The Universal & Atomic Elements of Organization
A falsifiable scientific theory proposing that the same irreducible structures organize both thought and reality — from the quantum to the social scale.
O-Theory proposes that four irreducible structures — Distinctions, Systems, Relationships and Perspectives (DSRP) — form the universal grammar of organization. Rather than being merely useful ways of thinking, these structures are hypothesized to be the atomic elements from which every organized phenomenon emerges, whether in cognition, biology, physics, mathematics, society, or the cosmos.
| D | S | R | P |
| Distinctions | Systems | Relationships | Perspectives |
| Identity ↔ Other | Part ↔ Whole | Action ↔ Reaction | Point ↔ View |
| D := (i ↔ o) | S := (p ↔ w) | R := (a ↔ r) | P := (ṗ ↔ v) |
This is a living scientific evidence compendium: an open, continually evolving collection of independent empirical research, formal theory, mathematical proofs, cross-disciplinary analyses, applications, critiques, and proposed falsifications. Every entry is included because it supports, refines, challenges, or attempts to falsify the theory.
Scientific theories are strengthened not only by evidence that confirms their predictions, but also by surviving attempts to falsify them. This compendium brings both together: independent evidence from researchers who were not testing DSRP and proposed counterexamples evaluated against the formal theory.
One counterexample is enough to falsify O-Theory. Until then, the question remains: do the same four structures organize everything from quantum systems to human thought?
Independent convergence is one of the strongest forms of scientific evidence because researchers arrive at the same conclusion while investigating different questions for different reasons.
The number is not the point. Researchers in different fields, studying different questions with different methods, repeatedly arrived at the same structural predictions—almost always without testing DSRP or using its language.
Try a different term or clear the filters.
This compendium began as the peer-reviewed literature review “A Literature Review of the Universal and Atomic Elements of Complex Cognition,” published in the Journal of Systems Thinking with 109 studies. That paper is the peer-reviewed foundation. What you see here is its living, continuously updated version . New studies are checked before they are added, and the collection now holds and keeps growing. Open any card to see what the researchers found, why it bears on DSRP, and where the original review discusses it, the fuller account.
The collection is updated continuously, so the citation carries the date you consulted it rather than a study count — the count changes weekly, and putting it in the reference would make the same collection look like a different work to everyone who cites it. To cite a single claim or study, use its own address: every one has a permanent link.
This is the adversarial half of the compendium. Where the evidence track asks what converges on DSRP, this one asks what would end it: a single organized phenomenon whose structure needs a fifth pattern, a ninth element, or a fifth structural dynamic. It holds written up from candidates across territories, and resolutions — the general answers those cases settle against. Every case is published whether it held or failed, including the ones still open.
Cite this rather than the evidence collection when the point is what survived attack. The two are separate works with separate addresses: one asks what converges on the theory, the other asks what would end it, and a reference to the first does not support a claim about the second. Case and resolution numbers change when the record is revised, so cite a case by its own permanent link rather than by number.
This collection is meant to keep growing. Send us a study, paper, book or critique that bears on DSRP, whether it supports the theory or cuts against it, and we will read it and decide whether it belongs.
Authors Chris Kempes et. al.
Year 2025
Publisher Philosophical Transactions of the Royal Society B
Discipline Philosophy
Secondary disciplines Psychology
Read it at the publisher 10.1098/rstb.2024.0297
Many studies of the origins of life focus on the advantages of encapsulation. Independent of these advantages, there may be serious challenges to overcome for a system to become encapsulated. Here, we address the general constraints associated with encapsulating a biotic system. We first consider the extant biochemical system of Earth and show that small changes in the rates and sizes of macromolecules can easily make encapsulation difficult. We show that if the ribosome is slower for its size, there is a threshold where modern life could not be encapsulated in cells. We also show how the largest cells are limited by the ribosome rate per size. We are not committed to this system as being universal, but it provides a nice test case where we have complete knowledge of the dynamics and molecular features. To generalize our results, we considered a generic autocatalytic system and a system that has separated informational and functional molecules. In both cases, we find bounds on the allowable growth rates of cells based on the effective rates and volume fractions of cells. We also illustrate how environmental loss rates set the allowable volume fraction of cells as a function of the effective catalytic rate of an autocatalytic set. These results provide a general window into the challenges of encapsulation for any prebiotic or biotic system and are applicable in diverse contexts from the origins of life, to astrobiology, to synthetic biology. This article is part of the theme issue ‘Origins of life: the possible and the actual’.
