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Statistics and Data Analysis for Microarrays Using R and
Bioconductor 2nd Edition Sorin Draghici Digital Instant
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Author(s): Sorin Draghici
ISBN(s): 9781439809754, 1439809755
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 Computer Science/Bioinformatics

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Using R and Bioconductor

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Statistics and Data Analysis
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 Statistics and Data Analysis
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 Published Titles
Algorithms in Bioinformatics: A Practical Exactly Solvable Models of Biological
Introduction Invasion
Wing-Kin Sung Sergei V. Petrovskii and Bai-Lian Li
Bioinformatics: A Practical Approach Gene Expression Studies Using
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A Comprehensive Approach Methods in Medical Informatics:
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Data Analysis Tools for DNA Microarrays Programming in Perl, Python, and Ruby
Sorin Draghici Jules J. Berman
Differential Equations and Mathematical Modeling and Simulation of Capsules
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Normal Mode Analysis: Theory and Statistics and Data Analysis for
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Pattern Discovery in Bioinformatics: Structural Bioinformatics: An Algorithmic
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 Statistics and Data Analysis
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Second Edition

Sorin Drăghici

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CRC Press
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 To Jeannette, my better half,
to Tavi, who brightens every day of my life,
and to Althea, whom I miss every day we are not together
This page intentionally left blank
Contents

List of Figures xxv

List of Tables xxxv

Preface xxxix

1 Introduction 1

1.1 Bioinformatics – an emerging discipline . . . . . . . . . . . . 1

2 The cell and its basic mechanisms 5

2.1 The cell . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

2.2 The building blocks of genomic information . . . . . . . . . . 13
2.2.1 The deoxyribonucleic acid (DNA) . . . . . . . . . . . 13
2.2.2 The DNA as a language . . . . . . . . . . . . . . . . . 19
2.2.3 Errors in the DNA language . . . . . . . . . . . . . . . 23
2.2.4 Other useful concepts . . . . . . . . . . . . . . . . . . 24
2.3 Expression of genetic information . . . . . . . . . . . . . . . 28
2.3.1 Transcription . . . . . . . . . . . . . . . . . . . . . . . 30
2.3.2 Translation . . . . . . . . . . . . . . . . . . . . . . . . 32
2.3.3 Gene regulation . . . . . . . . . . . . . . . . . . . . . . 35
2.4 The need for high-throughput methods . . . . . . . . . . . . 36
2.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

3 Microarrays 39

3.1 Microarrays – tools for gene expression analysis . . . . . . . 39

3.2 Fabrication of microarrays . . . . . . . . . . . . . . . . . . . 41
3.2.1 Deposition . . . . . . . . . . . . . . . . . . . . . . . . 41
3.2.1.1 The Illumina technology . . . . . . . . . . . 42
3.2.2 In situ synthesis . . . . . . . . . . . . . . . . . . . . . 48
3.2.3 A brief comparison of cDNA and oligonucleotide tech-
nologies . . . . . . . . . . . . . . . . . . . . . . . . . . 55
3.3 Applications of microarrays . . . . . . . . . . . . . . . . . . . 57
3.4 Challenges in using microarrays in gene expression studies . 58

ix
x Contents

3.5 Sources of variability . . . . . . . . . . . . . . . . . . . . . . 63

3.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

4 Reliability and reproducibility issues in DNA microarray

measurements 69

4.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
4.2 What is expected from microarrays? . . . . . . . . . . . . . . 70
4.3 Basic considerations of microarray measurements . . . . . . 70
4.4 Sensitivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
4.5 Accuracy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
4.6 Reproducibility . . . . . . . . . . . . . . . . . . . . . . . . . 77
4.7 Cross-platform consistency . . . . . . . . . . . . . . . . . . . 78
4.8 Sources of inaccuracy and inconsistencies in microarray mea-
surements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
4.9 The MicroArray Quality Control (MAQC) project . . . . . . 85
4.10 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87

5 Image processing 89

5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
5.2 Basic elements of digital imaging . . . . . . . . . . . . . . . . 90
5.3 Microarray image processing . . . . . . . . . . . . . . . . . . 95
5.4 Image processing of cDNA microarrays . . . . . . . . . . . . 96
5.4.1 Spot finding . . . . . . . . . . . . . . . . . . . . . . . . 99
5.4.2 Image segmentation . . . . . . . . . . . . . . . . . . . 100
5.4.3 Quantification . . . . . . . . . . . . . . . . . . . . . . 106
5.4.4 Spot quality assessment . . . . . . . . . . . . . . . . . 111
5.5 Image processing of Affymetrix arrays . . . . . . . . . . . . . 113
5.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115

6 Introduction to R 119

6.1 Introduction to R . . . . . . . . . . . . . . . . . . . . . . . . 119

6.1.1 About R and Bioconductor . . . . . . . . . . . . . . . 119
6.1.2 Repositories for R and Bioconductor . . . . . . . . . . 120
6.1.3 The working setup for R . . . . . . . . . . . . . . . . . 121
6.1.4 Getting help in R . . . . . . . . . . . . . . . . . . . . . 122
6.2 The basic concepts . . . . . . . . . . . . . . . . . . . . . . . . 122
6.2.1 Elementary computations . . . . . . . . . . . . . . . . 122
6.2.2 Variables and assignments . . . . . . . . . . . . . . . . 125
6.2.3 Expressions and objects . . . . . . . . . . . . . . . . . 126
6.3 Data structures and functions . . . . . . . . . . . . . . . . . 128
6.3.1 Vectors and vector operations . . . . . . . . . . . . . . 128
6.3.2 Referencing vector elements . . . . . . . . . . . . . . . 131
 Contents xi

6.3.3 Functions . . . . . . . . . . . . . . . . . . . . . . . . . 133

6.3.4 Creating vectors . . . . . . . . . . . . . . . . . . . . . 135
6.3.5 Matrices . . . . . . . . . . . . . . . . . . . . . . . . . . 137
6.3.6 Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
6.3.7 Data frames . . . . . . . . . . . . . . . . . . . . . . . . 141
6.4 Other capabilities . . . . . . . . . . . . . . . . . . . . . . . . 144
6.4.1 More advanced indexing . . . . . . . . . . . . . . . . . 144
6.4.2 Missing values . . . . . . . . . . . . . . . . . . . . . . 145
6.4.3 Reading and writing files . . . . . . . . . . . . . . . . 148
6.4.4 Conditional selection and indexing . . . . . . . . . . . 150
6.4.5 Sorting . . . . . . . . . . . . . . . . . . . . . . . . . . 151
6.4.6 Implicit loops . . . . . . . . . . . . . . . . . . . . . . . 154
6.5 The R environment . . . . . . . . . . . . . . . . . . . . . . . 159
6.5.1 The search path: attach and detach . . . . . . . . . . 159
6.5.2 The workspace . . . . . . . . . . . . . . . . . . . . . . 161
6.5.3 Packages . . . . . . . . . . . . . . . . . . . . . . . . . 163
6.5.4 Built-in data . . . . . . . . . . . . . . . . . . . . . . . 165
6.6 Installing Bioconductor . . . . . . . . . . . . . . . . . . . . . 165
6.7 Graphics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
6.8 Control structures in R . . . . . . . . . . . . . . . . . . . . . 169
6.8.1 Conditional statements . . . . . . . . . . . . . . . . . 170
6.8.2 Pre-test loops . . . . . . . . . . . . . . . . . . . . . . . 171
6.8.3 Counting loops . . . . . . . . . . . . . . . . . . . . . . 172
6.8.4 Breaking out of loops . . . . . . . . . . . . . . . . . . 173
6.8.5 Post-test loops . . . . . . . . . . . . . . . . . . . . . . 173
6.9 Programming in R versus C/C++/Java . . . . . . . . . . . . 174
6.9.1 R is “forgiving” – which can be bad . . . . . . . . . . . 174
6.9.2 Weird syntax errors . . . . . . . . . . . . . . . . . . . 175
6.9.3 Programming style . . . . . . . . . . . . . . . . . . . . 179
6.10 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
6.11 Solved Exercises . . . . . . . . . . . . . . . . . . . . . . . . . 183
6.12 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191

7 Bioconductor: principles and illustrations 193

7.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193

7.2 The portal . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
7.2.1 The main resource categories . . . . . . . . . . . . . . 195
7.2.2 Working with the software repository . . . . . . . . . 195
7.3 Some explorations and analyses . . . . . . . . . . . . . . . . 197
7.3.1 The representation of microarray data . . . . . . . . . 197
7.3.2 The annotation of a microarray platform . . . . . . . 199
7.3.3 Predictive modeling using microarray data . . . . . . 203
7.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
xii Contents

