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 (+/-)
DNA (+/-)
DNA-centrism (See gene/genocentrism)
junk
noncoding
code

(See machine-idea/code)

development (ontogeny)
epigenetics
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)

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

topical index


chromosome
  1. chromatin
    1. Genes and Organisms: Improvising the Dance of Life
    2. The Sensitive Nucleosome
    3. The Nucleosome as Mediator
    4. DNA and RNA brought to life
    5. How to Unthink Epigenetics
  2. dynamics
    1. Genes and Organisms: Improvising the Dance of Life
    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. The Dynamic Space of the Cell Nucleus
    2. Pervasive Transcription: Using Genomes “Every Which Way”
    3. The Complex Performance of the Three-Dimensional Chromosome
code
  1. (See machine-idea/code)
development (ontogeny)
  1. How Does an Organism Get Its Shape?
  2. The Embryo’s Eloquent Form
  3. The Divorce of Evolution from Development
  4. Plasticity, Stability, and DNA
  5. Form and the Electrified Organism
  6. Will the real Walter Gilbert please stand up?
  7. It Takes a Whole Context to Support Pluripotency
DNA
  1. Genes and Organisms: Improvising the Dance of Life
  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 to Unthink Epigenetics
  2. Paradoxes driving the new emphasis on epigenetics
  3. Metamorphosis of the Code
  4. The Sensitive Nucleosome
  5. Genes and Organisms: Improvising the Dance of Life
  6. A Thousand-Stranded Tapestry: How Organisms Employ Their Genes
  7. How the Organism Decides What to Make of Its Genes
  8. Epigenetics and the Inheritance of Acquired Characters
evolution
  1. Evolution and the Purposes of Life
  2. Evolution and the Illusion of Randomness
  3. Genes and the Central Fallacy of Evolutionary Theory
  4. The core logic of evolution
  5. Evolution as a Genetic Narrative
  6. Why DNA Seems So Central to Evolution
  7. A Story We Have Not Yet Learned to Narrate
  8. and development
    1. The Divorce of Evolution from Development
    2. Life Is an Activity, Not a Collection of Things
  9. fitness
    1. Can We Track Fitness?
    2. Fitness — An Irretrievably Obscure Concept
  10. inheritance
    1. Transgenerational Digital Fidelity
    2. DNA, Inheritance, and the Whole Organism
    3. of acquired characters
      1. Epigenetics and the Inheritance of Acquired Characters
    4. heritability
      1. Missing Heritability — Or Whole-Organism Inheritance?
  11. intelligent design
    1. Three Questions for Intelligent Design Theorists
    2. Evolution and the Purposes of Life
    3. A Sectarian Quarrel? Intelligent Design and Neo-Darwinism
    4. How Does an Organism Get Its Shape?
  12. as mindless process
    1. The “mindlessness” of biological science today
    2. Evolution and the Purposes of Life
    3. Letting the Reality of the Organism Speak
    4. A Sectarian Quarrel? Intelligent Design and Neo-Darwinism
    5. Evolution and Belief
    6. (See also: inwardness)
  13. mutations and
    1. Chance to the Rescue?
    2. Natural Genome Remodeling
    3. Couldn’t You Be More Explicit Here?
  14. sociobiology
    1. Vladimir Solovyov on Sexual Love and Evolution
explanation
  1. From Physical Causes to Organisms of Meaning
  2. biological
    1. The Problematic Effectiveness of Reason in Biology (Part 1 of “From Bodily Wisdom to the Knowing Self)”
    2. From Physical Causes to Organisms of Meaning
    3. What Changes at Death?
    4. Two Kinds of Description
    5. Some Views of the Living Organism
    6. Trying to Grasp the Whole Organism
    7. Biology — More Fundamental than Physics?
    8. How Does an Organism Get Its Shape?
    9. RNA: Dancing with a Thousand Partners at Once
    10. From Differences to Character
    11. The Paradox in “Explaining” Form
    12. Psyche, Soma, and the Unity of Gesture (Part 2 of “From Bodily Wisdom to the Knowing Self)”
    13. Let’s Loosen Up Biological thinking!
    14. Of Humans and Our Microbial Guests: A Dynamic and Living Balance
    15. Microbiome: It’s Less About the “Bad Guys” Than the Whole Organism
    16. Where Do Intelligence and Wisdom Reside? (Part 3 of “From Bodily Wisdom to the Knowing Self”)
  3. and causation
    1. Who Regulates the Regulators?
    2. Laws and Causes
    3. Beings in Context
    4. How Does an Organism Get Its Shape?
    5. Have Biologists Really Overcome Gene-Centered Thinking?
    6. The (Molecular) Lives of Our Days
    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
    9. It Takes a Whole Context to Support Pluripotency
    10. How to Unthink Epigenetics
  4. part and whole
    1. What Does “More Than the Sum of Its Parts” Mean?
    2. RNA: Dancing with a Thousand Partners at Once
    3. Who Are You and Who Am I and Who Are We?
    4. Vladimir Solovyov on Sexual Love and Evolution
    5. Of Humans and Our Microbial Guests: A Dynamic and Living Balance
    6. Microbiome: It’s Less About the “Bad Guys” Than the Whole Organism
  5. portrayal and
    1. To Explain or Portray?
    2. Can We Explain the Form of Organisms?
form
  1. molecular
    1. Molecular Machines
    2. Are “Disordered” Proteins Really Disordered?
    3. The Complex Performance of the Three-Dimensional Chromosome
    4. Eloquent Form
    5. Why Genetic Synonyms Are Not Synonymous
