Evolutionary Bioinformatics

THIRD Edition

 
Samuel Butler (1835-1902) who, with Ewald Hering, saw heredity as the transfer of stored information. This self portrait is reproduced with the permission of the Master and Fellows of St. John's College, Cambridge

The double-helical structure of DNA, with base A pairing with base T, and base G pairing with base C. This figure was kindly prepared for the book by  Richard R. Sinden

Erwin Chargaff (1905-2002) whose four "rules" provide the foundation for the book. This photograph is reproduced from the collection of the National Library of Medicine, Washington.

Donald R. Forsdyke

 
Third Edition 2016 Third Edition 2016 Third Edition 2016 Third Edition 2016 Third Edition 2016 Third Edition 2016

 

Published by Springer (2016) 

A substantial revision of the second edition (2011)

 

Books on bioinformatics began appearing in the mid 80s and primarily served gene-hunters, and biologists who wished to construct family trees showing tidy lines of descent. Given the great pharmaceutical industry interest in genes, this trend has continued in most subsequent texts. These deal extensively with the exciting topic of gene discovery and searching databases, but hardly consider genomes as information channels through which multiple forms and levels of information, including genic information, have passed through the generations. 

    This book identifies the types of information that genomes transmit, shows how competition between different types is resolved in the genomes of different organisms, and identifies the evolutionary forces involved. The early chapters relate the form of information with which we are most familiar, namely written texts, to the DNA text that is our genome. This lends itself well to introducing historical aspects dating back to the nineteenth century.

    Third edition revisions include expansion of the section on brain bioinformatics. All sections are updated with references. Attention is drawn to a new series of online tutorials for beginners in the field.

 

Notes on Second and Third Editions XVII
Prologue To Select is Not To Preserve  XXIII  
     
Chapters    
Part I. Information and DNA    
1 Memory – A Phenomenon of Arrangement 3
2 Chargaff’s First Parity Rule  25
3 Information Levels and Barriers    43
     
Part II. Parity and Non-Parity  
4 Chargaff’s Second Parity Rule 63
5 Stems and Loops  83
6 Chargaff’s Cluster Rule  103
     
Part III. Variation and Speciation  
7 Mutation  121
8 Species Survival and Arrival 141
9 The Weak Point 157
10 Chargaff's GC Rule 175
11 Homostability 193
     
Part IV. Conflict within Genomes  
12 Conflict Resolution 209
13 Exons and Introns  235
14 Complexity 253
     
Part V. Conflict between Genomes  
15 Self/Not-Self?  279
16 The Crowded Cytosol 305
     
Part VI. Sex and Error-Correction  
17 Rebooting the Genome   327
18 The Fifth Letter 351
     
Part VII. Information and Mind  

19

Memory - What to Arrange and Where 367
20 Certainty Now Uncertain 381
   
     
Epilogue To Preserve is Not To Select 395
 Appendix A What the Graph Says 409
 Appendix B Scoring Information Potential 415
 Appendix C Selection Level for PR2? 419
 Appendix D K-mer Probabilities and Genome Size 421
 Appendix E No Line? 425
   
Acknowledgements 435
Index 439

ISBN-13:978-3319287539  104 illustrations (20 in colour)  13 tables   eBook $189.00  Hardcover $249.00 

For e-book: (Click Here)

For institutions with access to a Springer eBook package, students can purchase a low-price black and white softcover edition, and individual chapters may be downloaded as PDF files

(Bookmetrix records for the 2nd edition 21470 downloads between Sept 2012 and Jan 2017)

(Bookmetrix records for the 3rd edition 9733 downloads between April 2016 and Jan 2017)  

Read the Reviews

Phillip Guddemi's Review in Cybernetics & Human Knowing (2016) 23(3): 93-103

The book ... consolidates a revolution in thinking that is contained in Forsdyke’s earlier publications, for example his 2001 book The Origin of Species Revisited. Like many revolutions Forsdyke’s is catalyzed by a renewed look at the past. Specifically, he has revived a number of questions about evolutionary process which were raised in the 19th Century by William Bateson—who was Gregory Bateson’s father and the inventor of the word genetics—and by the essayist Samuel Butler ... . These questions deal with the fundamental issue of the origin of species and how they diverge, but because they point away from natural selection as the only and total explanation they have by and large been ignored by the mainstream of evolutionary theorizing. ... Forsdyke goes far to show how processes which either can directly be called schismogenesis, or which might be analytically related to schismogenesis—processes which cannot be understood without very sophisticated molecular genetic analysis, and yet may have been anticipated conceptually by Butler among others—might be the answer to hybrid sterility and thus to some of the problems relating to the origins of species that niggled at William Bateson in his later years. By treasuring his conceptual exceptions, WB recognized that there was a residue problem that had not been fully explained by Darwin or by Mendel. Forsdyke has directly contributed to addressing that residue and explaining it in a 21st Century way.

 

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This page was established in 2016 and was last edited 26 Feb 2017 by D. R. Forsdyke. The double-helix figure was kindly prepared by Richard R. Sinden, adapted from his book DNA Structure and Function with the permission of the publisher. Permission to reproduce the photograph of Samuel Butler was given by the Master and Fellows of St. John's College, Cambridge. The photograph of Erwin Chargaff is from the collection of the National Library of Medicine, Washington, USA.