Evaluating Measurement Uncertainty in Amino Acid Racemization Analysis

399 Pages·2013·7.6 MB·English

EVALUATING MEASUREMENT UNCERTAINTY
IN AMINO ACID RACEMIZATION ANALYSIS:
TOWARDS A NEW CHRONOLOGY

Joanne Powell

PhD

2012

Evaluating Measurement Uncertainty
in Amino Acid Racemization Analysis:
Towards a New Chronology

Joanne Powell

PhD

University of York
Department of Archaeology
October 2012

Abstract

Unlike other Quaternary dating methods, amino acid racemisation (AAR)
geochronology has the potential to provide age estimates that span the entire Quaternary
period, a crucial period for understanding past climate change and human evolution. It has
become a critical technique for Quaternary Science and uses the time/temperature
dependent kinetics of protein decomposition to provide relative age estimates of fossil
samples. The accuracy of age estimates relies heavily on the accuracy of analytical data and
accurate determinations of uncertainty estimates.
This thesis takes internationally established principles of measurement uncertainty
determination and applies them to AAR. Analytical uncertainty is considered in the context
of intra- and inter-laboratory measurement results. A retrospective evaluation of intra-
laboratory precision using ANOVA is given, and results from an inter-laboratory proficiency
study, evaluated as estimates of bias, are summarised (paper submitted). The final sections
look at uncertainty from existing archaeological site data, including sampling effects. A
model is proposed that utilises decomposition correlations between amino acids to provide a
priori uncertainty estimates. These are then used to update observed site data using a
Bayesian approach to derive posterior uncertainty estimates and D/L values. A further model
is tentatively presented which could potentially be used to derive quantitative age estimates
once uncertainty within the kinetic and temperature models have been characterised and
accounted for.

