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To us, the most conspicuous feature of an animal is its appearance because, as visually oriented creatures, we perceive and respond quickly to varying colors and patterns. This chapter includes descriptions of animal colors and patterns, including physiological explanations of what produces the colors we see and ideas about the evolution of these patterns. Some colors and patterns are not very common in nature (bioluminescence, false heads, and aggressive mimicry), but they are spectacular to see. Others (seasonal forms, countershading) are common but subtle, and those having to do with deception (eyespots, camouflage) can be remarkable. Taken together, these appearances suggest that people are not the only living creatures responding strongly to what can be seen; clearly, vision is very important to many animals.

This chapter explains how humans, and nearly all animals on Earth, witness astonishing variation in their optical environment. Brightness changes by many orders of magnitude each day, and colors also shift dramatically. Those animals that enter forests and especially the water experience even larger changes. Given this, it is surprising that nearly all the natural light on Earth ultimately comes from two sources, the sun and bioluminescence. A final source of light that is potentially relevant to vision is mechanoluminescence. In this process, light is produced by mechanical processes, including deformation (piezoluminescence), fracturing (triboluminescence), and crystallization (crystalloluminescence). The latter two have been suggested as being at least partially responsible for ambient light at deep-sea vents.

This chapter considers if and why lightening the ventral regions (through pigmentation or bioluminescence) can act to make an organism more difficult to detect as a three-dimensional object. The most common explanation for this is that countershading acts to cancel out shadowing since more organisms are generally lit from above. This and alternative hypotheses are compared to the available empirical data in an attempt to evaluate the importance of countershading to crypsis and its ecological distribution.

This chapter examines light emission. There are only a few ways of making light, the main two categories being (1) thermal radiation, where light emission is related to the temperature of an object, and (2) luminescence, where light emission is related to specific changes in the energy levels of molecules. Other possibilities, such as light produced when matter meets anti-matter, are not likely to matter in biology. With few exceptions, light in the biological world ultimately comes from two sources, the sun and bioluminescence, which are exemplars of the two main mechanisms of light emission. The chapter also looks at mechanoluminescence and sonoluminescence.

This chapter looks at fluorescence. Fluorescence does not make light. This misunderstanding comes in two ways. 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. Because phosphorescence is closely related to fluorescence, the latter term has joined the party and is also often used synonymously with bioluminescence. While this mislabeling is ubiquitous, it is less pernicious than another misunderstanding, in which, while it is accepted that fluorescence is not bioluminescence, it is still believed that fluorescence makes light. Fluorescence can never make light, it can only take it away. Moreover, fluorescence cannot add more optical energy to the system.

The bioluminescence of Malaysian fireflies shows extremely precise synchronization, implying that each animal possesses an intrinsic timing device allowing synchronization of all animals in the swarm. A similar effect leads to the synchronization of coupled metronomes.

This chapter discusses deep-sea life, the largest life habitat on Earth. It focuses on the diversity of organisms living in the mesopelagic and bathypelagic depth zones of the ocean—that is, the twilight zone and the completely dark zones. The chapter examines the role of bioluminescence and other special adaptations that control the behavior of deep-sea animals. It also discusses depth zonation, systematic measurements of light transmission in the sea, and vertical migration. Vertical migration is an integral part of life in the mesopelagic zone—the migrating animals come up to feed and go down to hide. Among the fishes of the twilight zone, the lanternfishes and the hatchet fishes are prominent participants in daily vertical migration.

Below the euphotic epipelagic zone is the realm of deep-sea fishes. The depth zones of this major portion of the earth's oceans have been characterized by the physical features and types of organisms present. Many deep-sea fishes are bioluminescent, even though light production would seem to make them stand out in their dark world. The photophores of many mesopelagic and bathypelagic fishes are, however, arranged in rows along the ventral surface of the animal. These are thought to provide counterillumination by producing light that is similar to the ambient light in color, intensity, and angular dispersion. Near the seafloor of even the world's deepest oceans, one finds that the fishes are typically much larger, more substantial, and usually more active than those of the overlying midwaters. This chapter also presents general differences in the characteristics of fishes from the epipelagic through the benthopelagic regions of the open ocean.

Ever since life’s debut on the earth, biotic evolution has been a near-balancing act. On virtually every level, competition and cooperation, shifting endlessly between foreground and background, have tugged and teased evolving systems as they have wobbled through time along the edge of chaos. The emergence of cellular life from the world of complex carbon-based chemistry appears to have happened only once in the primordial dreamtime of planet Earth. Scientists base this conjecture on a number of virtually universal distributions of chemical structures and processes across the spectrum of living organisms. Despite their perhaps tenuous hold on life, the earliest cells, primitive bacteria and archea, possessed the keys to the opening of new potential for matter and energy—the capabilities of self-replication, controlled energy transduction, directed locomotion, and the regulation of an internal environment. Out of this cellular Big Bang there arose a totally new force field on planet Earth superimposed over the physical, chemical, and geological, but with tendrils pervading all of those realms. It was the beginning of the biosphere. Life pervaded and began to transform the lithosphere, hydrosphere, and atmosphere. The chapter highlights transitions of prokaryote to eukaryote via endosymbiosis. Also featured are: biofilms, bioluminescence, coral reefs, and ecological succession.

This chapter describes the blue moon phenomenon, the effect of anomalous aerosol light scattering, and the red tide and dead fish event caused by dinoflagellate and Gymnodinium brevis. Various studies on rhythmic leaf movements, circadian rhythm, and their control by the endogenous biological clock are presented. The chapter also discusses the incidence of bioluminescence in Gonyaulax polyedra, its mechanism, what causes it, and clock control. The role of melatonin in rhythms, biological rhythm research, and the circadian clock of Gonyaulax and its knowledge and usefulness are emphasized.