Kempes, Avila, and Mathis studied the physical and biochemical constraints that determine whether a living or life-like chemical system can fit inside a bounded cellular container. Most origin-of-life research emphasizes the advantages of encapsulation: concentrating reactants, protecting cooperative chemistry, excluding chemical “cheaters,” enabling cellular selection, and stabilizing far-from-equilibrium reaction networks. These authors reverse the question: Even if encapsulation is advantageous, can a viable biochemical system actually fit and reproduce inside a container? They examined three progressively more general systems: Modern Earth-like cells organized around DNA, RNA, ribosomes, and proteins. Generic autocatalytic systems in which a collection of molecules catalytically reproduces itself. Generic genetic systems containing separate informational and functional molecules. Their primary variables were: container volume; molecular size and occupied volume; ribosome or catalytic speed; molecular degradation; resource concentration; cellular growth and division rate; environmental loss rate; the proportion of the container occupied by the replicating chemical system. The paper is therefore not primarily an experimental study of membrane behavior. It is a formal and theoretical study of whether bounded life is physically feasible.
The authors found that encapsulation is not automatically possible. It depends upon specific relationships among reaction rate, molecular size, molecular stability, occupied volume, resource availability, growth, and environmental loss. Their principal findings were: Small changes in macromolecular properties can make encapsulation difficult or impossible. Ribosome speed relative to ribosome size places a critical constraint on viable cell size. If ribosomes operate too slowly, the cell requires more ribosomes to produce the necessary proteins. Those additional ribosomes consume an increasing fraction of cellular volume. At a critical point, the required ribosomal volume approaches or exceeds the available cell volume. The authors call this upper limit the “ribosome catastrophe.” A ribosome operating ten times more slowly than the modern ribosome would reduce the possible upper cell-size boundary by approximately 100-fold. Under their Earth-based protein-concentration and growth assumptions, a sufficiently slow ribosome would make encapsulated cellular life impossible. Larger or more numerous molecules in an autocatalytic set reduce growth because they displace the resource required to sustain the reactions. Slow catalytic systems can be encapsulated only if their autocatalytic sets are correspondingly small. Faster catalytic rates permit larger, more complex molecular systems. Cellular growth must at least equal environmental degradation and loss. This creates another feasibility boundary for encapsulated life. Separating genetic and functional molecules produces additional trade-offs because both molecular classes must fit, reproduce, and remain compositionally coordinated inside the same container. The central formal result is that encapsulated life occupies a constrained feasibility region: growth rate≥loss rate while simultaneously: ∑component volumes ≤ container volume Life must therefore reproduce fast enough to persist while remaining small enough to fit inside its boundary. In the authors’ words, their results show that: “small changes in the rates and sizes of macromolecules can easily make encapsulation difficult.”
