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BIOINFORMATICS
ALGORITHMS
BIOINFORMATICS
ALGORITHMS
Techniques and Applications

Edited by

Ion I. Măndoiu and Alexander Zelikovsky

A JOHN WILEY & SONS, INC., PUBLICATION

Copyright © 2008 by John Wiley & Sons, Inc. All rights reserved.

Published by John Wiley & Sons, Inc., Hoboken, New Jersey

Published simultaneously in Canada

No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or
by any means, electronic, mechanical, photocopying, recording, scanning or otherwise, except as
permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without either the prior
written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to
the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400, fax
978-646-8600, or on the web at www.copyright.com. Requests to the Publisher for permission should be
addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ
07030, (201)-748-6011, fax (201)-748-6008.
Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in
preparing this book, they make no representations or warranties with respect to the accuracy or
completeness of the contents of this book and specifically disclaim any implied warranties of
merchantability or fitness for a particular purpose. No warranty may be created or extended by sales
representatives or written sales materials. The advice and strategies contained herein may not be suitable
for your situation. You should consult with a professional where appropriate. Neither the publisher nor
author shall be liable for any loss of profit or any other commerical damages, including but not limited to
special, incidental, consequential, or other damages.
For general information on our other products and services please contact our Customer Care Department
within the U. S. at 877-762-2974, outside the U. S. at 317-572-3993 or fax 317-572-4002.
Wiley also publishes its books in a variety of electronic formats. Some content that appears in print,
however, may not available in electronic format.
Library of Congress Cataloging-in-Publication Data:
Bioinformatics algorithms : techniques and applications / edited by Ion I.
Mandoiu and Alexander Zelikovsky.
p. cm.
ISBN 978-0-470-09773-1 (cloth)
1. Bioinformatics. 2. Algorithms. I. Mandoiu, Ion. II. Zelikovsky,
Alexander.
QH324.2B5472 2008
572.80285–dc22
2007034307
Printed in the United States of America
10 9 8 7 6 5 4 3 2 1
CONTENTS

Preface ix

Contributors xi

1 Educating Biologists in the 21st Century: Bioinformatics Scientists

versus Bioinformatics Technicians 1
Pavel Pevzner

PART I TECHNIQUES 7

2 Dynamic Programming Algorithms for Biological Sequence

and Structure Comparison 9
Yuzhen Ye and Haixu Tang

3 Graph Theoretical Approaches to Delineate Dynamics

of Biological Processes 29
Teresa M. Przytycka and Elena Zotenko

4 Advances in Hidden Markov Models for Sequence Annotation 55

Broňa Brejová, Daniel G. Brown, and Tomáš Vinař

5 Sorting- and FFT-Based Techniques in the Discovery of Biopatterns 93

Sudha Balla, Sanguthevar Rajasekaran, and Jaime Davila

v
vi CONTENTS

6 A Survey of Seeding for Sequence Alignment 117

Daniel G. Brown

7 The Comparison of Phylogenetic Networks: Algorithms

and Complexity 143
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, and
Giancarlo Mauri

PART II GENOME AND SEQUENCE ANALYSIS 175

8 Formal Models of Gene Clusters 177

Anne Bergeron, Cedric Chauve, and Yannick Gingras

9 Integer Linear Programming Techniques for Discovering

Approximate Gene Clusters 203
Sven Rahmann and Gunnar W. Klau

10 Efficient Combinatorial Algorithms for DNA

Sequence Processing 223
Bhaskar DasGupta and Ming-Yang Kao

11 Algorithms for Multiplex PCR Primer Set Selection with

Amplification Length Constraints 241
K.M. Konwar, I.I. Măndoiu, A.C. Russell, and A.A. Shvartsman

12 Recent Developments in Alignment and Motif Finding

for Sequences and Networks 259
Sing-Hoi Sze

PART III MICROARRAY DESIGN AND DATA ANALYSIS 277

13 Algorithms for Oligonucleotide Microarray Layout 279

Sérgio A. De Carvalho Jr. and Sven Rahmann

14 Classification Accuracy Based Microarray Missing Value

Imputation 303
Yi Shi, Zhipeng Cai, and Guohui Lin

15 Meta-Analysis of Microarray Data 329

Saumyadipta Pyne, Steve Skiena, and Bruce Futcher
 CONTENTS vii

PART IV GENETIC VARIATION ANALYSIS 353

16 Phasing Genotypes Using a Hidden Markov Model 355

P. Rastas, M. Koivisto, H. Mannila, and E. Ukkonen

17 Analytical and Algorithmic Methods for Haplotype

Frequency Inference: What Do They Tell Us? 373
Steven Hecht Orzack, Daniel Gusfield, Lakshman Subrahmanyan,
Laurent Essioux, and Sebastien Lissarrague

18 Optimization Methods for Genotype Data Analysis

in Epidemiological Studies 395
Dumitru Brinza, Jingwu He, and Alexander Zelikovsky