8 Elements of statistics 207

8.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 207

8.2 Some basic concepts . . . . . . . . . . . . . . . . . . . . . . . 208
8.2.1 Populations versus samples . . . . . . . . . . . . . . . 208
8.2.2 Parameters versus statistics . . . . . . . . . . . . . . . 209
8.3 Elementary statistics . . . . . . . . . . . . . . . . . . . . . . 211
8.3.1 Measures of central tendency: mean, mode, and median 211
8.3.1.1 Mean . . . . . . . . . . . . . . . . . . . . . . 211
8.3.1.2 Mode . . . . . . . . . . . . . . . . . . . . . . 212
8.3.1.3 Median, percentiles, and quantiles . . . . . . 213
8.3.1.4 Characteristics of the mean, mode, and me-
dian . . . . . . . . . . . . . . . . . . . . . . . 214
8.3.2 Measures of variability . . . . . . . . . . . . . . . . . . 215
8.3.2.1 Range . . . . . . . . . . . . . . . . . . . . . . 215
8.3.2.2 Variance . . . . . . . . . . . . . . . . . . . . 216
8.3.3 Some interesting data manipulations . . . . . . . . . . 218
8.3.4 Covariance and correlation . . . . . . . . . . . . . . . 219
8.3.5 Interpreting correlations . . . . . . . . . . . . . . . . . 223
8.3.6 Measurements, errors, and residuals . . . . . . . . . . 230
8.4 Degrees of freedom . . . . . . . . . . . . . . . . . . . . . . . 231
8.4.1 Degrees of freedom as independent error estimates . . 232
8.4.2 Degrees of freedom as number of additional measure-
ments . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
8.4.3 Degrees of freedom as observations minus restrictions 233
8.4.4 Degrees of freedom as measurements minus model pa-
rameters . . . . . . . . . . . . . . . . . . . . . . . . . . 234
8.4.5 Degrees of freedom as number of measurements we can
change . . . . . . . . . . . . . . . . . . . . . . . . . . . 234
8.4.6 Data split between estimating variability and model pa-
rameters . . . . . . . . . . . . . . . . . . . . . . . . . . 235
8.4.7 A geometrical perspective . . . . . . . . . . . . . . . . 235
8.4.8 Calculating the number of degrees of freedom . . . . . 236
8.4.8.1 Estimating k quantities from n measurements 236
8.4.9 Calculating the degrees of freedom for an n × m table 237
8.5 Probabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
8.5.1 Computing with probabilities . . . . . . . . . . . . . . 243
8.5.1.1 Addition rule . . . . . . . . . . . . . . . . . . 243
8.5.1.2 Conditional probabilities . . . . . . . . . . . 244
8.5.1.3 General multiplication rule . . . . . . . . . . 247
8.6 Bayes’ theorem . . . . . . . . . . . . . . . . . . . . . . . . . . 247
8.7 Testing for (or predicting) a disease . . . . . . . . . . . . . . 250
8.7.1 Basic criteria: accuracy, sensitivity, specificity, PPV,
NPV . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
 Contents xiii

8.7.2 More about classification criteria: prevalence, incidence,

and various interdependencies . . . . . . . . . . . . . . 253
8.8 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
8.9 Solved problems . . . . . . . . . . . . . . . . . . . . . . . . . 257
8.10 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258

9 Probability distributions 261

9.1 Probability distributions . . . . . . . . . . . . . . . . . . . . 261

9.1.1 Discrete random variables . . . . . . . . . . . . . . . . 262
9.1.2 The discrete uniform distribution . . . . . . . . . . . . 265
9.1.3 Binomial distribution . . . . . . . . . . . . . . . . . . 266
9.1.4 Poisson distribution . . . . . . . . . . . . . . . . . . . 275
9.1.5 The hypergeometric distribution . . . . . . . . . . . . 278
9.1.6 Continuous random variables . . . . . . . . . . . . . . 281
9.1.7 The continuous uniform distribution . . . . . . . . . . 283
9.1.8 The normal distribution . . . . . . . . . . . . . . . . . 283
9.1.9 Using a distribution . . . . . . . . . . . . . . . . . . . 287
9.2 Central limit theorem . . . . . . . . . . . . . . . . . . . . . . 291
9.3 Are replicates useful? . . . . . . . . . . . . . . . . . . . . . . 292
9.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294
9.5 Solved problems . . . . . . . . . . . . . . . . . . . . . . . . . 295
9.6 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 296

10 Basic statistics in R 299

10.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 299

10.2 Descriptive statistics in R . . . . . . . . . . . . . . . . . . . . 300
10.2.1 Mean, median, range, variance, and standard deviation 300
10.2.2 Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . 304
10.2.3 More built-in R functions for descriptive statistics . . 305
10.2.4 Covariance and correlation . . . . . . . . . . . . . . . 307
10.3 Probabilities and distributions in R . . . . . . . . . . . . . . 308
10.3.1 Sampling . . . . . . . . . . . . . . . . . . . . . . . . . 308
10.3.2 Empirical probabilities . . . . . . . . . . . . . . . . . . 309
10.3.3 Standard distributions in R . . . . . . . . . . . . . . . 315
10.3.4 Generating (pseudo-)random numbers . . . . . . . . . 316
10.3.5 Probability density functions . . . . . . . . . . . . . . 316
10.3.6 Cumulative distribution functions . . . . . . . . . . . 317
10.3.7 Quantiles . . . . . . . . . . . . . . . . . . . . . . . . . 319
10.3.7.1 The normal distribution . . . . . . . . . . . . 321
10.3.7.2 The binomial distribution . . . . . . . . . . . 324
10.3.8 Using built-in distributions in R . . . . . . . . . . . . 326
10.4 Central limit theorem . . . . . . . . . . . . . . . . . . . . . . 329
10.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336
xiv Contents

10.6 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336

11 Statistical hypothesis testing 337

11.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 337

11.2 The framework . . . . . . . . . . . . . . . . . . . . . . . . . . 338
11.3 Hypothesis testing and significance . . . . . . . . . . . . . . 341
11.3.1 One-tailed testing . . . . . . . . . . . . . . . . . . . . 342
11.3.2 Two-tailed testing . . . . . . . . . . . . . . . . . . . . 346
11.4 “I do not believe God does not exist” . . . . . . . . . . . . . 348
11.5 An algorithm for hypothesis testing . . . . . . . . . . . . . . 350
11.6 Errors in hypothesis testing . . . . . . . . . . . . . . . . . . . 351
11.7 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355
11.8 Solved problems . . . . . . . . . . . . . . . . . . . . . . . . . 356

12 Classical approaches to data analysis 359

12.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 359

12.2 Tests involving a single sample . . . . . . . . . . . . . . . . . 360
12.2.1 Tests involving the mean. The t distribution. . . . . . 360
12.2.2 Choosing the number of replicates . . . . . . . . . . . 366
12.2.3 Tests involving the variance (σ 2 ). The chi-square distri-
bution . . . . . . . . . . . . . . . . . . . . . . . . . . . 370
12.2.4 Confidence intervals for standard deviation/variance . 374
12.3 Tests involving two samples . . . . . . . . . . . . . . . . . . . 375
12.3.1 Comparing variances. The F distribution. . . . . . . . 375
12.3.2 Comparing means . . . . . . . . . . . . . . . . . . . . 380
12.3.2.1 Equal variances . . . . . . . . . . . . . . . . 384
12.3.2.2 Unequal variances . . . . . . . . . . . . . . . 386
12.3.2.3 Paired testing . . . . . . . . . . . . . . . . . 387
12.3.3 Confidence intervals for the difference of means µ1 − µ2 388
12.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389
12.5 Exercises . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 392

13 Analysis of Variance – ANOVA 393

13.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . 393

13.1.1 Problem definition and model assumptions . . . . . . 393
13.1.2 The “dot” notation . . . . . . . . . . . . . . . . . . . . 397
13.2 One-way ANOVA . . . . . . . . . . . . . . . . . . . . . . . . 398
13.2.1 One-way Model I ANOVA . . . . . . . . . . . . . . . . 398
13.2.1.1 Partitioning the Sum of Squares . . . . . . . 399
13.2.1.2 Degrees of freedom . . . . . . . . . . . . . . . 401
13.2.1.3 Testing the hypotheses . . . . . . . . . . . . 401
13.2.2 One-way Model II ANOVA . . . . . . . . . . . . . . . 405
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“Then they praised him, soft and low,
Call’d him worthy to be loved,
Truest friend and noblest foe;
Yet she neither spoke nor moved.

“Stole a maiden from her place,

Lightly to the warrior stept,
Took the face-cloth from the face;
Yet she neither moved nor wept.

“Rose a nurse of ninety years,

Set his child upon her knee—
Like summer tempest came her tears—
‘Sweet my child, I live for thee.’”

