Evolutionary bioinformatics

Evolutionary Bioinformatics

Volumn , Issue , 2006, Pages 1-424

  Forsdyke, Donald R ^a  

^a QUEEN S UNIVERSITY   (Canada)

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[No Author keywords available]

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EID: 84900121977     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-0-387-33419-6     Document Type: Book

References (435)

1. Romano T (2002) Making Medicine Scientific. John Burdon Sanderson and the Culture of Victorian Science. John Hopkins University Press, Baltimore, p 105 [Sanderson was the great uncle of the twentieth century's "JBS'", John Burdon Sanderson Haldane, and may have partly inspired Lydgate in George Eliot's Middlemarch.]
2. Brenner S (2002) The tale of the human genome. Nature 416:793-794
3. Forsdyke DR (2001) Did Celera invent the Internet? The Lancet 357:1204
4. 6 cells with MLV integrations were injected into each child. Assuming that 20% of integrations are near transcription start sites, there will be... an average of 55 integrations into the 5' region of the LM02 locus per treatment."]
5. Brenner S (1991) Summary and concluding remarks. In: Osawa S, Honjo T (eds) Evolution of Life: Fossils, Molecules and Culture. Springer-Verlag, Berlin, pp 453-56
6. Little P (1995) Navigational progress. Nature 277:286-287
7. Hood L, Rowen L, Koop BF (1995) Human and mouse T-cell receptor loci. Genomics, evolution, diversity and serendipity. Annals of the New York Academy of Sciences 758:390-412
8. Baldi P (2001) The Shattered Self: The End of Natural Evolution. MIT Press, Cambridge, MA
9. Wolfram S (2002) A New Kind of Science. Wolfram Media, Champaign, 1L
10. Badash L (1972) The complacency of nineteenth century science. Isis 63:48-58
11. Butler S (1914) The Humour of Homer and Other Essays. Kennerley, New York, p 255
12. Gould SJ (2002) The Structure of Evolutionary Theory. Harvard University Press, Cambridge, MA, pp 36-37
13. Forsdyke DR, Mortimer JR (2000) Chargaff s legacy. Gene 261:127-137
14. Morris R (2001) The Evolutionists. Norton, New York
15. Forsdyke DR. (2005) Web-Pages. http://post.queenu.ca/~forsdyke/homepage. htm
16. Forsdyke DR (2001) The Origin of Species, Revisited. McGill-Queen's University Press, Montreal
17. Dunn LC (1965) A Short History of Genetics. McGraw-Hill, New York, p xxii
18. Dawkins R (1986) The Blind Watchmaker. Longman, Harlow, p ix [Dawkins' preface reads: "This book is written in the conviction that our own existence once presented the greatest of all mysteries, but that it is a mystery no longer because it is solved. Darwin and Wallace solved it, though we shall continue to add footnotes to their solution for a while yet." This appears to rest on the assumption that matter and energy - whatever they are - interchangeably exist, and there is nothing more fundamental. So it seems our task is to determine the mechanisms by which living beings arose from this raw material; see also Appendix 3]
19. Pope A (1711) Essay on Criticism. Macmillan, London (1896)
20. Darwin C (1859) The Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. John Murray, London, p 490
21. Bateson W (1899) Hybridization and cross-breeding as a method of scientific investigation. In: Bateson B (ed) William Bateson, F. R. S. Naturalist. His Essays and Addresses. Cambridge University Press (1928) pp 161-171
22. Darwin C (1872) Letter to Moggridge. In: Darwin F, Seward AC (eds) More Letters of Charles Darwin. John Murray, London (1903) Vol 1, p 337
23. Gelbart WM (1998) Databases in genome research. Science 282:659-661
24. Delbruck M (1971) Aristotle-totle-totle. In: Monod J, Borek F (eds) Of Microbes and Life. Columbia University Press, New York, pp 50-55
25. Lyell C (1863) Geological Evidences on the Antiquity of Man with Remarks on Theories of the Origin of Species by Variation. Childs, Philadelphia, p 467
26. Mendel G (1865) Versuche uber Pflanzen Hybriden. Verhandlung des naturforschenden Vereines in Brunn 4:3-47
27. Nägeli C von (1884) Mechianisch-physiologische Theorie der Abstammungslehre. Munich, p 73 [Translated in Darwin F (1908) British Association for the Advancement of Science. Presidential Address.]
28. Darwin C (1868) Provisional hypothesis of pangenesis. In: The Variation of Animals and Plants under Domestication. John Murray, London, Chapter 27
29. Dawkins R (1976) The Selfish Gene. Oxford University Press, Oxford
30. Huxley TH (1869) The genealogy of animals. In: Darwiniana. Collected Essays. Macmillan, London (1893)
31. Roux W (1881) der Kampf der Theile im Organismus. Liepzig
32. Hering E (1870) Über das Gedachtniss als eine allgemeine Function der organisirten Materie. Karl Gerald's Sohn, Vienna [On memory as a universal function of organized matter. A lecture delivered at the anniversary meeting of the Imperial Academy of Sciences at Vienna, translated in Butler S (1880) Unconscious Memory. David Bogue, London, pp 97-133.]
33. Butler S (1985) The Notebooks of Samuel Butler. Jones HF (ed) Hogarth Press, London, pp 58-59, 70-71
34. Bateson W (1909) Heredity and variation in modern lights. In: Bateson B (ed) William Bateson, FRS, Naturalist. His Essays and Addresses. Cambridge University Press, Cambridge (1928) pp 215-232
35. rd edition. Jonathan Cape, New York, pp 109, 152-160, 215, 240-250 [The first edition, dated 1878, appeared in December 1877. G. H. Lewes was a Victorian philosopher/biologist and member of the Physiological Society (London), who is best known as the partner of authoress George Eliot.]
36. Butler S (1872) Erewhon or Over the Range. Penguin Books, Harmondsworth (1935), pp 197-198
37. Romanes GJ (1884) Mental Evolution in Animals, with a Posthumous Essay on Instinct by Charles Darwin. Appleton, New York, p 131
38. Butler S (1884) Selections from Previous Works, with Remarks on Mr. G. J. Romanes' "Mental Evolution in Animals", and a Psalm of Montreal. Traubner, London, pp 228-254
39. Butler S (1880) Unconscious Memory. David Bogue, London, pp. 252, 269-273 [Tekke Turcomans were members of a nomadic tribe occupying an area somewhere to the north of what was then Persia.]
40. nd Edition. Jonathon Cape, London, pp 259-260 [The first edition was in 1887.]
41. Butler S (1914) The Humour of Homer and Other Essays. Kennerley, New York, pp 209-313
42. Provine WB (1971) The Origins of Theoretical Population Genetics. University of Chicago Press, Chicago
43. Olby R (1974) The Path to the Double Helix. University of Washington Press, Seattle
44. Crookes W (1866) On the application of disinfectants in arresting the spread of the cattle plague. In: Appendix to Third Report of the Commissioners Appointed to Inquire into the Origin and Nature, etc. of the Cattle Plague. Houses of Parliament, London, pp 187-201
45. Romano TM (2002) Making Medicine Scientific. John Burdon Sanderson and the Culture of Victorian Science. John Hopkins University Press, Baltimore, pp 63
46. Harris H (1999) Birth of the Cell. Yale University Press, New Haven, CT
47. Galton F (1872) On blood-relationship. Proceedings of the Royal Society 20:394-402 [Although not named as such, there is also here a distinction between the "phenotype" corresponding to "patent" elements, and "genotype" corresponding to both "patent" and "latent" elements.]
48. Weismann A (1904) The Evolution Theory, Vol 1. Edward Arnold, London, p 411
49. Vries H de (1910) Intracellular Pangenesis. Gager CS (translater) Open Court, Chicago
50. [Translated from Vries H de (1889) Intracellulare Pangenesis. Fischer. Jena.]
51. Olby R, Posner E (1967) An early reference on genetic coding. Nature 215:556
52. Romanes GJ (1893) An Examination of Weismannism. Open Court, Chicago, pp 182-183 [Romanes pointed out that Weismann's "germ-plasm" and Galton's equivalent (called "stirp" from the Latin stirpes = root), had in common the properties of stability and continuity. However, unlike today's DNA, "germ-plasm" as originally conceived by Weismann could only vary by the mixing with another germ-plasm through sexual reproduction. Galton held open the possibility that "stirp" might also vary by other means and, to "a very faint degree" (perhaps in deference to his cousin's theory of pangenesis"), Lamarckian principles were admitted.]
