Photobiology, the science of life and light 2nd ed l bjorn (springer, 2008)

Photobiology
Second Edition


Photobiology
The Science of Life and Light
Second Edition

Edited by

Lars Olof Björn
Lund University
Lund, Sweden


Lars Olof Björn
Department of Plant Physiology
Lund University
Sölvegatan 35
SE-223 62 Lund
Sweden


Library of Congress Control Number: 2007928823

ISBN: 978-0-387-72654-0

e-ISBN: 978-0-387-72655-7

Printed on acid-free paper.

© 2008 Springer Science+Business Media, LLC
All rights reserved. This work may not be translated or copied in whole or in part without the written
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987654321
springer.com


(Drawing by Per Nilsson)
Photobiology
I am lying on my back beneath the tree,
dozing, looking up into the canopy,
thinking: what a wonder!—I can see!
But in the greenery above my face,
an even greater miracle is taking place:
Leaves catch photons from the sun
and molecules from air around.
Quanta and carbon atoms become bound.
Life, for them, has just begun.
The sun not only creates life, it also takes away
mostly by deranging DNA.
Damage can be, in part, undone
by enzymes using photons from the sun.
Summer nears its end, already ’cross the sky
southward aiming birds are flying by.

Other birds for travel choose the night

relying on the stars for guiding light.
Imprinted in their little heads are Gemini,
Orion, Dipper, other features of the sky.
There is room for clocks that measure
day and night,
Correct for movement of the sky
and tell the time for flight
Deep into oceans, into caves
the sun cannot directly send its waves.
But through intricacies of foodweb’s maze,
oxygen from chloroplasts, luciferin, luciferase,
at times, in place,
where night and darkness seem to reign,
solar quanta emerge as photons
once again.
L.O. Björn 2002


Preface

I started my first photobiological research project almost exactly 50 years ago,
in the spring of 1957. My scientific interest ever since has been focused on
photobiology in its many aspects. Because I have been employed as a botanist,
my own research has dealt with the photobiology of plants, but throughout this
time I have been interested in other aspects, such as vision, the photobiology of
skin, and bioluminescence. A first edition of the present book was published in
2002, but this second edition is much expanded and completely updated. Several
new authors have been recruited among my eminent colleagues.

It has not been possible to cover all aspects of photobiology in one volume,
but I feel that we have managed to catch a fair and well-balanced cross section.
Many colleagues promised to help, but not all lived up to their promises. To
those who did, and who are coauthors to this volume, I direct my thanks; I think
that they have done an excellent job.
Living creatures use light for two purposes: for obtaining useful energy and
as information carrier. In the latter case organisms use light mainly to collect
information but also (e.g., by coloration and bioluminescence) for sending information, including misleading information, to other organisms of their own or
other species. Collection of free energy through photosynthesis and collection
of information through vision or other photobiological processes may seem to
be very different concepts. However, on a deep level they are of the same kind.
They use the difference in temperature between the sun and our planet to evade
equilibrium, i.e., to maintain and develop order and structure.
Obviously, all of photobiology cannot be condensed into a single volume.
My idea has been to first provide the basic knowledge that can be of use to
all photobiologists, and then give some examples of special topics. I have had
to limit myself, and one of the interesting topics that had to be left out is the
thermodynamics of processes in which light is involved.
Thus, this book is intended as a start, not as the final word. There are several
journals dealing with photobiology in general, and an even greater number
dealing with special topics such as vision, photodermatology, or photosynthesis. There are several photobiology societies arranging meetings and other
activities. And last but not least, up-to-date information can be found on the
Internet. The most important site, apart from the Web of Science and other
scientific databases, is Photobiology Online, a site maintained jointly by the
American and European Societies for Photobiology (ASP and ESP, respectively),
vii


viii

Preface

at http://169.147.169.1/POL.index.html or where
details about photobiology journals and books can be obtained.
The subtitle of this book may be somewhat misleading. There is only one
science. But I wanted to point out that the various disciplines dealing with light
and life have more in common than perhaps generally realized. I hope that
the reader will find that the same principles apply to seemingly different areas
of photobiology. For instance, we have transfer of excitation energy between
chromophores active in photosynthesis, in photorepair of DNA, and in bioluminescence. Cryptochromes, first discovered as components in light-sensing
systems in plants, are involved in the human biological clock, and probably
in the magnetic sense of birds and other animals, and they have evolved from
proteins active in DNA photorepair. The study of the photomagnetic sense of
birds has, in turn, led to new discoveries about how plants react to a combination
of light and magnetic fields.
Many colleagues have been helpful in the production of this book. Two of
my coauthors—Professors Helen Ghiradella and Anders Johnsson—who are also
close friends, have earned special thanks, because they have helped with more
chapters than those who bear their names. Helen has also helped to change my
Scandinavian English into the American twist of the islanders’ tounge, but we
have not changed the dialect of those who are native English speakers. Professor
Govindjee has contributed not only with his knowledge of photobiology, but
also with his great experience in editing. Drs. Margareta Johnsson and Helena
Björn van Praagh have helped with improvements and corrections, and Professor
Allan Rasmusson at our department in Lund has been very helpful when I and
my computer have had disagreements. I have enjoyed the friendliness and help
of other colleagues in the department. The staff of our biology library has been
very helpful and service-minded.
Many others have also helped, but special thanks go to my wife and beloved
photobiologist Gunvor, who has supported me during the work and put up with

paper and books covering the floor in our common home; to her I dedicate those
chapters of the book that bear my name.
Lars Olof Björn
Lund, Sweden
March 2007


Contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxi
1. The Nature of Light and Its Interaction with Matter . . . . . . . . . . . . . .
Lars Olof Björn
1.1. Introduction ...................................................................................
1.2. Particle and Wave Properties of Light .........................................
1.3. Light as Particles and Light as Waves, and Some Definitions....
1.4. Diffraction .....................................................................................
1.5. Polarization....................................................................................
1.6. Statistics of Photon Emission and Absorption .............................
1.7. Heat Radiation...............................................................................
1.8. Refraction of Light........................................................................
1.9. Reflection of Light ........................................................................
1.10. Scattering of Light ........................................................................
1.11. Propagation of Light in Absorbing and Scattering Media...........
1.12. Spectra of Isolated Atoms.............................................................
1.13. Energy Levels in Diatomic and Polyatomic Molecules...............
1.14. Quantum Yield of Fluorescence ...................................................
1.15. Relationship Between Absorption and Emission Spectra ............
1.16. Molecular Geometry of the Absorption Process ..........................
1.17. Transfer of Electronic Excitation Energy Between Molecules....

1.18. The Förster Mechanism for Energy Transfer ...............................
1.19. Triplet States .................................................................................
1.20. The Dioxygen Molecule................................................................
1.21. Singlet Oxygen..............................................................................
2. Principles and Nomenclature for the Quantification of Light . . . . . .
Lars Olof Björn
2.1. Introduction: Why This Chapter Is Necessary .............................
2.2. The Wavelength Problem..............................................................
2.3. The Problem of Direction and Shape ...........................................
2.4. Biological Weighting Functions and Units ..................................

1
1
1
6
7
8
9
11
14
15
18
19
22
23
29
30
31
33
34

35
36
37
41
41
42
43
46
ix


x

Contents

3. Generation and Control of Light . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Lars Olof Björn
3.1. Introduction ...................................................................................
3.2. Light Sources.................................................................................
3.2.1. The Sun ...........................................................................
3.2.2. Incandescent Lamps........................................................
3.2.3. Electric Discharges in Gases of Low Pressure ..............
3.2.4. Medium- and High-Pressure Gas Discharge Lamps......
3.2.5. Flashlamps ......................................................................
3.2.6. Light-Emitting Diodes ....................................................
3.2.7. Lasers ..............................................................................
3.3. Selection of Light..........................................................................
3.3.1. Filters with Light-Absorbing Substances .......................
3.3.2. Interference Filters ..........................................................
3.3.3. Monochromators .............................................................

4. The Measurement of Light . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Lars Olof Björn
4.1. Introduction ...................................................................................
4.2. Photothermal Devices ...................................................................
4.2.1. The Bolometer ................................................................
4.2.2. The Thermopile...............................................................
4.2.3. Thermopneumatic Devices .............................................
4.3. Photoelectric Devices....................................................................
4.3.1. A Device Based on the Outer Photoelectric Effect:
The Photomultiplier .........................................................
4.3.2. Devices Based on Semiconductors (Inner
Photoelectric Effect) ........................................................
4.4. Photochemical Devices: Actinometers and Dosimeters...............
4.5. Fluorescent Wavelength Converters (“Quantum Counters”) .......
4.6. Spectroradiometry .........................................................................
4.6.1. General ............................................................................
4.6.2. Input Optics.....................................................................
4.6.3. Example of a Spectroradiometer ....................................
4.6.4. Calibration of Spectroradiometers..................................
4.7. Special Methods for Measurement of Very Weak Light.............
4.7.1. Introduction .....................................................................
4.7.2. Direct Current Mode.......................................................
4.7.3. Chopping of Light and Use of Lock-In Amplifier ........
4.7.4. Measurement of Shot Noise ...........................................
4.7.5. Pulse Counting ................................................................
4.8. A Sensor for Catching Images: The Charge-Coupled Device.....

51
51
51

51
52
53
54
55
55
56
57
58
61
62
69
69
69
69
71
72
73
73
75
76
79
80
80
80
82
84
87
87
87

88
88
88
89

5. Light as a Tool for Biologists: Recent Developments . . . . . . . . . . . . . . 93
Lars Olof Björn
5.1. Introduction ................................................................................... 93


Contents

5.2.
5.3.
5.4.
5.5.
5.6.
5.7.
5.8.
5.9.
5.10.
5.11.
5.12.
5.13.

xi

Optical Tweezers and Related Techniques................................... 93
Use of Lasers for Ablation, Desorption, Ionization,
and Dissection ................................................................................ 95

Fluorescent Labeling ..................................................................... 96
Abbe’s Diffraction Limit to Spatial Resolution
in Microscopy ................................................................................ 97
Two-Photon Excitation Fluorescence Microscopy....................... 99
Stimulated Emission Depletion ................................................... 100
Near-Field Microscopy ................................................................. 101
Quantum Dots ............................................................................... 103
Photochemical Internalization....................................................... 108
Photogating of Membrane Channels ............................................ 110
Photocrosslinking and Photolabeling............................................ 113
Fluorescence-Aided DNA Sequencing ......................................... 115

