The Sacred Depths of Nature: How Life Has Emerged and Evolved [2 ed.] 0197662064, 9780197662069

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The Sacred Depths of Nature: How Life Has Emerged and Evolved [2 ed.]
 0197662064, 9780197662069

Table of contents :
Cover
THE SACRED DEPTHS OF NATURE
Copyright
Dedication
CONTENTS
Personal 1997 (first edition)
Personal 2022 (second edition)
Introduction
How This Book Is Put Together
1 Origins of the Earth
2 Origins of Life
3 How Life Works
4 How an Organism Works
5 How Evolution Works
6 The Evolution of Biodiversity
7 Awareness and the I-​Self
8 Interpretations and Feelings
9 Sex
10 Intimacy
11 Multicellularity and Death
12 Human Evolution
13 Human Morality and Ecomorality
Epilogue: Emergent Religious Principles
Epilogue: The Religious Naturalist Orientation
Endnotes 1: Legends to Cover and Chapter Frontispieces   and Text Figure Credits
Endnotes 2: Further Readings/​Resources and Text Credits
Index

Citation preview

ADVANCE PRAI S E F OR T HE SACRED DEP T H S OF NAT U R E

“This book is a gem. Not only are the science passages an exquisite introduction to astronomy, cell biology, and evolution, but her reflections on the meaning she personally derives from such knowledge leave the reader yearning for more. Her passages on the meaning of death—​indeed, a celebration of death, for the kind of life and love only it can call forth—​is unsurpassed by all the outpourings from the humanities. She is fully, intimately, restfully at home in the universe, in her version of divinity: the sacred depths of nature. And then, able to draw no more from either the science or her own soul, she offers up a poem or psalm from various of the world’s wisdom traditions.”—​Connie Barlow, Eco-​ activist, author of Green Space, Green Time: The Way of Science “A truly fascinating, wide-​ranging, beautifully written, and eye-​ opening book that considers the origins of earth, the origins of life itself, where we are now, where we are most likely heading, and the importance of developing a shared global cosmology and ecomorality that can benefit us all in the future.”—​Marc Bekoff,

Ecology and Evolution, University of Colorado, author of Rewilding our Hearts: Building Pathways of Compassion and Coexistence “Ursula Goodenough argues passionately, wisely, and even lyrically for a new, modern, scientifically informed worldview that can tell us both about the universe we inhabit and the moral rules we need to inhabit it well. This is a wonderful account of the history of life by a great biologist. It invites us to find in modern science the profound sense of wonder and belonging, and the deep ethical sense present in all the world’s religious traditions.”—​David Christian, History, Macquarie University, author of Origin Story: A Big History of Everything “Even better the second time around! Engagingly and clearly written, replete with striking metaphors—​especially ones from music—​and with conscientious respect for the scientifically untrained reader. A convincing demonstration of the integral relation between generously open-​minded natural science and equally receptive, non-​dogmatic religious thought. The two are shown to interact with, jointly inform, and mutually inspire one another in Goodenough’s engrossing version of Religious Naturalism. Here the compelling sacredness of all living and non-​living nature is brought into sharp focus.”—​Donald Crosby, Philosophy, Colorado State University, author of Sacred and Secular: Responses to Life in a Finite World “Not since Loren Eiseley or Lewis Thomas has biology had such an eloquent spokesperson, nor one with so much heart. Finally, someone who can breathe life into molecules and make us feel it.”—​ Terrence Deacon, Anthropology and Cognitive Science

Program, University of California, Berkeley, author of Incomplete Nature: How Mind Emerged from Matter “What perfect timing for this revised edition of Ursula Goodenough’s classic, The Sacred Depths of Nature. As we witness and experience, emotionally and socially, the unraveling of the biosphere and industrial civilization, a meaningful, reverential worldview grounded in evidence is more relevant than ever. An excellent introduction to the religious naturalist orientation! Only my wife, Connie Barlow’s Green Space Green Time, is even in the same league. Bravo, Ursula!”—​Michael Dowd, Ecotheologian, author of Thank God for Evolution “Tender, yet passionate, Goodenough immerses us in a collective spiritual vision, allowing us to discover and feel the numinous in science, synthesizing these understandings and the religious impulse without doing harm to either. Our best hope for a future.”—​Anne Druyan, Writer, director, and producer of COSMOS and cocreator with Carl Sagan of the motion picture CONTACT “The Sacred Depths of Nature is both a spiritual exercise and a sophisticated, crystal clear, and lyrical primer on what science teaches us about this wondrous universe and the mysterious gift that is being here at all.”—​Owen Flanagan, Philosophy, Duke University, author of The Geography of Morals “Hosanna! Here, now, this! The new revised version of The Sacred Depths of Nature is manna from heaven on earth. Muons and neutrinos, eukaryotic sex and somatic death, covenant with mystery, Goodenough’s Gospel of Life is the true myth we and our planet desperately need.”—​Michael S. Hogue, Meadville Lombard

Theological School, author of American Immanence: Democracy for an Uncertain World “At once expansive and intimate, empirical and immanent, analytical and intuitive, material and spiritual, science and poetry get to dance joyfully together in these pages. The Sacred Depths of Nature allows us to see and celebrate our fundamental kinship with all beings, united by the forces that propel life’s improbable unfolding. In this time of crisis, we urgently need the planetary ethic that resists the degradation of the shimmering world.”—​Robin Wall Kimmerer, Center for Native Peoples and the Environment, SUNY-​ ESF, author of Braiding Sweetgrass: Indigenous Wisdom, Scientific Knowledge, and the Teachings of Plants “This book is a treasure for all those who seek to connect with a deeper meaning in the universe without jettisoning empirical scientific evidence. Ursula Goodenough dissolves the conventional split between science and religious orientation, showing with delightful prose and breathtaking examples how a deeply scientific investigation can naturally lead us to a ‘covenant with mystery’ and a ‘credo of continuation.’ ”—​Jeremy Lent, author of The Patterning Instinct and The Web of Meaning “Thank you, Ursula Goodenough, for telling us the science-​based story of life on earth and the wonders of our universe in a way that brings them down to the level of our hearts, and deeper still, to the very place from where our prayers come.”—​Peter Mayer, Singer and songwriter, lyricist of “Blue Boat Home” “I am so glad this important book is being revised for our time. It is wise, calm, and compassionate; it treats us as the mature, complex, and fascinating creatures that we are, and in so doing helps point

the way towards a future where we act together far better than at present.”—​Bill Mckibben, Founder of 350.org, author of The Flag, the Cross, and the Station Wagon: A Graying American Looks Back at his Suburban Boyhood and Wonders What the Hell Happened “To experience the sacred, we need not ask the WHY question, which is, after all, unanswerable. In this absolutely amazing book, biologist Ursula Goodenough shows us that pondering the HOW of things brings us face-​to-​face with that which is sacred. Through science, poetry, and her own remarkable personal stories, Goodenough shares her profound religious stance as a Credo of Continuation.”—​Jennifer Morgan, President, Deeptime Network “An engaging, authoritative account of the evolution and molecular basis of life from the perspective of a religious naturalist who rejoices in the complexity and wonder of the natural world. A successful cell biologist and gifted writer, Goodenough weaves together our scientific understanding of the appearance, place, and workings of life on earth in the context of the diversity of religious traditions. The book will inspire both scientists and non-​scientists to appreciate the magic of our existence and the necessity to preserve that which makes it possible.”—​Thomas Pollard, Molecular, Cellular and Developmental Biology, Yale University, co-​author of Cell Biology, 4th edition “Goodenough’s masterpiece unites the beauty of biology and the wonders of evolution in a magnificent, heartfelt celebration of life. Like its author, this book is eloquent, vibrant, inspiring, and truly one-​of-​a-​kind.”—​Barbara Smuts, Psychology, University of Michigan, author of Sex and Friendship in Baboons

“Incisive, comprehensive, witty, and beautiful, with paragraph after paragraph of lucidity and significance. We could be witnessing one of the most important cultural events of the last three centuries—​ the moment when scientists themselves take their role seriously in forging a planetary wisdom.”—​Brian Swimme, Evolutionary cosmologist, California Institute of Integral Studies, coauthor of The Journey of the Universe “Goodenough gives us a new bridge between science and religion that is both eloquent and elegant. She offers us the poetry, power, and passion of her vision of nature, a vision born from scientific knowledge, nurtured by religious sensibility, and inspired by nature itself. Such a pathbreaking interdisciplinary work illumines the way for each of us—​embracing an ecomorality that is comprehensive and compelling.”—​Mary Evelyn Tucker, School of the Environment and Forum on Religion and Ecology, Yale University, coproducer of the film Journey of the Universe “A delicious account of the grandeur and intricacies of natural reality that will have you falling in love with the beauty of scientific knowledge while honoring the grand wisdom of religious valuing. The new chapters on human evolution, human morality, and ecomorality reveal why The Sacred Depths of Nature remains a remarkable gift for our generation. Goodenough demonstrates, in her inimitable lucid, poetic style, a religious naturalist orientation that is uniquely positioned to address—​all at once!—​such urgent topics as systemic, structural racism, cultural imperialism, and environmental injustices.”—​Carol Wayne White, Religious Studies, Bucknell University, author of Black Lives and Sacred Humanity: Toward an African American Religious Naturalism

“I have been waiting years for this paean to the universe. With lustrous turns of phrase, skillful explanations of nature, a profound vision of the past, and a prescient sense of the future, Ursula Goodenough reintroduces us to the present moment, the fulsome present, bursting with an invitation to gratitude and reverence. There’s not a single person on this planet who doesn’t need and deserve this book.”—​Wesley J. Wildman, School of Theology and Faculty of Computing and Data Sciences, Boston University, author of Spirit Tech “The first edition of The Sacred Depths of Nature was a revelation to me. Before reading it, I had no idea that the workings of a single cell were so elaborate as to be awe-​inspiring. This second edition has brought many more such revelations. Illustrated with lovely photos and poems from wise poets, this is a detailed short treatise on the science of life. It proves once again that a science book can be a page-​turner. I learned from every page and could not wait for the next one.”—​Paul Woodruff, Philosophy, University of Texas Austin, author of Living Toward Virtue: Practical Ethics in the Spirit of Socrates “What a beautiful, lyrical, lively, fascinating, and outstanding book. Delightful to read. Awesome achievement.”—​ Richard Wrangham, Human Evolutionary Biology, Harvard University, author of The Goodness Paradox: The Strange Relationship Between Virtue and Violence in Human Evolution

URSULA GOODENOUGH

THE SACRED DEPTHS OF NATURE How Life Has Emerged and Evolved SECOND EDITION

Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide. Oxford is a registered trade mark of Oxford University Press in the UK and certain other countries. Published in the United States of America by Oxford University Press 198 Madison Avenue, New York, NY 10016, United States of America. © Ursula Goodenough 2023 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, by license, or under terms agreed with the appropriate reproduction rights organization. Inquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above. You must not circulate this work in any other form and you must impose this same condition on any acquirer. Library of Congress Cataloging-​in-​Publication Data Names: Goodenough, Ursula, author. Title: The sacred depths of nature : how life has emerged and evolved / Ursula Goodenough. Description: Second edition. | New York, NY : Oxford University Press, [2023] | Includes bibliographical references and index. Identifiers: LCCN 2022030828 (print) | LCCN 2022030829 (ebook) | ISBN 9780197662069 (hardcover) | ISBN 9780197662083 (epub) Subjects: LCSH: Biology—Philosophy. | Biology—Religious aspects. | Naturalism—Religious aspects. | Nature—Religious aspects. Classification: LCC QH331 .G624 2023 (print) | LCC QH331 (ebook) | DDC 570.1—dc23/eng/20220923 LC record available at https://lccn.loc.gov/2022030828 LC ebook record available at https://lccn.loc.gov/2022030829 DOI: 10.1093/​oso/​9780197662069.001.0001 1 3 5 7 9 8 6 4 2 Printed by Sheridan Books, Inc., United States of America

For: Rachel Cowan Joan Goodwin Esther Hopkins

CON TEN T S

Personal 1997 (first edition)  Personal 2022 (second edition) 

xv xix

Introduction 

1

How This Book Is Put Together 

7

1 Origins of the Earth 

11

2 Origins of Life 

21

3 How Life Works 

41

4 How an Organism Works 

63

5 How Evolution Works 

75

6 The Evolution of Biodiversity 

87

7 Awareness and the I-​Self 

101

8 Interpretations and Feelings 

123

9 Sex 

135

10 Intimacy 

147

11 Multicellularity and Death 

157

12 Human Evolution 

167

13 Human Morality and Ecomorality 

187

Contents

Epilogue: Emergent Religious Principles 

211



Epilogue: The Religious Naturalist Orientation 

219



Endnotes 1: Legends to Cover and Chapter Frontispieces    and Text Figure Credits  Endnotes 2: Further Readings/​Resources and Text Credits  Index 

227 231 249



xiv

P ER SONAL 1997 (FI R S T EDI T ION )

No question about it: I’m writing this book because of my father. He started out as a Methodist preacher but became absorbed—​no, obsessed—​with a need to understand why people are religious. As Professor of the History of Religion, he poured out book after book on the ancient Jews and early Christians: their art, their texts, their motivations. And then he brought it all home, to me sitting there after dessert trying to look inconspicuous while he and the other Yale scholars drank a great deal of wine and held forth on Plato and Paul and Freud and Sartre. Dad began his famous undergraduate course, The Psychology of Religion, by announcing “I do not believe in God.” He ended one of his last books by admitting “I still pray devoutly, and when I do I forget my qualifications and quibbles and call upon Jesus—​and he comes to me.” He was a larger-​than-​life father, passionate and outrageous and adored. When he died of cancer when I was twenty-​two, it was almost more than any of us could bear. I went to college with 1950s expectations: find a husband, raise two children, and continue to read novels. But everything changed when I took Zoology 1 as a distribution requirement. Nothing in my girls-​school training had led me to understand that creatures are made up of cells and genes and enzymes, that life evolves, that kidneys control blood electrolytes. I was astonished. Better still, I

Personal 1997 (first edition)

was good at it. And Dad was quite as excited about my unexpected calling as I was. “Ursula a scientist! How splendid!” What a father. For the next twenty-​five years or so I played it straight: biology professorships, research projects, federal grants, graduate and undergraduate teaching. I still do all those things, and with as much pleasure and satisfaction as ever. But as my five children grew and there was more time for myself, my father’s question returned. Why are people religious? And then: Why am I not religious? But was that true? What is being religious anyhow? What about the way I feel when I think about how cells work or creatures evolve? Doesn’t that feel the same as when I’m listening to the St. Matthew Passion or standing in the nave of the Notre Dame Cathedral? So I joined Trinity Presbyterian Church and spent the next decade singing in the choir, reciting the liturgy and prayers, hearing the sermons, participating in the ritual. I came to understand how this tradition, as played out in a middle-​class, mostly white congregation, is able to elicit states of serious reflection, reverence, gratitude, and penance. But all of it was happening in the context of ancient premises and a deep belief in the supernatural. What about the natural? Was it possible to ground such religious sensibilities in the context of a fully modern, up-​to-​the-​minute understanding of Nature? And so I started reading and listening and reflecting, and out of it has emerged this book. Certainly the most important dialogue has been with Loyal Rue, who has explained to me most of what I understand about theology and philosophy and who has insisted that we scientists speak of what we know and feel. Early on I happened onto an improbable collection of people composing the Institute on Religion in an Age of Science (IRAS), and while the input of xvi

Personal 1997 (first edition)

many in IRAS has been seminal, this is particularly true for Gene d’Aquili, Connie Barlow, Michael Cavanaugh, Tom Gilbert, Ward Goodenough, Phil Hefner, Bill Irons, Sol Katz, Ted Laurenson, Karl Peters, Bob Schaible, and Barbara Whitaker-​Johns. Kirk Jensen of Oxford University Press has provided generous and unwavering support; Carl Smith has helped me understand and experience the religious impulse; John Heuser has continuously infused his perspectives and wisdom; Sine Berhanu and Jeanne Heuser have nurtured my spirituality; Pam Belafonte, Elizabeth Marincola, Sharon Olds, and Betsy Weinstock have nurtured my courage; my children—​Jason, Mathea, Jessica, Thomas, and James—​bless my life in countless ways; and no one can emerge from a consideration of religion without thanking William James.

xvii

PER SONAL 2022 (SECON D EDI T ION )

In the 25 years since I wrote the first edition of this book, I continued as a biology professor for 20 years and then retired to Martha’s Vineyard to celebrate my remaining years within oak forests abutting wetlands and the open ocean. Along the way I taught cell biology and evolution courses, participated in exciting scientific research with wonderful colleagues and trainees, and welcomed nine grandchildren. But after the book was published, I acquired a second life. As an advocate for the religious naturalist orientation (p. 219), I spoke at numerous venues—​college seminars, sermons, church-​basement discussion groups, conferences, book clubs. I wrote journal articles and blog essays and was interviewed and reviewed. I joined others in founding the Religious Naturalist Association (RNA, https://​religi​ous-​nat​ural​ist-​asso​ciat​ion.org) that in 2022 has some 900 members in 50 states and 40 countries. I shared ideas and feelings with those who embraced the religious naturalist trajectory and with those who offered critiques, thereby greatly expanding and clarifying my understandings. My second life has been both exhilarating and humbling, and the many new ideas and perspectives presented in this second edition were incubated in this rich context.

Personal 2022 (second edition)

The mentors, supporters, and family whom I acknowledged in 1997, most of whom, although sadly not all, are happily alive and well in 2022, are thanked again for their invaluable input and their continued belief in me. The concept of emergence anchored much of the first edition, but Terry Deacon and Jeremy Sherman have greatly expanded my understanding of its dynamics in their writings and in many conversations. Over the years, I have greatly benefited from the wisdom and support of Claude Bernard, Thomas Berry, Rachel Cowan, Susan Dutcher, Terry Findlay, Carol and Daniel Goodenough, Joan Goodwin, Billie Grassie, John Grim, Sam Guarnaccia, Joe Heitman, Michael Hogue, Esther Hopkins, Michael Kalton, Jason Keune, Kent Koeninger, Todd Macalister, Sandra Masur, Sabeeha Merchant, Jennifer Morgan, Janet Newton, Bill Orme-​Johnson, Irving, Sarah, and Alessandra Petlin, Lynne Quarmby, Edmund Robinson, Robyn Roth, Jeremy Rutledge, Sue Savage-​Rumbaugh, Barbara Smuts, JD Stillwater, Tricia Swift, Brian Swimme, Mary Evelyn Tucker, Sabine Waffenschmidt, Carol Wayne White, Wesley Wildman, Paul Woodruff, and Michael Wysession. I have also greatly benefited from the insights posted on IRAS and RNA social-​media forums. And my grandchildren—​Isabella, Delilah, Oliver, Lola, Zora, Luciano, Theodore, Leonardo, and Henry—​bless my life in countless ways.

xx

INTRODUCTION

W

hen people talk about religion, most soon mention the major religious traditions of our times, but then, thinking further, most mention as well the religions of indigenous peoples and of such vanished civilizations as ancient Greece and Egypt and Persia. That is, we have come to understand that there are—​and have been—​many different religions; anthropologists estimate the total in the thousands. They also estimate that there have been thousands of human cultures, which is to say that the making of a culture and the making of its religion go together: each religion is embedded in its cultural history. True, certain religions have attempted, and variously succeeded, in crossing cultural boundaries to “convert the heathens,” but the invaded cultures usually put their unmistakable stamp on what they import, as evinced by the pulsating percussive Catholic masses sung in Africa. In the end, each of these religions addresses two fundamental human concerns: How Things Are and Which Things Matter. How Things Are is articulated as a Cosmology or Cosmos: How the natural world came to be, how humans came to be, what happens after we die, the origins of evil and tragedy and natural disaster and love. Which Things Matter becomes codified as a Morality

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0001

The Sacr ed Depths of Natur e

or Ethos: the Judaic Ten Commandments, the Christian Sermon on the Mount, the Five Pillars of Islam, the Buddhist Vinaya, the Confucian Five Relations, and the understandings inherent in numerous indigenous traditions. The role of a religion is to integrate the Cosmology and the Morality, to render the cosmological narrative so rich and compelling that it elicits our allegiance and our commitment to its attendant moral understandings. As a culture evolves, a distinctive Cosmos and Ethos appear in its co-​evolving religion. For billions of us, back to the early humans, the stories, ceremonies, and art associated with our religions-​of-​origin have been central to our lives. I stand in awe of these religions. I have no need to take on their contradictions or immiscibility, any more than I would quarrel with the fact that Scottish bagpipe ceremonies coexist with Japanese tea ceremonies. And indeed, the failure of Soviet Marxism to obliterate Russian Orthodoxy, and of Maoism to obliterate Buddhism, Confucianism, or Daoism, and of Christianity to obliterate indigenous understandings, reminds us that projects designed to overthrow religious traditions face strong headwinds. My concern is very different. As I witness contemporary efforts to generate planetary consensus, I see many high-​minded and earnest people attempting to operate within an amalgam of economic, military, and political arrangements, and I find myself crying out “But wait! Where is the religion? What is orienting this project besides fear and greed? Where is the shared cosmology and the shared morality?” That we need a planetary ethic is so obvious that I need but list a few key words: climate change, ethnic cleansing, fossil fuels, habitat and species preservation, human rights, hunger, inland waterways, infectious disease, nuclear weapons, oceans, pollution, 2

Introduction

population pressures. To my ear, conversations on these topics are largely cacophonies of national, cultural, and denominational self-​ interest. Without a common religious orientation, we basically don’t know where to begin, nor do we know what to say or how to listen, nor are we motivated to respond. My agenda for this book is therefore to outline some possible foundations for such a planetary ethic, an ethic that would make no claim to supplant existing orientations but would seek to coexist with them, informing our global concerns while we continue to orient our daily lives in our cultural/​religious contexts. Any planetary foundation needs to be anchored in a shared worldview—​a culture-​independent, globally accepted consensus as to how things are. From my perspective, this part is easy. How things are is, well, how things are: our science-​based understandings of Nature: the Big Bang, the formation of stars and planets, the origin and evolution of life and sentience on Earth, the very recent advent of language-​based consciousness in humans, and the concomitant evolution of human cultures. As science-​based inquiry continues, our current understandings will deepen and evolve, but a core narrative is in place: The universe is a single reality—​one long, sweeping spectacular process of interconnected events. The universe is not a place where evolution happens, it is the evolution happening. It is not a stage on which drama unfolds, it is the unfolding drama itself. If ever there were a candidate for a universal story, it must be this story of cosmic evolution . . . .The story shows us in the deepest possible sense that we are all sisters and brothers—​fashioned from the same stellar dust, energized by the same star, nourished by the same planet, endowed with the same genetic code, and threatened by the same evils. This story, more than any other, humbles us before the magnitude and complexity of creation. Like no other story it

3

The Sacr ed Depths of Natur e bewilders us with the improbability of our existence, astonishes us with the interdependence of all things, and makes us feel grateful for the lives we have. And not the least of all, it inspires us to express our gratitude to the past by accepting a solemn and collective responsibility for the future. —​Loyal Rue

This, I believe, is the story that can unite us, because it is true for us all. It is Everybody’s Story. But that potential carries a crucial caveat. A cosmology works as a religious cosmology only if it resonates, only if it makes the listener feel religious. Yes, the beauty of Nature—​sunsets, woodlands, bird song—​readily elicits religious responses. We experience awe and wonder at the grandeur, the poetry, the richness of the natural world; it fills us with joy and thanksgiving. Our responses to accounts of the workings of Nature, on the other hand, are often far less positive. The scientific accounts of how things are, and how they came to be, are more likely, at least initially, to elicit alienation, disenchantment, anomie, and nihilism rather than the celebration just offered by Loyal Rue. Such responses are not likely to motivate allegiance or a spiritual/​ethical orientation. This alienation has several sources that are considered in various chapters of the book. Here I suggest that a primary source derives from the way that scientific understandings are commonly presented. The language of scientists, while conveying essential precision and depth to other scientists, too often conveys a view of the natural world that can feel cold and mechanical to the outsider. Moreover, the language is often obscure, generating the understandable response that “I can’t get my mind around all that stuff.” And, alas, our science curricula in the schools, while often creative and stimulating, have all too often been experienced as 4

Introduction

difficult, dry, and boring except for “those science nerds who were good at it.” This book therefore seeks to present an accessible and engaging account of our science-​based understandings of Nature, with a focus on planetary life, and then suggest ways that this account can elicit abiding, fulfilling, and joyous religious responses, generating what has been called a religious naturalist orientation (p. 219), an orientation poised to participate in the development of a planetary ethos. Once we experience a solemn gratitude that we exist at all, share a reverence for how life and the planet work, and acknowledge an imperative that both continue to flourish, our conversations will be infused with intimations of the sacred depths of Nature and our responsibility to nurture that which we deem sacred. A key component of any religious cosmology is its focus on the human. Even as we acknowledge that our advent on the planet was but an evolutionary moment ago, even as we gaze into the heavens with urgent questions about our significance, the significance and future of humankind remain central to our religious sensibilities. The religious naturalist orientation has no problem here. Being at home with our natural selves is the prelude to both morality and ecomorality, and there are many ways to see human beings as noble and distinctive even as we are also animals who are inexorably part of the whole. A planetary ethic must be anchored both in an understanding of human nature and an understanding of the rest of Nature. This, I believe, can be achieved if we all start out with the same kinds of perspectives on how human nature flows forth from whence we came.

5

HOW THIS BOOK IS PUT TOGETHER

A

Lutheran-​ raised friend who read an early draft of the first edition of this book remarked that it was set up like a Daily Devotional booklet, also found in Evangelical and Catholic traditions. A Daily Devotional, he explained, contains a collection of short bible-​based stories, each followed by a religious meditation on the story’s theme. While I wasn’t familiar with the genre, that’s basically how the chapters of this book are constructed. Each chapter begins with a story about the dynamics of Nature. Most are about biology since that is what I best understand, and most are about biology at the level of molecules and genes and cells, since this is what cries out to be understood. The stories recount what has been called the Epic of Evolution or Journey of the Universe or, my favorite, Everybody’s Story: our current understandings of the origins of the universe and the planet; the origins of chemistry and life; the workings of cells and organisms; the patterns of biological evolution and the resultant biodiversity; awareness and feelings; sex and intimacy; multicellularity and death; human evolution; and morality and ecomorality. Throughout, I have done my best to bridge C.P. Snow’s “two cultures”—​persons fluent in science-​based worldviews vs. persons oriented within the arts The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0002

The Sacr ed Depths of Natur e

and humanities. For readers not well versed in scientific concepts and terminology, I have tried to render my accounts accurate, understandable, and meaningful. Those who know the terrain will, I hope, find themselves engaged by the analogies and story lines that are used to explain the familiar. I often use anthropomorphic language in these descriptions—​ amino acids prefer to do something and enzymes recognize something—​because that’s how we humans think: we follow narratives with protagonists that have agency. Indeed, biologists use such analogies/​metaphors all the time; we speak of orphaned receptors and proteins that serve as chaperones and genes that hitchhike. While we hold robust science-​based understandings of the molecules and mechanisms of which we speak, it’s usually easier to communicate those understandings in carefully chosen anthropomorphic frames that convey the essence of a process. Then, at the end of each story, I offer a short response, the analogue of the Christian meditation, as a nontheistic religious naturalist (p. 219). These reflections draw heavily on traditional religious concepts and on readings and conversations, but in the end, each reflection is personal, describing the particular religious/​spiritual sensibility elicited in me when I think about a particular facet of the story. For example, the existence of the Cosmos invokes in me a sense of mystery; the exuberance of biodiversity invokes humility; and an understanding of the evolution of death offers me helpful ways to think about my own death. If the religious naturalist orientation is to flourish, it will be because other writers find themselves called to reflect on the dynamics of Nature from their own cognitive, experiential, and cultural perspectives—​in which case this book will become one of a series of Daily Devotionals. 8

How This Book Is Pu t Together

Human memory, they say, is like a coat closet: The most enduring outcome of education is that it creates rows of coat hooks so that later on, when you come upon a new piece of information about something, you have a hook to hang it on. Without a hook, the new information falls on the floor. Some readers with scanty scientific backgrounds have told me that while they were reading one of my stories about Nature, it felt like they understood everything I said, but the next day they could scarcely remember a thing about it. No hooks, I explain. Then I remind them that there isn’t going to be a test, and that as they were reading they were creating hooks for their next encounters with scientific explanation. And then the important part: The point of hearing a story for the first time is not to remember it but to experience it.

9

Chapter 1

ORIGINS OF THE EARTH INFINITIES AND INFINITESIMALS

T

o our knowledge, everything in our universe, including the Earth and its living creatures, obeys the laws of physics, laws that became manifest in the first moments of time. Much of what we know about the physical universe, like the curvature of spacetime and the behavior of sub-​atomic entities as both particles and waves, is very difficult to conceptualize, even for people who spend their lives thinking about such things (Richard Feynman: “If you think you understand quantum mechanics, you don’t understand quantum mechanics.”). As physicists and mathematicians probe ever more deeply, they present us with ever more mind-​boggling concepts, like the idea that sub-​atomic particles may in fact be minute, vibrating “superstrings” of space, that our four-​dimensional universe may actually be ten-​or eleven-​dimensional, that the observable universe may be much smaller than the true universe, and that there may be other universes besides our own. We are introduced to other stars that also have orbiting planets and presented with ever more bizarre observations about black holes. We learn that “ordinary matter”—​the subatomic particles and luminous atoms that we

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0003

The Sacr ed Depths of Natur e

and the Earth and the stars are made of—​is only ~5% of the universe. Much of the rest (~25%) is enigmatic “dark matter,” which doesn’t interact with light nor with ordinary matter in any way except through gravity. And most (~70%) is the even more enigmatic “dark energy” that participates in the expansion of the universe, characterized by a physicist friend as “pushy-​outty stuff.” Fascinating as these known and speculative manifestations of physics may be, they are not central to our story of life. Why? Because when Earth life was coming into being, some ten billion years after the universe had come into being, the laws of physics were a given. Life had no choice but to originate and evolve in the context of quantum indeterminacy and quarks held together by gluons and gravitational and magnetic fields and thermodynamics. Therefore, while the laws of physics underlie all of life, and constrain what can and cannot occur in living beings, we can describe how life works without referring to them, in much the same way that we can describe what a painting looks like without referring to the light-​absorption spectra of its pigments. What is central to the origination of Earth life is the history of the universe—​the cosmic dynamics that have yielded our galaxy, our star, our planet, and the atoms that form living beings. We can tell the story sparingly, without pausing to define terminology, allowing the flow of events to suggest the enormous times and distances involved.

THE UNIVERSE STORY The observable universe is currently estimated to be 13.8 billion years old. In the beginning, everything that is now 12

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the universe, including all of its ordinary matter and dark matter and dark energy, was concentrated in a singularity, smaller than the size of a pinhead, that was unimaginably hot (100,000,000,000,000,000,000,000,000,000,000 degrees Fahrenheit by some estimates) and unimaginably dense. It all let loose during an event called the Big Bang—​a misleading term in that there wasn’t an audible explosion. Instead, the singularity expanded very rapidly, carrying all the matter and energy with it, accompanied by an event called cosmic inflation that created inhomogeneities in the expanding space. During the first three minutes of this expansion, all sorts of high-​ energy physics took place that yielded the current tally of subatomic particles in the universe, including single protons (hydrogen nuclei), neutrons, and electrons. A small portion of the protons and neutrons went on to fuse into helium nuclei and an even smaller proportion into lithium nuclei. And then things started to settle down, with the space continuing to expand and cool until, after ~400,000 years, temperatures were low enough that the hydrogen and helium nuclei could acquire electron shells and become stable hydrogen and helium atoms. The expansion continued for another 13.8 billion years to yield the present observable universe estimated to be 60,000,000,000,000,000,000,000 miles in diameter. Once hydrogen atoms formed, the stage was set for the creation of galaxies and stars. The spatial inhomogeneities that had formed during cosmic inflation were amplified by the gravitational properties of dark matter, creating huge lumps called dark matter halos. Hydrogen atoms fell into the centers of these halos and initiated star formation. The gravitational field of each proto-​star pulled the hydrogen atoms closer and closer together, colliding with one another in a gaseous state until the temperatures became so 13

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high that they were stripped of their electrons. The resultant hydrogen nuclei then started to fuse, forming new helium nuclei. The fusion reactions released heat, causing the gas to expand and counterbalancing the tendency of the center to contract due to gravity. As a result, each star stabilizes in temperature and mass, burning its hydrogen nuclear fuel. What happens next depends on the mass of the star. Low-​mass stars, which are the most numerous, fuse all their hydrogen nuclei into helium nuclei without going through later stages, while intermediate-​and high-​mass stars follow more dramatic pathways. Once the hydrogen starts to run out in an intermediate-​mass star, its center starts to contract again, eventually becoming so dense and hot that its helium nuclei start to fuse together, forming larger nuclei like carbon, oxygen, nitrogen, and other “light elements” of the periodic table. Such a star, called a red giant, puffs away its outer layers, seeding its galaxy with its newly minted light elements, including most of the carbon in the universe, and leaving behind a remnant known as a white dwarf. A white dwarf may subsequently explode, releasing elements such as calcium and iron. A high-​mass star goes through a red-​giant phase as well, but its core keeps collapsing, getting hotter and hotter and forming heavier and heavier nuclei until it starts to make iron, which can’t be processed further. When a critical amount of iron accumulates, the core is crushed by gravity, and the shock waves generated by the crushing process cause a huge explosion in the star’s outer layers—​a supernova—​releasing its newly forged elements, including most of the oxygen and magnesium nuclei in the universe, and leaving behind a remnant called a neutron star. Neutron stars may subsequently collide/​merge with one another, creating 14

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and seeding the surrounding space with the nuclei of such “heavy elements” as gold, silver, and the radioactive thorium and uranium. The nuclei that are released into space from dying stars proceed to cool, acquire electrons, and become atoms. Some then join primordial hydrogen atoms to form more complex second-​ generation stars. The second-​generation stars proceed to burn their hydrogen, and the more massive ones then collapse, creating new elements in the process. Their released atoms proceed to join primordial hydrogen to form third-​generation stars that are yet again more complex. Such birth-​and-​death stellar cycles are destined to continue into the future, albeit the rate of star formation is decreasing as the universe ages. Stars cluster together within galaxies that are shaped by dark-​ matter halos. Our current universe contains ~200 billion massive galaxies, plus numerous small ones, each populated by ~100 billion stars. Which takes us to our own context: The Milky Way.

THE EARTH STORY The Milky Way (chapter frontispiece) is an enormous spiral galaxy, embedded in and surrounded by its dark-​matter halo, containing ~100 billion stars, and the Sun, located in one of its spiral arms, is a second-​or third-​generation intermediate-​mass star. The Sun is ~4.6 billion years old and has enough hydrogen to burn for another ~5 billion years. As its hydrogen begins to run out, it will follow the sequence described earlier for intermediate-​mass stars, becoming a red giant, and the Earth will spiral into it and be absorbed. Another important feature of the Sun, and any star, is that as it ages, it keeps getting brighter—​more luminous, radiating more 15

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photons—​an effect related to its ever-​increasing content of helium nuclei. A billion years from now, the Sun will be ~10% brighter than it is now, and the resultant heat is predicted to evaporate all the water from the Earth’s surface. It’s important to remember, in reading the previous sentence, that a billion years is a very long time. While the Sun was forming, some of the surrounding material assembled into aggregates that collided and merged with one another and eventually stabilized as its orbiting planets, moons, and comets. Planet Earth acquired generous endowments of iron that formed its broiling core, siliceous magma that formed its thick liquid mantle, and a thin silicon-​based crust that floated on top of the mantle. Gases that were trapped in the Earth’s interior, including water vapor, were released through fissures in the crust and became trapped by gravity to form the early atmosphere. The floating crust then settled into large masses, occasionally breached by volcanic magma, that drift and crash into one another in a slow but continuous geological activity called plate tectonics, defining and redefining the continents and ocean basins. After about a billion years of consolidation—​to repeat, a billion years is a very long time—​the physical conditions on Earth became such that life could originate and continue.

REFLECTIONS I’ve had a lot of trouble with the universe. It began soon after I was told about it in physics class. I was perhaps twenty and went on a camping trip, where I found myself in a sleeping bag gazing up into the crisp Colorado night. Before I could look around for Orion 16

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and the Big Dipper, I was overwhelmed with terror. The panic became so acute that I had to roll over and bury my face in my pillow. • All the stars that I see are part of but one galaxy. • There are billions of galaxies out there, with billions of stars in each one, occupying magnitudes of space that I cannot begin to imagine. • Each star is forming, dying, accreting, dying again, fusing atomic nuclei under enormous temperatures and pressures. • Our Sun too will die, frying the Earth to a crisp during its heat-​ death, spewing its bits and pieces out into the frigid nothingness of curved spacetime. The night sky was ruined. I would never be able to look at it again. I wept into my pillow, the long slow tears of adolescent despair. When I later encountered the famous quote from physicist Steven Weinberg—​“The more the universe seems comprehensible, the more it seems pointless”—​I wallowed in its poignant nihilism, and I froze before Stephen Hawking’s question: “What is it that breathes fire into the equations and makes a universe for humans to describe?” A bleak emptiness overtook me whenever I thought about what was going on out in the Cosmos or deep in the atom, so I did my best to not to think about such things, and thought about biology instead. But since then, I have found a way to defeat the nihilism that lurks in the infinite and the infinitesimal. I have come to understand that I can deflect the apparent pointlessness of it all by realizing that I don’t need to seek a Point. In any of it. Nor do I need an answer to Hawking’s question. Instead I can see it as the locus of Mystery. 17

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• The Mystery of why there is anything at all, rather than nothing. • The Mystery of where the laws of physics came from. • The Mystery of why the universe seems so strange. Mystery. Inherently shrouded in its own absence of category, its own absence of an answer. The word God is often used to name this mystery. A theological view known as Deism, for example, proposes that God created the universe, authored the equations and laws that govern it, orchestrated the Big Bang, and then stepped back and allowed things to pursue their own course. Deism doesn’t work for me because I can only think of a creator in human terms, and the concept of a human-​like creator of muons and neutrinos and black holes has no meaning for me. But more profoundly, Deism spoils my Covenant with Mystery. To assign attributes to Mystery, to give it a name and a mind, is to disenchant it, to take away its luminance. I think of the ancients ascribing thunder and lightning to godly feuds and I smile. The need for explanation pulsates in us all. Early humans, bursting with questions about Nature but with limited understanding of its history and dynamics, explained things in terms of supernatural persons and person-​animals who delivered the droughts and floods and plagues, took the dead, and punished or forgave the wicked. Explanations taking the form of unseen persons and animals were the best option when persons and animals were what we felt we best understood. Now, with our understanding of Nature arguably better than our understanding of persons, Nature can take its place as a strange but wondrous given. The realization that I needn’t have answers to the Big Questions, needn’t seek answers to the Big Questions, was an epiphany. I lie 18

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on my back under the stars and the unseen galaxies and I let their enormity wash over me. I assimilate the vastness of the distances, the impermanence, the fact of it all. I go all the way out and then I go all the way down, to the fact of photons without mass and gauge bosons that become massless at high temperatures. I take in the abstractions about forces and symmetries and they caress me, like Gregorian chants, the meaning of the words not mattering because the words are so haunting. Mystery generates wonder, and wonder generates awe. The gasp can terrify, or the gasp can emancipate. As I dwell within cosmic and quantum Mystery, I wander back through the centuries and encounter the essence of Lao Tzu: The Tao that can be told is not the eternal Tao. The name that can be named is not the   eternal name. The nameless is the beginning of heaven   and earth. The named is the mother of ten thousand   things. Ever desireless, one can see the mystery. Ever desiring, one sees the manifestations. These two spring from the same source    but differ in name. This appears as darkness, Darkness within darkness, The gate to all mystery. Lao Tzu, ~600 BCE

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Chapter 2

ORIGINS OF LIFE

M

ost religions have an account of the origins of life. The Abrahamic traditions offer two narratives: Genesis 1, the spare, poetic account of six days of creation whose sequence, from the simple to the complex, mirrors our current understanding of what happened over billions of years, and Genesis 2, the morality-​ laden account of the garden of Eden. The Pueblo peoples tell of a primordial home beneath a lake where humans, gods, and animals lived together while the earth above was still soft and “unripe.” The Kogi peoples of Columbia describe a Supreme Deity: “The mother of our songs, the mother of all our seed, bore us in the beginning of things. . . . She is the mother of the thunder, the mother of the streams, the mother of trees and of all things.” Certain Hindu teachings speak of the Brahmanda, the cosmic egg from which all creatures came forth. The Yaruro peoples of Venezuela tell of the water serpent Puana who created the world, his brother Itciai, a jaguar, who created water, and their sister Kuma, wife of the Sun, who made the Yaruro peoples. While these are wonderfully engaging narratives, we recognize their cultural embeddedness and their contradictions with our present understandings of the natural world. When we look

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0004

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to science-​based understandings for an origin story, we find a different kind of poetry.

THE PLANETARY MATRIX Geologists speak of the biosphere, the parts of the earth where life is found, but I prefer the concept of a planetary matrix, a matrix that came to include life. The word matrix derives from the Latin mater, meaning both mother and fertile woman, and is translated in late Middle English as womb. The planetary matrix came into being about a billion years before life originated (Chapter 1). Life then emerged from within it, using some of its materials, and flourished within the wondrous and ever-​changing habitats that it provided—​the oceans, skies, lands, and inland waterways. Life has distinctive properties, as we’ll be exploring throughout this book, but volcanos, plate tectonics and the atmosphere have distinctive properties as well. Life is one of the many manifestations of the ever-​transforming planetary matrix, a matrix that Thoreau experienced as being imbued with spirit:

The earth I tread on is not a dead inert mass. It is a body, has a spirit; is organic and fluid to the influence of its spirit and to whatever particle of that spirit is in me. —​Henry David Thoreau, 1851

and a matrix that Rachel Carson experienced geologically: For the differences I sense in this particular instant of time that is mine are but the differences of a moment, determined by our place

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Or igins of Life in the stream of time and in the long rhythms of the sea. Once this rocky coast beneath me was a plain of sand; then the sea rose and found a new shore line. And again in some shadowy future the surf will have ground these rocks to sand and will have returned the coast to its earlier state. And so in my mind’s eye these coastal forms merge and blend in a shifting, kaleidoscopic pattern in which there is no finality, no ultimate and fixed reality—​earth becoming fluid as the sea itself. —​Rachel Carson, 1955

To think about how life might have originated within this matrix, we’ll first look at what chemistry entails and then consider the kinds of chemistry needed to generate the first living organism. The organism we’ll consider, called an autogen, is hypothetical, an invention; no one knows what the first organism was really like. But as we get to know the autogen, we come to understand the basics of what it is to be alive in a biological sense.

THE ORIGINS OF CHEMISTRY In the beginning there was high-​energy physics, but with the cooling of the universe we encounter chemistry. The core participants in a chemical reaction are atoms, whose size is unimaginably small: enlarging an atom to the size of an apple is equivalent to enlarging an apple to the size of the Earth. An atom’s central nucleus carries a positive charge that is balanced by the negative charge contributed by its shell of electrons. When atoms lose or gain electrons from their shells they become either net positively charged or net negatively charged, a process called ionization. Chemistry allows atoms and ions to form various kinds of bonds

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with one another via a sharing of their electrons or a neutralization of their charge, thereby forming minerals and molecules; it also allows smaller molecules to associate into larger molecules. Like everything else, chemistry is reducible to physics, but chemistry takes place only under certain conditions. There are four conditions that are important to our story. • Chemistry requires the flow of energy—​the capacity to do work—​from a source to a sink. The Earth has two massive sources of energy: the Sun, of course, and also its own molten interior, pulsing with radioactivity, that helps warm the oceans and the continents. The energy sink is, ultimately, the universe itself, most of which is only a few degrees above absolute zero. As energy flows, bonds can form between atoms and hence chemistry can occur. • Chemistry cannot occur when atoms are so hot that they fall apart into subatomic particles, as in the interiors of stars. It also cannot readily occur when all the atoms are locked up together as solids. When temperatures are such that atoms and molecules can coexist in their various forms—​solids, liquids, and gases—​this is a sign that the system is enjoying energy flow and that chemistry can proceed. • Some atoms are more likely to engage in chemistry than others. Helium, for example, exists only as helium, whereas carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur—​the Big Six in modern organisms—​are poised to form electron-​sharing bonds with one another under conditions of energy flow: hydrogens readily share electrons with oxygens to form molecules of water; carbons readily share electrons with oxygens to form molecules of carbon dioxide. 24

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• The probability of forming chemical bonds can be influenced by the presence of materials called catalysts—​minerals or molecules that enhance the probability and hence the rate that a given interaction will occur without themselves being chemically altered in the process. Some catalysts are metals, like deposits of iron or copper, whose charged surfaces increase the likelihood that energy flow will occur between interacting atoms. Other catalysts are organic (carbon-​based) molecules called enzymes, whose shapes serve to bring reactants close enough together that bonds are likely to form between them.

