| 1. Domain | 1.1 Scope of the Domain | Boundaries | The range of phenomena the science includes and excludes. | Studies the history of life on Earth through fossils, including organisms, their environments, evolution, extinction, and biological interactions as preserved in the rock record. Includes body fossils, trace fossils, microfossils, paleoecology, taphonomy, and biostratigraphy. Excludes living organisms except as analogs, and excludes purely geologic processes unless related to fossil preservation or interpretation. |
| | Scale | The spatial, temporal, or organizational level at which the science operates (e.g., quantum, cellular, social, cosmic). | Operates from microscopic structures (pollen, spores, forams) → organismal anatomy → paleoecosystems → global biodiversity patterns → mass extinctions. Timescales from seconds (death/decay) to billions of years (evolutionary history). |
| 1.2 Ontological Commitments | Entities | The kinds of things assumed to exist within the domain (particles, organisms, agents, fields, etc.). | Organisms, fossils, skeletal elements, trace fossils, microfossils, ichnotaxa, communities, ecosystems, extinction events, stratigraphic ranges, taphonomic agents, evolutionary lineages. |
| | Properties | The fundamental attributes these entities possess (mass, charge, genotype, preference, etc.). | Morphology, size, ornamentation, phylogenetic characters, preservational state, chemical composition, isotopic signatures, abundance, diversity, ecological traits, functional attributes, stratigraphic position. |
| | Categories | The basic ontological types used to classify domain elements (substances, processes, relations, structures). | Fossil types (body, trace, chemical), taxonomic groups, taphonomic pathways, depositional environments, biostratigraphic zones, evolutionary clades, functional groups, preservational modes (permineralization, mold/cast, carbonization). |
| 1.3 State-Variables | Variables | The measurable or definable properties that describe system conditions. | Sedimentation rate, burial depth, redox conditions, temperature, pressure, decay rate, biological productivity, fossil abundance, diversity, isotopic ratios, stratigraphic ranges, evolutionary rates. |
| | Parameterization | How variables encode and represent the system’s state. | States encoded by facies data, preservation indices, morphological characters, isotopic signatures (δ¹³C, δ¹⁸O, etc.), diversity curves, phylogenetic metrics, depositional parameters, taphonomic grade. |
| 1.4 Admissible Idealizations | Simplifications | Conceptual reductions used to make the domain tractable (point masses, rational agents, perfect gases). | Treating fossils as complete/unaltered; assuming constant sedimentation; ignoring reworking; modeling organisms as static forms; assuming phylogenetic characters evolve at uniform rates; ignoring ecological complexity. |
| | Validity Conditions | The limits and contexts in which idealizations hold or break down. | Valid under slow sedimentation, low reworking, chemically stable environments, well-preserved fossil assemblages; breaks down in high-energy settings, heavy bioturbation, diagenetic alteration, long hiatuses, or biased fossilization regimes. |
| 1.5 Domain Assumptions | Structural Assumptions | Background ontological stances such as determinism, continuity, randomness, discreteness. | Life leaves material traces; fossils reflect original organisms; evolutionary relationships can be inferred from morphology/chemistry; fossil assemblages record past ecosystems; stratigraphic order reflects relative time. |
| | Implicit Commitments | Unstated but necessary assumptions that shape the field’s conceptual structure. | Assumes preservable features, measurable morphology, reliable stratigraphic context, interpretable taphonomic processes, continuity of evolutionary patterns, and applicability of uniformitarian principles. |
| 1.6 Internal Coherence Requirements | Consistency | The demand that domain concepts do not contradict one another. | Requires agreement among fossil morphology, taphonomic interpretation, sedimentary environment, stratigraphy, phylogeny, geochronology, and evolutionary models. |
| | Compatibility | The requirement that entities, variables, and assumptions fit together into a unified descriptive framework. | Must align with geology, sedimentology, stratigraphy, geochemistry, evolutionary biology, ecology, climate science, and planetary history in a coherent historical-biospheric framework. |
| 2. Evidence Layer | 2.1 Observable Phenomena | Observables | The aspects of the domain that can produce detectable signals accessible to measurement. | Fossil bones, shells, teeth, impressions, trace fossils (tracks, burrows, coprolites), microfossils, mineralized tissues, carbon films, articulated vs disarticulated remains, bedding-plane assemblages, diversity patterns, extinction horizons, biogeographic ranges. |
| | Detection Limits | The boundaries of what can be resolved or sensed by current instruments or methods. | Limited by fossil size, preservation quality, matrix hardness, weathering, incomplete exposures, resolution of microscopes/CT scans, low abundance of rare taxa, diagenetic alteration masking features, and sampling spacing in stratigraphy. |
| 2.2 Measurement Systems | Units | Standardized quantifications (meters, seconds, volts, decibels, dollars, etc.) necessary for consistent comparison. | Size (mm–m), counts/abundance, diversity indices, isotopic ratios (δ¹³C, δ¹⁸O, δ³⁴S), geochemical concentrations (ppm, wt%), stratigraphic thickness (m), age (Ma), sedimentation rate (mm/yr), morphological measurements (mm). |
