Physics of Life 4. Wave phenomena

Introduction to wave phenomena, focusing on electromagnetic radiation.

Wave phenomena include light and sound, which are fundamentally means of transmitting energy through waves: waves of elastic deformation in the case of sound, and waves of electromagnetic energy in the case of light. Wave transmission of energy, even in such disparate forms as electromagnetic radiation and sound, are described in fundamentally similar ways, including amplitude, wavelength, frequency, speed of transmission and so forth.

KW: sound; light; decibel; frequency; wavelength; transmission speed; electromagnetic energy;

Electromagnetic energy includes a broad range of wave phenomena, ranging from thermal radiation with very long wavelength, to gamma rays with very short wavelength. Light occupies only a very narrow band of this larger electromagnetic spectrum. Electromagnetic energy expresses two phenomena that otherwise might seem distinct: electricity and magnetism. They are in fact two dimensions of the same phenomenon.

KW: electromagnetic spectrum; magnetic induction; electron state; photon; thermodynamic temperature; cosmic ray; gamma ray; Planck’s law; wavelength; energy; color temperature; black body; Wien’s displacement law; solar spectrum;

Earth climate is fundamentally an energy balance that resolves energy inputs from solar radiation and ultimate loss of energy to the universe. These two streams of energy occur at very different bands of the electromagnetic spectrum, short-wave radiation from the sun, and long-wave radiation to the universe. Climate change boils down to understanding this energy balance.

KW: electromagnetic spectrum; solar energy spectrum; short-wave infrared; long wave infrared; solar temperature; atmospheric absorptance, carbon dioxide; water vapor; optical transmittance;

The key to understanding climate and climate change is the transmission and storage of incoming solar energy as the energy makes its way to ultimate loss to the universe. In this, the distribution of heat in oceanic and atmospheric currents plays a crucial role.

KW: oceanic conveyor; atmospheric circulation; Hadley cell; Ferrell cell; polar cell; water vapor; carbon dioxide; atmospheric opacity; long wave infrared; paleoclimate; ice age; interglacial; Cenozoic; solar energy output;

The Earth has a strong magnetic field, with lines of magnetic flux that run north to south. The lines of magnetic flux are oriented horizontally (north to south) but also have a vertical orientation that varies with latitude (vertical near the poles, horizontal at the equator). These provide a means for organisms to orient themselves with the magnetic field. The magnetotactic bacteria provide a striking illustration of this. These micro-organisms use the Earth’s magnetic field to orient their swimming so as to maintain them in their preferred habitat.

KW: magnetic field; vertical orientation; magnetic flux lines; magnetotactic bacteria; ferromagnetism; magnetosome; oxic zone; anoxic zone; sediments; oxic-to-anoxic transition zone; magnetite;

Navigation using a magnetic field involves knowing heading, that is the direction of travel with respect to some reference. Our magnetic navigation uses magnetic north as that reference. Various animals, like sharks, can use the magnetic field to navigate, but they do so in a different way. Sharks are conductors of current, and their moving through a magnetic field induces electric currents around them, which depend upon compass heading. The sharks sense their self-generated electric fields using electric field sensors like the ampullae of Lorenzini.

KW: shark; magnetic sense; electrical induction; electroreceptor; ampullae of Lorenzini; magnetic field; navigation; heading;

The weakly electric fish also use an electrical sense to navigate about their environment. In this instance, the electric field is generated by the fish itself using an electric organ, a living galvanic cell. The electric organ consists of modified muscle tissue that has been restructured to generate a high-frequency high-voltage AC electrical field.

KW: electric fish; galvanic cell; axial muscles; weakly electric fish; electric organ; membrane voltage; electroreceptors; AC electric field; electro plaque;

The weakly electric fish use their self-generated electric field to map their external environment. Depending upon the placement and orientation of objects in the environment that either conduct or impede the flow of current generated by the electric organ, this alters the distribution of current on the fish’s electroreceptors. These fish even use their electric organs as a means of communication with other electric fish.

KW: electric fish; galvanic cell; axial muscles; electro plaque; membrane voltage; electroreceptor; AC electric field; electrical current; mapping; cognition;

Magnetism is one significant dimension of electromagnetic wave phenomena. The earth has a powerful magnetic field, and this has a significant protective effect shielding the atmosphere against the powerful force of the solar wind, a stream of highly charged particles that radiates from the sun and streams toward the earth. At times, this protection can be overwhelmed by magnetic storms on the sun known as coronal mass ejections, which can have significant disruptive effects on the atmosphere.

