| 1. Domain | 1.1 Scope of the Domain | Boundaries | The range of phenomena the science includes and excludes. | Studies the physical and chemical processes used to separate components of mixtures based on their differing properties; excludes identity-only analysis (qualitative) or pure quantification without separation. |
| | Scale | The spatial, temporal, or organizational level at which the science operates (e.g., quantum, cellular, social, cosmic). | Operates from molecular-level interactions (partition coefficients, diffusion, adsorption) to macroscopic flow systems (chromatography columns, membranes, electrophoresis, bulk extraction). |
| 1.2 Ontological Commitments | Entities | The kinds of things assumed to exist within the domain (particles, organisms, agents, fields, etc.). | Analytes, mobile phases, stationary phases, ions, molecules, solvent systems, membranes, sorbents, charged species, micelles, droplets, gels, interfaces, matrix components. |
| | Properties | The fundamental attributes these entities possess (mass, charge, genotype, preference, etc.). | Polarity, charge, hydrophobicity/hydrophilicity, size, mass, diffusion coefficients, partition coefficients (K), electrophoretic mobility, affinity, volatility, adsorption strength. |
| | Categories | The basic ontological types used to classify domain elements (substances, processes, relations, structures). | Chromatography (GC, LC, IC), electrophoresis, extraction (liquid–liquid, solid–liquid), distillation, filtration, dialysis, precipitation, membrane separations, sorption-based methods. |
| 1.3 State-Variables | Variables | The measurable or definable properties that describe system conditions. | Flow rate, temperature, pressure, voltage, mobile-phase composition, pH, ionic strength, stationary-phase characteristics, viscosity, analyte concentration, retention time. |
| | Parameterization | How variables encode and represent the system’s state. | States encoded via retention factors (k), selectivity (α), resolution (Rs), partition coefficients (K), electrophoretic mobility (µep), plate numbers (N), diffusion constants, adsorption isotherms. |
| 1.4 Admissible Idealizations | Simplifications | Conceptual reductions used to make the domain tractable (point masses, rational agents, perfect gases). | Ideal plug flow, perfectly uniform stationary phase, equilibrium partitioning, no band broadening, no matrix interference, ideal laminar flow, constant temperature/pressure, negligible adsorption hysteresis. |
| | Validity Conditions | The limits and contexts in which idealizations hold or break down. | Valid under optimized method conditions and clean matrices; break down in overloaded columns, complex sample matrices, turbulent flow regimes, strong adsorption, non-ideal diffusion, temperature variability. |
| 1.5 Domain Assumptions | Structural Assumptions | Background ontological stances such as determinism, continuity, randomness, discreteness. | Differences in analyte physical/chemical properties reliably produce separations; partitioning and transport behavior are predictable; retention mechanisms are consistent across similar systems. |
| | Implicit Commitments | Unstated but necessary assumptions that shape the field’s conceptual structure. | Assumes reproducible stationary/mobile-phase behavior, stable analyte chemistry, meaningful plate theory descriptions, predictable retention mechanisms, and negligible uncontrolled interactions. |
| 1.6 Internal Coherence Requirements | Consistency | The demand that domain concepts do not contradict one another. | Requires consistency among retention times, chromatographic parameters (k, α, Rs), electrophoretic behavior, thermodynamic/kinetic models, and physical transport theory. |
| | Compatibility | The requirement that entities, variables, and assumptions fit together into a unified descriptive framework. | Demands alignment between thermodynamics (partitioning), kinetics (mass transfer), instrument physics (flow/voltage), and analyte–matrix interactions within a unified separation framework. |
| 2. Evidence Layer | 2.1 Observable Phenomena | Observables | The aspects of the domain that can produce detectable signals accessible to measurement. | Retention times, migration times, peak shapes, peak widths, peak asymmetry, solvent front movement, band broadening, color zones, conductance changes, pH shifts, membrane permeation rates, extraction layer formation. |
| | Detection Limits | The boundaries of what can be resolved or sensed by current instruments or methods. | Limited by detector sensitivity, baseline noise, column/membrane overloading, co-elution, low analyte abundance, matrix interferences, weak partitioning, diffusion limits, and small mobility differences. |
| 2.2 Measurement Systems | Units | Standardized quantifications (meters, seconds, volts, decibels, dollars, etc.) necessary for consistent comparison. | Time (min, s), voltage (V), current (A), flow rate (mL/min), pressure (bar/psi), wavelength (nm), conductivity (S/m), mass-to-charge (m/z), partition coefficients (dimensionless), viscosity (cP). |
| | Instruments | Devices and tools (microscopes, spectrometers, sensors, surveys, detectors) used to produce measurements. | HPLC/UPLC systems, GC systems, IC systems, CE (capillary electrophoresis), TLC plates, solid-phase extraction rigs, mass spectrometers, UV–Vis detectors, fluorescence detectors, refractive-index detectors, membrane setups. |