In this poem we see that desolation and despair have sealed the
fountain of tears in the widowed wife—that the light of love has
gone from her life and returns only through the influence of
childhood, with all its tender links and memories.
The last song, “Ask Me No More,” is like the sestette in a sonnet
—the application of all the preceding. These influences of the family,
with all its sacred ties and affections, are too much for the strong
and noble soul of the Princess, who throws aside all theories of
intellectual independence for woman, and, yielding to the impulse of
love and affection, proclaims the triumph of the womanly elements
in her nature in the following sweet and tender lines:

“Ask me no more: the moon may draw the sea;

The cloud may stoop from heaven and take the shape,
With fold to fold, of mountain or of cape;
But O too fond, when have I answered thee?
Ask me no more.

“Ask me no more; what answer should I give?

I love not hollow cheek or faded eye:
Yet, O my friend, I will not have thee die!
Ask me no more, lest I should bid thee live;
Ask me no more.

“Ask me no more: thy fate and mine are seal’d:

I strove against the stream and all in vain:
Let the great river take me to the main:
No more, dear love, for at a touch I yield;
Ask me no more.”

What bearing these six lyrics, which are truly miracles of

workmanship, have upon the main theme of the story will be readily
perceived. They not only contribute to the unity of the poem proper
but are in themselves linked together by a kindred bond and
purpose. They are the voice of the heart singing through the night,
cheered by the kindly stars of faith, hope and love.
Having analyzed the poem and reached its central thought, let us
now consider who is the hero or heroine of the story. Assuredly it is
not the Prince, for he has been ignominiously thrust out of Ida’s
gates in draggled female clothes. Nor is it his jovial-hearted
companion, Cyril, nor Arac, who cares for nothing save the
tournament. It cannot even be the high-souled and stately Princess,
for has she not been vanquished at the very moment of triumph?
The only one who comes out triumphantly is Psyche’s baby—she is
the real heroine of the epic. The little blossom, sweet Agläea, is the
central point upon which the plot turns. In the poem, in the songs—
everywhere—this unconscious child, the concrete embodiment of
nature itself, exerts an overpowering influence, shaping, directing,
nurturing the tender instincts of womanhood and clearing away all
intellectual theories which tend to usurp the sacred offices of mother
and home.
In the despatch which Ida sends to her brother she
acknowledges the power of the child in the following lines:
“I took it for an hour in mine own bed
This morning: there the tender orphan hands
Felt at my heart, and seemed to charm from thence
The wrath I nursed against the world.”

And again:

“I felt
Thy helpless warmth about my barren breast
In the dead prime.”

Notice, too, how ubiquitous the babe is. Ida carries it with her
everywhere. It is on her judgment seat, it shares in her song of
triumph when the tournament is ended, and is with her on the
battlefield when she is tending her wounded brothers.
The babe is indeed the heroine of the story, holding the epic
along the channel of its main motive, despite every current and
breeze stirred by foreign elements in its course.
It is not hard to read in this poem Tennyson’s solution of the
woman question, though there are some who maintain that it is
vague and unsatisfactory. Such persons forget that it is the office of
the poet not so much to affirm principles on a subject as to inspire
the sentiments which ought to preside over the solution.
It seems to us that the transfiguration of Ida’s nature under the
influence of the affections is the only solution possible that could be
offered by the poet for the questions raised in “The Princess.” It is
the office of poetry, not to guide the conclusions of the intellect, but
to tone the feelings in accordance with truth and duty. Poetry is not
to teach the truth—it is truth itself.
Those who have the interest of the true advancement of woman
at heart should remember that neither the whole race nor woman
herself can be benefited by any system of education for woman at
variance with Nature and not co-ordinate with the highest needs of
the race. It is idle to discuss the equality or inequality of gifts and
faculties as between man and woman. Every person knows that
woman is not only the equal of man in many respects, but his
superior in not a few; yet this does not justify her in waging a war
with Nature and, with her heart clothed in an iron panoply, riding
forth into the arena of dust and turmoil to perform services for which
the strong hand and knightly heart of man as well as the vocation of
centuries have fitted him alone.
As to her education, that which enables her every faculty to grow
and unfold its beauty and power, with no harm to her distinctive
womanhood—that should be her privilege and right to enjoy,
whether it be obtained in convent or co-education hall. That woman
needs a greater breadth and solidity of intellectual culture goes
without saying, and this for two reasons—to better fit her for the
high moral offices which belong to her domestic mission, and to
keep alive in her a just sympathy with the larger social movements
of which she is the passive, but ought not to be the uninterested
spectator.
If Ida’s theories were carried out, the child element in woman
and the feminine element in man would be crushed out, and it is this
very feminine element in man which gives him moral insight—it
constitutes the poetic side of his nature. Without the feminine
element in his nature Chaucer never could have written “The
Canterbury Tales.”
Ida was right in seeking for a more generous culture, but the
spirit in which she sought it was wrong. Mrs. Browning’s Aurora
Leigh would be an artist first and then a woman. Ida, too, would
crush out the womanly elements in her nature in her eagerness to
satisfy the claims of the intellect. She set the claims of the head
above those of the heart, and, like Aurora Leigh, she failed.
Enthusiasts often point to the glories achieved by women
through the centuries, and make this a pretext for their vagaries and
Utopian dreams. Because Corinna won the lyric prize from Pindar,
and Judith delivered her people from Holofernes, and Joan of Arc
repulsed the English from the walls of Orleans, and Queen Elizabeth
laid the foundation of England’s supremacy upon the sea, is it meet
that the whole social order should be turned upside down and
Nature wounded in its very heart? Such enthusiasts forget that the
mother of Themistocles was greater than the vanquisher of Pindar,
the mother of St. Louis of France greater than the Maid of Orleans,
and the mother of Shakespeare greater than she who held with firm
grasp the sceptre of English sovereignty during the closing years of
the Tudor period.
In spite, therefore, of all theories to the contrary, in spite of
many zealous but misguided women who are looking in the near
future for the reign of woman and the complete subserviency of
man, the true mission of woman is, and always will continue to be,
within the domestic sphere, where she conserves the accumulated
sum of the moral education of the race, and keeps burning through
the darkest night of civilization upon the sacred altar of humanity,
the vestal fires of Truth, Beauty, and Love.

POETRY AND HISTORY TEACHING

FALSEHOOD

POETRY AND HISTORY TEACHING

FALSEHOOD.

T he function of the poet is to speak essential truths as opposed to

relative truths, and Mrs. Browning in “Aurora Leigh” testifies to
this fact in the following lines:
 “I write so
Of the only truth-tellers now left to God,
The only speakers of essential truth
Opposed to relative, comparative,
And temporal truths; the only holders by
His sun-skirts, through conventional gray glooms;
The only teachers who instruct mankind
From just a shadow on a charnel wall
To find man’s veritable stature out
Erect, sublime,—the measure of a man;
And that’s the measure of an angel says
The Apostle.”

It is much to be regretted that the poetry of the present day

does not always fulfil this high purpose. The poets of to-day—and by
poets of to-day I mean the poets of the past half-century—are not
“the only truth-tellers now left to God.” Nay, they are often
disseminators of falsehood. It is true the non-Catholic poet—a
Wordsworth, a Byron, a Longfellow, or a Tennyson—by being true to
art and inspiration, which has as its basis Catholic truth, sometimes
unwittingly expresses a Catholic truth of the deepest significance.
But as poetry is only a reflection of life idealized, and as there is
nothing in poetry but what is in life, we may expect the anti-Catholic
seeds scattered about by prejudiced hearts in the garden of the
world to bear the poisonous blossoms of falsehood as they are
translated and reflected in the pages of modern poetry.
And this is sometimes done indirectly. Sometimes, too, it is done
by expressing a half truth or by seizing on some exceptional phase
of Catholic religious life and impressing it upon the non-Catholic
mind with an “Ab uno disce omnes.”
A concrete example will best illustrate this. Browning has a poem
entitled “The Bishop Orders His Tomb at St. Praxed’s Church.” Now
Browning’s poetic workshop was Italy, so this great psychological
poet wrote:
“Open my heart and you shall see
Graven on it Italy.”