EMERGENT PROPERTIES We are now poised to introduce a key concept, called emergence, that will appear in many contexts throughout this book. Stable chemical relationships between materials often generate what are called emergent properties: the tee-​shirt meme for this is “Something Else from Nothing But.” A water molecule is nothing but an oxygen atom and two hydrogen atoms bonded in a V-​shaped configuration, but when many liquid water molecules are frozen, their bonds form an open lattice with the emergent property called buoyancy—​ice floats. Under certain freezing conditions they can also generate the something-​else called the snowflake. A mineral displays the emergent property called its hardness; materials that foster the flow of chemical reactions possess the emergent property called catalytic capacity. Another tee-​ shirt meme: Emergence is Nature’s Mode of Creativity. 25

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THE PRIMORDIAL SOUP So, now back to our story of life’s origins. Two kinds of chemistry were needed to get life going: the chemistry that generated small “molecular building blocks” of life, such as water, carbon dioxide, methane, ammonia, and hydrogen sulfide, and the chemistry that combined these building blocks into larger but simple carbon-​based molecules such as formate, acetate, pyruvate, and urea, collectively forming what is called the “primordial soup.” Building blocks and soup molecules are posited to have been chemically forged in two kinds of factories. The first are tiny specks of matter, about the size of talcum particles, called interstellar dust because they form huge clouds of matter between the stars, soaking up the elements released from stellar catastrophes. Since they are floating out in space, the specks are inherently cold, but as nearby stars pulse them with radiation, they heat and cool, heat and cool, an energy flow that has allowed hundreds of different kinds of small carbon-​based molecules to form on their surfaces. As comets and meteors passed through the dust and crashed into the early Earth, they brought with them cargos of these molecules, which dissolved in its waters and became available to incipient life. The second factories are thought to have been deep-​sea hydrothermal vents, illustrated in the chapter frontispiece, wherein ocean water first seeps into fissures in the Earth’s crust, heats up, and then circulates back into the cold oceans, creating a gradient of energy flow that again permits the chemical synthesis of building blocks and carbon-​based soup molecules.

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THE AUTOGEN MODEL FOR THE ORIGIN OF LIFE We can now ask how life might have emerged out of such a primordial soup. All origin-​ of-​ life hypotheses are by definition speculations since the original lifeform, arising some 3.7 billion years ago, no longer exists, having instead evolved into the DNA-​ based, lipid-​membrane-​based, protein-​mediated organisms that live on Earth today. Considered here is an origin-​of-​life model that says nothing about what the first lifeforms were made of and instead focuses on how they might have organized themselves as stable entities, called autogens, using the soup molecules that were locally available. This allows us to lift up what being alive entails. Simple soup molecules have the potential to form bonds with one another and form larger molecules, but such reactions require a large energy flow and hence rarely occur on their own. Catalysts serve to bring molecules together in particular configurations, lowering this energy requirement and rendering such reactions far more probable. A key feature of the autogen is that it has the capacity to produce its own catalysts, using available soup molecules, and thereby to generate what are called autocatalytic cycles. A drawing of an autocatalytic cycle is shown in Figure 2.1. Soup molecules, generically called substrates, each have an individual shape, represented in the drawing as ovals, rectangles, and diamonds. Starting at the top, two rectangles form a chemical bond between themselves to create molecule B, a reaction catalyzed (+​sign) by molecule A. Molecule B, in turn, catalyzes the bonding of two diamonds to form C, and C catalyzes the bonding of two ovals to form A, and the cycle starts over again, and round

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The Sacr ed Depths of Natur e A catalyzes (+) the synthesis of B from substrates in soup. B catalyzes the synthesis of C from substrates in soup. C catalyzes the synthesis of A from substrates in soup.

A +

+

B

C +

Fig 2.1 Autocatalytic cycle (something else) using primordial soup molecules (nothing but).

and round it goes. As long as substrates are available, more and more of the A, B, and C catalysts will be synthesized. A cycle like the one drawn in Figure 2.1 would quickly come to a halt if the catalysts were to diffuse away from one another—​they need to be close together for the cycle to operate. Hence a second feature of the autogen is that it encloses its autocatalytic sets. Figure 2.2 shows a way that such containment might be accomplished. The upper drawing shows a second version of an autocatalytic cycle: in this case, catalyst C is generated from substrates A +​ B in the soup and catalyst F is generated from substrates D +​E. The key innovation is that F is a multi-​tasker: one of the flat surfaces of its triangular shape serves to catalyze the A +​B reaction, while its 28

Or igins of Life A+B Catalysis

F C D+E

F

A

D

C

B E

Autogen (C + F)

Fig 2.2  Autocatalytic cycle (upper) and autogens formed when catalysts are enclosed within self-​assembling capsids (lower).

edges associate with the edges of other F triangles to form a container or capsid, the catalytic surfaces facing the interior, which encloses sets of C catalysts and substrates. The art in the lower part of Figure 2.2 illustrates the essence of these events: it’s all about molecular shapes and shape-​shape interactions. 29

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The resulting hypothetical entity, drawn in Figure 2.2, is called an autogen. Its sequestered cycles come to a stop once it uses up its sequestered substrates, and it enters dormancy, analogous to becoming a bacterial spore or a seed. But if at some later time the capsid loses its integrity and new soup molecules penetrate it, the cycle starts up again, events drawn in Figure 2.3. The breach would subsequently be prone to re-​seal, but not before new catalysts and capsids molecules are synthesized. A third core feature of the autogen, called replication, is also illustrated in Figure 2.3. Successive rounds of the cycle have generated enough F molecules that, when assembly occurs, two catalyst-​containing capsids—​and hence two autogens—​are able to self-​assemble rather than just one. We need reminding at this juncture that any such original lifeforms presumably operated on a very leisurely time scale compared with the pace set by modern organisms. It might have been thousands of years before the first autogen gave rise to a second.

Substrates

Fig 2.3  Autogen capsid disruption (left) and autogen replication (right).

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There was no reason, of course, to be in any hurry. The important thing was to persist: the autogen became embodied and propagated that embodiment.

EMERGENT DYNAMICS We can now consider the autogen in the context of emergence (p. 25). Each of the soup molecules, and each of the catalysts, and each of the capsid subunits, is nothing but atoms-​bonded-​together, but these interactions generate something else—​distinctive molecular shapes that allow catalysts to interact with substrates and capsid molecules to fit together, as illustrated in Figure 2.2. In addition to these emergent properties that are based on shape, the autogen also displays what are called emergent dynamics. Autocatalysis and containment and propagation are dynamic in that each is causally connected over time: one thing leads to the next which leads to the next; something is happening. Molecular shapes again serve as the nothing-​buts, but in this case they yield emergent dynamics—​the operation of the cycle, the self-​assembly of the capsid, and the propagation of the autogen. Emergent dynamics arise as the consequence of constraints. The law of entropy describes what happens to materials over time in the absence of constraint—​a drift into random homogeneity. Autogens and subsequent lifeforms push back against this tendency by performing highly constrained chemistry, chemistry restricted to the regenerative interactions that keep them alive. The constraints are generated by shapes that render some chemical and morphogenetic associations highly probable, and hence the rest increasingly improbable. By constraining material interactions to 31

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generate useful emergent properties and dynamics, lifeforms are able to reverse the entropic tide and generate order and reproducibility and continuation.

DNA, RNA, AND PROTEIN The autogen displays key features of life—​ self-​ organization, substrate acquisition, propagation—​without possessing a separate coding mechanism to specify these features. By contrast, all modern lifeforms make use of coding systems called genomes, usually DNA-​based but sometimes RNA-​based, whose genes encode instructions for the synthesis of the proteins needed to generate the lifeforms. Proposals are on offer as to how autogen-​ like lifeforms might have become encoded, and many origin-​of-​ life proposals in fact reverse the sequence we’ve presented here, instead suggesting that RNA molecules came first (the “RNA World”), prior to any autogen-​like creature, and then in various ways came to encode embodied beings. In either case, RNA and DNA show up early in all origin-​of-​life scenarios. A key feature of DNA (and RNA) is that it is readily copied and hence distributed to daughter organisms. Four kinds of nucleotide molecules, called A, T, G, and C, line up in a particular sequence—​ e.g., CGCATTCC—​and are then bonded side-​by-​side to form a long strand or polymer called a polynucleotide. The shapes of the nucleotides in the polymer allow them to form associations with free-​floating nucleotides in accordance with the following rule: A always associates with T, and G always associates with C. Once the free nucleotides are lined up by such associations, they form side-​to-​side bonds with one another to create a second strand, a 32

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new daughter strand, whose nucleotide sequence, GCGTAAGG, is complementary to (akin to “the mirror image of”) the mother strand. When the daughter strand is subsequently copied, the CGCATTCC sequence of the mother is recapitulated in the granddaughter strand. The nothing-​buts here are the shapes of the nucleotides responsible for the A/​T and G/​C pairings and the enzymes that catalyze the bonding of the aligned nucleotides into strands; the something-​else is the emergent dynamic called DNA replication. A second key feature of DNA is that it is readily encoded via the sequence of nucleotides along its strands—​the CGCATTCC in our example—​a code we’ll consider in molecular detail in Chapter 5 when we explore the process of evolution. A coding mechanism is inherently just that—​a mechanism, consisting of a set of markers, like an alphabet or syllables, coupled with a process that can interpret them. Its interpretation acquires significance to the extent that it codes for something, something that is of use, like a catalyst in the case of encoded organisms. When coding systems are copied, the capacity to generate more such useful entities is introduced. When coding systems change (mutate), the capacity to generate novel entities arises. In adopting a coding system that employed RNA and DNA, early lifeforms continued to operate using the basic emergent dynamics of an autogen. But their continuation and evolution now came to depend as well on sets of instructions, encoded in polynucleotides, which they then translated into useful dynamics. Encoding offers independence. For example, an early DNA-​ based lineage might come to harbor instructions for synthesizing an essential substrate that it formerly needed to seek out in the primordial soup, generating a degree of autonomy and hence an 33

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expansion in its evolutionary potential. What continued through time was no longer the pattern adopted by a particular self-​ reproducing entity like an autogen, but instead the instructions for generating such a pattern and the possibility of exploring modified or alternative patterns. Life’s dynamics were no longer left to the vagaries of events like substrate availability and container disruption but were now independently specified and sequestered within in an emergent parameter called genetic instruction. We can pause at this juncture to address a key issue. One way to read this account—​a misreading, I will argue, but a common one—​is that the genes are driving the system, that genes are “selfish,” that genes rule. Not only is this misreading inherently depressing and religiously sterile; it also misses the point. While there are indeed examples of “selfish” DNA elements that hitch-​ hike onto existing genomes, the genomes themselves—​the DNA that encodes the instructions for producing organisms—​are in fact the handmaidens of life’s emergent properties and dynamics and not the other way around. Genomes represent a splendid convenience, a repository in the back room, consulted as needed, allowing organisms to be generated ever more efficiently and with increasing levels of dynamic complexity. But they are useless unless they confer organisms with the capacity to execute and regulate these dynamics. We were able to posit an autogen without an operational genome, but a set of genes that fails to specify or parasitize an operational organism is dead on arrival. The emergent outcomes generated by DNA-​based organisms are called biological traits; collectively they constitute the organism writ large. It is traits that rule; genes follow in their wake. Traits common to all organisms include purposiveness, awareness, and the pursuit of well-​being; traits common to social 34

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organisms include cooperation and sacrifice; traits common to birds and mammals include bonding and nurturance; traits common to humans include the ability to acquire symbolic language and hence share subjective experience. Transmission of mutable genomes is the steady drumbeat that keeps the whole life thing going; organisms, embedded in their planetary contexts, are the rest of the music.

THE SELF The origin of life marks a momentous event: the origin of the self. We usually use the word “self” to refer to our experience of being a person: we speak of having a narrative self, an I-​self, an identity. This human understanding of self will be explored in Chapter 7. But we can also use the word self to describe every organism, all the way back to autogen-​like beings, without imposing the stricture that they be aware of being a self. Each self is capable of doing self-​directed work. We can say that the autogen self-​maintains, using substrates from the soup to form its catalysts and containers; it self-​protects, sequestering catalysts within dormant containers; it self-​repairs, regenerating denatured catalysts and re-​sealing a disrupted capsid; and it self-​replicates, giving rise to daughter autogens. All present-​day lifeforms also engage in self-​ maintenance, self-​ protection, self-​ repair, and self-​replication. Most present-​ day selves are unicellular, including bacteria, archaea, protists, and most algae. We can think of them as one-​ man bands. Some selves, like us, are multicellular orchestras, the outcome of a collaborative project undertaken by many kinds of 35

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differentiated cells (liver cells, leaf cells) that collectively generate a single whole, a single self. Viruses and other parasites commandeer the self-​directed work of cells to generate infectious versions of their own selves. A foundational feature of all selves, be they unicellular or multicellular, is that they have aims. They embody teleology (end-​ directedness). Each self aims to make things happen, and it does so by generating constraints that channel energy into work that regenerates these selfsame constraints. Each set of aims has a collective goal –​to stay alive, to keep the self from falling apart. Hence the advent of selves marks the advent of purpose, not only on Earth but anywhere in the universe where selves come into being.

REFLECTIONS The origin of life has long been considered a miracle wrought by gods or God or Spirits. Now life can be understood as the perhaps inevitable consequence of our entangled thermal and chemical context—​our planetary matrix—​that fostered and continues to foster life’s emergent properties and dynamics. Miracle, from the Latin miraculum, in fact means an object of wonder. We can gasp in wonder at the miraculous origin of life without the need to invoke supernatural design or agency. Each lifeform is a self and each self has a purpose. In many religious contexts, Purpose is spelled with a capital P—​as in what is the Purpose of my life? The monotheistic credos, for example, tell us that one’s Purpose is to act out the will of God. The religious naturalist instead joins the East Asian and indigenous religions in 36

Or igins of Life

dwelling within a lower-​case understanding of purpose: the exuberant purposive dynamics that spring forth from every creature, every self, and infuse our every moment. Who made the world? Who made the swan, and the black bear? Who made the grasshopper? This grasshopper, I mean—​ the one who has flung herself out of the grass, the one who is eating sugar out of my hand, who is moving her jaws back and forth instead of up and down -​ who is gazing around with her enormous and complicated eyes. Now she lifts her pale forearms and thoroughly washes her face. Now she snaps her wings open, and floats away. I don’t know exactly what a prayer is. I do know how to pay attention, how to fall down into the grass, how to kneel down in the grass, how to be idle and blessed, how to stroll through the fields, which is what I have been doing all day. Tell me, what else should I have done? Doesn’t everything die at last, and too soon? Tell me, what is it you plan to do with your one wild and precious life? —​Mary Oliver, “The Summer Day”

The word “self” can suggest selfishness, going-​it-​alone, and the first self was most certainly a go-​it-​alone entity since, by definition, it inhabited an otherwise sterile planet. But as selves multiplied and evolved, their environments came to include other selves—​of their own kind and other kinds—​that both enabled and disrupted their flourishing. Many of their relationships entail communication, leading to the evolution of a myriad bacterial quorum sensors and insect pheromones and alarm calls and the like. Trees use their root systems and fungal mycorrhizal networks to communicate 37

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vital information about themselves to one another, and structured social lifestyles have evolved in numerous animal lineages, including our own. Hence the goal of a present-​day self is not only to be fit, to thrive within the physical parameters of its environment. Its goal is also to fit in, where thriving plays out in the context of the playing out of other lives. Our planetary matrix teems with the interactions and the interdependencies of selves within their geological habitats. The purpose of it all is that the selves, and hence their habitats, continue to flourish, where I, for one, would spell purpose here with a capital P. When we describe the geological world, we often use metaphoric personifications –​we might speak of the joy of the river freed of her pollutants, or the furor of a hurricane, or the anger of a decapitated mountain. This is the way we think (p. 8). Perspectives known as animistic go beyond such metaphors and include the belief that all of the entities in the planetary matrix—​not only the animals, plants, amoebae and bacteria, but also the rocks, mountains, rivers, oceans and clouds—​are actually living. Versions of animism are found in indigenous, Asian, and Celtic traditions and in some present-​day pagan orientations, and are of spiritual importance to many. The passage quoted earlier from Thoreau (p. 22) could be said to articulate this concept. Such animistic understandings of life clearly differ from the concepts of life that we’ve been developing in this chapter. A rock gives no indication that it is a self with aims, that it endeavors to roll down a hill or undergo erosion or internal crystallization; these things apparently happen as the consequence of its mineral composition and its geothermal circumstances. Hence the belief that a rock is living is based on a different set of understandings of 38

Or igins of Life

what is meant by living, where the animistic understandings are often said to be ascertained by “other ways of knowing.” I’ve not as yet been able to access these other ways of knowing, perhaps mirroring my inability to access connection with supernatural deities (Chapter 10). Hence my spiritual practice instead entails the joy of connecting with rivers and mountains not as living beings but on their own terms, sui generis—​marveling at their inherent magnificence, their inherent river-​ ness and mountain-​ness, and offering them my deepest respect and reverence. I hold a rock in my hand and I resonate with its heft and its patterns; I try to imagine its broiling history within the Earth’s interior; I rejoice in our co-​habitation within the planetary matrix; and I absorb the understanding that our atoms all came from the same stars, and that some of my atoms will come to inhabit rocks and that some of its atoms will come to inhabit lifeforms. For me, a belief that this rock is living, were I able to hold such a belief, would disrupt my potent immersion in its geological essence. The same goes for rivers and mountains.

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Chapter 3

HOW LIFE WORKS

E

ven well into the past century, even after it was clear that life works through myriad chemical reactions and that the instructions needed to set up this chemistry are encoded in genes, there were scientists who continued to believe that living systems also possessed an élan vital, a vital force, akin to the Hindu concept of prana, the vital breath that animates all beings. Although science-​based paradigms no longer invoke such a force—​we are convinced that life emerges from self-​constrained chemistry—​the sense that it exists is so widespread, so deeply rooted, that it almost seems instinctive. One explanation for the persistence of vitalism is that it serves as a bulwark to fend off reductionism. We are told that life is so many manifestations of biochemistry and we shudder, a long existential shudder. And then we defend. We dig in our heels and say No! That can’t be all it is! That does to life what astrophysics does to the night sky. Life reduced to its component molecules is life demeaned. Stop saying things like that! For me, a helpful way to think about reductionism is to invoke what we can call the Mozart metaphor. A Mozart piano sonata is a wondrous thing, beautiful beyond belief, sonorous, resonant, transporting. But it is also about notes and piano keys. Mozart’s

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0005

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magnificent brain conceived the work, to be sure; he then transcribed it into black specks on white paper to be translated into strings hit by tiny hammers to create vibrations heard by ears. We can thrill to a sonata without giving a thought to its notes. But we can also open up a score and follow the notes, or play them ourselves, without having the music diminished or demeaned. It is another way of experiencing the whole and, indeed, the only way to have a full understanding of what the sonata entails and what Mozart had in his mind. So let us go, then, to life reduced to its spare renderings, to the strings and hammers (the working parts) and the notes (the instructions) that generate the emergent properties and dynamics of all beings. I can assure you that it is very beautiful where we are going and not hard to understand.

THE MACROMOLECULES IN MODERN ORGANISMS The first lifeform—​modeled as an autogen in Chapter 2—​was doubtless a very simple creature, but things didn’t stay that way. As time elapsed, encoded lifeforms acquired the ability to synthesize the five kinds of macromolecules shown in Figure 3.1 that are essential to all present-​day creatures and hence essential to our story. To my science-​wary readers, a reminder: Figure 3.1 isn’t going to be on a test. It’s a photo gallery of the protagonists in our narrative. • RNA (RiboNucleic Acid) is a chain (polymer) of four small nucleotide molecules (p. 32), called A, G, C, and U, that

42

How Life Wor ks B. DNA

A. RNA

Adenine

Adenine N

H2N N

N

O

H

N

H

O

NH2 N

H

NH3

H

RNA

H

NH3

O

Thymine

O

H3C

N–H N

N

N N

O

Uracil H

H N

NH2

N N

N

Cytosine

Cytosine H

N

H–N

N

H

N

Guanine

Guanine H–N

H

N

N

H

N

H2N

H

H

DNA

O

H–N

O N–H O

D. Phospholipids in bilayer C. Protein

E. Polysaccharide (cellulose) CH2OH

CH2OH

CH2OH

H C O O O H C H C H H H C OH H C O C OH H C O C OH H C O C C C H C H C C H H

OH

H

OH

H

OH

Fig 3.1  Macromolecules essential to modern life.

usually exists as a linear strand (Figure 3.1A), but can fold back on itself, via A-​U and G-​C associations, to form finger-​like projections. In some cases, such RNA shapes are able to function as catalysts, enabling the formation of bonds between other molecules.

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• DNA (DeoxyriboNucleic Acid), a cousin of RNA, is also a polymer of A, G, and C but uses T rather than U and a different sugar. In its most stable configuration, two single-​ stranded DNA polymers associate with one another to form the famous double helix (Figure 3.1B), where one strand is the mother and the other is its daughter formed during DNA replication (p. 32). The “rungs” of the helix represent the A-​T and G-​C pairs that associate during the copying process (p. 32). • Proteins are polymers of small molecules called amino acids that also interact with one another to generate shapes. Protein shapes are more nuanced than RNA shapes, displaying pro­ tuberances and pockets and long straight parts and tightly coiled parts (Figure 3.1C and the chapter frontispiece), and they are responsible for most of the catalysis and morphogenesis in modern organisms. • Lipids are a diverse group of carbon-​based molecules whose common feature is their low solubility in water. Particularly important to life are phospholipids, each of which carries two fatty-​acid polymers that are prone to line up next to and opposite one another to form bi-​layered films, akin to soap bubbles (Figure 3.1D). These serve as the backbones of cellular membranes. • Polysaccharides are polymers of sugar molecules that are particularly abundant in the walls of fungi and insects (chitin) and plants (cellulose). Indeed, cellulose (Figure 3.1E) is the most abundant macromolecule on the planet. These five kinds of macromolecules collaborate to generate all forms of modern life. 44

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THE INSTRUCTIONS Every modern organism possesses a key feature that is absent from the posited autogen, namely, a complete set of instructions for how to make all of its components, instructions that are copied when the organism reproduces (Chapter 2). The instructions were likely first stored in RNA, but in modern organisms they are stored in the more stable DNA. DNA uses a code to specify the sequences of amino acids in protein chains. Each segment of DNA that encodes a protein is called a gene, and the collection of all the genes necessary to specify an organism is called its genome (the human genome, for example, contains ~23,000 genes). For a lineage to continue, the entire genome must be copied and then transmitted to the next generation, much as we now have numerous copies of the complete works of Mozart. We will have more to say about codes and genes and genomes in coming chapters. Here we will focus on the proteins encoded by genes, since they are the key players in virtually all of modern life’s operations.

PROTEINS Modern creatures are organized as cells, which are usually very small (0.01–​ 0.1 millimeters). Each modern cell resembles an autogen in two key respects: (1) it is surrounded by a fatty membrane (Figure 3.1D) that keeps the outside out and the inside in, equivalent to the capsid of the autogen (Figure 2.2); and (2) its aqueous interior, called the cytoplasm, is filled with molecules 45

The Sacr ed Depths of Natur e

that collaborate to carry out self-​maintenance, self-​protection, self-​repair, and self-​reproduction. In the autogen model, the nature of these molecules was left unspecified. In modern cells, most of these molecules are proteins. Proteins are synthesized by molecular machines called ribosomes that typically occupy 30% of the cytoplasm and whose operation consumes 30% of the cell’s oxygen supply. Ribosome architecture is dictated by the shapes created by ribosomal RNA (rRNA) molecules as they fold back on themselves to form loops. Ribosomes associate with linear RNA strands (Figure 3.1A), called messenger RNA (mRNA), that have been copied (transcribed) from the nucleotide sequences of genes using the same A-​T(U)/​G -​C pairing rules that we saw earlier for DNA replication (p. 32). Amino acids are lined up in the order specified by each associated mRNA, following a simple coding paradigm (Chapter 5), and the ribosome then catalyzes a bond, called a peptide bond, between each aligned amino acid, creating a chain called a polypeptide, much like those chains of cut-​out paper dolls connected by their hands and feet. As the chain elongates, it passes through a ribosomal exit tunnel and into the cytoplasm, or into a designated compartment within the cytoplasm, where it engages in its biological activity. Polypeptides are made of 20 different kinds of amino acids—​in our analogy, 20 different colors of paper dolls—​each with its own properties: glycine is small and greasy; phenylalanine is bulky and greasy; aspartic acid is long and slender and carries a net negative electrical charge. Since the instructions in a given gene, and hence its mRNA transcript, dictate the sequence of amino acids in a given polypeptide chain, one chain might start out with a glycine linked to a phenylalanine linked to an aspartic acid linked to another 46

How Life Wor ks

phenylalanine for a total length of 152 amino acids; a second chain might start out with tryptophan linked to glycine linked to aspartic acid for a total of 433 amino acids. Once one of these polypeptide chains is synthesized by the ribosome, it folds into a 3-​D jigsaw-​puzzle shape to form a protein with distinctive domains (Figure 3.1C and chapter frontispiece). Amino acids that prefer to be next to one another, like greasy ones, might associate to form a domain that associates with the fatty acids in cell membranes; amino acids with negative charges might line up next to amino acids with positive charges and stabilize the shape of a second domain; a bulky amino acid might cause a protuberant domain to stick out farther. Folding happens spontaneously, generating a protein with a distinctive overall shape and size. A second chain with a different sequence of amino acids will self-​assemble into a protein with a different overall size and a different set of folds. Dynamic functions, like enzyme catalysis, emerge from the nothing-​buts of protein folds, and the folds emerge from the nothing-​buts of amino-​acid shapes and their chemical properties. Emergence builds on emergence. So you’re doing a jigsaw puzzle, and you pick up a piece of sky that looks discouragingly like all the other pieces of sky, but you know to focus in on what’s important—​the shape and size and placement of the protuberances that you know are going to have to fit exactly into the pockets of adjacent blue pieces, yielding edges that are flush with one another. While some proteins act alone, most fit together in just this way to produce multiprotein complexes that perform most biological functions. The chapter frontispiece, for example, models a domain of a human antibody protein (upper) associating with a domain of the coronavirus spike protein (lower), where their topological fit triggers immune responses. 47

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Pockets are particularly important to proteins called enzymes, since it is in these pockets that biochemistry usually occurs.

ENZYMES Enzymes are catalysts, enhancing the probability of chemical-​ bond formation between substrates (p. 25). We introduced generic catalysts when we considered the autogen in Chapter 2; we can now zoom in on how present-​day proteins carry out catalytic activity in present-​day cells. When an enzyme folds into its three-​dimensional shape, some of the pockets that self-​assemble on its surface are shaped to interact with substrate molecules that the cell seeks to manipulate chemically. Consider an enzyme that takes a molecule of the sugar glucose and a molecule of the sugar galactose and facilitates the formation of a chemical bond between them to create glucose-​ galactose, also called lactose, the predominant sugar in milk. This enzyme will have a pocket that is just the right shape for a glucose molecule to fit into and an adjacent pocket that’s just the right shape for galactose, as drawn in Figure 3.2. What happens next is a bit hard to explain, but it’s the critical step. Once both sugars are snuggled into their pockets, the enzyme is no longer the same. Instead of empty pockets it has full pockets, meaning that the amino acids in these domains no longer have the same neighbors that they used to have, allowing them to form new associations. These new relationships cause the domains to flip into new configurations—​the pockets change shape—​and the glucose and galactose are brought close enough together to form a chemical bond, as drawn in Figure 3.2. The new lactose molecule 48

How Life Wor ks

OH OH

OH O

HO

OH

O

HO OH

O OH

Fig 3.2  Enzyme (black blob) bringing two sugar molecules together to facilitate their chemical bonding (red bar).

then pops out, the enzyme resumes its original shape, and the process starts over again. If you put many glucose and galactose molecules in a jar of water and wait a long time, two of them might spontaneously form a lactose molecule. But if you add our enzyme, the jar will quickly fill up with glucose-​galactose pairs. By offering its pockets so that the two substrates are constrained to line up just so, and by then changing its shape so that the reactive parts of the sugars are constrained 49

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to come together just so, the enzyme greatly enhances the probability that an electron-​sharing chemical bond will form—​the hallmark of biological catalysis. And that’s basically all there is to modern biochemistry. Each cell is packed with thousands of different kinds of enzymes, each able to catalyze one or several specific chemical reactions. Some, like our example, catalyze the formation of chemical bonds between substrates, while others catalyze the disruption of chemical bonds so that smaller molecules are generated from larger ones. Yet another might take lactose and add a third sugar on to it, and then a fourth, until a long chain, a polysaccharide (Figure 3.1E), is generated. The same kinds of recursive operations produce our key cellular components (Figure 3.1): long polymers of amino acids in proteins, long polymers of nucleotides in DNA and RNA, long polymers of acetate in fatty acids, and long polymers of sugars in polysaccharides. Last but hardly least, enzymes can self-​organize into cycles, much like the autocatalytic cycles of the posited autogen (Figures 2.1 and 2.2). An important example, called the Calvin-​Benson cycle, is found in all photosynthetic bacteria, algae, and land plants. An ancient enzyme called Rubisco catalyzes the bonding of atmospheric CO2 to a 5-​carbon sugar, forming a 6-​carbon sugar. Additional enzymes convert this to several additional kinds of sugars, eventually regenerating a 5-​carbon sugar that acquires another CO2 via Rubisco. And round and around it goes, producing more and more of the sugar molecules that feed all of life on Earth. Once the Calvin-​ Benson cycle was invented, organisms no longer needed to depend on the vagaries of primal soup molecules to keep themselves alive; they could either perform photosynthesis themselves or ingest nutrients that ultimately derive from photosynthetic sugars. 50

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Figure 3.3 displays the biochemical pathways, collectively called intermediary metabolism, that are operant in the human, where the astonishing complexity is evident even when it’s not possible to read any of the words. In the center is a second cycle, called the Krebs cycle, found in all aerobic organisms, which feeds sugar metabolites into linear biosynthetic pathways that generate amino acids and nucleotides and fatty acids and polysaccharides. This is how we roll. Figure 3.3 illustrates complexity, and it also illustrates constraint. Each pathway is catalyzed by enzymes whose shape renders the occurrence of a particular chemistry far more likely than other outcomes. Our human pathways have ancient origins: a diagram of a yeast cell or an aerobic bacterium would look very similar to Figure 3.3, with the same enzyme families catalyzing the same emergent outcomes. This how all of us roll.

BIOPHYSICS In addition to biochemistry, many cellular processes rely on the electrical properties of atoms. Atoms such as hydrogen, sodium, potassium, and calcium are prone to lose one or more of their electrons and become positively charged ions, while chlorine atoms and phosphorous compounds are prone to gain one or more extra electrons and become negatively charged ions. Charged ions in the environment are unable to move directly across the fatty membrane surrounding the cell (Figure 3.1D); therefore, they enter the cell via protein complexes, aptly called channels, that span the membrane. Each channel recognizes a particular ion and regulates its flux by changing the shape of its tiny internal pore. Also 51

Fig 3.3 Human metabolic pathways. For higher magnification, go to https://​www.pathw​ayz.org/​Tree/​Plain/​BIOC​HEMI​CAL+​PATHW​AYS

How Life Wor ks

embedded in membranes are protein complexes called pumps, which use chemical energy to move positively charged ions into a cellular region that is already positively charged, or negatively charged ions into a negative region, creating what are called ion gradients or electrical gradients. Ion gradients are key to the formation of small energy-​rich molecules called ATP, which collaborate with catalysts to drive numerous biochemical reactions and are essential to all lifeforms. In aerobic organisms, positively charged hydrogen ions (protons) are first driven to the outside of specialized membranes in an oxygen-​ dependent metabolic process, generating an outside-​to-​inside proton gradient. As the protons flow back across the membranes via proton channels, protein complexes adjacent to the channels are induced to rotate, in the plane of the membrane, at an astonishing ~100 revolutions per second. The rotation, in turn, activates adjacent enzymes called ATP synthases and leads to the formation of ATP molecules. Mind-​blowing. In addition to ion channels, cell membranes are spanned by channels called transporters that mediate the uptake of external nutrients from the environment and the bloodstream. Again, each is specific: a glucose transporter opens its pore only when glucose fits into an external domain; a lactose transporter is specific for lactose. Knowing this much, we can now step back and watch what’s going on inside a cell as if we were watching a movie. As we watch, we realize that life proceeds as a series of shape changes. We might observe three proteins fitting together to assemble a calcium ion channel that spans the cell membrane and watch the pore of the channel expand in size to allow calcium to enter the cell from the outside when it is needed. We’d next observe that the calcium flux 53

The Sacr ed Depths of Natur e

causes an internal enzyme to change its shape such that certain pockets, previously buried in its interior, become exposed. These pockets are now available to catalyze some biochemistry, one product of which goes on to induce yet another protein to change its shape, perhaps with the assistance of ATP, until we finally witness the functional outcome, such as motility or secretion, which again entails numerous shape transformations. And all the events that we’ve just described would typically occur within seconds.

BIOCHEMICAL AND SIGNAL TRANSDUCTION CASCADES In modern organisms, enzyme-​ catalyzed pathways may self-​ organize as recursive cycles, like the Calvin-​Benson and Krebs cycle examples (pp. 50–51), but they usually self-​organize as cascades, one thing leading to the next leading to the next—​analogous to a series of small waterfalls tumbling down a hill, each feeding the next, start to finish. Many hundreds of such biochemical cascades are represented by the straight lines in Figure 3.3. Cascades are also central to awareness—​the cell’s ability to distinguish and respond to features of its environment. We will consider awareness writ large in Chapter 7; here we can look at its molecular features. Awareness is usually mediated by proteins called receptors that span the outer membrane of a cell along with channels and transporters. One domain of a receptor faces outward, into the environment; a second domain bridges the membrane; and a third faces the cytoplasm. The outer domain carries a pocket that is shaped to fit some relevant molecule in the external world. 54

How Life Wor ks Inside Cell

Cell Membrane

Outside Cell

A

B

C

D

E

Fig 3.4  Odorant receptor binding odorant and initiating signal transduction cascade.

For example, the cell membranes in your nose are studded with receptors shaped to fit particular odorants. Figure 3.4 depicts such an olfactory receptor, whose outer pocket is shown associating with an odorant molecule (Figure 3.4A). Just as we saw with enzymes (Figure 3.2), this pocket-​occupancy causes the receptor to change its shape (Figure 3.4B), a shape change that propagates through its membrane-​spanning domain and stimulates the creation of a round-​shaped pocket in its interior domain (Figure 3.4C). A round molecule in the cytoplasm can now snuggle into this new site and the receptor, now acting 55

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as an enzyme, catalyzes a change in its shape (it acquires “ears”) (Figure 3.4D) such that it can interact with yet another molecule and bring about a change in its shape, perhaps triggering the opening of a channel to let in some sodium. And so on, down the line, one shape change stimulating the next until the organism experiences the odor. The signal—​the presence of the odorant—​ is said to set off a signal transduction cascade: the receptor transduces the external signal into a cascade of biochemical and biophysical responses. Even those of us trained in thinking about signal transduction cascades are astonished at their speed. All the events drawn in Figure 3.4, plus a great deal of brain-​centered biophysics necessary to process and evaluate the odor, takes place well within a second. We know this by experience, of course—​we know how long it takes to smell something—​but our intuition gives us no hint as what is going on during that second. If we now back off and watch the action more globally, we realize that the cytoplasm of cells like ours is set up to optimize the flowing of cycles and cascades. Proteins destined to interact with one another are endowed with domains called addresses that target them to common cellular locations. Each destination is set up to be optimal for particular biochemical reactions—​some locales are fatty and stolid, others aqueous and fluid, some acidic, some loaded with calcium—​and each is delimited by its own boundary, usually an intracellular membrane. Some of these compartments, like mitochondria and chloroplasts and the nucleus, retain their identity, but many undergo elaborate branching and anastomosis, mixing their membranes and products and then separating again. Thus each of our cells is like a community, its inner workings segregated into interacting compartments, its 56

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outermost membrane defining its interactions with the rest of the world.

CELLULAR HOMEOSTASIS Metabolic and biosynthetic cascades, channels and transporters and pumps and receptors, collectively establish what is called cellular homeostasis. Homeostasis literally means staying the same, but the process is hardly static; instead it involves making continuous adjustments. Too much calcium? Fire up the calcium pumps to get rid of it. Too little? Open up the calcium channels to let some in. The goal is to maintain a balance that is optimal for the smooth operation of that kind of cell given its ambient conditions, a balance conducive not just to survival but to flourishing. The same homeostatic dynamics also operate in multicellular bodies that have tissues and organs: Blood sugar levels too high? Secrete one set of hormones. Too low? Secrete a second set.

THE SONATA The notes are hammered by the piano keys and out flows the emergent sonata. Our attention might focus downward on the genomic DNA sequence of a wild rose, and then shift upward to take in some beautiful flowers, and then move back down to the cytoplasmic compartments swollen with red pigment to give the petals their flush. We reduce, and then we synthesize, and then we find another occasion to reduce. How did Mozart generate that modulation into B-​flat? Ah, with that chord. How lovely. 57

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REFLECTIONS Reductionism generates a hierarchy of truths. The hierarchy is not about parts versus wholes; it’s about sub-​wholes: when you look down, it feels like you’re looking at the whole thing, but when you look up, you realize you’ve only been looking at one aspect of what’s going on. To be sure, the wholes display emergent properties and dynamics that the parts do not, but this does not mean that the parts are somehow irrelevant, or somehow untrue, since it is from the parts that the wholes emerge. Reductionism is not the only operation that scientists know how to perform, as some people seem to believe, but reductionism is the operation that constantly monitors whether our understandings work all the way down. We reduce so that we are able to understand what the nothing-​buts are and what they are doing, and then we synthesize. Engagements in reductionism eventually encounter matter. Poor matter. This magical stuff that undergirds everything that we are is so often given disparaging qualifiers like “mere” matter or “just” matter or “only” matter. Loyal Rue calls it “the grunge theory of matter.” Religious naturalists instead offer a paean to matter: During the course of epic events, matter was

distilled out of radiant energy segregated into galaxies collapsed into stars fused into atoms swirled into planets spliced into molecules

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mutated into species compromised into thought, and cajoled into cultures.

All of this is what matter has done as systems upon systems of organization have emerged over thirteen billion years of creative natural histories. —​Loyal Rue

We also offer a paean to cellular homeostasis. In a musical composition, the chords and melodies and rhythms create sub-​wholes from which emerge the collective opus, the sonata, and during the composition process, ideas are discarded that imbalance the whole and ideas are added that help bring everything together. This same dynamic plays out continuously in every cell in every organism, and the cells don’t even need to “think it through”: excesses are pruned and shortfalls are replenished via a beautiful network of feedback and crosstalk to generate not only a viable cell but the best possible cell under the circumstances. We can recite the Mozart metaphor and the paeans to matter and homeostasis, and we can develop a deep understanding of, and admiration for, the notes and the strings and the keys of life. As a cell biologist immersed in these understandings, I experience the same kind of awe and reverence when I contemplate the structure of an enzyme or the flowing of a cascade as when I watch the moon rise or visit Machu Picchu. Same rush, same rapture. But many of us, and scientists are no exception, are vulnerable to the existential shudder that leaves us wishing that the foundations of life were something other than just so much biochemistry and biophysics. The shudder, for me at least, is different from the

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encounters with nihilism that have beset my contemplation of the universe (Chapter 1). There I can steep myself in cosmic Mystery. But the workings of life are not mysterious. My body is some 30 trillion of my own cells, plus some 40 trillion resident bacterial cells, differentiated into >200 cell types that occupy some 80 organs, all integrated by hormones and by ion fluxes flowing along my nerve cells. My thoughts and feelings are the result of neurotransmitters squirted on my brain cells. I look in the mirror and see the mortality and find myself fearful, yearning for less knowledge, longing to believe that I have an immaterial soul who will go to heaven and soar with the angels. William James: “At bottom, the whole concern of religion is with the manner of our acceptance of the universe.” The manner of our acceptance. It can be disappointed or resentful or fearful, or it can be the active response we call assent. When my awe at how life works gives way to self-​pity because it doesn’t work in ways I would have preferred, I call on assent—​the age-​old religious response to self-​pity, as in “Why Lord? Why this? Why ME?” And then, “Thy Will Be Done.” As a religious naturalist I say “What Is, Is” with the same bowing of the head, the same bending of the knee. Which then allows me to say “Blessed Be to What Is” with thanksgiving. After all, life had no choice but to use matter when it originated and evolved. Matter was the only thing on offer, the only game in town (p. 12). And it has turned out to be wondrously creative stuff. To give assent is to understand, incorporate, and then let go. With the letting go comes that deep sigh we call relief, allowing the joy-​of-​being-​alive-​at-​all to come tumbling forth again. Assent is a dignified word. Once it is freely given, one can move fluidly within it and beyond it. 60

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he Mozart metaphor began with our delight in the sonata. We then acknowledged that the music was the consequence of notes and hammers and strings. Invoking the concept of emergence (p. 25), we can now say that the music emerges from the notes. But there’s an intermediate level of emergence as well. From the notes emerge chords and phrases and tempos and melodies, and from these emerge the sonata as a whole. In the middle there are musical patterns. In biology it is the same. The biochemistry and biophysics are the required notes; they combine, collectively, to generate the experiencing unit of life—​the organism, the self. The intermediate level, the chords and tempos, relates to how the biochemistry and biophysics are organized, arranged, played out in space and time to produce an emergent creature who grows and propagates and is. In the middle there are biological patterns. The chords and tempos are orchestrated by regulating the expression of genes. The 23,000 protein-​encoding genes in your DNA genome are present in every cell in your body, but they are selectively expressed: the hemoglobin-​encoding gene is “ON” in the precursors to your red blood cells and “OFF” everywhere else; the insulin-​encoding gene is “ON” only in your pancreas.

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0006

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Not only that, each gene has a dimmer switch: the expression of the hemoglobin-​encoding gene is upregulated when you are at high altitudes; the insulin-​encoding gene is upregulated when blood-​sugar levels exceed a threshold. And many of the genes are regulated in time, such as those that control day/​night circadian rhythms, or cell-​division cycles, or the development of an embryo. Each gene encodes the sequence of amino acids of a protein, which in turn folds to adopt its functional shape and proceeds to participate in cellular processes (pp. 44 and 47). An organism emerges when the expression of these genes is coordinated and regulated in time and in space. We will start by following such events in a single-​celled amoeba (illustrated in the chapter frontispiece), since once there is an understanding of how an amoeba is orchestrated, most of the story falls into place. We will next consider the ways that multicellular patterning is different from amoebic patterning. And finally, we will reflect on experiencing the sacredness of our individual selves within this biological context.

REGULATION OF GENE EXPRESSION IN TIME The genome of an amoeba contains all the genes, all the instructions, for making all the proteins needed to generate that particular kind of an amoeba. Each protein has an address that tells it where to go in the cell, and each protein has a shape that dictates what it will associate with and the biochemical/​biophysical consequences of that association. Fine. But the trick to crafting an amoeba’s life out of this arrangement is to do one more thing: regulate the 64

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expression of these genes so that the proteins come and go as they are needed. Each gene has two contiguous segments: one, called the downstream sequence, encodes a protein; the other, the upstream sequence, encodes a switch that regulates the expression of its downstream neighbor. The downstream nucleotides are read off (transcribed) as messenger RNA (mRNA), and the mRNA is de-​ coded (translated) into protein sequences by ribosomes (p. 46). By contrast, the upstream nucleotides, called promoters, don’t encode protein sequences at all. Instead, they are recognized by proteins called activators and repressors—​collectively called transcription factors. When they bind a to promoter, the gene’s expression is either activated or repressed. Let’s look at an example. The job of the lactase enzyme is to catalyze the breakdown (metabolism) of the sugar lactose—​reversing the job of the enzyme depicted in Figure 3.2 which catalyzes the formation of a bond between glucose and galactose to form lactose. The lactase-​encoding gene is ordinarily OFF because amoebas don’t usually encounter lactose in their environment so it’s not needed, but should an amoeba crawl into a lactose-​rich environment, lactose is taken up by lactose transporters, the lactase gene is switched ON, lactase is made, lactose is cleaved, and the resultant glucose and galactose can be used as nutrients. How does this work? Embedded in the amoeba’s outer membrane are lactose receptors that display pockets shaped for lactose molecules. When they bind, the receptors change their shape, much as we saw earlier for olfactory receptors (Figure 3.4). This sets off a signal-​transduction cascade that eventually brings about a shape change in an activator such that it now recognizes, and binds to, the promoter of a 65

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lactase gene, triggering transcription of the downstream lactase-​ encoding sequences. Hence the sugar lactose is wearing two hats here: it is taken up as a food source, and it elicits the production of enzymes that catalyze its conversion into usable sugars. Once an adequate number of lactase enzymes has been produced, a second signal-​transduction cascade is triggered that leads to a reversal of the activator’s shape change so that it no longer binds to the promoter, and the lactase gene is switched OFF. A repressor protein may now come along, bind to a different region of the promoter, and inhibit expression more definitively. Further repression may then be imposed by what are called epigenetic modifications of the DNA itself and its associated proteins. An amoeba’s genome encodes some thousand different kinds of activators and repressors that govern the expression of thousands of genes. Each transcription factor is a protein, meaning that each is encoded by its own gene that possesses its own promoter and is subject to its own set of activators and repressors. So where does all of this end? It all gets coordinated by a series of complex feedback loops, reminiscent of the biochemical pathways we marveled at in Figure 3.3. And any failure in the system can have deleterious or lethal consequences. If the lactase promoter were to undergo a mutation such that a single nucleotide is changed, the activator might no longer bind, and the amoeba would be unable to feed on lactose.

