An Index for the “Biology Worthy of Life” Project

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topical index

1. chromatin
   1. How Our Genes Come to Expression (It Takes an Epigenetic Village)
   2. The Sensitive Nucleosome
   3. The Nucleosome as Mediator
   4. DNA and RNA brought to life
   5. How to Unthink Epigenetics
2. dynamics
   1. What Brings Our Genome Alive?
   2. The Dynamic Chromosome
   3. The Complex Performance of the Three-Dimensional Chromosome
   4. Hox Genes in Motion: Who’s Moving Whom?
3. in 3D space
   1. What Brings Our Genome Alive?
   2. The Dynamic Space of the Cell Nucleus
   3. Pervasive Transcription: Using Genomes “Every Which Way”
   4. The Complex Performance of the Three-Dimensional Chromosome

1. (See machine-idea/code)

1. Development Writ Large
2. Teleology and Evolution — Why Can’t We have ‘Evolution on Purpose’?
3. What Is the Problem of Form?
4. Why We Cannot Explain the Form of Organisms
5. Evolution Writ Small
6. How Does an Organism Get Its Shape?
7. The Embryo’s Eloquent Form
8. Form and the Electrified Organism
9. Will the real Walter Gilbert please stand up?
10. It Takes a Whole Context to Support Pluripotency

1. How Our Genes Come to Expression (It Takes an Epigenetic Village)
2. Metamorphosis of the Code
3. DNA’s Many Languages
4. Why Genetic Synonyms Are Not Synonymous
5. Look What’s Happened to Genetic Synonyms
6. Yet Another Face of DNA
7. Viruses, Cytoplasmic DNA, and the Web of Life
8. DNA and RNA brought to life
9. junk
   1. Pervasive Transcription: Using Genomes “Every Which Way”
   2. Why Genetic Synonyms Are Not Synonymous
   3. Look What’s Happened to Genetic Synonyms
10. noncoding
    1. Pervasive Transcription: Using Genomes “Every Which Way”
    2. How to Unthink Epigenetics

1. How Our Genes Come to Expression (It Takes an Epigenetic Village)
2. The Mystery of an Unexpected Coherence
3. There Is No Genetics — Only Epigenetics
4. How to Unthink Epigenetics
5. Paradoxes driving the new emphasis on epigenetics
6. Metamorphosis of the Code
7. The Sensitive Nucleosome
8. A Thousand-Stranded Tapestry: How Organisms Employ Their Genes
9. How the Organism Decides What to Make of Its Genes
10. Epigenetics and the Inheritance of Acquired Characters

1. The Evolution of Consciousness
2. All Science Must Be Rooted in experience
3. Reframing the Mind-Body Problem: An Exercise in Letting Go of Dualist Assumptions
4. A Modest Epistemological Exercise

1. Development Writ Large
2. Let’s Not Begin With Natural Selection
3. Evolution and the Illusion of Randomness
4. of consciousness
   1. The Evolution of Consciousness
   2. A Physicist, a Philologist, and the Meaning of Life
5. and development
   1. Inheritance (2): Genetics and the Particulate View of Life
   2. Inheritance (1): The Whole Organism
   3. Development Writ Large
   4. Teleology and Evolution — Why Can’t We have ‘Evolution on Purpose’?
   5. Evolution Writ Small
6. fitness
   1. Can We Track Fitness?
   2. Fitness — An Irretrievably Obscure Concept
7. inheritance
   1. Inheritance (2): Genetics and the Particulate View of Life
   2. Inheritance (1): The Whole Organism
   3. of acquired characters
      1. Epigenetics and the Inheritance of Acquired Characters
   4. heritability
      1. Missing Heritability — Or Whole-Organism Inheritance?
8. intelligent design
   1. Why Can’t Evolutionary Biologists Quit Believing in Intelligent Design?
   2. Three Questions for Intelligent Design Theorists
   3. Evolution and the Purposes of Life
   4. A Sectarian Quarrel? Intelligent Design and Neo-Darwinism
   5. How Does an Organism Get Its Shape?
9. as mindless process
   1. Is a Qualitative Biology Possible?
   2. Toward a Thought-Full Teleology
   3. The “mindlessness” of biological science today
   4. Evolution and the Purposes of Life
   5. Letting the Reality of the Organism Speak
   6. A Sectarian Quarrel? Intelligent Design and Neo-Darwinism
   7. Evolution and Belief
   8. (See also: inwardness)
10. and mutations
    1. Inheritance (2): Genetics and the Particulate View of Life
    2. Inheritance (1): The Whole Organism
    3. Chance to the Rescue?
    4. Natural Genome Remodeling
    5. Couldn’t You Be More Explicit Here?
11. sociobiology
    1. Vladimir Solovyov on Sexual Love and Evolution