6. Terrestrial Daylight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Lars Olof Björn
6.1. Introduction ................................................................................... 123
6.2. Principles for the Modification of Sunlight by the
Earth’s Atmosphere........................................................................ 123
6.3. The UV-A, Visible, and Infrared Components
of Daylight in the Open Terrestrial Environment Under
Clear Skies ..................................................................................... 124
6.4. Cloud Effects................................................................................. 127
6.5. Effects of Ground and Vegetation ................................................ 127
6.6. The UV-B Daylight Spectrum and Biological Action
of UV-B.......................................................................................... 128
7. Underwater Light . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Raymond C. Smith and Curtis D. Mobley
7.1. Introduction ...................................................................................
7.2. Inherent Optical Properties ...........................................................
7.3. Apparent Optical Properties..........................................................
7.4. Estimation of In-Water Radiant Energy .......................................

131
131
132
133
134

8. Action Spectroscopy in Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Lars Olof Björn
8.1. Introduction ................................................................................... 139
8.2. The Oldest History: Investigation of Photosynthesis by
Means of Action Spectroscopy...................................................... 141
8.3. Investigation of Respiration Using Action Spectroscopy ............ 143
8.4. The DNA That Was Forgotten ..................................................... 144
8.5. Plant Vision ................................................................................... 147
8.6. Protochlorophyllide Photoreduction to Chlorophyllide a ............ 151


xii

Contents

8.7.
8.8.

Limitations of Action Spectroscopy: The Elusive Blue
Light Receptor................................................................................ 152
Another Use for Action Spectra ................................................... 153

9. Spectral Tuning in Biology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155

Lars Olof Björn and Helen Ghiradella
9.1. Introduction ................................................................................... 155
9.2. Why Are Plants Green? ................................................................ 156
9.3. What Determines Spectra of Pigments? ....................................... 157
9.4. Relation Between the Absorption and Molecular Structure
of Chlorophylls .............................................................................. 159
9.5. Tuning of Chlorophyll a and b Absorption Peaks
by the Molecular Environment ...................................................... 161
9.6. Phycobiliproteins and Phycobilisomes ......................................... 162
9.7. Chromatic Adaptation of Cyanobacterial Phycobilisomes........... 165
9.8. Visual Tuning................................................................................ 166
9.9. Tuning of Anthocyanins................................................................ 171
9.10. Living Mirrors and the Tuning of Structural Color ..................... 177
9.10.1. Introduction ..................................................................... 177
9.10.2. Reflection in a Single Thin Layer.................................. 178
9.10.3. Reflection by Multilayer Stacks ..................................... 183
9.11. The Interplay of Spectra in the Living World.............................. 188
10. Photochemical Reactions in Biological Light Perception
and Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Lars Olof Björn
10.1. Introduction ................................................................................... 197
10.2. Cis-Trans and Trans-Cis Isomerization........................................ 198
10.2.1. Urocanic Acid ................................................................. 199
10.2.2. Eukaryotic Rhodopsin..................................................... 200
10.2.3. Archaean Rhodopsins ..................................................... 203
10.2.4. Photoactive Yellow Proteins (PYPs, Xanthopsins) ....... 205
10.2.5. Phytochrome ................................................................... 207
10.2.6. Photosensor for Chromatic Adaptation
of Cyanobacteria.............................................................. 209
10.2.7. Violaxanthin as a Blue-light Sensor in

Stomatal Regulation ........................................................ 210
10.3. Other Types of Photosensors ........................................................ 211
10.3.1. Cryptochromes ................................................................ 211
10.3.2. Phototropin...................................................................... 212
10.3.3. The Plant UV-B Receptor .............................................. 215
11. The Diversity of Eye Optics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
Lars Olof Björn
11.1. Introduction ................................................................................... 223


Contents

11.2.
11.3.
11.4.
11.5.
11.6.
11.7.
11.8.
11.9.
11.10.
11.11.
11.12.
11.13.

The Human Eye ............................................................................
An Eye in Water: The Problem ....................................................
An Eye in Water: The Solution ....................................................
Another Problem: Chromatic Aberration .....................................
Problems and Solutions for Amphibious Animals.......................

Feedback Regulation During Eye Development ..........................
Eyes with Extreme Light Sensitivity ............................................
Compound Eyes ............................................................................
Nipple Arrays on Insect Eyes .......................................................
Eyes with Mirror Optics ...............................................................
Scanning Eyes ...............................................................................
Evolution of Eyes..........................................................................

xiii

223
227
228
230
231
234
234
235
240
241
242
246

12. The Evolution of Photosynthesis and Its Environmental Impact . . . 255
Lars Olof Björn and Govindjee
12.1. Introduction ................................................................................... 256
12.2. A Short Review of Plant Photosynthesis...................................... 257
12.3. The Domains of Life..................................................................... 258
12.4. Predecessors of the First Photosynthetic Organisms.................... 259
12.5. The First Photosynthesis ............................................................... 260