| | Instruments | Devices and tools (microscopes, spectrometers, sensors, surveys, detectors) used to produce measurements. | Light microscopes, SEM/TEM, CT scanners, 3D laser scanners, microdrills, mass spectrometers (SIMS, TIMS, IRMS), XRF/XRD, thin-section microscopes, stable-isotope analyzers, field tools (GPS, total stations), micro-CT systems. |
| 2.3 Operational Definitions | Definitions | Terms defined by specific measurement procedures, ensuring empirical clarity. | Fossil defined as preserved remains or traces older than a threshold age; species defined by diagnosable morphological characters; biostratigraphic zone defined by index taxa; taphonomic grade defined by preservation features; paleoenvironment defined by facies + fossil assemblage. |
| | Procedures | The explicit steps required to perform a measurement in a reproducible way. | Excavation protocols, fossil preparation, thin-sectioning, CT scanning, morphological measurement, isotopic sampling, microfossil sieving/processing, taphonomic scoring, biostratigraphic logging, mapping fossil occurrences. |
| 2.4 Data Acquisition | Protocols | Formal processes for gathering data under controlled or standardized conditions. | Systematic field sampling, grid excavation, stratigraphic logging, multi-level sampling in cores/outcrops, replicate microfossil samples, repeated isotopic analyses, CT scan stacks, high-resolution photogrammetry. |
| | Sampling | Rules determining which subset of the domain is measured and how representative it is. | Multi-bed sampling, representative facies sampling, fossil census sampling, rarefaction subsampling, multiple individuals per horizon, microfossil splits, spatial transects across environments, vertical stratigraphic spacing. |
| 2.5 Data Character & Format | Data Types | The form raw evidence takes (time series, spectra, images, counts, qualitative records). | Fossil catalog tables, morphological matrices, isotopic datasets, CT volumes, thin-section images, taphonomic scoring tables, species-abundance distributions, diversity curves, biostratigraphic range charts, paleoenvironmental reconstructions. |
| | Resolution | The granularity or precision with which data is captured. | Determined by microscope/CT resolution, sample size, stratigraphic interval spacing, isotopic precision, grain-size effects on microfossil recovery, and temporal resolution of sedimentation versus preservation. |
| 2.6 Reliability & Calibration | Calibration | Adjustment procedures ensuring instruments produce accurate results. | Microscopy calibration, CT density calibration, isotope-standard calibration (IAEA/NBS), XRF/XRD reference materials, measurement-repeatability checks, fossil-ID cross-checking, inter-observer calibration of morphological/taphonomic scoring. |
| | Error Characterization | Identification and quantification of noise, uncertainty, bias, and measurement error. | Misidentification, compaction distortion, diagenetic alteration, sampling bias, time-averaging, reworking, contamination during prep, instrument noise, isotopic fractionation, limited preservation fidelity, incomplete sampling of rare taxa. |
| 3. Structural Layer | 3.1 Patterns & Regularities | Laws / Relations | Stable, repeatable patterns governing how observables behave across conditions. | Evolution follows branching phylogenetic patterns; extinction and origination follow statistical distributions; morphological change constrained by functional/phylogenetic rules; stratigraphic succession follows superposition; fossil preservation follows predictable taphonomic pathways; diversity responds to environmental forcing. |
| | Invariants | Quantities or properties that remain constant under transformations (symmetries, conservation laws). | Consistent morphological traits within taxa, invariant skeletal architectures (e.g., pentadactyl limb), repeated ecosystem structures, predictable fossil successions, conserved phylogenetic signals, stable isotopic fractionation patterns for given physiological types. |
| 3.2 Causal Architecture | Mechanisms | Underlying processes or structures that produce the observed regularities. | Evolution via natural selection, drift, speciation, extinction; taphonomic pathways (decay → burial → mineralization); ecological interactions (predation, competition); environmental drivers (climate, sea level); biogeographic dispersal; diagenetic modification. |
| | Pathways | Organized sequences of interactions forming a causal chain or network. | Organism death → decay → burial → preservation; environmental shift → ecological turnover → speciation/extinction; sedimentation → fossil accumulation → stratigraphic patterning; isotopic incorporation → fossilization → geochemical archive. |
| 3.3 Theoretical Vocabulary | Concepts | Core terms that encode the domain’s structure (force, gene, equilibrium, field). | Morphology, clade, phylogeny, speciation, extinction, adaptive radiation, stasis, punctuated equilibrium, diversity, disparity, biostratigraphy, taphonomy, functional morphology, paleoecology, Lagerstätten. |
| | Classifications | Taxonomies, categories, or typologies that organize entities and relations. | Fossil types (body/trace/chemical), taxonomic hierarchies, taphonomic grades, depositional environments, morphotypes, functional groups, biostratigraphic zones, evolutionary modes (gradualism, punctuated). |
| 3.4 Formal Representations | Equations | Mathematical constructs expressing laws, relations, or mechanisms. | Rates of speciation/extinction; survivorship curves; diversity metrics; isotopic fractionation equations; morphometric PCA equations; logistic or exponential diversification models; stratigraphic range models; phylogenetic distance metrics. |