KW: magnetic field; atmosphere; solar wind; Aurora; aurora borealis; aurora australis; coronal mass ejection; photosphere; sun; magnetic storm;

The Earth’s magnetic field is generated by fluid motions of iron rich minerals in the Earth’s outer core. The magnetic field comes from a so-called dynamo effect whereby energy of motion in a flowing ferromagnetic fluid is transformed into potential energy in a magnetic field.

KW: dynamo; magnetic field; magma; outer core; fluid motion; ferromagnetic element; iron;

Because the Earth’s magnetic field is a fluid phenomenon, it can change depending upon how the molten ferromagnetic minerals in the outer core flow. This can be seen in the well-known wandering of the magnetic poles, but is evident far more dramatically in the periodic reversals of the magnetic field that occur on average every 200,000 years or so. These dramatic changes in the magnetic field can have significant effects on the Earth’s atmosphere, because at those times, the protective shield of the magnetic field against the solar wind disappears.

KW: magnetic field; ferromagnetic minerals; magma flow; magnetic field reversal; Rayleigh-Taylor mixing; Kelvin-Helmhotz mixing; solar wind; atmospheric stripping; atmospheric composition;

The dramatic atmospheric effects of a magnetic field reversal make it likely that such periods would be accompanied by substantial changes in atmospheric composition and climate. This may have dramatic effects on the Earth’s biota, and this is reflected in the rough correlation of extinction rates and mass extinction events with periods of rapid magnetic field reversal.

KW: magnetic field reversal; atmospheric stripping; atmospheric composition; climate change; volcanism; extinction rates; mass extinction; Radiolaria;

Visible light namely the electromagnetic radiation that we can see, occupies only a very small band of the electromagnetic spectrum. This raises the obvious question: why is it only those wavelengths that can be sensed by photo receptors cells? Answering that question requires that we understand something about how photo receptors cells interact with light. Central to this ability are specialized molecules known as visual pigments, of which rhodopsin is the most common.

KW:: vision; light; visible spectrum; photoreceptor; rhodopsin; visual purple; retinal; opsin; phototransduction;

Electromagnetic radiation can carry information, which can be transmitted to antennas that are designed to intercept electromagnetic energy and converted into electrical current: induction, in a word. It is no different with vision. There must be some kind of antenna-a light antenna, if you will-, that can intercept the energy in the narrow band of electromagnetic radiation that is light, and use that to mobilize electrons to do the work of phototransduction. Part of the reason why the visible spectrum is so narrow is that light antennas are structured to capture energy within that narrow band.

KW: light antenna; rhodopsin; retinal; opsin; antenna design; wavelength; broadcast frequency; impedance; tuning; absorptance spectrum;

In visual pigments, variation in the opsin can tune a visual pigment to respond preferentially to particular wavelengths. This is the foundation of the ability to sense color, that is to discriminate between light of different wavelengths. In the vertebrate eye, this variation in absorptance is reflected in different kinds of photoreceptor cells that absorb light at different wavelengths. Despite there being many different types of visual pigments to be found among the eyes of vertebrates, all depend upon tuning of the interception of photons by retinal to different wavelengths.

KW: color vision; rods; cones; photoreceptor; absorptance spectrum; humans; mammals; bird; salamander; goldfish; retinal; opsin; tuning; phototransduction; ciliary photoreceptor; rhabdomeric photoreceptor;

Light is a rich medium of communication, because it can carry information in two separate sources of variation: wavelength, which is sensed as color, and amplitude, which is sensed as brightness. Light also can carry information in a third band, the so called plane of polarization. Sensitivity to the plane of light polarization is prevalent in the rhabdomeric photoreceptors of insects and other invertebrates. These creatures are able to use polarized light sensitivity as a means of navigation by sun compass.

KW: polarized light; plane of polarization; rhabdomeric photoreceptor; microvilli; sun compass navigation; insect; compound eye; ommatidium;

Visible light occupies only a narrow band of the electromagnetic spectrum, and this limitation is due to at least two factors. The first is the design limitations of light antennae, which must be small to correspond to the very small wavelengths of visible light. Cellular photo receptors meet that size criterion of light antenna design. Additionally, photo reception requires sufficient energy to excite electrons in photo receptors without imparting so much energy that the visual pigments and photo receptors suffer damage.

KW: visible light; visible light spectrum; electron energy; phototransduction; light antenna; wavelength; tuning;

Light is a medium for transmission of information, because information can be encoded in at least four independent channels: wavelength, amplitude, plane of polarization, and modulation with time. Living things have exploited the potentialities of this medium of communication in some extraordinary ways.

KW: light; wavelength; color; amplitude; brightness; polarized light; encoding; communication;

Living things can manipulate color through the use of pigments, which are molecules that selectively absorb certain wavelengths of visible light, allowing others to be transmitted, and in part to the pigment is color. Most biological pigments fall into two broad classes: the carotenoids, and the xanthophylls. The particular wavelengths that are absorbed depends upon the number and placement of alternating double bonds in these molecules.