12.6. Appearance of Oxygenic Photosynthesis ..................................... 262
12.7. From Cyanobacteria to Chloroplasts ............................................ 265
12.8. Evolution of Photosynthetic Pigments and
Chloroplast Structure ..................................................................... 267
12.9. Many Systems for the Assimilation of Carbon Dioxide
Have Been Tried in the Course of Evolution ............................... 270
12.10. C4 Metabolism .............................................................................. 272
12.11. Crassulacean Acid Metabolism..................................................... 274
12.12. Evolution of ATP-Synthesizing Enzymes .................................... 275
12.13. The Journey onto Land ................................................................. 275
12.14. Impact of Photosynthesis on the Biospheric Environment .......... 277
12.15. Conclusion..................................................................................... 280
13. Photosynthetic Light Harvesting, Charge Separation, and
Photoprotection: The Primary Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289
Villy Sundström
13.1. Introduction ................................................................................... 289
13.2. Photosynthetic Antennas: Light-Harvesting and Energy
Transfer .......................................................................................... 293
13.2.1. Theoretical Considerations for Energy Transfer
and Spectroscopy ............................................................. 294
13.2.2. Energy Transfer Between Weakly Dipole-Coupled
Chromophores: B800–B800 and B800–B850
Transfer in LH2 ............................................................... 295


xiv

Contents

13.3.

13.4.

13.5.
13.6.

13.2.3. Energy Transfer Between Strongly Coupled
Chromophores: B850 of LH2.......................................... 296
13.2.4. The Photosynthetic Unit: Intercomplex
Excitation Transfer .......................................................... 298
Photosynthetic Charge Separation: The Photosynthetic
Reaction Center.............................................................................. 300
13.3.1. The Structure and Function of the Bacterial
Reaction Center ............................................................... 300
13.3.2. The Mechanism of Primary Electron Transfer .............. 301
Carotenoid Photophysics and Excited State Dynamics:
The Basis of Carotenoid Light-Harvesting and
Non-Photochemical Quenching ..................................................... 303
13.4.1. Excited States of Carotenoids......................................... 305
Energy Transfer from Carotenoids to (Bacterio)Chlorophyll ...... 309
Quenching of Chlorophyll Excited States by Carotenoids:
Non-Photochemical Quenching ..................................................... 313

14. The Biological Clock and Its Resetting by Light . . . . . . . . . . . . . . . . . . 321
Anders Johnsson and Wolfgang Engelmann
14.1. Biological Clocks .......................................................................... 321
14.1.1. Spectrum of Rhythms ..................................................... 322
14.1.2. Function of Clocks.......................................................... 322
14.1.3. Current Concepts and Caveats ....................................... 323
14.1.4. Adaptive Significance and Evolutionary Aspects

of Circadian Clocks ......................................................... 324
14.1.5. Properties and Formal Structures of the Circadian
System.............................................................................. 324
14.2. Synchronization of Clocks ............................................................ 325
14.3. Clocks and Light in Cyanobacteria .............................................. 328
14.3.1. Photoreceptors and Zeitgeber ......................................... 328
14.3.2. Molecular Clock Model and Temporal
Orchestration of Gene Expression .................................. 330
14.4. Clocks in the Dinoflagellate Lingulodinium ............................... 331
14.5. Light Effects on Circadian Clocks in Plants: Arabidopsis .......... 332
14.5.1. Light as the Most Important Zeitgeber .......................... 333
14.5.2. Photoreceptors................................................................. 334
14.5.3. Clock Mechanism and Clock-Controlled Genes............ 336
14.5.4. Photoperiodism ............................................................... 337
14.6. Fungal Clocks and Light Resetting: Neurospora ........................ 338
14.6.1. The Circadian System of Neurospora............................ 338
14.6.2. Entrainment of the Circadian System ............................ 341
14.6.3. Photoreceptors of the Circadian System ........................ 342
14.6.4. Outputs of the Circadian System and
Photoperiodism ................................................................ 343
14.7. How Light Affects Drosophila’s Circadian System .................... 344


Contents

xv

14.7.1. Circadian Eclosion .......................................................... 344
14.7.2. Locomotor Activity Controlled by Several
Circadian Oscillators ....................................................... 345

14.7.3. Mechanism of Circadian Clock...................................... 347
14.7.4. Photoreceptors for the Entrainment
of the Locomotion Clock ................................................ 347
14.8. Light and Circadian Clocks in Mammals..................................... 351
14.8.1. SCN and Its Incoming and Outgoing Pathways ............ 351
14.8.2. Circadian Photoreceptors in the Retina.......................... 353
14.8.3. Pineal Organ, Melatonin, and Photoperiodism .............. 355
14.8.4. Clocks Outside the SCN................................................. 357
14.9. Light and the Human Circadian System ...................................... 358
14.9.1. Light Synchronizes the Human Circadian System ........ 359
14.9.2. Significance of Light in Shift Work and Jetlag ............. 360
14.9.3. Light Treatment in Sleep Disorders ............................... 361
14.9.4. Seasonal Affective Disorders and Endogenous
Depressions ...................................................................... 362
14.10. Models ........................................................................................... 363
14.10.1. Simple Model Description.............................................. 363
14.10.2. Some Mathematical Properties of Circadian Models .... 365
14.10.3. Single Versus Multioscillator Models—Outlook........... 366
15. Photoperiodism in Insects and Other Animals . . . . . . . . . . . . . . . . . . . . 389
David Saunders
15.1. Introduction ................................................................................... 389
15.2. Photoperiodic Regulation of Diapause and Seasonal
Morphs in Insects........................................................................... 391
15.3. Models for Photoperiodism........................................................... 393
15.4. Evidence for the Involvement of the Circadian System in
Photoperiodic Time Measurement................................................. 396
15.4.1. Nanda-Hamner Experiments........................................... 396
15.4.2. Night Interruption Experiments and the Bünsow
Protocol ............................................................................ 397
15.4.3. Skeleton Photoperiods and Bistability Phenomenon ..... 400