He found in the land of Dante and Michael Angelo fit subjects for his
dramatic monologues. The art world of Italy opened up to Browning
new themes, new thoughts. The intense life of its people, full of the
sweetness and aroma of virtue and the dark tragedy of vice, gave
him scope which he could not find elsewhere. Pity it is that he
presents only the dark side of Italian character. Pity it is that the
paganized and sensual Bishop of the Italian Renaissance depicted by
Browning in “The Bishop Orders His Tomb at St. Praxed’s Church”
did not find setting, in his poems, as a foil to the pure and pious
men and women who prayed before the shrines and in the cloisters
of Italy when the new wine of old classicism poured from Homeric
flasks and casks had intoxicated the head and heart of that garden
of Europe and turned possible saints into satyrs.
De Maistre, the great French publicist, has said that history for
the past three hundred years has been a conspiracy against truth.
Aye, and poetry, too, whose countenance should reflect the beauty
of heavenly truth, often wears the mask of the assassin. To-day
there are so-called advanced and up-to-date scholars in our
universities and clubs who hold that “The Bishop Orders His Tomb at
St. Praxed’s Church” is a true reflection of the religious life of the
Italian Renaissance. They quote Ruskin as saying of that poem:
“I know of no other piece of modern English, prose or poetry, in
which there is so much told as in these lines, of the Renaissance
spirit—its worldliness, inconsistency, pride, hypocrisy, ignorance of
itself, love of art, of luxury, and of good Latin. It is nearly all that I
have said of the Central Renaissance, in thirty pages of the ‘Stones
of Venice,’ put into as many lines, Browning’s being also the
antecedent work.”
We would say just here to students of literature and history: Let
not the shadow of a great literary name overawe you. John Ruskin
did a great deal for art and criticism, but he is far from being an
infallible apostle of truth in either domain; and though he loved the
lowly, brown-hooded friars of St. Francis, this love was not based on
spiritual affinity, but on the poetry and art bound up in their humble
lives.
John Ruskin and Robert Browning, respectively art critic and
poet, have done the religious life of the Italian Renaissance a
grievous wrong—nay, they grossly misrepresent it when they say
that this abnormal picture of a Renaissance Catholic bishop truly
represents and reflects the religious life of Italy at that period. No
doubt but a certain amount of abuses and corruption prevailed in the
Church at that time, largely as a consequence of the worldly spirit
which had gained entrance into it during its exile at Avignon.
However, all was not darkness and sin. The vivifying life of the
Church was not exemplified in the Bishop of St. Praxed’s. As the
great historian of the Popes of the Renaissance, Dr. Ludwig Pastor,
says, “If those days were full of failings and sins of every kind, the
Church was not wanting in glorious manifestations through which
the source of her higher life revealed itself. Striking contrasts—deep
shadows on the one hand and most consoling gleams of sunshine on
the other—are the special characteristics of this period. If the
historian of the Church of the fifteenth century meets with some
unworthy prelates and bishops, he also meets in every part of
Christendom with an immense number of men distinguished for their
virtue, piety and learning, not a few of whom have been, by the
solemn voice of the Church, raised to her altars.”
Limiting ourselves to the most remarkable individuals of the
period of which we are about to treat, we shall mention only the
saints and holy men and women given by Italy to the Church: St.
Bernardine of Siena, of the order of Minorites, whose eloquence won
for him the title of “Trumpet of Heaven and fountain of knowledge”;
around him are grouped his holy brothers in religion, Saints John
Capestran and Jacopo della Marca. St. Antonius, whose unexampled
zeal was displayed in Florence, the very centre of the Renaissance,
had for his disciples blessed Antonio Neyrot of Ripoli and Constanzio
di Fabriano. In the order of St. Augustine are the following who have
been beatified: Andrea, who died at Montereale in 1497; Antonio
Turriani, in 1494. In 1440 St. Frances, the foundress of the Oblates,
was working at Rome. The labors of another founder, St. Francis of
Paula, who died in 1507, belong in part to this period. These names,
to which many more might be added, furnish the most striking proof
of the vitality of religion in Italy at the time of the Renaissance. Such
fruits do not ripen on trees which are “decayed and rotten to the
core.”
Indeed, it is astonishing what nonsense is talked about this
period of the Italian Renaissance, especially as it influenced the
religious life of the people. In one breath our would-be professors
will tell you that the Italian Renaissance movement swept the
Catholic Church into a vortex of paganism—pope, cardinals, bishops,
and all; and in the next they will lead you to believe that the Catholic
Church set its face against the new revival of classical learning,
fearing that the development of the intellect would be prejudicial to
the faith of the people. Either slander will effect its end.
As we write we have before us two historical works of somewhat
recent publication: “Books and Their Makers During-the Middle
Ages,” by George Haven Putnam, A.M., and “A General History of
Europe,” by Professors Thatcher and Schwill, of Chicago University.
As the latter is now used as a text-book in many American High
Schools, we will deal with its worth and wisdom first.
There is but one Chicago University in the world, and we might
expect its distinguished professors of medieval and modern
European history to understand at least the elementary truths of the
Catholic Church and something of its spirit and policy.
Let us examine for a moment some of the statements contained
in this “General History of Europe,” by Professors Thatcher and
Schwill. Here is a choice morsel which will amuse the student of
Church history. The topic is “The Church and Feudalism.” The author
says: “As late as the eleventh century it was not at all uncommon for
the clergy to marry. Since fiefs were hereditary, it seemed perfectly
proper that their children should be provided for out of the Church
lands which they held. But unless all their children became
clergymen these lands would pass into the hands of laymen and
therefore be lost to the Church. One of the purposes of the
prohibition of the marriage of the clergy was to prevent this
alienation and diminution of the Church lands.”
And this little paragraph dealing with the Italian Renaissance,
found on page 264 of the same work: “Medieval life knew nothing of
the freedom, beauty and joy of the Greek world. . . . The medieval
man had no eye for the beauty of nature. To him nature was evil.
God had indeed created the world and pronounced it very good, but
through the fall of man all nature had been corrupted. Satan was
now the prince of the world. As a result no one could either study or
admire nature.” Pray note the force of the auxiliary “could.”
Just think of it! A Catholic—a medieval Catholic—was forbidden
to look at or admire a flower, a forest, or a mountain peak. How so
much of nature got mixed up in the singing of “Old Dan Chaucer,” a
Catholic poet of the fourteenth century, we know not. ’Tis a mystery.
Chaucer is essentially the poet of the daisy, and robed it in verse
long before Burns turned it over with his plough.
Then we have the brown-hooded and gentle Friar, St. Francis of
Assisi, who was wont to call the birds of the air and the beasts of
the field his brothers, and who composed canticles to the winds, the
flowers and the sun. Did the erudite professors of Chicago University
ever make a study of Gothic architecture, the distinct inspiration and
creation of medieval times? If so, they will remember that plants and
flowers play, in symbolism, an important part in ornamentation. The
hatred of nature as well as the hatred of art imputed to the early
Christians is simply a “fable convenue,” manufactured by the
partisan and superficial historian who is either too dishonest or
indolent to state or reach the real facts.
It is enough to say that Professors Thatcher and Schwill’s work is
actually teeming with historical inaccuracies and gross
misrepresentations of the Catholic Church. Whether by inference or
blunt statement, these two professors have written themselves down
in the pages of their history either as ignorant or dishonest
historians, and it is unworthy of a presumably great university, such
as Chicago, to give its imprimatur to such unreliable and unscholarly
works.
 But lest we may not have convicted as yet Professors Thatcher
and Schwill of having misrepresented the truth, life and policy of the
Catholic Church in the pages of their history, we shall cite one more
paragraph found on page 172. It deals with monasticism. The author
says: “The philosophic basis of asceticism is the belief that matter is
the seat of evil, and therefore that all contact with it is
contaminating. This conception of evil is neither Christian nor
Jewish, but purely heathen. Jesus freely used the good things of this
world and taught that sin is in nothing external to man, but has its
seat only in the heart. But His teaching was not understood by His
followers. The peculiar form which this asceticism in the Church took
is called monasticism. . . . After about 175 A.D. the Church rapidly
grew worldly. As Christianity became popular large numbers entered
the Church and became Christians in name; but at heart and in life
they remained heathen. The bishops were often proud and haughty
and lived in grand style. Those who were really in earnest about
their salvation, unsatisfied with such worldliness, fled from the
contamination in the Church and went to live in the desert and find
the way to God without the aid of the Church: her means of grace
were for common Christians. Those who would could obtain, by
means of asceticism and prayer, all that others received by means of
the sacraments of the Church. There were to be two ways of
salvation: one through the Church and her means of grace; the
other through asceticism and contemplation.”
There is assuredly something of the historical naïveté of the
schoolboy in the above. Mark when the Christian Church became
corrupt—nearly one hundred and fifty years before it was upheld by
the arm of Constantine and when it had been hiding for more than
one hundred years in the Catacombs carving and painting in symbol
the truths and mysteries of God. This was the corruption, that as
Christ had birth in the lowly manger of Bethlehem so the Church, His
Spouse, was cradled in humility, hidden away from the purple rage
of the Cæsars, and, like a little child whose dreams are of the past
and the future, was rudely fashioning her life and soul in terms of
eternity, in symbols of the palm, the dove and the lamb.
 Now let us cite from Putnam’s “Books and Their Makers in the
Middle Ages” an instance of historical contradiction within the
compass of three pages. It is said that he who misrepresents the
truth must have a good memory, but the author of “Books and Their
Makers in the Middle Ages” is evidently devoid of that faculty,
otherwise he would not have contradicted himself in almost
succeeding pages of his work. Here is the contradiction. He is
speaking of book-making at the time of the Italian Renaissance. On
page 331, Vol. I., the author says: “A production of Beccadelli’s,
perhaps the most brilliant of Alfonso’s literary protégés, is to be
noted as having been proscribed by the Pope, being one of the
earliest Italian publications to be so distinguished. Eugenius IV.
forbade, under penalty of excommunication, the reading of
Beccadelli’s “Hermaphroditus,” which was declared to be contra
bonos mores. The book was denounced from many pulpits, and
copies were burned, together with portraits of the poet, on the
public squares of Bologna, Milan and Ferrara.”
On page 333 of the same volume Putnam writes—and we beg
the reader will compare carefully the two statements: “Poggio is to
be noted as a free thinker who managed to keep in good relations
with the Church. So long as free thinkers confined their audacity to
such matters as form the topic of Poggio’s ‘Facetiae,’ Beccadelli’s
‘Hermaphroditus’ or La Casa’s ‘Capitolo del Farno’ the Roman Curia
looked on and smiled approvingly. The most obscene books to be
found in any literature escaped the Papal censure, and a man like
Aretino, notorious for his ribaldry, could aspire with fair prospects of
success to the scarlet of a Cardinal.”
These are the kind of books that stuff the shelves of the libraries
in our great secular universities.
There is perhaps no other period in the history of the world that
requires more careful investigation than that of the Renaissance in
Italy, and this because of its complex character. Speaking of this
complexity Dr. Pastor says: “In the nature of things it must be
extremely difficult to present a truthful picture of an age which
witnessed so many revolutions affecting almost all departments of
human life and thought, and abounded in contradictions and
startling contrasts. But the difficulty becomes enormously increased
if we are endeavoring to formulate a comprehensive appreciation of
the moral and religious character of such an epoch. In fact in one
sense the task is an impossible one. No mortal eye can penetrate the
conscience of a single man; how much less can any human intellect
strike the balance between the incriminating and the extenuating
circumstances on which our judgment of the moral condition of such
a period depends, amid the whirl of conflicting events. In a rough
way, no doubt, we can form an estimate, but it can never pretend to
absolute accuracy. As Burckhardt, author of ‘The Civilization of the
Period of the Renaissance in Italy,’ says: ‘In this region the more
clearly the facts seem to point to any conclusion the more must we
be upon our guard against unconditional or universal assertions.’”
It were well assuredly if some of our professors of history in the
great secular universities—professors who assume to understand the
Catholic Church and her policy better than her own clergy and laity—
it were well, we say, if these would lay to their historical souls
Pastor’s judicial words ere they indict the “Renaissance Period” and
blacken the character of its popes, its prelates and its people.
The truth is that few if any non-Catholic students read Catholic
historical works to-day. Jansen’s great work, dealing with the social
and religious life of Germany in the period that preceded the advent
of Luther, is considered to be the last word on this debatable
ground, and yet how many non-Catholic students have ever opened
its pages? The same may be said of Pastor’s monumental work.
“Lives of the Popes Since the Close of the Middle Ages.” When this
ignorance of Catholic fact is supplemented by the reading of such
misrepresentation as is found in Browning’s poem, “The Bishop
Orders His Tomb,” what hope can there be of justice to Catholic truth
and the Catholic faith in our great secular universities?
We see, then, that not alone are the facts of history falsified, but
the genius of the poet is enlisted to give glamor and glow to the
historical slander.
Take again Tennyson’s poem, “St. Simeon Stylites.” This is a
satire on ascetic life. Tennyson was a Broad Churchman, and it is
said that he was particularly careful not to write anything that would
offend the religious feelings of any of his friends. He saw, however,
at the time of the “Oxford Movement,” the English mind in certain
quarters look with favor on monasticism, and he wrote “St. Simeon
Stylites” as a rebuke to the movement. But is it a true picture of the
spirit and life of those early hermits of the desert? Not at all.
Tennyson as a satirist did not aim at truth, but rather at
exaggeration. So he puts into the mouth of this pillar-fixed saint
these words of pride:

“A time may come, yea, even now,

When you may worship me without reproach,
And burn a fragrant lamp before my bones,
When I am gathered to the glorious Saints.”

The essence of the Catholic faith is not “the torpidity of

assurance,” but the working out of one’s salvation in fear and
trembling. That pride should sometimes gain entrance into the
cloister and assume the garb of humility is no doubt true; but the
self-renunciation which is the true spirit of the cloister, giving up all
for the service of God, is in itself a mantle of virtue—a seamless
garment of grace which neither the false satire of a Tennyson nor
the flashlight of a Browning monologue can transform from a
beauteous raiment of light.
It is true that the same pen which gave us “St. Simeon” gave us
also these beautiful lines in “St. Agnes’ Eve,” a poem which is stirred
with the loveliness and tenderness of religious life. St. Agnes on the
very eve of death utters these ecstatic words in beatific vision:
“He lifts me to the golden doors;
The flashes come and go;
All heaven bursts her starry floors,
And strews her lights below,
And deepens on and up! The gates
Roll back, and far within
For me the heavenly Bridegroom waits
To make me pure of sin.
The Sabbaths of Eternity,
One Sabbath deep and wide—
A light upon the shining sea—
The Bridegroom with his bride.”

The student, before accepting Tennyson’s poetic or, more

correctly, satiric picture of the hermits of the desert in the early
centuries of the Church as represented in “St. Simeon Stylites,”
would do well to study the condition of the Christian, or rather
pagan, world at the time when the hermits fled to the desert. It is a
remote period in the life of the world, and like all remote periods you
must translate yourself into it if you would clearly and justly
understand it. But we warn you that Kingsley’s “Hermits” will not
enlighten you.
Catholics have no need to apologize for the life or policy of their
Church during its reign of nineteen hundred years. It is a book open
to the world, and every chapter in it is a record of the spiritual and
intellectual progress of man. There have been, indeed, twilight
epochs—spiritual eclipses—when man seemed to forget his divine
destiny; but the Church of God still stood at her altars waiting for
her people to kneel—waiting for the “Introibo ad altare Dei” to reach
the heart of king and noble, peasant and slave.
Therefore as a student of history and literature we protest
against every misrepresentation of Catholic truth, whether within the
pages of history, fiction or poetry, no matter who may be its author
—a professor in one of our New World universities, a Marie Corelli
counting her gains as she kneels at the shrine of a publisher, a
Tennyson striking the chords of falsehood and “looking down
towards Camelot,” or a Browning constructing his little monologue
chapel by the wayside to seduce from Catholic truth his poetic
pilgrim—it is ever misrepresentation wearing the specious garb of
truth, whether it be in history or fiction or poetry teaching falsehood.

THE STUDY AND INTERPRETATION

OF LITERATURE

THE STUDY AND INTERPRETATION OF

LITERATURE.

T he study of literature has of late years become somewhat sane

and rational in its aim and purpose. There was a time, and that
not very long ago, when literature was forced to yield up its spirit in
the class-room to mere analysis or a talk about grammar, philology,
rhetoric and sundry other irrelevant subjects.
To-day, however, in the best schools and colleges, this vicious
method, which has for years worked destruction to true literary
culture, has pretty well died out; nor is a through ticket by flying
express down the centuries from Chaucer to Tennyson any longer
regarded as satisfactory evidence that the privileged passenger
knows much of the glory which nestles on the way.
How any person can hope to become a literary scholar in the
highest and best sense of the word without assimilating the
INFORMING life of literature has always seemed to us a problem in dire
need of solution. We can well understand how one may possess
himself of the literature of knowledge without such assimilation, but
how he can become possessed of the literature of power without
responding to the inner life of an art product, is to us a question
incomprehensible.
Nor has the old spirit, we fear, been fully and wholly exorcised, as
yet, from the class and lecture room. There are still to be found
those who believe that the analytical exegesis of literature should be
the main purpose of the teacher—that to elucidate the intellectual
thought which articulates a poem, precipitating it from a concrete
creation into a barren abstraction—this and this alone should be the
aim and end of all literary study in the school or lecture room.
The fault with such persons is, that they do not fully understand
and appreciate the true meaning and import of literature, mistaking
its lesser coefficient for its chief and primary one. No definition of
literature can be at all adequate which does not take into
consideration the spiritual element as a factor. The late Brother
Azarias, whose study of literature was most profound, clear and
sympathetic, gives us a definition in the very opening chapter of his
charming little volume, “A Philosophy of Literature,” which is entirely
satisfactory. He regards literature as the verbal expression of man’s
affections, as acted upon in his relations with the material world,
society and his Creator. Literature may therefore be defined as the
expression in letters of the spiritual co-operating with the intellectual
man, the former being the dominant co-efficient.
Knowing, then, that the spiritual element constitutes the
INFORMING life of a poem, how can teachers fritter their time away
with brilliant analytics which do little or nothing for true literary
culture? Better, far better, that the students under their charge be
turned loose in some library—there to browse at will, free to follow
their literary tastes and inclinations.
We have long considered that examinations for certificates and
degrees are for the most part a detriment to literary studies—that
they dull the finer faculties of appreciation and magnify the
importance of mere acquisition. Assuredly, when a young man finds
that in order to reach his diploma or degree he must be able to
discuss the Elizabethan English as found in Shakespeare’s “Macbeth”
and “As You Like It,” or trace the gerundial infinitive through
Chaucer’s “Canterbury Tales,” he will pay little heed to either the
spirit of Shakespeare or Chaucer as embodied in their works.
In our great eagerness to fill our heads with facts, without any
co-ordination, we lose sight amid the stress and strain of our
educational work of the ONE GREAT FACT: That if we would be wisely
educated, we must seek it on the basis of a maximum of education
with a minimum of acquirement. It is impossible to play fast and
loose with the spirit of literature and not suffer for our insincerity.
Literature is a jealous mistress and will brook no rival. Those who
woo her must come with clean hearts and minds, setting aside all
thought of mercenary returns, for, as Mrs. Browning says:

“We get no good

In being ungenerous, even to a book,
And calculating profits—so much help
By so much reading. It is rather when
We gloriously forget ourselves and plunge
Soul-forward, headlong into a book’s profound
Impassion’d for its beauty and salt of truth—
’Tis then we get the right good from a book.”