THE CELL CYCLE AS AN INTERNAL CLOCK Amoebas, like all organisms, can switch genes on and off in response to short-​term changes in their environment as in this 66

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lactose/​lactase example. All organisms also harbor genes that respond to longer-​term environmental fluctuations, an example being circadian rhythms. A group of “clock” transcription factors activates some genes during the day and represses them at nightfall while a second group activates other genes during the night and represses them at daybreak. All of us creatures are attuned to the fact that our planet rotates. Another universal rhythm, called the cell cycle, is regulated internally, marching to its own drummer. An amoeba feeds and grows in size until a decision is made to copy its entire genome (DNA replication) (p. 32). Once replication is finished, a second decision is made that allows the amoeba to divide in two (mitosis), with one genome copy going to one daughter organism and the other to the other. And then two cell cycles are initiated, each daughter first growing, then replicating its DNA, then dividing by mitosis. Each “grow,” “replicate,” and “divide” decision is bracketed by a large number of sub-​decisions, and all are dictated by changing patterns of gene expression. Let’s say we start watching a cell cycle when the cohort of “replicate” genes has just switched on. Some of their protein products mediate DNA replication directly, while others activate the promoters of the “divide” genes that must next be expressed to kick off mitosis. Some of the resultant “divide” proteins participate directly in mitosis while others serve as repressors to switch off the “replicate” genes. And then, once cell division has completed, the daughters repress their “divide” genes and activate their “grow” genes to initiate their own cycles. The time it takes for a cell cycle to elapse is variable—​some kinds of bacteria can cycle every 20 minutes, others may take days—​and it is influenced by the environment—​a well-​fed amoeba cycles 67

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faster than a poorly fed one. But cell cycles have an inherent life of their own. Indeed, once the first cycle was traversed, the engine has never stopped: cell cycles have been continuously running, continuously generating daughter organisms, for billions of years. .

REGULATION OF GENE EXPRESSION IN SPACE: MULTICELLULARITY We need but one variation on the amoeba theme to take us to humans. In humans, the two daughter cells don’t drift or move away from each other after mitosis but instead stay together to form a two-​celled embryo and then a four-​celled embryo and so on. Multicellularity has arisen independently dozens of times during the course of biological evolution. Most multicellular lineages pursue relatively simple morphogenetic strategies, like the formation of blades (seaweeds) or mycelial networks (fungi). Animal and land plant lineages independently came up with the idea of producing embryos—​multicellular entities that mature into adult forms (illustrated in the chapter frontispiece). Embryogenesis opened up a vast array of morphological opportunities. A key participant in the evolution of multicellularity is sex, as we explore in Chapter 11, but essential as well has been a novel pattern of gene expression. In addition to regulating the expression of genes in time—​switching on a lactase gene after lactose is perceived or switching off “replicate” genes after the genome has been copied—​ multicellular organisms also regulate gene expression in space. We might imagine a two-​celled fantasy organism that is programmed to switch on a set of light-​detection genes in cell #1 and a set of motility genes in cell #2. We would now have an organism in 68

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which the motile cell is found pushing its light-​sensitive cell ahead of itself like a tiny eye. A four-​celled organism might expand on this idea, having one light-​detecting cell specialized for blue light and a second specialized for yellow light. Modern plants and animals set up such spatial patterns in embryos and maintain them throughout life. A multicellular animal. That’s what I am, we are. In humans, more than 30 trillion daughter cells remain together to form an organism. Each cell possesses the full set of genetic instructions for making a human being, but many of these instructions are only read in certain cell types: light-​detecting cells in the retina; odor-​ sensing cells in the nose; bone-​forming cells in the spine and limbs. Each type of cell is also cycling at its cell-​specific rate—​some cells in my gut divide twice a day, while my liver cells divide only once a year and most of my brain cells don’t divide at all—​patterns that generate the size and shape of an organism. This all gets set up during embryogenesis, where we can look at the human. A fertilized human egg divides in two and then four and then eight and, after 44 rounds, reaches 30 trillion, with each set of daughter cells making decisions that influence decisions, each decision marked by sets of genes switching on or off in particular cells in particular places at particular times in the developmental sequence. Decisions are deeply influenced by hormones and by cell-​cell contacts—​outgrowing eyes in the embryo trigger the overlying cells to form lenses—​and the process is highly dynamic (p. 31). And then, once it’s set up, once the correct cells form correct tissues and organs, the whole thing goes. Brains coordinate muscles and thoughts, hormones coordinate metabolism and fear, hearts pump blood and kidneys filter it, lungs breathe. The embryo becomes a baby. 69

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So we can return to Mozart and expand the metaphor. Patterns of gene expression are to organisms as melodies and harmonies are to sonatas. It’s all about which sets of proteins appear in a given cell at the same time (the chords) and which sets come before or after other sets (the themes) and at what rate they appear (the tempos) and how they modulate one another (the developments and transitions). When these patterns go awry, we may see malignancy. When they change by mutation, we can get new kinds of organisms. When they work, we get a creature.

REFLECTIONS At the baptismal ceremony in my church of origin, the parents hand the shining baby over to the minister, who looks down lovingly, dips his hand in the water, touches the luminous little head three times, and says, “I baptize you in the name of the Father, and the Son, and the Holy Spirit. You are a child of the Covenant, called by name, cherished, known, blessed by the grace of God.” Called by name. This brand-​new creature, called by name. I gasp every time I recall the words. Some of us were taught to sing “Jesus loves me this I know,” What do I do with yearnings to be special in some ultimate sense? I have come to understand that the self, my self, is inherently sacred. By virtue of its own improbability, its own miracle, its own emergence. I start with my egg cell, one of 400,000 in my mother’s ovaries, each one of them different (Chapter 9). It meets with one of the hundreds of millions of different kinds of sperm cells produced each day by my father. Astonishing that I happened at all, truly astonishing. 70

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And then I cleave, I implant in her uterus, I grow tiny fetal kidneys and a tiny heart. The genes of my father and the genes of my mother switch on and off and on again in all sorts of combinations, all sorts of chords and tempos, to create something both eminently human and eminently new. Once I am born, my unfinished brain slowly completes it maturation in the context of my unfolding experience, and during my quest to understand what it is to be a person, I come to understand that there can be but one me. And so I lift up my head, and I bear my own witness, with affection and tenderness and respect. And in so doing, I sanctify myself with my own grace. To the extent that I know myself, I am known. Any yearnings to be Known are relegated to the corridors of arrogance, and I sing my own song, with profound gratitude for my existence. With this comes the understanding that I am in charge of my own unfolding, my own emergence. It is not something that I must wait for, or pray for, but something to participate in achieving, something to delight in achieving.

When I am among the trees, especially the willows and the honey locust, equally the beech, the oaks, and the pines, they give off such hints of gladness. I would almost say that they save me, and daily.

I am so distant from the hope of myself, in which I have goodness, and discernment, and never hurry through the world    but walk slowly, and bow often. Around me the trees stir in their leaves and call out, “Stay awhile.” The light flows from their branches.

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And they call again, “It’s simple,” they say, “and you too have come into the world to do this, to go easy, to be filled with light, and to shine.” —​Mary Oliver, “When I Am Among the Trees”

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Chapter 5

HOW EVOLUTION WORKS

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ife may have originated as a simple autogenic self (Chapter 2), but what happened, of course, is that life underwent biological evolution, generating the breathtaking array of creatures that we encounter in the fossil record and in the countless present-​ day habitats provisioned by the planetary matrix. Charles Darwin: “From so simple a beginning, endless forms most beautiful and most wonderful have been, and are being, evolved.” To understand how this all happened, we can compare the history of life with the history of music. The music of a composer like Brahms did not spring from his brain de novo. A trained musicologist can go through a Brahms score and point out a Bach-​ like fugal texture here, a Handelian cadence there, a Hungarian folk melody somewhere else. As Brahms composed, bits of the old were woven together with the new to generate the next musical legacy. The same process occurs in improvisational groups like jazz ensembles, where old tunes are remembered and embellished and brought together in new ways. In the history of life, the evolution of life, it is the same. A good biochemical idea—​an enzyme domain that binds well to a substrate, a channel that’s just the right size for a calcium ion—​gets

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0007

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carried along through time, tweaked and modulated to best serve the needs of the current lineage but recognizable by its gene sequence throughout evolutionary history. These conserved ideas combine with occasional brand-​new genes and with modulated patterns of gene expression to generate new directions, new ways of negotiating new environmental circumstances. Evolution can be minimally defined as changes in the frequencies of distinctive sets of instructions for making organisms. So to understand evolution, we need to understand how the instructions work (encoding), how they become different (mutation), and then how the frequencies of variant sets of instructions are changed (natural and sexual selection). And then we can take in how this process has created a deeply interconnected web of life.

GENETIC INSTRUCTIONS AND THEIR TRANSLATION INTO PROTEINS We introduced the hypothetical first lifeform, the autogen, in Chapter 2. While capable of self-​assembly, self-​maintenance, self-​ protection, and self-​reproduction, we can readily think of ways that these activities might be improved: its catalysts might adopt new shapes that more efficiently recognize the soup molecules that enter its cycles; the shape of the capsid molecules might change to better undergo disruption and reassembly. The original autogen, we would then say, has evolved; the new versions differ from the progenitor version in ways that better serve autogenic aims.

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The salient difference between an autogen and all modern lifeforms is that it lacks a separate set of encoded instructions for carrying out self-​generation, instructions that are copied and transmitted to the next generation. Proposals are on offer as to how such a coding system might have arisen in early organisms (p. 32), but all are hypothetical—​as is, of course, the autogen itself. For our purposes, we need only to know that such an instructional system was somehow established, and once it was established, evolution could occur in a far more efficient and creative fashion. The modern instructional system is based on genes that are encoded in DNA. In the previous chapter we saw that each gene has two regions—​a “downstream” portion that encodes a protein and an “upstream” portion that regulates whether or not that protein is produced. There we focused on the operation of upstream regions. Now we can look at how the protein-​encoding part works, where the same code, with rare and minor variations, is used by every organism and every virus on the planet. DNA is composed of four small molecules called nucleotides: adenine (A), guanine (G), cytosine (C), and thymine (T); these are linked side-​by-​side into a long strand or polymer (p. 32). In its stable form, two such strands associate to form the famous DNA double helix (Figure 3.1B), but we only need a single strand to understand the encoding part. The code is very straightforward. Each of the 20 amino acids that are found in proteins is specified by one or more sets of three nucleotides, each set called a codon. The amino acid methionine is represented by the codon ATG, histidine is represented by CAC, tryptophan by TGG, and proline by CCC. So, if methionine,

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histidine, tryptophan, and proline are the first four amino acids in the enzyme lactase, then the lactase gene will begin with the sequence ATG,CAC,TGG,CCC . . . and continue until it reaches specialized codons that signal termination. That’s it! Next these instructions need to be converted into protein products, a process we considered earlier (p. 46) but can now revisit in the context of the code. The conversion process occurs in two steps, call transcription and translation. The gene sequence is first copied (transcribed) into a complementary messenger RNA (mRNA) sequence using the G/​C and A/​T(U) pairing rules we highlighted earlier (p. 32), and the resultant mRNA strand, carrying all the encoded information, then peels off the gene, moves to a ribosome, and displays its sequence of codons. The codons are recognized by small adaptor molecules called transfer RNAs (tRNA) that match codons up with amino acids, thereby translating the “codon language” into an “amino-​acid language.” So if the mRNA is a transcript of our lactase gene, an adaptor will respond to the first mRNA codon, ATG, by bringing in methionine; the next codon, CAC, will elicit the recruitment of histidine; the next, TGG, will bring in a tryptophan. As the amino acids line up side by side, the ribosome catalyzes the formation of peptide bonds between them—​recall our analogy to a chain of cut-​out paper dolls (p. 46)—​where in this case the chain will start out as methionine-​histidine-​tryptophan, the beginning of the lactase protein. When the entire mRNA is translated, a complete lactase protein is produced. We are now poised to understand how different kinds of genes, and hence different kinds of proteins, come into being, a process called mutation. 78

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MUTATION Mutate means change, and any nucleotide-​sequence change in a genome is called a mutation. In our lactase gene, a mutant version might read ATG,CAC,TGT,CCC and the resultant protein would have cysteine (TGT) rather than tryptophan (TGG) as its third amino acid. Such changes may result from an error during the copying process such that a T is inserted instead of a G, or they may occur as the consequence of chemical or physical damage to the nucleotides via environmental agents generically known as mutagens. The Covid-​19 pandemic has sensitized us to the occurrence of such “variants” in viral capsid-​encoding genes. Our lactase mutation can have one of three effects. If the tryptophan is critical for the lactase to work and cysteine is the wrong shape for that purpose, then the mutation is said to be deleterious—​ or lethal if the gene product is essential. If the cysteine allows the enzyme to work better, then the mutation is beneficial. And if the original and the new enzyme work pretty much the same way—​ perhaps position #3 doesn’t participate in forming an important protein domain—​then the mutation is said to be neutral. Mutations may also occur in upstream promoter sequences (p. 65), and these will also have deleterious, beneficial, or neutral consequences depending on which nucleotide is altered: an activator or repressor may recognize the sequences in a mutated promoter less well, better, or about as well as its predecessor. Most mutations affect a single nucleotide, but some are more extensive: copying errors or mutagenic damage may affect several adjacent nucleotides, in which case the resultant mutation is more likely to be deleterious. In some cases an extra nucleotide 79

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may be added or an existing nucleotide deleted, causing the entire triplet coding sequence to go “out of frame.” If, for example, we add a second G to our lactase gene, ATG,GCA,CTG,GCC,C.., then the protein sequence becomes methionine (ATG), arginine (GCA), leucine (CTG), alanine (GCC) . . . . Such a frame-​shifted protein is unlikely to fold into anything useful, and the mutation is called a nonsense mutation. Mutations known as duplications are major players in the generation of novelty; these arise when the DNA replication machinery gets confused and copies the same gene twice. Were this to happen with our lactase gene, then one of the duplicates can continue to cover the lactase-​producing task and the other duplicate is in effect a free agent. As it accumulates mutations over time, it generates new sequences of amino acids that fold into new shapes. Most of these will be duds, but should one prove to serve the organism in some new way, the lineage can be said to have acquired a new gene. Genes that encode proteins that are vital to an organism’s operation have been found to carry nucleotide modifications that reduce their susceptibility to mutation, but to a first approximation, every nucleotide in the genome is equivalently vulnerable to change, and every gene is equivalently vulnerable to duplication. By contrast, the fate of mutations is not at all random. Instead, organisms carrying new versions of genes and promoters are subjected to discriminating acts of selection.

NATURAL AND SEXUAL SELECTION Natural selection asks one question: How well does the organism carry on given its environmental context? For an amoeba 80

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dependent on lactose as its food source, a deleterious lactase mutation will likely be lethal and the mutant gene will fail to spread to future generations, whereas a beneficial mutation may allow it to grow and divide more rapidly and the new gene may become more prevalent in the population than the old one. If the population can also grow on maltose, then as long as maltose is available, its various lactase-​encoding genes will “drift” along through many generations without being a focus of selection. If, however, the maltose runs out and lactose is the only food option, then the selection pressures change completely. Now the ability to metabolize lactose becomes critical, and organisms with the most effective lactase activity will prevail. Importantly, natural selection does not “see” the genes or the proteins; it only “sees” their emergent influence on an organism’s well-​being. Once the trait has spread so that it influences the well-​being of a population, biological evolution can be said to have occurred. Sexual selection introduces a bias into natural selection: Organisms that are more likely to be chosen as mates by the opposite sex are more likely to transmit their genes to future generations. In some animal lineages this is accomplished by male-​ male competition or male-​female coercion; in others, the males display sexual “come-​ons” that are evaluated by females attuned to recognize “high-​quality males” (think peacocks and peahens). The come-​ons are typically complex—​“hard to fake”—​and hence are produced most successfully by members of the male population who are already flourishing overall, the criterion of importance to the female. So, mutations change genes, and hence can change traits. Natural and sexual selection modulate their frequency in a population. And the ongoing, underlying fact is that the process is 81

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totally dependent on context. Evolution is contingent on the circumstances in which it is occurring: lactose or maltose, warm or cold, prey or predators or symbionts, wet or dry. These are the agents that call the shots.

NOVELTY VERSUS CONSERVATION When we think about the evolution of life, most of us marvel at the vast diversity, the new kinds of shells and flowers and mating rituals. The chapter frontispiece lifts up examples of this diversity in birds. But at the gene level, evolution proves to be remarkably conservative. Once a gene sequence has arisen that encodes a useful protein domain—​a domain that binds well to DNA promoters, or a domain that can catalyze the transfer of a phosphate group onto a protein, or a domain that allows cells to find one another in an embryo—​that sequence shows up again and again, in different guises in different genes in different lineages. The lovely French word for this is bricolage: the construction of things using what is at hand, the patchwork quilt. As a consequence of bricolage, a great deal of homology exists between the genes/​proteins of all modern organisms, reflecting the fact that we have all evolved from the same common ancestor (Chapter 6) and have moved through evolution manipulating the same basic sets of protein domains. Gene families—​families of ion channels, receptors, transcription factors—​are found everywhere, deep in the sea and underneath rocks and flying about in the air. Conservation is most obvious in what are called “housekeeping proteins” that participate in such core biological activities as metabolism, ATP synthesis, DNA replication, and ion transport. 82

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While there are many embellishments, their basic parameters are baked in and can be thought of as “universals.” Indeed, a yeast cell carrying a deleterious mutation in one of its key metabolism genes, and hence unable to grow, can usually be “rescued” by providing that gene from a human cell, and vice-​versa. So, all the creatures on the planet today share a huge number of genetic ideas. Most of my genes are like most gorilla genes, but my housekeeping genes are also like most of the housekeeping genes in a diatom or a mushroom or a daffodil. We all have homologous piano keys even as we play them with different chords and tempos.

REFLECTIONS Fellowship and community are central to the religious impulse. Children of Israel. United in Christ. Umma in Islam. A friend who was raised Roman Catholic and who travels frequently to foreign cities tells me that she often seeks out the local church when she arrives, finding there the shared ritual, the known liturgy and prayers, the haven. Those of us who find a religious home feel deep affinity with those who have moved through with us and before us, congregating, including, supporting. We offer and receive sympathy and affection. The musicians sing their hushed responses or chant their solemn rhythms or dance their tribal legacies and we breathe together, sense our connectedness, heal. Religion. From the Latin religare, to bind together. The same linguistic root as ligament. We have throughout the ages sought, and found, religious fellowship with one another. And now we realize that we are connected to all creatures. Not just in food chains and ecological equilibria. We share common ancestry. We share genes 83

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for receptors and ion pumps and signal transduction cascades. We share evolutionary constraints and possibilities. We share the same basic aims and purpose. We are connected all the way down. I walk through the woods and the creatures are everywhere, seen and unseen, flying about or pushing through the soil or rummaging under the leaf litter, adapting and interacting and reproducing. I open my senses to them and we connect. I don’t need to anthropomorphize them, nor to value them because they are beautiful or amusing or needed for my survival. I see them as they are; I understand how they work. I think about their genes switching on and off, their cells dividing and differentiating in pace with my own, homologous to my own. I take in the sycamore by the river and I think about its story, the ancient versions of algae and mosses and ferns that came before, the tiny first lifeform that gave rise to it and to me. I try to guess why it looks the way it does—​ why the leaves are so serrated and the bark so white—​and imagine all sorts of answers, all manner of selections and adaptations that have yielded this tree to existence and hence to my experience.

You do not have to be good. You do not have to walk on your knees For a hundred miles through the desert repenting. You only have to let the soft animal of your body love what it loves. Tell me about despair, yours, and I will tell you mine. Meanwhile the world goes on. Meanwhile the sun and the clear pebbles of the rain are moving across the landscapes, over the prairies and the deep trees, the mountains and the rivers. Meanwhile the wild geese, high in the clean blue air, are heading home again.

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Whoever you are, no matter how lonely, the world offers itself to your imagination, calls to you like the wild geese, harsh and exciting—​ over and over announcing your place in the family of things. —​Mary Oliver, “Wild Geese”

Blessed be the tie that binds. It anchors us. We are embedded in the great story of biological evolution, the spare, elegant process of mutation and selection and bricolage. And this means that we are anything but alone.

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Chapter 6

THE EVOLUTION OF BIODIVERSITY THE GENERATION OF BIODIVERSITY Our description of how evolution works in the previous chapter could apply to any planet in any solar system in any galaxy. Once there’s a self-​ assembling, self-​ maintaining, self-​ repairing, self-​ protecting, and self-​ replicating entity, then any changes that improve upon any of these attributes will lead to more prevalent entities. If ours were a perfectly uniform planet with an unchanging environment, it would presumably come to be inhabited by a single kind of organism, maximally adapted to such a habitat. Happily for us, our planetary matrix is anything but homogeneous. Instead, it offers, and continuously generates, a seemingly endless diversity of parameters: arid and humid, fresh and salty, aerobic and anaerobic, hot and cold, populated by a panoply of other organisms. A collection of such parameters that generates the opportunity for habitation is called a niche. Organisms that populate a niche are attuned to operate in that context; organisms carrying genes that improve this possibility will fare better than those with genes that do not. Thus there is no such thing as the

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0008

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“fittest” organism. We can only talk about how an organism fits in and propagates in a given niche, how its life strategies have become, via selection, adapted to that niche. It is no more or less fit than another kind of organism that succeeds in that niche via a second set of adaptations. So because we have an endless array of niches, with plate tectonics and glaciation to stir things up in the long term, and tides and seasons and weather to modulate things in the short term, we have had an endless array of organisms. And what a windfall it has been! Minute and enormous, beautiful and hideous (to some eyes), enduring and evanescent, independent and parasitic and social. They occupy the most impossible (to our eyes) niches: ocean vents, arctic snows, desert cliffs, human eyelashes, lava outcrops (book cover). They form long complex food chains and provision our atmosphere with gases and our earth with soils and our organisms with fixed forms of carbon and nitrogen. We all know the story of the dinosaurs, how they came and went. We will consider the evolution of ourselves in Chapter 12. Here we can walk through the overall history of life, thinking about what happened to all the creatures and the genes they carried with them. And then we can think about our place in it all.

THE STORY OF BIOLOGICAL EVOLUTION Figure 6.1 outlines the course of biological evolution on Earth. We start with the emergence of life from the planetary matrix, explored in Chapter 2, which generates the hypothetical self that we have been calling an autogen. Once instantiated, the autogen evolves, with most of the new ideas, most of the branches, failing 88

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Fig 6.1 Evolutionary sequence from proto-​life to the three modern supergroups (BYA, billion years ago).

to make the cut and going extinct. One lineage, however, continues to persist, eventually generating what is called the Last Universal Common Ancestor or LUCA. At this juncture, there occurs a two-​way split: some LUCA descendants follow the branch leading to modern Bacteria, while others take the branch to modern Archaea. From this point onward, all the bacteria share a common ancestor, and all the archaea share a common ancestor, but the only ancestor that the two radiations share in common is the LUCA. At a later time, a subset of bacteria and archaea fuse together to generate a third path that leads to modern Eukaryotes, including humans. All the eukaryotes share a common ancestor, but the LUCA is the only ancestor they share with bacteria and archaea—​hence it is the last universal common ancestor. That there existed but a single version of a shared common ancestor, a single kind of LUCA, is inferred from the fact that the three emergent “super groups”—​the Bacteria, Archaea, and Eukaryotes—​share numerous genetic homologies. To understand what this means, a helpful analogy is to imagine you are a student of mythology and you discover that a 89

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particular story—​say, the slaying of a dragon by a giant Snake-​ God—​is found in the recorded texts of three modern civilizations in Persia, Ethiopia, and China. This finding would lead you to infer that the tale originated in yet an earlier civilization and was then transmitted, via migrant storytellers, to populations that founded the three modern civilizations. You would, in this case, expect to find embellishments specific to each culture: the Persian version might emphasize that the Snake God was female while the Ethiopian version might claim that a male Snake God ate the dragon’s heart and became human. You might also find that a feature is present in two of the accounts—​the dragon was blue—​and absent from the third, suggesting that the blue dragon was present in the original and was dropped by one of the branches. The lineages shown in Figure 6.1 have been deciphered by this same kind of reasoning. If a version of a particular cellular process is found in modern Bacteria, Archaea, and Eukaryotes, this indicates that the process was also operant in the LUCA, the ancestor common to all three groups. For example, all modern life features cells surrounded by membranes. All cells encode instructions in DNA, transcribe the genes into messenger RNA, and translate the messages into proteins using ribosomes. All have the same suite of enzymes that metabolize glucose in a process called glycolysis. Glycolysis requires the presence of ATP, meaning that all possess systems for generating ATP. Hence, it is deduced, the LUCA displayed all of these traits. The three super groups can then be characterized by their elaborations of LUCA-​ derived traits, much as we saw for elaborations on the core Snake God myth. For example, the ribosomes of Bacteria and Archaea are smaller than the ribosomes 90

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of Eukaryotes, suggesting that the LUCA ribosomes were small and had increased in size in the last eukaryotic common ancestor. Moreover, the small ribosomes of modern Bacteria and Archaea are now different from one another in several respects, indicating that each started from a core “small idea” but then followed different paths—​like the Snake God being female in one version and dragon-​eating in the other. Such evolutionary histories can now be exquisitely fine-​tuned given our current ability to decipher gene sequences. Recall that the instructions in a protein-​specifying gene are encoded in sets of three nucleotides called codons (p. 77). If one group of modern organisms is found to have the codon CAC at position #43 of the gene encoding hexokinase, a housekeeping enzyme in the glycolysis pathway, then it is posited to be more closely related to organisms with CAT at this position than it is to those with CGA or TAT at this position. When this kind of comparative analysis is iterated for many genes, familial relationships can be established with high accuracy. With this much background, we can consider, with astonishment, Figures 6.2 and 6.3. Modern representatives of the three super groups are shown at the periphery of each figure; their relationships to one other are depicted by ever-​deepening intersections toward the center, the LUCA. Moving out from the center, each bifurcation indicates the separation of two lineages from one another, with their common ancestor sitting at the node. The Bacteria and Archaea are emphasized in Figure 6.2 and the Eukaryotes in Figure 6.3. The two lower panels of Figure 6.3 show enlarged sectors of the Animal radiation, and when we zoom in on Homo sapiens, we find ourselves positioned between two rodents and two amphibians. Astonishing. 91

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DISTINCTIVE FEATURES OF ARCHEA, BACTERIA, AND EUKARYOTES Archaea (Figure 6.2) were until recently lumped in together with Bacteria as Prokaryotes—​ very small organisms (at most 1–​ 2 microns in size) that lack a nucleus (karyon)—​but they are now recognized as one of the two original radiations from the LUCA (Figure 6.1) and one of the three modern supergroups. They were first thought to be confined to hot springs and other extreme niches since that is where they were first discovered, but they have since been found in numerous habitats, including the open oceans where they play an important role in the planetary nitrogen cycle. Bacteria (Figure 6.2) are by far the most abundant organisms on Earth: there are as many bacteria in a handful of soil as there are humans on the planet, and there are as many bacterial residents in your body as there are your own cells. Bacteria can be thought of as biochemical specialists: their general strategy is to engage in the fastest metabolism, biosynthesis, and DNA replication possible given their environmental circumstances so that they divide as rapidly as possible and generate as many of themselves as they can, albeit many have evolved “quorum sensing” and biofilm systems to put a lid on population size. They occupy virtually every planetary niche and are essential to the planetary food chain: if bacteria were to disappear, all of life would quickly come to a halt. Many specialize in distinctive modes of energy generation, including groups that perform several versions of photosynthesis, and many are motile, propelled by elegant twirling appendages called flagella. Eukaryotes (Figure 6.3) sequester their genomes within membrane-​bound organelles called nuclei, organize their genomes 92

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into elaborate DNA/​protein complexes called chromosomes, and produce internal cytoskeletons that allow them to move about and adopt all manner of shapes. Most have remained unicellular, burrowing through the soil as amoebae and floating or swimming about in oceans and ponds as algae and protists, while some have adopted various modes of multicellularity. Simple multicellular 93

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body plans are found in sponges and in many fungi and algae; next came the “Cambrian explosion” (~550 million years ago) featuring an animal body plan governed by transcription factors called Hox (considered in Chapter 12); and then came the land-​plant explosion (~300 million years ago) featuring a plant body plan governed by transcription factors called Knox. If bacteria are biochemical specialists, then the eukaryotes can be thought of as morphogenetic artisans: their adaptive strategies depend more on form than on numbers. Amoebae send out long protuberances to capture their bacterial prey (Frontispiece to Chapter 3). Fungi produce mushrooms that rise up from the earth and allow their spores to disperse in the wind. Plants fashion flowers to fit the proboscises of specific insects and insects fashion proboscises to burrow into specific flowers. Animals make muscles to climb and ears to hear and claws to grab. Our mantra still holds: Evolution produces organisms that successfully fill niches, not organisms of increasing fitness. But it is also obvious that the multicellular eukaryotic organisms have vastly augmented the organismal complexity of the planetary matrix, coming up with elaborate embryonic and adult life strategies and, in the case of animals, brains that harbor consciousness (Chapter 7).

THE HYBRID NATURE OF EUKARYOTES We noted earlier that eukaryotes have had an unusual evolutionary history. After the LUCA had given rise to the Archaeal and Bacterial radiations, several branches within the Archaeal lineage collaborated to initiate the modern eukaryotic lineage (Figure 6.1). In addition, these progenitors internalized and domesticated bacteria, 95

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converting them into cellular organelles called mitochondria, a process called endosymbiosis. During this domestication process, many bacterial genes were spliced into the host chromosomes, meaning that modern eukaryotic genomes are hybrids of ancient archaeal and bacterial instructions that have evolved into present-​ day genes. Mitochondria and their derivatives are present in all eukaryotic cells. They harbor the Krebs-​cycle enzymes (p. 51) and serve as robust producers of ATP via ion gradients (p. 53). Later in evolution, an amoebic lineage, already endowed with mitochondria, established a second endosymbiosis, this time with a photosynthetic cyanobacterium, and domesticated it to become the organelle called the chloroplast. This event was also accompanied by gene transfer, meaning that the genomes of photosynthetic eukaryotes—​the algae and land plants—​are hybrids of ancient archaeal, bacterial, and cyanobacterial instructions.

A CENTRAL CONCEPT All the modern organisms at the outer tips of each radiation in Figures 6.2 and 6.3 are, evolutionarily, equally old. Some of the eukaryotes, like the single-​celled Trichomonads, branched off the eukaryotic “main line” early and later adapted to their current peculiar niches—​the stomachs of termites and wood-​eating cockroaches. The insects branched off later, then the vertebrates, then the land plants. But the flow of genetic instructions derived from the LUCA has been constant, diverted into countless culverts but moving steadily, from the beginning to the present. We are all, we creatures who are alive today, equally old, or equally recent. 96

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EVOLUTIONARY TIME This is a good place to pause and ask what it means to talk about millions or billions of years. These concepts are hard to grasp because our experience with time is so limited: we have no problem with 100 years, and it feels like we can maybe extrapolate back to the onset of European agriculture some 10,000 years ago, but we’re clueless about 100,000 years, let alone a million. When we say that human and non-​human apes diverged ~7 million years ago, we are saying two things: that the divergence was very recent given the billions of years of evolutionary history, and that, nevertheless, ~7 million years is still a very long time, a longer time than most of us, perhaps all of us, can imagine. A helpful way to think about time is in terms of walking. The human pace is about a yard/​meter, so if we call each pace a century, then to walk back to the time of Christ is to walk twenty yards, or two first downs of an American football field. With this scale in mind, to walk back to the ape divergence is to walk 40 miles, a 14-​hour journey. When we calculate the distance to the origin of the first animals at the dawn of the Cambrian era, ~550 million years ago, it comes to 3,000 miles, or a walk from New York to San Francisco. To go back to the origin of the Earth, 4.5 billion years ago, is to trek the entire circumference of the planet, 100 years a pace. Two more rounds of circumnavigation get you to the origin of the observable universe.

REFLECTIONS The wonders and majesty of Nature have been deep resources for religious orientation and reflection throughout human history. 97

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Particularly integral is the relationship between the natural world and the indigenous peoples of Native America, as expressed in this prayer of the Pawnee/​Osage/​Omaha: Remember, remember the circle of the sky the stars and the brown eagle the supernatural winds breathing night and day from the four directions. Remember, remember the great life of the sun breathing on the earth it lies upon the earth to bring out life upon the earth life covering the earth. Remember, remember the sacredness of things running streams and dwellings the young within the nest a heart for sacred fire the holy flame of fire.

The outpouring of biological diversity calls us to marvel at its fecundity. It also calls us to stand before its presence with deep, abiding humility. Earlier we sanctified our individual selfhood, and soon we will consider ways to think about our humanness with reverence and pride. But these affirmations must coexist with an understanding that we humans are but a tiny part of an enormous context. We are one of perhaps 30 million species on the planet today, and countless millions that have gone before and, it could be said, have died for us. We occupy, temporally, the very last moment of the animal radiation that began at least 550,000,000 years ago: Homo sapiens appeared in Africa only ~300,000 years ago (Chapter 12). And while we animals were radiating, so too were all

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the other lineages within the planetary matrix, generating a veritable sunburst of biological ideas (Figures 6.2 and 6.3). We are called to acknowledge not only our interrelatedness but also the interdependency of the web of life both for our subsistence and for countless aesthetic experiences: spring birdsong, swelling tree buds, the dizzying smell of honeysuckle. Rachel Carson: “Nowhere is the relation of a creature to its surroundings a matter of a single cause and effect; each living thing is bound to its world by many threads, weaving the intricate design of the fabric of life.” We are called to acknowledge that which we are not: we cannot survive near a deep-​sea vent, or fix nitrogen from the atmosphere, or create a forest canopy, or soar 300 feet in the air and then catch a fish in a spectacular nosedive. Many religious traditions ask us to bow and tremble in deference to the Divine, to walk humbly with thy God. Religious naturalists are asked to center such humility within the Earthly whole. Oren Lyons, Faithkeeper of the Onondaga Nation, conveyed this concept to an assembly at the United Nations: I do not see a delegation for the four-​footed. I see no seat for the eagles. We forget and we consider ourselves superior, we are after all a mere part of the Creation. And we must continue to understand where we are. And we stand between the mountain and the ant, somewhere and there only, as part and parcel of the Creation. It is our responsibility, since we have been given the minds to take care of these things.

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Chapter 7

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historic centerpiece of human pride has been our sense that we possess the capacity for a special kind of awareness which, in certain narratives, distinguishes us from the “dumb creatures” over which we have been assured we “have dominion.” No question, our mode of awareness is in some ways quite distinctive, ways that we will explore later in this chapter. But no question also, these capacities are reconfigured versions of the awareness inherent in all of life. Indeed, the Earth can be wonderfully thought of as a planet shimmering with awareness. Perhaps there are other planets that so shimmer, or perhaps ours is the only one. In any case, awareness is integral to life.

WHAT ARE ORGANISMS AWARE OF? To answer this question, we can start with our autogen. In Figures 2.2 and 2.3, the original autogen acquires a random bolus of primordial soup molecules each time its capsid is breached, some of which serve as substrates for its autocatalytic cycle and hence as nutrients.

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0009

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We can now posit that the original autogen evolves into autogens that are “choosy.” In one choosy variant, the capsid molecule might adopt a shape that allows a particular nutrient in the soup to associate with its outer surface. When the nutrient binds, the capsid molecule changes shape and loosens its attachment to its capsid neighbors, allowing the nutrient to selectively leak into the capsid interior. Such an arrangement would be formally equivalent to the transporter channels be considered earlier that populate the cell membranes of modern organisms and import specific nutrients (e.g., glucose) from the environment or the bloodstream (p. 53). In a second choosy variant, a capsid molecule might increase the strength of its attachment to its neighbors if an unwanted soup component—​a toxic substance—​associates with its surface, thereby preventing the toxin from entering the capsid. Each variation would enhance the autogen’s aims—​improved self-​maintenance in the case of nutrient entry and improved self-​protection in the case of toxin exclusion—​and such choosy autogens would be favored by natural selection. To be choosy is to be aware. The word aware/​ness has many usages. Here, awareness will refer to a process that occurs in all modern lifeforms and entails three steps: (1) something is specifically noticed, like the shape of an external molecule; (2) the molecule is evaluated as being good, bad, or of no interest; and (3) an appropriate response is elicited. Hence awareness, as we are using the term, entails far more than the detection of something external to the self; it entails as well an understanding of its meaning to the organism—​this bound soup molecule means that the capsid should leak—​and an evaluation of that meaning—​this molecule services my self-​maintenance and is therefore “good.” Awareness, that is, includes evaluation, a parameter that we will consider more fully in the next chapter. 102

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During the evolutionary period from the autogen to the DNA-​ based LUCA (Figure 6.1), and during the radiation of the three super groups (Figures 6.2 and 6.3), awareness systems have flourished. Numerous families of receptors have evolved that trigger the flow of signal-​ transduction cascades when presented with external stimuli. In animals, olfactory (Figure 3.4) and taste receptors detect molecular shapes, while other receptors detect various forms of energy: eyes are stimulated by photons of particular wavelengths; ears are sensitive to specific vibrations produced when air is compressed; heat receptors in the skin distinguish levels of molecular motion. A critical focus of this evolution has been the selection of receptors that pick out shapes and energy patterns that are of use to, or noxious to, the organism while ignoring most everything else that’s going on. Land plants, algae, and cyanobacteria, for example, are endowed with all manner of chlorophyll photoreceptors that selectively absorb those wavelengths of sunlight that best activate their photosynthetic pathways. They also produce pigments that absorb wavelengths that would be damaging to the chlorophylls, thereby providing self-​protection. More generally, much of biological evolution can be said to entail the evolution of what organisms are aware of. The first awareness systems focused on the physical and chemical properties of the planetary matrix, but once a sufficient number of organisms came into existence, they became intensely aware of one another as competitors or prey or predators or symbionts or parasites. And once eukaryotic sexuality was invented, countless systems were devised to recognize a mate of the correct species and the correct mating type or gender (Chapter 10). All organisms, be they unicellular or multicellular, are aware of their environment and one another using an array of sensory 103

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systems. Of recent interest are the extensive communication networks assembled by populations of trees. Here we will focus on animal nervous systems that utilize a cell type, called the neuron, that is specialized for generating awareness. Most neurons go on to associate as brains that coordinate the avenue of animal awareness called consciousness.

NERVOUS SYSTEMS All neurons work in much the same way, from jellyfish to insects to humans. They are long narrow cells, and the nucleus-​containing cell body at one end produces numerous extensions of its cell membrane to form what is called a dendritic tree. The dendrites are studded with receptors for particular stimuli, and when a stimulant binds, the receptors change shape, triggering dendritic ion channels to open and allow a flux of sodium ions to enter the cell. This influx stimulates neighboring channels to open, which in turn stimulates neighboring channels to open, the result being that an ion flux sweeps across the cell body and down the long length (axon) of the cell. The neuron is said to “fire.” When the ion-​flux cascade reaches the end of the axon, the tip of the axon is stimulated to release (secrete) small molecules, called neurotransmitters, onto the cell membrane of an adjacent target cell. The target membrane carries receptors for these neurotransmitters, and when the receptors bind to the neurotransmitters and change shape, they set off their own cascades of response. If the target cell is a muscle fiber, the neurotransmitter/​receptor interaction may trigger muscle contraction. If the target cell resides in the gut, the interaction may stimulate its secretion of digestive enzymes. 104

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In most cases, the target cell is in fact a second neuron whose dendrites carry receptors for the neurotransmitters secreted by the first neuron; the junction between the first axon and the second dendrite is called a synapse. For example, when an olfactory neuron in a mouse fires in response to an odorant in cheese, its axon secretes neurotransmitters onto a second neuron, located in the olfactory center of the brain, with which it is in synaptic contact. The brain neuron fires, causing it to secrete neurotransmitters at its synapse with a third neuron that is also located in the brain. This chain reaction continues until the last neurons in the cascade excite muscles in the mouse’s legs, at which point the mouse starts to move towards the cheese. Once neurons are set up in such a series, their activity can be regulated. For example, neurons that stimulate the mouse’s leg muscles can be induced to fire by odor perception as we have just described. But their dendrites are also in synaptic contact with neurons poised to secrete an inhibitory neurotransmitter that prevents them from firing. The inhibitory neurons are hooked up in series back to the mouse’s visual system, and if the mouse notices that a cat is crouching close to the cheese, the visual neurons activate these inhibitory pathways and the mouse, still sniffing, will nonetheless freeze in its tracks, and then likely abandon its quest for cheese and scurry back behind the refrigerator. A key feature of animal evolution has been the complexification of nervous systems. Primary receptors, like those in the nose and eye and skin, detect an enormous range of external stimuli, and many kinds of neurotransmitter/​receptor systems, some excitatory and some inhibitory, then transmit and modulate responses to these stimuli. Increasingly complex networks of synapses have generated increasingly complex patterns of response. And 105

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primitive memory systems have given rise to increasingly impressive abilities to learn from experience and, notably in our lineage, to transmit these experiences as cultural understandings.

BRAINS Most of the complexification has occurred in central processing organs called brains. The brain of every human contains about 86 billion (86,000,000,000) neurons; their axons have the collective length of several thousand miles—​impressive until you consider that our blood vessel system extends 100,000 miles. Some of our brain-​derived axons extend out into the body via the spinal cord to take in stimuli (itch) or trigger muscular responses (scratch); others extend directly to the viscera. But most stay in the brain and form synapses with one another, thereby coordinating the body as a whole. There are an estimated 100 trillion synapses in the human brain, meaning that an average dendritic tree is in synaptic contact with 1,000 other neurons—​an astonishing concept. Some of these synapses are excitatory and others inhibitory, and each neuron fires or fails to fire after integrating its various dendritic inputs. Its target, in turn, is usually a second brain neuron with 999 other potential synaptic influences. Brains started their evolution as loose collections of cell bodies called nerve rings or nerve nets, as found in modern jellyfish (Cnidaria) and sea urchins (Echinoderms), but in most modern animals they are located in heads and are differentiated into discrete functional modules that communicate extensively with one another. Figure 7.1 illustrates these modules in the vertebrate

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lineage, where familiar anatomical units, like the olfactory bulb and the optic lobe, reappear in each brain and carry out homologous functions. The cerebral cortex has increased in size during vertebrate evolution and, in humans, is much larger than expected given our body size. The nervous systems in organisms like worms are hardwired: a well-​studied nematode has 302 neurons in the same positions making the same synapses and performing the same functions. But as brains got larger and more complex, this stopped being the case. Instead, the process of brain construction is set up in the vertebrate embryo with general instructions indicating general areas toward which particular neuronal lineages should move in the cranium. The neurons then migrate toward these targets, with the fate of any particular cell highly dependent on the cells it moves past, the proteins they display on their surface membranes, and locally secreted growth-​promoting hormones. Some migrants proliferate, others die off. Hence the construction of each mammalian brain can be thought of as a kind of evolutionary event in itself, with much of the fine-​tuning left to contingency and selection. The overall organization of all human brains is the same, but the detailed “wiring” is unique in each person. Fortunately for us, most of the neural circuits that are set up during our brain development govern decisions that we never need to make and indeed are never even aware of. Brains process enormous amounts of physiological information to generate such results as appropriate blood pressure and breathing rate. Were it necessary to think about these matters, no poems or sonatas would ever have been written. Indeed, the processes that produce our conscious selves constitute but a small fraction of what our brains are doing; the cerebellum (Figure 7.1), for example, an 108

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ancient module that is deeply involved in “running the store,” has about four times as many neurons as the rest of the brain.

