Table Of ContentFrom Photon to Neuron
Bookcover: [Confocalfluorescencemicrograph.]Thevertebrateretinaismadeupoflayersofdifferent
cell types. To create this image, the rod photoreceptor cells of a mouse (in the outer nuclear layer,
far right) were labeled in red. Moving leftward, the next layers constitute the inner nuclear layer
(center): bipolar cells were labeled in green; the amacrine and horizontal cells were labeled in blue.
Nextcomestheinnerplexiformlayer(green filaments),includinginterconnections,andfinallyalayer
containing ganglion cell bodies (far left, blue). These cell types and their functions are described in
Chapter 11. The magnification is such that the cell diameters are about 5µm.
Ingreaterdetail,theexperimentersgeneratedDNAplasmidsthatdrovefluorescentproteinexpression,
either enhanced GFP or a red emitter named mCherry, in bipolar cells or rods respectively. They
also used short DNA segments (enhancers), that made the fluorescent proteins express in a cell
type-specific manner (similarly to methods discussed in Chapter 2). Other cell types in the inner
nuclear layer (INL, center) were tagged with fluorescent antibodies. (Yet other cell types that make
uptheretinawerenotlabeled,includingtheconephotoreceptorcellsandthemajorityofMu¨llerglia
cells. Rodoutersegmentsareonlyfaintlyvisibleonfar right becausemostofthefluorescentprotein
remained confined to the inner segment and cell body.) [CourtesyofDr.SuiWangandDr.Constance
Cepko;seealsoWangetal.,2014.]
The basic structural organization of the retina shown here is conserved across vertebrates and is
responsiblefordetecting,preprocessing,andconveyingallofthedifferentkindsofvisualinformation
about the outside world to the brain.
This image also demonstrates that specific cell types can be genetically manipulated in vivo, with
potential applications to therapy and basic science. For example, an optogenetic protein can be
introducedonlyinbipolarcells,renderingthemphotosensitive,anapproachbeingtakentocompensate
for loss of photoreceptors in disease (see Section 11.4.3).
Inset: Fragment from Albert Einstein’s 1905 article introducing the photon concept. The formula
appears in the text, in modern notation, as Equation 1.6 (page 34). [FromEinstein,1905.]
Facing page: Protein structures shown in Figure 10.13 (page 338). Vesicle: A1 - synaptobrevin; A2
- synaptotagmin; A3 - Rab; A4 - synaptophysin; A5 - vGlut; A6 - vesicular ATPase. Presynaptic
cytoplasm:B1-dystrophin;B2-actin;B3-NSF;B4-munc13(inactive);B5-GDI(guaninenucleotide
dissociation inhibitor); B6 - munc13/munc18; B7 - bassoon; B8 - RIM, CAST, etc.; B9 - ribeye; B10
- PRA1 (connection between bassoon and Rab); B11 - speculative bridging protein. Presynaptic
membrane: C1 - EAAT (excitatory amino acid transporter); C2 - SNAP25; C3 - syntaxin; C4 -
sidekick/DSCAM(speculative);C5-PSD-95;C6-voltage-gatedcalciumchannel;C7-dystroglycan;
C8 - src; C9 - LAR (receptor-type tyrosine-protein phosphatase); C10 - sodium/potassium ATPase.
Cleft: D1 - laminin; D2 - pikachurin. Postsynaptic membrane: E1 - iGluR; E2 - mGluR; E3 - G
protein; E4 - adenyate cyclase; E5 - TRPM1; E6 - nyctalopin; E7 - PSD-95/MAGI (speculative);
E8 - Fyn; E9 - potassium channel; E10 - ErbB (as a generic receptor tyrosine kinase). Postsynaptic
cytoplasm: F1 - GKAP; F2 - SHANK; F3 - Homer. [ArtbyDavidSGoodsell.]
From Photon to Neuron
Light, Imaging, Vision
B2
B1
C2
C1 B3 B4
B6 A1
C4
A2
A3
C2 B5
C7 C6 C5 C3
D2 C3 A4
C8 B10
D1 B8 B11
B8 B7 A5
B8
E9 C9
F2 B8
E8
F1 B8 B9
E7
C10
F3 E5 E6
E3 E4
E3 E2
E1
E10
A6
Philip Nelson
With the assistance of Sarina Bromberg,
Ann M. Hermundstad, and Jesse M. Kinder
Princeton University Press
Princeton and Oxford
Copyright c 2017 by Philip C. Nelson.