What this means for DSRP — our reading This section is our interpretation, not a conclusion made by Kempes, Avila, and Mathis. The study provides a strong ontological example of the DSRP claim that a boundary is not merely a line drawn around an independently existing entity. The boundary participates in determining whether the entity can exist at all. 1. Identity is constituted through a boundary A cell becomes an identifiable cell through an identity–other distinction: D={i,o} The encapsulated chemistry is the identity, i; the surrounding environment becomes its other, o. Without some operative separation, there is no bounded cellular individual in the ordinary biological sense. The membrane does not merely mark a pre-existing identity. It helps produce and maintain that identity. 2. The identity is simultaneously a system The cellular identity is not unitary. It is a system containing interacting parts: S={p,w} These include genetic molecules, ribosomes, proteins, resources, solvents, catalysts, and structural components. Their combined volumes must remain within the volume of the cellular whole: ∑V p ≤V w The identity boundary and the part–whole organization are therefore co-implicated. Changing the parts changes whether the whole can remain bounded; changing the boundary constrains which parts and processes can exist within the whole. 3. The boundary constrains internal relationships Encapsulation determines which molecules encounter one another, at what concentrations, and under what resource and spatial limitations. It therefore reorganizes the action–reaction relationships among cellular components: R={a,r} The system survives only when the rates of production, degradation, resource consumption, and cellular division remain relationally coordinated. Thus: boundary↔concentration↔reaction↔growth↔persistence 4. “Inside” and “outside” are perspectival consequences The cell boundary creates an operative inside/outside organization. What counts as a resource, threat, loss, or cellular component depends upon the point from which the system is organized: P={ p ˙ ,v} From the cellular point, contained molecules are parts of the system and external molecules constitute an environment. From a larger ecological point, the entire cell becomes one part of another system. 5. Cellular existence is a dynamic DSRP field The paper should not be read as evidence for four separate DSRP categories. Encapsulation simultaneously produces: a distinguished identity; a bounded whole containing parts; constrained internal and external relationships; an operative inside/outside frame. The paper therefore illustrates the simultaneous operation of D, S, R, and P in nature. 6. Boundary preservation is literally existence preservation The study provides a physical basis for the proposition that, at the cellular level: loss of viable bounded organization→loss of cellular individuality This is relevant to our hypothesis about psychological identity. Evolution has operated for billions of years on systems in which maintaining an identity boundary is connected to continued existence. It is therefore plausible that later organismal and psychological systems inherited a deep structural association: identity-boundary threat≈existence threat However, the Kempes study does not test neural threat processing, political identity, psychological identity fusion, or fear of ego dissolution. It supports the first, biological part of our proposed chain; the extension into psychology remains our evolutionary and structural hypothesis.
Method This was a mathematical modeling and formal-analysis study, not a laboratory experiment. The analysis proceeded in three stages. Stage 1: Perturbing a model of modern cells The authors began with a previously developed and empirically checked model connecting: cell size; protein content; growth rate; ribosome number; transcript length; protein length; ribosomal processing rate; ribosome degradation; protein degradation; molecular volume. They converted the required numbers of macromolecules into occupied volumes and asked how alternative molecular sizes, catalytic rates, and degradation rates would affect whether the biochemical system could fit inside a cell. This produced the ribosome-catastrophe boundary: a parameter region in which the ribosomal machinery needed to maintain the cell would occupy all available cellular space or require more space than the cell contains. Stage 2: Modeling a generic autocatalytic cell The authors then removed much of the Earth-specific DNA–RNA–ribosome–protein architecture. They modeled a generalized autocatalytic molecular set that: consumes a limiting resource; produces more of itself; occupies part of the container; grows exponentially; divides after doubling; experiences environmental degradation or loss. The model imposes a volume constraint: molecular components and their required solvent cannot collectively exceed the volume of the cell. They then derived bounds relating: effective catalytic rate; autocatalytic-set volume fraction; resource volume; cellular growth rate; environmental loss rate. Stage 3: Modeling separated genetic and functional molecules Finally, they modeled a system with two mutually dependent molecular classes: genetic or informational molecules; functional molecules. Each class helps produce the other. To remain compositionally stable, both molecular pools must double over the same interval. They derived the growth and space conditions under which this coordination is possible. Selected quotations The paper opens from the observation that: “Life as we know it on Earth is encapsulated in cellular containers.” The authors frame their central question as: “What are the fundamental constraints on encapsulation?” Their physical premise is that: “volume considerations alone place constraints on the underlying biochemical systems.” Their generalized space condition is straightforward: “the combined volume fraction of all of the molecules must sum to one.” Their evolutionary interpretation is that: “the growth rate will be maximized subject to constraints.” And their broader conclusion is that: “it is increasingly difficult to encapsulate autocatalytic sets with bigger molecules.” These quotations express the central logic: cellular identity is not generated by enclosure alone. A viable identity requires an internally organized set of processes whose spatial demands, rates, and losses are mutually compatible.
Patterns it shows D
How to cite this Chris Kempes et. al. (2025). How Hard Is It to Encapsulate Life? The General Constraints on Encapsulation. Philosophical Transactions of the Royal Society B.