53. Bateson W (1894) Materials for the Study of Variation Treated with Especial Regard for Discontinuity in the Origin of Species. Macmillan, London, p33
54. Bateson W (1908) The methods and scope of genetics. In: Bateson B (ed) William Bateson, FRS, Naturalist. His Essays and Addresses. Cambridge University Press, Cambridge (1928), p 317-333
55. Bateson W (1913) Problems of Genetics. Yale University Press, New Haven, p 86
56. Bateson W (1914) Presidential address to the British Association, Australia. In: Bateson B (ed) William Bateson, FRS, Naturalist. His Essays and Addresses. Edited by Bateson B, Cambridge University Press, Cambridge (1928) pp 276-316
57. Schrodinger E (1944) What is Life? The Physical Aspect of the Living Cell. Cambridge University Press, Cambridge
58. Portugal FH, Cohen JS (1977) A Century of DNA. MIT Press, Cambridge, MA
59. Loewenstein WR (1999) The Touchstone of Life. Molecular Information, Cell Communication, and the Foundations of Life. Oxford University Press, Oxford
60. Kay LE (2000) Who Wrote the Book of Life? A History of the Genetic Code. Stanford University Press, Stanford
61. Weismann A (1904) The Evolution Theory, Vol 2. Edward Arnold, London, p63
62. Celarius (alias Butler S) (1863) Darwin among the machines. The Press, Christchurch, New Zealand [Reprinted in
63. Butler S (1914) The First Year in Canterbury Settlement with Other Early Essays. Fifield, London.]
64. Kellogg VL (1907) Darwinism Today. Holt, New York, pp 274-290
65. th edition. Jonathan Cape, New York, p 35 [The original edition was in 1879.]
66. Haeckel E (1909) Charles Darwin as an Anthropologist. In: Darwin and Modem Science. Cambridge University Press, Cambridge, pp 137-151
67. Jablonski NG, Chaplin G (2000) The evolution of human skin coloration. Journal of Human Evolution 39:57-106
68. Darwin C (1871) The Descent of Man, and Selection in Relation to Sex. Appleton, New York, pp 57-59 [The survival of favored words in individual nervous systems was considered in R. Semon's Mnemic Psychology (1923; Allen and Unwin, London): "There is thus - and perhaps this is at the bottom of all Mneme, a competition between what has been and what is and continues; there is the victory of the present, which accepts from the past only as much as it can integrate with its substance and turn to its uses."]
69. Watson JD, Crick FHC (1953) Molecular structure of nucleic acids. A structure for deoxyribose nucleic acid. Nature 171:737-738
70. Chargaff E (1951) Structure and function of nucleic acids as cell constituents. Federation Proceedings 10:654-659
71. Wyatt GR (1952) Specificity in the composition of nucleic acids. Experimental Cell Research, Supplement 2:201-217
72. Wyatt GR, Cohen SS (1953) The bases of the nucleic acids of some bacterial and animal viruses. Biochemical Journal 55:774-782
73. Israelachvili J, Wennerstrom H (1996) Role of hydration and water structure in biological and colloidal interactions. Nature 379:219-224
74. Muller HJ (1941) Resume and perspectives of the symposium on genes and chromosomes. Cold Spring Harbor Laboratory Symposium on Quantitative Biology 9:290-308
75. Sinden RR (1994) DNA Structure and Function. Academic Press, San Diego
76. Watson JD, Crick FHC (1953) Genetical implications of the structure of deoxyribonucleic acid. Nature 171:964-967
77. Kornberg A (1989) For the Love of Enzymes: the Odyssey of a Biochemist. Harvard University Press, Cambridge, MA
78. Muller HJ (1936) The needs of physics in the attack on the fundamental problems of genetics. Scientific Monthly 44:210-214
79. Crick F (1970) Molecular biology in the year 2000. Nature 228:613-615
80. Gatlin LL (1972) Information Theory and Living Systems. Columbia University Press, New York
81. Burton DW, Bickham JW, Genoways HH (1989) Flow-cytometric analyses of nuclear DNA contents in four families of neotropical bats. Evolution 43:756-765
82. Hughes AL, Hughes MK (1995) Small genomes for better flyers. Nature 377:391
83. Waring MJ, Britten RJ (1966) Nucleotide sequence repetition: a rapidly reassociating fraction of mouse DNA. Science 154:791-794
84. Bateson G (1967) Cybernetic explanations. American Behavioural Scientist 10:29-32
85. Romanes GJ (1891) Aristotle as a naturalist. Contemporary Review 59:275-289
86. Delbruck M (1971) Aristotle-totle-totle. In: Monod J. Borek F (eds) Of Microbes and Life. Columbia University Press, New York, pp 50-55
87. Lyell C (1863) The Geological Evidences of the Antiquity of Man with Remarks on Theories of the Origin of Species by Variation. Childs, Philadelphia, p 467
88. Shaw GB (1913) Pygmalion. In: Bernard Shaw. Complete Plays with Prefaces. Volume I. Dodd, Mead, New York (1963)
89. Galton F (1876) A theory of heredity. Journal of the Anthropological Institute 5:329-348
90. rd Edition. Jonathan Cape, London, pp 140-147, 163-165 ["Locus poenitenliae" is Latin for a "place of repentance." Legally the term signifies a, perhaps brief, temporal safe-haven where there is an opportunity to change one's mind. Thus, between the last bid and the fall of the auctioneer's hammer there is a locus poenitenliae for a decision, which cannot be stretched out for ever.]
91. Olby R, Posner E (1967) An early reference on genetic coding. Nature 215:556
92. Jenkin F (1867) The origin of species. The North British Review 46:277-318
93. rd Edition. Garland Publishing, New York, p 340
94. nd Edition. Worth Publishers, New York, p 789
95. Goldschmidt R (1956) Portraits from Memory. Recollections of a Zoologist. University of Washington Press, Seattle [Goldschmidt refers to Richard Semon who wrote two books on the theory of the "mneme." Building on the work of Butler, Semon proposed that memory was "the consequence of an accumulation of mnemetic engrams produced by environmental action", which can compete for neural space. Richard Dawkins was unaware of this when he suggested the word "meme", which could be "thought of as relating to memory" and is defined as "a self-replicating element of culture, passed on by imitation;" see A Devil's Chaplain by Dawkins (2003) Houghton Mifflin, Boston.]
96. Bateson W (1894) Materials for the Study of Variation Treated with Especial Regard to Discontinuities in the Origin of Species. Macmillan, London, pp 16, 69 [While there are many references to Galton, there is no reference to Jenkin, and Romanes is cited only with respect to his work on jelly fish.]
97. Galton F (1869) Hereditary Genius. Macmillan, London
98. Bateson G (1973) Steps to an Ecology of Mind. Paladin, St. Albans, p 127
99. Lipset D (1980) Gregory Bateson: The Legacy of a Scientist. Prentice-Hall, Englewood Cliffs, p 208 [This is also a splendid mini-biography of William Bateson.]