THE EVOLUTIONARY PLASTICITY OF BRAINS During the course of animal evolution, brains have on occasion changed their configurations to adapt to new circumstances. One option that we can call rewiring is exemplified by the blind mole rat. During its embryonic brain development, neurons that would have migrated into the optic lobes of its sighted cousins, like the porcupine, instead grow into the lobes governing smell and touch, augmenting these important senses for underground living. Hence there is no such thing as a prefabricated “visual neuron”; neurons acquire their functions in the contexts of the brain domains that they come to inhabit. A second option that we can call de-​wiring is exemplified by an Asian bird called the white-​r umped munia. In the wild, munia males are sexually selected (p. 81) to sing highly stereotyped songs—​motif A is always followed by B which is followed by C—​ that advertise their fitness and availability to female munias. About 250 years ago, a few munias were brought to Japan by breeders and subjected to a completely different mode of selection: birds with particularly colorful plumage were mated to one another and their progeny sold to bird fanciers. There was no selection for the stereotypic birdsong in these domesticated birds for over a thousand generations, and the songs of the present-​day domesticates prove to be unconstrained and individualized: motif A may be followed by motif C or by something else altogether. Some of our distinctive human traits, such as language facility, may similarly 109

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have initiated with the degradation of “hardwired” instinctual networks and their replacement by more fluid and multifaceted capabilities.

CONSCIOUSNESS The word consciousness has acquired multiple meanings with little consensus. In some usages it refers only to human forms of awareness; in others it can refer to the awareness states of land plants as well as animals; in others it is also a property of atoms; in others it is an ineffable condition that fills the universe, moves in and out of lifeforms, and lacks all materiality. Here, consciousness will refer to brain-​based frames of mind—​ and hence animal frames of mind—​ wherein sensations and feelings and memories feed into and are integrated by the brain. The outcome is a continuous state of coordinated experience, the apprehension of the world within and the world around. Consciousness is a quintessential example of emergence. As Anil Seth puts it: “The way in which things in the world appear in perceptual experience is a construction of the brain . . . When we perceive something, the content of what we perceive is not carried in the sensory signals themselves; instead it emerges from the brain’s implicit knowledge about how actions and sensations are coupled.” Which is to say that we animals don’t perceive the world directly “as it is” like single-​celled organisms do; we perceive what our brains tell us about it, with editorial preference given to what’s important to know. The experience of smell, for example, dominates the consciousness of a dog. Each kind of animal inhabits a distinctive interiority. 110

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So is my cat conscious? Well of course she is. She takes in the world and her feeling states and memories and coordinates these experiences in her brain; she responds appropriately and learns and remembers. Indeed, the domains of the brain that have been shown to participate in the moment-​to-​moment flow of human consciousness—​the thalamus and cerebral cortex—​are present in all reptiles, birds, and mammals. Then how about a snail? I hesitate. Cats and sparrows and alligators are a lot more like me than a snail, as are their brains (Figure 7.1). But when I put aside this anthropocentrism, and recall that snail brains, although anatomically different, coordinate their sensory and bodily inputs and remember experiences, then my answer is yes—​the snail is doing its version of being conscious. A fascinating arrangement has evolved in the octopus; Peter Godfrey-​Smith remarks that “if we want to understand other minds, the minds of cephalopods are the most other of all.” The large and intelligent octopus brain controls basic bodily functions and many behavioral decisions, but it makes no connections with the neurons that control its skin and its tentacles. The skin, on its own, generates changes in total-​body camouflage to match its surrounds, and the tentacles, on their own, engage in complex coordinated behaviors in response to the environment. In the octopus, consciousness has been “distributed.”

SELF-​AWARENESS While my cat is for sure conscious in a non-​octopus way, inhabiting and responding to the reality constructed within her brain, I am strongly convinced that she does not reflect on her 111

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I-​self, on her own cat-​hood, even though there is no obvious way to prove that this is so. She just is her conscious self. Her experience is in-​the-​moment: this is followed by that is followed by that. I would say that this is the case as well for a human baby. Self-​ awareness as we experience it is a trait that kicks in during child development and comes to dominate human mentality. Our I-​ selves, our autobiographical selves, our narrative selves—​we all know exactly what this means, even if none of us can describe it very well. Versions of I-​selves may well be experienced by other animals, such as nonhuman primates, dolphins, and elephants, and neuropsychology is still far away from being able to explain how any version of self-​awareness works. But theories abound. A widely held perspective holds that the human version co-​evolved with our ability to use symbolic language; that language somehow enables us to be spectators of our own consciousness. The human brain is said to construct a sub-​symbolic ongoing consciousness like other animals, integrating sensory stimuli with feelings and memories as we have just described, and that somehow, some of these perceptions are delivered to something called the working memory in the form of symbolic concepts and narratives, which then “come to mind.” There’s obviously a lot of hand-​waving going on in that last sentence. No one yet understands where or what such a working memory might be, nor what might be involved in converting the sub-​symbolic to the symbolic, nor how anything comes to mind. But there’s no questioning the outcome: humans not only experience things as conscious beings like all other animals do; each of us also develops an I-​self that feels as though it has authorship and exerts executive control over these experiences, that it possesses 112

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a version of free will. William James described all this as well as anyone in 1902: It is as if there were in the human consciousness a sense of reality, a feeling of objective presence, a perception of what we may call “something there,” more deep and more general than any of the special and particular “senses” by which the current psychology supposes existent realities to be originally revealed.

Our human I-​selves go on to imagine as well as perceive, and we use the same sets of feelings for both. Imagined dangers can elicit the same fear response as real dangers, imagined accolades the same infusion of pleasure, imagined works of art the impetus and courage to produce them.

AN ODE TO SYMBOLIC LANGUAGE We humans share the planetary matrix with countless other kinds of creatures, and share brain-​based consciousness with all other animals, but we also live in a world that no other species has access to. We inhabit a world full of abstractions, impossibilities, and paradoxes. We alone brood about what didn’t happen and spend a large part of each day imagining the way things could have been if some event had transpired differently. Narrative is our foundational modality: we construct and control the stories we tell others—​and ourselves—​about who we are, and we make use of these stories to organize our lives and kindle our art and ground our capacity for mindful understanding. The doorway into this world is posited to have opened to the Homo species with the evolution of language. Language is not 113

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merely a mode of communication; it is also the outward expression of an unusual mode of thought—​symbolic representation. Without symbolization, this world is out of reach and indeed inconceivable. The way that language represents objects, events, and relationships provides a uniquely powerful economy of reference. It offers the means to generate an essentially infinite variety of scenarios and an unprecedented ability to predict events, organize memories, plan behaviors, and inhabit our cultures. Terrence Deacon sums it up: “Biologically we are just another ape. Mentally, we are a new phylum of organism.”

REFLECTIONS When we considered the autogen in Chapter 2, we developed the concept that it was a self that had aims, had purposes, embodied telos. Here we have considered autogens that evolved “choosiness,” producing capsids that enhance uptake of nutrients and minimize uptake of toxins, variants that better achieve the aims of self-​maintenance and self-​protection and hence are favored during the process of natural selection. Choosiness may have started out as a crude ability to bind to a useful external molecule or avoid a toxic one, but it has evolved into something highly refined, a condition that we can call attunement. All present-​day selves are highly attuned to the environments that they inhabit, aiming to find what they need, or need to avoid, and ignoring most everything else. So how might we describe human attunement? We are, of course, conscious of numerous features of our circumstances like all other animals. But most of our awareness comes to us 114

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indirectly, via the I-​self, who dominates our every moment when we are awake, who stars in our dreams when we sleep, and who disappears with anesthesia. Some have developed in meditative practice the ability to turn down its volume and access other modes of conscious experience—​a friend calls this accessing his “froggy self”—​but it pops back up again when it’s time to prepare dinner or meet with a friend. Each I-​self emerges from a mélange of experience and memories and feelings and developmental genetics, and hence each is unique. And each is also enduring. In my nearly eight decades of life, much about me has changed, yet I retain my core sense of who I am, my autobiographical self. As do we all. What is remarkable about this human sense of self is that it feels immaterial. While I have no doubt whatsoever that it is brain-​ based, my experience is that it is something else altogether, an essence, intangible. We have, throughout the ages, spoken of a spirit or a soul that somehow “inhabits” the body. The sense of an immaterial self presumably grounds the concept, encountered in numerous religious traditions, that this self, this soul, this spirit will survive the death of the body and experience an afterlife or some form of immortality—​in some cases disembodied and in some cases reunited with one’s former body or other bodies. Familiar to many readers are the heaven/​ hell concepts of Christianity and Islam, as in an oft-​spoken child’s prayer from the Protestant tradition:

Now I lay me down to sleep. I pray the Lord my soul to keep. If I should die before I wake I pray the Lord my soul to take.

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Hinduism and Buddhism are embedded in the concept of reincarnation cycles, and Buddhists voice the concept of interbeing:

This body is not me. I am not limited by this body. I am life without boundaries. I have never been born, and I have never died.



Look at the ocean and the sky filled with stars, manifestations from my wondrous true mind. Since before time, I have been free.



Birth and death are only doors through which we pass, sacred thresholds on our journey. Birth and death are a game of hide-​and-​seek.



So laugh with me, hold my hand, let us say good-​bye, say good-​bye, to meet again soon.



We meet today. We will meet again tomorrow. We will meet at the source every moment. We meet each other in all forms of life. —​Thich Nhat Hanh

The Bwende in the Congo carved icons to the Four Moments of the Sun: Dawn (the beginning of life), Noon (life at its fullest), Sunset (the end of life’s journey), and a Second Dawn (for those who have lived an exemplary life). The Egyptians envisioned an elaborate Afterlife ruled by King Osiris and inhabited by numerous gods. The Daoists look to Fei-​Sheng, the ascension to heaven in daylight. The Fang of Gabon speak of the khun, the disincarnated spirit, which can appear as a ghost. 116

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The human sense of an immaterial and hence “other-​worldly” self also feeds into what are called mystical experiences that may occur spontaneously or be actively sought in prayer and ritual, encounters that are intensely personal and described, if at all, with a halting tongue. During a prototypical experience, a powerful external immaterial presence—​the divine, the spirit within the totem, the numinous other—​is first encountered, and this presence then permeates one’s being and becomes a reality within it. In Christian traditions, one is said to experience Immanence, as in this prayer.

Spirit of the living God, fall afresh on me. Melt me, mold me, fill me, use me. Spirit of the living God, fall afresh on me. —​Daniel Iverson, 1926

In the Buddhist meditative tradition, one instead seeks a loss of the narrative I-​self, an emptying out, a receptivity, in order to experience an at-​one-​ness, an interbeing. Many Asian traditions speak of a spiritual communion with universal consciousness. So we raise our eyes to the heavens and we ask, Is this Other? Is this a supernatural God? The Great Spirit? The Perfection of Understanding? Or are these overwhelmingly powerful brain-​ based experiences, with Immanence a particularly intense form of self-​awareness and universal communion a detachment from self-​ awareness so that all else can penetrate? How can we tell? As a nontheistic religious naturalist, I call upon the concept of emergence—​something else from nothing but—​to help me understand the widespread sense that humans have immaterial souls that can interact with immaterial spirits and can continue

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their existence after the death of the body. The emergentist approach suggests that to experience our experience without perceiving its underlying material mechanisms, the neural/​hormonal collaborations, is the kind of thing one might expect of emergent dynamics. While the outcome has been given reverent names like spirit or soul, names that conjure up the apparent absence of materiality, we need not interpret this as evidence of some parallel immaterial world. We can now say that the experience of soul or spirit as immaterial is a reflection of the way the process of emergence distances each new level from the details below. Given such understandings, I have no qualms about referring to my sense of myself as my soul, a soul emergent from material and biological complexity, a soul that will die when my body dies, but nonetheless a soul provisioned with endless opportunities for what some call immanent or mystical experiences and others describe as a fullness, an overwhelming richness. The concept that these experiences entail access to some independent spiritual realm doesn’t resonate with me, whereas to think of the mystical dimension as emergent from my mind and heart makes it all the more wondrous and exciting to be a human. I am called to access the mysticism inherent in my participation in the planetary matrix. The most beautiful emotion we can experience is the mystical. It is the source of all true art and science. He to whom this emotion is a stranger, who can no longer wonder and stand rapt in awe, is as good as dead. —​Albert Einstein

Immanent experience is for me very different from cosmic Mystery (Chapter 1). It is immediate and known. It becomes a part of myself 118

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that I most cherish, the part that most deeply celebrates the fact that I am alive, the part that sustains me through discouragement and loss. Immanence can be contrasted with what is known as transcendence. Transcendence is usually configured vertically, directed skyward, entailing access to an overarching non-​material realm or Presence that supersedes the natural world or has greater reality than the natural world. In contrast to experiencing an immanental spiritual presence within one’s being, one transcends into a different, and “higher,” modality. Michael Kalton has suggested that transcendence can instead be configured horizontally: an immersion within the natural world as a participating critter. That the capacity for horizontal transcendence is an intrinsic human trait is readily affirmed by taking a young child for a walk in the woods or by the sea and witnessing her innate astonishment and delight in all that she beholds. The delight has nothing to do with the aesthetic appreciation of sunsets or mountain vistas, things that we adults tend to notice. The delight is with the particular: the ladybug crawling on the rock, the fuzzy moss, the tickly dune grass, the mucky mud by the river. Children connect with the immediate and become a part of it. The mud isn’t messy, or rather, its messiness is what makes it wonderful. Children are inherently attuned to Nature. The attunement of the child is the attunement of all animals, whose conscious experience is all about participation with their natural surrounds. Whether a child’s pleasure in this participation feels the same as it does to other mammals is not easily proven, but when I watch a child and a dog running through a field of grass, laughing and barking, it looks pretty much the same to me. The 119

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difference is that the child may later describe the romp in symbolic language or draw a picture of it for all to see. The child inhabits the natural world both as a conscious critter and as an emerging I-​self. As our I-​ selves “mature,” our critter-​ based attunement is all too often left by the wayside or at least neglected as we immerse ourselves in our cultural contexts. But this need not be so. Opportunities for horizontal transcendence abound throughout our lives, in both urban and non-​urban contexts, and wherever and whenever they are sought and cultivated, they nourish and deepen our souls. For me, they are experiences of unity, of being completely a part of all that’s going on around me (p. 84), and this yields joy and wonder and richness and tranquility.

When despair for the world grows in me and I wake in the night at the least sound in fear of what my life and children’s lives may be I go and lie down where the wood drake rests in his beauty on the water, and the great heron feeds. I come into the peace of wild things who do not tax their lives with forethought of grief. I come into the presence of still water. And I feel above me the day-​blind stars waiting with their light. For a time I rest in the grace of the world, and I am free. —​Wendell Berry, “The Peace of Wild Things”

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Chapter 8

INTERPRETATIONS AND FEELINGS

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he arrival of choosy lifeforms (Chapter 7) marked the advent of awareness on the planet. Awareness, as we are using the term, entails noticing something, evaluating that something as being good or bad, and launching an appropriate response. Awareness, that is, entails perception, interpretation, and some form of what we can generically call behavior. Natural selection has favored selves that execute adaptive choices, that interpret and respond to their surrounds in ways that promote their aims. We humans are so awash in our language-​based systems of interpretation that we need to be reminded that we possess a specialized, albeit very powerful, version of what all selves possess: the ability to ascribe both meaning and value to that of which they are aware. Evaluation—​this is good, that is bad, that is too much or not enough, that doesn’t matter—​is at the heart of awareness. This chapter will focus on what is known about how evaluation systems work in present-​day animals, including humans, but first we should pause in wonderment at the array of stimuli that earthly creatures are capable of evaluating. Unicellular organisms, and multicellular fungi and land plants, have come up with a huge variety of complex sensibilities, all The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0010

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accomplished with no nervous systems and no brains whatsoever. In some land-​plant lineages, for example, when nitrogen-​fixing bacteria bind to the roots, this is interpreted as beneficial and the plant constructs nodules to facilitate bacterial colonization. By contrast, when pathogenic bacteria bind, this induces the synthesis and deployment of bactericides. In most vascular plants, a shortening day length is interpreted by the elegant phytochrome system as the time to initiate flowering, and the tissues respond by producing hormones that stream through the vascular system and govern the flowering process. Animals deploy a panoply of sensory systems, including electromagnetic detectors in sharks and sonar in bats, which transmit information to ever-​complexifying brains, brains that are in extensive neural and hormonal communication with the rest of the body, to generate integrated interpretations of a myriad sensations that are experienced as consciousness. In humans, our animal brains evolved an additional capacity: the use of language to symbolize our thoughts and ideas, to integrate them as narratives, store them in our long-​term memories, access them in our working memories, and present them to ourselves and to others. We go on to symbolize these concepts in our literature and other arts, where imagination flourishes. Importantly, our thoughts and narratives and memories and imaginations are invariably infused with our feelings about them.

EVALUATION USING HOMEOSTATIC AND EMOTIONAL FEELINGS All modern creatures are choosy and hence all evaluate. The virus must bind to the correct cell-​surface protein before it activates 124

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its infection program. The amoeba perceives and then moves a pseudopod toward a food source (Frontispiece to Chapter 4); it perceives and then moves away from a toxic stimulus. We move away from a dead rat; a housefly moves toward it; we move toward it, holding our noses, when our trained sensibilities remind us that we are obliged to dispose of it. Such evaluations are rapid: long before I have “thought about” what to do about the dead rat, I am already feeling disgust at the odor. Animals with brains evaluate using what can generically be called feelings. Two kinds of feelings have been distinguished, called homeostatic and emotional. Homeostatic feelings are elicited by internal states—​well-​being versus non-​well-​being: indigestion, hunger, thirst, fatigue. Much of the feedback on these states is conveyed via interactions between neural tissue and non-​neural tissue, such as the gut and its bacterial microbiome. In neurobiological language, signals from these interior networks reach nuclei in the brain stem, the amygdala, and the basal forebrain, which then coordinate and inform domains in the insula and cingulate regions of the cerebral cortex, letting them know how things are going throughout the body. The information in this circuitry is said to be “implicit”—​ it doesn’t reach consciousness—​but the accompanying feelings permeate consciousness and are the substrates of many moods and motivations. Emotional feelings, such as anger and elation, also contribute to moods and motivations, but they are triggered by external events. A well-​studied example is the so-​called fight-​or-​flight response to a stimulus that elicits the emotion called fear. When our mouse in Chapter 7 sees the cat, this perception, again using neurobiological language, connects in series to the amygdala, 125

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which proceeds to activate the autonomic nervous system, which stimulates the adrenal gland to release the hormone adrenaline/​ epinephrine, which causes changes in her blood pressure and heart rate, all without her “knowledge.” These outcomes are experienced as fear. The same set of responses occurs in the frightened human: our basic emotional reactions are ancient and hardwired survival systems that mediate key evaluative interactions with the external world. That said, humans may be unique in experiencing emotional feelings not only in response to external events but also in response to inner narratives—​thoughts and memories. Our storied understandings, when brought to mind, may frighten or empower or disgust or elate us. My cat likely remembers where she caught the mouse yesterday, and may return there in hopes of another catch, but to my knowledge she does not spend time pondering, or even recalling, the joy she felt when she caught it. Her joy was in the moment, in the here-​and-​now. We humans experience joy in the moment as well, but we also have minds that are able to reflect upon, and hence re-​experience, that joy.

I wandered lonely as a cloud That floats on high o’er vales and hills, When all at once I saw a crowd, A host, of golden daffodils; Beside the lake, beneath the trees, Fluttering and dancing in the breeze.



Continuous as the stars that shine And twinkle on the milky way, They stretched in never-​ending line Along the margin of a bay: Ten thousand saw I at a glance, Tossing their heads in sprightly dance.

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The waves beside them danced; but they Out-​did the sparkling waves in glee: A poet could not but be gay, In such a jocund company: I gazed—​and gazed—​but little thought What wealth the show to me had brought:



For oft, when on my couch I lie In vacant or in pensive mood, They flash upon that inward eye Which is the bliss of solitude; And then my heart with pleasure fills, And dances with the daffodils. —​William Wordsworth, “I Wandered Lonely as a Cloud”, 1804

Homeostatic and emotional feelings often overlap—​a sense of internal well-​being may be reinforced by the release of pleasure-​ stimulated hormones like serotonin and dopamine that enhance that interpretation—​and all animals integrate both the quality and intensity of their various feeling states while they are generating an evaluation. Our mouse first evaluated the cheese in the context of her homeostatic feeling of hunger; the emotional feeling of fear then kicked in with the sight of the cat and trumped her hungry frame of mind.

THE INTEGRATION OF THOUGHTS AND FEELINGS Just as various domains of the brain somehow deliver sets of symbolic narratives depicting our cognitive “thoughts,” so too do other domains in the brain, networked with bodily systems, somehow 127

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deliver information about our underlying “feelings” about those thoughts. In fact, it is likely impossible to have a thought without simultaneously having a feeling about it: this thought makes me anxious, that delights me, that’s a good idea, that’s dumb. As neuroscientist Antonio Damasio writes: “Nature appears to have built the apparatus of rationality not just on top of the apparatus of biological regulation, but also from it and with it.” Most of us are not likely to have difficulty dealing with this kind of analysis for a feeling such as fear—​we’re not enamored with fear in any case and tend to regard it as a “primitive instinct.” But a neurobiological view of love or joy or transcendence may be more troubling. Neuroscientists in fact have as yet little to tell us about love or joy or transcendence, but once they are understood, it will doubtless be the case that all human feelings, including those we consider most deeply human, will be found to be created the same way that all experience comes about—​by creating mental representations of the workings of underlying processes. Reductionism again. Now you scientists are turning my most cherished feelings into mechanisms! Damasio can help us here with his lucid version of the Mozart metaphor: To discover that a particular feeling depends on activity in a number of specific brain systems interacting with a number of body organs does not diminish the status of that feeling as a human phenomenon. Neither anguish nor the elation that love or art can bring about are devalued by understanding some of the myriad biological processes that make them what they are. Precisely the opposite should be true: Our sense of wonder should increase before the intricate mechanisms that make such magic possible.

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Very well, you might say, but does this rule out the possibility there are feeling pathways that are unique to humans? After all, our capacity for symbolic language seems to have shown up only once in all of evolutionary history, so might our brains be working with more than just ancient feelings like hunger and fear and lust and anger and nurture? Might there not be novel emotional centers that give rise to exclusively human feelings? Perhaps. But given Nature’s track record for conservative tinkering (p. 82), it seems far more likely that our feelings represent elaborate combinations and syntheses of prior configurations, experienced by us in emergent ways, without in any way being the less compelling or important. So, our working memory—​what “comes to mind”—​is not presented with stand-​alone “thoughts” and stand-​alone “feelings” but rather with intricate integrations of the two. My grandmother comes to mind, and as I experience her smile and her stride and memories of our times together, I also experience my admiration for her energy and my impatience with her fussiness and my deep sorrow that she is no longer alive. The impatience may come as a remembered feeling with little impact, but the grief wells up in my body as a primal heaviness and infuses her smiling image. My grandmother has become a complex symbol of cognitive meanings and profound feelings.

REFLECTIONS Anyone who has raised children or had siblings can testify that each child manifests, early on, a temperament, expressed along numerous axes—​serene/​restive, shy/​outgoing, focused/​daydreamy, 129

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optimistic/​pessimistic, somber/​jovial, daring/​cautious—​qualities that are retained throughout a lifetime: “Joey has always been like that.” Temperament describes a person’s baseline feeling configuration—​the myriad hormones and neurotransmitters and receptors, and the neuronal maps and connections, that generate our moods and motivations. Studies of identical twins reared apart document that temperament is significantly heritable, but to say that temperaments are influenced by genetic endowment is not to suggest that there is a “gene for,” say, conviviality: numerous gene products collaborate in numerous developmental contexts to produce the outcomes that are manifested as temperaments. Moreover, each outcome is expected to be individualistic, displaying a distinctive panoply of neurotransmitter levels, synaptic configurations, thresholds of reactivity, and so on. There are lots of ways to be focused or daydreamy. To the extent that there is such a thing as human nature, it is robustly rooted in temperament, and since there are numerous temperamental blends—​ numerous weightings of the various feeling axes—​this means that there are numerous versions of human nature. Primatologist Frans de Waal was asked to describe the ways that chimpanzees and bonobos are different from humans, and he responded that there are obvious cognitive differences, but then he paused and remarked thoughtfully: “But you know, in terms of their emotional makeup, their feeling states, once you’ve spent time with these animals you come to understand that they’re basically the same as we are.” Primatologist Barbara Smuts recalls Gombe chimpanzee Fifi as being confident and calm, Patty as being insecure and excitable, Figan as being friendly and extroverted, and

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Goblin as being aggressive and unpredictable. Our temperaments are a robust legacy from our evolutionary history. Given this rainbow of temperaments, we can now ask: What are the feeling states associated with religious frames of mind? These turn out to have much in common. Let’s begin with William James. “There must be something solemn, serious, and tender about any attitude we denote religious. If glad, it must not grin or snicker; if sad, it must not scream or curse.” A visit to the Brooklyn Museum of Art validated this insight. In collection after collection, I found I had no difficulty figuring out which pieces were considered “religious” and which “secular,” even when the works came from cultures I knew nothing about. The religious pieces were infused with feeling and immediacy, but always in the context of a solemnity or a tenderness. The masks, however frightening, were also noble; the fertility figures were lush; the totems and sarcophagi were carved with deep respect for the beliefs that they symbolized. And then there was the symbolism itself. Each was redolent with meaning, and each conveyed complex feelings, like hope or assent or sorrow. A powerful metaphor demonstrates the depth of one’s understandings, and this is what religious art and ceremony have always been about. Each totem elicits religious sentiments central to the tradition and made manifest by the artisans. Each crucifix calls us to the pathos of Christ. Each image of the Buddha elicits a reflective serenity. Each embodies the sacred. “Being religious” can be said to mean “being deeply committed to the sacred,” where the religious naturalist considers the natural world itself to be eminently sacred.

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A feeling state that also accompanies most religious frames of mind is variously known as empathy, compassion, humaneness, or loving kindness: the ability to imagine what it is like for another being to feel distress, the ability to put oneself in another’s shoes and experience their distress in one’s own being; and the impulse to help ameliorate that distress. Empathy has deep roots. Versions of empathy have often been witnessed in other mammals and in birds, and are particularly evident in nonhuman apes. A young bonobo was observed to fatally injure a bird while playing with it. She picked up the comatose body, carried it with her to the top of a tree, and opened out her hand. When the bird still lay there limply, she wrapped her legs around the tree trunk, held the bird by its wings, and then opened and closed the wings several times, apparently trying to help it start to fly. It is as we can imagine being the least of these that we can begin to experience the anguish of poverty or deprivation. It is as we are able to identify with the oil-​soaked shore bird and the bewildered moose and the stranded polar bear that they come to embody our environmental concerns. And accompanying our sense of compassion, often at variance with our self-​focused aims, is our haunting sense that things should be fair. We will return to these sensibilities in Chapter 13.

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Chapter 9

SEX

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ll cells reproduce themselves by copying their genomes and allotting one full copy to each of two daughter cells. Many and probably all modern organisms are also capable of acquiring short segments of DNA from an external source and incorporating them into their genomes. Bacteria, for example, often take up and propagate pieces of DNA released from other bacteria that specify antibiotic resistance or other useful traits. Sex describes a distinctive mode of genetic exchange, carried out only by eukaryotes, that involves combining entire genomes and not just incorporating pieces. The process is both ancient and ubiquitous. While the original eukaryotic organisms, produced as fusions between archaeal and bacterial cells (Figure 6.1), may not yet have invented it, the common ancestor to all modern eukaryotes had certainly done so, since all the eukaryotic radiations (Figure 6.3) include sexual lineages. Eukaryotic sex entails the coming together of two complete genomes, two complete sets of instructions, one carried by a gamete typically called a female egg, the other a gamete typically called a male sperm. In some lineages, these two genomes may derive from the same organism—​hermaphrodites and many plants produce both eggs and sperm and can fertilize themselves—​but

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0011

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in most cases it necessitates finding a second organism, a mate. Therefore, the origin of sex marks the onset of biological relationship, a theme developed in the next chapter. In multicellular animals and land plants, sexual reproduction has been handed over to what is called the germ line—​to ovaries and testes and flowers that produce eggs and sperm that fuse to generate embryos and immature offspring and adults. The generation of offspring is essential for the continuation of the lineage, and the nurture and protection of these offspring marks the onset of a second mode of biological relationship. In animals, such nurture and protection are often entrusted to strong instincts and feeling states, as we consider later in the chapter. But first we need to look at how sex works.

WHAT DOES SEX ENTAIL? A genome contains all the instructions needed to make that kind of an organism, but in eukaryotes it is not encoded in a single strand of DNA as it is in bacteria and archaea. Instead, it is divided up into a number of DNA strands called chromosomes. A useful analogy here is to a printed encyclopedia. All the information in the encyclopedia could be printed in a single huge volume that is rolled about in a wheelbarrow, but it is more manageably organized as a set of volumes, the first containing all the A–​B information, the second the C information, for a total of, say, 19 volumes. A chromosome is equivalent to a volume, and the full set of 19 volumes comprises a genome. The genome of each species is apportioned to distinctive numbers of chromosomes: cats have 19, humans 23, goldfish 50, flies 4, corn 10, yeast 16. 136

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The chromosomes reside in the nuclei of eukaryotic cells. We have considered in Chapter 4 how their encoded genes give rise to organisms and how they are replicated and allotted to daughter cells during the mitotic cell cycle. Now our focus is how they are transmitted sexually from parent to offspring. Sex features two kinds of cells: haploid cells—​called gametes in a sexual context—​ each possess a single complete set of chromosomes, while diploid cells each possess two complete sets of chromosomes, sets that were acquired when two haploid gametes fused together. We can look at each cell type in turn.

FORMING DIPLOID CELLS The fusion of two haploid gametes—​egg and sperm—​is called fertilization, and the resultant diploid cell is called a zygote. In multicellular lineages like land plants and animals, the zygote proceeds to divide by mitosis into two cells, then four, then eight, to form an embryo. Some of these cells differentiate to form the germ line that produces haploid gametes; the rest differentiate to form the many diploid cell types—​liver, leaf, skin—​that collectively form the adult organism (Chapter 4). Returning to the encyclopedia analogy, if we could color all 19 volumes from the sperm set blue and all 19 volumes from the egg set pink, the diploid zygote and all the subsequent adult cells would have a complete set of blue volumes and a complete set of pink volumes, 38 in all, such that every entry, every gene, is represented twice. There are important advantages to having two sets of instructions. Let’s say there’s a large printer’s error in the Calcium Ion Channel entry in the blue volume 2. Chances are that the pink 137

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volume 2, printed in a different year in a different city by a different typesetter, won’t have this same error (although it may well have other errors in other entries). If you have both volumes, you have access to readable information from the pink version and hence can construct a serviceable ion channel. Expressing this in genetic terms, we say that the printer’s error corresponds to a mutation (Chapter 5), and that diploid cells, carrying two sets of instructions for making each kind of protein, are less vulnerable to deleterious mutations than haploid cells are. This allows us to understand why inbreeding—​mating with close relatives—​is associated with decreased viability: the two relatives, from the same genetic “city,” may both carry the same calcium-​channel printer’s error/​mutation and hence be unable to transport calcium properly.

FORMING HAPLOID CELLS Now we can look at the reciprocal process, the formation of haploid cells from diploids, which is more complicated but totally elegant. This happens in numerous contexts. We can consider here how it occurs in the testis of a cat. The task is to generate haploid sperm cells with 19 chromosomes from diploid testicular cells that have 38 chromosomes, 19 of which are pink (from the cat’s mother) and 19 blue (from his father). If this were accomplished by grabbing 19 chromosomes at random, the result would almost certainly be a disaster. A given sperm might wind up carrying, say, a pink and a blue chromosome #1, no chromosome #2, a pink chromosome #3, no chromosome #4, and so on. That is, you’d almost certainly create a sperm with an incomplete set of instructions for making a cat. 138

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Therefore, the rule is that you have to include a complete set of chromosomes—​a complete set of encyclopedia volumes—​in every haploid sperm nucleus. But this doesn’t mean that they have to all be pink or all be blue. You can have a pink #1 and #2, a blue #3, a pink #4, and a blue #5, so long as you wind up with one copy of each, a complete set of 19. All this partitioning takes place during an intricate process called meiosis—​the hallmark of sex in all eukaryotes—​during which the chromosomes are carefully assorted such that complete haploid sets are generated. And the consequences are profound. Our original diploid male had 19 pink and 19 blue chromosomes, whereas each sperm he produces will contain a distinctive full set of chromosomes, some pink and some blue. When any of his sperm manages to fertilize an egg, the egg nucleus will contain a set of 19 chromosomes—​we can call them paternal purple and maternal orange—​that has also been shuffled by meiosis. Therefore, while the resultant diploid zygote and kitten will have 38 chromosomes—​ some blue, some pink, some purple, some orange—​these will be very different from the sets that were present in the parents, and very different from the sets present in the other kittens in the litter. To mix things up even further, events called crossing over frequently occur during meiosis, creating patchwork chromosomes. For example, if the two copies of chromosome #11 in an egg precursor cell have undergone crossing over, then the top third of the first one might be purple and its bottom two-​thirds orange, while the top third of the second one might be orange and its bottom two-​thirds purple—​an outcome created by a precise cut-​and-​ paste swapping process. Hence eggs and sperm not only contain a sampling of each of set of parental chromosomes; they also contain new kinds of patchwork chromosomes. 139

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Another way of stating this is to say that although parents each contribute half of their genetic endowment to their children, they basically end up with strangers.

WHAT DOES SEX ACCOMPLISH? If we look at the female cat who generated the egg just fertilized, her orange and purple and patchwork chromosomes are expected to carry a different spectrum of gene sequences from the pink/​ blue/​patchwork set contributed by the sperm. Specifically, the calcium-​ion gene in the orange version of her chromosome #2 might specify a channel that transports ions particularly rapidly, whereas her purple chromosome #2 might carry a slow-​channel gene. If one of her eggs with an orange chromosome is fertilized by a sperm carrying a pink chromosome, the resultant kitten will have two kinds of channels, one rapid (orange) and one normal (pink). A littermate might inherit orange and blue versions of the gene and hence only transport calcium rapidly since the blue version is dysfunctional. In genetic terminology, we say that each kitten carries two alleles of the channel gene, where allele means “a different version.” Now we can go to all cats and look at every calcium channel gene in every chromosome #2 in the entire species. We might in this case find 12 alleles of the gene—​we can drop our color-​ coding and call them C1–​C12. Some will encode nonfunctional proteins, like our blue example, with deleterious mutations at various positions in the gene sequence. Others will carry codon changes that make no difference to the basal rate of calcium flux—​so-​called neutral alleles. Others will specify channels that 140

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work more slowly or more rapidly. The survey will also reveal that some alleles are more abundant than others: 62% might be C2, 13% C3, 3% C12, and 0.1% C8. But all are presented in the cat “gene pool.” If we move along chromosome #2, we come to the next gene, called B, that codes for an enzyme involved in making black fur. Looking at all cats, we find that 44% have the allele B1 which results in jet black hair, 17% have allele B2 which yields charcoal gray, and 39% have B3–​B16, all of which encode dysfunctional enzymes so the hair is white. The next gene, I, might be involved in implantation of the fertilized egg in the uterus, the next, P, with purring, each with its spectrum of alleles. It follows that virtually every cat chromosome #2 in the gene pool will be different from every other. The first might read C1 B3 I6 P3, the second C1 B7 I6 P1, and so on. The same will also be true of the other 18 chromosomes. Since the cat genome contains ~20,000 genes, each chromosome will on average carry 1,000 genes, meaning that the cat species harbors huge chromosomal diversity and huge allelic diversity. Running through these concepts one more time with the encyclopedia analogy, we can imagine thumbing through numerous printings of our 19-​volume encyclopedia, each volume having on average 1,000 entries. The first entry in volume 1 is always Aardvark, but there may be 18 versions (alleles) of the Aardvark spiel in the world-​wide volume-​1 pool, some informative, some different but equally informative (neutral), and some unintelligible. The second entry is always Aaron, with 27 versions. If you pick up a volume 1 in one bookstore you might find Aardvark 17 followed by Aaron 3; the next bookstore might have Aardvark 9 followed by Aaron 14. 141

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EVOLUTIONARY STRATEGY And now, finally, we can put all of this together. There are 19 different kinds of cat chromosomes, each one of its kind carrying a unique lineup of alleles. If we think of the whole pool of cat chromosomes on the planet as a gigantic collection of playing cards, then in one generation the cards are dealt out as complete sets of 19 cards held in countless gamete hands. Each fertilization brings two sets together and creates a diploid kitten that, as it matures and makes sperm or eggs, shuffles its two sets together and deals out new haploid hands. Any one of these then combines with a second new gametic hand to make a new diploid kitten, with many such fertilizations creating the next cat generation. What this means is that each sexual generation is, in effect, a whole new card game, with each cat holding a unique diploid hand and the entire gene pool dealt into countless diploid hands, all subject to natural and sexual selection. The hands—​and hence the cards—​that make it to the next generation are crossed-​over and shuffled and dealt again, with the next generation of diploid kittens again substrates for selection. Obviously, this strategy is beautifully configured to generate variety. Each diploid hand is in effect a new experiment in making a cat. Even subtle differences in the timing of gene expression or the shape or stability of the various protein products may generate differences in the cat’s ability to hunt, resist disease, or produce viable offspring. A second diploid with a different palette of alleles will come up with a different version of a cat. In genetic terminology we say that there are countless genotypes—​allelic profiles—​producing countless phenotypes—​how the organism turns out. 142

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Sexual populations deal all their hands, strut their stuff, at each generation rather than going out on a limb and specializing in one particular phenotype the way an asexual population tends to do. Asexual specialization can sometimes be a good idea over the short haul, when a particular facet of a niche can be exploited by a particular phenotype. But over the long haul, environments change, and the specialized populations lack allelic reserves to enable going with the environmental flow. A classic example of sexual population dynamics involves moths (see Frontispiece to Chapter 6). Prior to the industrial revolution, light-​colored moths in England were camouflaged from their bird predators by resting on tree limbs covered with gray-​green lichens. When industrial pollution killed the lichens, exposing the underlying dark bark, dark-​colored moths were camouflaged and came to predominate. When pollution came under control and the lichens re-​established themselves, the light moths returned. Both the light and the dark sets of alleles were harbored in the moth populations; natural selection influenced their relative frequencies. Overall, then, two reproductive strategies seem to win the evolutionary lottery every time. The first is to be asexual and make as many specialized organisms as you can before the niche changes—​the strategy of bacteria, archaea, and self-​fertilizing multicellular organisms. The second is to be sexual and out-​ crossing, making enough different kinds of organisms in one generation that at least some will flourish in the niches available and the whole enterprise—​the whole lineage—​keeps going. The fact that eukaryotic sex persists in all modern eukaryotic lineages despite its inconveniences indicates that it usually wins the eukaryotic lottery. 143

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NURTURE In land plants and animals, genomes are entrusted to a new class of individuals: the immature offspring that emerge from embryos. Therefore, the nurture of offspring is fully as important as surviving long enough to produce them. Nurture is manifested in countless ways. Land plants go to great lengths to ensure that their fertilized ovules are surrounded with nutritious endosperm and hardy seed coats. Butterfly pupae snuggle in cocoons. The social insects stagger out of disturbed nests with larvae in their mouths to carry to the next refuge. The vertebrates, and particularly the mammals and birds, engage in a stunning array of behaviors to assure the survival and maturation of their progeny. Our love for our children has deep roots.

REFLECTIONS We have thus far considered two ways to think about caring for others. We have acknowledged our deep genetic homology with all of life and the affinity, the fellowship, that emerges from that knowledge (Chapter 6). We have also celebrated our capacity to experience empathy with other creatures and respond to their concerns as our own (Chapter 8). And now we encounter our biological imperative to nurture our offspring, sacrificing, if need be, our lives on their behalf. My own experience with this imperative came when, alone on a beach with my youngest son, I saw him being dragged out to sea. I jumped in, fully clothed, and as I swam out, I realized that I was taking in huge amounts of water as I navigated the strangely 144

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turbulent surf. My brain displayed the headline: This Is How People Drown in Rip Tides. I looked ahead at James’s terrified face bobbing above the waves, and the next realization came to me not as a headline but as an understanding: Either both of us survive or both of us drown. I reached him and helped him to shore with a calm conviction that was somehow outside myself, and as we stood together on the empty beach, I absorbed my new self-​ knowledge: I am endowed with an inherent maternal altruism, unrehearsed, that is poised to flood my being whenever my children are in danger. There is no way to describe the joy that attends this kind of knowledge. It seems likely that the emotions evoked when we absorb our evolutionary affinity with other creatures, and when we are infused with compassion, will turn out to map closely onto the pathways that drive our basal parental and nurturing instincts, emotions that generate such feelings as tenderness and warmth and protectiveness. These same emotions extend to our understanding that the Earth, the planetary matrix, must be nurtured as well, an understanding embedded in many religious traditions and explored in Chapter 13. We nurture our children selflessly, and we also recognize them as our most tangible sources of renewal. For a child, the world is always new. Renewal has been a religious theme throughout the ages, be it the Jews exhorted to return to Jerusalem after their exile in Babylon or the disciples exhorted by Jesus and Mohammed to petition God/​Allah for redemption of the spirit. All of us see in children—​our own children and all children—​the hope and promise of what we humans can become. As the forbears of our children, we are called to transmit to them a joyous vision of their future—​meaning that we are each called to develop such a vision. 145

Chapter 10

INTIMACY

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e have seen in the last chapter that sex is a core feature of the eukaryotic way of doing things and that it can generate the core imperative to nurture offspring. But sex generates another necessity as well: Gametes carrying haploid genomes must, at each sexual generation, fertilize other gametes to create new diploid organisms. Bacteria and asexual amoebae have no such burden: their sole commitment is to go through a cell cycle, divide in two, go through another cell cycle, divide in two again, ad infinitum. By contrast, obligately sexual creatures must also, at a minimum, produce gametes that find, recognize, and fuse with gametes of the same species and opposite mating type, a far more ambitious proposition. Still more ambitious are the animals that keep their gametes inside their bodies rather than spewing them out into the water or the air and hoping for the best. In these cases, it becomes necessary to first identify the animal of the correct species and opposite gender and then engage in successful copulation with that animal such that the gametes can fuse. These animal strategies entail relationship, if only briefly, between sexually mature males and females, and they presumably share homologies with the elaborate emotional networks

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0012

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that undergird human sexual relationships in their various manifestations. They are also manifest in the embedded relationships that develop between two parents and between parents and their offspring—​ both illustrated in the chapter frontispiece—​and, in humans, in our relationships with close friends and with other animals. All represent various versions of intimacy, a word that has come to connote sexual intimacy but is used here in its original sense: from the Latin intimus, innermost, and intimare, to make familiar. We come to know one another deeply; these relationships have been described as “thick,” as contrasted with the “thin” relationships we hold with most other beings.

