The Importance of Defense Mechanisms
Corals are sessile, colonial organisms, forever fixed in a certain position by attaching as young polyps to a substrate such as a rock or existing coral. This makes the ocean a very dangerous place for these immobile animals. However, in an effort to combat their immobility, many corals have developed different types of defense mechanisms to protect themselves from the ocean's looming dangers--leading to the production of some of the most lethal toxins found in nature.  In this sense, chemical defense is vital to the life of the coral, whose life depends upon its ability to protect itself from predators and invasive species. In fact, some 73% of all coral is toxic to fish, and most of the other species of coral maintain some physical type of defense mechanism to protect against fish predation. 
Chemical Defense Mechanisms
Bioluminescence has been observed for millennia and found its way into myths and folklore of multiple ethnicities, including Polynesians, Siberians and Scandinavians. Although fireflies were first reported in religious writings from India and China, bioluminescence wasn’t characterized until Aristotle in the fourth century BCE . In his book, De Anima, he identified luminescence as “cold light” recognizing that it doesn’t produce heat, and he was able to reference multiple luminescent species such as squid, glowworms, and fireflies. Following in the first century CE, Pliny the elder wrote about various bioluminescent organisms, but it was not until much that later that any scientific discoveries were made about the process .
In the 1667, Robert Boyle observed that there was an “air” requirement for the luminescence to occur. Although oxygen had not yet been discovered, his documentation extended beyond simple visual characterization and addressed the chemistry behind the process. Later, in in the 19th century, Raphael Dubois finally identified the necessary components of the bioluminescence: luciferin and luciferase . Shortly after, E.Newton Harvey searched extensively for the luciferin-luciferase system in nature . He was able to isolate some of the components and is responsible for most of our current knowledge of bioluminescence.
How it works
Bioluminescence is the result of a simple, chemical reaction between a substrate, luciferin, and oxygen. Luciferin is oxygenated into an exited state of oxyluciferin, and as the oxyluciferin returns to its ground state, photons of light are emitted. The reaction is catalyzed by either the enzyme luciferase or by a photoprotein. This process produces cold light, meaning that less that 20% of the light generates heat .
In fireflies, the chemical reaction occurs in the following two steps: luciferin + ATP → luciferyl adenylate + pyrophosphate
luciferyl adenylate + O2 → oxyluciferin + AMP + light
[[File:Euprymna_scolopes_-_image.pbio.v12.i02.g001.png|Euprymna scolopes - image.pbio.v12.i02.g001]|320| Bioluminescent Squid]
The bioluminescent color is determined by the arrangement of the luciferin molecules. Species acquire their luciferin through either synthesis or absorption from another species. Midshipman fish absorb luciferin from the “seed shrimp” they consume while other species, such as squid, typically house bioluminescent bacteria in a symbiotic relationship . The color can range all over the visible spectrum for example appearing yellow for fireflies or blue-green in Dinoflagellates. The blue-green color is typical for marine species because it is more easily detected in the deep ocean, and some marine organisms can only process blue-green colors. Some species can even luminesce in multiple colors. The railroad worm is an example of an organism with this capability. Its head glows red and the rest of its body glows green.
While the luciferin arrangement is responsible for the color, the luciferases are responsible for the bioluminescent expression. Most species use their light organs to flash for very short periods of time while other organisms express bioluminescence continuously. This expression can occur locally or throughout an organism’s entire body .
Quorum sensing communication in general with cells and application in reefs
Bacteria communicate with one another using chemical signal molecules. As in higher organisms, the information supplied by these molecules is critical for synchronizing the activities of large groups of cells. In bacteria, chemical communication involves producing, releasing, detecting, and responding to small hormone-like molecules termed autoinducers.. This process, termed quorum sensing, allows bacteria to monitor the environment for other bacteria and to alter behavior on a population-wide scale in response to changes in the number and/or species present in a community..
Difference in bioluminescence and fluorescence
The major difference between bioluminescence and fluorescence is that florescence is not the result of a chemical reaction. In fluorescence, light is simply absorbed and re-emitted, and in the absence of a light source, fluorescence is not possible. Additionally, phosphorescence is a type of florescence involving phosphorus. Through this process light is able to be re-emmited for long periods of time. Glow-in-the-dark stickers are a common example of phosphoresces , but again, without prolonged exposure to a light source, no light can be re-emitted.