100. Bateson G (1963) The role of somatic change in evolution. Evolution 17:529-539
101. Wilson NG (1999) Archimedes: the palimpsest and the tradition. Byzantinische Zeitschrift 92:89-101
102. Crick F (1988) What Mad Pursuit. A Personal View of Scientific Discovery. Basic Books, New York
103. Forsdyke DR (2006) Heredity as transmission of information, (submitted for publication)
104. Dickens C (1837) The Posthumous Papers of the Pickwick Club. Chapman-Hall, London
105. Moliere (1670) Le Bourgeous Gentilhomme. In: Oliver TE (ed) Ginn, New York (1914)
106. Bok C (2001) Eunoia. Coach House Books, Toronto
107. Perec G (1972) Les Revenentes. Julliard, Paris
108. Perec G (1969) La Disparition. Denoel, Paris
109. Ohno S (1991) The grammatical rule of DNA language: messages in palindromic verses. In: Osawa S, Honjo T (eds) Evolution of Life. Springer-Verlag, Berlin, pp 97-108
110. Rudner R, Karkas JD, Chargaff E (1968) Separation of B. subtilis DNA into complementary strands. III. Direct analysis. Proceedings of the National Academy of Sciences USA 60:921-922
111. Bell SJ, Forsdyke DR (1999) Accounting units in DNA. Journal of Theoretical Biology 197:51-61
112. Darwin C (1871) The Descent of Man and Sex in Relation to Sex. John Murray, London, p 316
113. Edwards AWF (1998) Natural selection and the sex ratio. American Naturalist 151:564-569
114. Forsdyke DR (2002) Symmetry observations in long nucleotide sequences. Bioinformatics 18:215-217
115. Prabhu VV (1993) Symmetry observations in long nucleotide sequences. Nucleic Acids Research 21:2797-2800
116. Forsdyke DR (1995) Relative roles of primary sequence and (G+C) % in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species. Journal of Molecular Evolution 41:573-581
117. Russell GJ, Subak-Sharpe JH (1977) Similarity of the general designs of protochordates and invertebrates. Nature 266:533-535
118. Bultrini E, Pizzi E, Guidice P Del, Frontali C (2003) Pentamer vocabularies characterizing introns and intron-like intergenic tracts from Caenorhabditis elegans and Drosophila melanogaster. Gene 304:183-192
119. Forsdyke DR, Bell SJ (2004) Purine-loading, stem-loops, and Chargaff s second parity rule: a discussion of the application of elementary principles to early chemical observations. Applied Bioinformatics 3:3-8
120. Baisnee P-F, Hampson S, Baldi P (2002) Why are complementary strands symmetric? Bioinformatics 18:1021-1033
121. Sueoka N (1995) Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. Journal of Molecular Evolution 40:318-325
122. Nussinov R (1981) Eukaryotic dinucleotide preference rules and their implications for degenerate codon usage. Journal of Molecular Biology 149:125-131
123. Delbruck M (1949) Transactions of the Connecticut Academy of Arts and Sciences 38:173-190
124. Salser W (1970) Discussion. Cold Spring Harbor Symposium in Quantitative Biology 35:19
125. Ball LA (1972) Implications of secondary structure in messenger RNA. Journal of Theoretical Biology 36:313-320
126. Forsdyke DR (1998) An alternative way of thinking about stem-loops in DNA. Journal of Theoretical Biology 192:489-504
127. Seffens W, Digby D (1999) mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Research 27:1578-1584
128. Tinoco I, Uhlenbeck OC, Levine MD (1971) Estimating secondary structure in ribonucleic acids. Nature 230:362-367
129. Allawi HT, Santa Lucia J (1997) Thermodynamics and NMR of internal GT mismatches in DNA. Biochemistry 36:10581-10589
130. Zuker M (1990) Predicting optimal and suboptimal secondary structure for RNA. Methods in Enzymology 183:281-306
131. Bass BL (2002) RNA editing by adenosine deaminases that act on RNA. Annual Review of Biochemistry 71:8I7 846
132. Chargaff E (1963) Essays on Nucleic Acids. Elsevier, Amsterdam, p 148
133. Szybalski W, Kubinski H, Sheldrick P (1966) Pyrimidine clusters on the transcribing strands of DNA and their possible role in the initiation of RNA synthesis. Cold Spring Harbor Symposium in Quantitative Biology 31:123-127
134. Smithies O, Engels WR, Devereux JR, Slightom JL, Shen S (1981) Base substitutions, length differences and DNA strand asymmetries in the human GX and AX fetal globin gene region. Cell 26:345-353
135. Saul A, Battistutta D (1988) Codon usage in Plasmodium falciparum. Molecular Biochemistry and Parasitology 27:35-42
136. Bell SJ, Forsdyke DR (1999) Deviations from Chargaff s second parity rule correlate with direction of transcription. Journal of Theoretical Biology 197:63-76
137. Lao PJ, Forsdyke DR (2000) Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Research 10:1-20
138. Schattner P (2002) Searching for RNA genes using base-composition statistics. Nucleic Acids Research 30:2076-2082
139. Szybalski W, et al. (1969) Transcriptional controls in developing bacteriophages. Journal of Cellular Physiology 74, supplement 1:33-70
140. Frank AC, Lobry JR (1999) Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 238:65-77
141. Tillier ERM, Collins RA (2000) Replication orientation affects the rate and direction of bacterial gene evolution. Journal of Molecular Evolution 51:459-463
142. Brewer BJ (1988) When polymerases collide. Cell 53:679-686;
143. French S (1992) Consequences of replication fork movement through transcription units in vivo. Science 258:1362-1365
144. Olavarrieta L, Hernandez P, Krimer DB, Schvartzman JB (2002) DNA knotting caused by head-on collision of transcription and replication. Journal of Molecular Biology 322:1-6
145. Chargaff E (1951) Structure and function of nucleic acids as cell constituents. Federation Proceedings 10:654-659
146. Elson D, Chargaff E (1955) Evidence of common regularities in the composition of pentose nucleic acids. Biochemica Biophysica Acta 17:367-376
147. Wang H-C, Hickey DA (2002) Evidence for strong selective constraints acting on the nucleotide composition of 16S ribosomal RNA genes. Nucleic Acids Research 30:2501-2507
148. Forsdyke DR, Bell SJ (2004) Purine-loading, stem-loops, and Chargaff s second parity rule: a discussion of the application of elementary principles to early chemical observations. Applied Bioinformatics 3:3-8
149. Eguchi Y, Itoh T, Tomizawa J (1991) Antisense RNA. Annual Reviews of Biochemistry 60:631-652
150. Brunei C, Marquet R, Romby P, Ehresmann C (2002) RNA loop-loop interactions as dynamic functional motifs. Biochimie 84:925-944
151. Cristillo AD, Heximer SP, Forsdyke DR (1996) A "stealth" approach to inhibition of lymphocyte activation by oligonucleotides complementary to the putative G0/G1 switch regulatory gene G0S30/EGR1/ZFP6. DNA and Cell Biology 15:561-570
152. Paz A, Mester D, Baca I, Nevo E, Korol A (2004) Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes. Proceedings of the National Academy of Sciences USA 101:2951-2956
153. Spees JL, Olson SD, Whitney MJ, Prockop DJ (2006) Mitochondrial transfer between cells can rescue aerobic respiration. Proceedings of the National Academy of Sciences USA 103:1283-1288
154. Bennett JH (1983) Natural Selection, Heredity and Eugenics. Including Selected Correspondence of R. A. Fisher with Leonard Darwin and Others. Clarendon Press, Oxford, p 122 [Mathematicians with an interest in biological problems need a biologist to help them along. Fisher had Leonard Darwin. His American adversary, Sewall Wright, had Theodosius Dobzansky.]
155. Butler S (1862) Darwin and the origin of species. Reproduced from The Press of Christchurch. In: Streatfeild RA (ed) The First Year in Canterbury Settlement with Other Early Essays. Fifield, London, (1914) pp 149-164
156. Fisher RL (1930) The Genetical Theory of Natural Selection. Oxford University Press, Oxford
157. Darwin C (1856) Letter to J. D. Hooker. In: Darwin F (ed) Life and Letters of Charles Darwin. Volume 1. Appleton, New York (1887) p 445
158. Bateson W (1909) Heredity and variation in modern lights. In: Bateson B (ed) William Bateson FRS, Naturalist. His Essays and Addresses. Cambridge University Press, Cambridge (1928) pp 215-232
159. Bateson W (1894) Materials for the Study of Variation Treated with Especial Regard for Discontinuity in the Origin of Species. Macmillan, London, pp 85, 573
160. Bossi L, Roth JR (1980) The influence of codon context on genetic code translation. Nature 286:123-127
161. Simonson AB, Lake JA (2002) The transorientation hypothesis for codon recognition during protein synthesis. Nature 416:281-285
162. Eigen M, Schuster P (1978) The hypercycle. A principle of natural self-organization. Part C. The realistic hypercycle. Naturwissenschaften 65:341-369
163. Shepherd JCW (1981) Method to determine the reading frame of a protein from the purine/pyrimidine genome sequence and its possible evolutionary justification. Proceedings of the National Academy of Sciences USA 78:1596-1600
164. Akashi H (2001) Gene expression and molecular evolution. Current Opinion in Genetics and Development 11:660-666
165. Forsdyke DR (2002) Selective pressures that decrease synonymous mutations in Plasmodium falciparum. Trends in Parasitology 18:411-418
166. Forsdyke DR (2006) Positive Darwinian selection. Does the comparative method rule? (submitted for publication).
167. Fitch WM (1974) The large extent of putative secondary nucleic acid structure in random nucleotide sequences or amino acid-derived messenger-RNA. Journal of Molecular Evolution 3:279-291
168. Bernardi G, Bemardi G (1986) Compositional constraints and genome evolution. Journal of Molecular Evolution 24:1-11
169. Wolfe KH, Sharp PM (1993) Mammalian gene evolution: nucleotide sequence divergence between mouse and rat. Journal of Molecular Evolution 37:441-456
170. Novella LA, Zarate S, Metzgar D, Ebendick-Corpus, BE (2004) Positive selection of synonymous mutations in vesicular stomatitis virus. Journal of Molecular Biology 342:1415-1421
171. th edition, Darwin was more seriously thinking that some acquired characters might be inherited (Lamarckism). This is probably why he then questioned the sufficiency of natural selection as an explanation for evolutionary advance.]