Another fault which characterizes the literary studies of to-day is,

that we grasp at too much, and not a little that we fain would
compass is, as far as literary training and culture are concerned,
entirely unimportant. A few great literary personages—epochal men
—who have handed the intellectual torch down the centuries—these
are worthy of a devoted study. We think it is Ruskin who says that
he who knows the history of Rome, Venice, Florence, Paris and
London has a full knowledge of medieval and modern civilization.
Twenty authors are not many, still they largely cover the great
masterpieces of poetic thought, both ancient and modern. Homer,
Virgil and Dante, Calderon, Molière and Goethe, Chaucer, Spenser,
Shakespeare, Milton, Wordsworth and Tennyson—these contain
much of the best poetic thought in all ages, and yet we have but
named little more than half of the twenty. There is a flood of
ephemeral literature—chiefly novels—day by day deluging the land,
which fashion and frivolity set up for literary study. How much harm
these novels do, lashing with their waves the moral shores of life.
God alone knows. To-day, in the minds of many, the novel has
supplanted the Bible, and the ethics of George Eliot take precedence
of the Sermon on the Mount. It is doubtful if either Cardinal Newman
or John Ruskin ever read a line of Tolstoi, Ibsen or Kipling, and yet
both hold respectable places in literature.
Passing now from the subject of literature in itself to a
consideration of its interpretation, we desire to touch upon a subject
of vital import: The Vocal Interpretation of Literature. The spiritual
element in a poem is indefinite and cannot be formulated in terms of
x and y. No examination on paper, be it ever so thorough, can
satisfactorily reach it. The only full response to this spiritual element,
this essential life of a poem, that can be secured by the teacher is
through a vocal rendering of it. But before he is capable of doing so
he must first have sympathetically assimilated the INFORMING life of
the poem. This is why no person need hope to become a great
reader without a deep and sympathetic study of literature, nor a
great interpreter of literature—which means a great teacher of
literature—without the vocal capabilities requisite for voicing the
indefinite or spiritual element which constitutes the soul of an art
product. A true literary scholar is one who grows soulward. It is not
enough that he store his mind with intellectual facts, he should grow
vitalized at every point of his soul in his literary studies.

“Let knowledge grow from more to more,

But more of reverence in us dwell.”

Knowledge is of the intellect, wisdom and reverence of the soul.

We should aim, in our study of literature, to pierce through the show
of things—to reach the vital, quickening, spiritual element, by
breaking through the baffling and perverting mesh of words which
hide and blind it. How true are the lines of the late Poet Laureate:
 “I sometimes hold it half a sin
To put in words the thoughts I feel,
For words, like nature, half reveal
And half conceal the soul within.”

Herein, then, comes the office of the voice in literary

interpretation—to aid in laying bare the soul within. When the same
time is given in preparing the voice for the high office of literary
interpretation that is now devoted to it in preparation for the
operatic and concert stage, then we may look for the best and
highest results in literary study. Then, indeed, will the throbbing
pulse of poetry be felt in the class and lecture room, and the divine
infection of inspiration will do its benign work, cheating the lazy and
indifferent student of his hours and days.
Many make the mistake of believing that they may become
capable vocal interpreters of literature in a month or a year, whereas
the great work should cover a lifetime. Professor Corson, of Cornell
University, who is acknowledged to be the ablest vocal interpreter of
literature in America, once told the writer that he had made it a
custom to read aloud for an hour each day for more than twenty-five
years. Those who have been privileged to hear Professor Corson
interpret vocally the great masterpieces of poetic literature, as found
in Shakespeare, Tennyson, Coleridge, Wordsworth, Milton and
Browning, can better understand and appreciate the true value of
vocal culture as a factor in the great work of literary interpretation.
If we could combine the voice work of our best schools of
elocution and oratory with the fullest and most comprehensive
courses in literature found in our best universities, we might soon
hope for the very summit of literary culture and training. The worst
of our elocution schools are a positive injury to vocal training as a
worthy factor in the interpretation of literature, inasmuch as they
induce both superficiality and artificiality, their chief ambition being
to graduate pretty girls with pretty gowns who can recite some
catch-penny piece of current literature, before an assemblage of
admiring friends, according to the numbers or lines upon an
elocutionary chart or fashion plate. When these graduates leave
their schools after a six months’ course, all equipped and prepared
to voice the depths of Shakespeare, the heights of Milton, or the
zigzag involutions of Browning, they never fail, also, as a rule, to
carry with them the brand or trade-mark of their respective
manufactories.
In the best of our elocution schools, such as are found in Boston,
Philadelphia and New York, where saner and more thorough
methods are pursued and a certain measure of literary scholarship
finds a habitation and a name, respectable attention is given to
some of the chief masterpieces of literature, and a graduate knows
something more than the scrappy selections found in a few
recitation books.
Still the aim of all these schools is to turn out readers and
teachers of reading, and this very aim precludes a deep, serious and
comprehensive study of literature.
In many of our leading colleges and universities there is a
professor of oratory, who trains young men for declamation and
intercollegiate contests in oratory and debate, but here again the
aim determines the character and limitations of the work done. The
most suitable department for voice training in a college or university
is that of English literature, for it is as needful in the dramas of
Shakespeare as in the orations of Webster and Burke; as requisite in
the lyrics of Moore, Burns and Longfellow as in the glorious epics of
Homer, Dante and Milton; as potent in the sonnets of Cowper and
Wordsworth as in the tender elegies of a Shelley, an Arnold or a
Tennyson.
But what about the vocal interpretation of literature in our
primary and intermediate schools—in our academies preparatory to
college and university work? It is here where the great work of vocal
culture should begin—and begin in earnest, too. But it should never
be pursued as an accomplishment or means of frivolous display. The
aim should be, in every class, the adequate voicing of literary
thought. Teachers will find in the voice an invaluable aid in the work
of interpreting, particularly lyrics.
 The lyric being subjective, and its very lifeblood being feeling, a
sympathetic vocal interpretation of it will give a better insight into its
poetic moment or inspirational thought, around which centres the
whole structure, than hours of sentence chopping and phrase
stitching. For the purpose of illustrating this fact let us take
Tennyson’s exquisite lyric, “Break, Break, Break,” which embodies or
crystallizes a mood. Here is the delightful little gem:

“Break, break, break,

On thy cold gray stones, O Sea!
And I would that my tongue could utter
The thoughts that arise in me.

“O well for the fisherman’s boy

That he shouts with his sister at play!
O well for the sailor-lad,
That he sings in his boat on the bay.

“And the stately ships go on

To their haven under the hill;
But O for the touch of a vanish’d hand,
And the sound of a voice that is still!

“Break, break, break,

At the foot of thy crags, O Sea!
But the tender grace of a day that is dead
Will never come back to me.”

It will be remembered that this lyric, as well as another poem, “In

the Valley of Cauteretz,” though not contained in the linked elegy of
“In Memoriam,” are practically a part of it, and are co-radical as to
their subject of inspiration—the sorrow borne by Tennyson for young
Hallam. Here are the lines of the second poem:
“All along the valley, stream that flashest white,
Deepening thy voice with the deepening of the night,
All along the valley, where thy waters flow,
I walked with one I loved two and thirty years ago.
All along the valley, while I walk’d to-day,
The two and thirty years were a mist that rolls away;
For all along the valley, down thy rocky bed,
Thy living voice to me was as the voice of the dead.
And all along the valley, by rock and cave and tree,
The voice of the dead was a living voice to me.”

It is easy to find the poetic moment in the first lyric, as it may be

seen and FELT at once that the whole poem-thought centres around
the inspirational lines:

“But O for the touch of a vanished hand,

And the sound of a voice that is still.”