PART V STRUCTURAL AND SYSTEMS BIOLOGY 417

19 Topological Indices in Combinatorial Chemistry 419

Sergey Bereg

20 Efficient Algorithms for Structural Recall in Databases 439

Hao Wang, Patra Volarath, and Robert W. Harrison

21 Computational Approaches to Predict Protein–Protein

and Domain–Domain Interactions 465
Raja Jothi and Teresa M. Przytycka

Index 493
PREFACE

Bioinformatics, broadly defined as the interface between biological and computational

sciences, is a rapidly evolving field, driven by advances in high throughput technolo-
gies that result in an ever increasing variety and volume of experimental data to be
managed, integrated, and analyzed. At the core of many of the recent developments in
the field are novel algorithmic techniques that promise to provide the answers to key
challenges in postgenomic biomedical sciences, from understanding mechanisms of
genome evolution and uncovering the structure of regulatory and protein-interaction
networks to determining the genetic basis of disease susceptibility and elucidation of
historical patterns of population migration.
This book aims to provide an in-depth survey of the most important develop-
ments in bioinformatics algorithms in the postgenomic era. It is neither intended as
an introductory text in bioinformatics algorithms nor as a comprehensive review of
the many active areas of bioinformatics research—to readers interested in these we
recommend the excellent textbook An Introduction to Bioinformatics Algorithms by
Jones and Pevzner and the Handbook of Computational Molecular Biology edited
by Srinivas Aluru. Rather, our intention is to make a carefully selected set of ad-
vanced algorithmic techniques accessible to a broad readership, including graduate
students in bioinformatics and related areas and biomedical professionals who want
to expand their repertoire of algorithmic techniques. We hope that our emphasis on
both in-depth presentation of theoretical underpinnings and applications to current
biomedical problems will best prepare the readers for developing their own extensions
to these techniques and for successfully applying them in new contexts.
The book features 21 chapters authored by renowned bioinformatics experts who
are active contributors to the respective subjects. The chapters are intended to be
largely independent, so that readers do not have to read every chapter nor have to read
them in a particular order. The opening chapter is a thought provoking discussion of
ix
x PREFACE

the role that algorithms should play in 21st century bioinformatics education. The
remaining 20 chapters are grouped into the following five parts:

Part I focuses on algorithmic techniques that find applications to a wide range of

bioinformatics problems, including chapters on dynamic programming, graph-
theoretical methods, hidden Markov models, sorting the fast Fourier transform,
seeding, and phylogenetic networks comparison approximation algorithms.

Part II is devoted to algorithms and tools for genome and sequence analysis.
It includes chapters on formal and approximate models for gene clusters, and
on advanced algorithms for multiple and non-overlapping local alignments and
genome things, multiplex PCR primer set selection, and sequence and network
motif finding.

Part III concentrates on algorithms for microarray design and data analysis.
The first chapter is devoted to algorithms for microarray layout, with next two
chapters describing methods for missing value imputation and meta-analysis
of gene expression data.

Part IV explores algorithmic issues arising in analysis of genetic variation across
human population. Two chapters are devoted to computational inference of
haplotypes from commonly available genotype data, with a third chapter
describing optimization techniques for disease association search in epidemi-
ologic case/control genotype data studies.

Part V gives an overview of algorithmic approaches in structural and systems bi-
ology. First two chapters give a formal introduction to topological and structural
classification in biochemistry, while the third chapter surveys protein–protein
and domain–domain interaction prediction.

We are grateful to all the authors for their excellent contributions, without which
this book would not have been possible. We hope that their deep insights and fresh
enthusiasm will help attracting new generations of researchers to this dynamic field.
We would also like to thank series editors Yi Pan and Albert Y. Zomaya for nurturing
this project since its inception, and the editorial staff at Wiley Interscience for their
patience and assistance throughout the project. Finally, we wish to thank our friends
and families for their continuous support.

Ion I. Măndoiu and Alexander Zelikovsky

 CONTRIBUTORS

Sudha Balla, Department of Computer Science and Engineering, University of

Connecticut, Storrs, Connecticut, USA
Sergey Bereg, Department of Computer Science, University of Texas at Dallas, Dal-
las, TX, USA
Anne Bergeron, Comparative Genomics Laboratory, Université du Québec à
Montréal, Canada
Paola Bonizzoni, Dipartimento di Informatica, Sistemistica e Comunicazione, Uni-
versità degli Studi di Milano-Bicocca, Milano, Italy
Broňa Brejová, Department of Biological Statistics and Computational Biology,
Cornell University, Ithaca, NY, USA
Dumitru Brinza, Department of Computer Science, Georgia State University,
Atlanta, GA, USA
Daniel G. Brown, Cheriton School of Computer Science, University of Waterloo,
Waterloo, Ontario, Canada
Zhipeng Cai, Department of Computing Science, University of Alberta, Edmonton,
Alberta, Canada
Cedric Chauve, Department of Mathematics, Simon Fraser University, Vancouver,
Canada
Bhaskar DasGupta, Department of Computer Science, University of Illinois at
Chicago, Chicago, IL, USA
Sérgio A. de Carvalho Jr., Technische Fakultät, Bielefeld University, D-33594
Bielefeld, Germany
xi
xii CONTRIBUTORS