172. Darwin C (1857) Letter to T. H. Huxley. In: Darwin F (ed) More Letters of Charles Darwin, Vol 1. Appleton, New York (1903) p 102
173. Hooker J (1860) On the origination and distribution of species. Introductory essay on the flora of Tasmania. American Journal of Science and Arts 29:1-25, 305-326
174. Mendel G (1865) Versuche uber Pflanzen Hybriden. Verhandlung des naturforschenden Vereines in Brunn 4:3-47 [The pea plant was a happy choice for Mendel. In this species the height character can be treated largely as a unigenic trait.]
175. th May. Wellcome Museum of the History of Medicine, London. [Romanes cited Mendel in an article on "Hybridism" in the Encyclopaedia Britannica, 1881.]
176. Darwin C (1866) Letter to A. R. Wallace. In: Marchant J (1916) Alfred Russel Wallace. Letters and Reminiscences. Harper, New York
177. rd Edition. Jonathan Cape, London, pp. 135-160
178. Bateson W, Saunders ER (1902) Report 1. Reports to the Evolution Committee of the Royal Society. Harrison, London
179. Forsdyke DR (2001) The Origin of Species, Revisited. McGill-Queen's University Press, Montreal
180. nd November. The William Bateson Archive. University of Cambridge [His sister had sent him copies of Nature with Romanes' articles.]
181. Galton F (1872) On blood relationship. Proceedings of the Royal Society 20:394-402 [Bateson's concept of a "residue", may have derived from Galton's earlier postulate that "patent elements" responsible for the hereditary transmission of characters constituting "the person manifest to our senses" (i.e. phenotype), had a material base, which was separate from that of a much larger "residue" containing the "latent elements." These were responsible for the hereditary transmission of ancestral characters that were not manifest in the current phenotype.]
182. Richmond ML, Dietrich MR (2002) Richard Goldschmidt and the crossingover controversy. Genetics 161:477-482 [In his Natural Inheritance (1889) Galton used the metaphor of a necklace as "the main line of hereditary connection", and equated the elements responsible for personal characters (genes to the modern reader) to "pendants attached to its links."]
183. Goldschmidt R (1940) The Material Basis of Evolution. Yale University Press, New Haven, pp 205-6, 245-248 [The term "reaction system"' was introduced to distinguish large genetic units between which recombination was restricted (i.e. each was an individual "reaction system"), from individual genes that exhibited standard Mendelian behaviour;
184. Goodspeed TH, Clausen RE (1917) American Naturalist 51:31-46, 92-101.]
185. Avery OT, Macloed CM, McCarty M (1944) Studies on the chemical transformation of pneumococcal types. Journal of Experimental Medicine 79:137-158
186. Chargaff E (1951) Structure and function of nucleic acids as cell constituents. Federation Proceedings 10:654-659
187. Sueoka N (1961) Compositional correlations between deoxyribonucleic acid and protein. Cold Spring Harbor Symposium on Quantitative Biology 26:35-43
188. Forsdyke DR (2001) The Origin of Species, Revisited. McGill-Queen's University Press, Montreal
189. Dawkins R (1986) The Blind Watchmaker. Longman, Harlow, p 267
190. Gratia JP, Thiry M (2003) Spontaneous zygogenesis in Escherichia coli, a form of true sexuality in prokaryotes. Microbiology 149:2571-84
191. Bellgard M, Schibeci D, Trifonov E, Gojobori T (2001) Early detection of G + C differences in bacterial species inferred from the comparative analysis of the two completely sequenced Helicobacter pylori strains. Journal of Molecular Evolution 53:465-468
192. Grantham R, Perrin P, Mouchiroud D (1986) Patterns in codon usage of different kinds of species. Oxford Surveys in Evolutionary Biology 3:48-81
193. Page AW, Orr-Weaver TL (1996) Stopping and starting the meiotic cell cycle. Current Opinion in Genetics and Development 7:23-31
194. Metz CW (1916) Chromosome studies on the Diptera. 11. The paired association of chromosomes in the Diptera, and its significance. Journal of Experimental Zoology 21:213-279
195. Muller HJ (1922) Variation due to change in the individual gene. American Naturalist 56:32-50
196. Carlson EA (1981) Genes, Radiation and Society. The Life and Work of H. J. Muller, Cornell University Press, Ithaca, NY, p 390
197. Crick F (1971) General model for chromosomes of higher organisms. Nature 234:25-27
198. Sobell HM (1972) Molecular mechanism for genetic recombination. Proceedings of the National Academy of Sciences USA 69:2483-2487
199. Wagner RE, Radman M (1975) A mechanism for initiation of genetic recombination. Proceedings of the National Academy of Sciences USA 72:3619-3622
200. Doyle GG (1978) A general theory of chromosome pairing based on the palindromic DNA model of Sobell with modifications and amplification. Journal of Theoretical Biology 70:171-184
201. Gerton JL, Havvley RS (2005) Homologous chromosome interactions in meiosis: diversity amidst conservation. Nature Reviews Genetics 6:477-487
202. Weiner BM, Kleckner N (1994) Chromosome pairing via multiple interstitial interactions before and during meiosis in yeast. Cell 77:977-991
203. Wong BC, Chiu S-K, Chow SA (1998) The role of negative superhelicity and length of homology in the formation of paranemic joints promoted by RecA protein. Journal of Biological Chemistry 273:12120-12127
204. Forsdyke DR (1996) Different biological species "broadcast" their DNAs at different (G+C) % "wavelengths." Journal of Theoretical Biology 178:405-417
205. Dong F, Allawi HT, Anderson T, Neri BP, Lyamichev VI (2001) Secondary structure prediction and structure specific sequence analysis of singlestranded DNA. Nucleic Acids Research 29:3248-3257
206. Chen J-H, Le S-Y, Shapiro B, Currey KM, Maizel JV (1990) A computational procedure for assessing the significance of RNA secondary structure. CABIOS 6:7-18
207. Forsdyke DR (1998) An alternative way of thinking about stem-loops in DNA. A case study of the human G0S2 gene. Journal of Theoretical Biology 192:489-504
208. Bronson EC, Anderson JN (1994) Nucleotide composition as a driving force in the evolution of retroviruses. Journal of Molecular Evolution 38:506-532
209. Levy DN, Aldrovandi GM, Kutsch O, Shaw GM (2004) Dynamics of HIV-1 recombination in its natural target cells. Proceedings of the National Academy of Sciences USA 101:4204-4209
210. Michel N, Allespach I, Venzke S, Fackler OT, Keppler OT (2005) The nef protein of human immunodeficiency virus established superinfection immunity by a dual strategy to downregulate cell-surface CCR5 and CD4. Current Biology 15:714-723 [The authors state: "Primate lentiviruses appear to have evolved time windows during which the permission or prevention of superinfection is regulated by gene expression. According to this model, after infection and prior to early HIV gene expression, superinfection can readily occur in order to permit recombination. As the most abundant early viral gene product, Nef defines the start point of a successful productive infection and functions as a master switch for the establishment of superinfection resistance by downregulating the entry receptor complex."]