SEXUAL ATTRACTION All sexual eukaryotes locate their mates, or the gametes of their mates, by some form of attraction/​recognition. When we considered sexual organisms in Chapter 9, we described multicellular eukaryotes like cats and land plants, but in fact, unicellular eukaryotes are the original sexual organisms, and sex continues to be a common feature of their life cycles, where attraction and recognition play key roles. As an example, we can consider a single-​celled green alga called Chlamydomonas, which lives in temperate ponds and soils and swims using a pair of motile appendages called cilia. Each haploid cell, about 10 micrometers in diameter, divides by mitosis to produce more haploid cells, but under adverse conditions, in this case nitrogen-​depletion, each also has the capacity to differentiate into a gamete and fuse with another gamete to form a diploid zygote. The zygote secretes a protective wall around itself to 148

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become a dormant spore and then, when conditions improve, the spore undergoes a canonical deck-​shuffling meiosis, generating haploids that hatch from the spore wall and proceed to divide mitotically until, at a later stage, some are triggered by nitrogen depletion to undergo gametogenesis. This life-​cycle pattern is said to employ “facultative sex”—​sex isn’t required at each generation as in multicellular organisms but is instead employed on occasion to take advantage of the card-​shuffling benefits of chromosomal reassortment, the gamble being that some of the recombinant progeny will be better at navigating future environmental challenges. There are two Chlamydomonas mating types, called plus and minus. When plus cells are induced to undergo gametogenesis, they express sets of plus-​specific genes; minus cells switch on minus-​specific genes. Each plus gamete produces proteins called plus agglutinins that are displayed on its ciliary membranes; each minus gamete produces and displays complementary minus agglutinins. When opposite-​type gametes swim past each other, their agglutinins stick to one another, triggering signal transduction cascades that first activate cell-​fusion programs and then the stages of zygote maturation. Similar kinds of adhesive interactions initiate fertilization between the eggs and sperm produced by multicellular plants and animals: proteins on the surfaces of starfish sperm bind to receptors on the surfaces of starfish eggs. Such simplicity can become highly complex. Land plants, for example, produce elaborate flowers so that insects or birds will be lured to brush against their anthers and transport their pollen grains to the stigmas of other flowers, promoting outcrossing. Each pollen grain then sends a long tube down into the ovule where it locates an egg by a set of surface 149

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receptors; when contact is made, the tube ruptures, releasing two sperm cells whose egg-​binding proteins then mediate egg-​sperm recognition and fusion. Animals take the behavioral possibilities for sexual attraction to every imaginable extreme, where it is usually the males who call attention to themselves and the females who evaluate their efforts, with differential success often leading to the evolutionary dynamic called sexual selection (p. 81). Fireflies pulse, fruit flies beat their wings, moths seek out musk, fish dance, frogs croon, mammals strut and preen, birds display feathers, sing, and dance (Frontispiece to Chapter 8). If this is a planet shimmering with awareness, then a great deal of that awareness is focused on the sexual signals that eukaryotic creatures send to one another. When we look to our closest relatives, the bonobos and the chimpanzees, we find distinctive approaches to sexuality. Bonobos copulate freely, and the females also have sexual encounters with one another many times a day, sometimes to reduce levels of conflict or solidify friendships, but often just because they seem to enjoy doing so. The chimpanzees, in contrast, engage only in heterosexual copulation, and only when the female is in heat. Neither group is monogamous, and while dominant male chimpanzees may attempt to monopolize access to one or several females, dalliances occur frequently, often with males in a neighboring troop. The range of human sexual behavior includes all of the above. Many humans also enter into committed partnerships/​marriages and engage in co-​parenting. This commitment feeds into the second facet of sexuality, the need for other, and its generation of intimate relationship. 150

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THE NEED FOR OTHER All sexual organisms depend on interacting with mates if they are to transmit their shuffled genomes to the next generation, interactions that animals doubtless experience consciously. In addition, animals who co-​parent their young, like the albatross in the chapter frontispiece and the swans in the Frontispiece to Chapter 5, create ties with one another that can in many cases last a lifetime. In addition, newborn birds and mammals form vital bonds with their all-​important parent or parents and engage in intimate interactions, both playful and snuggly, with their siblings. Our human feelings of affection for our mates and parents and siblings flow through longstanding networks. Human pair-​ bonding and co-​ parenting are encountered in all human cultures, and parent-​child bonding happens at every human birth. Psychologists have long posited that our love/​need for our mates shares many feeling systems with those that accompany our love/​need for our parents, albeit expressed at different stages of maturity and experienced very differently, and that these feelings extend to siblings and close friends and beloved animals. Certainly they have in common a rich intensity. Our thick relationships can be compelling and joyous. Alas, of course, they can also be fraught with conflict. We confront, often clumsily, the imperative that we separate from our parents while retaining our affection for them. We struggle to accommodate our love for our mates, and our need for their reliability and trust, with the experience that we elect to call temptation. When we find ourselves estranged from or betrayed by our mates or friends or children, we can be torn apart by jealousy, loneliness, desolation, and anger; hence we carry fears of disapproval 151

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and abandonment. Should we encounter a fluidity in gender identification or sexual preference, these self-​understandings are often subject to scorn or attack by our intimates, frequently in the name of religious taboos. Intimacy can bring both joy and sorrow.

REFLECTIONS We humans not only experience the richness of our own self-​ experience (Chapter 7). We also engage in intimate connection with other human beings, both families and friends, and with nonhuman beings, most commonly our dogs and cats. But given the complexities of human-​style intimacy, an enormous attraction of theistic religions has been that they offer the opportunity for intimate relationship with a deity or deities. Indeed, they often suggest that the most stable and fruitful outlet for intimacy is with the Divine. These relationships can be abstract, as in indigenous prayers to cosmic concepts like the Great Spirit or the Earth Mother, or they can be intensely personal, as in the devotion accorded to Krishna in some Hindu traditions. The Abrahamic traditions contain images of God as stern and judgmental, to be sure, but Judaism includes as well the concept of a protective and affectionate father, as in Psalm 23:

The Lord is my shepherd; I shall not want. He maketh me to lie down in green pastures. He leadeth me beside the still waters. He restoreth my soul. He leadeth me in the paths of righteousness for his name’s sake. Yea, though I walk through the valley of the shadow of death,

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Such personal relationships are particularly salient in the Christian traditions. The reward of Christian faith, we learn, is the inexhaustible, unconditional love that flows from God the Father and Mary the Mother and Christ the Redeemer and, in Catholic traditions, a panoply of saints. They are there for us, they listen and respond, they offer forgiveness, they will never abandon us and seek only our love in return. As in these hymns and prayers. Jesus, the very thought of thee with sweetness fills the breast; But sweeter far thy face to see, and in thy presence rest. O hope of every contrite heart, O joy of all the meek, To those who fall, how kind thou art! How good to those who seek. But what to those who find? Ah, this nor tongue nor pen can show; The love of Jesus what it is, none but his loved ones know.

—​Bernard of Clairvaux, 1153

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The Sacr ed Depths of Natur e Jesus, priceless treasure, source of purest pleasure, Truest friend to me, Long my heart hath panted, till it well-​nigh fainted Thirsting after thee. Thine I am, O spotless Lamb, I will suffer naught to hide thee, Ask for naught beside thee. —​Johann Frank, 1653

Jesus, lover of my soul, let me to thy bosom fly, While the nearer waters roll, while the tempest still is high. Hide me, O my Savior hide, till the storm of life is past; Other refuge I have none, hangs my helpless soul on thee; Leave, ah! leave me not alone, still support and comfort me. All my trust on thee is stayed, all my help from thee I bring. —​Charles Wesley, 1740

So we arrive here at what is, for many, the heart of it all. If there is a major tension between a nontheistic approach like the religious naturalist orientation and the monotheistic traditions, it centers on the question of whether or not one experiences some version of a personal God or gods. Most people immersed in monotheism would probably say that “being religious” includes “having a relationship with God.” Indeed, when reminded that personal gods are not inherent in many other religious traditions, they might question whether these traditions are really religions and not philosophies. For me, and probably for all of us, the concept of an interested and caring god can be appealing. In times of sorrow or despair, I often wonder what it would be like to be able to pray to God or Allah or Jehovah or Mary or Krishna and believe that I was heard, believe that my petition for relief and comfort might be answered.

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When I sing the hymns of faith in Christ’s love, I am drawn by their intimacy, their allure, their poetry. But in the end, such faith simply isn’t available to me. I can’t go there. I lack the resources to render my capacity for love and my need to be loved to supernatural Beings. And so I have no choice but to pour these capacities and needs into thick relationships with human and nonhuman beings, fragile and mortal and difficult as they can sometimes be. Earthly intimacy is a gift, filling our lives with experiences of loving and being loved in all sorts of beautiful ways. There are creatures whose children float   away at birth, and those who throat-​feed their   young for weeks and never see them again. My   daughter is free and she is in me—​no, my love of her is in me, moving in my heart, changing chambers, like something poured from hand to hand, to be weighed and then   reweighed. —​Sharon Olds, “High School Senior”

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Chapter 11

MULTICELLULARITY AND DEATH THE GERM/​SOMA DICHOTOMY

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ost eukaryotes are single-​celled organisms, including some fungi (e.g., the yeasts used in baking and brewing), most algae (e.g., Chlamydomonas, introduced in Chapter 10), and all protists (a generic term for numerous radiations, including amoebae and ciliates and diatoms (Figure 6.3)). They originated via a fusion between an archaeal cell and a bacterial cell, which was converted into a mitochondrion. One lineage went on to ingest and domesticate a photosynthetic cyanobacterium that became a chloroplast (p. 96). All variously populate the oceans, lakes, streams, and soils of the Earth, and all are key constituents of the food chains in the planetary matrix. As we saw in Chapter 10 for Chlamydomonas, many unicellular eukaryotes engage in “facultative” sex: they commonly reproduce by mitotic cell divisions, but particularly under adverse environmental circumstances, they may instead differentiate into sexual gametes of opposite mating type, fuse to form resting spores, undergo meiosis when circumstances improve, and re-​initiate

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0013

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mitotic growth. Some unicellular lineages may have lost this ability and are truly asexual, but many may instead engage in facultative sex so infrequently, or under such unusual circumstances, that it has not yet been documented. Animals evolved from a sexual protist, probably some sort of amoeba, ~600 million years ago, and land plants evolved from a lineage of sexual unicellular green algae ~300 million years ago. All modern multicellular lineages are sexual, and indeed, the invention of sex was necessary for multicellularity to evolve. To understand what this means, we can consider the diploid zygote—​the fertilized egg—​of a multicellular animal. Whereas the Chlamydomonas zygote has admirable but modest potential—​it can form a protective spore wall and it can engage in meiosis—​the animal zygote proceeds to cleave into two, then four, then eight diploid cells, with the daughter cells remaining together as a developing embryo (Frontispiece to Chapter 4). And then all of them start to specialize. We considered the basics of this specialization process in Chapter 4. To expand the story, let’s focus on one of the cells in a hypothetical 8-​cell embryo—​we can call it Cell #6—​a cell programmed to switch on a certain subset of genes. In the ensuing 16-​cell embryo, both of the #6 daughter cells have synthesized the proteins encoded by these genes, and some of them activate promoters associated with a second subset of genes. In the 32-​ cell embryo, the proteins encoded by the second subset include components of a signal-​transduction cascade, which is triggered in the four Cell #6 granddaughters when they detect a hormone secreted by cells elsewhere in the embryo. The cascade endows the granddaughters with the ability to move together to a new region of the embryo, and several cleavages later, the Cell #6 descendants 158

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move in unison to the embryo interior, a process called gastrulation, where the now 512 descendants are subject to several fates: 64 of them, at one end of the embryo, activate a subset of genes that allow their daughters to eventually differentiate into brain cells; another 128, near the midline, activate a program that ultimately generates heart cells; and so on. We can next focus on Cell #3 in our 8-​cell embryo. It activates the expression of genes that commit its descendants to become germ-​line cells—​cells capable of undergoing meiosis to generate eggs or sperm. These migrate into regions that will become the gonads. If the animal is a female mammal, the germ cells undergo meiosis in the fetus, and the resultant eggs—​~400,000 in humans—​are stored in the ovaries until individually released at and after puberty. If the animal is a male mammal, the germ cells remain dormant until puberty, at which time they activate their capacity to undergo meiosis and produce, in human testes, several million sperm cells per day. In flowering plants, the commitment to produce a germ line and construct gonadal equivalents (pistils and stamens) occurs later in adulthood, but the same goal is achieved: the germ line is segregated from the rest of the mature organism (chapter frontispiece). We can now stand back and appreciate the beauty of this arrangement. The dichotomy between the germ-​line cells and remaining somatic (body) cells effectively parcels out the job of being alive. Transmission of the genome to the next generation is entrusted to the germ line, while negotiating the niche so that the germ cells are successfully transmitted is entrusted to the soma. The germ line is safely sequestered in the gonads or pistils/​stamens, nurtured by surrounding tissues, its genomes released only at appropriate times; the somatic cells are the ones that perceive and 159

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move and photosynthesize and sprout feathers and pump blood and make love.

MORTALITY AND IMMORTALITY One of the fates that is often programmed into particular cells or cellular lineages during the course of embryogenesis or during post-​natal maturation is that those cells should die, a process known as apoptosis. Thus the limbs of a human embryo initially grow out as blunt stubs, after which sets of cells die in order to create separate fingers and toes. And every autumn, in every deciduous tree, the cells at the base of each leaf stem are programmed to undergo apoptosis such that the flow of nutrients is cut off and the leaves themselves die and detach, as illustrated in the chapter frontispiece. The more general fate of the multicellular soma is that the whole soma dies. If this death is premature, before its genome has had time to be successfully transmitted to the next generation, we say that the organism was either unfit (an insect incapable of flight) or unlucky (an insect eaten by a bird). But if death happens after genome transmission to sons and daughters has taken place, then we say that that organism, that self, has carried out its long-​term biological aim of self-​reproduction. Natural death may occur after only a few days of life, as with some kinds of adult insects, or it may be postponed for hundreds of years, and hundreds of procreation cycles, as is the case for some kinds of trees. Eventually, though, the sequoias die just like the fruit flies. If we don’t die by malnutrition or accident or infection or a dysfunctional organ system, we die because we just 160

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get old. A friend describes her husband’s last two years before his death at the age of ninety-​one: “It just got slower and slower, and less and less, and then he stopped being interested in eating, and then drinking, and then he stopped breathing.” So is there such a thing as an immortal organism? The answer is yes, but immortal organisms are by definition of limited complexity. There is no death programmed into the life cycle of a bacterium or an amoeba. For sure, the cells can be killed by boiling or starvation—​the cells are fully mortal—​but they don’t have to die. The same is true for the alga Chlamydomonas: the cells need to have occasional sex in their natural habitats—​they must form heavy-​walled spores to protect their genomes from freezing and desiccation—​but in the laboratory they keep on dividing indefinitely as long as we provide them with light and moisture and appropriate salts. By the same token, tumor cells, in scientific terminology, are said to be “immortalized”: they carry mutations in key cell-​cycle genes (p. 67) such that they don’t know when to stop dividing, either in our bodies or in the laboratory. But once you have a life cycle with a germ line and a soma, then immortality is handed over to the germ line. This allows the soma to instead focus on staying alive long enough for the gametes to be transmitted. And since morphogenesis is the key niche-​ negotiating strategy of eukaryotes (p. 95), multicellular somas have generated every complex morphological structure imaginable: wings, gills, eyes, leaves, glands, talons, bark, nostrils, root hairs. All of these parts are highly specialized, and although each cell in each part retains two full copies of the genome, transmission of their somatic genomes to the next generation is not included in the arrangement. The arrangement is that the parts will do their utmost to keep the organism flourishing long enough to 161

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ensure the transmission, and the nurture, of the germ line, and then they die. One of these “parts” is my brain, the locus of my self-​awareness, my I-​self. My brain developed with nary a backward look at gene transmission or immortality. The whole point was to make synapses, modulate and reconfigure them, with countless neurons dying in the process by apoptosis and countless more dying during my lifetime, many as I sit here typing. It is because these cells were not committed to the future that they could specialize and cooperate in the construction of this most extraordinary, and most here-​and-​now, center of my perception and feelings. So our brains, and hence our minds, are destined to die with the rest of the soma. And it is here that we arrive at one of the central ironies of human existence, which is that our sentient brains are capable of experiencing deep regret and sorrow and fear at the prospect of our own deaths, yet it was the invention of death, the invention of the germ/​soma dichotomy, that make possible the existence of our brains.

REFLECTIONS All religious traditions offer ways to think about death, usually in the context of some form of immortal soul, a parameter that we considered in Chapter 7. For those of us who do not “believe in” immortal souls, there are two kinds of responses to death. The first is the response to the death of someone loved, or a death that is premature or senseless like a school shooting or a bird hitting the window. These directly ravage our personal sense of relationship and activate our 162

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compassion, and we experience unmitigated grief. I was told of a school-​age child whose mother was killed in a car crash—​how weeks later he would go into her clothes closet and bury his face in her dresses so that he could smell her smell. I am undone by his savage loss, and outraged by her death, even though these people are strangers to me. Our sorrow at the death of others is a universal human emotion that transcends cultural and religious particularities. And indeed, elephant, dolphin, whale, and nonhuman primate mothers have been observed carrying their dead babies around for several days, indicating that grieving far antedates our humanness. And then there is the response to the fact of death itself and, in particular, to the fact of my own inevitable death. When I wonder what it will feel like to be dead, I tell myself that it will be like before I was born, an understanding that has helped me to cope with my fear of being dead. But what about the fact that I will die? Does death have any meaning? Well, yes, it does. Sex without death gets you single-​celled algae and fungi and protists; sex with a mortal soma gets you the rest of the eukaryotic creatures. Death is the price paid to have oaks and clams and geese and grasshoppers, and death is the price paid to have human-​style consciousness, to be aware of all that shimmering awareness and all that love. My somatic life is the wondrous gift wrought by my forthcoming death.

O’er all the hilltops Is quiet now, In all the treetops Hearest thou Hardly a breath;

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HUMAN EVOLUTION BIOLOGICAL SPECIATION

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ukaryotic sex has been foundational to the evolution of nurture (Chapter 9), the evolution of intimacy (Chapter 10), and the evolution of multicellularity and death (Chapter 11). Here we consider a fourth manifestation: Sexual eukaryotes came to adopt the evolutionary pattern known as biological speciation, which can follow many pathways but eventually segregates organisms into those that will and will not mate to produce fertile offspring. Such segregation allows each species to specialize in distinctive traits suited to distinctive habitats and has generated the splendid biodiversity of eukaryotes that we admired in Chapter 6 (Figure 6.3). Diverging species rapidly evolve new mating phenotypes that reinforce their segregation: sister species of Chlamydomonas algae produce new pairs of ciliary agglutinins (p. 148); fruit flies come up with new versions of their dances; fireflies pulse with new frequencies; birds display feathers with novel patterns and colors. Figure 12.1 depicts the overall pattern of the speciation process. Each species is represented by an inverted teardrop, where the length of each teardrop indicates how long that species exists before going extinct, and the width indicates the “niche dimensions”

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0014

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Niche Dimensions = extinction bar

Fig 12.1  Speciation patterns.

of the species—​the range of the available habitats that can be successfully negotiated by members of the population at each generation. Each narrow sideways branch represents a speciation event, during which a new species not only becomes sexually isolated but also comes to inhabit a distinctive niche dimension. The “extinction bar” in the middle of the drawing represents a catastrophic change in the niche that wipes out the three mid-​positioned species, but the lineage as a whole keeps going, and indeed, with time, the devasted niche is restored and becomes repopulated with new species in the lineage. Figure 12.1 can also be viewed through the lens of common ancestry (Chapter 6): the species colored blue is the common ancestor to all the others on the left; the species colored orange is the common ancestor to all those on the right. Biologists have codified such relationships into taxonomies. A group of similar species that shares common ancestry is called a genus; groups of 168

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genera that share common ancestry are called Families; Families are grouped into Orders, Orders into Classes, Classes into Phyla, and Phyla into the three super groups (Figures 6.1–​6.3). Present-​day finches, for example, all belong to the Order Passeriformes and the Family Fringillidae, which contains more than 200 identified species belonging to 50 genera. Their most recent common ancestor lived 10–​20 million years ago, and numerous extinctions have occurred during the interval. In this chapter we will focus on speciation in the Great Ape Family (Hominidae), which branched from within the Primate Order at least 10 million years ago. Particular attention will be given to a lineage, called the hominins, that diverged from the great-​ape tree ~7 million years ago and birthed the modern human genus, called Homo, some 6.7 million years later, with now-​extinct genera like Australopithecus branching off along the way. Modern humans are by definition all members of the same species, Homo sapiens, since we are fully interfertile. We will close the chapter by looking again at the key trait that distinguishes the modern human species from our modern great-​ ape cousins—​our fluent use of symbolic language—​and consider how it might have evolved in the context of our brains and our cultures.

GREAT APE SPECIATION Figure 12.2 shows the human family tree, where we branch in the thick of the other great apes ~7 million years ago, with chimpanzees and bonobos, hereafter collectively called chimps, diverging after we split off. The dashed circle marks the common ancestor to modern 169

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Human

Gorilla

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10

15 Millions of years ago

Fig 12.2  Evolutionary tree of the great apes. Dashed circle: the common ancestor to chimpanzees, bonobos, and humans.

chimpanzees, bonobos, and humans. To think about this common ancestor is to absorb important concepts about who we are. You may recall our account of the Snake God story (p. 90), where parts of the story were conserved and parts reconfigured as it spread to new civilizations. Applying this thinking to the evolution of bonobos, humans, and chimpanzees, we can say that if a trait is evident in all three lineages, then it was likely found in our common ancestor as well, meaning that the common ancestor had a chimp body plan, dexterous hands, dark skin, a complex sociality, robust emotions, and an intelligence that includes self-​ recognition in a mirror and the ability to learn features of human symbolic communication. We can further say that a trait displayed 170

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by only one of the three lineages probably arose after the three-​ way divergence; this would include an inborn facility with symbolic language for humans. And finally, we can say that if a trait shows up in two of the three, it was likely present in the common ancestor and subsequently lost by one of the branches. So, chimps are arboreal and covered with thick hair, humans are not; hence the common ancestor was presumably arboreal and hairy, and humans lost both traits along the way.

COMPARING CHIMP AND HUMAN GENOMES Fossilization is rare in the rainforest habitats of nonhuman apes; hence the physical features of our common ancestor (Figure 12.2) have been difficult to document. The quest to understand our origins has therefore centered on the fossil record that is found in genome sequences. When chimp and human genomes are compared, 99% of their protein-​encoding sequences prove to be near-​ identical, and most of the proteins with distinctive amino-​acid sequences are involved with traits such as immunity, olfaction, and male fertility. Such protein conservation should not surprise us. As we’ve noted (p. 158), the development of multicellular organisms has everything to do with the timing and spatial segregation of gene expression in the embryo; the genes themselves, and the proteins they encode, usually have ancient histories. Same piano keys, different chords and melodies. Hence the search for the sources of great-​ape differences has shifted to looking at the non-​protein-​encoding parts of the genome, where sequences that regulate gene expression are known to reside. Here the terrain is challenging. In chimps and humans (and 171

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most vertebrates), only ~1.5% of genomic DNA contains protein-​ encoding genes. The remaining 98.5%, corresponding to some 3 billion nucleotides in great apes, was originally called “junk” since it is loaded with quasi-​parasitic elements (transposons) that play no known role in constructing an organism. But some of the remaining junk sequences are proving to be vitally important, including regions that function as enhancers. You may recall that protein-​encoding genes consist of two domains: the downstream sequences encode the amino-​acid sequence of the protein, and the contiguous upstream sequences contain regulatory domains, called promoters, that are recognized by transcription factors and govern whether and when and where the gene is expressed (p. 65). It turns out that gene expression in multicellular plants and animals is also influenced by DNA sequences called enhancers. Enhancers are found in the vicinity of, but not necessarily contiguous to, protein-​encoding genes; they also bind to transcription factors and somehow influence the transcription of target genes even when the targets reside thousands of nucleotides away. Enhancers are hard to identify, but some that have been identified carry pronounced sequence differences between humans and chimps, suggesting that they may have played roles in generating chimp/​human divergence, perhaps during embryonic and fetal development.

COMPARING EARLY DEVELOPMENT IN CHIMPS AND HUMANS Animal embryos, including chimp and human, are all constructed on the same basic body plan, governed by a family of genes called 172

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Hox that encodes a family of transcription factors. One combination of Hox proteins initiates a cascade of gene expression that designates a region of the embryo as the head, another combination initiates thorax, another legs, another tail. Additional genes convey additional positional instructions–​dorsal vs. ventral, external vs. internal. This body-​plan theme has been subjected to countless variation for more than 500 million years: in each animal lineage, the Hox genes have divergent sequences and are expressed at distinctive rates and in all sorts of temporal and spatial combinations to produce all manner of embryos and hence all manner of adults. As in the musical form called theme and variations, the core Hox theme is always present: there’s always a head, a middle, and a tail end, be it worm, fly, fish, bird, or human. Hence our bodily differences with chimps—​foot anatomy (Figure 12.2), arm length, jaw size, hair distribution—​represent recent riffs on the theme called the great-​ape body plan and, more deeply, the animal body plan. Hox genes also pattern the overall anatomy of the brain (Figure 7.1), and the embryonic neurons that migrate into the cranium express brain-​specific transcription factors. The protein sequences of these transcription factors are virtually identical in all vertebrates, but the expression of their encoding genes is often regulated by enhancers, and in some cases, the DNA sequences of these enhancers are found to be very different when humans are compared with other apes. Possibly, then, in the developing human brain, such novel enhancers promote expression of conserved target genes for longer developmental periods, or during different developmental stages, or in different parts of the brain than in developing chimps, resulting in variant brain organization and hence specialization. 173

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Given such understandings, it is obviously inaccurate to speak of a gene as being “for” a particular mental capacity. True, a mutant allele encoding an aberrant protein may in some cases generate an atypical or even lethal brain-​function outcome, but this is not because that gene encodes that outcome; it’s because the aberrant protein is defective in pointing neurogenesis in a particular direction. Humans develop slowly compared with other apes: our neonates are basically helpless whereas newborn chimps soon scamper about. Moreover, the length of human childhood is considerably extended: the average onset of puberty is 9 years in chimps and 13 years in humans. By slowing things down, the developing human brain has presumably had more time to explore and consolidate cognitive trajectories, including those needed for symbolic-​language facility. However it happened, during the 7 million years since our hominin lineage diverged from the other apes, human brains got three times larger, mostly due to expansions of the cerebral cortex and prefrontal cortex, domains that execute or coordinate most of the “higher” functions of vertebrate brains. These expansions presumably participated in generating our cognitive distinctiveness.

HOMININ EVOLUTION The oldest known hominin fossil, in the genus Sahelanthropus, lived 6–​7 million years ago in west-​central Africa; Lucy, the most famous early fossil, in the genus Australopithecus, lived 3.2 million years ago in east Africa. These early hominins had taken the important step of evolving human-​style upright posture, while 174

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their brain size remained about the same as that of a chimp (~400 cubic centimeters). Increased brain size (~600 cc) is seen in early fossils of the genus Homo ~2.8 million years ago and continues through Homo erectus (~900 cc) and then, explosively, in both Homo neanderthalensis and Homo sapiens (~1,350 cc), whose most recent common ancestor lived in Africa ~800,000 years ago. The history of the Homo genus, defined by human-​ like proportions of arms and legs, is fascinating. The earliest fossils of H. erectus, found in Africa, date to ~2 million years ago. A subset of this African population then initiated journeys into Asia ~1.8 million years ago, and their most recent fossils, found in Java, Indonesia, date to 110,000 years ago. Which is to say that H. erectus survived for nearly 2 million years before it went extinct. Early H. erectus chipped rocks to produce sharp edges and later fashioned sophisticated axes. There is as yet no evidence that they used symbolic language. Meanwhile, back in Africa, a second Homo lineage arose ~800,000 years ago and branched, ~500,000 years ago, into two anatomically distinctive species, Homo neanderthalensis and Homo sapiens, both of whom possessed large brains. Subsets of the H. neanderthalensis population then undertook journeys into Europe and Asia ~450,000 years ago; their most recent fossils, found in Spain, date to 40,000 years ago. Recent H. neanderthalensis lived in social groups, produced a sophisticated panoply of tools, fashioned hides into clothing, used shells to make jewelry, created pictorial art, and buried their dead with ceremony. The time-​ worn characterization of Neanderthals as stupid brutes is clearly incorrect. A lone fossil of Homo sapiens dating ~200,000 years ago has been found in Greece, indicating that our predecessors occasionally 175

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took short-​lived sojourns to the north, but in general H. sapiens stayed in Africa, where the oldest fossils date to ~300,000 years ago and an indubitably modern human skull from Ethiopia, illustrated in the chapter frontispiece, dates to ~160,000 years ago. Hence human evolution occurred in Africa. Local coalitions formed but migration and interbreeding were common, generating what is called a pan-​African population. Subsets of this population then began migrating out of Africa ~100,000 years ago, first populating southern Asia and Oceania, then Europe ~54,000 years ago, and then the rest of the world, with some of the migrants’ descendants returning to Africa to interbreed with those who had elected not to travel. During the course of these migrations, humans encountered pockets of H. neanderthalensis and engaged in interbreeding, which is to say that while H. neanderthalensis and H. sapiens are clearly distinct species by anatomical criteria, they did not reach the stage of obligate reproductive isolation (p. 168). Moreover, some of the migrants who reached southeast Asia encountered yet another now-​extinct Homo population called the Denisovans, with whom they also interbred. Hence the genomes of some modern humans now carry a small proportion of Neanderthal and/​or Denisovan DNA sequences.

EVOLUTION OF SYMBOLIC LANGUAGE The richest and most flexible meaning systems make use of symbols. A symbol, when perceived, brings something in addition to itself into awareness, such as an object or an emotion or an idea or a cultural tradition, and symbols encoded as words can be 176

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combined via syntactical conventions to construct narratives and convey information (teach). So far as we know, humans are unique among extant creatures in their innate ability to create and manipulate symbols as neural representations, as languages, and as art. We can teach nonhuman apes to understand certain features of our languages, but to humans these understandings come spontaneously at about two years of age. Children are “language-​ready.” Human evolution has included the co-​ evolution of three modalities—​the brain, symbolic language, and culture—​each feeding into and responding to the other two and hence generating complex patterns and outcomes. During the co-​evolution of brains and language, for example, children’s brains began to acquire the capacity to learn and use symbolic language. Symbolic language, in turn, evolved so as to more readily be learnable by children’s brains which, in turn, evolved to better utilize and understand the new configurations of symbolic language, and so on. While the capacity to learn symbolic language is inborn in the human child, the languages themselves are not, in contrast to such animal communication systems as alarm calls and mating vocalizations and laughter. Instead, the responsibility for language transmission has been off-​loaded onto the cultures that humans construct. Once language-​based communication became key to human life, culture effectively became an artificial but vital niche to which human brains, and hence human beings, have adapted, much as beavers have adapted to the aquatic niches they create. The evolution of the human ability to think and communicate symbolically was likely an incremental process, involving multiple brain domains and spread out over many hundreds of thousands of years of African history. Recent examples of this ability are manifested in African stone art (140,000 years ago), 177

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jewelry (75,000 years ago), and bone flutes (45,000 years ago) and in the cave paintings of Indonesia (45,000 years ago) and Europe (30,000 years ago). We have no idea when humans began talking to one another, nor what they were saying, but an intriguing notion is that a facility with language, and hence an ability to convey one’s romantic feelings during courtship, was a focus of what is called sexual selection or mate-​choice (p. 81). The enhanced mating success of articulate wooers might have translated into an accelerated, perhaps even runaway, evolution of nuanced language capabilities.

EVOLUTION OF HUMAN CULTURE Our Eurocentric histories depict humans as living in small hunter-​ gatherer groups, migrating to obtain resources, until ~10,000 years ago when they invented agriculture, settled down, established the principle of land ownership, and lived in caste-​structured fiefdoms often ruled by warring monarchs. In fact, our cultural history is far richer, more diverse, and more interesting than this. Archeologists have encountered numerous examples of elaborate large-​scale human communities throughout Eurasia, North America, and Mesoamerica that were established well before the European settlements and that engaged in a mixture of agricultural and hunting/​gathering practices. Their architecture and artifacts indicate that land was communal and that governance did not usually include a dominant ruler. To be sure, monarchy-​style power structures were in some cases able to insert themselves into such communities, but such power structures are by no means an obligate feature of human social organization. 178

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DOMESTICATION Humans have been domesticating nonhuman animals for millennia. Domesticated animals share a suite of anatomical features called the domestication syndrome, allowing archeologists to identify their bones in excavation sites. Domesticated dogs show up 15,000 years ago, domesticated sheep 11,000 years ago, and cattle, pigs, and cats shortly after that. Present-​day domesticated animals have more recently been found to share a suite of embryological patterns and hormonal and neurotransmitter profiles, expanding the inventory of domestication-​syndrome traits. A key trait in the domestication syndrome is a low propensity to engage in what is called reactive aggression, variously described as impulsive, angry, fearful, or “hot.” Instead, domesticated animals are relatively docile; breeders who engage in present-​day domestication projects report that they select young animals who are friendly and trusting. While domesticates may squabble and may even inflict injury, they rarely attack to kill, and individuals who do so repeatedly, including our dogs and cats, are subjected to training programs, isolation, or, as a last resort, euthanasia. A tempered reactivity to provocation undergirds the domesticate’s ability to get along with both humans and with one another, in contrast to their “wild” counterparts who are constitutively poised to attack and perhaps kill in response to behaviors perceived as threatening. Humans and bonobos prove to exhibit some of the phenotypic traits of the domestication syndrome, including a low tendency to display reactive aggression, notwithstanding the reactive outliers whom we will consider more fully in Chapter 13. To be sure, humans most certainly kill one another, but this is usually in the context of a different mode of aggression, called proactive 179

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aggression, that entails planning and activates different neural pathways from reactive aggression, again as considered more fully in Chapter 13. In general, both humans and bonobos are strikingly peaceful and tolerant animals. Chimpanzees, by contrast, do not display domestication-​syndrome traits, and they frequently engage in reactive aggression, most often in the context of defending male hierarchical dominance. So Homo sapiens can be considered a domesticated species. And it’s even more interesting than that. We’re a self-​domesticated species. Our domestication wasn’t guided by the selection protocols of external breeders. We did it ourselves, starting way back in Africa, in the context of the cultures that we constructed and inhabited. Selection for non-​reactive temperaments presumably set the stage for such cultures, enabling our ancestors to form coalitions that reinforced domesticated frames of mind with norms, practices, and religious worldviews. Self-​ domestication in bonobos followed a different evolutionary trajectory. The social structure of bonobo troops is based on coalitions of females offering respect to their female leader and friendship to one another. A male’s status is more dependent on his mother’s status than on displays of aggression, and the fluid sexual practices of bonobos (p. 150) are conducive to collaboration.

COALITION FORMATION There are several theories as to how reactive aggressiveness was tamed during the course of Homo sapiens evolution: some emphasize the use of capital punishment for reactive behavior; others emphasize mate choice; others suggest that the brain evolved more 180

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robust emotional self-​control in general. However it happened, the taming paved the way for our proclivity to form coalitions (Latin, coalescere, to coalesce, fuse). Once we came to trust others to be even-​tempered and congenial, collaboration became a viable and adaptive social arrangement; indeed, there may well have occurred positive selection—​perhaps sexual selection (p. 81)—​for collaborative traits in addition to negative selection for antisocial traits. Human coalitions often increase in size, a dynamic accompanied by their propensity to become differentiated. Throughout our history and in all parts of the globe, such coalitions have come to inhabit distinct regions and speak distinct languages and engage in distinct cultural and religious practices. An astonishing example is the island system comprising Papua New Guinea, where close to 1,000 different languages are spoken by close to 1,000 tribal groups; a single river valley may contain speakers of six languages holding unique cosmological beliefs. Large archaic coalitions have been shown to split up into small groups during hunting/​foraging seasons and then re-​assemble for ceremonial festivals held in sophisticated sacred edifices. The downside of coalitions, of course, is that they often engage in proactive aggression against one another—​war, acquisition of lands and resources and slaves, racist violence—​and thereby do great harm, as we explore more extensively in Chapter 13. Fortunately, proactive aggression is not a necessary feature of a coalition—​there are countless peaceable examples—​and in theory and often in practice, the aggression can be suppressed or eradicated internally. This leaves us with the highly salubrious features of coalition formation: members are inherently poised to be kind and helpful and cooperative, and they devise and teach cultural 181

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norms of behavior that cultivate our inborn pro-​sociality, generating moral sensibilities and aspirations—​the topic of our next chapter.

REFLECTIONS Distinctiveness. We have encountered this concept several times. We have celebrated our individual selves as organisms, as self-​ aware creatures, and as recipients of such spiritual experiences as reverence and immanence and transcendence, even as we have also honored the experience of humility, of being but a small part of the planetary matrix within which we are joyfully immersed. Here we can lift up our distinctiveness as a lineage. We are the most recent manifestations of the ~15,000 generations of Homo sapiens that preceded ours, to whom we are called to offer our heartfelt gratitude for forging such rich trajectories on our behalf. Our Homo cousins—​H . erectus, H. neanderthalensis, and the Denisovans—​are no longer with us, but happily we are privileged to share the planet with our deeper kin, the orangutans and gorillas and chimpanzees and bonobos. All of us great apes are highly intelligent animals with impressive abilities to learn by both experience and imitation and to remember what we have learned. We display a similar range of temperaments generated by similar emotional and feeling systems (p. 130). We have much to learn from one another, and I would say that the preservation of the habitats and dignity of nonhuman apes emerges as a commandment. And then we turn to our present-​day selves. The global human gene pool harbors a huge trove of alleles (p. 140), some variously 182

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distributed in particular geographic/​ethnic groups, which means that each of us is distinctive, and each of our children will be distinctive. But all of us are also members of the interfertile Homo sapiens species. Indeed, species derives from the same linguistic root as special. As eco-​minded religious naturalists we have learned to value and defend the planetary diversity of species in general and endangered species in particular. We are here called to celebrate human distinctiveness with the same full-​throated thanksgiving that we offer the blue whale and the spotted owl. The whale and the owl are magnificent, but so are we. • We are a symbolic species, unique in our capacity to engage not just in communication but in language (Chapter 7). To repeat Terrence Deacon’s maxim: “Biologically, we are just another ape. Mentally, we are a new phylum of organism.” Our symbolic languages, coupled with our emotional sensibilities (Chapter 8), allow us to build scenarios, plan for the future, and articulate and transmit our cultural and personal understandings. They are the wellspring of our uniqueness. • All beings have the capacity to interpret the reality that they perceive; we humans also have the capacity and the curiosity to analyze reality, to ask questions that yield answers that generate new questions. All of us, that is, are scientists—​even as young children, we construct hypotheses and test them out. Our impulse to understand how things work and how things came to be has extended to our universe and planet and brains, to our emotions and sexuality and cultures, and we use these understandings to generate our technologies and to guide the construction of our social institutions. 183

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• We have as well the capacity to take off from reality, molding it into the distinctively human forms we call art. We brim with imagination. As we create art, and respond to the art of others, we acquire much of our truth, and much of our nobility and grace. • We are teachers. Many animals can learn by imitation, such as chimpanzees watching others using a stick to retrieve termites from a mound and then trying it themselves. But humans also learn by listening to and absorbing explanations and narratives from their teachers and passing them on to others, conveying and expanding their embedded wisdom. • And finally, we are religious. Our forebears buried their dead and set flowers and icons beside or within their graves, and all cultures, present and past, include religious cosmologies and practices. We seek answers to existential questions. We want to believe in things, to structure and orient our lives in ways that make sense and offer hope, to identify values and ideals, to both interconnect and transcend. And happily, we have the capacity to transmit our accumulated religious understandings to one another and our children through our narratives and our arts, allowing them to endure and evolve.

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HUMAN MORALITY AND ECOMORALITY

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he format of this chapter differs from the daily-​devotional format of the other chapters (p. 8) in that my reflections permeate the whole rather than being restricted to a concluding section. I first explore Nature-​embedded moral understandings as they pertain to human-​human relationships, and I then consider them in the context of human-​Earth relationships, offering pathways to an ecomorality. I am presenting my own perspectives throughout, bringing in understandings that I have gleaned from religious and philosophical traditions as well as science-​based findings, and there are many other perspectives on offer. The hope is that they will collectively contribute to fruitful conversations on how we might best move forward.

DISTINGUISHING ETHICS AND MORALITY The words ethics and morality are often used interchangeably; here they will be distinguished as follows. Ethics will refer to cultural norms, established by human coalitions (Chapter 12), that distinguish “right” from “wrong.” They articulate expectations/​

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0015

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rules/​laws for pro-​social behavior and civic punishments for behavior deemed anti-​social, ranging from ostracism to fines to capital punishment. Laws may be established by a consensus of elders, historically mature males within the coalition, or by rulers or monarchs in cases where such persons acquire power within a coalition. Ethics, in this usage, is a political term (Gr. politiká, affairs of the city). Morality will refer to pro-​social concepts and ideals writ large, historically envisioned as derived from and monitored by supernatural sources, that distinguish “good” from “bad” or “evil.” A good person, it is said, will receive some version of salvation—​ grace, heaven, beneficial karma—​and an evil person some form of damnation—​misfortune, hell, toxic karma. Morality, in this usage, is a religious term. In practice these distinctions have often been blurred: certain foundational laws (“Thou shalts, thou shalt nots”) are often claimed to have been conveyed and hence validated by deities, and the concept of “the divine right of kings” has existed in numerous guises. Laws are often culture-​specific: a rule leading to severe punishment when transgressed in some coalitions (e.g., a prohibition of sorcery) is often absent in other coalitions. Morals, on the other hand, tend to be trans-​cultural: visions of the good person and the bad person are found to be widely shared. Universals suggest a deep-​rootedness in human nature and hence a rootedness in our evolutionary history. Social behavior has evolved independently numerous times: quorum-​ sensing in bacteria, hives in social insects, schooling in fish, flocking in birds (Frontispiece to Chapter 5), and packs/​herds in many mammals. Here we will consider our immediate lineage, first outlining the pro-​social orientations and 188

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sentiments found in our primate cousins and then considering their manifestations in human moral concepts.

PRO-​SOCIALITY IN NONHUMAN PRIMATES A commonly voiced concern about evolutionary theory is that it leads to moral relativism. Tom DeLay (R-​TX) famously declaimed that the Columbine school massacre in Colorado was the result of exposure to evolutionary theory, that “our school systems teach the children that they are nothing but glorified apes who are evolutionized [sic] out of some primordial soup.” Inherent in this mode of thinking is the notion that animals are “brutes,” and therefore, if we believe that we “evolutionized” from brutes, we are by nature brutes as well. Studies of our primate cousins refute this notion, however, instead documenting that these animals self-​organize into effective and coherent social systems wherein versions of numerous pro-​social sensibilities are readily discerned. In this light, to be glorified apes is a promising moral starting point. Lists of pro-​social sentiments in nonhuman apes usually begin with empathy, a parameter we considered in Chapter 9 when we recounted the story of the young bonobo trying to help an injured bird to fly. Empathic responses are encountered in numerous mammals and birds, including some that do not adopt formal social lifestyles. Nonhuman apes who witness an altercation have been observed to console the loser, offering reassuring body contact such as a hug. Empathic feelings involve domains of the mammalian brain that are also activated by physical pain; hence the phrase “I feel your pain” goes all the way down. 189

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The list of primate pro-​social building blocks continues with other entries; translations into human moral vocabulary are offered in parentheses: • helping your offspring and your group (nurture and altruism) • reciprocal exchange of benefits (friendship) • participation in conflict resolution (reconciliation and forgiveness) • deference to superiors (reverence) • division of disputed resources while respecting prior possession (fairness)

HUMAN-​HUMAN MORALITY: THE VIRTUES So in what ways, and by what means, have humans differentiated from our cousins on the moral axis? The idea that resonates with me is that during our brain/​language/​culture co-​evolutionary trajectory outlined in Chapter 12, the pro-​social sensibilities resident in our common ancestor with chimpanzees and bonobos were most certainly not left in the evolutionary dustbin, nor are these sensibilities experienced in the same way that present-​day nonhuman apes experience them. Rather, they are experienced as humans experience things: via our symbolic subjectivity, our feeling-​laden I-​selves (Chapters 7 and 8). A human’s moral framework, while based on our pro-​social building blocks, is not some set of instincts that just bubbles up. It is something that develops in each of us, with varying levels of conscious consideration, building upon our inherited tendencies in the context of our cultural teachings and prioritizations. 190

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Versions of our inherent moral capacities are given names—​ yamas in Hinduism, wu chang (five virtues) in Confucianism, Pāramitās in Buddhism, the Seven Sacred Teachings in the First Nations. In English translation they have historically been called virtues. The word virtue has acquired prissy self-​important connotations, but its Latin root is virtus—​valor or merit—​which conveys a cultivated pro-​social frame of mind. Virtues describe ideals of what we best hope to attain: to be virtuous is an ongoing process and not an achievement; anyone who claims to be virtuous doesn’t understand the concept. In Aristotle’s words, “We have the virtues neither by nor contrary to our nature. We are fitted by our nature to receive them”—​an aphorism that brings to mind the concept that our childhood brains are fitted to learn and use the symbolic languages acquired from our cultures. A woman who took great risks to shelter Jews in Holland during WWII commented: “I don’t think it was such a courageous thing to do. For some people it was a self-​evident thing to do.” There are many lists of virtues. Here we will consider four: • compassion (the capacity to resonate with and care about the suffering of others) • fair-​mindedness (the capacity to recognize and act upon what is just) • reverence (the capacity for awe, respect, and humility) • courage (the capacity for tempered confidence, enabling creativity and leadership) Virtues are not, of course, stand-​alone items—​they are all of a piece. Cowardice will undermine fair-​mindedness and injustice is 191

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incompatible with compassion. Therefore, to develop virtue is to nurture capacities that are interwoven and interdependent. Importantly, the path to virtue has consequences. When we fail to act in accordance with our developing virtues, we feel shame and remorse. When we witness inhumane, unjust, and irreverent behaviors in others, we feel various versions of outrage and call upon our courage to voice and act upon our concerns. An outcome of developing one’s capacity for virtue is to experience well-​being and be graced by the love and respect of others. Those who engage in compassion, fair-​mindedness, reverence, and courage report deep satisfaction with these frames of mind—​they are found to be good and beautiful—​and they are held in esteem by others. Indeed, such traits likely served, and continue to serve, as criteria for sexual selection (p. 81): persons who evince these qualities are apt to be favored as partners, anticipating their nurture and provision of kindness and moral wisdom to forthcoming families. This perspective—​a version of a philosophical tradition called virtue ethics—​asks us to understand humans as emergent moral entities, expanding core primate capacities and sensibilities and celebrating their beauty and value in art, literature, and religious teachings. The myths and metaphors that come to us from thousands of wisdom and religious traditions convey timeless understandings of how best to develop virtue and hence foster both personal wholeness and social coherence.