KW: carotenoid, xanthophyll, pigment, transmission, absorption, alternating double bonds, super orbitals, absorptance spectra;

Carotenoid and xanthophyll pigments impart colors in the red to yellow ranges. Colors on the other end of the spectrum, the violets, blues, and greens, arise from a different mechanism known as interference color. Interference color depends upon the manipulation of wavelengths through the use of multiple and closely spaced reflective surfaces.

KW: structural color; melanin; retraction; constructive interference; destructive interference; interference color; iridescence; viewing angle;

Skin color is a means of signaling using light. Among the fishes and amphibians and reptiles, skin color is changeable, and this is due to a specialized set of cells in the skin known as the dermal chromatophore unit. The dermal chromatophore unit includes cells that filter incident light through pigments, reflect it off of colored granules, and generates iridescent color.

KW: carotenoid; xanthophyll; dermal chromatophore unit; melanophore; xanthophore; iridophore; filtering; melanin; guanine; structural color;

Iridescent colors can also arise from birds feathers, which generate iridescence through an entirely different mechanism from the reflecting plates of an iridophore. Blue colors arise from Tyndall scattering through arrays of keratin fibers in the feathers, and iridescence arises from incoherent scattering of light from numerous tiny voids within the feather shaft, the same mechanism that produces the brilliant colors of a rainbow.

KW: feather; iridescence; Tyndall scattering; refraction scattering; incoherent iridescence; coherent iridescence;

Iridescence is a phenomenon of reflected ambient light. It can also arise from self generated light in the form of bioluminescence. Bioluminescence is a phenomenon largely bacterial in origin, and many animals use bioluminescence through symbiotic associations with bioluminescent bacteria. These associations are exploited by animals in a variety of ways, including the use by squids of bioluminescence to provide a form of camouflage related to the well-known phenomenon of counter shading, namely counter illumination.

KW: symbiosis; Vibrio fischeri; squid; Euprymna scolopes; light organ; counter shading; counter illumination; metabolic control; bioluminescence; signaling; switching;

Many animals use light as a kind of semaphore signaling, encoding messages in patterns and rates of flashing light. Bioluminescence that arises from bacterial symbionts is on more or less constantly, but various animals like the flashlight fish in squids can modulate light output by occluding the light organ various means. Flashlight fish blink, covering the light organ with a shade, and squids use irises over the assemblages of skin cells called photophores. In the case of the squid, signaling can be encrypted using polarized light.

KW: flashlight fish; squid; semaphore; signaling; photophore; blink; polarized light; encryption;

Sound is the propagation of an elastic wave of pressure through a medium, which can include fluids as well as solids. Sound generation is basically a thermodynamic problem, with work being done on a vibrating surface, with the vibrating surface doing work on the medium in three forms, known as inertial work, capacitative work, and dissipative work. Of the three, dissipative work is sound. For animals creating sounds efficiently, the challenge is to maximize the energy devoted to dissipative work, and to minimize the energy devoted to inertial and capacitative work.

KW: sound; energy balance; elastic wave; inertial work; capacitative work; dissipative work;

A common way to maximize sound production efficiency is to reduce the amount of energy that goes into other forms of work, including inertial work and capacitative work. A very simple method for eliminating inertial work entirely is to surround the sound generator with a baffle. Baffles are commonly found in sound generating structures of insects, including the cricket, in which the vibrating membrane is surrounded by the stiffer membranes of the wing. Baffles can also be constructed from things like leaves, which some crickets used to enhance their own sound production.

KW: sound; inertial work; dissipative work; baffles; loudspeaker; vibrating membrane; cricket; leaves;

Another way of increasing sound production efficiency is to reshape broad-spectrum sound into particular bands of frequency. Musical instruments, like organ pipes, do this. In an organ pipe, broad-spectrum turbulence is channeled into resonant musical notes, which consist of a fundamental frequency, and a number of overtones, or harmonics. This structure of sounds arises from the production of standing waves inside a resonating pipe.

KW: sound; organ pipe; resonant frequency; fundamental frequency; overtones; harmonics; spectrogram; frequency spectrum; bird song; syrinx; body size;

Resonant pipes, like organ pipes, are not perfect emitters of sound, in part because sound energy within the pipe can be reflected back into the pipe, making it unavailable for projection from the pipe. This is a problem of capacitative work, and this can be minimized by encasing the sound generator in an exponential horn, which reduces these reflections almost to nothing. Certain animals, mole crickets, and hence sound production by singing from burrows that are shaped like an exponential horns.