211. Goldschmidt R (1940) The Material Basis of Evolution. Yale University Press, New Haven, p 220
212. Matassi G, Melis R, Macaya G, Bernardi G (1991) Compositional bimodality of the nuclear genome of tobacco. Nucleic Acids Research 19:5561-5567
213. Bernardi G (2001) Misunderstandings about isochores. Part 1. Gene 276:3-13
214. Cohen N, Dagan T, Stone L, Graur D (2005) GC composition of the human genome: in search of isochores. Molecular Biology and Evolution 22:1260-1272
215. Matsuo K, Clay O, Kunzler P, Georgiev O, Urbanek P, Schaffner W (1994) Short introns interrupting the Oct-2 POU domain may prevent recombination between POU family genes without interfering with potential POU domain 'shuffling' in evolution. Biological Chemistry Hoppe-Seyler 375:675-683
216. Newgard CB, Nakano K, Hwang PK, Fletterick RJ (1986) Sequence analysis of the cDNA encoding human liver glycogen phosphorylase reveals tissue-specific codon usage. Proceedings of the National Academy of Sciences USA 83:8132-8136
217. Moore R C, Purugganan MD (2003) The early stages of duplicate gene evolution. Proceedings of the National Academy of Sciences USA 100:15682-15687
218. Zhang Z, Kishino H (2004) Genomic background drives the divergence of duplicated Amylase genes at synonymous sites in Drosophila. Molecular Biology and Evolution 21:222-27
219. Montoya-Burgos JI, Boursot P, Galtier N (2003) Recombination explains isochores in mammalian genomes. Trends in Genetics 19:128-130
220. Skalka A, Burgi E, Hershey AD (1968) Segmental distribution of nucleotides in the DNA of bacteriophage lambda. Journal of Molecular Biology 34:1-16
221. Vizard DL, Ansevin AT (1976) High resolution thermal denaturation of DNA: thermalites of bacteriophage DNA. Biochemistry 15:741-750
222. Bibb MJ, Findlay PR, Johnson MW (1984) The relationship between base composition and codon usage in bacterial genes and its use for the simple and reliable identification of protein-coding sequences. Gene 30:157-166
223. Wada A, Suyama A (1985) Third letters in codons counterbalance the (G+C) content of their first and second letters. Federation of European Biochemical Societies Letters 188:291-294
224. Kudla G, Helwak A, Lipinski L (2004) Gene conversion and GC-content evolution in mammalian Hsp70. Molecular Biology and Evolution 21:1438-1444
225. Williams GC (1966) Adaptation and Natural Selection. Princeton University Press, Princeton, pp 24-25
226. Dalgaard JZ, Garrett A (1993) Archaeal hyperthermophile genes. In: Kates M, Kushner DJ, Matheson AT (eds) The Biochemistry of Archaea (Archaebacteria). Elsevier, Amsterdam, pp 535-562
227. Forterre P, Elie C (1993) Chromosome structure, DNA topoisomerases, and DNA polymerases in archaebacteria (archaea). In: Kates M, Kushner DJ, Matheson AT (eds) The Biochemistry of Archaea (Archaebacteria). Elsevier, Amsterdam, pp 325-345
228. Galtier N, Lobry JR (1997) Relationships between genomic G+C content, RNA secondary structures, and optimal growth temperature in prokaryotes. Journal of Molecular Evolution 44:632-636
229. Lambros R, Mortimer JR, Forsdyke DR (2003) Optimum growth temperature and the base composition of open reading frames in prokaryotes. Extremophiles 7:443-450
230. Filipski J (1990) Evolution of DNA sequence. Contributions of mutational bias and selection to the origin of chromosomal compartments. Advances in Mutagenesis Research 2:1-54
231. Oshima T, Hamasaki N, Uzawa T, Friedman SM (1990) Biochemical functions of unusual polyamines found in the cells of extreme thermophiles. In: Goldembeg SH, Algranati ID (eds) The Biology and Chemistry of Polyamines. Oxford University Press, New York, pp 1-10
232. Friedman SM, Malik M, Drlica K (1995) DNA supercoiling in a thermotolerant mutant of Escherichia coli. Molecular and General Genetics 248:417-422
233. Holliday R (1968) Genetic recombination in fungi. In: Peacock WJ, Brock RD (eds) Replication and Recombination of Genetic Material. Australian Academy of Science, Camberra, pp 157-174
234. Galton F (1876) A theory of heredity. Journal of the Anthropological Institute 5:329-348 [He did not think that the "germs" would be linearly arranged: "It is difficult to suppose the directions of the mutual influences of the germs to be limited to lines, like those that cause the blood corpuscles to become attached face to face, in long rouleaux, when coagulation begins."]
235. Schaap T (1971) Dual information in DNA and the evolution of the genetic code. Journal of Theoretical Biology 32:293-298
236. Grantham R (1972) Codon base randomness and composition drift in coliphage. Nature New Biology 237:265
237. Grantham R, Perrin P, Mouchiroud D (1986) Patterns in codon usage of different kinds of species. Oxford Surveys in Evolutionary Biology 3:48-81
238. Sharp PM, Stenico M, Peden JF, Lloyd AT (1993) Codon usage: mutational bias, translation selection, or both? Biochemical Society Transactions 21:835-841
239. Cox EC, Yanofsky C (1967) Altered base ratios in the DNA of an Echerichia coli mutator strain. Proceedings of the National Academy of Sciences USA 58:1895-1902
240. Muto A, Osawa S (1987) The guanine and cytosine content of genomic DNA and bacterial evolution. Proceedings of the National Academy of Sciences USA 84:166-169
241. Forsdyke DR (2004) Regions of relative GC% uniformity are recombinational isolators. Journal of Biological Systems 12:261-271
242. Lee J-C, Mortimer JR, Forsdyke DR (2004) Genomic conflict settled in favour of the species rather than of the gene at extreme GC% values. Applied Bioinformatics 3:219-228
243. Wada A, Suyama A, Hanai R (1991) Phenomenological theory of GC/AT pressure on DNA base composition. Journal of Molecular Evolution 32:374-378
244. D'Onofrio G, Bernardi G (1992) A universal compositional correlation among codon positions. Gene 110:81-88
245. Orr HA (2004) A passion for evolution. The New York Review of Books 51: no. 3, pp 27-29
246. Paz A, Kirzhner V, Nevo E, Korol A (2006) Coevolution of DNA-interacting proteins and genome "dialect." Molecular Biology and Evolution 23:56-64
247. Lao PJ, Forsdyke DR (2000) Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine. Genome Research 10:228-236
248. Mortimer JR, Forsdyke DR (2003) Comparison of responses by bacteriophage and bacteria to pressures on the base composition of open reading frames. Applied Bioinformatics 2:47-62
249. Rayment JH, Forsdyke DR (2005) Amino acids as placeholders. Base composition pressures on protein length in malaria parasites and prokaryotes. Applied Bioinformatics 4:117-130
250. Lin F-H, Forsdyke DR (2006) Prokaryotes that grow optimally in acid have purine-poor codons in long open reading frames, (submitted for publication)
251. Hamming RW (1980) Coding and Information Theory. Prentice-Hall, Englewood Cliffs
252. Federoff NV (1979) On spacers. Cell 16:687-710
253. Scherrer K (2003) The discovery of 'giant' RNA and RNA processing. Trends in Biochemical Sciences 28:566-571
254. Gilbert W (1978) Why genes in pieces? Nature 271:501
255. Weber K, Kabsch W (1994) Intron positions in actin genes seem unrelated to the secondary structure of the protein. EMBO Journal 13:1280-1288
256. Stoltzfus A, Spencer DF, Zuker M, Logsdon JM, Doolittle WF (1994) Testing the exon theory of genes: evidence from protein structure. Science 265:202-207
257. Sakharkar M, Passetti F, Souza JE de, Long M, Souza SJ de (2002) Exlnt: an Exon Intron Database. Nucleic Acids Research 30:191-194
258. Blake C (1983) Exons - present from the beginning. Nature 306:535-537
259. Naora H, Deacon NJ (1982) Relationship between the total size of exons and introns in protein-coding genes of higher eukaryotes. Proceedings of the National Academy of Sciences USA 79:6196-6200
260. Raible F, et al. (2005) Vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii. Science 310:1325-1326
261. Liu M, Grigoriev A (2004) Protein domains correlate strongly with exons in multiple eukaryotic genomes - evidence of exon shuffling? Trends in Genetics 20:399-403
262. Forsdyke DR (1981) Are introns in-series error-detecting codes? Journal of Theoretical Biology 93:861-866
263. Bernstein C, Bernstein H (1991) Aging, Sex and DNA Repair. Academic Press, San Diego
264. Williams GC (1966) Adaptation and Natural Selection. Princeton University Press, Princeton, pp 133-138
265. Forsdyke DR (1995). A stem-loop "kissing" model for the initiation of recombination and the origin of introns. Molecular Biology and Evolution 12:949-958
266. 2 genes. An application of FORS-D analysis. Molecular Biology and Evolution 12:1157-1165
267. Forsdyke DR. (1996) Stem-loop potential: a new way of evaluating positive Darwinian selection? Immunogenetics 43:182-189
268. Forsdyke DR (1995) Reciprocal relationship between stem-loop potential and substitution density in retroviral quasispecies under positive Darwinian selection. Journal of Molecular Evolution 41:1022-1037
269. Zhang C-Y, Wei J-F, He S-H (2005) The key role for local base order in the generation of multiple forms of China HIV-1 B/C intersubtype recombinants. BMC Evolutionary Biology 5:53
270. Alvarez-Valin F, Tort JF, Bernardi G (2000) Nonrandom spatial distribution of synonymous substitutions in the GP63 gene from Leishmania. Genetics 155:1683-1692
271. Bustamente CD, Townsend JP, Hartl DL (2000) Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Molecular Biology and Evolution 17:301-308
272. Heximer SP, Cristillo AD, Russell L, Forsdyke DR (1996) Sequence analysis and expression in cultured lymphocytes of the human FOSB gene (G0S3). DNA Cell Biology 12:1025-1038
273. Forsdyke DR (1991) Programmed activation of T-lymphocytes. A theoretical basis for short term treatment of AIDS with azidothymidine. Medical Hypothesis 34:24-27
274. Williams SA, Chen L-F, Kwon H, Fenard D, Bisgrove D, Verdin E, Greene WC (2005) Prostratin antagonizes HIV latency by activating NF-kappaB. Journal of Biological Chemistry 279:42008-12017 [HIV may have an Achilles heel, but first latent HIV must be "flushed" from the genome using "inductive therapy."]