1. All Science Must Be Rooted in experience
2. From Physical Causes to Organisms of Meaning
3. The Reduction Complex
4. Can We Learn to Think Like a Plant?
5. biological
   1. The Keys to This Book
   2. The Organism’s Story
   3. The Problematic Effectiveness of Reason in Biology (Part 1 of “From Bodily Wisdom to the Knowing Self)”
   4. From Physical Causes to Organisms of Meaning
   5. What Changes at Death?
   6. Two Kinds of Description
   7. Some Views of the Living Organism
   8. Trying to Grasp the Whole Organism
   9. Biology — More Fundamental than Physics?
   10. How Does an Organism Get Its Shape?
   11. RNA: Dancing with a Thousand Partners at Once
   12. From Differences to Character
   13. The Paradox in “Explaining” Form
   14. Psyche, Soma, and the Unity of Gesture (Part 2 of “From Bodily Wisdom to the Knowing Self)”
   15. Let’s Loosen Up Biological thinking!
   16. Of Humans and Our Microbial Guests: A Dynamic and Living Balance
   17. Microbiome: It’s Less About the “Bad Guys” Than the Whole Organism
   18. Where Do Intelligence and Wisdom Reside? (Part 3 of “From Bodily Wisdom to the Knowing Self”)
   19. Why Can’t Evolutionary Biologists Quit Believing in Intelligent Design?
6. and causation
   1. A Mess of Causes
   2. Who Regulates the Regulators?
   3. Laws and Causes
   4. Beings in Context
   5. How Does an Organism Get Its Shape?
   6. Have Biologists Really Overcome Gene-Centered Thinking?
   7. The Sensitive, Muscular Cell
   8. The (Molecular) Lives of Our Days
   9. Of Humans and Our Microbial Guests: A Dynamic and Living Balance
   10. Microbiome: It’s Less About the “Bad Guys” Than the Whole Organism
   11. It Takes a Whole Context to Support Pluripotency
   12. How to Unthink Epigenetics
7. part and whole
   1. Inheritance (2): Genetics and the Particulate View of Life
   2. Context: Dare We Call It Holism?
   3. The Organism’s Story
   4. What Does “More Than the Sum of Its Parts” Mean?
   5. RNA: Dancing with a Thousand Partners at Once
   6. Who Are You and Who Am I and Who Are We?
   7. Vladimir Solovyov on Sexual Love and Evolution
   8. Of Humans and Our Microbial Guests: A Dynamic and Living Balance
   9. Microbiome: It’s Less About the “Bad Guys” Than the Whole Organism
8. portrayal and
   1. To Explain or Portray?
   2. Can We Explain the Form of Organisms?

1. What Is the Problem of Form?
2. Why We Cannot Explain the Form of Organisms
3. Can the New Science of Evo-Devo Explain the Form of Organisms?
4. What is Life?
5. molecular
   1. Our Bodies Are Formed Streams
   2. Molecular Machines
   3. Are “Disordered” Proteins Really Disordered?
   4. The Complex Performance of the Three-Dimensional Chromosome
   5. Eloquent Form
   6. Why Genetic Synonyms Are Not Synonymous
   7. Look What’s Happened to Genetic Synonyms
   8. The Unexpected Phases of Life
6. organismal
   1. Is a Qualitative Biology Possible?
   2. The Embryo’s Eloquent Form
   3. The Paradox in “Explaining” Form
   4. To Explain or Portray?
   5. How Does an Organism Get Its Shape?
   6. Can We Explain the Form of Organisms?
   7. Form and the Electrified Organism
   8. RNA: Dancing with a Thousand Partners at Once
   9. Hox Genes in Motion: Who’s Moving Whom?

