Evolutionary Bioinformatics
Evolutionary Bioinformatics aims to make the "new" information-based (rather than gene-based) bioinformatics intelligible both to the "bio" people and the "info" people. Books on bioinformatics have traditionally served gene-hunters, and biologists who wi
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Donald R. Forsdyke
Evolutionary Bioinformatics
Second Edition
Donald R. Forsdyke Department of Biochemistry Queen’s University Kingston Ontario Canada [email protected]
ISBN 978-1-4419-7770-0 e-ISBN 978-1-4419-7771-7 DOI 10.1007/978-1-4419-7771-7 Springer New York Dordrecht Heidelberg London © Springer Science+Business Media, LLC 2011 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com)
In memory of Erwin Chargaff whose studies of the base composition ‘accent’ of DNA underlie everything in this book, and of Susumo Ohno who first understood that DNA ‘speaks’ in palindromic verses; with many thanks to Vinay Prabhu whose neat little 1993 paper showed the way.
Erwin Chargaff (1905-2002)
Contents Note on Second Edition ……………………………………ix Abbreviations …………..…………………………….……...x
Prologue – To Select is Not to Preserve………….…...xi Part 1 Information and DNA 1. Memory – A Phenomenon of Arrangement………….……..3 2. Chargaff’s First Parity Rule……………………….………27 3. Information Levels and Barriers……………….………….47
Part 2 Parity and Non-Parity 4. Chargaff’s Second Parity Rule……………….……………69 5. Stems and Loops…………………………….…………….91 6. Chargaff’s Cluster Rule……………………….………….111
Part 3 Variation and Speciation 7. Mutation……………………...……………….………….131 8. Species Survival and Arrival……………………………..153 9. The Weak Point…………………………………………..171 10. Chargaff’s GC Rule…..……………………….………….189
VIII
Contents
11. Homostability…………………………………………….205
Part 4 Conflict within Genomes 12. Conflict Resolution………………………………………221 13. Exons and Introns………………………………………...249 14. Complexity……………………………………………….267
Part 5 Conflict between Genomes 15. Self/Not-Self?.....................................................................295 16. The Crowded Cytosol……………….……………………319
Part 6 Sex and Error-Correction 17. Rebooting the Genome………………….…..……………341 18. The Fifth Letter…………………………….…………….363
Part 7 Information and Mind 19. Memory – Where to Arrange and Where?.........................377
Epilogue To Preserve is Not To Select……….…..….391 Appendix 1 What the Graph Says……………………………...405 Appendix 2 Scoring Information Potential……...…….……..…411 Appendix 3 No Line?...................................................................415 Acknowledgments...........................................................
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