275. Kurahashi H, Lnagaki H, Yamada K, Ohye T, Taniguchi M, Emanuel BS, Toda T (2004) Cruciform DNA structure underlies the etiology for palindrome-mediated human chromosomal translocations. Journal of Biological Chemistry 279:35377-35383
276. Lang DM (2005) Imperfect DNA mirror repeats in E. coli TnsA and other protein-coding DNA. Biosystems 81:183-207
277. Barrette IH, McKenna S, Taylor DR, Forsdyke DR (2001) lntrons resolve the conflict between base order-dependent stem-loop potential and the encoding of RNA or protein. Further evidence from overlapping genes. Gene 270:181-189
278. Grantham R (1974) Amino acid difference formula to help explain protein evolution. Science 185:862-864 [To construct a "PAM matrix", the observed frequency of interchanges between two amino acids is divided by the expected interchanges calculated by multiplying the respective frequencies of each amino acid in the data set. There being 20 amino acids, a 20 x 20 matrix is generated. Of the 400 values, 20 are on the diagonal and the remaining 380 are duplicates, so that 190 values form the final matrix. Two proteins whose amino acid differences generate a low total PAM score would be held to be closely related evolutionary.]
279. Bateson G (1964) The logical categories of learning and communication. In: Steps to an Ecology of Mind. Paladin, St. Albans (1973) pp 250-279
280. Sibbald PR (1989) Calculating higher order DNA sequence information measures. Journal of Theoretical Biology 136:475-483
281. Wan H, Wootton JC (2000) A global complexity measure for biological sequences. AT-rich and GC-rich genomes encode less complex proteins. Computers and Chemistry 24; 71-94
282. Cristillo AD, Mortimer JR, Barrette IH, Lillicrap TP, Forsdyke DR (2001) Double-stranded RNA as a not-self alarm signal: to evade, most viruses purine-load their RNAs, but some (HTLV-1, EBV) pyrimidine-load. Journal of Theoretical Biology 208:475-491
283. Forsdyke DR (2002) Selective pressures that decrease synonymous mutations in Plasmodium falciparum. Trends in Parasitology 18:411-418
284. Xue HY, Forsdyke DR (2003) Low complexity segments in Plasmodium falciparum proteins are primarily nucleic acid level adaptations. Molecular and Biochemical Parasitology 128:21-32
285. Pizzi E, Frontali C (2001) Low-complexity regions in Plasmodium falciparum proteins. Genome Research 11:218-229
286. Forsdyke DR (1996) Stem-loop potential: a new way of evaluating positive Darwinian selection? Immunogenetics 43:182-189
287. McMurray CT, Kortun LV (2003) Repair in haploid male cells occurs late in differentiation as chromatin is condensing. Chromosoma 111:505-508
288. Suhr ST, Senut M-C, Whitelegge JP, Faull KF, Cuizon DB, Gage FH. (2001) Identities of sequestered proteins in aggregates from cells with induced polyglutamine expression. The Journal of Cell Biology 153:283-294
289. Tian B, White RJ, Xia T, Welle S, Turner DH, Mathews MB, Thornton CA (2000) Expanded CUG repeat RNAs form hairpins that activate the doublestranded RNA-dependent protein kinase PKR. RNA 6:79-87
290. Peel AL, Rao RV, Cottrell BA, Hayden MR, Ellerby LM, Bredesen DE (2001) Double-stranded RNA-dependent protein kinase, PKR, binds preferentially to Huntington's disease (HD) transcripts and is activated in HD tissue. Human Molecular Genetics 10:1531-1538
291. Ranum LPW, Day JW (2004) Pathogenic RNA repeats: an expanding role in genetic diseases. Trends in Genetics 20:506-512
292. Trifonov EN, Sussman JL (1980) The pitch of chromatin DNA is reflected in its nucleotide sequence. Proceedings of the National Academy of Sciences USA 77:3816-3820
293. Schieg P, Herzel H (2004) Periodicities of 10-11 bp as indicators of the supercoiled state of genomic DNA. Journal of Molecular Biology 343:891-901
294. Trifonov EN (1998) 3-, 10.5-, 200-, and 400-base periodicities in genome sequences. Physica A 249:511-516
295. Li W, Holste D (2004) An unusual 500, 000 base long oscillation of guanine and cytosine content in human chromosome 21. Computational Biology and Chemistry 28:393-399
296. Shaw HW (1866) Josh Billings, His Sayings. Carleton, New York
297. Mira A (1998) Why is meiosis arrested? Journal of Theoretical Biology 194:275-287
298. Johnson J, Canning J, Kaneko T, Pru JK, Tilly JL (2004) Germ line stem cells and follicular renewal in the post-natal mammalian ovary. Nature 428:145-150
299. Granovetter M (1983) The strength of weak ties. A network theory revisited. Sociological Theory 1:201-233
300. Pancer Z, Amemiya CT, Ehrhardt GRA, Ceitlin J, Gartland GL, Cooper MD (2004) Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature 430:174-180
301. Zhang S-M, Adema CM, Kepler TB, Loker ES (2004) Diversification of Ig Superfamily Genes in an Invertebrate. Science 305:251-254
302. Brücke E (1861) Die Elementarorganismen. Sitzungsberichte der Akademie der Wissenschaften Wein, Mathematische-wissenschaftliche Classe 44:381-406
303. Forsdyke DR, Madill CA, Smith SD (2002) Immunity as a function of the unicellular state: implications of emerging genomic data. Trends in Immunology 23:575-579
304. Ohno S (1972) So much "junk" DNA in our genome. Brookhaven Symposium on Biology 23:366-370
305. Plant KE, et al. (2001) Intergenic transcription in the human B-globin gene cluster. Molecular and Cellular Biology 21:6507-6514
306. Kapranov P, et al. (2002) Large-scale transcriptional activity in chromosomes 21 and 22. Science 296:916-919
307. Johnson JM, Edwards S, Shoemaker D, Schadt EE (2005) Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. Trends in Genetics 21:93 102
308. Darwin C (1871) Descent of Man, and Selection in Relation to Sex. Appleton, New York, pp 156-157
309. Cristillo AD, Mortimer JR, Barrette LH, Lillicrap TP, Forsdyke DR (2001) Double-stranded RNA as a not-self alarm signal: to evade, most viruses purine-load their RNAs, but some (HTLV-1, EBV) pyrimidine-load. Journal of Theoretical Biology 208:475-91
310. Wilkins C, Dishongh R, Moore SC, Whitt MA, Chow M, Machaca K (2005) RNA interference is an antiviral defence mechanism in Caenorhabditis elegans. Nature 436:1044-1047
311. Lauffer MA (1975) Entropy-driven Processes in Biology. Springer-Verlag, New York
312. Levanon EY, et al. (2004) Systemic identification of abundant A-to-I editing sites in the human transcriptome. Nature Biotechnology 22:1001-1005
313. Ota T, et al. (2004) Complete sequencing and characterization of 21243 full-length human cDNAs. Nature Genetics 36:40-45
314. Waddington CH (1952) Selection of the genetic basis for an acquired character. Nature 169:278
315. Kipling R (1891) If. In: Rudyard Kipling's Verse. Inclusive Edition 1885-1918, Copp Clark, Toronto (1919) pp 645
316. Fulton AB (1982) How crowded is the cytoplasm? Cell 30:345-347
317. Wainwight M (2003) Early history of microbiology. Advances in Applied Microbiology 52:333-355
318. Forsdyke DR (1995) Entropy-driven protein self-aggregation as the basis for self/not-self discrimination in the crowded cytosol. Journal of Biological Systems 3:273-287
319. Lauffer MA (1975) Entropy-driven Processes in Biology. Springer-Verlag, New York [In addition to entropy, "volume exclusion" may play a role in some crowding phenomena;
320. see Minton AP (2001) The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. Journal of Biological Chemistry 276:10577-10580.]
