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The Optics of Life

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

Sönke Johnsen
Copyright Date: 2012
Pages: 376
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  • Book Info
    The Optics of Life
    Book Description:

    Optics--a field of physics focusing on the study of light--is also central to many areas of biology, including vision, ecology, botany, animal behavior, neurobiology, and molecular biology.The Optics of Lifeintroduces the fundamentals of optics to biologists and nonphysicists, giving them the tools they need to successfully incorporate optical measurements and principles into their research. Sönke Johnsen starts with the basics, describing the properties of light and the units and geometry of measurement. He then explores how light is created and propagates and how it interacts with matter, covering topics such as absorption, scattering, fluorescence, and polarization. Johnsen also provides a tutorial on how to measure light as well as an informative discussion of quantum mechanics.

    The Optics of Lifefeatures a host of examples drawn from nature and everyday life, and several appendixes that offer further practical guidance for researchers. This concise book uses a minimum of equations and jargon, explaining the basic physics of light in a succinct and lively manner. It is the essential primer for working biologists and for anyone seeking an accessible introduction to optics.

    eISBN: 978-1-4008-4066-3
    Subjects: Biological Sciences, Physics

Table of Contents

  1. Front Matter
    (pp. i-vi)
  2. Table of Contents
    (pp. vii-viii)
    (pp. ix-xii)
  4. CHAPTER ONE Introduction
    (pp. 1-7)

    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...

  5. CHAPTER TWO Units and Geometry
    (pp. 8-30)

    The number one complaint I get from people who want to learn optics is about units. Although a photon (or light wave) has only three properties—frequency, wavelength, and polarization—the long history of light measurement and its association with human vision has left a trail of perplexing and comical units. Only in optics do people still publish papers using units like stilbs, nits, candelas, trolands, and my personal favorite, foot-lamberts. Unless you work in human visual psychophysics, where these units are entrenched, my advice is simple. If you know what these units are, forget them. If they are unfamiliar...

  6. CHAPTER THREE Emission
    (pp. 31-74)

    Even a casual look at the most boring of surroundings, for example my office, quickly reveals a dazzling diversity of color, sheen, polarization, and other effects. In fact, the diversity of visual phenomena is at least partially responsible for the complex and messy history of optics—for ages people have naturally wanted to catalog and understand what they saw. So it can be surprising to realize that there are few natural sources of light. In fact, there are actually only a few ways of making light, the main two categories being (1) thermal radiation, where light emission is related to...

  7. CHAPTER FOUR Absorption
    (pp. 75-115)

    Absorption has been called the “death of photons” (Bohren and Clothiaux, 2006). While the energy of a photon is never truly lost (reincarnation is a fact in physics), most people find the conversion of photons into heat and chemical reactions less appealing than their original emission. I admit that I enjoy watching bioluminescent plankton more than contemplating the blackness of my T-shirt.

    Without absorption, though, the earth would be a far less colorful place, with no paintings, flowers, leopard spots, or stained-glass windows. There would still be some colors due to interference and scattering (to be discussed in chapters 5...

  8. CHAPTER FIVE Scattering
    (pp. 116-150)

    As mentioned in the previous chapter, optics is primarily photons interacting with electrons, atoms, and molecules. If the energy of the photon matches the difference in energy between two levels of excitation, then the photon vanishes, its energy converted into other forms (heat, etc.). However, if the photon’s energy doesn’t find a match among the differences in possible energy states, a new photon will quickly be emitted. The new photon is usually the same energy (and thus the same wavelength) as the old one, making it appear as if the original photon bounced, which is why this nonabsorptive interaction is...

  9. CHAPTER SIX Scattering with Interference
    (pp. 151-180)

    Light does not bend in a lens, it doesn’t bounce off the surface of glass, and it doesn’t spread out after passing through a small hole. It doesn’t even travel in a straight line. The happiest day of my scientific life came when I read Feynman’sQEDand learned that refraction, reflection, and diffraction—things I had known since fifth grade—were all lies. More accurately, they are illusions. Itappearsthat light bends, bounces, and spreads out. The illusion is so good that you can base solid mathematical predictions on them, but careful thought and further experiments show that...

  10. CHAPTER SEVEN Fluorescence
    (pp. 181-202)

    Fluorescence does not make light! There, I have been waiting six chapters to say that and finally got it out of my system. I don’t have many pet peeves—I find them peevish—but this one matters. The misunderstanding comes in two flavors. The first is a common misuse of terms. Historically, bioluminescence was often referred to as phosphorescence, and many people, even biologists, still consider the terms synonymous. This is not helped by tourist brochures for local bioluminescence hotspots that refer to the places as, for example, “phosphorescent bays.” Even more unfortunately, because phosphorescence is closely related to fluorescence...

  11. CHAPTER EIGHT Polarization
    (pp. 203-236)

    Edwin Land was a remarkable person. Though he never finished college, Land was a dominating figure in photography and optics for much of the twentieth century and made fundamental contributions to the understanding of color vision. His two most famous inventions were the Polaroid camera and the polarizing filter. The latter, developed late at night using equipment and space stolen from Columbia University, opened the door for a myriad of technical and scientific applications, ranging from 3D movies to the study of honeybee navigation. So, it is with his inspiring, and somewhat intimidating, example that I tackle the issue of...

  12. CHAPTER NINE Measuring Light
    (pp. 237-270)

    While it can often appear as simple as turning on a machine and recording a number, light measurement has many nasty pitfalls. It is easy to measure the wrong thing, to measure the right thing in the wrong way, or to have a worthless number and not know it. The main reason for this is that we don’t measure light in our daily lives. Since childhood, we develop an intuitive sense of weights, lengths, area, temperature, and so on. For example, we can guess someone’s height to within 5% and weight to within 10%–20%. However, even after a decade...

  13. CHAPTER TEN What Is Light, Really?
    (pp. 271-286)

    Nothing in this chapter is relevant to biologists considering light in their work, but it is interesting. Also, you might want to know what a weird substance you are dealing with.

    The modern theory of light falls within the field of quantum mechanics. At first glance, quantum mechanics does not seem that strange—its name is based on the fact that light comes in units (i.e., photons) and that electrons have discrete energy states. So far, no big deal. It also includes the uncertainty principle, which states that you cannot know certain pairs of physical properties with perfect precision. Using...

  14. APPENDIX A Converting Spectral Irradiance to Lux
    (pp. 287-289)
  15. APPENDIX B Calculating the Absorbance Spectrum of a Visual Pigment
    (pp. 290-291)
  16. APPENDIX C Refractive Indices of Common Substances
    (pp. 292-292)
  17. APPENDIX D Optical Properties of Very Clear Water
    (pp. 293-294)
  18. APPENDIX E Optical Properties of Natural Waters
    (pp. 295-296)
  19. APPENDIX F Useful Formulas
    (pp. 297-301)
  20. APPENDIX G Equipment and Software Suppliers
    (pp. 302-306)
    (pp. 307-318)
  22. INDEX
    (pp. 319-336)
  23. [Illustrations]
    (pp. None)