| 2.3 Operational Definitions | Definitions | Terms defined by specific measurement procedures, ensuring empirical clarity. | Retention factor (k), selectivity (α), resolution (Rs), plate number (N), capacity factor, electrophoretic mobility (µep), breakthrough volume, extraction efficiency, membrane flux. |
| | Procedures | The explicit steps required to perform a measurement in a reproducible way. | Sample injection, column equilibration, gradient programming, voltage application (CE), extraction workflows, membrane conditioning, washing/elution sequences, standardized detection protocols. |
| 2.4 Data Acquisition | Protocols | Formal processes for gathering data under controlled or standardized conditions. | Multi-run chromatographic sequences, time-series electrophoretic scans, extraction time curves, fraction collection, repeated detector scans, gradient ramps, multi-wavelength monitoring, internal standard tracking. |
| | Sampling | Rules determining which subset of the domain is measured and how representative it is. | Triplicate injections, replicate extractions, cross-matrix sampling, multi-fraction collection, repeated elutions, subsampling for heterogeneity, randomization of sample order, multi-point gradient sampling. |
| 2.5 Data Character & Format | Data Types | The form raw evidence takes (time series, spectra, images, counts, qualitative records). | Chromatograms, electropherograms, extraction curves, membrane flux graphs, peak-integration tables, retention/migration-time datasets, multi-wavelength spectral traces, fraction profiles. |
| | Resolution | The granularity or precision with which data is captured. | Determined by detector sensitivity, column efficiency (N), electrophoretic field strength, instrument dead volume, gradient-program precision, membrane pore uniformity, and baseline noise. |
| 2.6 Reliability & Calibration | Calibration | Adjustment procedures ensuring instruments produce accurate results. | Retention-time referencing, flow-rate calibration, pressure-sensor calibration, mass-axis calibration (MS detectors), wavelength referencing, membrane-flux calibration, voltage and current verification. |
| | Error Characterization | Identification and quantification of noise, uncertainty, bias, and measurement error. | Identifying co-elution, peak overlap, injection-volume error, sample carryover, matrix-induced retention shifts, gradient inaccuracies, diffusion-induced band broadening, membrane clogging, and detector drift. |
| 3. Structural Layer | 3.1 Patterns & Regularities | Laws / Relations | Stable, repeatable patterns governing how observables behave across conditions. | Partitioning laws (Nernst distribution), chromatographic retention relationships (k, α), Van Deemter equation trends, electrophoretic mobility laws, adsorption isotherms, membrane-flux laws, distillation vapor–liquid equilibria. |
| | Invariants | Quantities or properties that remain constant under transformations (symmetries, conservation laws). | Conserved selectivity (α) under constant conditions, invariant elution order in given separation modes, reproducible mobility hierarchy, constant phase-equilibrium relationships for defined systems, consistent peak-capacity behavior. |
| 3.2 Causal Architecture | Mechanisms | Underlying processes or structures that produce the observed regularities. | Mass transfer between phases, adsorption/desorption, diffusion, ion migration in electric fields, convection, solvent–analyte interactions, chemical complexation in separations, mechanical sieving. |
| | Pathways | Organized sequences of interactions forming a causal chain or network. | Stepwise migration through stationary/mobile phases, gradient-elution pathways, selective binding–release cycles, extraction partitioning sequences, electrophoretic zone formation, membrane permeation sequences. |
| 3.3 Theoretical Vocabulary | Concepts | Core terms that encode the domain’s structure (force, gene, equilibrium, field). | Partition coefficient (K), retention factor (k), selectivity (α), resolution (Rs), plate number (N), Van Deemter parameters (A, B, C terms), dead volume, stationary/mobile phase, electrophoretic mobility, adsorption isotherm (Langmuir/Freundlich), breakthrough volume. |
| | Classifications | Taxonomies, categories, or typologies that organize entities and relations. | Chromatographic modes (normal-phase, reverse-phase, ion-exchange, size-exclusion, affinity), electrophoresis types (capillary, gel, micellar), extraction classes (liquid–liquid, solid-phase), membrane separations (ultra/micro/nanofiltration), distillation classes (simple, fractional, azeotropic). |
| 3.4 Formal Representations | Equations | Mathematical constructs expressing laws, relations, or mechanisms. | Van Deemter equation, Nernst partition law, Rs equation, k and α definitions, electrophoretic mobility equation, adsorption isotherm equations, mass-transfer equations, membrane-flux J = (ΔP – Δπ)/R. |
| | Models | Structured representations—mathematical, computational, or conceptual—used to predict and explain phenomena. | Plate theory, rate theory, diffusion–convection models, adsorption models (Langmuir, Freundlich), electrophoretic migration models, membrane-transport models, chromatographic peak-shape models. |