321. Forsdyke DR (2001) Adaptive value of polymorphism in intracellular self/not-self discrimination. Journal of Theoretical Biology 210:425-434
322. Moreau-Aubry A, Le Guiner S, Labarriere N, Gesnel M-C, Jotereau F, Breathnach R (2000) A processed pseudogene codes for a new antigen recognized by a CD8+ T cell clone on melanoma. Journal of Experimental Medicine 191:1617-1623
323. Goldschmidt R (1940) The Material Basis of Evolution. Yale University Press, New Haven, pp 266-271
324. Hickman HD, et al. (2003) Class 1 presentation of host peptides following human immunodeficiency virus infection. Journal of Immunology 171:22-26
325. Darnell RB (1996) Onconeural antigens and the paraneoplastic neurological disorders: at the intersection of cancer, immunity and the brain. Proceedings of the National Academy of Sciences USA 93:4529-1536
326. Pardoll D (2002) T cells take aim at cancer. Proceedings of the National Academy of Sciences USA 99:15840-15842
327. Lane C, Leitch J, Tan X, Hadjati J, Bramson JL, Wan Y (2004) Vaccination-induced autoimmune vitiligo is a consequence of secondary trauma to the skin. Cancer Research 64:1509-1514
328. Heaman EA (2003) St. Mary's. The History of a London Teaching Hospital. McGill-Queen's University Press, Montreal, p 322
329. Shull GH (1909) The "presence and absence" hypothesis. American Naturalist 43:410-419
330. Forsdyke DR (1994) The heat-shock response and the molecular basis of genetic dominance. Journal of Theoretical Biology 167:1-5
331. Sangster TA, Lindquist S, Queitsch C (2004) Under cover: causes, effects and implications of Hsp90-mediated genetic capacitance. BioEssays 26:348-362
332. Zinkemagel RM, Doherty PC (1974) Restriction of in vitro T cell-mediated cytotoxicity in lymphocytic choriomeningitis within a syngeneic or semiallogeneic system. Nature 248:701-702
333. Forsdyke DR (1975) Further implication ofatheory of immunity. Journal of Theoretical Biology 52:187-198 [The "affinity/avidity" model for positive repertoire selection presented here is now generally accepted.]
334. Forsdyke DR (1991) Early evolution of MHC polymorphism. Journal of Theoretical Biology 150:451-456
335. Forsdyke DR (2005) "Altered-self' or "near-self in the positive selection of lymphocyte repertoires. Immunology Letters 100:103-106
336. Naveira HF, Maside XR (1998) The genetics of hybrid male sterility in Drosophila. In: Howard DJ, Berlocher SH (eds) Endless Forms and Speciation. Oxford University Press, Oxford, pp 329-338
337. Delboeuf J (1877) Les mathematiques et le transformisme. Une loi mathematique applicable a la theorie du transformisme. La Revue Scientifique 29:669-679
338. Bernstein C, Bernstein H (1991) Aging, Sex and DNA Repair. Academic Press, San Diego, CA
339. Ridley M (2000) Mendel's Demon. Gene Justice and the Complexity of Life. Orion Books, London, pp 167-201
340. Medvinsky A, Smith A (2003) Fusion brings down barriers. Nature 422:823-825
341. Butler S (1914) The Humour of Homer and Other Essays. Kennerley, New York, pp 209-313
342. Noort V van, Worning P, Ussery DW, Rosche WA, Sinden RR (2003) Strand misalignments lead to quasipalindrome correction. Trends in Genetics 19:365-369
343. Lolle SJ, Victor JL, Young JM, Pruitt RE (2005) Genome-wide non-Mendelian inherence of extra-genomic information in Arabidopsis. Nature 434:505-509
344. Forsdyke DR (2001) The Origin of Species, Revisited. McGill-Queen's University Press, Montreal
345. Darwin C (1871) Descent of Man, and Selection in Relation to Sex. Appleton, New York, pp 245-311
346. Haldane JBS (1922) Sex ratio and unidirectional sterility in hybrid animals. Journal of Genetics 12:101-109
347. Coyne JA (1992) Genetics and speciation. Nature 355:511-515
348. Forsdyke DR (1995) Fine tuning of intracellular protein concentrations, a collective protein function involved in aneuploid lethality, sexdetermination and speciation. Journal of Theoretical Biology 172:335-345
349. Chandley AC, Jones RC, Dott HM, Allen WR, Short RV (1974) Meiosis in interspecific equine hybrids. 1. The male mule (Equus asinus X E. caballus) and hinny (E. caballus X E. asinus). Cytogenetics and Cell Genetics 13:330-341
350. Vries H de (1889) Intracellular Pangenesis. Open Court, Chicago, (1910) pp 18-19
351. Darwin C (1851) A Monograph on the Subclass Cirripedia, vol. 1. The Ray Society, London, pp 281-293
352. Bateson W (1922) Evolutionary faith and modern doubts. Science 55:55-61
353. Goldschmidt R (1940) The Material Basis of Evolution, Yale University Press, New Haven, pp 233-236
354. Forsdyke DR (2000) Haldane's rule: hybrid sterility affects the heterogametic sex first because sexual differentiation is on the path to species differentiation. Journal of Theoretical Biology 204:443-452
355. Romanes GJ (1886) Physiological selection: an additional suggestion on the origin of species. Journal of the Linnean Society (Zoology) 19:337-411
356. Romanes GJ (1897) Darwin, and After Darwin:3. Isolation and Physiological Selection. Longmans Green, London
357. Roller PC, Darlington CD (1934) The genetical and mechanical properties of the sex chromosomes. 1. Rattus norvegicus. Journal of Genetics 29:159-173
358. Montoya-Burgos JI, Boursot P, Galtier N (2003) Recombination explains isochores in mammalian genomes. Trends in Genetics 19:128-130
359. Willard HF (2003) Tales of the Y chromosome. Nature 423:810-813
360. Warburton PE, Giordano J, Cheung F, Gelfand Y, Benson G (2004) Inverted repeat structure of the human genome: the X chromosome contains a preponderance of large, highly homologous inverted repeats that contain testes genes. Genome Research 14:1861-1869
361. Ironside JE, Filatov DA (2005) Extreme population structure and high interspecific divergence of the Silene Y chromosome. Genetics 171:705-713
362. Bachtrog D (2003) Adaptation shapes patterns of genome evolution on sexual and asexual chromosomes in Drosophila. Nature Genetics 34:215-219
363. Carrel L, Cottle AA, Goglin KC, Willard HF (1999) A first-generation X-inactivation profile of the human X chromosome. Proceedings of the National Academy of Sciences USA 96:14440-14444
364. Forsdyke DR (1994) Relationship of X chromosome dosage compensation to intracellular self/not-self discrimination: a resolution of Muller's paradox? Journal of Theoretical Biology 167:7-12
365. Bateson W (1924) Letter to G. H. Hardy. Bateson Archive, Cambridge University
366. Johnson TB, Coghill RD (1925) The discovery of 5-methyl-cytosine in tuberculinic acid, the nucleic acid of the tubercle bacillus. Journal of the American Chemical Society 47:2838-2844
367. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes and Development 16:6-21
368. Galagan JE, Selker EU (2004) RIP: the evolutionary cost of genome defence. Trends in Genetics 20:417-423
369. Takai D, Jones PA (2002) Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proceedings of the National Academy of Sciences USA 99:3740-3745
370. Krieg AM (2002) CpG motifs in bacterial DNA and their immune effects. Annual Reviews of Immunology 20:709-760
371. Fraga MF, et al. (2005) Epigenetic differences arise during the lifetime of monozygotic twins. Proceedings of the National Academy of Sciences USA 102:10604-10609
372. Surani MA (2001) Reprogramming of genome function through epigenetic inheritance. Nature 414:122-127
373. Holmgren C, Kanduri C, Dell G, Ward A, Mukhopadhya R, Kanduri M, Lobanenkov V, Ohlsson R (2001) CpG methylation regulates the Igf2/H19 insulator. Current Biology 11:1128-1130
374. Bateson W, Pellew C (1915) On the genetics of "rogues" among culinary peas (Pisum sativum). Journal of Genetics 5:15-36
375. Stam M, Mittelsten Scheid O (2005) Paramutation: an encounter leaving a lasting impression. Trends in Plant Science 10:283-290
376. Pembrey ME, Bygren LO, Kaati, G, Edvinsson S, Northstone K, Sjostrom M, Golding J (2006) Sex-specific, male-line transgenerational responses in humans. European Journal of Human Genetics 14:159-166
377. Eliot G (1876) Daniel Deronda. William Blackman, London;
378. st, 1884, pp 282-283). In an article in Nineteenth Century (1890) Romanes pointed to Theophrastus as "the earliest botanist whose writings have been preserved.'"]
