Evolution since Coding: Cradles, Halos, Barrels, and Wings

177 Pages·2017·13.9 MB·English

by  Zachary F. Burton

Evolution Since Coding
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Evolution Since Coding
Cradles, Halos, Barrels, and Wings
Zachary F. Burton
Michigan State University
East Lansing, MI, United States
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Contents
Preface ix
Introduction xi
1. Big Questions 1
2. What This Book Is About 3
3. Scientific Acronyms 7
4. Molecular Graphics 9
Section I
The Old Testament of Gene Regulation
5. Evolution as a Cutout Doll Problem I 13
6. Evolution as a Cutout Doll Problem II 17
7. The Best Art 21
8. Intelligent Design 23
9. Polymers 25
10. LEGO (Trademark) Life 27
11. α /β Proteins 33
12. The Inevitability of α/β Folds 45
13. E volution Puts the Y (Why) in Biology 49
14. E volution Is Not Anti-Religion 51
15. Computers in Biology 53
16. T he Old and New Testaments of Gene Regulation 55
17. E volution as a Cutout Doll Problem III 59
18. M ulti-Subunit RNA Polymerases Book I 65
Double-Ψ–β-Barrels (The Active Site) 67
The Bridge Helix 68
v
vi Contents
The Trigger Loop 68
σ Factor Binding to Promoter DNA 68
Zn1 and Zn2 69
Do Not Try This at Home 71
19. M ulti-Subunit RNA Polymerases Book II 73
20. T he Chemical Synthesis of Life 83
21. The RNA World 85
22. Ribosomes 87
23. The RNA-Protein World 89
24. Transfer RNA 91
Generation of Sequence Repeats 103
“Intellectual Property” in Biology and Evolution 104
Try This at Home 104
Now Try This 105
25. T he Three Domains of Life on Earth and Scientific
Working Hypotheses 107
Last Universal Common (Cellular) Ancestor 107
Archaea 109
Bacteria 109
Eukaryotes 110
Descriptions and Predictions 111
26. LUCA 113
27. G eneral Transcription Factors and Promoters 115
Try This at Home 121
28. Archaea 123
29. Bacteria 125
30. Methane and Oxygen 129
Section II
The New Testament of Gene Regulation
31. LECA 133
32. E ukaryotic Multi-Subunit RNA Polymerases,
General Transcription Factors, and the CTD 139
33. Patchwork Eukaryotic Phylogenomics 145
34. Plants 147
35. The Permian–Triassic Extinction 149
Contents vii
36. The Triassic–Jurassic Extinction 151
37. The Cretaceous–Paleogene Extinction 153
38. T he Paleocene–Eocene Thermal Maximum 155
39. P romoter Proximal Pausing and the CTD Interactome 157
40. Human Evolution 161
Of Mice and Men 162
41. Human Cancer 165
42. H omology Modeling and Cryoelectron Microscopy 169
43. Human Extinction 171
44. Evolution Versus Faith 173
45. Concept in Biology 175
46. O ther Books and Studies 177
References 181
Supplementary Materials 185
Index 187
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Preface
Public discussions of evolution versus “intelligent design” or a deity are no
more enlightening than public discussions of man-made global warming and
ocean acidification with an oil executive. Basically, one is having the wrong
conversation with the wrong people. Evolution is no more anti-religion than
wristwatches or jet airplanes. As recognized by Arrhenius (late 1800s to early
1900s), carbon dioxide is a greenhouse gas that dissolves in water to produce
acid. So, why argue about that? What evolution appears to do is to render a deity
unnecessary, at least, for the genesis of life on earth, a story that now can be told
with surprising details, confidence, and authority.
I wrote this book to tell a simple, brutal story of genesis that integrates RNA
structure/function, protein structure/function, RNA synthesis, protein synthesis,
metabolism, and phylogenomics. As living organisms, our story is rich and wonder-
ful, and I hope I tell some of our most ancient stories well. I have certainly learned a
lot writing this book. Perhaps regrettably, my best studies in the scientific literature
were written based on my ancient evolution studies of transcription systems and
cloverleaf tRNA. This book is an attempt to reach a larger, perhaps less-specialized
but more enthusiastic audience. I have great passion for this book and subject.
So, why might you be interested in Evolution Since Coding?
Although you may not think so, you wish to learn molecular graphics, and
I will encourage you to do so. Initially, low-level proficiency with molecular
graphics programs takes a few hours. Of course, ultimately, this core life skill
will cause you much frustration, anguish, and pain. But, if you do not want a life
of thwarted dreams, you should avoid biology.
I tell a very straightforward story of evolution of life on earth. I am amazed
at how simple, integrated, and predictive the story of genesis has become.
This is a story of code breaking. The codes are dumb, but not so dumb that
scientists could not break them. Genetic codes provide a written and historic
record of evolution, and much of the initial print remains legible.
Transcription (RNA synthesis) systems resemble a Rube Goldberg construc-
tion with seemingly endless add-ons and compensations. Evolution makes sur-
prising sense out of otherwise incomprehensible transcription systems.
Translation (protein synthesis) systems comprise a Rube Goldberg contrap-
tion with a distinct history. Evolution of transfer RNA (tRNA) provides the core
narrative and makes conceptual sense out of translation systems.
The evolution of metabolism is conceptualized. A simplified evolutionary
description may be a useful complement to the perplexing treatment presented
ix