| 3.5 Idealized Structures | Simplified Models | Purposeful abstractions that capture essential dynamics while omitting irrelevant detail. | Perfectly uniform stationary phase, ideal plug flow, no band broadening, uniform pore size, instantaneous partitioning equilibrium, purely laminar flow, no matrix effects, ideal reversible adsorption. |
| | Limit Conditions | Regimes where specific models or approximations hold (classical vs. quantum, linear vs. nonlinear). | Break down with overloaded columns, non-ideal packing, strong adsorption hysteresis, turbulent flow, complex or dirty matrices, temperature instability, molecular interactions altering retention/mobility, or polymeric membrane fouling. |
| 3.6 Integrative Frameworks | Unifying Theories | Higher-order structures that connect disparate laws or mechanisms under a coherent whole. | Integration of thermodynamics (partitioning), kinetics (mass transfer), fluid dynamics (flow), and electrostatics (migration) into unified separation models; chromatographic, electrophoretic, and extraction sciences connected by transport and equilibrium theory. |
| | Interdisciplinary Links | Points where the theory connects to adjacent sciences or larger explanatory systems. | Connects to chemical engineering, materials science (membranes, sorbents), environmental science (remediation), biochemistry (affinity separations), pharmacology (purification), and nanoscience (selective transport). |
| 4. Method Layer | 4.1 Inquiry Design | Experimental Design | Structured plans for manipulating variables to test causal claims. | Controlling mobile-phase composition, flow rate, voltage (CE), temperature, pressure, stationary-phase chemistry, gradient profiles, injection volume, and sample prep to test separation efficiency and selectivity. |
| | Observational Design | Systematic approaches for gathering non-manipulated data (surveys, field studies, natural experiments). | Monitoring spontaneous drift in retention/migration times, peak broadening, solvent-front behavior, membrane fouling, column-aging effects, and natural matrix-induced shifts without deliberate intervention. |
| 4.2 Testing & Validation | Hypothesis Testing | Procedures for evaluating whether evidence supports or contradicts specific claims. | Comparing predicted retention, selectivity, resolution, migration order, and extraction efficiency with observed chromatograms/electropherograms/extraction curves to confirm or reject mechanism-based expectations. |
| | Replication | The requirement that results be independently reproducible under similar conditions. | Performing replicate injections, duplicate extractions, repeated gradient runs, multi-batch column testing, repeated membrane-flux measurements, and multi-lab reproducibility checks. |
| 4.3 Inference & Evaluation | Statistical Inference | Rules for drawing conclusions from noisy or incomplete data. | Determining retention factors, selectivity ratios, resolution values, theoretical plate numbers, migration-order confidence, extraction efficiencies, and uncertainty in separation performance metrics. |
| | Model Comparison | Criteria (fit, simplicity, predictive accuracy, robustness) used to evaluate competing models. | Evaluating plate theory vs rate theory models, competing retention/mobility mechanisms, adsorption models, membrane transport models, and computational predictions vs experimental retention behavior. |
| 4.4 Error Management | Error Analysis | Identification and quantification of random and systematic errors. | Identifying co-elution, peak tailing, column overloading, band broadening, sample carryover, baseline drift, matrix suppression/enhancement, membrane clogging, gradient inaccuracy, and injection-volume error. |
| | Bias Control | Methods for minimizing subjective, instrumental, or procedural biases. | Randomizing injection order, using blanks and standards, verifying column conditioning, applying internal standards, maintaining constant temperature/pressure, washing steps, and blinding chromatogram interpretation when needed. |
| 4.5 Adjudication & Revision | Peer Scrutiny | Collective evaluation of claims through critique, review, and debate. | Independent evaluation of retention assignments, peak-integration accuracy, mechanism claims, efficiency/resolution calculations, membrane performance data, and suspected method artifacts. |
| | Theory Revision | Procedures for modifying, replacing, or discarding models based on new evidence. | Updating retention mechanisms, revising mass-transfer models, adjusting gradient/voltage strategies, modifying extraction workflows, and recalibrating plate/efficiency models in response to new evidence. |
| 4.6 Integrity Conditions | Transparency | Requirements to disclose methods, data, assumptions, and limitations. | Full disclosure of column/membrane specifications, mobile-phase recipes, gradient programs, instrument settings, sample-prep protocols, calibration procedures, and all data-processing assumptions. |
| | Ethical Standards | Norms ensuring responsible conduct in experimentation, data handling, and publication. | Honest reporting of co-elutions, low resolution, failed separations, matrix interference, column/membrane deterioration, and all limitations impacting the reliability of the separation. |