15.4.4. The Effects of Transient or Non–Steady-State
Entrainment on Diapause Induction................................ 401
15.5. Using Overt “Indicator” Rhythms as “Hands of the Clock” ....... 403
15.6. The “Hourglass” Alternative: Damping Oscillations ................... 404
15.7. Photoreception and Clock Location.............................................. 405
15.8. Diapause Induction in Drosophila melanogaster and the
Potential Molecular Analysis of Photoperiodic Induction ............ 408
16. Photomorphogenesis and Photoperiodism in Plants . . . . . . . . . . . . . . . 417
James L. Weller and Richard E. Kendrick
16.1. Introduction ................................................................................... 417


xvi

Contents

16.2. Photomorphogenic Photoreceptors ............................................... 418
16.2.1. Phytochromes.................................................................. 418
16.2.2. Cryptochromes ................................................................ 423
16.2.3. Phototropins .................................................................... 424
16.2.4. Other Photoreceptors ...................................................... 425
16.3. Physiological Roles of Photoreceptors ......................................... 425
16.3.1. Germination .................................................................... 426
16.3.2. Seedling Establishment................................................... 427
16.3.3. Phototropism ................................................................... 429
16.3.4. Shade Avoidance ............................................................ 430
16.4. Photoreceptor Signal Transduction............................................... 431
16.4.1. Primary Reactions of Photoreceptors ............................. 431
16.4.2. Mutants and Interacting Factors ..................................... 432
16.4.3. Expression Profiling ....................................................... 436

16.4.4. Pharmacological Approaches ......................................... 437
16.5. Photoperiodism.............................................................................. 438
16.5.1. Light and the Circadian Clock ....................................... 438
16.5.2. Signaling in Photoperiodism .......................................... 445
16.6. Photomorphogenesis and Photoperiodism in the Natural
Environment ................................................................................... 447
16.6.1. Improving Energy Capture ............................................. 448
16.6.2. Light and the Seed Habit................................................ 449
16.6.3. Avoidance or Survival of Unfavorable Conditions ....... 450
16.7. Concluding Remarks ..................................................................... 451
17. The Light-Dependent Magnetic Compass . . . . . . . . . . . . . . . . . . . . . . . . . 465
Rachel Muheim
17.1. The Involvement of Light in the Magnetic Compass
Orientation in Animals................................................................... 465
17.1.1. The Magnetic Inclination Compass................................ 466
17.2. Light-Dependent Effects on Orientation at Different
Wavelengths and Irradiances ......................................................... 467
17.2.1. Evidence for an Antagonistic Spectral Mechanism
Mediating Magnetic Compass Orientation in Newts...... 467
17.2.2. Magnetic Compass Orientation of Birds Depends
on Wavelength and Irradiance ........................................ 468
17.3. Localization of the Light-Dependent Magnetoreceptor ............... 469
17.4. Mechanisms of Light-Dependent Magnetoreception ................... 470
17.4.1. Chemical Magnetoreception Based on a Radical
Pair Mechanism ............................................................... 471
17.4.2. Involvement of Cryptochromes
as Magneto-Sensitive Photoreceptors?............................ 471
17.4.3. RF Fields as Diagnostic Tool for Testing
the Radical Pair Mechanism............................................ 473
17.5. Outlook .......................................................................................... 474

Contents

xvii

18. Phototoxicity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 479
Lars Olof Björn and Pirjo Huovinen
18.1. Introduction ................................................................................... 479
18.2. Phototoxicity in Plant Defense ..................................................... 482
18.3. Phototoxins of Fungal Plant Parasites .......................................... 484
18.4. Phototoxic Drugs and Cosmetics.................................................. 485
18.5. Metabolic Disturbances Leading to Phototoxic Effects of
Porphyrins or Related Compounds................................................ 487
18.6. Polycyclic Aromatic Hydrocarbons as Phototoxic
Contaminants in Aquatic Environments........................................ 489
18.6.1. Nature and Occurrence of PAHs.................................... 489
18.6.2. Mechanisms of PAH Phototoxicity................................ 490
18.6.3. Factors Affecting Exposure to Phototoxicity
of PAHs in Aquatic Systems........................................... 492
18.6.4. Phototoxicity of PAHs to Aquatic Biota........................ 493
19. Ozone Depletion and the Effects of Ultraviolet Radiation . . . . . . . . . . 503
Lars Olof Björn and Richard L. McKenzie
19.1. Introduction ................................................................................... 503
19.2. The Ozone Layer........................................................................... 504
19.3. Ozone Depletion............................................................................ 506
19.4. Molecular Effects of UV-B Radiation.......................................... 508
19.4.1. Effects of Ultraviolet Radiation on DNA ...................... 511
19.4.2. Photolyases and Photoreactivation ................................. 513
19.4.3. Formation and Effects of Reactive Oxygen Species ..... 515