MINDFULNESS AND MINDFUL VIRTUE The virtues are the outcome of forging our pro-​social endowments into moral ways of being, and it is essential that their development 192

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be fully embedded in reality, free of delusion. Hence an important complement to the cultivation of virtue is the cultivation of mindfulness. Mindfulness is a central concept in Buddhism, where it is found both as a way-​of-​being and as a meditative practice. The mindful person, Buddhism tells us, assumes the attitude of pure observation, freed of personal needs and prejudices and dogmatism. The mindful person really really sees. The development of mindfulness, like the development of virtue, is described as an ongoing process, animated by new understandings, ready for surprise. It entails both the acquisition of knowledge and a connection with what you come to know. As you become mindful of something, your feelings and your behavior toward it are transformed. It becomes a part of your being. Every day I see or hear something that more or less kills me with delight, that leaves me like a needle in the haystack of light. It was what I was born for—​ to look, to listen, to lose myself inside this soft world—​ to instruct myself over and over

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The Sacr ed Depths of Natur e In joy, and acclamation. Nor am I talking about the exceptional, the fearful, the dreadful, the very extravagant—​ but of the ordinary, the common, the very drab, the daily presentations. Oh, good scholar, I say to myself, how can you help but grow wise with such teachings as these—​ the untrimmable light of the world, the ocean’s shine, the prayers that are made out of grass? —​Mary Oliver, “Mindful”

It is essential that virtue be mindful virtue, freed from personal needs and prejudices and dogmatism. Reverence for an fraudulent tyrant is not mindful reverence.

AGGRESSION To look at the primates and lift up only their pro-​social capacities is of course to tell only part of the story. The origin of life marked the origin of the self—​self-​maintaining, self-​repairing, self-​protecting, 194

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and self-​reproducing (p. 35). Therefore, in social lineages such as ours, the mandate is both to flourish as an individual self and to flourish in community, where our inherited and cultivated pro-​ social sensibilities navigate the inevitable tensions that arise between self-​interest and group cooperation. Aggression is a useful word to characterize self-​ interested behaviors that disrupt the coherence and well-​being of a group. We noted in Chapter 12 that aggression can take two forms—​ reactive (impulsive, on-​the-​defense) and proactive (planned, on-​ the-​offense)—​that engage different regions of the brain. We can consider them here in greater depth. Reactive aggression is a common occurrence in modern chimpanzees and uncommon, although certainly not absent, in modern bonobos and humans. Those humans who are prone to reactive aggression are usually male, and their attacks are usually abusive or violent—​verbal assaults, beatings of women and children, drunken fights in bars. The behavior is typically triggered by perceived insult or threat. Reactive aggressiveness has a heritable component, but it is exacerbated by childhood instability, stress, and alcohol, and can in many cases be remediated by therapy and medication. Proactive aggression is occasionally practiced by nonhuman apes—​chimpanzees have been observed in the wild to band together and kill a member of a neighboring troop—​but it is largely confined to humans because it entails premeditation and scenario-​ building and hence is greatly enabled by the planning skills conferred by symbolic language—​it’s not easy for chimpanzees to plan very far ahead. Small-​scale proactive aggressions, carried out by individuals or, more commonly, a group of co-​conspirators, include murdering 195

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an enemy, robbing a bank, defrauding an elderly couple, where the motive is typically revenge or economic gain. They can also take the form of random violence, such as school shootings, where motives range widely and are usually delusional. Our ethical systems include laws that prohibit and punish such behaviors. Large-​ scale proactive aggressions are carried out by the coalitions we variously call tribes, governments, or nations: waging war against another coalition; confiscating lands or resources; oppressing a particular population. The motive can again be revenge or economic gain, but the practice is typically infused with racism: the “enemy” is identified by ethnicity, race, and/​or religious beliefs. Self-​interest, in these cases, has been transferred to membership in the coalition—​the coalition’s success against the enemy becomes the individual’s success. Regional and global institutions attempt to enact laws that prohibit and punish forms of large-​scale proactive aggression, and nations enter into non-​ aggression treaties, but these laws and treaties are challenging to enforce given the collective power of coalition psychology and xenophobia/​racism. Large-​scale proactive aggression remains an enormous impediment to global social coherence.

XENOPHOBIA AND RACISM Xenophobia and racism have distinct but overlapping definitions. Xenophobia describes a fear and hatred of persons perceived to be strange or foreign, including persons with nonnormative sexual or gender orientations and persons holding different religious, cultural, or ethnic identifications. Racism amplifies xenophobia by including the belief that racial differences are linked to the inherent 196

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superiority of a particular race, legitimizing proactive aggressive attacks against persons of “inferior” races. Racism is exacerbated by conditions wherein humans find themselves physically or emotionally impoverished, humiliated, or insecure, fostering the dehumanization and demonization of persons identified as the “cause” of these conditions, and permitting their exclusion and often brutalization. Such conditions also render humans vulnerable to the call of rigid political fundamentalisms, many labeled as religious, that promise deliverance from their stressful circumstances and offer implicit or explicit validation of their racist perspectives. While racism can be exacerbated by stress, structural and systemic racism is just that: structural and systemic, a global pandemic, pitting Arab against Asian against Black against Brown against Native American against Jew against White in countless toxic and often lethal combinations and manifestations. Religious naturalists are heartbroken by the devastation that racism wreaks on our social fabric, and we seek its eradication in ourselves and in others. We also lift up an important fact: xenophobia and racism are both fundamental errors, since both ignore modern human history. As we saw in Chapter 12, the multiple human migrations out of Africa began only ~100,000 years ago and the European migrations only ~54,000 years ago, time spans we can almost imagine if we use the adoption of European agriculture ~10,000 years ago as a scale bar. About a mile in our walking analogy (p. 97). And those migrants were all fully pan-​African (p. 176). Geoffrey Miller says it well: It should go without saying, but I’ll say it anyway: all of the significant evolution in our species occurred in populations with brown and black skins living in Africa. At the beginning of hominin evolution

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The Sacr ed Depths of Natur e seven million years ago, our ape-​like ancestors had dark skin just like chimps and gorillas. When modern Homo sapiens showed up three hundred thousand years ago, we still had dark skins. When brain sizes tripled, they tripled in Africans. When sexual choice shaped human nature, it shaped Africans. When language, music, and art evolved, they evolved in Africans. Lighter skins evolved in some European and Asian populations long after the human mind evolved its present capacities. The skin color of our ancestors does not have much scientific importance. But it does have a political importance given the persistence of anti-​black racism in many populations. I think that a powerful antidote to such racism is the realization that the human mind is a product of black African females favoring intelligence, kindness, creativity, and articulate language in black African males, and vice versa. Afrocentrism is an appropriate attitude to take when we are thinking about human evolution.

Our fully shared, fully ligated humanity—​our deep kinship—​is a foundational concept and, when absorbed, a potent counterforce to systemic and structural racism.

ECOMORALITY As humans, our most immediate ecosystems are our cultures, cultures that we alone construct and inhabit and modify and value. That said, our cultures are fully embedded in the natural world, and it is our relationship with the rest of the planetary matrix—​ our ecomorality—​to which we now turn. As we do so, it is essential that we keep in mind and heart the words of Pope Francis: We cannot presume to heal our relationship with nature and the environment without healing all fundamental human

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Hum an Mor alit y and Ecomor alit y relationships . . . . A sense of deep communion with the rest of nature cannot be real if our hearts lack tenderness, compassion and concern for our fellow human beings . . . . Concern for the environment thus needs to be joined to a sincere love for our fellow human beings and an unwavering commitment to resolving the problems of society.

Ecomorality can be thought of as a reconfiguration of our inherited and cultivated pro-​social sentiments, an enlargement of our moral vision, such that we come to care not just about the well-​being of family and village and tribe but also about the rest of the natural world. We are asked to respect, cherish, nurture, and celebrate that from which we have come and upon which we depend, to consider it sacred. The moral challenge is to forge relationships with Nature that sustain and enhance both our human cultures and the planetary matrix within which these cultures are embedded. A philosophical argument claims that “you can’t get values from facts,” that Nature does not come pre-​packaged with moral recommendations. Philosopher Loyal Rue responds: Religious naturalists treat the integrity of natural systems as an absolute value, implied by the principle that any vision of the good presupposes life, and that life presupposes the integrity of natural systems . . . . Nature is the sacred object of humanity’s ultimate concern. Nature is the ultimate ground of natural facts, and eco-​centric values are therefore justified by the claim that Nature is sacred.

Indigenous peoples have held and fostered ecomoral sensibilities for millennia, as in the following examples: Native American teachings describe the relations all around—​ ­animals, fish, trees, and rocks—​as our brothers, sisters, uncles,

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The Sacr ed Depths of Natur e and grandpas . . . These relationships are honored in ceremony, song, story and life that keep relations close—​to buffalo, sturgeon, salmon, turtles, bears, wolves, and panthers. These are our older relatives—​the ones who came before and taught us how to live. —​Winona LaDuke (Ojibwe Nation) Sustain the ones who sustain you and the earth will last forever. —​Robin Wall Kimmerer (Potawatomi) [Sustainable practice] can be done only if all of us . . . can again see ourselves as part of the earth, not as an enemy from the outside who tries to impose its will on it. Because we . . . know that, being a living part of the earth, we cannot harm any part of her without hurting ourselves. —​Lame Deer (Lakota) The mountains, I become part of it . . . The herbs, the fir tree, I become part of it. The morning mists, the clouds, the gathering waters, I become part of it. The wilderness, the dew drops, the pollen I become part of it. —​Navajo chant

Similar sensibilities can be found in other religious traditions. Even as a mother protects with her life Her child, her only child, So with a boundless heart Should one cherish all living beings, Radiating kindness over the entire world, Spreading upward to the skies, And downward to the depths, Outward and unbounded. —​Metta Sutta, Buddhism

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Hum an Mor alit y and Ecomor alit y Heaven is my father and earth is my mother And even such a small creature as I finds an intimate place in their midst. Therefore, that which extends throughout the universe I regard as my body and that which directs the universe I consider as my nature. All people are my brothers and sisters, and all things are my companions. —​Chang Tsai, Confucianism The Word is living, being, spirit, all verdant greening, all creativity. This Word manifests itself in every creature. —​Hildegard of Bingen (1098–​1179), Christianity We have forgotten that we ourselves are dust of the earth; our very bodies are made up of her elements, we breathe her air and we receive life and refreshment from her waters. —​Pope Francis, Christianity Christians are called to accept the world as a sacrament of communion, as a way of sharing with God and our neighbors on a global scale. It is our humble conviction that the divine and the human meet in the slightest detail in the seamless garment of God’s creation, in the last speck of dust of our planet. —​Ecumenical Patriarch Bartholomew, Christianity

Traditional ecomoral sensibilities have in recent times been supplemented with understandings of the sacred depths of the natural world, its molecular and genetic and atomic and cosmic underpinnings, understandings that were birthed by human curiosity, developed by creative science-​based inquiry, and validated by their countless technological applications. These science-​based understandings, many narrated in this book, fully confirm longstanding perceptions that we originated from the Earth, that we 201

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are interrelated and interdependent with all living beings, and that we are fully dependent on our shared planetary matrix.

ECOMORAL VIRTUES The four virtues that we listed earlier in considering our human-​ human relations—​compassion, fair-​mindedness, reverence, and courage—​are central as well to our human-​Earth relations. We considered eco-​compassion in Chapter 8, where we noted that it is as we identify with the oil-​soaked bird and the bewildered moose that they come to symbolize our environmental concerns. Eco-​compassion entails first accepting, and then rejoicing in, one’s own critterhood, one’s connectedness with all other present and prior beings in the planetary matrix. It then entails experiencing sorrow when these fellow beings are subjected to suffering, followed by efforts to reverse the suffering. Eco-​fairmindedness entails seeking and advocating just and sustainable environmental configurations, the goal being a planet wherein human cultural ecosystems co-​ habit with planetary ecosystems in ways that preserve and restore the integrity and dignity of both. Reverence, the sense of there being entities larger than ourselves to which we accord awe and respect and which we approach with humility, is readily expanded to eco-​reverence—​a reverence for the spectacular whole of which we are privileged to be a part. Courage, the capacity for confidence, is also readily expanded to eco-​courage—​the germ of creative activism, a commitment to resist the degradation of the sacred.

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The eco-​ virtues, like human-​ focused virtues, carry with them the potential for shame and outrage. When we fail to offer earthly compassion and reverence or tip the scales away from environmental justice so as to favor our own self-​interests, we feel ashamed. When we encounter others who engage in Earthly abuse, we feel outrage and marshal the courage to voice and activate protest. Shame and outrage are crucial manifestations of both morality and ecomorality, measures of the depth of our commitment to what we value. The eco-​virtues are not just about how we think and feel. They represent the wellsprings of our eco-​centric action. To say that I care about my ideals is to say that I feel an obligation toward them, a responsibility. Taking responsibility, like acting on outrage, requires courage: it entails engagement and strong character and a sense of honor, and it yields both respect and self-​respect. Religious naturalists take Nature to heart (p. 219), and when we encounter the widespread desecration of Nature, our hearts can be broken. The more one cares, the more one is vulnerable to feelings of violation and despair. But passive despair is neither a moral response nor an ecomoral response, as voiced by Dr. Martin Luther King Jr.: We are now faced with the fact that tomorrow is today. We are confronted with the fierce urgency of now. In this unfolding conundrum of life and history, there is such a thing as being too late. This is no time for apathy or complacency. This is a time for vigorous and positive action.

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ECOMORALITY AND THE WAY FORWARD Like it or not, we have the capacity to dictate the condition of most every feature of the planet and its inhabitants: remove the mountaintop; dam the river; warm the oceans; kill any inconvenient creature; nuke the whole thing. The human race is challenged to demonstrate our mastery, not over nature but of ourselves. —​Rachel Carson We humans are the only species with the power to destroy the earth as we know it. The birds have no such power, nor do the insects, nor does any other mammal. Yet if we have the capacity to destroy the earth, so, too, do we have the capacity to protect it. —​The Dalai Lama

The human capacity to protect the Earth can be put into practice in numerous ways. Here I will lift up three that seem important to me. First, it is essential that we cultivate sustainable practices in our own lives and in our communities. As Patrick Geddes first put it in 1915: Think globally, act locally. Most readers are doubtless familiar with lists of such practices: reduce or eliminate meat consumption; drive a hybrid or electric vehicle; take busses and trains; ride a bike; adopt sustainable landscaping practices; purchase local organic foods when available; turn down the thermostat and wear a sweater; buy what you need and want what you have; join local groups engaged in habitat protection or advocacy of sustainability, and participate in peaceful protests. We are called as well to become teachers, or even evangelists, passing on ecomoral principles by word and by example to our communities. Such local 204

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efforts may at times seem trivial or even useless given so much planetary upheaval, like recycling a chewing-​gum wrapper, but each is in fact a strand in the weaving of a meshwork, a mycelium, of global ecomoral sensibility. As anthropologist Margaret Mead is said to have put it: “Never doubt that a small group of thoughtful, committed citizens can change the world. Indeed, it’s the only thing that ever has.” Importantly, if I find that I am joined in a river cleanup project by people who are so engaged because the river is the Lord’s or Allah’s Creation, or because the river is inhabited by Spirits, that’s fantastic. My perspectives as a religious naturalist and the perspectives of those holding traditional religious beliefs have arrived at the same place: an imperative that the planetary matrix and its creatures be respected and cherished and, when necessary, remediated. As our group gathers up the plastic bags and soda cans and sops up the oil slicks and removes invasive growth, all of us are engaging our religious sensibilities in doing what needs to be done. We share a common purpose—​I would say a common Purpose. And as the afternoon progresses, some of us become good friends. A second capacity we bring to the table is our ability to form coalitions (p. 180), in this case political and religious associations that seek to redress climate change, promote habitat preservation, and support numerous other eco-​centered goals. Any impatience with their seemingly slow progress should be replaced by deep gratitude for what they have been able to accomplish given the enormous cultural, political, and economic headwinds they face. It is imperative that we join and support these associations. A third human capacity is our ability to devise technologies. Science and technology, although interwoven, are distinct enterprises. Science entails discovering how the natural world 205

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works; technology entails the use of these understandings to make things. Technology was practiced by our early ancestors when they used their knowledge of the natural world to forge weapons and cutlery and develop herbal medicines and agriculture. Virologists who study the coronavirus infection process are doing science; bioengineers who use these understandings to create vaccines are doing technology. Some environmentalists are skeptical and even fearful of “technological solutions,” noting that the Earth operated just fine before technology came along and that technologies have often wreaked havoc with ecosystems. But as Robin Kimmerer notes: “To love a place is not enough. We must find ways to heal it.” Healing will be anchored in the practice of earth-​centered living and the support of local and global coalitions, but the use of mindful technologies will be essential as well, often to reverse the damage already wrought by mindless technologies. Solar, wind, and geothermal technologies are engaged in replacing the use of fossil fuels; biotechnologies are engaged in the rescue of coral reefs and other vital habitats. The list is long. Importantly, a key feature of any technology is that humans, and humans alone, get to decide whether or not to develop it or employ it. We can’t make judgments about how Nature works: Nature just is. But we can evaluate proposed technologies, after which we can elect to pursue those that would ameliorate prior damage and/​or encourage earthly/​human flourishing and to disallow those that pose threats, obvious examples being unfettered fossil-​fuel extraction and pesticide abuse. Such evaluations need to be anchored in our science-​based understandings of the planetary matrix; they must also be made with mindful eco-​compassion, eco-​reverence, eco-​fairmindedness, and eco-​courage. 206

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The Senegalese conservationist Baba Dioum summarizes the foundational tenets of ecomorality: “In the end, we will conserve only what we love, we will love only what we understand, and we will understand only what we are taught.” We lifted up earlier our deep affinity with the natural world, our inborn capacity for horizontal transcendence (p. 119). Baba Dioum calls us to interweave this sensibility with our deep knowledge of the natural world, creating narratives and teachings that help all of us understand what it is that we love—​and to then insist that its sacred presence be conserved for future generations. If we will have the wisdom to survive, to stand like slow-​growing trees on a ruined place, renewing, enriching it, if we will make our seasons welcome here, asking not too much of earth or heaven, then a long time after we are dead the lives our lives prepare will live here, their houses strongly placed upon the valley sides, fields and gardens rich in the windows. The river will run clear, as we never know it, and over it, birdsong like a canopy. On the levels of the hills will be green meadows, stock bells in noon shade. On the steeps where greed and ignorance cut down the old forest, an old forest will stand, its rich leaf-​fall drifting on its roots. The veins of forgotten springs will have opened. Families will be singing in the fields. In their voices they will hear a music risen out of the ground. They will take nothing from the ground they will not return, whatever the grief at parting. Memory,

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The Sacr ed Depths of Natur e native to this valley, will spread over it like a grove, and memory will grow into legend, legend into song, song into sacrament. The abundance of this place, the songs of its people and its birds, will be health and wisdom and indwelling light. This is no paradisal dream. Its hardship is its possibility. —​Wendell Berry, 1999, “A Vision”

AN ODE TO THE LICHEN My science-​based research has recently focused on small creatures, most ranging in size from one millimeter to one centimeter, called lichens. I’ve had the honor and pleasure of connecting with them in the woodlands and burrowing deep into their cellular interiors using microscopy—​reductionism and holism entwined. Along the way, I’ve come to realize that lichens can serve as evocative metaphors to guide our quest for planetary sustainability. Lichens are relative newcomers to the planet, showing up ~250 million years ago, which is ~50 million years after the vascular land plants and ~300 million years after the animals. The Earth presently harbors some 20,000 distinct lichen species, and they dominate an estimated 12% of the planet’s terrestrial ecosystems, including arid deserts and vast expanses of Arctic tundra. A lichen found in the Arctic has been determined to be 8,600 years old, to our knowledge the world’s oldest living organism. Humans are generally unaware of and/​or uninterested in lichens since they are sparse in urban environments and are rarely used for food or fuel. In fact, they can’t really be said to be useful for much of anything. 208

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They just are, providing the planetary matrix with some of its fixed carbon and much of its beauty. A lichen is an organism created by genetically scripted interactions between three kinds of organisms—​a filamentous multicellular fungus, a unicellular green alga, and many kinds of bacteria—​each deriving from separate evolutionary radiations (Figures 6.2 and 6.3). Each can grow independently, but when they encounter one another, they collectively construct a new organism: the fungus self-​organizes into several layers, with the algae in between and the bacteria on the top and bottom, to form an elaborate and often elegant edifice that attaches to bark or stone. Every lichen is both an organism and a bounded, fully balanced ecosystem. Its fungi, algae, and bacteria carry out niche construction, photosynthesis, nitrogen fixation, metal acquisition, air/​ water relationships, and biosynthetic/​metabolic processes that collectively ensure the survival of each inhabitant, the preservation of their shared and co-​constructed habitat, and the continuation of the lichen writ large—​the lichen self. A lichen is structured to be resilient, bounding back after desiccation, freezing, and UV bombardment. It does no harm to other organisms or ecosystems and is vulnerable to only a few exogenous agents, notably urban air pollutants, caribou, and certain snails. It harbors no internal predators or pathogens—​even the bacteria are well behaved. Lichens grow very slowly—​typically a few millimeters per year—​ with growth rates dependent on environmental circumstances, and they stop growing when they reach a genetically specified size. They have been able to spread throughout the terrestrial world, including its most inhospitable terrains, because they bring their 209

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self-​sustaining ecosystems with them, and because they aren’t in any hurry. We humans would do well to keep lichens in mind as we envision pathways to planetary co-​habitation and sustainability. An ecological concept called niche partitioning describes the differential use of resources and space by the various creatures in an ecosystem, allowing for their coexistence and their mutual flourishing. Countless billions of lichens have figured out how to do this in 20,000 different ways. We should be able to figure it out as well.

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EPILOGUE: EMERGENT RELIGIOUS PRINCIPLES

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hen the responses elicited by Everybody’s Story are gathered together, several religious principles emerge with the potential to serve both as the framework for a religious naturalist orientation and as a promising framework for conversations about our planetary future.

TAKING ON ULTIMACY We are all, each one of us, ordained to live out our lives in the context of The Big Questions, such as: • Why is there anything at all rather than nothing? • Where did the laws of physics come from? • Why does the universe seem so strange? My response to such questions has been to articulate a Covenant with Mystery (Chapter 1), but others prefer to respond with answers, answers that often include a concept of God or other supernatural beings or forces. Such answers are by definition interpretations

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0016

Epilogue

that can neither be proven nor refuted; their adoption entails what is called Belief. They may be gleaned from existing faith traditions or from personal search or experience. God may be apprehended as a remote Author without present-​day agency, or as an interested Presence with whom one forms an intimate relationship, or as Pantheistic—​Inherent in All Things. Central to human experience is the opportunity to develop Beliefs in response to questions of ultimacy—​including the choice that I’ve made, which is to adopt no Beliefs and dwell in mystery. The important part, I would say, is that the questions be openly considered. To ask Why Are Things as They Are is to generate the basis for everything else.

GRATITUDE Imagine that you and some other humans are in a spaceship, roaming around in the universe, looking for a home. You land on a planet that proves to be ideal in every way. It has deep forests and fleshy fruits and surging oceans and gentle rains and cavorting creatures and rich soils and dappled light from its star. Everything is perfect for human habitation, and everything is astonishingly beautiful. This is how the religious naturalist thinks of our human advent within the planetary matrix. We arrived but a moment ago and found it to be perfect for us in every way. And then we came to understand that it is perfect because we arose from it and are a part of it. Hosannah! Not in the highest, but right here, right now, this. Once such gratitude flows from our beings, it can be offered to God, as in this poem, or to Mystery or the Great Spirit or Cosmic 212

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Evolution or Mother Earth or Brahman. Or, just offered. One can feel deeply grateful for a gift without needing to identify the giver. i thank You God for most this amazing day: for the leaping greenly spirits of trees and a blue true dream of sky; and for everything which is natural which is infinite which is yes (i who have died am alive again today, and this is the sun’s birthday; this is the birth day of life and of love and wings: and of the gay great happening illimitably earth) how should tasting touching hearing seeing breathing any—​lifted from the no of all nothing—​human merely being doubt unimaginable You? (now the ears of my ears awake and now the eyes of my eyes are opened) —​e e cummings, “i thank You God”

REVERENCE AND HUMILITY Our story tells us of the sacredness of life—​the astonishing complexity of cells and organisms and the vast lengths of time it took to generate their splendid diversity—​and the sacredness of the planetary matrix within which life is embedded. Reverence is the capacity to perceive the sacred, to harbor the sense that there are entities larger and more important than the self to which one accords awe and gratitude and to which one develops obligation and commitment. Theistic persons traditionally offer reverence to a supernatural deity or deities, while nontheistic religious 213

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naturalists are called to revere the whole enterprise of planetary existence, the whole and all of its myriad living beings as they catalyze and replicate and mutate and evolve and synergize as ecosystems. Reverence also endows us with humility and hence defeats our susceptibility to self-​absorption. Ralph Waldo Emerson invites us to express our reverence in the form of prayer. “Prayer,” he writes, “is the contemplation of the facts of life from the highest point of view. It is the soliloquy of a beholding and jubilant soul.”

NURTURE AND COMPASSION All creatures, including all humans, are embedded in self-​interest; our basal biological mandate is to pursue our aims and foster our well-​being. As communal animals, we are also endowed with pro-​ social sentiments, urging us to nurture one another and to foster social coherence in family and community. Religious orientations suggest ways to integrate these often conflicting endowments and develop virtue. A core virtue is the capacity for compassion—​to resonate with and care about the suffering of others and to do what can to reverse or ameliorate their suffering. Religious naturalists join many religious traditions in expanding these pro-​ social understandings to include the planetary matrix and all of its beings.

CREDO OF CONTINUATION Evolution is often thought of as being about prevalence, about how many copies there are of which kinds of genomes. But it is 214

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quite as accurate, and I believe far more germinative, to think of evolution as being about the continuation of organisms. Genomes that provision organisms with instructions that lead to well-​being are found in future organisms. Key adaptations that generate well-​being include awareness, valuation, and purpose, features that were doubtless present in primordial selves. In order to continue, genomes must specify organisms that are aware of their environmental circumstances, evaluate these inputs correctly, and respond with intentionality. And so, I profess my Faith. For me, the existence of all this biological complexity and awareness and intent and beauty and relationship, embedded in its wondrous planetary matrix, serves as the ultimate meaning and the ultimate value. The continuation of life reaches around, grabs its own tail, and forms a sacred circle that requires no further justification, no Creator, no superordinate Meaning, no Purpose other than that the continuation continue until the Earth collapses into the sun or the final meteor collides. I confess a Credo of Continuation. And in so doing, I confess as well as credo of human continuation. We may be the only questioners in the universe, the only ones who have come to understand the astonishing dynamics of cosmic and biological evolution. If we are not, if there others out there who Know, it is highly unlikely that we will ever encounter one another. We are also, for better or worse, the dominant species and hence the stewards of this planet. If we can revere how things are, and can find ways to express gratitude for our existence, then we should be able to figure out, with a great deal of work and good will, how to take care of the place, how to share the planetary matrix with other creatures, how to restore and preserve its elegance and grace, and how to commit ourselves to love and joy and laughter and hope. 215

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It goes back in the end to my father’s favorite metaphor. “Life is a coral reef. We each leave behind the best, the strongest deposit we can so that the reef can grow. But what’s important is the reef.”

OUR RELIGIONS OF ORIGIN So we harvest from the natural world all the meaning and guidance and spiritual subsistence that we can, and we bring these mindful understandings with us as we set out to chart future paths. And then we come back to our religions of origin, the faiths of our mothers and fathers. What do we do with them? What have I done with mine? Theologian Philip Hefner offers a weaving metaphor. The tapestry maker first strings the warp, long strong fibers anchored firmly to the loom, and then interweaves the weft, the patterns, the color, the art. Everybody’s Story is our warp, destined to endure, commanding our universal gratitude and reverence. And then, after that, we are all free to be artists, to render in story and painting and song and dance the hopes and concerns and understandings embedded in our human natures. We are free to partake in one of our most cherished gifts: Imagination. Throughout the ages, the weaving of our religious wefts has been the province of prophets and gurus and liturgists and elders and shamans and a panoply of artists and musicians. The texts and art and ritual that come to us from these revered ancestors may include claims about Nature and agency that are no longer plausible. They used a different warp. But for me at least, this is just one of those historical facts, something that can be acknowledged and then put aside as I encounter the imagination and wisdom 216

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embedded in these traditions and the abundant opportunities that they offer to experience transcendence and immanence and moral clarity. I love traditional religions. Whenever I wander into distinctive churches or mosques or temples, or visit museums of religious art, or am invited to participate in indigenous ceremonies, or hear performances of sacred music, I am enthralled by the beauty and solemnity and power they offer. Once we have our understandings and feelings about Nature in place, then I believe that we can also find ways to call ourselves Buddhist or Christian or Confucian or Daoist or Hindu or Hopi or Jew or Muslim. Or some of each. The words in the traditional texts may sound different to us than they did to their authors, but they often continue to resonate with our religious selves. We know what they are intended to mean. The word myth has been debased—​it now commonly refers to an account that is false—​but originally it meant a grand compelling narrative, a Myth, that fully engages the mind and heart and imagination. Humans need Myths that help to orient us in our lives and in the cosmos. Everybody’s Story is such a Myth, beautifully suited to anchor our mindful search for planetary consensus, telling us of our nature, our place, our context. Moreover, responses to this Myth—​what we are calling a religious naturalist orientation (p. 219)—​can yield abiding interpretive grounding, spiritual experience, ecomoral commitment, and celebration. And then there are other stories on offer as well, human-​ centered Myths that embody our ideals and our passions. These stories come to us, often via experiences called revelation, from the spiritual and artistic and wisdom traditions of past and present times, and they burnish our souls.

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EPILOGUE: THE RELIGIOUS NATURALIST ORIENTATION

T

he first edition of this book was written from the perspective of a religious naturalist, an orientation with many historical roots but considered at the time to be a general concept. Since then, in books, articles, conferences, and conversations, a number of religious naturalists have contributed to developing a more specific framework. An overview of such a framework is presented here. Many resources can be found in the endnotes to this book and at https://​religi​ous-​nat​ural​ist-​asso​ciat​ion.org.

WHO IS A NATURALIST? Scientific inquiry has provisioned us with mind-​blowing new ways of understanding the natural world, generating a narrative that has been called the New Story, the Epic of Evolution, the Universe Story, Big History, Journey of the Universe, and, my preference, Everybody’s Story. Naturalists dwell within these understandings, recognizing that they will certainly deepen and that some may be revised with further scientific discoveries, and they adopt this

The Sacred Depths of Nature. Ursula Goodenough, Oxford University Press. © Ursula Goodenough 2023. DOI: 10.1093/​oso/​9780197662069.003.0017

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account as a core narrative. A naturalist is at home in the natural world writ large.

WHAT IS ENTAILED BY BEING RELIGIOUS? People can “be religious” in many ways, some participating in traditional rituals and adopting traditional moral codes as a way of life without engaging in deep explorations of their dynamics. When the dynamics are probed, some common themes emerge. A religious person self-​orients within a core narrative (a Mythos, a large story), historically accessed in sacred texts or oral accounts, that tells How Things Are, and develops responses to the narrative along three axes—​the interpretive, the spiritual, and the moral. 1. The interpretive axis involves asking the Big Questions along philosophical/​existential axes in the context of the narrative. Why is there anything at all rather than nothing? What does the narrative tell me about Death? Love? Evil? The Meaning of Life? God? In indigenous and traditional religions, answers to these questions are usually included in the narratives themselves and are then further interpreted by elders and clerics. 2. The spiritual axis involves exploring inward responses to the mythos, including awe, wonder, gratitude, assent, commitment, humility, reverence, joy, and the astonishment of being alive at all. In traditional and indigenous religions, art, ritual, and meditative practice foster and deepen spiritual modalities in the context of the mythos. 3. The moral axis involves exploring outward responses to the mythos, including nurture, compassion, fairness, 220

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responsibility, and communion. In indigenous and traditional religions, moral precepts are usually woven into the fabric of their texts, traditions, and ceremonies and are then further interpreted by elders and clerics. A religious person integrates these three axes into a coherent whole—​the oft-​uttered concept of being “spiritual but not religious,” for example, leaves out the interpretive and moral aspects of being religious. Persons who adopt the core tenets of an indigenous or traditional religion are said to hold Beliefs, and they are likely to participate in communities of fellow believers. The adjective religious does not mean the same thing as the noun religion. Most religions establish and advocate a set of codified Beliefs and practices and support a formal clergy of some kind. A religious person may, or may not, elect to adopt such a religion. Importantly, the noun religion is inapplicable to the religious naturalist trajectory, where interpretations and practices are shared and celebrated but not codified. Since there is no such thing as, nor is there likely to be, a canonical religious natural-​ism, but rather many versions thereof, we speak of a religious naturalist orientation, albeit the term religious naturalism often serves as useful shorthand.

WHO IS A RELIGIOUS NATURALIST? A religious naturalist is a naturalist who, having adopted Everybody’s Story as a core narrative, goes on to explore its religious potential, developing interpretive, spiritual, and moral/​ethical responses in the context of the natural world. The search for 221

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social justice, for example, is guided by an understanding of the evolutionary antecedents to our social sensibilities. Foundational to this orientation is Ecomorality—​seeking right relations between the Earth and its creatures, mindful of our interrelatedness and interdependence. None of these religious responses is front-​ loaded into Everybody’s Story as they are in the traditional and indigenous religious texts and traditions. Nature Just Is. Therefore, the religious naturalist engages in an exploration, accompanied by fellow explorers, developing and sharing interpretive, spiritual, and moral understandings and feelings. Each odyssey is informed and guided by mindful explorations of our human cultural traditions, including art, literature, philosophy, and the religions of the world, all of which are also part of Nature. The reflections offered in this book are written primarily in what I would call a spiritual voice. Some readers, I have come to learn, are uncomfortable with the word spiritual, seeing it as connoting a supernatural framework. But the word comes from spiritus, Latin for breath, and connotes essence. For religious naturalists, our spiritual selves, our most deeply felt selves, are fully essential and fully natural. Naturalistic understandings greatly expand and deepen the parameters of spiritual experience. I can look at a sunset and thrill to its outrageous beauty, then toggle to marveling at the nuclear fusions generating the helium and the heat, then switch to gratitude for the sunlight-​driven photosynthesis that generates the oxygen that I am breathing, and then become infused with joy that we have such a spectacular star. Naturalistic understandings also expand and deepen the parameters of our moral sensibilities to include ecomorality (Chapter 13). 222

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WHAT ABOUT GOD(S)? The concept of god(s) who actively guide and alter the course of natural events and human lives is not a naturalist view, and persons for whom this concept is important will presumably prefer another religious orientation. Most religious naturalists, including myself, do not elect to use god language at all, but some adopt the word as metaphor (e.g., God is a personification of sacred dimensions of reality), or to connote the unknown and perhaps unknowable substrate of order (e.g., God is the ground of all being), or to connote a large and revered human dynamic (e.g., God is serendipitous creativity), or to characterize a pantheistic framework (e.g., God is the sum of the natural and physical laws of the universe). I call myself a religious nontheist and not atheist because an atheist is considered to have a belief about God—​that there isn’t one. I find god-​belief conversations to be irrelevant to my religious sensibilities, but many, of course, consider them to be fundamental.

A RELIGIOUS NATURALIST TAKES NATURE TO HEART A naturalist takes Nature to mind. A religious naturalist takes Nature to mind. A religious naturalist also takes Nature to heart. Loyal Rue, who coined this phrase, illustrates what this would mean in an Islamic context: If I were to say that I have taken the Koran to heart, you might infer that the teachings of the Koran now

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Epilogue shape how I think, feel and act. I now take Allah’s will as my own, and I have a newly clarified sense of who I am, where I came from, and where I am going. Taking the Koran to heart alters the fabric of my self-​understanding, it shifts my teleological center of gravity, and I operate differently in my efforts to live in harmony with that reality.

Transposing to a religious naturalist context, we get this: If I were to say that I have taken Nature to heart, you might infer that my understandings of the natural world now shape how I think, feel and act. I now take the natural world as my own, and I have a newly clarified sense of who I am, where I came from, and where I am going. Taking Nature to heart alters the fabric of my self-​understanding, it shifts my teleological center of gravity, and I operate differently in my efforts to live in harmony with that reality.

PERSPECTIVE A religious naturalist is anchored in and dwells within her understandings of the natural world. He finds religious orientation within that meta-​narrative and develops mindful religious responses to it—​interpretive, spiritual, and moral. A religious naturalist takes Nature to mind and to heart. Importantly, the religious responses developed in religious naturalist orientations often deeply overlap those espoused by existing traditions. The adoption of a meta-​narrative does not alter the human impulse toward common spiritual and moral sensibilities; rather, it influences how we get there. 224

The R eligious Natur alist Or ientation Listen! On the hillside Trees are singing, Chalice gold with praise. The sun blurts a dazzling Sermon. In maroon and caramel Maples whisper amazements. You see in the pond’s perfect placidity Where years of prayer And stillness will take you. It’s so still here you can almost hear The leaves hymning as they lilt down Distributing communion to the Earth. Feel their bliss as they bob, On the periphery Of eternity. The trees meditate, plunging Deeper, ever deeper into wisdom’s Watery dark. Here and there circles silver: Softly, Shyly the depths are offering themselves To you. As day bows to the setting sun, And fills the sky with millions of votive candles, Incense rises everywhere And you, at last, Become The temple. —​Duane Tucker, “The Temple of Autumn”

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E N DNOT E S 1 : LEGEN DS TO COV ER A ND CHAP TER FRON T I SP I EC E S A ND TE X T FIGURE CREDI T S

Cover: Male giant tortoise (Chelonoidis vandenburghi) at sunrise near the Alcedo volcano of Isabela Island, Galápagos, Ecuador, where Charles Darwin began his analysis of evolution during his voyage on the Beagle, and where Tui de Roy https://​www.tuide​roy.com has been photographing wildlife for decades. She also contributed the beautiful cover photograph of the first edition.

Chapter Frontispieces The opportunity to use color in this edition allowed the selection of wonderful photographs as frontispieces; these are identified and acknowledged below. They join the elegant black-​and-​white drawings created by Ippy Patterson as the frontispieces for the first edition. Chapter 1: Our context. Upper: The Milky Way as visualized by an artist (from NASA/​ JPL-​ Caltech/​ R. Hurt (SSS/​ Caltech)). Lower: Earth (from https://​www.nasa.gov/​top​ics/​earth/​ima​ges/​index.html). Chapter 2: Hydrothermal vents. Upper: Black smokers emitting liquid rich in barium, calcium, silicon, and carbon dioxide at the Champagne vent, Northwest Eifuku volcano, Marianas Trench. Lower: White smokers emitting dark, sulphureous plumes (credit: Ocean Exploration Trust). Chapter 3: A portion of a human antibody protein (top) attached to the spike protein of the coronavirus (bottom). The protein strands adopt three internal configurations based on local amino-​acid sequences: random coil (orange); beta-​sheet (red); and alpha-​helical (blue). This architecture generates the shapes of the human and viral domains that interact with one another (credit: Markus Buehler https://​pubs.acs.org/​doi/​10.1021/​acsn​

Endnotes 1 ano.9b02​180 and https://​news.mit.edu/​2021/​symph​ony-​antib​ody-​prot​ ein-​body-​makes-​neu​tral​ize-​coro​navi​r us-​0521). Chapter 4: Single-​celled vs. multicellular organisms. Upper: Amoeba proteus extending its pseudopodia. Lower: Sea urchin embryo (Paracentrotus lividus) at the four-​cell stage (from open-​access on-​line sources). Chapter 5: Evolution. Upper: Herring gulls (Larus smithsonianus) displaying the social behavior called flocking. Lower: Mute swans (Cygnus olor) displaying the sexual behavior called monogamous co-​ parenting, which gulls also practice. Both from Martha’s Vineyard, Massachusetts (credit: Maria Thibodeax www.mariat​hibo​deau​phot​ogra​phy.com). Chapter 6: Biodiversity. Upper: Trilobite (Gabriceraurus mifflinensis), Ordovician (485–​ 4 44 million years ago), from Platteville Formation, Wisconsin (credit: Matt Heaton/​FossilEra). Lower: Pawpaw sphinx moths (Dolba hyloeus) from Martha’s Vineyard, Massachusetts (credit: Maria Thibodeau). Chapter 7: Awareness and the I-​Self. Upper: Leopard frog (Lithobates kauffeldi). Lower: Osprey hawk (Pandion haliaetus). Both from Martha’s Vineyard, Massachusetts (credit: Maria Thibodeau). Chapter 8: Interpretations and Feelings. Upper: Kaleb, a bonobo ape (Pan paniscus), clinging in fear to his mother’s fur after being chased by larger bonobos, from Jacksonville Florida Zoo (credit: Marian Brickner http://​ www.marian​bric​kner​phot​ogra​phy.com/​phot​ogra​phy/​). Lower: Blue-​ footed booby (Sula nebouxii), a favorite bird of Charles Darwin, displaying joy during his mating dance, from Lobos De Tierra Island, Peru (credit: Tui de Roy). Chapter 9: Sex. Upper: Dandelion (Taraxacum erythrospermum), which engages in apomictic self-​ fertilization. Lower: Coltsfoot (Tussilago farfara), which engages in out-​crossing. Both from Martha’s Vineyard, Massachusetts (credit: Maria Thibodeau). Chapter 10: Intimacy. Upper: Lorel (mother) and Lucy (daughter) bonobo apes (Pan paniscus), from Jacksonville Florida Zoo (credit: Marian Brickner; see also Mathea Levine and Marian Brickner, I’m Lucy: A Day in the Life of a Young Bonobo (Blue Barque Press, 2008)). Lower: Pair of Laysan albatross (Phoebastria immutabilis) co-​parenting a chick, from Midway Atoll, Hawaii (credit: Tui de Roy).

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Endnotes 1 Chapter 11: Death. Upper: Corn plants (Zea mays) in autumn. Lower: Maple leaves (Acer saccharum) released via apoptosis in autumn. Both from Martha’s Vineyard, Massachusetts (credit: Maria Thibodeau). Chapter 12: Human evolution. Upper: Homo sapiens skull, 160,000 years old, Afar region of eastern Ethiopia (from open-​access on-​line source). Lower: Infant Homo sapiens (credit: Maria Thibodeau). Chapter 13: Morality and Ecomorality. Minimalist human sculpture created next to a California mountain stream (credit: Bruce Fox).

Figure Credits Figures 2.1, 2.3, 3.2, 3.4, and 6.1 were drawn by Jae-​Hyeok Lee (University of British Columbia). Figure 2.2 From Terrence Deacon, “Reciprocal linkage between self-​ organizing processes is sufficient for self-​reproduction and evolvability” (Biological Theory 1: 136–​1 49, 2006). Figure 3.1 Images obtained from open-​source sites on the internet. Figure 3.3 was obtained from https://​www.pathw​ayz.org/​Tree/​Plain/​BIOC​ HEMI​CAL+​PATHW​AYS Figure 6.2 is from Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, and Banfield JF. A new view of the tree of life. Nature Microbiology 1: 16048 (2016). Figure 6.3 was created by David Hillis, Derrick Zwickl, and Robin Gutell, University of Texas Austin, http://​www.zo.ute​xas.edu/​facu​lty/​antise​nse/​ Downl​oadf​i les​ToL.html Figure 7.1 was obtained from Truex, RC, and Carpenter, MB, Strong & Elwyn's Human Neuroanatomy, Fifth edition. 1964. Baltimore: The Williams & Wilkins Co.; Edinburgh: Livingstone. Figure 12.1 was adapted from Stanley, S, Clades versus clones in evolution: why we have sex, Science 190: 382 (1975). Figure 12.2 was adapted from "Our Family Tree" from Demonic Males by Dale Peterson and Richard Wrangham. Copyright (c) 1996 by Richard Wrangham and Dale Peterson. Used by permission of HarperCollins Publishers.