Jaime Davila, Department of Computer Science and Engineering, University of

Connecticut, Storrs, Connecticut, USA
Gianluca Della Vedova, Dipartimento di Statistica, Università degli Studi di Milano-
Bicocca, Milano, Italy
Riccardo Dondi, Dipartimento di Scienze dei Linguaggi, della Comunicazione e
degli Studi Culturali, Università degli Studi di Bergamo, Bergamo, Italy
Laurent Essioux, Hoffmann-La Roche Ltd, Basel, Switzerland
Bruce Futcher, Department of Molecular Genetics and Microbiology, Stony Brook
University, Stony Brook, NY, USA
Yannick Gingras, Comparative Genomics Laboratory, Université du Québec à
Montréal, Canada
Daniel Gusfield, Department of Computer Science, University of California, Davis,
CA, USA
Robert W. Harrison, Department of Computer Science, Georgia State University,
Atlanta, GA, USA
Jingwu He, Department of Computer Science, Georgia State University, Atlanta,
GA, USA
Raja Jothi, National Center for Biotechnology Information, National Library of
Medicine, National Institutes of Health, Bethesda, MD, USA
Ming-Yang Kao, Department of Electrical Engineering and Computer Science,
Northwestern University, Evanston, IL, USA
Gunnar W. Klau, Mathematics in Life Sciences Group, Department of Mathematics
and Computer Science, University Berlin, and DFG Research Center Matheon
“Mathematics for Key Technologies,” Berlin, Germany
Mikko Koivisto, Department of Computer Science and HIIT Basic Research Unit,
University of Helsinki, Finland
Kishori M. Konwar, Department of Computer Science and Engineering, University
of Connecticut, Storrs, Connecticut, USA
Guohui Lin, Department of Computing Science, University of Alberta, Edmonton,
Alberta, Canada
Sebastien Lissarrague, Genset SA, Paris, France
Ion I. Măndoiu, Department of Computer Science and Engineering, University of
Connecticut, Storrs, Connecticut, USA
Heikki Mannila, Department of Computer Science and HIIT Basic Research Unit,
University of Helsinki, Finland
Giancarlo Mauri, Dipartimento di Informatica, Sistemistica e Comunicazione,
Università degli Studi di Milano-Bicocca, Milano, Italy
 CONTRIBUTORS xiii

Steven Hecht Orzack, Fresh Pond Research Institute, Cambridge, MA, USA
Pavel Pevzner, Department of Computer Science and Engineering, University of
California, San Diego, CA, USA
Teresa M. Przytycka, National Center for Biotechnology Information, National Li-
brary of Medicine, National Institutes of Health, Bethesda, MD, USA
Saumyadipta Pyne, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
Sven Rahmann, Bioinformatics for High-Throughput Technologies, Department of
Computer Science 11, Technical University of Dortmund, Dortmund, Germany
Sanguthevar Rajasekaran, Department of Computer Science and Engineering,
University of Connecticut, Storrs, Connecticut, USA
Pasi Rastas, Department of Computer Science and HIIT Basic Research Unit, Uni-
versity of Helsinki, Finland
Alexander C. Russell, Department of Computer Science and Engineering, Univer-
sity of Connecticut, Storrs, Connecticut, USA
Yi Shi, Department of Computing Science, University of Alberta, Edmonton, Al-
berta, Canada
Alexander A. Shvartsman, Department of Computer Science and Engineering, Uni-
versity of Connecticut, Storrs, Connecticut, USA
Steve Skiena, Department of Computer Science, Stony Brook University, Stony
Brook, NY, USA
Lakshman Subrahmanyan, University of Massachusetts Medical School,
Worcester, MA, USA
Sing-Hoi Sze, Departments of Computer Science and of Biochemistry and Bio-
physics, Texas A&M University, College Station, Texas, USA
Haixu Tang, School of Informatics and Center for Genomic and Bioinformatics,
Indiana University, Bloomington, IN, USA
Esko Ukkonen, Department of Computer Science and HIIT Basic Research Unit,
University of Helsinki, Finland
Tomáš Vinař, Department of Biological Statistics and Computational Biology,
Cornell University, Ithaca, NY, USA
Patra Volarath, Department of Computer Science, Georgia State University,
Atlanta, GA, USA
Hao Wang, Department of Computer Science, Georgia State University, Atlanta,
GA, USA
Yuzhen Ye, The Burnham Institute for Medical Research, San Diego, CA, USA
xiv CONTRIBUTORS