Uses in Nature
Most aquatic organisms luminesce in some way. Bio-luminescence is used to startle, as counter-illumination, misdirection, to distract, burglar alarm, sacrificial tag, warning coloration, lure prey, stun or confuse pray, illuminate prey, mate attraction or recognition. .
Locations where the organisms that bioluminesce live
The majority of complex, bioluminescent organisms live deep in the ocean. There is no example of bioluminescence in freshwater species even though some freshwater bodies have comparably low levels of light, similar to the ocean depths. Scientists have ample data to study the phenomenon where it exists, however pinpointing why it doesn't is much more challenging. .
Applications to science
There are many possible applications of bioluminescence and fluorescence. Probably the most important use in science today is with Green fluorescent protein. GFP is used as a reporter gene in many biology laboratories and is essential to modern research. Green fluorescent protein can easily be attached to other genes to mark there presence in a cell making it possible for researchers to trace and monitor the activity of a target gene. Other fluorescent proteins such as red and yellow fluorescent proteins are additionally used to mark and trace gene activity and can be used simultaneously with the GFP to study multiple genes at once.
From an experimental perspective, bioluminescence could also be used to power streetlights or house lamps as an efficient source of light. In addition, it shows potential as a method of signaling for crops. If the plants need water or are unhealthy this could be signaled using bioluminescence, which could revolutionize agriculture worldwide.
Bioluminescence in the news
Many corals possess toxic defense mechanisms for protection. Toxicity levels of different corals were naturally selected for, which has resulted in a direct relationship between how toxic a particular type of coral is and how much nutrition it provides to those who prey upon it. For instance, fish began preying more often upon those corals that had more nutritional benefits, so those corals had to increase their levels of toxicity in order to protect themselves and survive. Corals that had lower nutritional values were less susceptible to predation, so they did not adapt and increase their toxicity levels the way other types had to. 
Despite their toxic defense mechanisms, most corals are relatively harmless to humans, with one exception: fire coral. The particular type of proteinaceous toxin in fire coral affects humans, but only mildly — most reactions just involve stinging pain and inflammatory effects, and the more severe, but rare, side effect is nausea or vomiting . The most common toxins are neurotoxins, and there are three main types. Saxitoxins block sodium channels in the body of species it comes in contact with, causing paralysis and respiratory failure.  Palytoxins act on the antiporters that control cell membrane activity, thus disrupting the proper functioning of kidneys and red blood cells and leading to kidney, respiratory and heart failure. The third common type of toxin, the lophototoxin, causes muscle contractions and potential paralysis or respiratory failure by blocking the synapses where nerves connect with muscles.
Physical Defense Mechanisms
In a cross between a chemical and physical defense mechanism, most corals also have nematocytes for protection — stinging cells on the end of coral tentacles that are used to sting, capture and kill off small prey and neighboring coral in a continuous battle for space. The nematocytes look like double-walled structures that each contain a coiled, venomous thread with a barb at the end, so that when the nematocyte is stimulated either physically or chemically, the thread releases, penetrates its victim's skin and releases poison. 
Nematocysts are incredibly efficient, especially for their small size and relatively simple structure. When the nematocysts are activated, they fire a barb into the potential victim, which is the physical defense aspect. Then, the barb burrows through the skin of the prey and leaves a hollow filament in its wake, and poison is injected into the new space. The poison then immobilizes the prey, protecting the reef. .
A cnidocyte is the explosive, stinging cell that contains the nematocyst. While cnidarians are incredibly diverse in form, every cnidarian has a cnidoycte for protection. Cnidocytes help the usually quite defenseless cnidarians, like coral, capture prey and defend against predators. When the cnidocyte is stimulated, it fires the nematocyte — the coiled, threadlike structure that contains the toxic — through the cnidocyte wall and into the prey.[]
Other Marine Organisms with Unique Defense Mechanisms
The Glaucus nudibranch steals the stinging nematocysts of some cnidarians like jellyfish and uses them against the jellyfish and the nudibranch's own predators. Watch this cool video: http://vimeo.com/84585526
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