This chapter discusses interactions between microbes and higher plants and animals. Symbiosis is sometimes used to describe all interactions, even negative ones. The chapter focuses on interactions that benefit both partners (mutualism) or one partner while being neutral to the other (commensalism). Microbes are essential to the health and ecology of vertebrates, including Homo sapiens. Microbial cells outnumber human cells on our bodies, aiding in digestion and warding off pathogens. In consortia similar to the anaerobic food chain of anoxic sediments, microbes are essential in the digestion of plant material by deer, cattle, and sheep. Different types of microbes form symbiotic relationships with insects and help to explain their huge success in the biosphere. Protozoa are crucial for wood-boring insects; symbiotic bacteria in the genus Buchnera provide sugars to host aphids while obtaining essential amino acids in exchange; and fungi thrive in subterranean gardens before being harvesting for food by ants. Analogous to some insect–microbe relationships, wood-boring marine invertebrates depend on microbes for digesting cellulose and other biopolymers in wood. At hydrothermal vents in some deep oceans, sulphur-oxidizing bacteria fuel an entire ecosystem where symbiotic bacteria support the growth of giant tube worms. Higher plants also have many symbiotic relationships with bacteria and fungi. Symbiotic nitrogen-fixing bacteria in legumes and other plants fix more nitrogen than free-living bacteria. Fungi associated with plant roots (‘mycorrhizal’) are even more common and potentially provide plants with phosphorus as well as nitrogen.

This chapter provides an overview of the structure and function of insect photoreceptors, highlighting some problems (and solutions) peculiar to aquatic insect taxa. The physical properties of light underwater are described and their potential restrictions considered throughout the subsequent discussions of visual function. First is a discussion of the basic structure and the different types of compound eye, and the basic optical units, the ommatidia. The structure of compound eyes influences how they function, including image formation, movement detection, resolution, sensitivity to light levels, and wavelength (e.g., colour vision and polarization sensitivity). The following sections consider the other eye types, ocelli and stemmata, which are less complex than compound eyes, but still provide important kinds of photosensory information to aquatic insects. The final section provides a brief discussion of bioluminescence, which a few aquatic insects use in communication.

The book ends with a chapter devoted to discussing interactions between microbes and higher plants and animals. Symbiosis is sometimes used to describe all interactions, even negative ones, between organisms in persistent, close contact. This chapter focuses on interactions that benefit both partners (mutualism), or one partner while being neutral to the other (commensalism). Microbes are essential to the health and ecology of vertebrates, including Homo sapiens. Microbial cells outnumber human cells on our bodies, aiding in digestion and warding off pathogens. In consortia similar to the anaerobic food chain of anoxic sediments, microbes are essential in the digestion of plant material by deer, cattle, and sheep. Different types of microbes form symbiotic relationships with insects and help to explain their huge success in the biosphere. Protozoa are crucial for wood-boring insects, symbiotic bacteria in the genus Buchnera provide sugars to host aphids while obtaining essential amino acids in exchange, and fungi thrive in subterranean gardens before being harvested for food by ants. Symbiotic dinoflagellates directly provide organic material to support coral growth in exchange for ammonium and other nutrients. Corals are now threatened worldwide by rising oceanic temperatures, decreasing pH, and other human-caused environmental changes. At hydrothermal vents in some deep oceans, sulfur-oxidizing bacteria fuel an entire ecosystem and endosymbiotic bacteria support the growth of giant tube worms. Higher plants also have many symbiotic relationships with bacteria and fungi. Symbiotic nitrogen-fixing bacteria in legumes and other plants fix more nitrogen than free-living bacteria. Fungi associated with plant roots (“mycorrhizal”) are even more common and potentially provide plants with phosphorus as well as nitrogen. Symbiotic microbes can provide other services to their hosts, such as producing bioluminescence, needed for camouflage against predators. In the case of the bobtail squid, bioluminescence is only turned on when populations of the symbiotic bacteria reach critical levels, determined by a quorum sensing mechanism.

The propagation of light in the sea is of interest in many areas of oceanography: light provides the energy that powers primary productivity in the ocean; light diffusely reflected by the ocean provides the signal for the remote sensing of subsurface constituent concentrations (particularly phytoplankton pigments); light absorbed by the water heats the surface layer of the ocean; light absorbed by chemical species (particularly dissolved organics) provides energy for their dissociation; and the attenuation of light with depth in the water provides an estimate of the planktonic activity. Engineering applications include the design of underwater viewing systems. The propagation of light in the ocean-atmosphere system is governed by the integral-differential equation of radiative transfer, which contains absorption and scattering parameters that are characteristic of the particular water body under study. Unfortunately, it is yet to be shown that these parameters are measured with sufficient accuracy to enable an investigator to derive the in-water light field with the radiative transfer equation (RTE). Furthermore, the RTE has, thus far, defied analytical solution, forcing one to resort to numerical methods. These numerical solutions are referred to here as “simulations.” In this chapter, simulations of radiative transfer in the ocean-atmosphere system are used (1) to test the applicability of approximate solutions of the RTE, (2) to look for additional simplifications that are not evident in approximate models, and (3) to obtain approximate inverse solutions to the transfer equation, e.g., to derive the ocean’s scattering and absorption properties from observations of the light field. The chapter is based on a lecture presented at the Friday Harbor Laboratories of the University of Washington directed to both students and experts. For the students, I have tried to make the material as self-contained as possible by including the basics, i.e., by providing the basic definitions of the optical properties and radiometry for absorbing-scattering media, developing the approximate solutions to the RTE for testing the simulations, detailing the model used for scattering and absorbing properties of ocean constituents in the simulations, and briefly explaining the simulation method employed. For the experts, I hope I have provided some ideas worthy of experimental exploration.