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An Index for the “Biology Worthy of Life” Project

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This document is part of the “Biology Worthy of Life” project. Original posting of this index: August 2, 2013. Copyright 2015 The Nature Institute. All rights reserved.

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Index Headings
Click on "(+/-)" in the listing of headings to expand and collapse the submenus.
chromosome (+/-)
code

(See machine-idea/code)

development (ontogeny)
DNA (+/-)
DNA-centrism (See gene/genocentrism)
junk
noncoding
epigenetics
epistemology
evolution (+/-)
explanation (+/-)
form (+/-)
gene (+/-)
gene regulation
genome (+/-)
genomic hype
organization
plasticity

(See plasticity/genome)
remodeling

holism (+/-)
contextual
language of

(See explanation)

“more than the sum of its parts”

(See explanation/part and whole

organism as a “formed stream”
as polarity
versus mysticism and vitalism
information

(See machine-idea/code)

inwardness (intention, idea, meaning)
machine-idea (+/-)
manipulation and control

(See machine-idea and
explanation/and causation)

meaning in biology

(See inwardness)

mysticism

(See holism/versus mysticism and vitalism)

phase transitions

(See form/molecular)

plasticity (+/-)
protein (+/-)
qualities

(See especially explanation/portrayal;
also explanation/part and whole, and holism

RNA
signaling (+/-)
transcription (+/-)
translation
Special Topics
circadian rhythms
microbiome
pluripotency (+/-)

