(June, 2011 from FTPress Science)

INTRODUCTION: EVOLUTION IN THE NEW CENTURY
(non-DNA inheritance, cell decision-making, computer evolution and cognition, language and cultural evolution, evolution of practical innovations)

PART I: SENSING, SIGNALING & DECISION-MAKING IN CELL REPRODUCTION
• How E. Coli Chooses The Best Sugar To Eat
• Proofreading DNA Replication
        - Exonuclease_proofreading.html
• DNA Damage Repair And Mutagenesis
        - Translesion_mutator_polymerases.html
        - Chromatin in DNA proofreading and repair
• Cell Cycle Checkpoints
• From the Cell Surface to the Genome: Pheromone Response in the Sexually Aroused Yeast Cell
• The Role Of Intercellular Signals In The Cell Death Decision
         - Apoptosis.html
• Revisiting the Central Dogma of Molecular Biology
    microRNA-targeted chromatin silencing
    Non-coding RNA in genome expression
    Pervasive genome transcription

PART II: THE GENOME AS A READ-WRITE (RW) STORAGE SYSTEM
• Genome Formatting For Properly Accessing Stored Information
       - Regulatory_Networks.html
• Genome Compaction, Chromatin Formatting And Epigenetic Regulation
        - Transgenerational_Epigenetic_Effects.html
        - LifeHistoryEventsAlterEpigenome.html
        - microRNA-directed silencing
        - Epigenetic involvement in targeting retrotransposon and retroviruse insertions
• Genome Formatting For Replication And Transmission To Daughter Cells
• Distinct Classes Of DNA In The Genome
        - Bacterial_Transposons.html
        - DNA_Transposons
       - Endogenous_Retroviruses.html
        - LTR Retrotransposons.shtml
      - Non-LTR_Retrotransposons.html
• The Molecular Mechanisms Of Natural Genetic Engineering
      - Competence_for_DNA_Uptake.html
      - Bacterial_Surface_Structures.html
      - Site-specific_Recombination.html
      - Integrons_Super-integrons.html
      - Specialized_Transduction_and_in_vivo_Cloning.html
      - Bacterial_Transposons.html
      - Endogenous_Retroviruses.html
      - Retrovirus_Integration.html
      - Non-LTR_Retrotransposons.html
      - LINE_SINE_Retrotransduction.html
      - RNA_Reverse_Transcription_and_Genome_Insertion.html
      - Group_II_introns.html
      - NHEJ.html
      - Legitimate_and_Illegitimate_Recombination.html
• Natural Genetic Engineering As Part Of The Normal Life-Cycle
    - Antigenic_Variation.html
        - Phase_antigenic_variation.html
        - DNA_changes_cell_differentiation.html
    - Ciliate_macronuclear_development.html
      -Immune system

            VDJ_joining.html
           Somatic_hypermutation.html
               Ig_Class_isotype_switching.html

• Cellular Regulation Of Natural Genetic Engineering
      - Adaptive_mutation.html
      - CRISPRs.html
    - RNA_interference_and_epigenetic_regulation.piRNA.html
    - Germline_Specificity.html
      - Hybrid_dysgenesis_interspecific_hybridization.html
        - StimuliDocumentedActivateNGE.html
        - GenomicResponsesToChangesInPloidyInterspecificHybridization.html
• Targeting Of Natural Genetic Engineering Within The Genome
      - Mating-type_Switching.html
        - Tn7.html
    - P_factor_homing.html
        - Retrotransposons and retroviruses
• Natural Genetic Engineering in Cancer
        - Kataegis
        - Chromothripsis
• Reviewing What Cells Can do to Rewrite Their Genomes Over Time

Part III: EVOLUTIONARY LESSONS FROM MOLECULAR GENETICS AND GENOME SEQUENCING
• Antibiotic Resistance And Horizontal DNA Transfer
         - The Virosphere as Evolutionary R & D
           - Viral_Composites.html
           - Amoebal_Viruses.html
• The Modular And Duplicative Nature Of Protein Evolution
      - Exon_shuffling_and_protein_families.html
• Molecular Taxonomy And The Discovery Of A New Cell Type
• Symbiogenesis And The Origin Of Eukaryotic Cells
   - Origins_of_eukaryotic_cell.html
       - Secondary_and_tertiary_symbioses.html
   - Intracellular_Horizontal_Transfer.html
   - Gonadal_Symbiosis.html
       - Human_Microbiome.html
       - Bacterial_Cell_Biology_In_Pathogenesis_and_Symbiosis.html
       - SymbiosisInfectionStress.html
• Natural Genetic Engineering and Evolutionary Genomic Innovation
      - Interkingdom_and_Eukaryotic_Horizontal_Transfer.html
     - Origin_of_New_Protein_Domains.html
     - Exon_formation.html
     - Exon_Shuffling.html
     - Genome_Size.html
     - LTR_retrotransposons_and_genome_evolution.html
     - Retroviral_involvement_in_placenta_evolution.html
     - Retrogenes_Retroelements.html
     - GenomeDuplicationsAmplifications.html
     - Chromosome_Rearrangements_by_Repeat_Recombination.html
     - Chimp_to_Human_Chromosome_Fusion.html
       - Natural_genetic_engineering_and_multimolecular_networks.html
• Use And Reuse Of Evolutionary Inventions
       - Hox_HigLevelComplexes.html
• What Makes A Man Different From A Mouse?
• Whole Genome Doubling At Critical Stages Of Evolutionary Innovation And Divergence
• Reviewing What The DNA Record Reveals About Cell Activities Over Evolutionary Time

PART IV: A NEW CONCEPTUAL BASIS FOR EVOLUTIONARY RESEARCH IN THE 21^ST CENTURY
• A Systems Approach To Generating Functional Novelties
• Reorganizing Established Functions To Generate Novelty
• Generation Of Novel Components
• Retention, Duplication And Diversification Of Evolutionary Inventions
• The Implications Of Targeting Genome Restructuring
• Can Genomic Changes Be Linked To Ecological Disruptions?
        - Fossil_Record.html
• What Might A 21^st Century Theory Of Evolution Look Like?
• Where Does Evolution Fit In 21^st Century Science?

PRINTED REFERENCES (with PubMed links)
TABLES (with linked references)
    Table II.1 DNA content in higher eukaryotes
     Table II.2 Different classes of annotated repetitive genome components
    Table II.5 Control of bacterial protein synthesis (phase variation) and modification of protein structure (antigenic variation) by natural genetic engineering
    Table II.6. Applications of site-specific recombination to different functions in bacterial cells
    Table II.7. Various stimuli documented to activate natural genetic engineering
    Table II.8. Genomic responses to changes in ploidy and interspecific hybridization in plants and animals
    Table II.9. RNA-based defense against viruses and plasmids in bacteria, archaea, fungi and plants
    Table II.10. Life history events that alter the epigenome (DNA methylation and chromatin formatting).
    Table II.11. Examples of targeted natural genetic engineering
    Table III.1. Examples of intercellular and interkingdom DNA transfer
    Table III.2. Natural Genetic Engineering Documented in the Evolution of Sequenced Genomes

ONLINE APPENDICES (with linked references)
    Appendix I.1 The lac operon control circuit
    Appendix I.2 S. cerevisiae pheromone response signal network
    Appendix ii.1 Formatting the genome for transcriptional control
    Appendix II.2 Natural genetic engineering in B lymphocytes
            - Immune system

Suggested readings for non-professionals (mostly from Scientific American)