Alexander Zelikovsky, Department of Computer Science, Georgia State University,

Atlanta, GA, USA
Elena Zotenko, National Center for Biotechnology Information, National Library
of Medicine, National Institutes of Health, Bethesda, MD, USA and Department
of Computer Science, University of Maryland, College Park, MD, USA
1
EDUCATING BIOLOGISTS IN THE
21ST CENTURY: BIOINFORMATICS
SCIENTISTS VERSUS
BIOINFORMATICS TECHNICIANS1
Pavel Pevzner
Department of Computer Science and Engineering, University of California, San Diego,
CA, USA

For many years algorithms were taught exclusively to computer scientists, with
relatively few students from other disciplines attending algorithm courses. A biology
student in an algorithm class would be a surprising and unlikely (though not entirely
unwelcome) guest in the 1990s. Things have changed; some biology students now
take some sort of Algorithms 101. At the same time, curious computer science
students often take Genetics 101.
Here comes an important question of how to teach bioinformatics in the 21st
century. Will we teach bioinformatics to future biology students as a collection of
cookbook-style recipes or as a computational science that first explain ideas and
builds on applications afterward? This is particularly important at the time when
bioinformatics courses may soon become required for all graduate biology students
in leading universities. Not to mention that some universities have already started
undergraduate bioinformatics programs, and discussions are underway about adding
new computational courses to the standard undergraduate biology curriculum—a
dramatic paradigm shift in biology education.

1 Reprinted from Bioinformatics 20:2159–2161 (2004) with the permission of Oxford University Press.

Bioinformatics Algorithms: Techniques and Applications, Edited by Ion I. Mǎndoiu

and Alexander Zelikovsky
Copyright © 2008 John Wiley & Sons, Inc.

1
2 EDUCATING BIOLOGISTS IN THE 21ST CENTURY

Since bioinformatics is a computational science, a bioinformatics course should

strive to present the principles and the ideas that drive an algorithm’s design or explain
the crux of a statistical approach, rather than to be a stamp collection of the algorithms
and statistical techniques themselves. Many existing bioinformatics books and courses
reduce bioinformatics to a compendium of computational protocols without even try-
ing to explain the computational ideas that drove the development of bioinformatics in
the past 30 years. Other books (written by computer scientists for computer scientists)
try to explain bioinformatics ideas at the level that is well above the computational
level of most biologists. These books often fail to connect the computational ideas
and applications, thus reducing a biologist’s motivation to invest time and effort into
such a book. We feel that focusing on ideas has more intellectual value and represents
a long-term investment: protocols change quickly, but the computational ideas don’t
seem to. However, the question of how to deliver these ideas to biologists remains an
unsolved educational riddle.
Imagine Alice (a computer scientist), Bob (a biologist), and a chessboard with a
lonely king in the lower right corner. Alice and Bob are bored one Sunday afternoon
so they play the following game. In each turn, a player may either move a king one
square to the left, one square up, or one square “north–west” along the diagonal.
Slowly but surely, the king moves toward the upper left corner and the player who
places the king to this square wins the game. Alice moves first.
It is not immediately clear what the winning strategy is. Does the first player (or
the second) always have an advantage? Bob tries to analyze the game and applies a
reductionist approach, and he first tries to find a strategy for the simpler game on a
2 × 2 board. He quickly sees that the second player (himself, in this case) wins in
2 × 2 game and decides to write the recipe for the “winning algorithm:”

If Alice moves the king diagonally, I will move him diagonally and win. If Alice moves
the king to the left, I will move him to the left as well. As a result, Alice’s only choice
will be to move the king up. Afterward, I will move the king up again and will win the
game. The case when Alice moves the king up is symmetric.

Inspired by this analysis Bob makes a leap of faith: the second player (i.e., himself)
wins in any n × n game. Of course, every hypothesis must be confirmed by experi-
ment, so Bob plays a few rounds with Alice. He tries to come up with a simple recipe
for the 3 × 3 game, but there are already a large number of different game sequences
to consider. There is simply no hope of writing a recipe for the 8 × 8 game since the
number of different strategies Alice can take is enormous.
Meanwhile, Alice does not lose hope of finding a winning strategy for the 3 × 3
game. Moreover, she understands that recipes written in the cookbook style that Bob
uses will not help very much: recipe-style instructions are not a sufficiently expressive
language for describing algorithms. Instead, she begins by drawing the following table
that is filled by the symbols ↑, ←, , and ∗. The entry in position (i, j) (that is, the ith
row and the jth column) describes the move that Alice will make in the i × j game.
A ← indicates that she should move the king to the left. A ↑ indicates that she should
move the king up. A  indicates that she should move the king diagonally, and ∗
Exploring the Variety of Random
Documents with Different Content
The Project Gutenberg eBook of The Philistine
This ebook is for the use of anyone anywhere in the United
States and most other parts of the world at no cost and with
almost no restrictions whatsoever. You may copy it, give it away
or re-use it under the terms of the Project Gutenberg License
included with this ebook or online at www.gutenberg.org. If you
are not located in the United States, you will have to check the
laws of the country where you are located before using this
eBook.

