Introduction to Computational Biology: Maps, Sequences and Genomes. by M. S.
Waterman
Biometrics, Vol. 54, No. 1 (Mar., 1998), pp. 398-399
Published by: International Biometric Society
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398 Biometrics, March 1998
FERGUSON, T. S. A Course in Large Sam- L. Simon) and the application of Bayesian un-
ple Theory. Chapman & Hall, London, 1996. certainty analysis to the problem of radiological
ix + 245 pp. ?27.50/$45.95. ISBN 0-412-04371- protection (R. Haylock and A. O'Hagan).
8. The four papers on air quality deal with con-
structing spatial designs for monitoring air pol-
This book is intended for a first year gradu- lution using subset regression (D. Nychka, Q.
ate course in asymptotic theory. Graduate stu-
Yang, and J. A. Royle), local polynomial regres-
dents from a variety of disciplines (including bio-
sion and its applications in environmental statis-
statistics and biomathematics) have taken the
tics (D. Ruppert), statistical analysis of trend
author's courses on which the book is based. in urban ozone (H. Vaquera-Huerta, J. A. Vil-
Essential prerequisites are good undergraduate lasenor, and J. Hughes), and forecasting air pol-
courses in analysis and mathematical statistics. lution with causal probabilistic networks (L. E.
The text has been structured with self study in Sucar and J. C. Ruiz-Suairez). Concerning wa-
view. It is divided into 24 short sections, each ter quality, there are papers on non-point-source
dealing with a specific topic. The basic idea or pollution of surface waters over a watershed (N.
central result of a section is stated as a theo-
Cressie and J. J. Majure), geostatistics applied
rem. All except one of the sections end with ex- to hydrology problems and tools (D. Myers),
ercises for the reader. The sections are grouped
and optimal screening methods in the detection
into four parts: Basic probability; Basic statisti-
of water contamination (M. A. Amaral Turkman
cal large sample theory; Special topics; Efficient
and K. F. Turkman).
estimation and testing. There is a lengthy ap-
Health issues are examined in the next three
pendix containing solutions to all the exercises,
papers: interpolating air pollution data for
a list of 34 references, and a good subject index.
health impact assessment (J. V. Zidek), laten-
cies, exposure to environmental hazards, and
BARNETT, V. and TURKMAN, K. F. (edi- cancer rates (Y. Mao and I. B. MacNeill), and
tors). Statistics for the Environment 3: Pol- an investigation of the effect of road traffic pol-
lution Assessment and Control. Wiley, lution on asthma using geographical informa-
Chichester, England, 1997. xii + 345 pp. ?60.007 tion systems (M. McCready, S. Patel, and K.
$85.00. ISBN 0-471-96435-2. Rennolls). The final 'paper is on statistical is-
The SPRUCE 3 Conference (Statistics in Pub- sues in the environmental monitoring and as-
lic Resources, Utilities and in Care of the Envi- sessment of anthropogenic pollution (L. H. Cox
ronment, 3) was held in Merida, Mexico, in De- and N. P. Ross); the authors pinpoint the twin
cember 1995 on the important multidisciplinary challenges of the application of sound statisti-
topic of environmental pollution. The aim was cal methods to combine existing environmental
to discuss ways in which statistical models and data and the development of cost-effective meth-
methods can assist the understanding of pollu- ods for the monitoring, analysis, and display of
tion problems and to collate and classify such primary data.
methods. The following six major themes were
studied: Sampling and monitoring of pollution; BOOKSTEIN, F. Morphometric Tools for
Radiation; Air quality; Water quality; Health Landmark Data, paperback edition. Cam-
impact from pollution; and Policy and manage- bridge University Press, Cambridge, England,
ment of pollution. The book "presents a struc- 1997. xvii + 433 pp. ?24.95/$34.95. ISBN 0-
tured and comprehensive review of the mate- 521-58598-8 (pbk).
rial of the conference with chapters prepared to This paperback edition of Bookstein's impor-
cover all the invited papers and some of the con- tant volume on the theory of geometric mor-
tributed papers". phometrics will be very welcome, not least for
Chapter 1 (V. Barnett) looks at the scale of its reasonable price (one-third that of the hard-
the application of statistical methods to pol- back edition). The latter first appeared in 1991.
lution problems; it identifies over 1000 papers It was recommended to all biometricians con-
in the previous five years, largely (88%) out- cerned with the analysis of shape by R. A. Rey-
side the standard statistical journals and mainly ment in a detailed review in the December 1992
(75%) involving routine methods. Professor Bar- (48, 1301) issue of Biometrics.
nett puts forward a classification scheme and
uses it to analyse the scope and methods of some
WATERMAN, M. S. Introduction to Com-
500 papers published in 1993-1995.