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E NDNOTE S 2: FURT HER R E A DI NGS/​R E SOURCE S AN D TE X T CREDI T S

INTRODUCTION Many of the concepts presented were articulated by Loyal Rue in Amythia: Crisis in the Natural History of Western Culture (University of Alabama Press, 1989) and developed in his subsequent books: By the Grace of Guile: The Role of Natural History in Human Affairs (Oxford University Press, 1994); Everybody’s Story (SUNY Press, 1999), from which the Rue quote in the chapter derives; Religion is Not about God: How Spiritual Traditions Nurture our Biological Nature and What to Expect When They Fail (Rutgers University Press, 2006); and Nature is Enough: Religious Naturalism and the Meaning of Life (SUNY Press, 2012). My understanding of the nature of religion is indebted to: Erwin R. Goodenough, Religions in Antiquity: Essays in Memory of Erwin Ramsdell Goodenough (Wpf and Stock, 2004); William James, Varieties of Religious Experience: A Study in Human Nature (Longmans, Green & Co, 1903); and Mary Evelyn Tucker and John Grim, Ecology and Religion (Island Press, 2014). Karen Armstrong surveys religious myths in A Short History of Myth (Canongate Canons, 2022). The history of the religious naturalist orientation is reviewed by Jerome Stone in Religious Naturalism Today: The Rebirth of a Forgotten Alternative (SUNY Press, 2009), and numerous perspectives are offered in Donald Crosby and Jerome Stone, The Routledge Handbook of Religious Naturalism (Routledge Press, 2018). An outline of the orientation is presented on p. 219 of this book, with further readings listed in the final section of these Endnotes. Planetary ethical statements that have already been crafted and are ripe for consideration include: the Earth Charter https://​earth​char​ter.org/​read-​ the-​earth-​char​ter/​; the Declaration Toward a Global Ethic https://​www. glo​bal-​ethic.org/​decl​arat​ion-​tow​ard-​a-​glo​bal-​ethic/​; and the Charter for Compassion https://​chart​erfo​rcom​pass​ion.org.

Endnotes 2 HOW THIS BOOK IS PUT TOGETHER C.P. Snow, The Two Cultures (Barakaldo Books, 2020 [original, 1959]), re-​visited in Marcelo Gleiser, Great Minds Don’t Think Alike: Debates on Consciousness, Reality, Intelligence, Faith, AI, Immortality, and the Human (Columbia University Press, 2022). George Lakoff and Mark Johnson, Metaphors We Live By (University of Chicago Press, 2008).

CHAPTER 1 Origins of the Earth Joel Primack kindly vetted and corrected my understandings of cosmic and planetary history, some aspects of which have been simplified in this chapter. Classic accounts of cosmology and quantum theory include: Lucretius and Martin Smith translator, On the Nature of Things (Hackett Publishing Company 2001 [original ~50 BC]); Carl Sagan, Cosmos (Ballantine Books, 2013 [original 1980]); Steven Weinberg, Dreams of a Final Theory (Pantheon, 1992) and The First Three Minutes: A Modern View of the Origins of the Universe (updated Bantam, 1996); and Stephen Hawking, A Brief History of Time: From the Big Bang to Black Holes (Bantam, 1998). Brian Swimme offers poetic accounts in The Universe is a Green Dragon: a Cosmic Creation Story (Bear and Company, 1984) and The Universe Story: From the Primordial Flaring Forth to the Ecozoic Era—​A Celebration of the Unfolding of the Cosmos (HarperOne, 1994). The film Journey of the Universe featuring Brian Swimme is available here https://​vimeo​pro.com/​yale​fes/​jour ​ney-​of-​the-​unive​r se-​materi​alsusing the password JOTU2014. Recent accounts include: Joel Primack and Nancy Abrams, The View from the Center of the Universe: Discovering our Extraordinary Place in the Cosmos (Riverhead Books, 2007); Carlo Rovelli, Seven Brief Lessons on Physics (Riverhead Books, 2016), The Order of Time (Riverhead Books, 2018), and Helgoland: Making Sense of the Quantum Revolution (Riverhead Books, 2021); Marcia Bjornerud, Timefulness: How Thinking Like a Geologist Can Help Save the World (Princeton University Press, 2018); Sean Carroll, Spacetime and Geometry: An Introduction to General Relativity (Cambridge University Press, 2019) and Something Deeply Hidden: Quantum Worlds and the Emergence of Spacetime (OneWorld Publications, 2021); Brian Cox and Andrew Cohen, The Planets (William Collins, 2019); Eric Scerri, The Periodic Table: Its Story

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Endnotes 2 and its Significance, 2e (Oxford University Press, 2019); DK, Universe, Third Edition (DK, 2020); Katie Mack, The End of Everything (Astrophysically Speaking) (Scribner, 2020); Janna Levin, Black Hole Survival Guide (Knopf, 2020); Neil deGrasse Tyson, Michael Strauss, and J. Richard Gott, A Brief Welcome to the Universe: A Pocket-​Sized Tour (Princeton University Press, 2021); Chanda Prescod-​Weinstein, The Disordered Cosmos: A Journey into Dark Matter, Spacetime, and Dreams Deferred (Bold Type Books, 2021); Brian Green, Until the End of Time: Mind, Matter, and our Search for Meaning in an Evolving Universe (Vintage, 2021); Andrew Knoll, A Brief History of Earth: Four Billion Years in Eight Chapters (Custom House, 2021); Alan Lightman, Probable Impossibilities: Musings on Beginnings and Endings (Pantheon, 2021); Chandra Prescod-​Weinstein, The Disordered Cosmos: A Journey into Dark Matter, Speacetime, and Dreams Deferred (Bold Type Books, 2021), and Frank Wilczek, Fundamentals: Ten Keys to Reality (Penguin Press, 2021). Feynman quote is from The Character of Physical Law (MIT Press, 1995); the Steven Weinberg quote is from The First Three Minutes: A Modern View of the Origins of the Universe (updated Bantam, 1996); the Steven Hawking quote is from A Brief History of Time: From the Big Bang to Black Holes (Bantam, 1998); the passage from Lao Tzu is “Verse One” from Tao Te Ching, translated by Gia-​Fu Feng and Jane English © 1972, copyright renewed 2000 by Carol Wilson and Jane English, used by permission of Alfred A. Knopf, an imprint of the Knopf Doubleday Publishing Group, a division of Penguin Random House LLC.

CHAPTER 2 Origins of Life Four sourcebooks provided much of my material on comparative religion for the first edition: John Bowker, The Oxford Dictionary of World Religions (Oxford University Press, 1997) and the beautifully illustrated World Religions: The Great Faiths Explored and Explained (Dorling Kindersley, 1997); Åke Hultkrantz, Native Religions of North America: The Power of Visions and Fertility (HarperSanFrancisco, 1987, a volume in the Religious Traditions of the World series); and Dennis Tedlock and Barbara Tedlock, Teachings from the American Earth: Indian Religion and Philosophy (Liverite, 1975) from which comes the quote from the Kogi peoples. Barbara Sproul compiles accounts of creation in Primal Myths: Creation Myths Around the World (HarperCollins, 1991). Robert Bellah covers many bases in Religion in Human Evolution: From the Paleolithic to the Axial Age (Belknap Press, 2017).

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Endnotes 2 Humberto Maturana and Francisco Varela made key contributions to our understandings of self-​organization/​autopoiesis, starting with Autopoiesis and Cognition: The Realization of the Living (D. Reidel Publishing Company, 1980). Stuart Kauffman introduces the concept of emergent properties in At Home in the Universe (Oxford University Press, 1995); Terrence Deacon and Ursula Goodenough expand the concept in “The Sacred Emergence of Nature” (Oxford Handbook of Religion and Science, P. Clayton, ed., Oxford University Press, 2006). Deacon presents the autogen model in “Reciprocal linkage between self-​organizing processes is sufficient for self-​reproduction and evolvability” (Biological Theory 1: 136-​1 49, 2006), from which Figure 2 derives, and develops the concepts of emergent dynamics and the self in Incomplete Nature: How Mind Emerged from Matter (W.W. Norton & Co., 2013). Jeremy Sherman explores Deacon’s paradigms in Neither Ghost Nor Machine: The Emergence and Nature of Selves (Columbia University Press, 2017) and Andreas Weber articulates similar self concepts in The Biology of Wonder: Aliveness, Feeling, and the Metamorphosis of Science (New Society Publishers, 2016). Deacon proposes a model for the origins of life’s semiotic systems in “How molecules became signs” (Biosemiotics https://​doi.org/​10.1007/​s12​304-​021-​09453-​9, 2021). The what-​is-​life question is also explored by Carl Zimmer in Life’s Edge: The Search for What It Means to Be Alive (Dutton, 2021) and by Paul Nurse in What Is Life? Five Great Ideas in Biology (W.W. Norton & Co., 2021). Tyler Volk provides a synthesis in Quarks to Culture: How We Came to Be (Columbia University Press, 2017). Animism is explored in the following: Gregory Cajete, Look to the Mountain: An Ecology of Indigenous Education (Kivaki Press 1994); David Abram, The Spell of the Sensuous: Perception and Language in a More-​Than-​ Human World (Vintage, 1997) and Becoming Animal: An Earthly Cosmology (Vintage, 2010); Jane Bennett, Vibrant Matter: A Political Ecology of Things (Duke University Press Books, 2010); Graham Harvey, The Handbook of Contemporary Animism (Routledge, 2015); Mark Wallace, When God Was a Bird: Christianity, Animism, and the Re-​Enchantment of the World (Fordham University Press, 2019); and Sam Mickey, Mary Evelyn Tucker, and John Grim, Living Earth Community: Multiple Ways of Being and Knowing (Open Book Publishers, 2020). Thoreau quote is from A Year in Thoreau’s Journal: 1851 (Penguin Classics, 1993): the Carson quote is from The Edge of the Sea (Mariner Books, 1998 [first published 1995]).

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Endnotes 2 Mary Oliver poem, “The Summer Day,” is reprinted by the permission of The Charlotte Sheedy Literary Agency as agent for the author. Copyright © NW Orchard LLC 1990 with permission by Bill Reichblum.

CHAPTERS 3 & 4 How Life Works and How Organisms Work Listed here are some highly regarded textbooks and trade books on the topics covered in these chapters: Eric H. Davidson, The Regulatory Genome: Gene Regulatory Networks in Development and Evolution (Academic Press, 2006); Sean Carroll, Endless Forms Most Beautiful: The New Science of Evo Devo (W.W. Norton, 2006); Jamie Davies, Life Unfolding: How the Human Body Creates Itself (Oxford University Press, 2015); Kriti Sharma, Interdependence: Biology and Beyond (Fordham University Press, 2015); Denis Noble, Dance to the Tune of Life: Biological Relativity (Cambridge University Press, 2017); Michael Barresi and Scott Gilbert, Developmental Biology, 12th edition (Sinauer, 2019); Bill Bryson, The Body: A Guide for Occupants (Doubleday, 2019); David Nelson et al., Lehninger Principles of Biochemistry, 8th edition (W.H. Freeman, 2021); and Bruce Alberts et al., Molecular Biology of the Cell, 7th edition (W.W. Norton, 2022). Memorable essays are found in Lewis Thomas, The Lives of a Cell: Notes of a Biology Watcher (Penguin, 1978). An excellent animation of sub-​cellular processes is found at https://​www. yout​ube.com/​watch?v=​7Hk9​jct2​ozY. William James offered a version of the Mozart metaphor in 1897 in The Will to Believe (reprinted in Digireads.com, 2021): “A Beethoven quartet is truly, as someone has said, a scraping of horses’ tails on cats’ bowels, and may be exhaustively described in such terms; but the application of this description in no way precludes the simultaneous applicability of an entirely different description.” Loyal Rue presents the grunge theory of matter in Emergence: Nature’s Mode of Creativity: A Guide to Thinking About Emergence, Zygon 42: 829–​835 (2007), and his paean to matter is from Religion is Not about God: How Spiritual Traditions Nurture our Biological Nature and What to Expect When They Fail (Rutgers University Press, 2006); the James quote is from The Varieties of Religious Experience: A Study in Human Nature (Digireads.com 2002 [original 1902]). Mary Oliver poem, “When I Am Among the Trees,” is reprinted by the permission of The Charlotte Sheedy Literary Agency as agent for the author. Copyright © NW Orchard LLC 2006 with permission by Bill Reichblum.

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Endnotes 2 Figure 6 was obtained from https://​ www.pathw​ ayz.org/​ Tree/​ Plain/​ BIOC​HEMI​CAL+​PATHW​AYS

CHAPTERS 5 & 6 How Evolution Works and The Evolution of Biodiversity Books on evolution include: Charles Darwin, On the Origin of Species (Penguin Classics, 1984 [original 1859]), from which the “endless forms most beautiful” quote derives, and The Descent of Man, and Selection in Relation to Sex (Read & Co Books, 2020 [original 1871]); Jacques Monod, Chance and Necessity: An Essay on the Natural Philosophy of Modern Biology (Knopf, 1971); Richard Dawkins, The Ancestors Tale: A Pilgrimage to the Dawn of Evolution (Mariner Books, 2005); Sean Carroll, Endless Forms Most Beautiful: The New Science of Evo Devo (W.W. Norton & Co, 2006); Marc Kirschner and John Gerhart, The Plausability of Life: Resolving Darwin’s Dilemma (Yale University Press, 2006); Neil Shubin, Your Inner Fish: A Journey into the 3.5-​Billion-​Year History of the Human Body (Vintage, 2009); Jerry Coyne, Why Evolution is True (Penguin Books, 2010); Brian Swimme and Mary Evelyn Tucker, Journey of the Universe (Yale University Press, 2011); Patrick Keeling and Eugene Koonin, eds. Origin and Evolution of Eukaryotes (Cold Spring Harbor Laboratory Press, 2014); David Christian, Origin Story: A Big History of Everything (Little, Brown Spark, 2019); and Henry Gee, A (Very) Short History of Life on Earth: 4.6 Billion Years in 12 Pithy Chapters (St. Martin’s Press, 2021). Books on biodiversity include: John Muir, A Thousand Mile Walk to the Gulf (Doublebit Press, 2020 [original 1916]); Edward Ricketts and Jack Calvin, Between Pacific Tides: Fifth Edition (Stanford University Press, 1992 [original 1948]); Rachel Carson, The Sea Around Us (Canongates Canons, 2021 [original 1951]) and The Edge of the Sea (Mariner Books, 1995 [original 1955]); Edward O. Wilson, The Diversity of Life: With a New Preface (Belnap Press, 2010); Peter Wohlleben, The Hidden Life of Trees: What They Feel, How They Communicate (Greystone Books, 2016) and The Secret Network of Nature: The Delicate Balance of All Living Things (Vintage, 2019); J. Drew Lanham, The Home Place: Memoirs of a Colored Man’s Love Affair with Nature (Milkweed Editions, 2017); Ed Yong, I Contain Multitudes: The Microbes Within Us and a Grander View of Life (Ecco, 2018); Enric Sala, The Nature of Nature: Why We Need the Wild (National Geographic, 2020); DK, Oceanology: The Secrets of the Sea Revealed (DK, 2020), and Natural History, second edition (DK, 2021); and Scott

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Endnotes 2 Weidensaul, A World on the Wing: The Global Odyssey of Migratory Birds (W.W. Norton, 2021). Mary Oliver poem, “Wild Geese” is from DREAM WORK, copyright © 1986 by Mary Oliver. Used by permission of Grove/​Atlantic, Inc. Any third party use of this material, outside of this publication, is prohibited. Oren Lyons quote is from The Essential Mystics: Selections from the World’s Great Wisdom Traditions, A. Harvey, ed. (HarperSanFrancisco, 1996). “Remember, remember the circle of the sky”—​Pawnee/​Osage/​Omaha Indian Song from Earth Prayers by Elizabeth Roberts and Elias Amidon. Copyright (c) 1991 by Elizabeth Roberts and Elias Amidon. Used by permission of HarperCollins Publishers. The walking/​time analogy is also developed by Richard Dawkins in River Out of Eden: A Darwinian View of Life (Basic Books, 1995). An interactive tree of life is found here https://​www.onez​oom.org Figure 9 is from Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, Butterfield CN, Hernsdorf AW, Amano Y, Ise K, Suzuki Y, Dudek N, Relman DA, Finstad KM, Amundson R, Thomas BC, Banfield JF. A new view of the tree of life. Nature Microbiology 1: 16048 (2016). Figure 10 is from David Hillis, Derrick Zwickl, and Robin Gutell, University of Texas Austin, http://​www.zo.ute​xas.edu/​facu​lty/​antise​nse/​Downl​oadf​ iles​ToL.html The Rachel Carson quote is from The Edge of the Sea (Mariner Books, 1998; originally published 1955).

CHAPTERS 7 & 8 Awareness and the I-​Self; Interpretations and Feelings In writing the first edition, my major resources for neurobiology were: Antonio Damasio, Descartes’ Error: Emotion, Reason, and the Human Brain (Putnam, 1994); Joseph LeDoux, The Emotional Brain: The Mysterious Underpinnings of Emotional Life (Simon and Schuster, 1996); and Steven Pinker, How the Mind Works (Norton, 1997). Additional insights for this edition have come from: Terrence Deacon, The Symbolic Species: The Co-​Evolution of Language and the Brain (Norton, 1998) and Incomplete Nature: How Mind Emerged from Matter (W.W. Norton & Co., 2013); Antonio Damasio, Feeling

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Endnotes 2 and Knowing: Making Minds Conscious (Pantheon, 2021); and Anil Seth, Being You: A New Science of Consciousness (Dutton, 2021). Recent books that consider awareness, consciousness, and emotion/​ feeling include: Thomas Metzinger, Being No One: The Self-​Model Theory of Subjectivity (Bradford Book, 2004); Marc Bekoff, The Emotional Lives of Animals: A Leading Scientist Explores Animal Joy, Sorrow, and Empathy—​And Why They Matter (New World Library, 2008); Carl Safina, Beyond Words: What Animals Think and Feel (Henry Holt, 2015) and Becoming Wild: How Animal Cultures Raise Families, Create Beauty, (Henry Holt, 2020); Peter Godfrey-​ Smith, Other Minds: The Octopus, the Sea, and the Deep Origins of Consciousness (Farrar, Straus and Giroux, 2016) and Metazoa: Animal Life and the Birth of the Mind (Farrar, Strauss and Giroux, 2020); Jonathan Balcombe, What a Fish Knows: The Inner Lives of Our Underwater Cousins (Farrar, Straus and Giroux, 2016); Daniel Siegel, Mind: A Journey to the Heart of Being Human (W.W. Norton and Comany, 2017); Robert Wright, Why Buddhism Is True: The Science and Philosophy of Meditation and Enlightenment (Simon and Schuster, 2017); Frans de Waal, Are We Smart Enough to Know How Smart Animals Are? (W.W. Norton and Company, 2017); Annaka Harris, Conscious: A Brief Guide to the Fundamental Mystery of the Mind (Harper, 2019); Joseph Ledoux, The Deep History of Ourselves: The Four-​Billion-​Year Story of How We Got Conscious Brains (Penguin, 2019); Matthew Cobb, The Idea of the Brain: The Past and the Future of Neuroscience (Basic Books, 2020); Frans de Waal, Mama’s Last Hug: Animal Emotions and What They Tell Us About Ourselves (W.W. Norton & Co, 2020); Melanie Challenger, How to Be Animal: A New History of What It Means to Be Human (Penguin Books, 2021); Steven Pinker, Rationality: What It Is, Why It Seems Scarce, Why It Matters (Viking, 2021); Jeff Hawkins, A Thousand Brains: A New Theory of Intelligence (Basic Books, 2021); Rebecca Schwarzlose, Brainscapes: The Warped, Wondrous Maps Written in Your Brain—​ And How They Guide You (Mariner Books, 2021); Mark Solms, The Hidden Spring: A Journey to the Source of Consciousness (W.W. Norton & Co, 2021); Eric Kandel and colleagues, Principles of Neuroscience, 6th edition (McGraw-​Hill Education, 2021); Iain McGilchrist, The Matter with Things: Our Brains, Our Delusions, and the Unmaking of the World (Perspective Press, 2021); and Ed Wong, An Immense World: How Animal Senses Reveal the Hidden Realms Around Us (Random House, 2022). Mystical experience is explored in the following: Eugene d’Aquili and Andrew Newberg, The Mystical Mind: Probing the Biology of Religious Experience

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Endnotes 2 (Fortress Press, 1999); Ann Taves, Fits, Trances, and Visions: Experiencing Religion and Explaining Experience from Wesley to James (Princeton University Press, 1999); William Richards, Sacred Knowledge: Pyschedelics and Religious Experience (Columbia University Press, 2016); Andrew Newberg and Mark Waldman, How Enlightenment Changes Your Brain: The New Science of Transformation (Avery, 2017); Wayne Teasdale, The Mystic Heart: Discovering a Universal Spirituality in the World’s Religions (New World Library, 2001), and Jeremy Lent, The Web of Meaning: Integrating Science and Traditional Wisdom to Find Our Place in the Universe (New Society Publishers, 2021). The concept of humans as storytellers is developed in Daniel Dennett, Consciousness Explained (Back Bay Books, 1992). The concept of transcendence as a fullness and richness is developed in Charles Taylor, A Secular Age (Belnap Press, 2018). William James quote is from The Varieties of Religious Experience: A Study in Human Nature (Longmans, Green & Co, 1903); the Einstein quote is from The World As I See It (Philosophical Library, 1934); the Anil Seth quote is from Being You: A New Science of Consciousness (Dutton, 2021); the Peter Godfrey-​Smith quote is from Other Minds: The Octopus, the Sea, and the Deep Origins of Consciousness (Farrar, Straus and Giroux, 2016); the first Damasio quote is from Feeling and Knowing: Making Minds Conscious (Pantheon, 2021); the second Damasio quote is from Descartes’ Error: Emotion, Reason, and the Human Brain (Putnam, 1994); the Deacon quote is from The Symbolic Species: The Coevolution of Language and the Brain (Norton, 1998). Thich Nhat Hanh, “Contemplation on No-​Coming and No-​Going,” Plum Village https://​plum​vill​age.org/​contem​plat​ion-​on-​no-​com​ing-​and-​no​going/​ Daniel Iverson, “Spirit of the Living God,” © 1935, 1963 Birdwing Music (ASCAP), administered by EMI Christian Music Publishing. All Rights Reserved. Used by Permission. Wendell Berry poem “The Peace of Wild Things” from New Collected Poems. Copyright © 2012 by Wendell Berry. Reprinted with the permission of The Permissions Company, LLC on behalf of Counterpoint Press, counterpointpress.com. William Wordsworth poem, “I Wandered Lonely as a Cloud,” in The Complete Poetical Works of William Wordsworth, Late Poet Laureate (Franklin Classics, 2018).

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Endnotes 2 Figure 11 is from W. Hudos, “Evolutionary interpretation of neural and behavioral studies of living vertebrates,” in: F.O. Schmidt, ed., Neurosciences: Second Study Program, 1970, by copyright permission of the Rockefeller University Press.

CHAPTERS 9 & 10 Sex and Intimacy Classic books on sex and sexuality include: Charles Darwin, The Descent of Man, and Selection in Relation to Sex (Read & Co Books, 2020 [original 1871]), and G.C. Williams, Sex and Evolution (Princeton University Press, 1975). Recent books include: Geoffrey Miller, The Mating Mind: How Sexual Choice Shaped the Evolution of Human Nature (Anchor Press, 2011); Sexual Interactions in Eukaryotic Microbes, Danton O’Day, ed. (Academic Press, 2012); Barbara Fredrickson, Love 2.0: How Our Supreme Emotion Affects Everything We Feel, Think, Do, and Become (Hudson Street Press, 2013); Helen Fisher, Anatomy of Love: A Natural History of Mating, Marriage, and Why We Stray (W.W. Norton & Co., 2017); Richard Prum, The Evolution of Beauty: How Darwin’s Forgotten Theory of Mate Choice Shapes the Animal World—​and Us (Anchor, 2018); and Carl Zimmer, She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity (Dutton, 2019). “Thick” relationships are described in Avishai Margalit, On Betrayal (Harvard University Press, 2017). Sharon Olds poem, “High School Senior,” is from WELLSPRING: POEMS by Sharon Olds, copyright © 1996 by Sharon Olds. Used by permission of Alfred A. Knopf, an imprint of the Knopf Doubleday Publishing Group, a division of Penguin Random House LLC. All rights reserved.

CHAPTER 11 Multicellularity and Death A collection of essays on death is found in The End of Life, J.D. Roslansky, ed. (North-​Holland Publishing, 1973), one of which, “The Origin of Death” by George Wald, also considers the importance of the germ/​soma dichotomy; see also George Wald, Therefore Choose Life (House of Anansi Press, 2017). William Clark develops this idea as well in Sex and the Origins of Death (Oxford University Press, 1996). Camille Dungy anthologizes books of poetry on grief and mourning here https://​orionm​agaz​ine.org/​2021/​12/​fift​een-​poe​try-​reco​mmen​d ati​ons-​ about-​grief-​and-​mourn​ing-​for-​our-​dark​est-​nig​hts/​

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Endnotes 2 The concept that being dead is like before being born has been attributed to the poet Lucretius (~99 BC—​55 BC).

CHAPTER 12 Human Evolution Books on human evolution include: Frans de Waal and Frans Lanting, Bonobo: The Forgotten Ape (University of California Press, 1997); Terrence Deacon, The Symbolic Species: The Coevolution of Language and the Brain (Norton, 1998); Merlin Donald, A Mind So Rare: The Evolution of Human Consciousness (W.W. Norton and Company, 2001); Richard Wrangham, Catching Fire: How Cooking Made Us Human (Basic Books, 2010) and The Goodness Paradox: The Strange Relationship Between Virtue and Violence in Human Evolution (Vintage, 2019); Svante Pääbo, Neanderthal Man: In Search of Lost Genomes (Basic Books, 2015); Martin Muller et al., Chimpanzees and Human Evolution (Belknap Press, 2017); Robert Sapolsky, Behave: The Biology of Humans at Our Best and Worst (Penguin Press, 2017); Yuval Harari, Sapiens: A Brief History of Humankind (Harper Perennial, 2018); Rebecca Sykes, Kindred: Neanderthal Life, Love, Death and Art (Bloomsbury Sigma, 2020); Rutger Bregman, Humankind: A Hopeful History (Little Brown and Company, 2020); Lesley Newson and Peter Richerson, The Story of Us: A New Look at Human Evolution (Oxford University Press, 2021); David Graeber and David Wengrow, The Dawn of Everything: A New History of Humanity (Farrar, Straus and Giroux, 2021); Tom Higham, The World Before Us: The New Science Behind Our Human Origins (Yale University Press, 2021); Brian Kaas, Corruptible: Who Gets Power and How It Changes Us (Scribner, 2021); Franz de Waal, Different: Gender Through the Eyes of a Primatologist (W.W. Norton & Co, 2022);and Jennifer Raff, Origin: A Genetic History of the Americas (Twelve, 2022). The concept of anchoring language facility with sexual selection is developed in Geoffrey Miller, The Mating Mind: How Sexual Choice Shaped the Evolution of Human Nature (Anchor Press, 2011); the concept of human self-​ domestication is developed in Richard Wrangham, The Goodness Paradox: The Strange Relationship Between Virtue and Violence in Human Evolution (Vintage, 2019). Deacon quote is from The Symbolic Species: The Coevolution of Language and the Brain (Norton, 1998).

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Endnotes 2 Figure 12 is adapted from Steven Stanley, Clades versus clones in evolution: why we have sex, Science 190: 382 (1975). Figure 13 is adapted from Richard Wrangham and Dale Peterson, Demonic Males: Apes and the Origins of Human Violence (Houghton Mifflin, 1996).

CHAPTER 13 Morality and Ecomorality Books on virtue ethics and mindfulness include: Martin Oswald, Aristotle: Nicomachean Ethics, Translated with Introduction and Notes (Bobbs-​ Merril, 1962); Thich Nhat Hahn, The Miracle of Mindfulness (Beacon Press, 1975); Alasdair MacIntyre, After Virtue: A Study in Moral Theory (University of Notre Dame Press, 1981); Martha Nussbaum, The Fragility of Goodness: Love and Ethics in Greek Tragedy and Philosophy (Cambridge University Press, 1986); Roger Crisp and Michael Slote, eds., Virtue Ethics (Oxford University Press, 1998); Rosalind Hursthouse, On Virtue Ethics (Oxford University Press, 1999); Jon Kabat-​Zinn, Wherever You Go, You Are There: Mindfulness Meditation in Everyday Life (Hachette Books, 2005); Paul Woodruff, Reverence: Renewing a Forgotten Virtue (Oxford University Press, 2014); and John Teasdale, What Happens in Mindfulness: Inner Awakening and Embodied Cognition (The Guilford Press, 2022). Books on the evolution of human morality include: Robert Wright, The Moral Animal: Why We Are the Way We Are: The New Science of Evolutionary Psychology (Pantheon, 1994); Matt Ridley, The Origins of Virtue: Human Instincts and the Evolution of Cooperation (Penguin, 1998); Larry Arnhart, Darwinian Natural Right: The Biological Ethics of Human Nature (State University of New York Press, 2008); Frans de Waal, Primates and Philosophers: How Morality Evolved (Princeton University Press, 2006) and The Bonobo and the Atheist: In Search of Humanism among the Primates (W.W. Norton & Co., 2014); Sam Harris, The Moral Landscape: How Science Can Determine Human Values (Free Press, 2010); Geoffrey Miller, The Mating Mind: How Sexual Choice Shaped the Evolution of Human Nature (Anchor Press, 2011); Jonathan Haidt, The Righteous Mind: Why Good People Are Divided by Politics and Religion (Vintage Books, 2012); Karen Armstrong, Fields of Blood: Religion and the History of Violence (Anchor, 2015); Michael Tomasello, A Natural History of Human Morality (Harvard University Press, 2018); Richard Wrangham, The Goodness Paradox: The Strange Relationship Between Virtue and Violence in Human Evolution (Vintage, 2019); Nicholas Christakis, Blueprint: The Evolutionary Origins of a Good Society

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Endnotes 2 (Little, Brown Spark, 2020); and Owen Flanagan, How to Do Things with Emotions: The Morality of Anger and Shame across Cultures (Princeton University Press, 2021). Books on the relationship between religions and ecology include: J. Baird Caldicott, Earth’s Insights: A Multicultural Survey of Ecological Ethics from the Mediterranean Basin to the Australian Outback (University of California Press, 1994); Sarah Taylor, Green Sisters: A Spiritual Ecology (Harvard University Press, 2009); Mary Evelyn Tucker and John A. Grim, Ecology and Religion (Island Press, 2014); Pope Francis, Encyclical Letter Laudato Si’ of the Holy Father Francis On Care for our Common Home (Liberia Editrice Vaticana, 2015); Jerome Stone, Sacred Nature: The Environmental Potential of Religious Naturalism (Routledge, 2017); Willis Jenkins, Mary Evelyn Tucker, and John Grim, Routledge Handbook of Religion and Ecology (Routledge, 2018); Iyad Abumoghli, Faith for Earth: A Call for Action (United Nations Environment Programme, 2020); and Tyson Yunkaorta, Sand Talk: How Indigenous Thinking Can Save the World (HarperOne, 2021). A deep resource is found here https://​fore.yale.edu with a comprehensive consideration of ecomorality here https://​fore.yale.edu/​Eco​just​ice. A rich collection of conversations on ecomorality is found here https://​vimeo​ pro.com/​yale​fes/​jour​ney-​of-​the-​unive​rse-​materi​als where the password is JOTU2014. Books on racism include: Douglas Massey, Categorically Unequal: The American Stratification System (Russell Sage Foundation, 2008); Dee Brown, Bury My Heart at Wounded Knee: An Indian History of the American West, illustrated edition (Sterling Innovation, 2009); Alison Alkon, ed., Cultivating Food Justice: Race, Class, and Sustainability (MIT Press, 2011); Carolyn Finney, Black Faces, White Spaces: Reimagining the Relationship of African Americans to the Great Outdoors (University of North Carolina Press, 2014); Carol Wayne White, Black Lives and Sacred Humanity: Toward an African-​American Religious Naturalism (Fordham University Press, 2016); Richard Delgado and Jean Stefancic, Critical Race Theory: An Introduction, 3rd edition (NYU Press, 2017); Carl Anthony, The Earth, the City, and the Hidden Narrative of Race (New Village Press, 2017); Michael Hogue, American Immanence: Democracy for an Uncertain World (Columbia University Press, 2018); Isabel Wilkerson, Caste: The Origins of Our Discontents (Random House, 2020); Joe Feagin, The White Racial Frame, 3rd edition (Routledge, 2020); Christopher Carter, The Spirit of Soul Food: Race, Faith, and Food Justice (University of Illinois Press,

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Endnotes 2 2021); Eduardo Bonilla-​Silva, Racism without Racists: Color-​Blind Racism and Persistence of Racial Inequality in America, 6th edition (Rowman and Littlefield Publishers, 2021); and Charles Mills, The Racial Contract (Cornell University Press, 2022). Classic books on environmental activism include: Aldo Leopold, A Sand County Almanac: And Sketches Here and There (Oxford University Press, 2020 [1949]); Rachel Carson, Silent Spring (Houghton Mifflin Harcourt, 2002 [1962]); and Bill McKibben, The End of Nature (Random House Trade Paperbacks, 2006 [1989]). Recent books on environmental activism include: Barbara Kingsolver, Animal, Vegetable, Miracle (HarperCollins, 2007); Jonathan Foer, Eating Animals (Penguin Books, 2011); Rebecca Solnit, Hope in the Dark: Untold Histories, Wild Possibilities (Haymarket Books, 2016); Edward O. Wilson, Half-​Earth: Our Planet’s Fight for Life (Liveright, 2017); Martin Mulligan, An Introduction to Sustainability: Environmental, Social and Personal Perspectives, 2nd edition (Routledge, 2018); Eileen Crist, Abundant Earth: Toward an Ecological Civilization (University of Chicago Press, 2019); Mark Bekoff, Rewilding Our Hearts: Building Pathways of Compassion and Coexistence (New World Library, 2014); Richard Powers, The Overstory: A Novel (W.W. Norton, 2019); Belden Lane, The Great Conversation: Nature and the Care of the Soul (Oxford University Press, 2019); Holmes Rolston, A New Environmental Ethics, 2nd edition (Routledge, 2020); F. Stuart Chapin, Grassroots Stewardship: Sustainability within Our Reach (Oxford University Press, 2020); Joan Fitzgerald, Greenovation (Oxford University Press, 2020); David Wallace-​Wells, The Uninhabitable Earth: Life after Warming (Tim Duggan Books, 2020); Bill McKibben, Falter: Has the Human Game Begun to Play Itself Out? (Holt Paperbacks, 2020); Katharine Hayhoe, Saving Us: A Climate Scientist’s Case for Hope and Healing in a Divided World (Atria/One Signal Publishers, 2021); Eelco Rohling, Rebalancing Our Climate: The Future Starts Today (Oxford University Press, 2021); Emma Marris, Wild Souls: Freedom and Flourishing in the Non-​Human World (Bloomsbury Publishing, 2021); Michelle Nijhuis, Beloved Beasts: Fighting for Life in an Age of Extinction (W.W. Norton, 2021); Ayana Johnson and Karen Wilkinson, All We Can Save: Truth, Courage, and Solutions for the Climate Crisis (One World, 2021); Tyson Yunkaporta, Sand Talk: How Indigenous Thinking Can Save the World (HarperOne, 2021); Wahinkpe Topa and Darcia Narvaez, Restoring the Kinship Worldview: Indigenous Voices Introduce 28 Precepts for Rebalancing Life on Planet Earth (North Atlantic Books, 2022); and John Reid and Thomas Lovejoy, Ever Green: Saving Big Forests to Save the Planet (W.W. Norton, 2022).

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Endnotes 2 Loyal Rue quote is from Religion Is Not about God: How Spiritual Traditions Nurture Our Biological Nature and What to Expect When They Fail (Rutgers University Press, 2006); the Chang Tsai quote is from Wing-Tsit Chan, A Sourcebook in Chinese Philosophy (Princeton University Press, 1963); the Pope Francis quotes are from Laudato Si’ (Liberia Editrice Vaticana, 2015); the quote from Patriarch Bartholomew is also found in Laudato Si; the Winona LaDuke quote is from All Our Relations: Native Struggles for Land and Life (South End Press, 1999); the Robin Kimmerer quotes are from Braiding Sweetgrass: Indigenous Wisdom, Scientific Knowledge, and the Teachings of Plants (Milkweed Editions, 2013); the Lame Deer quote is from Lame Deer, Seeker of Visions (Washington Square Press, 1994); the Navajo chant is from Jared Kieling, The Gift of Prayer: A Treasury of Personal Prayer from the World’s Spiritual Traditions (Continuum Intl Pub Group, 1995); the Martin Luther King quote is from his address I Have a Dream (Washington DC, 1963); the Rachel Carson quote is from Silent Spring (Houghton Mifflin Harcourt, 2002 [1962]); the Dalai Lama quote is from Ancient Wisdom, Modern World: Ethics for the New Millennium (Time Warner Books UK, 2001); and the Baba Dioum quote is from a paper presented in New Delhi in 1968 to International Union for the Conservation of Nature and Natural Resources. An evocative video of lichens created by Connie Barlow is here https://​ youtu.be/​PpU8​s3so​pFo. Mary Oliver poem “Mindful” is reprinted by the permission of The Charlotte Sheedy Literary Agency as agent for the author. Copyright © NW Orchard LLC 2004 with permission by Bill Reichblum. Wendell Berry poem “A Vision” is from New Collected Poems. Copyright © 1977 by Wendell Berry. Reprinted with the permission of The Permissions Company, LLC on behalf of Counterpoint Press, counterpointpress.com.

EPILOGUE: EMERGENT RELIGIOUS PRINCIPLES e.e. cummings poem, “i thank you God for this amazing.” Copyright 1950, (c) 1978, 1991 by the Trustees for the E.E. Cummings Trust. Copyright (c) 1979 by George James Firmage, from COMPLETE POEMS: 1904–​1962 by E. E. Cummings, edited by George J. Firmage. Used by permission of Liveright Publishing Corporation.

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Endnotes 2 The Emerson quote is from “Self-​ Reliance,” in Ralph Waldo Emerson, R. Poirier, ed. (Oxford University Press,1990); the Hefner metaphor is expanded in “The spiritual task of religion in culture: An evolutionary perspective,” Zygon 33: 535–​544 (1998). I am grateful to Richard Dawkins for narrating the spaceship metaphor to me; his wonderful version is found in Unweaving the Rainbow (Houghton Mifflin, 1998).

Religious Naturalist Orientation Names that have been given to the narrative history of the Universe include: The New Story [Thomas Berry, The New Story (Anima Books, 1978)]; The Epic of Evolution [Edward O. Wilson, On Human Nature (Harvard University Press, 1978)]; The Universe Story [Brian Swimme, The Universe Story: From the Primordial Flaring Forth to the Ecozoic Era—​A Celebration of the Unfolding of the Cosmos (HarperOne, 1994)]; Everybody’s Story [Loyal Rue, Everybody’s Story: Wising Up to the Epic of Evolution (SUNY Press, 1999)]; Journey of the Universe [Mary Evelyn Tucker and Brian Swimme https://​ www.journ​eyof​theu​nive​rse.org]; and Big History [David Christian, Origin Story, A Big History of Everything (Little, Brown Spark, 2019 and https://​ en.wikipe​dia.org/​wiki/​Big_​Hist​ory)]. A comprehensive consideration is given at Deep Time Network https://​dtnetw​ork.org. Classic books that speak to the religious naturalist orientation include: Epicurus (341-​270 BC), The Best of Epicurus (The Classics Cave, 2021); Henry David Thoreau, Walden (Delhi Open Books, 2018; first published 1854); Henry Beston, The Outermost House (Holt Paperbacks, 2003; first published 1928); Aldo Leopold, A Sand County Almanac (Oxford University Press, 1949); Loren Eiseley, The Immense Journey: An Imaginative Naturalist Explores the Mysteries of Man and Nature (Vintage, 1959); Annie Dillard, Pilgrim at Tinker Creek (Harper and Row, 1974); Lewis Thomas, The Lives of a Cell: Notes of a Biology Watcher (Penguin, 1978); Thomas Berry, writings archived here https://​thom​asbe​rry.org; Carl Sagan, Cosmos (1980; reprinted Ballantine Books, 2013) and Varieties of Scientific Experience: A Personal View of the Search for God (Penguin Books, 2006; from 1985 Gifford Lectures); Chet Raymo, Honey from Stone: A Naturalist’s Search for God (Hungry Mind Press, 1987); and Lou Reich, Hume’s Religious Naturalism (University Press of America, 1998).

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Endnotes 2 More recent books that speak to the religious naturalist orientation include: Michael Cavanaugh, Biotheology: A New Synthesis of Science and Religion (University Press of America, 1995); Lou Reich, Hume’s Religious Naturalism (University Press of America, 1998); Stephen Batchelor, Buddhism Without Beliefs: A Contemporary Guide to Awakening (Riverhead Books, 1998); Thomas Berry, The Great Work: Our Way into the Future (Bell Tower, 1999); Rebecca Elson, A Responsibility to Awe (Carcanat Press, 2002); David Wilson, Darwin’s Cathedral: Evolution, Religion, and the Nature of Society (University of Chicago Press, 2003); William Murry, Reason and Reverence: Religious Humanism for the 21st Century (Skinner House Books, 2006); Chet Raymo, When God is Gone, Everything is Holy: The Making of a Religious Naturalist (Ave Maria Pr, 2008); Sharman Russell, Standing in the Light: My Life as a Pantheist (Basic Books, 2008); Bron Taylor, Dark Green Religion: Nature Spirituality and the Planetary Future (University of California Press, 2009); Michael Dowd, Thank God for Evolution: How the Marriage of Science and Religion Will Transform Your Life and Our World (Plume, 2009); Michael Hogue, The Promise of Religious Naturalism (Rowman and Littlefield Publishers, 2010) and American Immanence: Democracy for an Uncertain World (Columbia University Press, 2018); Stephen Kellert and Timothy Farnham, The Good in Nature and Humanity: Connecting Science, Religion, and Spirituality with the Natural World (Island Press, 2010); Stuart Kauffman, Reinventing the Sacred: A New View of Science, Reason, and Religion (Basic Books, 2010); Nancy Abrams and Joel Primack, A New Universe and the Human Future: How a Shared Cosmology Could Transform the World (Yale University Press, 2011); Paul Harrison, Elements of Pantheism: A Spirituality of Nature and the Universe (Create Space Independent Publishing Platform, 2013); David Haskell, The Forest Unseen: A Years Watch in Nature (Penguin Books, 2013) and The Songs of Trees: Stories from Nature’s Great Connectors (Penguin Books, 2018); Nancy Abrams, A God That Could Be Real: Spirituality, Science, and the Future of our Planet (Beacon Press, 2015); Carol Wayne White, Black Lives and Sacred Humanity: Toward an African-​ American Religious Naturalism (Fordham University Press, 2016) and Religious Naturalisms In: Bloomsbury Religion in North America (Bloomsbury Academic, 2021); Andres Weber, The Biology of Wonder: Aliveness, Feeling, and the Metamorphosis of Science (New Society Publishers, 2016) and Matter and Desire: An Erotic Ecology (Chelsea Green Publishing, 2017); Sean Carroll, The Big Picture: On the Origins of Life, Meaning, and the Universe Itself (Dutton, 2017); Jeremy Lent, The Patterning Instinct: A Cultural History of Humanity’s Search for Meaning (Prometheus Books, 2017) and The Web of Meaning: Integrating

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Endnotes 2 Science and Traditional Wisdom to Find Our Place in the Universe (New Society Publishers, 2021); Robert Corrington, Deep Pantheism: Toward a New Transcendentalism (Lexington Books, 2017); Todd Macalister, Einstein’s God: A Way of Being Spiritual Without the Supernatural (Apocryphile Press, 2018) and Looking to Nature: Exploring a Modern Way of Being Spiritual Without the Supernatural (Apocryphile Press, 2020); Donald Crosby and Jerome Stone, eds, Routledge Handbook of Religious Naturalism (Routledge, 2018); Jack Cohen, The Case for Religious Naturalism: A Philosophy for the Modern Jew (Wipf and Stock, 2019); Mark Green, Atheopaganism: An Earth-Honoring Path Rooted in Science (Green Dragon Publications, 2019); Robin Wall Kimmerer, Braiding Sweetgrass: Indigenous Wisdom, Scientific Knowledge, and the Teachings of Plants (Milkweed Editions, 2013);Clare Carlisle, Spinoza’s Religion: A New Reading of the Ethics (Princeton University Press, 2021); Victoria Loorz, Church of the Wild: How Nature Invites Us into the Sacred (Broadleaf Books, 2021); Randy Woodley, Becoming Rooted: One Hundred Days of Reconnecting With Sacred Earth (Broadleaf Books, 2022); Lowell Gustafson and colleagues, Science, Religion, and Deep Time (Routledge India, 2022); and Karen Armstrong, Sacred Nature: Our Ancient Bond with the Natural World (Knopf, 2022). Connie Barlow’s writings are archived here http://​thegre​atst​ory.org/​CB-​writi​ngs. html; Donald Crosby’s writings are archived here https://​religi​ous-​nat​ural​ ist-​asso​ciat​ion.org/​don​ald-​a-​cro​sby/​; Ursula Goodenough’s writings are archived here https://​religi​ous-​nat​ural​ist-​asso​ciat​ion.org/​urs​ula-​goo​deno​ ugh-​2/​; Karl Peters’ writings are archived here https://​religi​ous-​nat​ural​ ist-​asso​ciat​ion.org/​karl-​pet​ers/​, plus Christian Naturalism (Wipf and Stock, 2022); and Loyal Rue’s books are listed above in Endnotes: Introduction. A list of books and websites pertaining to the religious naturalist orientation is found here https://​reli​giou​snat​ural​ism.org/​variet​ies-​of-​religi​ous-​ nat​ural​ism/​ The cited god concepts derive, respectively, from Michael Dowd, Paul Tillich, Gordon Kaufman, and Baruch Spinoza. “Religious naturalists take nature to heart” was first voiced by Loyal Rue in Nature Is Enough: Religious Naturalism and the Meaning of Life (SUNY Press, 2011), from which the quote derives. Duane Tucker provided the author with his poem The Temple of Autumn.