Title: The Philistine

a periodical of protest (Vol. I, No. 4, September 1895)

Author: Various

Editor: Harry Persons Taber

Release date: June 23, 2022 [eBook #68384]

Language: English

Original publication: United States: The Society of the

Philistines, 1895

Credits: hekula03 and the Online Distributed Proofreading Team

at https://www.pgdp.net (This book was produced from
images made available by the HathiTrust Digital
Library.)

*** START OF THE PROJECT GUTENBERG EBOOK THE

PHILISTINE ***
 The Philistine
A Periodical of Protest.
I have peppered two of them: two I’m sure I have paid, two
rogues in buckram.—King Henry IV.

Printed Every Little While for The Society

of The Philistines and Published by Them
Monthly. Subscription, One Dollar Yearly

Single Copies, 10 Cents. September,

1895.
 THE PHILISTINE.
Edited by H. P. Taber.

CONTENTS FOR SEPTEMBER, 1895.

The Birth of the Flower.
John Northern Hilliard
A Notable Work.
Elbert Hubbard
The Manners Tart.
Clara Cahill Park
A Matter of Background.
William McIntosh
In Slippery Places.
W.
A Lantern Song.
Stephen Crane
The Rubaiyat of O’Mara Khayvan.
W. M.
Notes.

The Philistine is published monthly at $1 a year, 10 cents a

single copy. Subscriptions may be left with newsdealers or sent
direct to the publishers.
Business communications should be addressed to The
Philistine, East Aurora, New York. Matter intended for publication
may be sent to the same address or to Box 6, Cambridge,
Massachusetts.
Entered at the Postoffice at East Aurora, New York, for
transmission as mail matter of the second class.
COPYRIGHT, 1895, by H. P. Taber.
 THE PHILISTINE.

no. 4. September, 1895. vol. 1.

 THE BIRTH OF THE FLOWER.
In the Beginning, God, the Great Workman,
Fashioned a seed;
Cunningly wrought it from waste-stuff left over
In building the stars;
Then, in the dust and the grime of His Workshop,
He rested and pondered—
Then, with a smile, flung the animate atom
Far into space.

As the seed fell through the blue of the heavens

Down to the world,
Wind, the Great Gardener, seized it in triumph
And bore it away;
Then, at a sign of the Master, who made it,
He planted the seed:—
Thus into life sprang the first of the flowers
On earth.

—John Northern Hilliard.

