Introduction: Sequences, Sequences, and Sequences
0.1 The World in One Dimension
0.2 The Linguistic Model in Biology
0.3 Shoulders to Stand On
0.4 What to Expect from This Book
Chapter One: The Problem of Sequentialization
1.1 Our World as Sequences See It
1.2 Persistence of One-Dimensional Patterns
1.3 Sequences, In and Out of Time
1.4 Sequences are History
1.5 Collapsing Three Dimensions to One
1.6 Low-Energy Sequences
1.7 Matter Matters, Except When It Doesn’t
1.8 Laws are Not Rules, and Vice Versa
1.9 Sequential and Self-Referential
1.10 Sequences Made Explicit
Chapter Two: The Emergence of Constraint
2.1 Sequences at the Dinner Table
2.2 Meet the Constraint
2.3 Alternatives and Decisions
2.4 Classification, and then Reclassification
2.5 Sequences are Invisible Boundaries
2.6 Constraining Individuals in a Collection
2.7 Levels of Description and Control
2.8 Loosely-Coupled and Nearly-Decomposable
2.9 Hierarchical Patterns in Sequences
Chapter Three: The Grammar of Interaction
3.1 Interactions, Ordinary and Specific
3.2 The Folding Transformation
3.3 How the Improbable Becomes Probable
3.4 Molecular Pattern Recognition
3.5 Enzymes, Robots, and Perception
3.6 All That the Environment Affords
3.7 Affordances Great and Small
3.8 The Eye of the Enzyme
3.9 Genes Go to Pieces
Chapter Four: The Grammar of Extension
4.1 Where Does the Body End (and the World Begin)?
4.2 Puppet Masters and Their Puppets
4.3 The Affordances of Extension
4.4 Social Constraints and Affordances
4.5 Situating the Grammar of Interaction
4.6 How Does Language Acquire Children?
4.7 The Grammar of Extension
4.8 The Extended Genome
Chapter Five: The Grammar of Abstraction
5.1 Freedom’s Just Another Word
5.2 Shape Shifting Constraints
5.3 Blue- and White-Collar Sequences
5.4 When Is a Sequence Not a Sequence?
5.5 Who Constrains the Constraints?
5.6 The Grounding of Abstraction
Chapter Six: The Conundrum of Replication
6.1 What is Self-Replication?
6.2 Von Neumann and the Problem of Complexity
6.3 Turing’s Pristine Sequences
6.4 Enter the Self-Reproducing Automaton
6.5 Theory vs. Reality in Self-Reproduction
6.6 Lessons Learned from Von Neumann
6.7 Description, Construction, and the Central Dogma
6.8 The Central Dogma of Civilization?
Chapter Seven: The Threshold of Complication
7.1 What Makes a Threshold?
7.2 And Before DNA There Was?
7.3 Living by RNA Alone
7.4 Entangling the Central Dogma
7.5 A Civilized Threshold
7.6 Get It in Writing
7.7 Stability, Random Access, and Self-Reference
7.8 What Does the Thermostat Say?
7.9 Hand Me the Pliers
7. 10 Complication Great and Small
Chapter Eight: The Institution of Sequences
8.1 Of Constraints and Chimeras
8.2 The Fallibility of Constraints
8.3 A Recipe for Learning
8.4 Configured by Memes
8.5 The Microbial Sharing Economy
8.6 A Network Lovely as a Tree
8.7 Constraints, Institutionalized
8.8 The State of Sequences
Chapter Nine: The Continuum of Abstraction
9.1 Universal at Both Ends
9.2 The Universality of One-Dimensional Patterns
9.3 Feeling Special?
Appendix: Just Enough Molecular Biology
A.1 Why Mess with Molecules?
A.2 One-Dimensional Patterns in Biopolymers
A.3 DNA Replication: Complementary Base-Pairing
A.4 Transcription: DNA to Messenger RNA (mRNA)
A.5 The Genetic Code: Mapping RNA to Amino Acids
A.6 How Translation Happens: Transfer RNA (tRNA)
A.7 Constructing the Finished Protein: Ribosomes
References