379. Chargaff E (1978) Heraclitean Fire. Sketches from a Life before Nature. Warner Books, New York [After being prematurely "retired", Chargaff obtained some laboratory space at the Roosevelt Hospital, New York, until 1992.]
380. Forsdyke DR (2000) Tomorrow's Cures Today? Harwood Academic, Amsterdam
381. Wilszek F, Devine B (1987) Longing for the Harmonies. Norton, New York, pp 111, 209
382. Kant I (1781) The Critique of Pure Reason. Guyer P, Wood AW (eds) Cambridge University Press, Cambridge (1998)
383. Haldane JS (1891) Letter to Louisa Trotter. 3 December. In: Romano T (2002) Making Medicine Scientific. John Burdon Sanderson and the Culture of Victorian Science. John Hopkins University Press, Baltimore (2002), pp 128
384. Darwin C (1868) Letter to Alfred Wallace. 27 February. In: Darwin F, Seward AC (eds) More Letters of Charles Darwin. John Murray, London (1903), pp 301
385. Olby RC (1966) Origins of Mendelism. Schocken Books, New York [They may have been unaware of Mendel, but in 1876 in an article in Nature E. R. Lankester drew the Victorians' attention to the work of Ewald Hering.]
386. Dawkins R (1983) Universal Darwinism. In: Bendall DS (ed) Evolution from Molecules to Man. Cambridge University Press, Cambridge, pp 403-425
387. Forsdyke DR (2001) The Origin of Species, Revisited. McGill-Queen's University Press, Montreal
388. Gould SJ (1982) The uses of heresy. Forward to reprint of: Goldschmidt R (1940) The Material Basis of Evolution. Yale University Press, New Haven, pp xiii-xlii
389. Gould SJ (1980) Is a new and general theory of evolution emerging? Paleobiology 6:119-130
390. Gould SJ (2002) The Structure of Evolutionary Thought. Harvard University Press, Cambridge, MA, pp 1002-1003
391. Forsdyke DR (2004) Grant Allen, George Romanes, Stephen Jay Gould and the evolution establishments of their times. Historic Kingston 52:94-98
392. Smith, JM (1995) Genes, memes and minds. The New York Review of Books 42: ino. 19, pp 17-19 [The terms "ultra-Darwinian" and "neo-Darwinian'" were used by Romanes to disparage Wallace's and Weismann's inflexible advocacy of the power of natural selection.]
393. Tooby J, Cosmides L (1997) [A letter to the editor of The New York Review of Books that was not accepted for publication: see http://cogweb.ucla.edu/ Debate/]
394. Adams MB (1990) La genetique des populations etait-elle une genetique evolutive? In: Fischer J-L, Schneider WH (eds) Histoire de la Genetique, pp 153-171. ARPEM, Paris
395. [See also: Adams MB. Little evolution, big evolution. Rethinking the history of population genetics. (Personal communication. 2003)]
396. Provine WB (1992) Progress in evolution and the meaning of life. In: Waters CK, Helden A van (eds) Julian Huxley, Biologist and Statesman of Science. Rice University Press, Houston, pp 165-180
397. Bateson P (2002) William Bateson: a biologist ahead of his time. Journal of Genetics 81:49-58
398. Butler S (1914) The Humour of Homer and Other Essays. Kennerley, New York, pp 245-313
399. Galison P (2003) Einstein's Clocks, Poincare's Maps: Empires of Time. Norton, New York
400. Butler S (1985) The Notebooks of Samuel Butler. Jones HF (ed) Hogarth Press, London, pp 360-378
401. Barber B (1961) Resistance by scientists to scientific discovery. Science 134:596-602
402. Sacks O (2001) Uncle Tungsten. Knopf, New York, pp 104-105
403. Hook EB (2002) Prematurity in Scientific Discovery. On Resistance and Neglect. University of California Press, Berkeley
404. Dawkins R (2003) A Devil's Chaplain: Reflections on Hope, Lies, Science and Love. Houghton Mifflin, Boston, p 48
405. Fisher RA (1932) Letter to T. H. Morgan. In: Bennett JH (ed) Natural Selection, Heredity and Eugenics. Including Selected Correspondence of R. A. Fisher with Leonard Darwin and Others. Clarendon Press, Oxford (1983), p 239
406. Somerville MA (2002) A postmodern moral tale: the ethics of research relationships. Nature Reviews Drug Discovery 1:316-320 [Somerville's point was also independently made in the Globe and Mail of Toronto by myself (May 5, 2001) and John Polanyi (July 7, 2005), and in a letter to Science (2005) by forty Canadian scientists. Commenting on the latter Polanyi remarked: "What is excellent... is a revelation. It is precisely because it surprises us that it is resistant to being planned. To find 40 scientists willing to challenge authority is also a surprise. Canadian science is coming of age."]
407. Huxley AL (1931) Letter to R. A. Fisher. In: Bennett JH (ed) Natural Selection, Heredity and Eugenics. Including Selected Correspondence of R. A. Fisher with Leonard Darwin and Others. Clarendon Press, Oxford (1983), p 220
408. Forsdyke DR (1966) Letter to Editor. Survival 8:36
409. Forsdyke DR (1969) Book review. Survival 11:69-70
410. Roll-Hansen N (2005) The Lysenko effect: undermining the autonomy of science. Endeavour 29:143-147
411. Nirenberg M (2004) Historical review: deciphering the genetic code - a personal account. Trends in Biochemical Sciences 29:46-54
412. Meadows AJ (1972) Science and Controversy. A Biography of Sir Norman Lockyer. MIT Press, Cambridge, p 209-237
413. Punnett RC (1950) Early days of genetics. Heredity 4:1-10
414. Bennett JH (1983) Notes. In: Natural Selection, Heredity and Eugenics. Including Selected Correspondence of R. A. Fisher with Leonard Darwin and Others. Clarendon Press, Oxford, p 118
415. Forsdyke DR (2003) William Bateson, Richard Goldschmidt, and non-genic modes of speciation. Journal of Biological Systems 11:341-350
416. Forsdyke DR (2004) Chromosomal speciation: a reply. Journal of Theoretical Biology 230:189-196
417. Orr HA (2000) In: Crow JF, Dove WF (eds) Perspectives in Genetics. Anecdotal, Historical and Critical Commentaries 1987-1998. University of Wisconsin Press, Wisconsin, pp 555-559
418. Cove D (2002) Book review. Genetics Research 79:265
419. th February. In: The Complete Works of Voltaire, Vol 120. The Voltaire Foundation, Banbury, 1975, p 18 [The full translation reads: "The number of wise men will always be small. It is true that it is increasing, but it is nothing compared with the number of fools and, although they say it is regrettable, God is always for the big battalions. It is necessary that honest people quietly stick together. There is no way their little force can attack the host of the closed-minded who occupy the high ground."]
420. Eliot G (1874) Middlemarch. A Study of Provincial Life. Haight GS (ed). Houghton Mifflin, Boston (1956) p 613
421. Rushdie S (2003) Step Across the Line. Random House, Toronto
422. Gould SJ (1999) Rocks of Ages. Science and Religion in the Fullness of Life. Ballantine, New York
423. Ruse M (2001) Can a Darwinian be a Christian? The Relationship between Science and Religion. Cambridge University Press, Cambridge
424. Jones HF (1919) Samuel Butler. A Memoir. Macmillan, London
425. th January. The William Bateson Archive, University of Cambridge
426. Machiavelli N (1950) The Prince and the Discourses. Random House, New York
427. Huxley TH (1948) Selections from the Essays. Huxley. Castell A (ed) AHM Publishing, Northbrook
428. Forsdyke DR (2001) The Origin of Species, Revisited. McGill-Queen's University Press, Montreal
429. Wilczek F, Devine B (1987) Longing for the Harmonies. Norton, New York
430. Crick F (1988) What Mad Pursuit. Basic Books, New York
431. Dawkins R (1986) The Blind Watchmaker. Longman, Harlow, p ix
432. Chardin PT de (1959) The Phenomenon of Man. Collins, London
433. Butler S (1985) The Notebooks of Samuel Butler. Jones HF (ed) Hogarth Press, London, pp 59, 299
434. Huxley TH (1896) Darwiniana Essays. Macmillan, London, pp 447-175
435. Shakespeare W (1599) Julius Caesar. In: Rowse AL (ed) The Annotated Shakespeare. Orbis, New York (1988)