocky a plausible biological, social, and technological biography, making him and his kind a ready-made species against which to test ideas about the emergence of intelligence and material civilization.

Rocky does not have eyes. He perceives his surroundings through sound, including a biological form of echolocation precise enough for him to navigate a spacecraft, operate tools, build machinery, and make sense of a human being whose body must be nearly as peculiar to him as his is to us. By the end of the novel, Rocky is not merely an alien intelligence. He is a person we care about: funny, brave, impatient, technically gifted, occasionally annoying, and intensely loyal. An alien species is an abstraction. Rocky is someone we know.

As I thought about Rocky I started to wonder: what would life be like with echolocation and no vision? Rocky arrives in a Cadillac of a spaceship, so however much the absence of vision handicapped the Eridians, they appear to have worked through it. But on Earth, humans and other creatures benefit enormously from being able to distinguish colors. Being able to distinguish colored regions on a flat surface does a lot more for us than being able to read a clock. Infections are often detectable by color change in the affected tissue. Ripeness of crops can be judged by color. Vision also reveals objects at a distance and gives us some idea how far away they are. Knowing that something exists beyond the reach of touch, smell, or hearing may be more important than measuring the distance precisely. And perhaps most important, vision makes causal sequences visible. In a Paleolithic world, it could reveal that certain clouds mean rain, that others bear lightning, and that lightning ignites fires.

This line of inquiry might help us understand the kinds of sensory systems life can build and what each makes available to the organism possessing it. It might also help us anticipate the kinds of life we should expect to find elsewhere. It would certainly tell us something about ourselves. We might learn that we possess an unusual sensor configuration or we might learn we possess the only sensors capable of supporting the emergence of intelligence.

Vision makes some relations in the world unusually easy to notice. Other senses make other relations available. But noticing something and making it available to another mind are different achievements. For the second problem, Earth supplies plenty of improbable creatures of its own.

From One Mind to Another

YouTube is full of parrots who tease their owners, reprimand household cats, ask for particular things, protest when they do not get them, become demonic when they learn it’s time to visit the veterinarian, and deploy human phrases with comic timing that is difficult to dismiss as random. African grey parrots do not possess human language, but they can produce intelligible speech appropriate to the immediate context. Chaser, a border collie, learned to identify 1,022 objects by name.[2] An orca named Wikie learned to imitate recognizable human speech sounds, although imitation by itself does not establish understanding.[3]

These are different capacities, not scattered pieces of a whale-parrot-dog language waiting to be assembled. Their distribution still sharpens the question: if understanding, imitation, reference, learned signaling, and context-appropriate use are available in other lineages, why did none independently produce open-ended language?

Before a word could be shared, some recurring portion of continuous experience had to be treated as the same thing. A sound, movement, object, individual, relation, or situation had to become sufficiently stable in one organism's represented world that a signal could point toward it. Another organism then had to reconstruct enough of that distinction for the signal to alter its attention or behavior.

The two organisms need not experience the referent identically. Grace and Rocky plainly do not experience one another identically. Communication requires alignment sufficient for use, not the transfer of one private world into another. A signal succeeds when a distinction available to one organism becomes consequential to another.

Something changes when that success can be repeated. A signal that works again may become a convention. A convention learned by participants who were not present at its creation can begin to outlive the original encounter. Later organisms enter a representational environment they did not invent. They inherit not only genes and bodies but names, categories, expectations, and distinctions made available by other minds.

Some researchers have argued that recognizably modern language may extend back to the common ancestor of modern humans and Neanderthals roughly half a million years ago, with implications for Denisovans as well.[4] The evidence is indirect and the claim remains contested. There are no recordings, and the first speaker was inconsiderate enough not to leave notes. But even an incomplete reconstruction might help reveal how speech emerged rather than merely when a completed form appeared.

Once a representation can move among organisms, one mind no longer has to begin where every previous mind began. That makes accumulation possible, but it does not make civilization inevitable.

The Fermi paradox is usually introduced as a problem of arithmetic. The universe contains an extravagant number of stars and planets. If life is not impossibly rare, and if some of that life becomes intelligent and spreads, someone should have become conspicuous by now. Where is everyone?