topical index


chromosome
  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
code
  1. (See machine-idea/code)
development (ontogeny)
  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
  11. Evolution As It Was Meant To Be — An Overview
DNA
  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
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
epistemology
  1. All Science Must Be Rooted in experience
  2. Reframing the Mind-Body Problem: An Exercise in Letting Go of Dualist Assumptions
  3. A Modest Epistemological Exercise
evolution
  1. Development Writ Large
  2. Let’s Not Begin With Natural Selection
  3. Evolution As It Was Meant To Be — An Overview
  4. Evolution and the Purposes of Life
  5. Evolution and the Illusion of Randomness
  6. of consciousness
    1. A Physicist, a Philologist, and the Meaning of Life
  7. and development
    1. Inheritance (1): The Whole Organism
    2. Development Writ Large
    3. Teleology and Evolution — Why Can’t We have ‘Evolution on Purpose’?
    4. Evolution Writ Small
    5. Evolution As It Was Meant To Be — An Overview
  8. fitness
    1. Can We Track Fitness?
    2. Fitness — An Irretrievably Obscure Concept
    3. Evolution As It Was Meant To Be — An Overview
  9. inheritance
    1. Inheritance (1): The Whole Organism
    2. Evolution As It Was Meant To Be — An Overview
    3. of acquired characters
      1. Epigenetics and the Inheritance of Acquired Characters
    4. heritability
      1. Missing Heritability — Or Whole-Organism Inheritance?
  10. 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?
  11. as mindless process
    1. Toward a Thought-Full Teleology
    2. Evolution As It Was Meant To Be — An Overview
    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)
  12. and mutations
    1. Inheritance (1): The Whole Organism
    2. Chance to the Rescue?
    3. Natural Genome Remodeling
    4. Couldn’t You Be More Explicit Here?
  13. sociobiology
    1. Vladimir Solovyov on Sexual Love and Evolution
explanation
  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. Biology’s Missing Ideas
    3. The Organism’s Story
    4. The Problematic Effectiveness of Reason in Biology (Part 1 of “From Bodily Wisdom to the Knowing Self)”
    5. From Physical Causes to Organisms of Meaning
    6. What Changes at Death?
    7. Two Kinds of Description
    8. Some Views of the Living Organism
    9. Trying to Grasp the Whole Organism
    10. Biology — More Fundamental than Physics?
    11. How Does an Organism Get Its Shape?
    12. RNA: Dancing with a Thousand Partners at Once
    13. From Differences to Character
    14. The Paradox in “Explaining” Form
    15. Psyche, Soma, and the Unity of Gesture (Part 2 of “From Bodily Wisdom to the Knowing Self)”
    16. Let’s Loosen Up Biological thinking!
    17. Of Humans and Our Microbial Guests: A Dynamic and Living Balance
    18. Microbiome: It’s Less About the “Bad Guys” Than the Whole Organism
    19. Where Do Intelligence and Wisdom Reside? (Part 3 of “From Bodily Wisdom to the Knowing Self”)
    20. 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. Context: Dare We Call It Holism?
    2. The Organism’s Story
    3. What Does “More Than the Sum of Its Parts” Mean?
    4. RNA: Dancing with a Thousand Partners at Once
    5. Who Are You and Who Am I and Who Are We?
    6. Vladimir Solovyov on Sexual Love and Evolution
    7. Of Humans and Our Microbial Guests: A Dynamic and Living Balance
    8. 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?
form
  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. 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
  5. organismal
    1. The Embryo’s Eloquent Form
    2. The Paradox in “Explaining” Form
    3. To Explain or Portray?
    4. How Does an Organism Get Its Shape?
    5. Can We Explain the Form of Organisms?
    6. Form and the Electrified Organism
    7. RNA: Dancing with a Thousand Partners at Once
    8. Hox Genes in Motion: Who’s Moving Whom?
gene
  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. Biology’s Missing Ideas
    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
    10. Richard Dawkins and the Missing Organism
  3. indefinability
    1. Indefinable Genes and the “Wild West” Genomic Landscape
  4. mutation
    1. What Absent Genes Don’t Do — and How Can We Know?
    2. (See also: evolution/and mutations)
gene regulation
  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
genome
  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?
holism
  1. Inheritance (1): The Whole Organism
  2. How Our Genes Come to Expression (It Takes an Epigenetic Village)
  3. What Is the Problem of Form?
  4. Why We Cannot Explain the Form of Organisms
  5. The Sensitive, Muscular Cell
  6. The Unbearable Wholeness of Beings
  7. From Physical Causes to Organisms of Meaning
  8. On Being Wholehearted
  9. Facing Down to Life
  10. Shattering the Genome
  11. A Thousand-Stranded Tapestry: How Organisms Employ Their Genes
  12. Pervasive Transcription: Using Genomes “Every Which Way”
  13. What Absent Genes Don’t Do — and How Can We Know?
  14. RNA: Dancing with a Thousand Partners at Once
  15. Richard Dawkins and the Missing Organism
  16. contextual
    1. A Mess of Causes
    2. Biology’s Missing Ideas
    3. The Mystery of an Unexpected Coherence
    4. Context: Dare We Call It Holism?
    5. The Organism’s Story
    6. How to Unthink Epigenetics
    7. Who Are You and Who Am I and Who Are We?
    8. Cancer and Context
    9. Signals and the Whole Organism
    10. Trying to See the Organism Whole
    11. How Does an Organism Get Its Shape?
    12. Of Humans and Our Microbial Guests: A Dynamic and Living Balance
    13. Microbiome: It’s Less About the “Bad Guys” Than the Whole Organism
    14. 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. Free Life and Confining Form
  21. versus mysticism and vitalism
    1. Biology’s Missing Ideas
    2. A question for biologists: Are you and I machines?
    3. From Physical Causes to Organisms of Meaning
    4. Animistic Impulses in Biology
    5. Fear of Vitalism
    6. How Does an Organism Get Its Shape?
inwardness (intention, idea, meaning)
  1. Toward a Thought-Full Teleology
  2. Teleology and Evolution — Why Can’t We have ‘Evolution on Purpose’?
  3. The Keys to This Book
  4. Biology’s Missing Ideas
  5. Context: Dare We Call It Holism?
  6. The Organism’s Story
  7. All Science Must Be Rooted in experience
  8. Evolution As It Was Meant To Be — An Overview
  9. Scenes of Life
  10. Evolution and the Purposes of Life
  11. A Physicist, a Philologist, and the Meaning of Life
  12. The Inwardness of Beings
  13. How Biologists Lost Sight of the Meaning of Life
  14. The Problematic Effectiveness of Reason in Biology (Part 1 of “From Bodily Wisdom to the Knowing Self”)
  15. Psyche, Soma, and the Unity of Gesture (Part 2 of “From Bodily Wisdom to the Knowing Self)”
  16. Let’s Loosen Up Biological thinking!
  17. How Does an Organism Get Its Shape?
  18. RNA: Dancing with a Thousand Partners at Once
  19. How to Unthink Epigenetics
  20. The Embryo’s Eloquent Form
  21. Why Can’t Evolutionary Biologists Quit Believing in Intelligent Design?
  22. Three Questions for Intelligent Design Theorists
  23. Vladimir Solovyov on Sexual Love and Evolution
  24. Where Do Intelligence and Wisdom Reside? (Part 3 of “From Bodily Wisdom to the Knowing Self”)
  25. (See also: evolution/as mindless process)
machine-idea
  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)
mysticism
  1. (See holism/versus mysticism and vitalism)
plasticity
  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)

protein
  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?
RNA
  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
signaling
  1. Horror graphs
  2. Yet Another Face of DNA
  3. contextual
    1. Signals and the Whole Organism
transcription
  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
translation
  1. Why Genetic Synonyms Are Not Synonymous
  2. Look What’s Happened to Genetic Synonyms!


Special Topics
circadian rhythms
  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
microbiome
  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
pluripotency
  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