The Optics of Life: A Biologist's Guide to Light in Nature

346 Pages·2011·6.63 MB·English

by  Sönke Johnsen

THE OPTICS OF LIFE
THE OPTICS OF LIFE
A Biologist’s Guide to Light in Nature
Sönke Johnsen
PRINCETON UNIVERSITY PRESS
PRINCETON AND OXFORD
Copyright © 2012 by Princeton University Press
Published by Princeton University Press, 41 William Street,
Princeton, New Jersey 08540
In the United Kingdom: Princeton University Press, 6 Oxford Street,
Woodstock, Oxfordshire OX20 1TW
press.princeton.edu
Jacket Photo: An undescribed species of Hydromedusa in the genus Tetrorchis shows various optical
effects, including transparency, absorption by pigments, and iridescence caused by coherent scattering.
Courtesy of Steven Haddock.
All Rights Reserved
Library of Congress Cataloging-in-Publication Data Johnsen, Sönke.
The optics of life : a biologist’s guide to light in nature / Sonke Johnsen.
p. cm.
Includes index.
ISBN 978-0-691-13990-6 (hardback) — ISBN 978-0-691-13991-3 (paperback) 1. Photobiology. 2.
Physiological optics. 3. Polarization (Light) I. Title.
QH515.J64 2011
571.4'55—dc23 2011021796
British Library Cataloging-in-Publication Data is available This book has been composed in Garamond
Premier Pro Printed on acid-free paper. ∞
Printed in the United States of America 10 9 8 7 6 5 4 3 2 1
For my parents, my first and best teachers
CONTENTS
Acknowledgments
CHAPTER ONE Introduction
CHAPTER TWO Units and Geometry
CHAPTER THREE Emission
CHAPTER FOUR Absorption
CHAPTER FIVE Scattering
CHAPTER SIX Scattering with Interference
CHAPTER SEVEN Fluorescence
CHAPTER EIGHT Polarization
CHAPTER NINE Measuring Light
CHAPTER TEN What Is Light, Really?
APPENDIX A Converting Spectral Irradiance to Lux
APPENDIX B Calculating the Absorbance Spectrum of a Visual pigment
APPENDIX C Refractive Indices of Common Substances
APPENDIX D Optical Properties of Very Clear Water
APPENDIX E Optical Properties of Natural Waters
APPENDIX F Useful Formulas
APPENDIX G Equipment and Software Suppliers
Bibliography
Index
ACKNOWLEDGMENTS
I’m not sure why I wrote this book. I do enjoy writing, but this was a lot of
work, so there must have been a reason. When I pitched the project to my editor,
I told her that it would fill a niche, but I’ve never been one to lose sleep over
unfilled holes. I also told her that optics was important to biology. It is, but so
what? My colleague Steve Vogel told me once that writing books is wonderful
because it transforms you from a competitor into an enabler. I do hope this book
helps people use optics in their research, but honestly I still feel competitive.
Maybe I just want people to stop me in the hall and say, “Nice book!” I’d be
lying if I said this didn’t matter. I’m shallow, and flattery goes a long way with
me.
There’s more though. While not conventionally religious, I am often
overcome by this world—it’s like being given a prize over and over. The most
remarkable part to me is that we are able to appreciate and at least partially
understand it. Being a biologist, I can mumble about scientific curiosity being an
epiphenomenon of natural selection for cooperative hunting, foraging, individual
recognition, and so on, but that doesn’t make it any less incredible. As the
physicist Isidor Rabi said when the muon was discovered, “Who ordered that?”
However we acquired this ability to appreciate and understand the world, it
would be rude to waste it. So I wrote this book to share this feeling, this
amazement at what is all around us.
I got a lot of help. Laurie McNeil, Craig Bohren, and my father, Rainer
Johnsen, patiently went over some of the finer physical points with me. Craig, in
particular, went far beyond the call of duty, sending wonderfully detailed
answers to so many of my questions. Frankly, his books are better than mine;
read them if you can understand the math. Laurie McNeil, Eric Warrant, John
Endler, Tamara Frank, Marianne Moore, and members of my lab all read parts of
this book, helping with language, ideas, and making sure that biologists would
understand and appreciate it. Alison Sweeney, Andrij Horodysky, Andrew
Smith, my father, and two anonymous reviewers read and edited the whole
thing. Many colleagues allowed me to use their figures and photos. A week at
Friday Harbor’s Helen Whiteley Center finally broke six months of writer’s
block. Finally, Alison Kalett, Marsha Kunin, Stefani Wexler, and Karen Carter
at Princeton Press turned my draft into a real book.
I’d also like to thank my shipmates over the years, Tammy, Edie, Erika, Steve,
Alison, Brad, Justin, Jamie, Dan, and so many others—crazy pirates, all of them
—for sharing the excitement and fun of life at sea. Finally, I thank my wife,
Lynn, for being there and reminding me—every time I come home excited about
some new result—to tell her why she should care, and my daughter, Zoe, for
reminding me that “Dad’s just a dad.”
THE OPTICS OF LIFE
CHAPTER ONE
Introduction
In the right light, at the right time, everything is extraordinary.
— AARON ROSE (quoted in Live in the Light: A Journal of Self-Enlightenment, Mary
Engelbreit)
Of all the remarkable substances of our experience—rain, leaves, baby toes—
light is perhaps the most miraculous. Essentially indefinable, it is the ultimate
food for our planet’s life and allows us to perceive the world in nearly magical
detail and diversity. Via warmth, vision, and photosynthesis, and its darker
aspects such as radiation damage, light interacts fundamentally with nearly all
forms of life. Only certain subterranean species may be free from its influence.
Despite this, light remains relatively unstudied by biologists. In my own field
of oceanography, we have instruments known as “CTDs” that measure salinity
and temperature as a function of depth. These devices are ubiquitous, and the
characterization of a body of water is considered incomplete without the data
they provide. However, even though light is known to fundamentally affect the
distribution, ecology, and behavior of marine organisms, it is seldom measured,
despite the availability of economical light-meter attachments made specifically
for this instrument. Oceanography is a field known for the tight connections it
provides between biology and physics; in other biological fields light
measurement is rare. Even worse, many light measurements are taken
incorrectly. It is no fun to tell a colleague that, because they didn’t put a two-
inch cardboard tube around their detector, the data they collected over the last
three years is unsalvageable.
In my opinion, the relative lack of optics in biology is primarily the result of a
few factors. First, biologists receive very little training in the subject. What they
do get is usually confined to the electromagnetism portion of an introductory
physics course that derives Maxwell’s equations and Coulomb’s Law but gives
little practical advice about working with light. While there are some good
laboratory courses in optics, they’re generally populated by physics majors.
Second, no other field uses such an arcane and confusing collection of units.