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I NDE X

For the benefit of digital users, indexed terms that span two pages (e.g., 52–​53) may, on occasion, appear on only one of those pages. Figures are indicated by f following the page number abandonment, 151–​52 acceptance, 60 activator protein, 65–​66 adaptation, 84, 87–​88, 95, 96, 109, 123, 177, 180–​81, 215 address (of protein) 56–​57, 64–​65 adrenaline, 125–​26 affinity, 83, 144, 207 Africa, 98–​99, 174–​76, 177–​78, 180, 197–​98 religions, 1, 116 aggression, 179–​82, 194–​97 aging, 160–​61 agriculture, 178, 205–​6 algae, 35–​36, 50, 84, 92–​95, 96, 103, 148–​3, 157–​58, 161, 163, 167, 209 alienation, 4 Allah, 145, 154–​55, 203, 224 allele, 140–​43, 174, 182–​83 altruism, 144–​45, 190 amino acid, 44, 45, 46–​47, 48–​49, 51, 64, 77–​78, 80

amoeba, Frontispiece to Chapter 4, 38, 64–​68, 80–​81, 92–​95, 124–​25, 147, 157, 158, 161 amphibian, 91 amygdala, 125–​26 ancestry, common, 88–​91, 135, 168f, 168–​71, 170f, 174–​75, 190, 197–​98. See also LUCA anger, 125–​26, 129, 151–​52, 179 anguish, 124, 132 animals, 5, 18, 21, 37–​38, 68, 69, 81, 84, 91–​95, 94f, 97, 98–​99, 103–​4, 105–​13, 119–​20, 123–​1, 125, 130–​31, 136, 137, 144, 147–​48, 149–​51, 158–​14, 172–​73, 179–​80, 182, 184, 189, 199–​200, 214 animism, 38–​39 anther, 149–​50 anthropocentrism, 111 anthropomorphism, 8, 84 ape, 97, 114, 132, 169–​74, 170f, 175, 177, 182, 183, 189, 190, 195, 197–​98. See also bonobo; chimpanzee; human apoptosis, 160, 162

Inde x archaea, 35–​36, 89f, 89–​92, 93f, 95–​96, 135, 136, 143, 157 Aristotle, 191 art, 2, 113, 118, 124, 128, 131, 175, 176–​78, 184, 192, 197–​98, 216–​17, 220, 222. See also music asexuality, 143, 147 Asia, 164, 175–​76, 197–​98 Asian religions, 37, 117. See also Buddhism; Confucianism; Daoism; Hinduism assent, 60, 131, 220 atheism, 223 atmosphere, 16, 22, 88, 99 atom, 11–​15, 17, 23–​25, 31, 39, 51–​53, 58, 110, 201–​2 ATP, 48, 53–​54, 82–​83, 90, 96 attraction, sexual, 148, 150 attunement, 66–​67, 81, 87–​88, 114–​ 15, 119–​20 Australopithecus, 169, 174–​75 autocatalysis, 27–​29, 28f, 29f, 31, 50, 101 autogen, 23, 27–​32, 29f, 30f, 33–​35, 42, 45–​46, 48, 50, 75, 76–​77, 88–​89, 89f, 101–​3, 114 awareness, 34–​35, 54–​55, 101–​4, 108–​9, 110, 111–​12, 114–​15, 117, 123–​47, 150, 162, 163, 176–​77, 182, 208–​9, 215 awe, 2, 4, 19, 59, 60, 118, 191, 202, 213–​14, 220 axon, 104–​6   bacteria, 30, 35–​36, 37–​38, 50, 51, 59–​60, 67–​68, 89f, 89–​92, 93f, 95–​96, 103, 123–​24, 125, 135, 136, 143, 147, 157, 161, 188–​89, 209 cyanobacteria, 96, 103, 157

baptism, 70 Bartholomew, Patriarch, 201 beauty, 4, 75, 84, 88, 118, 120, 155, 159–​60, 192, 209, 212, 215, 217, 222 beaver, 177 behavior, 11, 111, 113–​14, 123, 144, 150, 179, 180–​82, 187–​89, 192, 193, 195–​96 belief, 38–​39, 131, 181, 196–​97, 205, 211–​12, 221, 223. See also faith Bernard of Clairvaux, 153 Berry, Wendell, 120, 207 Big Bang, 3, 12–​13, 18 Big History, 219–​20 biochemistry, 41, 48, 50–​54, 56–​57, 59–​60, 63, 64–​65, 66, 75–​76, 92 biodiversity, 7–​8, 82, 87–​99, 141, 167, 183, 213 biophysics, 51–​54, 56, 59–​60, 63 bird, Frontispieces Chapters 5, 7, 8, and 10, 107f behavior, 34–​35, 81, 84, 99, 132, 143, 144, 149–​50, 151, 163, 167, 188–​89 endangerment, 132, 183 evolution, 82, 109–​10, 111, 168–​69, 172–​73 song, 4, 99, 109–​10, 207 black hole, 11–​12, 18 blessing, 37, 60, 70, 85 blind mole rat, 109 bond, chemical, 23–​25, 27–​28, 32–​33, 42–​43, 46, 48–​50, 49f, 78, 169–​71 bonobo, Frontispieces to Chapters 8 and 10, 130–​31, 132, 150, 169–​71, 170f, 179–​80, 182, 189, 190, 195 Brahms, Johannes, 75

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Inde x brain, 56, 59–​60, 69, 70–​71, 103–​4, 105, 106–​9, 107f, 110–​12, 115, 117, 123–​24, 125, 127–​29, 158–​59, 162, 173–​75, 177–​78, 180–​81, 189, 190–​91, 195, 197–​98 de-​wiring, 109 re-​wiring, 109–​10 breath, 41, 69, 83, 98, 108–​9, 160–​61, 163, 201, 213, 222 bricolage, 82, 85 Brooklyn Museum of Art, 131 Buddhism, 2, 116, 191, 193, 200 building blocks, 26, 190 butterfly, 144 Bwende, 116   calcium, 14, 51–​54, 56–​57, 75–​76, 137–​38, 140–​41 Calvin-​Benson cycle, 50, 54 Cambrian, 92–​95, 97 capsid, 28–​31, 35, 45–​46, 76, 79, 101–​2, 114 carbon, 14, 24–​25, 26, 44, 50, 88, 208–​9 Carson, Rachel, 22, 99, 204 cascade biochemical, 54, 57 ion flux, 104–​5 signal transduction, 54–​57, 55f, 65–​66, 103, 149, 158–​59, 172–​73 cat, 107f behavior, 111–​12, 126 genetics, 138–​42 pet, 152, 179 catalysis, 25, 27, 31, 32–​33, 35, 42–​43, 44, 46, 47, 48–​51, 54, 65–​66, 76, 78, 82. See also autocatalysis Catholic, 1–​2, 7 cave painters, 177–​78

celebration, 4, 118–​19, 144, 182, 183, 192, 199, 217, 221 cell, 190 body, 104 cycle, 66–​68, 137, 147, 161 death, 160, 162 division , 63–​64, 67, 157–​58 (see also mitosis) germ, 159–​60 cellulose, 43f, 44 Celtic, 38 cerebellum, 108–​9 Chang Tsai, 201 channel, 51–​54, 55–​56, 57, 75–​76, 82, 102, 104, 137–​38, 140–​41 chemistry, 23–​25, 26, 31–​32, 41, 51. See also biochemistry children, Frontispiece to Chapter 12, 70, 111–​12, 115, 119–​20, 129–​30, 140, 144–​45, 151–​52, 155, 162–​63, 174, 176–​77, 183, 184, 189, 191, 195, 200 chimpanzee, 130–​31, 150, 169–​75, 170f, 179–​80, 182, 184, 190, 195, 197–​98 Chlamydomonas, 148–​49, 157–​58, 161, 167 chlorophyll, 103 chloroplast, 56–​57, 96, 157 Christ. See Jesus Christianity, 1–​2, 8, 115, 117, 153, 201, 217 chromosome, 92–​96, 136–​37, 138–​42 church, 70, 83, 193 cilia, 148–​49 ciliates, 157 circadian rhythm, 63–​64, 66–​67 coalition, 176, 180–​, 187–​88, 196, 206

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Inde x code, genetic, 3–​4, 32–​34, 45, 65, 66, 77–​80, 91, 140–​41 codon, 77–​78, 91, 140–​41 comet, 16, 26 commandment, 1–​2, 182, 188 commitment, 2, 131, 150, 159, 162, 198–​99, 202–​3, 204–​5, 213–​14, 215, 217, 220 communication, 37–​38, 103–​4, 106–​8, 113–​14, 123–​24, 170–​71, 177–​78, 183 communion, 117, 198–​99, 201, 220–​21, 225 community, 56–​57, 83, 178, 194–​95, 204–​5, 214, 221 compassion, 132, 145, 162–​63, 191–​92, 198–​99, 202, 203, 206, 214, 220–​21. See also empathy complexity, 3–​4, 15, 21, 34, 51, 66, 81, 88, 95, 105–​6, 118, 123–​24, 149–​ 50, 152, 161–​62, 177, 213, 215 Confucianism, 1–​2, 191, 201, 217 connection, 3–​4, 39, 76, 83–​84, 119, 152, 184, 193, 202, 208 consciousness, 3, 103–​4, 108–​9, 110–​12, 123–​2 4 human, 111–​15, 117–​19 (see also I-​Self) constraint, 31–​32, 36, 51, 83–​84 continent, drift, 16 Continuation, Credo, 214–​16 copulation, 147, 150 coral reef, 206, 216 cortex cerebral, 106–​8, 111, 125, 174 prefrontal, 174 cosmic inflation, 12–​14 cosmology/​cosmos, 1–​2, 4, 5, 8, 17, 181, 184, 193 courage, 191, 192, 202–​3, 206 Covenant with Mystery, 18, 211–​12

creation, 3–​4, 13–​14, 21, 99, 201, 205 Credo of Continuation, 215 crossing over, 139 culture, human, 1–​2, 3, 7–​8, 58, 89–​90, 113–​14, 151, 177, 178, 180, 183, 184, 188, 198, 199 cummings, e.e. 213 cyanobacteria, 96, 103, 157 cytoplasm, 45–​46, 54–​57 cytoskeleton, 92–​95   daily devotional, 7, 8, 187 Dalai Lama, 204 Damasio, Antonio, 127–​28 Daoism, 2, 116, 217 dark energy, 11–​13 dark matter, 11–​14, 15 Darwin, Charles, 75 Deacon, Terrence, 114, 183 de Waal, Frans, 130–​31 death, 8, 115, 116, 117–​18, 160–​63, 220 stellar, 15, 17 Deism, 18 Deity. See God Delay, Tom, 189 dendrite, 104–​5 Denisovan, 176, 182 Deoxyribonucleotide. See DNA despair, 17, 84, 120, 154–​55, 203 development. See embryology dignity, 60, 182, 202 dinosaur, 88 Dioum, Baba, 207 diploid, 137–​39, 142, 148–​49, 158 disease, 2–​3, 142 distinctiveness, 5, 22, 47, 76, 92–​95, 101, 109–​10, 130, 135, 136, 150, 167–​68, 171, 172–​73, 174, 175, 176, 181, 182–​83, 184, 193, 208–​9 diversity. See biodiversity

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Inde x divine, 99, 117, 152, 188, 201. See also God DNA, 32–​35, 43f, 44, 45, 50, 63–​64, 66, 67, 77, 80, 82–​83, 90, 92–​95, 135, 136, 171–​72, 176 dog, 110, 119–​20, 152, 179 dolphin, 112, 162–​63 domain, protein, 47, 48–​49, 75–​76, 82–​83 domestication, 95–​96, 109–​10, 179–​80 dopamine, 127 drift, genetic, 80–​81 duplication, gene, 80 dynamics. See emergence   earth, Frontispiece to Chapter 1, 11–​12, 15–​16, 22–​23, 24, 26, 50, 88, 97, 98, 99, 101, 145, 152, 155, 157, 200, 201–​2, 203, 204, 206, 207, 212–​13, 215, 221–​22, 225 ecology, 83–​84, 210 ecomorality, 5, 187, 198–​208, 217, 222 egg, 21, 69, 70–​71, 135–​36, 137, 139, 142, 149–​50, 157–​58, 159, 171, 173, 179 Einstein, Albert, 118 élan vital, 41 electrical charge, 46–​47, 51–​53, 204–​5 electron, 13–​14, 15, 23–​24, 49–​50, 51–​53 element, atomic, 14–​15, 26, 201 elephant, 112, 162–​63 embryology, Frontispiece to Chapter 4, 63–​64, 68–​69, 82, 108, 109, 136, 137, 144, 158–​60, 174 emergence, 22, 25, 27, 31, 33–​35, 36, 41, 42, 47, 51, 57–​58, 59, 63–​64, 70, 71, 80–​81, 110, 115, 117–​18, 129, 144, 192, 211

emergent dynamics, 31–​33, 47 emergent properties, 25, 31 Emerson, Ralph Waldo, 214 emotion, 125–​26, 127–​29, 130–​31, 145, 147–​48, 162–​63, 170–​71, 176–​77, 182, 183, 196–​97 anger, 125–​26, 129, 151–​52, 179, 180–​81 fear, 2, 59–​60, 69, 113, 120, 125–​26, 127, 128, 129, 151–​52, 163, 179, 193, 196–​97, 206, 220, 222 elation, 125–​26 joy, 4, 5, 38, 39, 60, 120, 126, 128, 144–​45, 150, 151–​52, 153, 182, 193, 211 sorrow, 129, 131, 151–​52, 154–​55, 162–​63, 202 empathy, 132, 144, 189. See also compassion encyclopedia analogy, 136–​41 endangered species, 183 endosymbiosis, 95–​96 energy, 11–​13, 23–​25, 26, 27, 36, 51–​53, 58, 92, 103 enhancer, 171–​73 entropy, 31–​32 environment, 37–​38, 53, 54–​55, 65, 66–​68, 75–​76, 79, 80–​81, 87, 92, 103–​4, 111, 114, 132, 143, 148–​49, 157–​58, 198–​99, 202, 203, 206, 208–​10 enzyme, 25, 32–​33, 47, 48–​51, 49f, 53, 54, 55–​56, 59, 65–​66, 75–​76, 79, 90, 96, 104, 141, 221–​22 Epic of Evolution, 7–​8, 219–​20 epigenetic modification, 66 epiphany, 18–​19 ethics, 2–​3, 4, 5, 187–​88, 192, 195–​96, 221–​22 Ethos, 1–​2, 5

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Inde x eukaryote, 89f, 89–​91, 92–​96, 93f, 135–​37, 139, 143, 147, 148, 150, 157–​58, 161–​62, 163, 167 evaluation, 56, 81, 102, 123–​26, 127, 150, 206, 215 Evangelical, 7 Everybody’s Story, 4, 7–​8, 211, 216, 217, 219–​20, 221–​22 evolution, 3–​4, 7–​8, 11–​19, 27, 33–​34, 37–​38, 60, 68, 75–​85, 87–​99, 102–​3, 105–​8, 109–​10, 111, 112, 113–​14, 124, 129, 130–​31, 142–​43, 145, 151–​52, 154–​55, 158, 162–​63, 188–​89, 190, 197–​98, 209, 213, 214–​15, 221–​22 human, 89, 97, 167–​84 existential, 41, 59–​60, 184, 220 extinction, 89, 167–​69, 168f, 175, 176   fair-​mindedness, 132, 190, 191–​92, 202, 206, 220–​21 faith, 99, 153, 154–​55, 211–​12, 215, 216. See also belief father, 70–​71, 138, 201, 216 fatty acid, 44, 47, 50, 51 fear, 2, 59–​60, 69, 113, 120, 125–​26, 127, 128, 129, 151–​52, 163, 179, 193, 196–​97, 206 feedback, 59, 66, 125, 138, 152, 153 feelings, 59–​60, 110, 111, 112, 113, 115, 124–​32 emotional, 125–​26 homeostatic, 125 fellowship, 83–​84, 144 female, 81, 109–​10, 135–​36, 147–​48, 150, 159, 177, 180, 198 fertility figure, 131 fertilization, 69, 135–​36, 137–​4 4, 147, 149–​50, 158, 199–​200

Feynman, Richard, 11 finch, 168–​69 fish, 107f, 150, 172–​73, 188–​89 fitness, 38, 87–​88, 91, 95, 109–​10, 160 fitting in, 38, 87–​88 flagella, 92 flower, 57, 82, 95, 123–​24, 136, 149–​50, 159, 184 food chain, 83–​84, 88, 92, 157 forgiveness, 153, 190 fossil, Frontispieces to Chapters 6 and 12, 75, 168–​69, 174–​76 Francis, Pope, 198, 201 Frank, Johann, 154 free will, 112–​13 friend, 147–​48, 150, 151–​52, 154, 180, 190, 205 frog, Frontispiece to Chapter 7, 107f, 114–​15, 150 fungi, 37–​38, 44, 68, 92–​95, 94f, 123–​24, 157, 163, 209. See also yeast   galactose, 48 galaxy, Frontispiece to Chapter 1, 12, 14, 15, 17, 87 gamete, 135–​36, 137, 147, 148–​49, 157–​ 58, 161–​62. See also egg; sperm gastrulation, 158–​59 Geddes, Patrick, 204–​5 gender, 103, 147, 151–​52, 196–​97 gene, 32, 34–​35, 45, 46–​47, 63–​71, 77–​ 84, 90, 91, 95–​96, 130, 140–​41, 158–​59, 162, 171–​74 downstream sequence, 65 duplication, 80 expression, 63–​70, 158–​59, 171–​72 family, 75–​76, 82 housekeeping, 82–​83, 91 pool, 140–​41, 142, 182–​83

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Inde x selfish, 34 upstream sequence, 65 Genesis, 21 genetics, 3–​4, 33–​34, 69, 83, 89, 96, 115, 130, 135, 137–​38, 140, 144, 191–​92, 209 genome, 32, 34–​35, 45, 63–​65, 66, 67, 79, 80, 92–​96, 135–​36, 141, 144, 147, 159–​60, 161–​62, 171–​72, 176, 214–​15 geology, 16, 22, 38–​39 germ/​soma dichotomy, 157, 162 germ line, 136, 137, 159–​60, 161–​62 glaciation, 88 glucose, 48–​50, 53, 57, 65, 90, 102 glycolysis, 90 God, 18, 21, 36–​37, 70, 89–​90, 99, 116, 117, 145, 152, 153, 154–​55, 201, 211–​13, 220, 223 Godfrey-​Smith, Peter, 112 Goethe, Johann, 163 gonad, 159–​60. See also ovary; testis Goodenough, Erwin, ix, 193 gorilla, 83, 170f, 182, 197–​98 grace, 70, 71, 120, 184, 188, 192, 193 gratitude, 3–​4, 5, 71, 182, 205, 212–​14, 215, 216, 222 gravity, 11–​12, 13–​15, 16, 223, 224 greed, 2, 207 guru, 216–​17 gut, 69, 104, 125–​26   habitat, 2–​3, 22, 38, 39, 75, 87–​88, 92, 161, 167–​68, 171, 182, 204–​5, 206, 209, 210, 212, 223, 224 haploid, 137–​39, 148–​49 heart, 69, 70–​71, 98, 118, 125–​26, 153, 154, 155, 158–​59, 198–​99, 200, 203, 217

heaven, 5, 19, 59–​60, 115, 116, 117, 188, 190, 207 Hefner, Philip, 193 helium, 13–​14, 15–​16, 24, 222 hell, 115, 188 hemoglobin, 63–​64 hierarchy, 58, 179–​80 Hildegard of Bingen, 201 Hinduism, 21, 41, 116, 152, 191, 193 history, 1, 12, 18, 39, 75–​76, 88, 95–​96, 97–​98, 129, 130–​31, 175, 177–​78, 181, 188, 197, 203, 219–​20 holy, 70, 98 homeostasis, 57, 59, 125, 127 Hominidae, 169 hominins, 169, 174–​75, 197–​98 Homo, 169, 174–​75, 176 erectus, 174–​75, 182 neanderthalensis, 174–​75, 176, 182 sapiens, 91, 98–​99, 113–​14, 169, 175–​76, 180–​81, 182–​83, 197–​98 (see also human) homology. See protein homology hope, 71, 131, 145, 153, 184, 187, 191, 193, 216 Hopi, 193 hormone, 57, 59–​60, 69, 108, 123–​24, 125–​26, 127, 129–​30, 158–​59 Hox genes, 92–​95, 172–​73 human, 2, 5, 8, 9, 13–​14, 34–​35, 51, 89, 98–​99, 101, 109–​10, 111–​12, 117, 118, 119, 123, 125–​26, 128–​29, 136, 151–​52, 155, 162–​63, 167–​84, 170f, 187–​98. See also Homo sapiens body, 160, 172–​73, 174–​76 brain, 106–​8, 107f, 112–​13, 124, 173, 174–​75 culture (see culture) embryology, 68, 69, 174

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Inde x human (cont.) evolution, 89, 97, 112, 167–​82 genome, 45 language (see language) morality (see morality) nature, 5, 130, 188, 191, 197–​98, 216, 217 sexuality, 149, 152, 159, 178 humaneness, 132 humility, 3–​4, 98–​99, 182, 191, 202, 214, 220 hunger, 2–​3, 125, 127, 129 hydrogen, 13–​14, 15, 24, 25, 26, 51–​53 hydrothermal vents, Frontispiece to Chapter 2, 26, 99 hymn, 153, 154–​55, 225   ideals, 188, 191, 203, 217 imagination, 84, 113, 124, 132, 184, 216–​17 immanence, 117, 119, 182, 216–​17 immortality, 161–​63 indigenous, 1–​2, 21, 36, 38, 97–​98, 131, 152, 199–200, 217, 220–​21, 222 insect, 37–​38, 44, 95, 96, 104, 144, 149–​50, 160–​61, 188–​89, 204 instinct, 41, 109–​10, 128, 136, 145, 190 instructions, genetic, 32, 33–​34, 42, 45, 46–​47, 63–​64, 69, 76–​77, 78, 90, 91, 95–​96, 108, 135–​36, 137–​ 38, 172–​73, 214–​15. See also gene insulin, 63–​64 intent, 215 interdependence, 3–​4, 38, 99, 191–​92, 201–​2, 221–​22 interpretation, 33, 123–​24, 127, 183, 188–​89, 193, 220–​22, 224 interrelatedness, 99, 201–​2, 221–​22 interstellar dust, 26 intimacy, 147–​55, 201, 211–​12

ion, 23–​24, 51–​53 iron, 14–​15, 16, 25 I-​self/​self-​awareness, 35, 111–​13, 115, 117, 119–​20, 162 Islam, 1–​2, 83, 115, 223 Iverson, Daniel, 117   James, William, x–​xi, 60, 113, 131 jealousy, 151–​52 Jehovah, 154–​55 jellyfish, 104, 106–​8 Jesus, 70, 83, 131, 145, 153, 154–​55 jigsaw puzzle analogy, 47 Journey of the Universe, 7–​8, 219–​20 joy, 4, 5, 38, 39, 60, 120, 126, 128, 144–​45, 150, 151–​52, 153, 182, 193, 214, 215 Judaism, 145, 152, 191, 197, 217 junk DNA, 171–​72 justice, 191–​92, 203, 221–​22. See also fair-mindedness   Kalton, Michael, 119 karma, 188 kidney, 69, 70–​71 Kimmerer, Robin, 200, 206 King, Martin Luther Jr. 203 Knox genes, 92–​95 Koran, 223 Krebs cycle, 51, 54, 96   lactase, 65 lactose, 48, 65 LaDuke, Winona, 199–​200 Lame Deer, 200 language, symbolic, 3, 8, 34–​35, 109–​10, 112–​14, 119–​20, 123, 124, 127–​28, 129, 169, 170–​71, 174, 175, 176–​78, 181, 183, 190, 191

256

Inde x Lao Tzu, 19 larva, 144 laughter, 116, 119–​20, 177, 215 learning, 105–​6, 111, 170–​71, 177, 182, 184, 191 lichen, 143, 208–​10 life, 12 cycle, 148–​49, 161–​62 evolution of (see evolution) origins of, 16, 21–​39, 60 workings of, 41–​60 liturgy, 83 loneliness, 59–​60, 84, 95–​96, 126, 151–​52 loss, 117, 118–​19, 162–​63 love, 1–​2, 70, 84, 128, 144, 151–​52, 153, 154–​55, 159–​60, 163, 192, 198–​99, 206, 207, 213, 215, 220 LUCA, 88–​92, 89f, 95–​96, 103 lust, 129 Lyons, Oren, 99   magic, 58, 128 male, 81, 109–​10, 135–​36, 139, 147–​48, 150, 159, 171, 179–​80, 187–​88, 195, 198 malignancy, 70 mammal, 34–​35, 103, 108, 111, 119–​20, 132, 144, 150, 151, 159, 167, 188–​ 89, 204 Maoism, 2 marriage, 150 Marxism, 2 Mary, 153, 154–​55 mask, 131 mate, 82, 103, 109–​10, 135–​36, 137–​38, 147, 148, 149, 151–​52, 157–​58, 167, 177, 178 choice, 178, 180–​81

maternal, 139, 144–​45 mathematics, 11–​12 matter, 11–​14, 15, 26, 58–​59, 60 Mead, Margaret, 204–​5 meaning, 18, 102, 123, 129, 131, 163, 176–​77, 215, 216, 220 meditation, 7, 8, 114–​15, 117, 193, 220, 225 meiosis, 139, 148–​49, 157–​58, 159 membrane, 27, 44, 45–​46, 47, 51–​57, 65–​66, 90, 92–​95, 102, 104, 108, 149 memory, 9, 105–​6, 110, 111, 112–​14, 115, 124, 126, 129, 207 working, 112–​13, 129 mentality, 111–​12, 114, 128, 174 metabolism, 51, 52f, 53, 57, 65, 69, 80–​81, 82–​83, 90, 92, 209 metaphor, 8, 38, 41–​42, 59, 63, 70, 128, 131, 192, 208, 216, 223 meteor, 26, 215 Milky Way, Frontispiece to Chapter 1, 15, 126 mindfulness, 113–​14, 192–​94, 206, 216, 217, 221–​22, 224 miracle, 36, 70 mirror test, 178 mitochondrion, 56–​57, 95–​96, 157 mitosis, 67–​68, 137, 148–​49, 157–​58. See also cell division molecule, 7–​8, 23–​25, 26–​33, 41, 42–​44, 45–​46, 48–​50, 53, 54–​56, 58, 65–​ 66, 76, 77, 78, 101–​3, 114, 201–​2 monogamy, 149–​50 monotheism, 36–​37, 154 moon, 16, 59 moose, 132, 202 morality, 1–​2, 5, 21, 181–​82, 187–​208, 216–​17, 220–​22, 224

257

Inde x morphogenesis, 31–​32, 44, 68, 95, 161–​62 mortality, 59–​60, 155, 160–​62, 163. See also death mother, 16–​17, 19, 21, 22, 70–​71, 138, 153, 162–​63, 168–​69, 190, 200, 212–​13, 216 Moth, Frontispiece to Chapter 6, 143 motility, 53–​54, 68–​69, 92, 95, 148–​49 mouse, 105, 125–​26, 127 Mozart metaphor, 41–​42, 45, 57, 59, 63, 70, 128 multicellularity, 35–​36, 57, 64, 68–​70, 92–​95, 103–​4, 123–​24, 136, 137, 143, 148–​50, 157–​64, 167, 171, 172, 209 munia, white-​r umped, 109–​10 muscle, 69, 95, 104–​5, 216–​17 mushroom, 83, 95 music, 34–​35, 41–​42, 59, 63, 83, 172–​73, 197–​98, 207 Muslim, 193 mutation, 33, 59, 66, 70, 76, 78–​83, 85, 137–​38, 140–​41, 161, 162, 213–​14 beneficial, 79, 80–​81 deleterious, 79, 140–​41 duplication, 80 lethal, 79, 80–​81, 174 neutral, 79, 140–​41 nonsense, 79–​80 mycelia, 68, 204–​5 mystery, 8, 17–​18, 19, 59–​60, 118–​19, 211–​13 mysticism, 117, 118 myth/​mythos, 89–​91, 192, 217, 220–​21   narrative, 2, 3, 8, 21–​22, 35, 42, 101, 111–​12, 113, 117, 124, 126, 127–​28, 176–​77, 184, 201–​2, 207, 217, 219–​20, 221–​22, 224

Native American, 197, 199–​200. See also indigenous naturalism, religious. See religious naturalist orientation naturalist, 219–​20, 221–​22, 223 natural selection, 80–​81, 102, 114, 123, 143 nature, 3, 4, 5, 7–​8, 18, 97–​98, 119, 127–​28, 129, 187, 198–​99, 203, 204, 206, 216–​17, 222, 223–​24 neanderthal. See Homo neanderthalensis nerve ring/​net, 106–​8 nervous system, 59–​60, 104–​6, 108, 123–​24, 125–​26. See also brain neuron, 103–​9, 111, 129–​30, 162, 173 neurotransmitter, 59–​60, 104–​6, 129–​30, 179 neutron, 13 neutron star, 14–​15 New Story, 219–​20 niche, 87–​88, 92, 95, 96, 143, 159–​60, 161–​62, 167–​68, 170f, 177, 209 partitioning, 210 nihilism, 4, 17, 59–​60 nitrogen, 14, 24, 88, 92, 99, 123–​24, 148–​49 nontheism, 8, 117–​18, 154, 213–​14, 223 nose. See olfactory nuclear weapons, 2–​3 nucleic acid, 42–​4 4. See also DNA; RNA nucleotide, 32–​33, 42–​43, 43f, 46, 50, 51, 65, 66, 77–​78, 79–​80, 91, 171–​72 nucleus atomic, 13–​16, 17, 23–​24 brain, 125 cellular, 56–​57, 92–​95, 104, 137, 139

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Inde x numinous other, 117 nurture, 5, 34–​35, 129, 136, 144–​45, 147, 159–​60, 161–​62, 167, 190, 191–​92, 199, 214, 220–​21   oceans, 2–​3, 16, 22, 24, 26, 38, 88, 92–​ 95, 116, 144–​45, 157, 193, 204, 212 octopus, 111 odor. See olfactory offspring, 136, 137, 142, 144, 147–​48, 167, 190 Olds, Sharon, 155 olfactory, 44, 54–​56, 55f, 65–​66, 69, 99, 103, 105–​8, 109, 110, 124–​25, 162–​63, 171 Oliver, Mary, 37, 71, 84, 193 Onondaga, 99 orangutans, 182 organelle, 92–​96 outrage, 162–​63, 192, 203 ovary, 70–​71, 142, 159 ovule, 144, 149–​50 owl, 183 oxygen, 14–​15, 24, 25, 46, 53, 222   pagan, 38 pair bonding, 151 pan-​African, 176, 197 pantheism, 211–​12, 223 paper-​doll chain analogy, 46–​47, 78 parent, 137, 139, 140, 145, 147–​48, 150–​52 pathogen, 123–​24, 209 Patriarch Bartholomew, 201 Pawnee, 98 perception, 105, 110, 112, 113, 123, 125–​26, 162, 201–​2 Perfection of Understanding, 117 periodic table, 14

pheromone, 37–​38 philosophy, 154, 187, 192, 199, 220, 222 phospholipid, 43f, 44 phosphorous, 24, 44, 51, 82 photon, 15–​16, 18–​19, 103 photoreceptor, 103 photosynthesis, 50, 92, 96, 103, 157, 159–​60, 209, 222 physics, 11, 12, 13, 16–​17, 18, 23–​24, 41. See also biophysics phytochrome, 123–​24 pigment, 12, 57, 103 planet, 2–​4, 5, 11–​12, 37–​38, 44, 58, 66–​67, 77, 83, 87, 92, 97, 98–​99, 101, 123, 142, 150, 182, 183, 201, 202, 204–​5, 208–​9, 210, 211, 212, 213–​14, 215, 217. See also earth planetary matrix, 22, 36, 38, 39, 75, 87–​89, 89f, 95, 98–​99, 103, 113, 118, 145, 157, 182, 198, 199, 201–​2 plants, Frontispieces to Chapters 9 and 11, 38, 44, 50, 68–​69, 92–​95, 94f, 96, 103, 110, 123–​24, 135–​36, 137, 144, 148, 149–​50, 158, 159, 172, 208–​9 plate tectonics, 16, 22, 88 playing card analogy, 142 pleasure, 113, 119–​20, 126, 127, 154, 208 pocket. See protein poetry, 4, 22, 154–​55. See also art pollen, 149–​50, 200 pollution, 2–​3, 143 polymer, 32–​33 polynucleotide, 32–​33 polypeptide, 46–​47 Pope Francis, 198, 201

259

Inde x polysaccharide, 43f, 44, 50, 51 population, 2–​3, 80–​82, 92, 103–​4, 143, 167–​68, 175–​76, 196, 197–​98 poverty, 132 prayer, 37, 83, 97–​98, 115, 117, 152, 153, 193, 195, 224 predator, 82, 103, 143, 209 Presbyterian, x preservation, 2–​3, 182, 205, 209 prevalence, 214–​15 prey, 81–​82, 95, 103 pride, 98–​99, 101 primate, 112, 163, 169, 189–​90, 192, 194–​95. See also ape; human primordial soup, 26, 27, 28f, 33–​34, 101, 189 proboscis, 95 progenitor, 76, 95–​96 promoter, 65–​66, 67, 79, 80, 82, 158–​59, 172 prophet, 216–​17 protein, 27, 32, 44, 45–​48, 50, 53–​54, 63–​64, 82 address, 56–​57, 64–​65 domain, 47, 48–​49, 75–​76, 82–​83 encoding, 76–​78 homology, 82–​83, 84, 89, 106–​8, 144, 147–​48, 171 housekeeping, 82–​83, 91 pocket, 44, 47–​50, 53–​56, 65–​66 regulation of expression, 64–​66, 70, 172–​73 structure, Frontispiece to Chapter 3, 43f protist, 35–​36, 92–​95, 94f, 157, 158, 163 proton, 13, 53 Psalm, 152 Pueblo, 21

pump (ion) 51–​53, 57, 83–​84 purpose, 34–​35, 36–​37, 38, 84, 114, 205, 215   quantum theory, 11, 12, 19 quorum sensing, 38, 92, 188–​89   race/​racism, 181–​82, 196–​98 radioactivity, 14–​15, 24 receptor, 54–​56, 57, 65–​66, 82, 83–​ 84, 103, 104–​6, 129–​30, 149–​50 redemption, 145 red giant, 14–​15, 138 reductionism, 22, 41–​42, 57–​58, 128, 208 regulation, genetic. See gene regulation reincarnation, 116 relationship, 37–​38, 98, 136, 147–​48, 150–​52, 153, 154–​55, 162–​63, 198–​200–​, 212, 215 thick, 147–​48 relief, 60, 154–​55 religion/​religious traditions, x–​xi, 1–​2, 7, 8, 21, 36–​37, 38, 58, 83–​84, 99, 115, 117, 131, 132, 152, 153, 154, 162, 187, 192, 200, 205, 211–​12, 213–​14, 216–​17, 220–​21, 222, 224 religious, ix, 2–​3, 4, 5, 7, 8, 22, 34, 60, 83–​84, 97–​98, 99, 128, 131–​32, 151–​52, 154, 162–​63, 180, 181, 184, 188, 192, 196–​97, 205, 211, 214, 216–​17, 220–​21, 223 religious naturalist orientation, xiii, 5, 8, 36–​37, 58, 60, 99, 117–​18, 131, 154, 183, 197, 199, 203, 205, 211, 212, 214, 219–​25 renewal, 145, 207 replication, 30f, 30, 32–​33, 35, 44, 46, 67, 68, 80, 82–​83, 87, 92, 137, 213–​14

260

Inde x repressor protein, 65, 66–​67, 79 reproduction, 32, 33–​34, 45–​46, 76, 84, 135, 136, 143, 157–​58, 160, 176, 194–​95 reptile, 107f, 111 respect, 39, 71, 131, 180, 190, 191, 192, 199, 202, 203, 205 responsibility, 3–​4, 5, 99, 203, 220–​21 revelation, 193 reverence, x, 5, 22, 59, 98–​99, 117–​18, 181, 182, 190, 191, 192, 194, 202, 203, 206, 213–​14, 215, 216–​17, 220, 223 ribonucleotide, 43f ribosome, 46–​47, 65, 78, 90–​91 ritual, x, 83, 117, 193, 220 river, Frontispiece to Chapter 13, 38, 39, 84, 119, 204, 205, 207 RNA, 32–​33, 42–​43, 43f, 44, 45, 46–​47, 50, 65, 78, 90 messenger, 46, 65, 78, 90 ribosomal, 46 transfer, 78 world, 32 Russian Orthodoxy, 2   sacred, 5, 64, 70, 98, 116, 131, 181–​82, 191, 199, 201–​2, 207, 213–​14, 215, 217, 220, 223 sadness. See sorrow Sahelanthropus, 174–​75 salvation, 188 sanctify, 55–​56, 213 sarcophagi, 131 science, x–​xi, 3, 4–​5, 7–​8–​, 21–​22, 41, 42, 58, 59–​60, 116, 127–​28, 161, 183, 187, 198, 201–​2, 205–​6, 208, 219–​20 sea urchin, Frontispiece to Chapter 4, 106–​8

seaweeds, 68 secretion, 53–​54, 57, 104–​5, 108, 148–​ 49, 158–​59 seed, 14–​15, 21, 30, 144 selection. See natural selection; sexual selection self, 35–​39, 45–​46, 63, 70, 75, 88–​89, 98–​99, 102, 111–​12, 114–​15, 117, 160, 194–​95, 209, 213–​14. See also I-​self self-​assembly/​organization, 29f, 30, 31, 32, 47, 48, 50, 54, 76, 87, 189, 209 self-​awareness. See I-​self self-​pity, 60 self-​interest/​selfish, 34, 37–​38, 193, 195, 196, 203, 214 serendipity, 223 serenity, 129–​30, 131 serotonin, 127 Seth, Anil, 110 sex, Frontispieces to Chapters 9 and 11, 68, 81, 103, 135–​45, 147–48, 157–​58, 161, 163, 167–​68, 180, 183, 196–​97 facultative, 149 sexual selection/​choice, 76, 81–​82, 109–​10, 142, 150, 178, 180–​81, 192, 198 shame, 192, 203 shape, 25, 27–​33, 42–​4 4, 46, 47–​50, 51–​56, 64–​66, 69, 76, 79, 80, 92–​ 95, 102–​3, 104, 142, 197–​98, 223 signal transduction cascade. See cascade silicon, 16 Smuts, Barbara, 130–​31 snail, 111, 209 snow, C.P. 7–​8

261

Inde x social, 34–​35, 37–​38, 88, 144, 170–​71, 175, 178, 180–​82, 183, 187–​91, 192–​93, 194–​95, 196, 197, 199, 214, 221–​22 solemnity, 4, 5, 83, 131, 193 soma, 159–​60, 161–​62, 163 sorrow, 129, 131, 151–​52, 154–​55, 162–​63, 202, 214, 217 soul, 59–​60, 115, 117–​18, 120, 152, 154, 162–​63 soup. See primordial soup space cosmic, 11–​13, 14–​15, 17, 26 organismal, 63, 64, 68–​70 spaceship metaphor, 189 species/​Speciation, 2–​3, 58, 98–​99, 103, 113–​14, 136, 141, 147, 167–​71, 175, 176, 180, 182–​83, 197–​98, 204, 208–​9, 215 sperm, 70–​71, 135–​36, 137, 138–​40, 142, 149–​50, 159 spine, 69, 108 spirit/​spiritual, 4, 8, 22, 36, 38, 39, 70, 115, 116–​18, 119, 145, 152, 182, 201, 205, 212–​13, 216, 217, 220, 221–​22, 224 sponge, ​95 spore, 30, 95, 148–​49, 157–​58, 161 stamen, 159–​60 star, 3–​4, 11–​12, 13–​16, 17, 18–​19, 24, 26, 39, 58, 98, 116, 120, 126, 212, 222 starfish, 149–​50 stewardship, 215 stigma, 149–​50 story, 3–​4, 7–​8, 9, 12–​16, 21–​22, 24, 26, 42, 64, 84, 85, 88–​91, 158–​59, 170–​71, 189, 194–​95, 199–​200, 213, 216, 220. See also Everybody’s Story subatomic particles, 11–​12, 13, 24 sugar, 37, 44, 48–​51, 49f, 57, 63–​64, 65–​66

sulfur, 24 sun, 4, 15–​16, 17, 21, 24, 84, 98, 103, 116, 119, 213, 215, 222, 225 super groups, 89, 90–​91, 93f, 103, 168–​69 supernaturalism, x, 18, 36, 39, 98, 117, 155, 188, 211–​12, 213–​1 4, 222 supernova, 14–​15 survival, 57, 84, 99, 115, 125–​26, 144–​45, 175, 207, 209 sustainability, 118–​19, 199, 200, 202, 204–​5, 208, 209–​10 symbiosis, 81–​82, 103 symbol, 112–​13, 129, 131, 176–​77, 202. See also language, symbolic synapse, 105–​8, 130, 162   taste, 103 taxonomy, 168–​69 technology, 183, 201–​2, 205–​6 temperament, 129–​31, 180, 182 temperature, 12–​14, 17, 18–​19, 24 temple, 193, 225 temptation, 151–​52 tenderness, 71, 131, 145, 198–​99 termite, 96 terror, 16–​17 testis, 136, 138, 159 thanksgiving. See gratitude theism, 152, 213–​14 theology, x–​xi, 18, 193 Thich Nhat Hanh, 116 Thoreau, Henry David, 22, 38 time, 11, 12, 15–​16, 17, 22–​23, 30–​31, 33–​34, 42, 63–​66, 67–​68, 75–​76, 80, 97, 116, 129–​30, 151, 167–​68, 169, 197, 203, 207, 213 toolmaking, 175 totem, 117, 131 toxin, 102, 114, 124–​25, 188, 197

262

Inde x trait, 34–​35, 44, 47, 81–​82, 90–​91, 110, 111–​12, 119, 135, 167, 169, 170–​71, 179–​81, 192 transcendence, 119–​20, 128, 182, 207, 216–​17 Transcription, 41–​42, 46–​47, 65–​67, 78, 82, 90, 92–​95, 172–​73 factor, 65 translation, 41–​42, 65, 78, 90 transporter, 53, 54–​55, 57, 65, 82–​83, 110, 140 tree, Frontispiece to Chapter 11, 21, 37–​38, 71, 84, 99, 103–​4, 126, 143, 160–​61, 163, 199–​200, 207, 213, 225 evolutionary, 43f, 93f, 94f, 168f, 169–​70, 170f Trichomonads, 98 trilobite, Frontispiece to Chapter 6 trust, 151–​52, 154, 179, 181 Tucker, Duane, 225 tumor, 161   ultimacy, 70, 199–​200, 211–​12, 215 unicellularity, 35–​36, 92–​95, 103–​4, 123–​24, 148, 157–​58, 209 universe, 3–​4, 11–​15, 16–​17, 18, 23–​24, 36, 59–​37, 97, 110, 183, 201, 212, 215, 223 Universe Story, 219–​20

value, 84, 123, 128, 183, 184, 192, 198, 199, 203, 215 virtue, 190–​94, 202, 203, 214 virus, 35–​36, 47, 77, 124–​25, 205–​6 viscera, 106 vision, 145, 188, 199, 208, 210 vitalism, 41 volcano, 22   walking/​time analogy, 97, 197 water, 2–​3, 16, 21, 22, 24, 25, 26, 44, 120, 147, 152, 154, 200, 201, 209, 225 weaving metaphor, 193 web of live, 76 Weinberg, Steven, 17 Wesley, Charles, 154 whale, 162–​63, 183 white dwarf, 14 worm, 108, 172–​73 xenophobia, 196–​98   Yaruro, 21 yearning, 59–​60, 70, 71 yeast, 51, 82–​83, 136, 157   zygote, 137, 139, 148–​49, 158

263