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Table of Contents
CHAPTER 1. INTRODUCTION ............................................................................... 1
1.1 QUATERNARY GEOCHRONOLOGY ................................................................... 1
1.1.1 Defining the Quaternary ............................................................................ 2
1.1.2 Subdivisions of the Quaternary ................................................................. 3
1.2 A CONTINUOUS RECORD ................................................................................ 5
1.2.1 Deep Sea cores ........................................................................................... 5
1.2.2 Ice Cores ..................................................................................................... 8
1.2.3 Marine-Terrestrial Correlation................................................................... 9
1.2.4 The British Chronological Framework ...................................................... 12
1.3 DATING METHODS ........................................................................................ 13
1.3.1 Amino Acid Racemisation ........................................................................ 14
1.3.1.1 Background and application ............................................................. 14
1.3.1.2 Precision ............................................................................................ 17
1.3.1.3 Measurement Uncertainty (MU) in AAR ........................................... 18
1.4 AIMS & OBJECTIVES ...................................................................................... 20
1.4.1 Thesis Structure ....................................................................................... 22
1.4.2 Terminology ............................................................................................. 23
CHAPTER 2. MEASUREMENT UNCERTAINTY ...................................................... 24
2.1 INTRODUCTION ............................................................................................. 24
2.2 ACCURACY AND FITNESS FOR PURPOSE ....................................................... 26
2.3 DEFINING MEASUREMENT UNCERTAINTY .................................................... 30
2.3.1 Measurement Uncertainty and Measurement Error .............................. 32
2.3.2 Fitness for Purpose and Quality Assurance ............................................. 32
2.3.2.1 Personnel........................................................................................... 34
2.3.2.2 Accommodation and Environmental conditions ............................... 34
2.3.2.3 Method selection, validation and uncertainty .................................. 35
2.3.2.4 Equipment ......................................................................................... 36
2.3.2.5 Measurement Traceability ................................................................ 36
2.3.2.6 Sampling ........................................................................................... 37
2.3.2.7 Handling of test and calibration items.............................................. 37
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2.3.2.8 Assuring the quality of test and calibration results (QC and
proficiency testing schemes) ............................................................. 37
2.3.2.9 Reporting the results ......................................................................... 38
2.4 MEASUREMENT UNCERTAINTY EVALUATION .............................................. 38
2.4.1 Quantifying Standard Uncertainty components ...................................... 39
2.5 THE MODELLING APPROACH, (UNCERTAINTY BUDGET, “BOTTOM-UP” OR
GUM APPROACH) .......................................................................................... 41
2.5.1.1 Type A evaluation of standard uncertainty (after JCGM 100, 2008,
p10, 4.2) ............................................................................................ 41
2.5.1.2 Pooled experimental standard deviation .......................................... 42
2.5.1.3 Type B evaluation of standard uncertainty (after JCGM 100, 2008,
p11, 4.3) ............................................................................................ 43
2.6 INTER-LABORATORY COLLABORATIVE TRIAL OR “TOP DOWN” METHOD ... 45
2.7 SINGLE LABORATORY METHOD VALIDATION APPROACH ............................ 48
2.7.1 Method Validation ................................................................................... 48
2.7.2 Quality Control Activities ......................................................................... 50
2.7.2.1 Internal Quality Control .................................................................... 50
2.7.3 Proficiency Testing (External Quality Control) ......................................... 50
2.7.4 Method Comparisons .............................................................................. 51
2.8 COMBINING STANDARD UNCERTAINTIES ..................................................... 52
2.9 EXPRESSING MU AS AN EXPANDED UNCERTAINTY (95% CL) ....................... 53
2.10 CONCLUSIONS ........................................................................................... 54
CHAPTER 3. ANALYTICAL UNCERTAINTY IN AAR; AN INTRA-LABORATORY
PERSPECTIVE ................................................................................. 56
3.1 INTRODUCTION ............................................................................................. 56
3.2 EVALUATING SOURCES OF UNCERTAINTY .................................................... 57
3.2.1 Specification of the measurand ............................................................... 57
3.2.2 Description of the measurement procedure ........................................... 58
3.2.3 Quantitative Expression ........................................................................... 60
3.2.4 Weighing up the uncertainty budget ....................................................... 62
3.2.5 Combining individual uncertainty contributions ..................................... 64
3.2.6 A “Top-Down” perspective ...................................................................... 65
3.3 UNCERTAINTY ESTIMATES AT THE UNIVERSITY OF YORK ............................. 73
3.4 USE OF REFERENCE MATERIALS (RMS) ......................................................... 74
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3.4.1 RMs in Validation ..................................................................................... 75
3.4.1.1 Precision ............................................................................................ 75
3.4.1.2 Bias .................................................................................................... 77
3.4.1.3 Calibration ......................................................................................... 80
3.4.2 RMs in Internal Quality Control (IQC) ...................................................... 83
3.4.2.1 Blanks ................................................................................................ 83
3.4.2.2 Calibrants .......................................................................................... 84
3.4.2.3 Spiked samples .................................................................................. 84
3.4.2.4 Replicate analyses ............................................................................. 85
3.4.2.5 QCMs and Control Charts.................................................................. 85
3.5 CONCLUSIONS ............................................................................................... 87
CHAPTER 4. A RETROSPECTIVE ANALYSIS OF MU IN AAR ................................... 88
4.1 INTRODUCTION ............................................................................................. 88
4.1.1 Evaluating precision in AAR ..................................................................... 89
4.1.1.1 Analysis of Variance, ANOVA ............................................................ 90
4.2 REFERENCE SOLUTIONS ................................................................................ 93
4.2.1 Instrumental stability in uncalibrated data: LhomoArginine ................... 93
4.2.2 Evaluating Normality and Identifying Outliers in Standard Solutions .... 96
4.2.2.1 Student’s t-Test for Significant Differences ....................................... 97
4.2.2.2 Scatter Plots .................................................................................... 100
4.2.2.3 Repeatability ................................................................................... 102
4.2.2.4 Boxplots........................................................................................... 102
4.2.2.5 Frequency histograms & Kolmogorov-Smirnov Normality test ...... 105
4.2.2.6 Outlier removal ............................................................................... 105
4.2.3 Re-evaluating Normality ........................................................................ 106
4.2.3.1 Considerations of Outlier removal .................................................. 109
4.2.3.2 Robust Mean Evaluations ............................................................... 113
4.2.3.3 Robust Mean and Kernel Density Evaluations ................................ 115
4.2.3.4 Difference between instruments ..................................................... 121
4.2.4 Summing up ........................................................................................... 123
4.3 PRECISION EVALUATION BY ANOVA; STANDARD SOLUTIONS ................... 124
4.3.1 Cochran’ and Grubb’s Outlier Tests ....................................................... 127
4.3.1.1 Cochran’s outlier test ...................................................................... 127
4.3.1.2 Grubb’s outlier test. ........................................................................ 128
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4.3.2 Analytical Precision Estimates ............................................................... 131
4.3.3 Repeatability limit .................................................................................. 134
4.3.4 Effect of Sample Size .............................................................................. 135
4.3.5 Summarising Precision estimates .......................................................... 137
4.3.6 Confidence Intervals .............................................................................. 142
4.4 PRECISION EVALUATION BY ANOVA; BIOMINERAL MATRICES................... 146
4.4.1 Mollusc shell, ILC-A, B and C materials. ................................................. 146
4.4.2 Precision estimates from Proficiency Test (PT) data ............................. 149
4.4.2.1 Observations on D/L value precision estimates .............................. 152
4.4.2.2 Observations on isomer concentration precision estimates ........... 153
4.4.2.3 Further comments ........................................................................... 154
4.4.3 Combined uncertainty and Covariance. ................................................ 164
4.5 QUALITY CONTROL ...................................................................................... 168
4.5.1 Repeatability .......................................................................................... 168
4.5.2 Control Charts ........................................................................................ 171
4.5.3 Bias Evaluation: Standard Solutions ...................................................... 175
4.5.3.1 Does D-Aile/L-Ile really = 1.3? ......................................................... 184
4.5.4 Calibration Curves .................................................................................. 186
4.6 CONCLUSION ............................................................................................... 190
CHAPTER 5. INTER-LABORATORY PROFICIENCY STUDY .................................... 191
5.1 ABSTRACT .................................................................................................... 191
5.2 INTRODUCTION ........................................................................................... 193
5.2.1 Amino Acid Racemization ...................................................................... 193
5.2.2 Accuracy or Precision ? .......................................................................... 194
5.2.3 Previous AAR Inter-laboratory studies .................................................. 195
5.2.4 Proficiency Testing ................................................................................. 199
5.3 2010-11 AAR PROFICIENCY TEST ................................................................. 200
5.3.1 Design and Organisation ........................................................................ 200
5.3.2 Test Materials ........................................................................................ 201
5.3.3 Homogeneity Evaluation........................................................................ 203
5.3.4 Performance Evaluation ........................................................................ 204
5.3.4.1 The Assigned Value, .................................................................... 205
5.3.4.2 Derivation of the Assigned Values, .............................................. 206
5.3.4.3 The Target Standard Deviation; σ .................................................. 207
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