We have seen an examination paper strewn with questions upon

this lyric, among them being one asking for the reason why the first
line, “Break, break, break,” is shorter in the number of its feet than
the others which follow. As well ask for the reason of the
permanency of parental or filial affection. The question is entirely
gratuitous to one who has assimilated the poem in its essential life
and can voice it properly. To those who have not responded, or,
worse, cannot respond, to the INFORMING life of the lyric, a technical
answer is of as much value as are many of the treatises that assume
to deal with the subject of versification. But enough. Let the reader
be assured of one thing: That the vocal interpretation of literature is
in every way a subject worthy of his attention, and that he is the
best interpreter of literature whose every faculty is fully developed—
not the least of which is the voice—and who brings to his work a full
and vitally spiritualized life.
Now as to the best method of taking up the study of literature—
and we refer particularly to that department of it known as poetry—
in our primary and secondary schools and colleges, why, we should
say that the less method put into the work the better. For indeed
there is no best method in the study and interpretation of literature.
A poem being a work of art, the approach to it must be along the
same lines as is the approach to every work of art.
As a matter of fact, no two interpreters of literature—we use the
word interpreter here rather than that of teacher, since the study of
literature is entirely subjective—will ever approach a poem along
exactly the same lines. Why? Because the poem makes to each a
different appeal. Nothing is truer than the statement that you get
out of a poem what you bring to it. But the teacher of literature
should ever remember that the primary purpose in the study of
poetry is not discipline and instruction but exaltation and inspiration.
Dr. Hamilton Mabie, the well-known American critic and author,
writing upon the study of poetry, says: “So much has been said of
late years about methods of literary study that we are in danger of
missing the ends of that study; in the multiplication of mechanical
devices of all kinds and in the elaboration of systems the joy which
ought to flow from a true work of art escapes us, and we are
disciplined and instructed where we ought to be exalted and
inspired. There are other studies which train the mind and impart
information; the study of poetry ought to do more; it ought to
liberate the imagination and enrich the spirit of the student.”
Dr. Corson, now Professor Emeritus of English Literature at
Cornell University, N.Y., to whom reference has already been made,
whose sympathetic interpretation of poetry will remain a gift and
memory to every student who has ever had the rare privilege of
sharing in his instruction and enjoying the fine infection of his
inspiring lectures, has this to say with respect to the study of poetry:
“In studying a poem with a class of students, the purpose being
literary culture (that is, spiritual culture), the aim of the teacher
should be to hold the minds of the class up as near as possible,
which at best may not be very near, to the height of the poet’s
thought and feeling. He should carefully avoid loosening, so to
speak, more than there is need the close texture of the language;
for it is all-important that the student should be encouraged to think
and feel as far as he is able in the idealized language of the higher
poetry.”
Nor should it be forgotten that much of our best poetry is
expressed under the form of a symbol. Take, for instance,
Longfellow’s little simple lyric, “Excelsior.” Think you that the full
meaning of that poem lies upon the surface? Instead of representing
the failure of a youth climbing the Alpine peaks of life, does the
poem not rather represent the triumph of a soul over all earthly
difficulties, freed from every worldly allurement? Is not the voice we
hear at the close “from the sky serene and far” but the voice of
triumphant immortality?
If the student would indeed know what poetry really means, and
what is its function, and what the office of a poet, he should read
Tennyson’s “The Poet’s Mind” and “The Lady of Shalott,” the Fifth
Book of Mrs. Browning’s “Aurora Leigh,” and her “Musical
Instrument,” and Browning’s poem, “Popularity.” In nearly all these
poems the meaning is expressed in symbol.
Another thing to remember in the interpretation of poetry is that
its value is constant; nor has it one message or meaning for the boy
and another for the man. But in order that this may be realized it
would be well to take up first for interpretation in the classes the
poets whose work is chiefly confined to the lyric, the idyl and the
ballad, and leave for mature years—the years of philosophic thought
—the study of poets of the more complex and philosophic school.

THE DEGRADATION OF
SCHOLARSHIP
 THE DEGRADATION OF SCHOLARSHIP.