19.4.4. Effects of Ultraviolet Radiation on Lipids..................... 517
19.4.5. Photodestruction of Proteins........................................... 518
19.4.6. UV Absorption Affecting Regulative Processes............ 518
19.4.7. UV-Induced Apoptosis ................................................... 519
19.5. Ultraviolet Effects on Inanimate Matter of Biological
Relevance ....................................................................................... 519
19.6. UV-B Radiation in an Ecological Context ................................... 520
19.6.1. Aquatic Life .................................................................... 520
19.6.2. Terrestrial Life ................................................................ 522
19.7. Effects on Human Eyes................................................................. 523
20. Vitamin D: Photobiological and Ecological Aspects . . . . . . . . . . . . . . . 531
Lars Olof Björn
20.1. Introduction ................................................................................... 531
20.2. Chemistry and Photochemistry of Provitamin and Vitamin D .... 532
20.3. Transport and Transformation of Vitamin D in the
Human Body .................................................................................. 536
20.4. Physiological Roles of 1,25-Dihydroxyvitamin D in
Vertebrates ..................................................................................... 536


xviii

Contents

20.5. Cellular Effects and the Vitamin D Receptor: Two Basic
Modes of Action ............................................................................ 537
20.6. Evolutionary Aspects .................................................................... 538
20.7. Distribution of Provitamin and Vitamin D in the
Plant Kingdom ............................................................................... 540
20.8. Physiological Effects of Provitamin and Vitamin D in

Plants and Algae ............................................................................ 541
20.9. Roles of Provitamin and Vitamin D in Plants.............................. 541
20.10. Biogeographical Aspects............................................................... 542
20.11. The Bright and Dark Sides of Sunlight........................................ 545
20.12. Non-Photochemical Production of Vitamin D ............................. 546
21. The Photobiology of Human Skin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 553
Mary Norval
21.1. Introduction ................................................................................... 553
21.2. The Structure of Skin and the Skin Immune System................... 554
21.2.1. Skin Structure ................................................................. 554
21.2.2. The Skin Immune System .............................................. 555
21.2.3. Contact and Delayed-Type Hypersensitivity ................. 556
21.2.4. Effect of Solar UV Radiation on the Skin: Action
Spectra.............................................................................. 557
21.3. Pigmentation and Sunburn ............................................................ 557
21.3.1. Pigmentation and Phototypes ......................................... 557
21.3.2. Sunburn and Minimal Erythema Dose........................... 558
21.4. Photoageing ................................................................................... 559
21.5. Photocarcinogenesis ...................................................................... 560
21.5.1. Nonmelanoma Skin Cancer ............................................ 561
21.5.2. Malignant Melanoma ...................................................... 563
21.5.3. Animal Studies of Skin Cancer ...................................... 564
21.6. Immunosuppression....................................................................... 565
21.6.1. UV-Induced Immunosuppression ................................... 565
21.6.2. UV-Induced Immunosuppression and Tumors .............. 568
21.6.3. UV-Induced Immunosuppression and Microbial
Infection Including Vaccination ...................................... 568
21.7. Photodermatoses............................................................................ 570
21.7.1. Genodermatoses: Xeroderma Pigmentosum .................. 570
21.7.2. Idiopathic Photodermatoses: Polymorphic

Light Eruption.................................................................. 571
21.7.3. Cutaneous Porphyrias ..................................................... 571
21.7.4. Photoallergic Contact Dermatitis.................................... 572
22. Light Treatment in Medicine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 577
Theresa Jurkowitsch and Robert Knobler
22.1. Introduction ................................................................................... 577


Contents

xix

22.2. Phototherapy (Use of Light Without Applied
Photosensitizer) .............................................................................. 578
22.2.1. UV-B ............................................................................... 578
22.2.2. Long-Wave (>340 nm) UV-A (“UV-A1”).................... 580
22.2.3. Visible Light ................................................................... 580
22.3. Photochemotherapy ....................................................................... 581
22.3.1. PUVA (Photochemotherapy Mediated
by UV-A Radiation with a Psoralen Derivative
as Photosensitizer) ........................................................... 581
22.3.2. Implementation of Phototherapy
and Photochemotherapy .................................................. 582
22.3.3. Extracorporeal Photochemotherapy................................ 582
22.3.4. Photodynamic Therapy (PDT) with Porphyrins
or Chlorins as Photosensitizers ....................................... 584
23. Bioluminescence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 591
Lars Olof Björn and Helen Ghiradella
23.1. Introduction ................................................................................... 591
23.2. Evolution and Occurrence Among Organisms............................. 592