In 1961, Frank Drake devised an equation to organize the first scientific meeting devoted to SETI.[5] It estimates the number of detectable civilizations in the Milky Way:

N = R^* × f_p × n_e × f_l × f_i × f_c × L

Most of its terms concern stars, planets, life, detectability, and duration. The transition that concerns us is compressed between two of them. f_i is the fraction of life-bearing planets on which intelligence emerges. f_c is the fraction of “civilizations” that develop technology producing detectable signs of their existence. The equation does not separately ask how intelligent organisms become a civilization capable of preserving and combining discoveries across bodies and generations. That transition is bundled into the movement from intelligence to detectable technology.

The compression is understandable. Drake designed the equation as an agenda for SETI, not as a theory of civilization. But it encourages a sequence in which intelligence appears and technological civilization follows without its own explanatory machinery. Earth gives us little reason to treat that passage as automatic.

Sperm whales live in intensely social, culturally differentiated communities. Their patterned clicks, called codas, are learned and vary among vocal clans.[6] Recent work has found contextual and combinatorial structure in their exchanges, while leaving the meanings of most codas unknown.[7] This is not a claim that sperm whales possess a submerged human language. It is enough that they are intelligent, social animals whose lives depend upon learned communication and cultural inheritance. They have still not produced material civilization.

Why should they have? Intelligence is a capacity of organisms. Civilization requires capacities to be assembled across organisms, generations, bodies, materials, and environments. Discoveries must survive their discoverers. Techniques must be teachable or recoverable. Useful changes must be preserved, tested, and combined. A sophisticated culture can remain exquisitely fitted to a form of life without beginning an ascent toward radio telescopes.

The Fermi paradox therefore contains a question prior to galactic silence: what are the prerequisites of civilization? A universe containing many minds need not contain many technological civilizations. Even on Earth, intelligence may be less exceptional than the conjunction that allowed some representations to accumulate outside individual bodies and become tools, procedures, records, structures, and institutions. Civilization, however, does not turn those representations into one shared account of the world.

Agreement Without Agreement

Bitcoin makes this unusually easy to see. Most familiar assets give valuation an anchor outside the stories told about them. A share of stock carries a claim on an enterprise and its possible earnings. A bond promises specified payments. Real estate can be occupied or rented. A commodity may be consumed in production. None of those anchors determines a single correct price, and every market is saturated with stories. But ownership of bitcoin conveys no claim on earnings, cash flows, productive assets, or redemption into something independently valued. The protocol has real properties and imposes real constraints. It does not contain a formula telling us what one bitcoin is worth.

Bitcoin therefore gives us an unusually clear connection between lore and price. The asset has one protocol history and trades through connected markets, yet the communities encountering it may see entirely different things: money, digital gold, political resistance, speculative technology, a treasury reserve, an environmental offense, or a confidence game. Some are openly hostile to one another's description of the object.

Contrast the bitcoin HODLer and the corporate chief financial officer. For the HODLer, refusing to sell can express conviction, identity, resistance, and membership in a community organized around scarcity and endurance. For the CFO, the same asset must earn its right to live in a world of treasury policy, custody, audit, volatility, risk limits, and fiduciary justification. The two need not agree about what Bitcoin is. Their decisions nevertheless meet in the same available supply and market price.

This is not coordination of ideas or values. It is coordination of attention, expectation, valuation, and action through a common object despite disagreement about the object. Each representation makes different behavior sensible. Those actions alter the infrastructure, law, legitimacy, risk, and price surrounding Bitcoin. The changed object becomes the starting point for the next person deciding what it is.

At the collective level, representations do more than describe groups. They help assemble them. A collection of intelligent organisms does not automatically become a coherent agent. Its members possess different information, purposes, loyalties, models, and power. Acting together requires ways to represent relationships: who belongs, who owes what, who may decide, whose account counts as evidence, what constitutes a violation, and who may revise the categories.