 A NOTABLE WORK.
In Mr. Cudahy’s remarkable book entitled The Pawns of Chance
there are Sixteen Women who Did. Its sure success is prophesied
on this account, for of the five novels that have made ten-strikes
during the past year each has contained at least One Woman who
Did, and in two instances Several.
And right here, before referring further to Mr. Cudahy’s book, I
wish to place on file a modest word of protest concerning the modern
sex novel.
Just now the stage and story-book seem to vie with one another in
putting on parade the Men and Women who Did for the delectation
of those who Have or May. The motif in all these books and plays is
to depict the torturing emotions that wring and tear the hearts of
these unhappy mortals. The Camp of Philistia does not boast that
there are in it no People who Did, neither do we deny the reality of
the heartaches and tears that come from unrequited love and
affection placed not wisely. But from a somewhat limited experience
in wordily affairs I arise to say that life does not consist entirely in
these things, and furthermore that the importance given to the Folks
who Have is quite out of proportion to their proper place with the
procession. There are yet loves that are sweet and wholesome;
there are still ambitions that are manly and strong. Let’s write and
talk of these.
But still even in spite of a morbid plot and many incidents that are
rather bluggy, Mr. Cudahy has produced a work that probably will
outsell any of the other volumes issued by Chicago’s Enterprising
Decadent Publishers. This book has a few positive virtues. Evidently
it is a collaboration. I think the author has employed some
exceptionally bright apprentices and like Dumas the Elder, Mr.
Cudahy is to be congratulated on the rare discrimination shown in
choosing his help. In literature, as in commerce or war, much
depends on selecting one’s aides: every good general must be
properly reinforced.
The prospectus of The Pawns of Chance describes the binding of
the book as “a symphony in pig-skin.” And the volume is certainly
very pleasing to the eye. The paper is hand-made—deckle edge; the
illustrations and etchings on Japan paper; and the portrait of the
author that serves as frontispiece is a genuine work of art.
The space in The Philistine at my disposal will not admit of an
extended criticism, so I will briefly trace the plot, and make a few
casual remarks on the more important situations, trusting that my
readers will procure the work and each read for himself. For while its
faults are many, yet there are here and there redeeming features,
and in the moral at the close is a suggestion that is worth one’s
while.
Now for the story:
James Hunks, known on the bills as Signor De June, was in 1875
proprietor of a Ballet Troupe. The corps de ballet consisted of sixteen
ladies who were personally selected by Signor De June, and trained
by him so that they performed some very wonderful terpsichorean
evolutions. Eight of these women were blondes and eight brunettes.
Surprising to state, none were over thirty and none under twenty
years of age. But they were all Women who Did—that is to say,
Ladies with a Past.
Not that they were selected on this account; indeed, Signor De
June did not interest himself in their Experiences—he only wanted
form and intellect—but mostly form. Yet a coryphee must have
brains, else she could not learn to conduct her airy shape through
the mazy evolutions of the dance.
But it came about by degrees that Signor De June learned that all
of his ladies were Ladies with a History. And being a philosopher, he
reasoned it out that the ballet was the only respectable calling that
was open to a woman who had been the victim of misplaced love.
Such is the bitter cruelty of a sham-virtuous society.
 And thus on page 141 Signor De June muses as follows: “Had my
ladies been possessed of homely faces and crusty manners, no
temptation could have come to them, and they would all have lived
and died virtuous maidens; or at best been the contented (or
discontented) wives of farmers, molders, bricklayers or mill hands.
But being loving and gracious and sympathetic and withal beautiful,
they have been unfortunate. Furthermore no woman should ever
speak of her virtue unless she hates her husband and loves another
man.”
So Signor De June was very kind and gentle with these ladies—
aye! tender. He loved them all; he guarded and shielded them from
every fierce temptation. It was a pure paternal love—more properly
Platonic. He only wished to make them happy—that was all.
They gave exhibitions in the principal cities of the United States
and were everywhere successful. Occasionally a husband or a
former lover of one of these Women who Did would appear upon the
scene, and whenever this happened the Signor, who was a large
man and ambi-dextrous, would take the offender neck and crop and
throw him out. This always cooled the most amorous follower, but it
kept Signor De June quite busy. Yet it must not be thought that the
Signor was brutal—far from it: all were welcome to worship his
ladies, but it must be done from the parquette or dress circle.
So they were all very prosperous and very happy, until one day the
wife of Signor De June appeared and camped upon his trail. He had
gotten an Indiana divorce from this woman five years before, but the
courts had pronounced it invalid, and now she was upon him neck
and crop, just as he had been upon the lovers and husbands. He
tried to explain to her that he loved the Corps de Ballet, not the
ladies individually. He loved them as a Whole, not singly. Moreover,
his love was idyllic—Platonic. The wife explained that the thing did
not exist except in books, and further stated her belief that the love
was Plutonic if anything; and moreover it must cease.
No doubt the woman really loved Mr. Hunks. He, too, had a little
regard for her, although they quarrelled. But he was essentially
commercial—a man of peace. He had no stomach for a legal battle
with his wife’s attorneys, who had taken the case on speculation,
and he could not run away. The woman utterly refused to be bought
off for a reasonable sum, and she also declined joining the Ballet
herself, in spite of De June’s assertions that he could love seventeen
as well as sixteen, for in love capacity increases through use.
“Try it for a month and you will see that it is Platonic,” said De
June.
“I’ve no doubt I’d find it so,” said the wife.
She still was firm. He must choose between her and the Troupe. If
he chose the Troupe he’d have her, like the poor, always with him. If
he chose her alone she would still resemble the poverty stricken; but
there would come times when vigilance might relax and he could slip
a way.
But what to do with the Troupe! He could not throw these beautiful,
susceptible women on a struggling, seething, wicked world. He could