putational Biology: Maps, Sequences and
The following six sections of the book deal
Genomes. Chapman Hall, New York, 1995. xv
with the six major themes listed above. Chap-
+ 431 pp. ?29.95/$54.95. ISBN 0-412-99391-0.
ters 2 and 3 are on sampling and the efficient
use of data for characterizing polluted areas (A. The author admits that the the title of this book
Stein) and statistical models for the semi-arid is uninformative. "Introduction to Computa-
land-surface-atmosphere program, an integrated tional Biology" is the short title that might pref-
monitoring experiment (F. Avila). Chapters 4 ace many disparate volumes. The remainder of
and 5 move on to consider the geostatistical anal- the title "Maps, Sequences and Genomes" is to
ysis of residual contamination from nuclear let the reader know that this is a book about
weapons testing (P. J. Diggle, L. Harper, and S. applications in molecular biology. Even that is
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All use subject to JSTOR Terms and Conditions
Book Reviews 399
too short: "Introduction to computational biolo- methods used by reliability engineers". It is in-
gy.. ." should be "Introduction to computation- tended to be a one-semester text for advanced
al, statistical, and mathematical biology..." . undergraduates and graduates with a calculus-
Professor Waterman is one of the founders of based background in probability and statistics.
the fast growing subject of mathematical molec- The emphasis is strongly on reliability engineer-
ular biology. In this book he has tried "to strike ing; the author hopes, nevertheless, that it will
a balance between... fundamentals unlikely to be useful for biostatistics and actuarial students.
change and those data structures and problems
whose relevance could be eliminated tomorrow PFAFFENBERGER, B. Protect Your Pri-
by a clever piece of technology". vacy on the Internet. Wiley, New York, 1997.
Although the book has the flavour of a text- vii + 326 pp. $00.00/?24.95. ISBN 0-471-18143-
book, with introductory material on experimen- 9 (pbk/CD).
tal molecular biology, computer algorithms, and
problems for the student with hints and solu- We all continue to make ever increasing use of
tions, there is far too much material here for a the Internet in one way or another, as more and
single course. The author recommends as a one- more organizations (including the IBS) join in
semester course: Chapters 1 and 2 (introduc- and set up Web pages. This book is a timely
tory molecular biology and restriction maps), and cautionary reminder of the general lack of
6.1 (mapping by fingerprinting), 8 (data-bases security surrounding our Internet activities, par-
and rapid sequence analysis), 9 (dynamic pro- ticularly visiting Web sites and communicating
gramming alignment of two sequences), 11.4-6 by e-mail. The author describes how detailed
(some of the chapter on probability and statis- records of an individual's Internet activities are
tics for sequence alignment), 14 (trees and se- routinely recorded, how access can be gained to
quences), and as much as possible of 12 (proba- such records, and how the information may be
bility and statistics for sequence patterns). But used and/or abused. Modern technology makes
this would ignore important material on, for ex- it easy to link and process information from dif-
ample, mapping by anchoring, sequence assem- ferent records to create what may be a distur-
bly, RNA secondary structure, and the author's bingly detailed profile of the individual. The au-
overview of key original material and current re- thor suggests various practical strategies for re-
search directions. ducing one's vulnerability when using the Web.
All biometricians should know something He discusses in detail the use of methods for en-
about this rapidly developing subject. With Pro- crypting e-mail messages and also the encryp-
fessor Waterman's help we have no excuse if we tion of other sensitive files. Other topics include
fail to grasp the basics before the task of catch- the creation of secure passwords, securing your
ing up becomes yet more difficult. personal computer system, totally deleting un-
wanted files, and restricting Web access by other
users of your machine. Details of Web sites that
LEEMIS, L. M. Reliability: Probabilistic
carry information and relevant software on pri-
Models and Statistical Methods. Prentice
vacy and security topics are given. The accom-
Hall, Englewood Cliffs, New Jersey, 1995. xv +
panying CD-ROM contains various privacy free-
319 pp. $83.00/?68.95. ISBN 0-13-720517-1.
ware and shareware for Windows PCs. The
The aim of this clearly written and well-pro- whole book is written predominantly for PC
duced book is "to give an elementary introduc- users, though devotees of the Macintosh will still
tion to the probabilistic models and statistical find it both informative and helpful.
CORRECTIONS
Corrections to "Comparing two diagnostic tests against the same "gold standard" in
the same sample" by D. A. Bloch; 53, 73-85, March 1997.
On page 81, equation (25) should read
var[ki (r)] =[rr(1 - PI) + (1 - r) (1 -T)p]
{ -( Tr) KI(r)-1 Sel (I -Sel)
nI
(7r - I+r)(1]2
[) (r)- SP, (1-SPi)}
n2
On page 81, the second line below equation (26) should read:
1lii/ni for PF111,7TrSe2+ (1 -,Tr)(1 - SP2) for P2, and so on. Once again...
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