23.3. Biological Roles: What Is Bioluminescence Good for? .............. 593
23.3.1. Reproduction ................................................................... 593
23.3.2. Protection from Predation............................................... 594
23.3.3. Food Acquisition............................................................. 595
23.3.4. Protection from Reactive Oxygen Species..................... 596
23.3.5. DNA Repair .................................................................... 596
23.4. Mechanisms of Light Production.................................................. 597
23.5. Dragonfishes: Long-Wave Bioluminescence
and Long-Wave Vision.................................................................. 601
23.6. Control of Bioluminescence.......................................................... 603
23.7. Human Exploitation of Bioluminescence ..................................... 607
23.8. Photosynthetic Afterglow.............................................................. 608
23.9. Ultraweak Light Emission ............................................................ 609
24. Hints for Teaching Experiments and Demonstrations . . . . . . . . . . . . .
Lars Olof Björn
24.1. Introduction ...................................................................................
24.2. A Good Start .................................................................................
24.3. The Wave Nature of Light............................................................
24.4. Singlet Oxygen..............................................................................
24.5. Complementary Chromatic Adaptation of Cyanobacteria ...........
24.6. What Is Color? The Benham Disk ...............................................
24.7. Photoconversion of Rhodopsin .....................................................
24.8. Photosynthesis of Previtamin D....................................................
24.9. Photoconversion of Protochlorophyllide ......................................
24.10. Separation of Chloroplast Pigments .............................................

617
617
618
619

620
620
622
623
624
625
627


xx

Contents

24.11. Light Acclimation of Leaves: The Xanthophyll Cycle................ 629
24.11.1. Introduction to the Xanthophyll Cycle........................... 630
24.11.2. Experiment ...................................................................... 633
24.12. Ultraviolet Radiation Damage and Its Photoreactivation............. 635
24.13. Ultraviolet Damage to Microorganisms ....................................... 637
24.14. Photomorphogenesis in Plants and Related Topics...................... 638
24.14.1. Photomorphogenesis of Bean Plants .............................. 638
24.14.2. Regulation of Seed Germination by Phytochrome ........ 639
24.14.3. Effects of Blue and Red Light on Development
of Fern Prothallia ............................................................ 640
24.15. Spectrophotometric Studies of Phytochrome In Vivo.................... 640
24.16. Bioluminescence............................................................................ 642
24.16.1. Fireflies ........................................................................... 642
24.16.2. Bacteria ........................................................................... 642
24.17. Miscellaneous Teaching Experiments and Demonstrations......... 643
25. The Amateur Scientist’s Spectrophotometer . . . . . . . . . . . . . . . . . . . . . .
Lars Olof Björn

25.1. Introduction ...................................................................................
25.2. Construction ..................................................................................
25.3. Calibration of Wavelength Scale ..................................................
25.4. Measurement and Manipulation of Spectra..................................
25.5. Suggestions for Further Experimentation .....................................

647
647
648
648
652
656

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 659


Contributors

Lars Olof Björn
Lund University, Department of Cell and Organism Biology, Sölvegatan 35,
SE-223 62 Lund, Sweden

Wolfgang Engelmann
Schlossgartenstr. 22, D-72070 Tübingen (Germany), Tel.: int+49-7071-68325

Helen Ghiradella
University at Albany, Department of Biology, Albany, New York 12222, USA

Govindjee
Prof.Em., Biochemistry, Biophysics and Plant Biology, Department of Plant

Biology, University of Illinois, 265 Morrill Hall, MC-116, 505 South Goodwin
Avenue, Urbana, IL 61801–3707, USA, Fax: int+01-217-244-7246

Pirjo Huovinen
Centro de Investigación y Desarrollo de Recursos y, Ambientes Costeros
(i∼mar), Universidad de Los Lagos, Camino a, Chinquihue Km 6, Casilla 557,
Puerto Montt, Chile

Anders Johnsson
Norwegian University of Science and Technology (NTNU), Department of
Physics, NO-7491 Trondheim, Norway

Theresa Jurkowitsch
Medical University of Vienna, Wahringerguertel 18–20, A-1090 Vienna, Austria

Richard E. Kendrick
Department of Plant Science, Wageningen University, The Netherlands
xxi


xxii

Contributors

Robert Knobler
Div. of Special and Environmental Dermatology, Medical University of Vienna,
Wahringerguertel 18–20, A-1090 Vienna, Austria

Richard L. McKenzie
National Institute of Water and Atmospheric Research, (NIWA), Lauder, PB

50061 Omakau, Central Otago 9352, New Zealand

Curtis D. Mobley
Sequoia Scientific, Inc., 2700 Richards Rd. Suite 107, Bellevue, WA 98005

Rachel Muheim
Virginia Polytechnic Institute and State University, Department of Biological
Sciences, Derring Hall, Blacksburg, VA 24061–0406, USA

Mary Norval
University of Edinburgh Medical School, Biomedical Sciences

David Saunders
21, Leadervale Road, Edinburgh EH16 6PB, Scotland U.K.

