Review of Bioinformatics Basics

Publisher’s information

Bioinformatics Basics: Applications in Biological Science and Medicine
by Hooman H. Rashidi and Lukas K. Buehler
December 1999
ISBN 0-8493-2375-4
CRC Press
$69.95

Review of Bioinformatics Basics

A Terrible Mistake

CRC Press made a terrible mistake. They accidentally published the rough—very rough—draft of the manuscript of Bioinformatics Basics. OK, OK, I’m sure that if you asked them, CRC Press would deny that they made that mistake. But they made the mistake of publishing this book.

This hodge-podge of disconnected ideas, half-baked sentences, and misinformation should never have been published. The chaos of disorganization begins on the first page and continues throughout the book. Entire sections of the book are incomplete or even missing, as if the authors ran out of time. Ideas are taken up but never developed. Some topics, such as mRNA splicing, are mentioned repeatedly but never addressed directly in a coherent way.

This book is intended to present the basics of bioinformatics. Unfortunately, the presentation is so confusing, disorganized, and incomplete, that a beginner will never make sense of the book. The background material is presented so badly that only a trained biologist will understand it. The material on databases and tools available from NCBI, EBI, DDBJ, or KEGG is barely adequate, and you’ll do better to go directly to their web sites and read their documentation.

Because the book was published in December, 1999, many of the facts related to the genome projects are now out of date. But some of the tables were out of date even at the time of publication. The latest date in the Progress Report of Databases on p. 8 is June, 1998, 17 months prior to the publication date.

Tortured Prose

The writing style is almost uniformly terrible, and no one edited the manuscript. It’s almost too easy to find examples of tortured prose in this book, but here are a few:

Academic research is powered by people who are knowledge driven. (p. 3)

DNA sequences are often found based on predictive tools, meaning that sequence similarities of newly discovered genes yield information about their physiological functions and structures, PCR (polymerase chain reaction), finding sequence fragments of significance (how is significance judged? By predictive biology, once again), finding distribution of genes or mRNAs (often an indicator of gene activity in an organism), and amplifying the amount of DNA for purification, sequencing, and mutational analysis. (p. 83)

A gene is a sequence of base pairs, and despite the ability to predict a protein’s function, experimental work to study the biochemistry and physiology of the actual protein is necessary. (p. 85)

There is no evidence that CRC Press assigned an editor, a proofreader, or an indexer to this project. It’s obvious that the authors did not write from an outline. The whole job, except for the typesetting, book design, printing, and binding, is the most amateurish job. The index is completely unreliable. Subjects do not agree with their verbs in many places throughout the text. Several pictures of web pages are included but with the URLs hidden. The Chapter 2 overview promises a section on sequence alignment tools, but the section is missing.

Numerous inaccuracies

The book is replete with errors. Among the inaccuracies, the color plate for Chapter 1, color figure 2, of the DNA helix shows a left-handed helix. The E value of a BLAST search does not range from 0 to 1 (p. 98); the smallest genome of a eubacterium is not about 15 million base pairs (p. 106).

My recommendation

Save your $70 and your time for some other book.

Other Reviews

William Sheridan of Insite Reviews wrote a favorable review.

In a review at amazon.com, John Rachlin gives the book one star (out of five possible) and says the presentation is “incoherent”.

Finally, there is a review available at whatislife.com, a web site founded by Lukas K. Buehler, one of the authors of Bioinformatics Basics.

Table of Contents

• Chapter 1: Introduction to Bioinformatics
  • Biology and Bioinformatics
  • Computers in Biology and Medicine
  • Biological Macromolecules
• Chapter 2: Databases and Search Tools
  • Computational Tools and Databases
  • Database Mining Tools
• Chapter 3: Genome Analysis
  • DNA Cloning and PCR
  • Computatinal Tools for DNA Sequence Analysis
  • Genome Analysis
  • Functional Genomics
• Chapter 4: Proteome Analysis
  • Proteomics
  • Metabolic Reconstruction
• Chapter 5: The Computer Revolution in Neurobiology
  • Human Brain Project
  • Computer Simulations and Visualization of Molecular Structures
  • Predictive Biology