KW: sound; resonance; horns; Klipsch horn; mole cricket; Gryllotalpa; exponential horn; conical horn;

Sound is produced by vibration, either of a vibrating string, or of a vibrating membrane. These vibrating structures exhibit the same kind of resonant phenomena that one sees in organ pipes, and these are commonly employed in sound producing organs of animals, including the larynx of mammals, and the syrinx of birds.

KW: sound; resonance; vibrating string; vibrating membrane; larynx; syrinx; modes of vibration;

Quality of sound is a property distinct from simple amplitude and frequency, and this constitutes an independent channel for communication. Quality of sound is expressed in a property known as timbre. Different musical instruments have different sounds because they have different timbres, and this comes about by the different instruments shaping the sound in particular ways. Timbre is a phenomenon of voice as well, and this is shaped by various so-called formants, which can include dynamic changes in shape of the trachea, oral cavity, and nasal cavity.

KW: timbre; formant; amplitude; frequency; speech; vowels;

For sound to be a communications medium, it must be projected. In other words, the intensity of sound at the receiving end of a sound message should be loud enough for the receiver to hear it. Working against effective communication is the property of attenuation, which is the diminishing of sound intensity with distance from the sound transmitter. This property shapes the ability of animals to use sound as a communications medium, and there are various clever tricks that animals use to be able to circumvent attenuation.

KW: attenuation; inverse square attenuation; viscous attenuation; body size; bats; elephants; infrasound; ultrasound; sound bubble;

Bats use sound as an echo locating device. However, bats face a significant physical limitation that stems from their small body size. Specifically, bats can emit sounds mostly in the ultrasound range. Viscous attenuation is particularly high at these frequencies. Therefore bats must shape the projection of their sound in various ways, to ensure that sound energy is more directed. This they do by molding their faces into very sophisticated reflectors.

KW: bats; echolocation; ultrasound; reflection; faces; ranging; sound bubble; auditory threshold;

Echolocation in bats involves some sophisticated manipulation and encoding of sound signals. To range properly, bats must be able to associate chirps with returning echo’s, and this bats do by modulating chirp intervals as they fly, hunt, and close in on their prey. Bats also have some sophisticated ways of encoding their chirps to not only provide information on range to pray, but also to enable sound to be an effective substitute for vision in these creatures.

KW: bats; echolocation; CF bats; constant frequency bats; FM bats; frequency modulation bats; CF/FM bats; chirp interval; pipistrelle bat;

Sound is energy, and this means that sound can be used to do work, sometimes very strenuous work as in when sound can be used as a weapon. In many cases, weaponized sound comes from its modification of other uses for sound, such as echolocation. The next four lectures will look at weaponized sound, concentrating on marine animals. In this lecture, we look at how dolphins use sound generally employed for echolocation to direct very energetic sound beams forward, which can kill or disable the fish upon which they prey.

KW: sound energy; sound focusing; melanin; dolphin; sound reflector; sound echolocation; sound intensity;

One of the most impressive creatures in the sea is the sperm whale, marked by the distinctive box shaped profile of its head. The head is shaped in this way because it houses a large acoustic lens in the form of the so-called melon. The sperm whale also has a number of other adaptations for focusing intense sound beams forward and direction. The sound beams can be intense enough to stun or kill the giant squid upon which these whales typically prey. The sperm whale is also unusual in that it must generate the sounds during a breath hold dive, which means it has to have mechanisms for recycling air within the air spaces of the lungs and head.

KW: sperm whale; melon; acoustic beam; air recycling; monkey lips; giant squid;

Killer whales also are known to weaponized sound, but they produce weaponized sound in an entirely different way. Even though killer whales have a well developed echolocation sense, they do not use vocalizations as a means of disabling prey. Rather these creatures employ the chaotic sound that follows the production of cavitation bubbles, that result from the forceful downward slap of its tail flukes. In combination with other hunting tactics, the sound produced by the thousands of cavitation bubbles following a tail slap are sufficient to confuse and disorient their prey, enabling them to more easily capture the fish.

KW: killer whale; hunting; turbulent; cavitation bubble; law of Laplace;

It’s not just large animals like killer whales that produce cavitation bubbles. Small animals can do so as well, and sometimes to lethal effect. One such creature is the pistol shrimp, which uses stored energy in elastic tissues and its large claw to generate cavitation bubbles in a jet that is directed forward from the claw. The cavitation bubble is produced by a great deal of energy, and the bubbles collapse is accompanied by the release of large quantities of energy. The energy so released is sufficient to kill or stunned the small shrimp or fish that these creatures prey upon.

KW: pistol shrimp; cavitation bubble; plasma temperature; bubble collapse; law of Laplace; supersonic; shockwave;