Raymond C. Smith
Geography Department and ICESS, University of California, Santa Barbara,
Santa Barbara, CA 93106

Villy Sundström
Department of Chemical Physics, Lund University, Box 124, SE-22100 Lund,
Sweden
James L. Weller
School of Plant Science, University of Tasmania, Private Bag 55, Hobart,
Tasmania 7001, Australia



1
The Nature of Light and Its Interaction

with Matter
Lars Olof Björn

Abstract:

This chapter provides a physical background to the following ones. It
describes the particle and wave properties of light, and the diffraction,
polarization, refraction, reflection, and absorption of light, statistics of
photon emission and absorption. Planck’s law of heat radiation is described
in various mathematical and graphical ways. One section is devoted to
a simplified description of the propagation of light in absorbing and
scattering media. The final sections are devoted to interactions between
light and matter: spectra of and energy levels in atoms and molecules, the
relation between absorption and emission spectra, the molecular geometry
of absorption and emission, and the transfer of electronic excitation energy
between molecules, including the Förster mechanism, triplet states, and the
photobiologically important properties of the dioxygen molecule.

1.1. Introduction
The behavior of light when it travels through space and when it interacts with
matter plays a central role in the two main paradigms of twentieth-century
physics: relativity and quantum physics. As we shall see throughout this book,
it is also important for an understanding of the behavior and functioning of
organisms.

1.2. Particle and Wave Properties of Light
The strange particle and wave properties of light are well demonstrated by a
modification of Young’s double slit experiment. In Young’s original experiment
(1801), a beam of light impinged on an opaque screen with two parallel, narrow
slits. Light passing through the slits was allowed to hit a second screen. Young did

not obtain two light strips (corresponding to the two slits) on the second screen,
but instead a complicated pattern of several light and dark strips. The pattern
1


2

L. O. Björn

obtained can be quantitatively explained by assuming that the light behaves as
waves during its passage through the system.
It is easy to calculate where the maxima and minima in illumination of the
last screen will occur. We can get some idea of the phenomenon of interference
by just overlaying two sets of semicircular waves spreading from the two slits
(Fig. 1.1), but this does not give a completely correct picture.
For the experiment to work, it is necessary for the incident light waves to be
in step, i.e., the light must be spatially coherent. One way of achieving this is
to let the light from a well-illuminated small hole (in one more screen) hit the
screen with the slits. The pattern produced (Fig. 1.2) is a so-called interference
pattern or, to be more exact, a pattern produced by a combination of diffraction
(see the next section) in each slit and interference between the lights from the
two slits. It is difficult to see it if white light is used, since each wavelength
component produces a different pattern. Therefore, at least a colored filter should
be used to limit the light to a narrower waveband. The easiest way today (which
Young could not enjoy) is to use a laser (a simple laser pointer works well),
giving at the same time very parallel and very monochromatic light, which is
also sufficiently strong to be seen well.
In a direction forming the angle with the normal to the slitted screen (i.e., to
the original direction of the light), waves from the two slits will enhance each
other maximally if the difference in distance to the two slits is an integer multiple

of the wavelength, i.e., d.sin = n. , where d is the distance between the slits,
the wavelength, and n a positive integer (0, 1, 2, …). The waves will cancel each
other completely when the difference in distance is half a wavelength, i.e., d.sin
= (n + 1/2). . To compute the pattern is somewhat more tedious, and we need
not go through the details. The outcome depends on the width of each slit, the
distance between the slits, and the wavelength of light. An example of a result
is shown in Fig. 1.2.
So far so good—light behaves as waves when it travels. But we also know
that it behaves as particles when it leaves or arrives (see later). The most direct
demonstration of this is that we can count the photons reaching a sensitive
photocell (photomultiplier).
But the exciting and puzzling properties of light stand out most clearly when
we combine the original version of Young’s experiment with the photon counter.
Instead of the visible diffraction pattern of light on the screen, we could dim the
light and trace out the pattern as a varying frequency of counts (or, if we so wish,
as a varying frequency of clicks as in a classical Geiger counter) as we move
the photon counter along the projection screen (Fig. 1.3a). Since we count single
photons, we can dim the light considerably and still be able to register the light.
In fact, we can dim the light so much that it is very, very unlikely that more than
one photon at a time will be in flight between our light source and the photon
counter. This type of experiment has actually been performed, and it has been
found that a diffraction pattern is still formed under these conditions. We can do
the experiment also with an image forming device such as a photographic film
or a charge coupled diode (CCD) array as the receiver and get a picture of where


1. Nature of Light and Its Interactions

3

Figure 1.1. (Top) Light waves impinge from below on a barrier with only one slit open
and spread from this in concentric rings. (Bottom) Light waves impinge from below on
a barrier with two slits open. The two wave systems spreading on the other side interfere
and in some sectors enhance, in others extinguish one another. The picture is intended
only to simplify the understanding of the interference phenomenon and does not give a
true description of the distribution of light.


4

L. O. Björn

Figure 1.2. Interference pattern produced in Young’s double slit experiment (computer
simulation). The width of each slit is 1 mm, the distance between slit centers 4 mm, and
the wavelength 0.001 mm (1 μm). The distance from the center of the screen is along
the horizontal axis and the irradiance (“light intensity”) along the vertical axis, both in
relative units. Note that the vertical scale is linear in the upper diagram, logarithmic in
the lower one.

the photons hit. A computer simulation of the outcome of such an experiment is
shown in Fig. 1.3b.
If you think a little about what this means, you will be very puzzled indeed.
For the diffraction pattern to be formed we need two slits. But we can produce
the pattern by using only one photon at a time. There can be no interaction
between two or more photons, which have traveled different paths, e.g., one