    6. Look What’s Happened to Genetic Synonyms
    7. The Unexpected Phases of Life
  2. 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. From Differences to Character
    2. What Absent Genes Don’t Do — and How Can We Know?
  2. genocentrism
    1. Putting Genes in Perspective
    2. The Seat of Power: Nucleus or Cytoplasm?
    3. How to Unthink Epigenetics
    4. Free Life and Confining Form
    5. Have Biologists Really Overcome Gene-Centered Thinking?
    6. Evolution as a Genetic Narrative
    7. Why DNA Seems So Central to Evolution
    8. Form and the Electrified Organism
    9. Shattering the Genome
    10. The (Molecular) Lives of Our Days
  3. indefinability
    1. Indefinable Genes and the “Wild West” Genomic Landscape
    2. Genes and Organisms: Improvising the Dance of Life
  4. mutation
    1. What Absent Genes Don’t Do — and How Can We Know?
    2. (See also: evolution/and mutations)
gene regulation
  1. Genes and Organisms: Improvising the Dance of Life
  2. Getting Over the Code Delusion
  3. The Sensitive Nucleosome
  4. A Thousand-Stranded Tapestry: How Organisms Employ Their Genes
  5. How the Organism Decides What to Make of Its Genes
  6. RNA: Dancing with a Thousand Partners at Once
  7. How to Unthink Epigenetics
  8. Why Genetic Synonyms Are Not Synonymous
  9. Look What’s Happened to Genetic Synonyms
  10. The Unexpected Phases of Life
  11. Symptoms: Notes from Biological Literature (1)
  12. Viruses, Cytoplasmic DNA, and the Web of Life
  13. Functional vs. Nonfunctional DNA Binding
genome
  1. genomic hype
    1. are chimps almost human?
  2. organization
    1. The Complex Performance of the Three-Dimensional Chromosome
    2. Genes and Organisms: Improvising the Dance of Life
  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?
    4. Genes and Organisms: Improvising the Dance of Life
holism
  1. Genes and Organisms: Improvising the Dance of Life
  2. The Unbearable Wholeness of Beings
  3. From Physical Causes to Organisms of Meaning
  4. On Being Wholehearted
  5. Facing Down to Life
  6. Shattering the Genome
  7. A Thousand-Stranded Tapestry: How Organisms Employ Their Genes
  8. Pervasive Transcription: Using Genomes “Every Which Way”
  9. What Absent Genes Don’t Do — and How Can We Know?
  10. RNA: Dancing with a Thousand Partners at Once
  11. contextual
    1. Genes and Organisms: Improvising the Dance of Life
    2. How to Unthink Epigenetics
    3. Who Are You and Who Am I and Who Are We?
    4. Cancer and Context
    5. Signals and the Whole Organism
    6. Trying to See the Organism Whole
    7. How Does an Organism Get Its Shape?
    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
    10. It Takes a Whole Context to Support Pluripotency
  12. language of
    1. (See explanation)
  13. “more than the sum of its parts”
    1. (See explanation/part and whole)
  14. organism as a “formed stream”
    1. The Organism Is Not a Machine
    2. The Nucleosome as Mediator
    3. A Living Vortex
    4. The Unexpected Phases of Life
  15. as polarity
    1. Free Life and Confining Form
  16. 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. A Story We Have Not Yet Learned to Narrate
    6. How Does an Organism Get Its Shape?
inwardness (intention, idea, meaning)
  1. Evolution and the Purposes of Life
  2. The Inwardness of Beings
  3. How Biologists Lost Sight of the Meaning of Life
  4. The Problematic Effectiveness of Reason in Biology (Part 1 of “From Bodily Wisdom to the Knowing Self”)
  5. Psyche, Soma, and the Unity of Gesture (Part 2 of “From Bodily Wisdom to the Knowing Self)”
  6. Let’s Loosen Up Biological thinking!
  7. How Does an Organism Get Its Shape?
  8. RNA: Dancing with a Thousand Partners at Once
  9. How to Unthink Epigenetics
  10. The Embryo’s Eloquent Form
  11. Three Questions for Intelligent Design Theorists
  12. Vladimir Solovyov on Sexual Love and Evolution
  13. Where Do Intelligence and Wisdom Reside? (Part 3 of “From Bodily Wisdom to the Knowing Self”)
  14. (See also: evolution/as mindless process)
machine-idea
  1. Biology’s Shameful Refusal to Disown the Machine-Organism
  2. On Being Wholehearted
  3. A question for biologists: Are you and I machines?
  4. Demise of Lock-and-Key Proteins
  5. The Organism Is Not a Machine
  6. Laws and Causes; Beings in Context
  7. Three Questions for Intelligent Design Theorists
  8. The (Molecular) Lives of Our Days
  9. Evolution and the Purposes of Life
  10. 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
  11. 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. Genes and Organisms: Improvising the Dance of Life
  3. genome
    1. Pervasive Transcription: Using Genomes “Every Which Way”
    2. Viruses, Cytoplasmic DNA, and the Web of Life
    3. (See also: chromosome/chromosome/dynamics)
  4. 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. Are “Disordered” Proteins Really Disordered?
RNA
  1. RNA: Dancing with a Thousand Partners at Once
  2. Genes and Organisms: Improvising the Dance of Life
signaling
  1. Horror graphs
  2. Yet Another Face of DNA
  3. contextual
    1. Signals and the Whole Organism
transcription
  1. Genes and Organisms: Improvising the Dance of Life
  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. 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

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