1. as difference-maker
   1. Inheritance (1): The Whole Organism
   2. From Differences to Character
   3. What Absent Genes Don’t Do — and How Can We Know?
2. genocentrism
   1. Inheritance (2): Genetics and the Particulate View of Life
   2. Putting Genes in Perspective
   3. The Seat of Power: Nucleus or Cytoplasm?
   4. How to Unthink Epigenetics
   5. Free Life and Confining Form
   6. Have Biologists Really Overcome Gene-Centered Thinking?
   7. Form and the Electrified Organism
   8. Shattering the Genome
   9. The (Molecular) Lives of Our Days
3. indefinability
   1. Indefinable Genes and the “Wild West” Genomic Landscape
4. mutation
   1. Inheritance (2): Genetics and the Particulate View of Life
   2. What Absent Genes Don’t Do — and How Can We Know?
   3. (See also: evolution/and mutations)

1. How Our Genes Come to Expression (It Takes an Epigenetic Village)
2. The Mystery of an Unexpected Coherence
3. There Is No Genetics — Only Epigenetics
4. What Brings Our Genome Alive?
5. Getting Over the Code Delusion
6. The Sensitive Nucleosome
7. A Thousand-Stranded Tapestry: How Organisms Employ Their Genes
8. How the Organism Decides What to Make of Its Genes
9. RNA: Dancing with a Thousand Partners at Once
10. How to Unthink Epigenetics
11. Why Genetic Synonyms Are Not Synonymous
12. Look What’s Happened to Genetic Synonyms
13. The Unexpected Phases of Life
14. Symptoms: Notes from Biological Literature (1)
15. Viruses, Cytoplasmic DNA, and the Web of Life
16. Functional vs. Nonfunctional DNA Binding

1. genomic hype
   1. are chimps almost human?
2. organization
   1. What Brings Our Genome Alive?
   2. The Complex Performance of the Three-Dimensional Chromosome
3. plasticity
   1. (See plasticity/genome)
4. remodeling
   1. Natural Genome Remodeling
   2. Shattering the Genome
   3. Will the real Walter Gilbert please stand up?

1. Inheritance (2): Genetics and the Particulate View of Life
2. Inheritance (1): The Whole Organism
3. How Our Genes Come to Expression (It Takes an Epigenetic Village)
4. What Is the Problem of Form?
5. Why We Cannot Explain the Form of Organisms
6. The Sensitive, Muscular Cell
7. The Unbearable Wholeness of Beings
8. From Physical Causes to Organisms of Meaning
9. On Being Wholehearted
10. Facing Down to Life
11. Shattering the Genome
12. A Thousand-Stranded Tapestry: How Organisms Employ Their Genes
13. Pervasive Transcription: Using Genomes “Every Which Way”
14. What Absent Genes Don’t Do — and How Can We Know?
15. RNA: Dancing with a Thousand Partners at Once
16. contextual
    1. A Mess of Causes
    2. The Mystery of an Unexpected Coherence
    3. Context: Dare We Call It Holism?
    4. The Organism’s Story
    5. How to Unthink Epigenetics
    6. Who Are You and Who Am I and Who Are We?
    7. Cancer and Context
    8. Signals and the Whole Organism
    9. Trying to See the Organism Whole
    10. How Does an Organism Get Its Shape?
    11. Of Humans and Our Microbial Guests: A Dynamic and Living Balance
    12. Microbiome: It’s Less About the “Bad Guys” Than the Whole Organism
    13. It Takes a Whole Context to Support Pluripotency
17. language of
    1. (See explanation)
18. “more than the sum of its parts”
    1. (See explanation/part and whole)
19. organism as a “formed stream”
    1. Our Bodies Are Formed Streams
    2. The Organism Is Not a Machine
    3. The Nucleosome as Mediator
    4. A Living Vortex
    5. The Unexpected Phases of Life
20. as polarity
    1. Is a Qualitative Biology Possible?
    2. Free Life and Confining Form
21. versus mysticism and vitalism
    1. A question for biologists: Are you and I machines?
    2. From Physical Causes to Organisms of Meaning
    3. Animistic Impulses in Biology
    4. Fear of Vitalism
    5. How Does an Organism Get Its Shape?