| | Models | Structured representations—mathematical, computational, or conceptual—used to predict and explain phenomena. | Evolutionary-tree models, morphometric shape models, community-assembly models, macroevolutionary diversification models, taphonomic bias models, fossil-preservation probability models, biostratigraphic correlation models. |
| 3.5 Idealized Structures | Simplified Models | Purposeful abstractions that capture essential dynamics while omitting irrelevant detail. | Perfect fossil record, uniform preservation, constant evolutionary rates, complete sampling, no reworking, simple morphometric variation, linear phylogenetic divergence, homogeneous environments. |
| | Limit Conditions | Regimes where specific models or approximations hold (classical vs. quantum, linear vs. nonlinear). | Break down with incomplete or biased fossil records, strong taphonomic overprinting, rapid environmental change, cryptic species, convergence, diagenetic distortion, highly time-averaged assemblages. |
| 3.6 Integrative Frameworks | Unifying Theories | Higher-order structures that connect disparate laws or mechanisms under a coherent whole. | Integrates evolution, ecology, sedimentology, geochemistry, and taphonomy into a unified framework linking organisms → environments → fossilization → stratigraphic patterns → macroevolutionary trends. |
| | Interdisciplinary Links | Points where the theory connects to adjacent sciences or larger explanatory systems. | Intersects with evolutionary biology, ecology, geology, sedimentology, stratigraphy, climatology, geochemistry, morphology, and planetary paleobiology. |
| 4. Method Layer | 4.1 Inquiry Design | Experimental Design | Structured plans for manipulating variables to test causal claims. | Controlling burial conditions, sedimentation rate, chemical environment, decay rate, and mechanical pressure in taphonomy experiments; varying light, temperature, and abrasion in functional–morphology tests; manipulating environmental variables in analog ecological experiments. |
| | Observational Design | Systematic approaches for gathering non-manipulated data (surveys, field studies, natural experiments). | Systematic field mapping of fossil occurrences, excavation without manipulation, observing natural decay sequences, documenting in-situ fossil assemblages, recording natural biostratinomic processes, and tracking fossil distribution in stratigraphy. |
| 4.2 Testing & Validation | Hypothesis Testing | Procedures for evaluating whether evidence supports or contradicts specific claims. | Comparing predicted phylogenetic relationships, morphological trends, diversity curves, isotopic signatures, and taphonomic pathways with field data, lab experiments, morphometric analyses, and stratigraphic patterns. |
| | Replication | The requirement that results be independently reproducible under similar conditions. | Repeating fossil ID, morphometric measurements, isotopic analyses, CT scans, sediment–fossil association assessments, taphonomic scoring, and biostratigraphic correlations across observers, localities, or analytical runs. |
| 4.3 Inference & Evaluation | Statistical Inference | Rules for drawing conclusions from noisy or incomplete data. | Estimating uncertainties in species abundance, diversity indices, morphometric variables, isotopic ratios, stratigraphic ranges, evolutionary rates, phylogenetic branch lengths, and preservation biases; performing rarefaction and completeness analyses. |
| | Model Comparison | Criteria (fit, simplicity, predictive accuracy, robustness) used to evaluate competing models. | Evaluating competing phylogenetic trees, diversification models, extinction/origination scenarios, morphometric models, preservation-bias models, stratigraphic correlation models, and isotope–environment interpretations. |
| 4.4 Error Management | Error Analysis | Identification and quantification of random and systematic errors. | Identifying misidentifications, sampling bias, taphonomic overprinting, diagenetic isotopic shifts, morphological deformation, time-averaging effects, reworking, analytical contamination, and uncertainty in stratigraphic placement. |
| | Bias Control | Methods for minimizing subjective, instrumental, or procedural biases. | Blinding fossil identifications, standardizing morphometric protocols, cross-checking taxonomy with multiple experts, using replicate samples, correcting for sampling effort, applying completeness metrics, and avoiding selective sampling of “good-looking” fossils. |
| 4.5 Adjudication & Revision | Peer Scrutiny | Collective evaluation of claims through critique, review, and debate. | Independent review of phylogenies, morphometric datasets, taphonomic interpretations, biostratigraphic correlations, diversity metrics, and paleoenvironmental reconstructions across teams or labs. |
| | Theory Revision | Procedures for modifying, replacing, or discarding models based on new evidence. | Updating phylogenies, revising stratigraphic ranges, correcting species assignments, modifying evolutionary-rate models, refining paleoenvironmental interpretations, and incorporating contradictory fossil or isotopic evidence. |
| 4.6 Integrity Conditions | Transparency | Requirements to disclose methods, data, assumptions, and limitations. | Full reporting of collection methods, preparation steps, imaging protocols, stratigraphic placement, analytical calibrations, data exclusions, uncertainty treatment, and assumptions in phylogenetic or morphometric analyses. |
| | Ethical Standards | Norms ensuring responsible conduct in experimentation, data handling, and publication. | Ethical field collection (permits, landowner consent), fossil provenance transparency, responsible curation, honest reporting of uncertainties, avoiding specimen damage, and maintaining integrity in taxonomy, description, and data handling. |