not put them on a farm, for who would look after, correct, discipline
and restrain them as he had done? If allowed to scatter they would
marry, and marriage according to civilized methods, so-called, was a
failure; had he not tried it?
But De June was a man of resource (he was from Chicago). They
were in Denver and women were scarce. He would select husbands
for his ladies, himself.
He did so, choosing sixteen strong fine young miners. Calling the
men out one side, he made known to them his plan. Each man was
to have a wife on payment of the trifling fee of two hundred dollars
“matriculation” (Sic). The men were delighted—but had the ladies
been consulted? No, that was not necessary—there was to be a
return to primitive methods, which indeed were ever best: civilization
was artificial, unnatural and corrupt.
These sixteen ladies were all of fair intelligence, good hearted,
able to work, willing to obey. More than that they had great capacity
for loving, for had not this excess of love been their misfortune? The
love only needed proper direction, like all of our other gifts.
 The sixteen gentlemen that the philosophic De June selected were
of fair intelligence, healthy and good natured, prosperous and all
men of fine physique. There was no choice in the men; there was no
choice in the women; they were on the same intellectual plane—they
were well mated and De June would not defeat the God of Chance
by allowing any personal selection. One man offered a thousand
dollars for first choice, but Mr. Hunks was a man of honor and could
not be bought.
The gentlemen were to be in the parquette. When the ladies
appeared on the stage, at the word “Go” from De June, the sixteen
men were to make a rush for the stage and each seize his future
wife. All after the manner of the Romans who captured the Sabine
women—and I guess the Roman Nation is not to be sneezed at!
Cæsar, Antony, Brutus and all the rest of those honorable men were
products of just such marriages.
The rush was made—the women screamed, some fainted, but
each man held his prize. The electric lights were turned off, the
audience got out as best it could. Then the doors were locked, the
curtain dropped and Signor De June stepped forward and in gentle
words assured the sixteen ladies that no harm should come to them.
All had been arranged for the best. They must be good honest
wives, and the men must be good honest husbands, and Mr. Hunks,
being a Justice of the Peace, declared them all man and wife—that
is sixteen wives and sixteen husbands.
The women, it must be confessed, had grown a trifle weary of the
De June Idyllic Plan; and in the good old-fashioned womanly way, oft
in the night season, each had confessed in her own heart, that one
loving husband for each woman was what Nature intended. So they
accepted the situation, and each began to use those winning ways
that Herbert Spencer says are woman’s weapons: woman conquers
through her intuition.
At a word from De June the women repaired to their dressing
rooms and soon appeared in customary feminine attire. This time the
ladies had to pick their mates, for the change in dress greatly
mystified the hirsute miners. There was a slight scramble among the
ladies when three of them selected the same man, but the Signor
soon brought order out of chaos. This scene, which occurs in
chapter XXXIII, is quite dramatic.
All being amicably settled De June gave each woman a chaste
kiss on the cheek, shook hands with the grateful miners and went
sorrowfully back (with his $3,200.00) to the hotel where his Mary
Jane sat up awaiting him.
That night Mr. Hunks and his wife left for Chicago. There he went
into real estate and was very successful. Having resolved to face his
fate, he treated Mary Jane as gently as he could and she repaid it all
in kindness. So things were really not so bad as the Signor had
imagined.
Ten years passed and Mr. Hunks went back to Denver and found
that the sixteen couples were living happily. Many little pledges had
appeared to cement the bonds. All were content and perfectly
mated, although several of the men were a bit henpecked—but a
man soon gets used to such things. (See page 491, line 16). The
women having had Experience were resolved to hold their new
found mates with love’s own bonds; and the men fearing to lose
such beautiful treasures were ever kind. There was a little doubt in
the minds of all concerning De June’s commission as Justice of the
Peace, and then certain requirements of the divorce courts had not
been fully met, but these irregularities put all on their good behavior.
For it is a fact that if a mortal knows that his mate cannot get away
he is often severe and unreasonable.
And the curious part of all this is that the story is true. Mr. Cudahy
protests it on his honor, and declares that these sixteen worthy
couples laid the foundation for the elite of Denver society, and are
now the leading lights in that beautiful city.
The story is somewhat marred by such ungrammatical
expressions as “has came,” “shouldn’t ought,” etc. There are also a
needless number of French and Latin phrases, culled from a lexicon
I fear, and a striving after Latin derivatives. It is also a pity that more
pains was not taken with the proof reading, as exasperating errors
are on nearly every page. Still these are minor points.
 In the last four chapters there is considerable symbolism, which
one cannot but wish had been put in plain English. Like Zangwill’s
The Master, the moral is left for the last. It is a little clouded, but I
take it that Mr. Cudahy believes that civilization’s plan of selection is
very faulty. He suggests indirectly that Congress should appoint
Matrimonial Commissioners for each district—men of discretion,
experience and judgment. The Commissioner is to select from
society sixteen marriageable young women and place them in a
room, and then take a like number of young men and let them make
a rush, and this, says Mr. Cudahy, would doubtless do away with
many of our matrimonial misfits.
Lovers of literature will look anxiously for Mr. Cudahy’s next book,
and in the meantime I am sure that the Young Decadents will reap a
rich harvest from The Pawns of Chance. I am in receipt of a letter
from the distinguished author wherein he says that he is positively
declining all invitations to lecture in the provinces, but that he may
appear late in the season in a few of our principal cities.
It may interest the Philistines to know that R. G. Dun & Co. rate
Mr. Cudahy Z Z xxx 1, while Hobart Chatfield-Chatfield Taylor is only
Y x 2 3·4 and Mrs. Reginald De Koven ranks K x 4. At the present
moment I can recall but two residents of Grub Street who have
ratings so high as Mr. Cudahy, these being William Waldorf Astor
and Walter Blackburn Harte.
Elbert Hubbard.
 THE MANNERS TART.
An old and worn out Tart once sat on the pantry shelf and as it dried
and stiffened, thus it soliloquized: “In my youth men fought over me,