N othing is more evident in this our day than the degradation to

which scholarship is subjected at the hands of certain so-called
educators. Indeed, it has become a malady which sooner or later
must prove fatal to the life and welfare of the body educational. How
could it be otherwise when pedantry with all its assumption and
presumption usurps the throne of scholarship, and true culture often
finds but little welcome in the class-rooms and academic halls of our
land?
Nor is this an exaggerated picture of the educational conditions
which obtain right here in the Province of Ontario. No person at all
acquainted with the character of work done in our primary and
secondary schools but knows that in many respects it is not only
inferior, but that much that bears the name of scholarship is only the
merest pedantry tricked out in the feathers and pomp of a school
curriculum.
Should you ask for a proof of this statement you have but to visit
with an open and unbiased mind the primary and secondary schools
of our Province and learn for yourself of their lack of efficiency in the
foundation subjects of reading, writing, composition and spelling.
Should your desire lead you further to ascertain something of the
character of the work that is being done in the departments of what
may be designated culture subjects, such as Latin, French and
German, you will quickly find proof that here it is pedantry rather
than scholarship which obtains.
As to the subject of reading, it is conceded on all sides that it is
badly taught in both the Public and High Schools, and that along this
line little progress has been made for a number of years. The High
School teachers lay the blame for this at the door of the Public
Schools, alleging that the pupils read very badly when they enter the
High Schools, forgetting meantime that the charge recoils upon
themselves, since the teachers of the Public Schools are the product
of the High Schools.
The fault lies in the fact that neither teachers nor inspectors of
Public or High Schools in Ontario have had any training in the
subject of reading; or, if they have had, it has only been along the
line of barren and worthless theorizing. This is borne out by the fact
that teachers who have from time to time boldly ventured to prepare
manuals of reading have not been able to apply their own principles,
and as readers or vocal interpreters of literature have been and are
pronounced failures.
If the teacher whose spirit has been quickened by the deeper
sympathies and experiences of life cannot read, how, pray, can you
expect the boy or girl to do so? If “Learn by doing” is pedagogically
of great value to the pupil, should it not be of equal value to the
teacher?
Now turn we for a moment to the subject of composition, and
what do we find? A condition which reveals manifest defects in its
teaching. We can readily put our finger on its weak spots, and with
Goethe say, “Thou ailest here and ailest there.” In the first place, the
translations in the secondary schools from Greek, Latin, French and
German authors are so badly done, so inaccurately done, so
inelegantly done, that what should be a daily practice in English
composition in the construction of sentences and paragraphs, the
disposal of phrases, and the choice of the exact word, becomes
almost worthless. The introduction of no fad like oral composition
will or can compensate for this.
Again, while the Public and High Schools are being provided with
libraries—in many instances quite an unnecessary expense being
entailed—little direction is given to the reading, and pupils gabble
thoughtlessly through books in mental gallop from chapter to
chapter without adding to the capital of their scholarship a single
new thought or idea, or to their vocabulary a single new word. Was
it not at a convention of teachers, held but a short time ago in an
Ontario city, that a Public School teacher boasted of the fact that
one of his pupils had read sixty books in three months? And not a
teacher present—not even the Inspector—protested.
 Then, too, in many cases the teachers cannot teach composition,
since they cannot write themselves. What does a teacher know
about sentence or paragraph construction, or the logical and artistic
expression of thought, who has never served his time as an
apprentice in the great laboratory of composition? It is but a few
years since a leading Canadian journalist told the writer that among
the letters sent to his paper many of the worst and most faulty came
from teachers.
Lastly, the study of literature, which should be an auxiliary to
composition, nay, be its right arm, is often such in our schools as to
aid the student but little in the work of composition.
There yet remain to be considered, of the foundation subjects,
writing and spelling. Perhaps nowhere else in the world can be found
as many slovenly and bad writers as here in the schools of Ontario.
Go to England, Ireland, Scotland, Germany or Switzerland, and you
will find that a boy or girl of fifteen years of age writes a hand
marvellously clear and legible. Why is this? Because in Europe its
importance is emphasized, and it counts for quite as much in the
estimate of acquirements as arithmetic or grammar or history or
geography. We also know of no word in the school vocabulary of
Europe—in any language—that exactly corresponds in meaning to
our word for school exercise book—“scribbler.” Sometimes a word
when traced to its origin is very significant.
Now just here it will be well, lest it might be thought that we are
making statements without any facts to support them, to quote from
the official report of McGill University matriculation examination held
at Montreal and the various examining centres of Canada in June,
1908. Touching the subjects of writing and spelling, the chief
examiner in his report says: “The handwriting of some of the
candidates was so unformed and untidy that it was hard to believe
that the writers were actually candidates at a matriculation
examination. Certainly such candidates will stand a poor chance of
being accepted should they look for any employment in which
writing is a factor. It is regrettable that a number of papers
otherwise excellent showed conspicuous lapses in this particular.
This will explain to some candidates thoroughly well up in their
subject why their marks were not high. A word of warning might be
given them that if they wish to have a high standing in English when
they come to college they must give their days and nights to the
study of the spelling-book—or the dictionary, perhaps, for there are
no spelling-books nowadays.” This is frank criticism, and if
hearkened to by schools and colleges cannot but prove a benefit
educationally. There is no attempt here to consider the work of the
examiner as “confidential.” Such criticism is, indeed, the basis of
progress.
But pray enter the temple of higher studies and see what we
find. Assuredly the work done in Latin is not thorough. How could it
be so when a course that demands six or eight years of study in Old
World schools is completed here in three? Is it any wonder that the
Canadian matriculant, when pursuing his classical studies at the
University, ever lives on intimate terms with his “crib” or “pony”?
How extensive can be the vocabulary of a student in Latin whose
class work has covered but four thirty-minute spaces a week for
three years? What will be his grasp of the Latin grammar? During his
third year he has been “sight reading.” Is he really prepared for such
work at the end of the second year? It is quite true that “sight
reading,” or translation without preparation, is excellent practice in
the study of any language, but does it not presuppose a solid
grounding in the grammar and a wide vocabulary? The boy’s
teacher, fresh from the academic halls of his alma mater, has
pathetically bid farewell to his “crib” or “pony,” and now goes out
into the cold classical world alone to teach “sight reading” to his
class, that have been tiptoed into Latin. What is the result? In most
instances the work is worthless—a loss of time which could have
been far better devoted to the Latin grammar or the extension of his
vocabulary. But it looks well, you know, in a High School curriculum.
In the department of modern languages—that is to say, French
and German—a still worse condition exists. After a three or four
years’ course in those languages in an Ontario High School, what
does the student carry away? The ability, think you, to converse in
those languages, to write them and read them easily? Not at all.
Though in many cases the students have been taught by so-called
specialists, their accent in reading French or German is in most
instances unlike that of either “Christian, pagan or man.” They have
prepared for an examination and have passed. That is all.
The purpose in studying modern languages in Europe is to be
able to speak and write them with ease. Here gabbling through
syntax and making application of its rules to the prescribed text
seem to constitute the chief aim in their study. Indeed, an Ontario
teacher who went to Europe a couple of years ago for the purpose
of taking a summer course in modern languages complained on his
return that over there too much attention was given to the speaking
of the languages and not enough to the grammar. He was probably
disappointed with Old World scholarship, finding that it was so
devoid of pedantry. No doubt grammar has its place, but its role is a
secondary one in the acquisition of any modern language.
Let us for a moment consider next how the important subject of
history is taught in our secondary schools. No one will deny how
large a place this subject should hold in a curriculum of well ordered
studies in either a High School or a University. For what is history but
a record of the activities of the human race, and to have a thorough
knowledge of this is in itself equivalent to a liberal education.
But the student who pursues a course in history in the High
Schools of Ontario is beset with a double danger—that of
endeavoring to cover too much ground and thereby getting but a
superficial knowledge of the facts and great movements of history,
and that of basing his judgments on data drawn from only one
source.
The course in history, as at present constituted in the High
School curriculum of Ontario, comprises five years. Now, certainly a
good deal should be done in that time, but it would be the sheerest
folly to think that any boy or girl could within that time gain even a
fair knowledge of the history of Greece, Rome, Canada, England,
medieval and modern Europe. This tiptoeing the pupils in history is
not a whit better than tiptoeing them in Latin, French or German.
Indeed, we are not sure but it works greater harm to true
scholarship. We are living in an age when education is becoming so
widely diffused that scholarship as a consequence is becoming very
superficial and thin.
As we write we have before us the Syllabus of the Ontario High
School Course in Medieval and Modern History. It briefly outlines the
scope of the work to be done and gives a list of books to be
consulted as works of reference. Now, the scientific method of
studying history warns you to take nothing for granted. First you
must verify the facts by examining the witnesses that testify to these
facts. Secondly, you must properly appreciate or value these facts
from the point of view of principles that ought to govern human
actions, and thirdly, these facts should be explained by going back to
the causes, whether particular or general, that produced them. That
is, the scientific method in history requires, first, verification;
secondly, appreciation or valuation; and thirdly, explanation of
historic facts.
In a High School it is true there is not sufficient time for historical
research or investigation, but there is sufficient time to study a
question on more than one side; there is sufficient time to be
honest; there is sufficient time to prefer truth to falsehood; and
where in a mooted point the policy and teachings of the Catholic
Church are involved there should be sufficient time and sufficient
honesty to consult authors who know whereof they write. Take for
example the history of the Middle Ages. Without a thorough and
correct knowledge of the policy, teachings and work of the Catholic
Church, how, I ask, may the student hope to follow and understand
the great movements of history in those centuries? In the first place,
the Catholic Church in the Middle Ages was the bulwark of
sovereignty, law and order, the founder of universities, the patron of
letters, the inspiration of art, the shield of the oppressed, and a very
staff and guide to the halting and stumbling steps of civilization. She
was knowledge, she was authority, she was order, she was
reverence.
Taking up now the books of reference recommended in the
Syllabus of the High School Course in Medieval and Modern History
in Ontario, we find the work of but one Catholic author on the
reference list—“English Monastic Life,” by Dom Gasquet, the
Benedictine. Is this not truly a one-sided study of history that
obtains in the secondary schools of Ontario? Yet the teachers of
history in those schools are supposed to be broad-minded and
cultured men. Why, then, should they refuse to read the Catholic
point of view in the study of historical periods and historical
movements in which the Catholic Church was the greatest factor?
It will not do to say that Catholic authors are not available.
Translations have been made of many of the most valuable works in
medieval and modern history written by leading Catholic scholars of
Europe. We usually find what we look for. Why, for instance, not put
on the list of reference books the lives of St. Benedict, St. Dominic,
St. Francis and St. Ignatius written by members of their own
communities? They should best understand the meaning, spirit and
purpose of the religious society in which they live. Why not put on
the list the great German historian Jansen’s work dealing with the
history of Germany on the eve of the Lutheran revolt, or Father
Denifle’s monumental work, “The Life of Luther”? For the beginnings
of Christianity why not put on the list Dr. Shahan’s excellent studies
in this subject, as well as his scholarly work on the Middle Ages? For
a study of the Thirteenth Century, which saw the founding of the
medieval university, the rise of the Gothic cathedral, the
development of scholastic philosophy, the birth of Dante, the world’s
greatest epic poet, the composition of the great Latin hymns, the
foundation of great libraries, and the origin of democracy, Christian
socialism and self-government, is there a better work of reference
than Dr. J. J. Walsh’s “The Thirteenth, Greatest of Centuries”? Why,
then, not put it on the list? And beside this, why not put on the list
Pastor’s “Lives of the Popes Since the Close of the Middle Ages”?
If the purpose in the study of history be to reach truth, why
accept in the court of history the testimony of but one set of
witnesses? Such a proceeding is neither judicial nor just. It would
not be permitted in the law courts of our land; why, then, permit it
in the history courts of our schools and colleges?
Nor is this ex-parte study of history more obvious in the
curriculum of the High Schools of Ontario than is the objectionable
character of many of the poems that are assigned for literary study.
In the selections from Browning of last year this choice stanza
greeted the Catholic pupils in their study and appreciation of “Up at
a Villa—Down in the City”:

“Or a sonnet with flowery marge to the Reverend Don So and So,
Who is Dante, Boccaccio, Petrarca, St. Jerome and Cicero.
‘And moreover’ (the sonnet goes rhyming), ‘the skirts of St. Paul has
reached,
Having preached us those six Lent-lectures more unctuous than ever
he preached.’
Noon strikes,—here sweeps the procession! our Lady borne smiling
and smart
With a pink gauze gown all spangles and seven swords stuck in her
heart!
Bang-whang-whang goes the drum, tootle-te-tootle the fife;
No keeping one’s haunches still: it’s the greatest pleasure in life.”

It may, we think, be legitimately questioned whether either the

study in our secondary schools of a one-sided presentation of the
facts of history or the interpretation of poems which ridicule the
tenets and ceremonies of any Church conduces to that breadth of
scholarship and culture and to the upbuilding of that large-minded
Canadian citizenship which we all so heartily desire in our land.
Is it not on the plea that these higher institutions of learning—
High Schools and Normal Schools—are broad and just and free from
prejudice in their teaching that the Roman Catholic Separate School
System has been persistently denied by successive Governments in
this Province the right to develop beyond an elementary status,
though this right is manifestly inherent or implied in the very pact
which made provision for the establishment of Separate Schools for
the minorities in the Provinces of Quebec and Ontario. The
Government of Quebec has recognized the right; the Government of
Ontario refuses to do so.
Now a word as to certain conditions educational which prevail in
Ontario and which have not only led to abuses but are contributing
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