Those arrangements can preserve knowledge and enable action beyond the capacity of any member. They also become inherited starting points, making some actions routine, others expensive, and some alternatives difficult even to recognize. They can preserve error, exclusion, and domination as readily as capability. Persistence is not proof of truth or virtue. The same machinery that carries capability across generations can carry injuries no living participant personally chose.

This is why a group cannot simply be treated as a large organism. Collective action is assembled from partial alignments, unequal authority, negotiated expectations, and sometimes coercion. The question is not how a social body acquires one mind. It is how many minds, none fully rational and none seeing the whole, form durable groupings and govern what they have made together.

Why These Questions?

Biological systems organize their worlds around distinctions. This is food. That is not. This is a partner. That is a rival.

When Rocky boards the Hail Mary, he enters a vessel built for a creature that understands its world through vision. Position, trajectory, status, the stars themselves: all of it is offered to eyes. The ship was not built for echolocation. And still Rocky can work with a human being whose senses, body, and world are not his. They do not have to inhabit the same experience. A distinction only has to become stable enough that another creature can act on it.

That is not yet civilization. Sperm whales live in learned, culturally divided communities and still leave no accumulating material record of tools, cities, or telescopes. Intelligence can stay inside a form of life. Civilization begins only when some of those distinctions survive their makers — in words, techniques, objects, and later in ledgers and laws — and become part of the environment the next mind has to enter.

Even then, common objects do not produce common worlds. Bitcoin has one protocol and many incompatible stories about what it is. People who do not agree still meet in the same price. Institutions work the same way. They do not give a group one mind. They make some representations durable enough that later people have to navigate them whether they share the original story or not.

That is the terrain these essays keep walking into. Not because a rock spider, a first word, a silent galaxy, and a market price are the same thing, but because each one shows a different stage of the same problem: how a living system comes to have a world at all, how pieces of that world get out of a single body, and what happens when they do.

Notes

[1] Robert Lawrence Kuhn, “A Landscape of Consciousness: Toward a Taxonomy of Explanations and Implications,” Progress in Biophysics and Molecular Biology 190 (2024): 28–169. Kuhn’s taxonomy organizes approximately 225 scientific, philosophical, metaphysical, and theological theories and explanatory positions. The count is deliberately broad; these are not 225 equally mature neuroscientific models.

[2] John W. Pilley and Alliston K. Reid, “Border Collie Comprehends Object Names as Verbal Referents,” Behavioural Processes 86, no. 2 (2011): 184–195. Across four experiments, Chaser learned and retained the proper-name labels of 1,022 objects and distinguished object names from commands.

[3] Josep Z. Abramson et al., “Imitation of Novel Conspecific and Human Speech Sounds in the Killer Whale (Orcinus orca),” Proceedings of the Royal Society B: Biological Sciences 285, no. 1871 (2018): 20172171. The study demonstrated vocal imitation; it did not establish semantic understanding of the imitated human sounds.

[4] Dan Dediu and Stephen C. Levinson, “On the Antiquity of Language: The Reinterpretation of Neandertal Linguistic Capacities and Its Consequences,” Frontiers in Psychology 4 (2013): 397. Their proposal that recognizably modern language predates the modern-human–Neanderthal split is an inferential and contested position, not a direct archaeological finding.

[5] Seth Shostak, “The Drake Equation,” SETI Institute, updated July 2021. The equation was devised by Frank Drake in 1961 as an organizing agenda for the Green Bank SETI meeting. The SETI Institute defines f_i as the fraction of life-bearing planets on which intelligence emerges and f_c as the fraction of civilizations that develop technology producing detectable signs.

[6] Maurício Cantor et al., “Multilevel Animal Societies Can Emerge from Cultural Transmission,” Nature Communications 6 (2015): 8091. The study combines eighteen years of empirical observation with agent-based modeling to examine the cultural transmission of sperm-whale coda repertoires and the emergence of vocal clans.

[7] Pratyusha Sharma et al., “Contextual and Combinatorial Structure in Sperm Whale Vocalisations,” Nature Communications 15 (2024): 3617. The study identifies context-sensitive and combinatorial structure in codas while emphasizing that the communicative functions of most codas remain unknown.