not to possess me, but that each should pass me to his neighbor.
“I was a fair Tart, greatly to be prized, but the manners of all were
such that I was left alone on the table, the last of my kind, the
Manners Tart, and they all withdrew, feigning indifference.
“The cook, having made many of my brethren, cared not for me,
so I, created to rejoice the soul of man, sit here, a cold and cheerless
thing at which the rats gnaw nightly.
“There was a little boy at the table, but why speak of him? He
stretched out his hand for me, but detecting a slight frown between
the eyebrows of his mother, he withdrew it and my chance was gone.
“The little boy was the only one that sympathized with me; he
knew that a Tart is short lived at best; that the only modest ambition
of a Tart is to gladden some one in life and to overhear a few words
of praise as it passes away.
“But alas! I am a failure, and all because I move in a circle that
makes a merit of self-sacrifice. I do not understand such things, but
——” here a pang of mold struck to the Tart’s heart and it relapsed
into unconsciousness.
If it had understood it would have said—“there are many joys in
the world that die unrejoiced over because no man will have the
courage to do what he wants to do.”
Clara Cahill Park.
Detroit, August, 1895.
 A MATTER OF BACKGROUND.
If the war in the extreme East just ended has done no more for
humanity, it has demonstrated the unfitness in these days of a nation
that has no perspective. Philosophers we have had, and eke
reformers, who saw no farther than their noses. But here is a great
people whose polity is exclusive, whose art recognizes no relation of
distance, whose social code is rigidly formal and openly mercenary,
whose methods in war consisted up to a late date of noise and
stenches and hideous banners designed to frighten an enemy. With
rare powers of detail, the art of China is lifeless and without
spirituality or suggestive force. With centuries of training in literary
industry, its lore is the elaborate repetition of didactic sayings
thousands of years old. There is no background in its pictures. There
is no constructive basis in its social theory. All is flat surface,
repression, imitation. Yet here is the oldest nation in the world in
continuous history. We need not wonder it has fallen at last. The
marvel is that it stood so long. The student of history may well ask
what has held back destroying hands through so many centuries of
the world’s unrest.
Lack of a sense of proportion and distance is not peculiar,
however, to Orientals. Even in the light of western civilization
philosophers have forgotten yesterday and to-morrow, and the
foreground has usurped the canvas. Impatience is a sign of modern
degeneration if the oracle who has a caveat on that warning is good
authority. It is strange to find in the prophet himself the fault he
attributes to our time. For in all ages the world has been on the point
of going to the dogs, according to some voice crying in the
wilderness or on the house tops, as he is crying now. From Jonah
warning luxurious Nineveh down to Max Simon Nordau listing
crooked ears as the breeder counts his cross-billed chicks as proof
that the race is “running out,” the warning has been unceasing. And
yet the race lives, and builds on its ruins.
 Our nerves have worn us out, according to Mr. Nordau. If Count
Tolstoi knows, amatory passion is the cause of the wreck, and high
feeding back of that. If Mr. Ibsen is right, artificiality has destroyed
the virtues. M. Zola is sure that bestiality has brought judgment upon
at least one modern Sodom. Mynheer Maartens is Philistine enough
to ascribe most of our ills to repression of sincerity, of naturalness in
social life. And so a score of doctors describe special symptoms,
each empirically, each truthfully. The wisest of them—those who
have a sense of perspective—see beyond the immediate ailment the
persistent vitality which is never wholly conquered.
We have specialized philosophy and literature as we have
medicine. These are not quacks who tell us the world is going to
wreck through the extravagances of society, through the repression
of humanities, through the lusts of gross living. They are students of
particular phases of distemper. The world, not the men in its clinics,
is to blame when it hails each as a cure-all. The realism of a Zola or
a Nordau is not a finality. While the knife is in hand the ulcer is pre-
eminently in evidence. Its removal is the business in order. But the
genius of a Zola that divines the cancer in the vitals of society
presupposes the life that is behind it—and that is the main factor in
his surgery.
He would be a false teacher who should put the immediate in the
place of the permanent in any such calculation. The world that
listens has an equal responsibility. The greatest artist can only paint
passing phases of the limitless evolution going on about him. It is
heresy in itself fatal to put a phase in the place of the infinite
process. Grant that society is always at war with itself, always
repressing truth, always promoting animalism by its very more or
less disguises. The paradox of these results can never be wholly
escaped. The teacher who sees what is and was in due proportion
will judge what is to be, though no son of a prophet. The new realism
for which Philistines contend is no expose of the evils of modern
society, no uncovering of a witch’s pot. It holds all these
manifestations in perspective, but substitutes none of them for a
general view of life and human destiny. It would make health instead
of disease infectious, substituting for blind Oriental imitation a truer
standard of custom, freer from convention that has no warrant of
purpose, more direct in its expression of natural and normal vitality in
personal living and thinking. “From within outward,” is its motto. It
would depose and outgrow self-consciousness—the vampire fungus
that signalizes arrested development and decay in thought or in
letters or in the self-projection of social life. The realism of the
Philistines is manifested in the recognition of healthy life that we find
in some of the new literature—in the heroic romance of Anthony
Hope, in the charming tenderness and sweetness of Maartens’s
Hollandais and in the fresh-witted islanders, full of arterial blood, of
Hall Caine and the wizard who lies buried on the mountain top of his
own beloved island—that second one to the left after you leave San
Francisco.
Even the modern stage, corrupted by French intensities and the
commercial idea of filling the house, is showing signs of a reaction.
Not more than nine-tenths of the standard attractions of the coming
season are based on infractions of the seventh commandment or of
that similar law which every chivalrous man knows, though it was
never traced in fire on the Sinaitic stone.
William McIntosh.