(cid:13)
Published by Princeton University Press, 41 William Street, Princeton, New Jersey 08540
In the United Kingdom: Princeton University Press, 6 Oxford Street, Woodstock, Oxfordshire OX201TR
press.princeton.edu
Cover: The retina is responsible for detecting and preprocessing visual information about the outside
world and conveying that information to the brain. [Courtesy Constance Cepko, Harvard Medical School
Department of Genetics and Ophthalmology and Howard Hughes Medical Institute, and Sui Wang,
Stanford Medical School Department of Ophthalmology.] The inset shows a fragment from Albert
Einstein’s 1905 article introducing the photon concept.
All Rights Reserved
ISBN 978-0-691-17518-8
ISBN (pbk.) 978-0-691-17519-5
British Library Cataloging-in-Publication Data is available.
Publication of this book has been aided by the United States National Science Foundation.
This book was composed using the LATEX typesetting system.
The publisher would like to acknowledge the author of this volume for providing the print-ready files
from which this book was printed.
Printed on acid-free paper.
∞
Printed in the United States of America.
1 3 5 7 9 10 8 6 4 2
For Scott Weinstein and William Berner
And yet, protest it if we will,
Some corner of the mind retains
The medieval man, who still
Keeps watch upon those starry skeins
And drives us out of doors at night
To gaze at anagrams of light.
— Adrienne Rich
Brief contents
Prologue: Preliminaries 1
PART I Doorways of Light
Chapter 1 What Is Light? 23
Chapter 2 Photons and Life 61
Chapter 3 Color Vision 107
Chapter 4 How Photons Know Where to Go 145
Chapter 5 Optical Phenomena and Life 180
PART II Human and Superhuman Vision
Chapter 6 Direct Image Formation 209
Chapter 7 Imaging as Inference 247
Chapter 8 Imaging by X-Ray Diffraction 272
Chapter 9 Vision in Dim Light 290
Chapter 10 The Mechanism of Visual Transduction 318
Chapter 11 The First Synapse and Beyond 352
PART III Advanced Topics
Chapter 12 Electrons, Photons, and the Feynman Principle 381
Chapter 13 Field Quantization, Polarization, and the Orientation of a Single Molecule 398
vii
viii
Chapter 14 Quantum-Mechanical Theory of FRET 415
Epilogue 423
Appendix A Global List of Symbols 431
Appendix B Units and Dimensional Analysis 439
Appendix C Numerical Values 446
Appendix D Complex Numbers 449
Contents Index Notation
Detailed contents
Web resources xx
To the student xxi
To the instructor xxv
Prologue: Preliminaries 1
0.1 Signpost: Uncertainty 1
0.2 Discrete Probability Distributions 2
0.2.1 Aprobabilitydistributionsummarizesourknowledgeaboutanuncertainsituation 2
0.2.2 Conditionalprobabilityquantifiesthedegreetowhicheventsarecorrelated 4
0.2.3 Arandomvariablecanbepartiallydescribedbyitsexpectationandvariance 4
0.2.4 Jointdistributions 6
0.2.5 Someexplicitdiscretedistributions 7
0.3 Dimensional Analysis 9
0.4 Continuous Probability Distributions 10
0.4.1 Probabilitydensityfunctions 10
0.4.2 Someexplicitcontinuousdistributions 12
0.5 More Properties of, and Operations on, Probability Distributions 14
0.5.1 Transformationofaprobabilitydensityfunction 15
0.5.2 Thesamplemeanofmanyindependent,identicallydistributedrandomvariableshaslowervariancethan
anyoneofitsconstituents 15
0.5.3 CountdataaretypicallyPoissondistributed 16
0.5.4 Thedifferenceoftwonoisyquantitiescanhavegreaterrelativestandarddeviationthaneitherby
itself 16
0.5.5 Theconvolutionoftwodistributionsdescribesthesumoftheirrandomvariables 16
0.6 Thermal Randomness 17
Big Picture 17
Key Formulas 18
Problems 19
PART I Doorways of Light
Chapter 1 What Is Light? 23
1.1 Signpost: Photons 23
1.2 Light Before 1905 24
1.2.1 Basiclightphenomena 25
1.2.2 Lightdisplayswavelikebehaviorinmanysituations 25
1.3 Light Is Lumpy 26
1.3.1 Thediscreteaspectoflightismostapparentatextremelylowintensity 27
1.3.2 Thephotoelectriceffect 30
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