1. The Evolution of Consciousness
2. Toward a Thought-Full Teleology
3. Teleology and Evolution — Why Can’t We have ‘Evolution on Purpose’?
4. The Keys to This Book
5. Context: Dare We Call It Holism?
6. The Organism’s Story
7. All Science Must Be Rooted in experience
8. Scenes of Life
9. Evolution and the Purposes of Life
10. A Physicist, a Philologist, and the Meaning of Life
11. The Inwardness of Beings
12. How Biologists Lost Sight of the Meaning of Life
13. The Problematic Effectiveness of Reason in Biology (Part 1 of “From Bodily Wisdom to the Knowing Self”)
14. Psyche, Soma, and the Unity of Gesture (Part 2 of “From Bodily Wisdom to the Knowing Self)”
15. Let’s Loosen Up Biological thinking!
16. How Does an Organism Get Its Shape?
17. RNA: Dancing with a Thousand Partners at Once
18. How to Unthink Epigenetics
19. The Embryo’s Eloquent Form
20. Why Can’t Evolutionary Biologists Quit Believing in Intelligent Design?
21. Three Questions for Intelligent Design Theorists
22. Vladimir Solovyov on Sexual Love and Evolution
23. Where Do Intelligence and Wisdom Reside? (Part 3 of “From Bodily Wisdom to the Knowing Self”)
24. What is Life?
25. (See also: evolution/as mindless process)

1. Toward a Thought-Full Teleology
2. Puzzles of the Microworld
3. What Is the Problem of Form?
4. Why We Cannot Explain the Form of Organisms
5. Biology’s Shameful Refusal to Disown the Machine-Organism
6. On Being Wholehearted
7. A question for biologists: Are you and I machines?
8. Demise of Lock-and-Key Proteins
9. The Organism Is Not a Machine
10. Laws and Causes; Beings in Context
11. Three Questions for Intelligent Design Theorists
12. The (Molecular) Lives of Our Days
13. Evolution and the Purposes of Life
14. Why Can’t Evolutionary Biologists Quit Believing in Intelligent Design?
15. code
    1. Getting Over the Code Delusion
    2. The Poverty of the Instructed Organism: Are You and Your Cells Programmed?
    3. The Organism Does Not Compute
    4. Why Genetic Synonyms Are Not Synonymous
    5. Look What’s Happened to Genetic Synonyms
    6. Shattering the Genome
    7. The Unexpected Phases of Life
    8. Ghosts in the Evolutionary Machinery
16. molecular
    1. (See form/molecular)

1. (See holism/versus mysticism and vitalism)

1. Who Are You and Who Am I and Who Are We?
2. genome
   1. How Our Genes Come to Expression (It Takes an Epigenetic Village)
   2. Pervasive Transcription: Using Genomes “Every Which Way”
   3. Viruses, Cytoplasmic DNA, and the Web of Life
   4. (See also: chromosome/chromosome/dynamics)
3. molecular

   (See form/molecular)

1. Demise of Lock-and-Key Proteins
2. The Unexpected Phases of Life
3. DNA and RNA brought to life
4. disordered
   1. Our Bodies Are Formed Streams
   2. Are “Disordered” Proteins Really Disordered?

1. How Our Genes Come to Expression (It Takes an Epigenetic Village)
2. The Mystery of an Unexpected Coherence
3. RNA: Dancing with a Thousand Partners at Once

1. Horror graphs
2. Yet Another Face of DNA
3. contextual
   1. Signals and the Whole Organism

1. How Our Genes Come to Expression (It Takes an Epigenetic Village)
2. A Thousand-Stranded Tapestry: How Organisms Employ Their Genes
3. How the Organism Decides What to Make of Its Genes
4. pervasive
   1. Pervasive Transcription: Using Genomes “Every Which Way”
5. transcription factors
   1. How Our Genes Come to Expression (It Takes an Epigenetic Village)
   2. Functional vs. Nonfunctional DNA Binding

1. Why Genetic Synonyms Are Not Synonymous
2. Look What’s Happened to Genetic Synonyms!

1. Section in “The Unbearable Wholeness of Beings”
2. Section in “From Physical Causes to Organisms of Meaning”
3. The (Molecular) Days of our Lives

1. Of Humans and Our Microbial Guests: A Dynamic and Living Balance
2. Microbiome: It’s Less About the “Bad Guys” Than the Whole Organism

1. induced
   1. It Takes a Whole Context to Support Pluripotency

This document: http://BiologyWorthyofLife.org/comm/inx.htm

Steve Talbott :: An Index for the “Biology Worthy of Life” Project