His exalted name, “Light,” touches the darkness
and everywhere is filled with light.
The letters written from a brilliant world
are revealed to the hearts;
Then the Divine command,
“Read in the name of your Lord!”
descends and becomes our intentions.

We look around the Earth and believe that we start to sail into the dark upon reaching the depths of the skies, the land, and the oceans. But if we look with care, we may notice that the inhabitants of those places often inform us of the beauties they are created with.

The depths of the oceans, especially, are where what we see leave us amazed. From microscopic bacteria to giant squids, and from tiny lighted jellyfish to spiny skin, many creatures, from ascidians to some sharks and stingrays, turn on their lights, literally, illuminating the darkness of the deep sea. This biological light-producing process in the body of some animals is called bioluminescence. It is astounding that these creatures can emit biological light with no change in their body temperature. Normally, light is formed by emitting heat. This basic principle applies to some of the most common sources of light that we know of, such as campfires and electrical lightbulbs.

A mechanism that produces light without heat has been created in some insects living under the sea as well as those on land. The basis of biological light production is generally the oxidation of luciferin, i.e. its conversion to oxyluciferin. The enzyme necessary for this chemical reaction to occur is luciferase.

Most living creatures that can produce bioluminescence live in deep, dark areas of the world’s various seas and oceans. Some of the inhabitants of these depths emit strong blue (secondarily green) light at an average wavelength of 475 nm. An interesting note is that underwater life forms are often created with sensitivity to the wavelengths of blue-green lights mentioned above. In rare cases, there are also sea creatures that emit light in the yellow-red wavelength range.

Animals with the ability to emit light are also usually given excellent control mechanisms so that they can use their equipment as a weapon. They can turn their lights on and off in a flash and can utilize complex chemical and neurological mechanisms that provide functions such as adjusting the intensity, color, and direction of the light. Creatures that produce light underwater sometimes do not need to use the light in order to see where they are going. Instead, they tend to use these marvelous gifts in a variety of strategic ways. Some will try to attract the attention of their prey; others will attempt to ward off predators and aggressors; still others will use their lights to indicate that they are ready for reproduction. It is even possible for some creatures to utilize several of these functions at the same time.

Let us now examine some specific species and how they employ bioluminescence.

Light vomiting shrimp

One of the most interesting examples of bioluminescence in animals is the light-emitting deep-sea shrimp Acanthephyra purpurea. This shrimp will actually vomit light from its mouth as a last-ditch effort to deter predators. The intent is to disorient, confuse, and even temporarily blind other creatures, similar to the effect of a flashbang grenade, so that the shrimp can retreat into the dark. As a result of their research on the shrimps, marine biologist Edith Widder states that the chemical substances sprayed are not blue when they are in the body and that the blue light production occurs when the luciferin substance in the sprayed liquid comes into contact with the oxygen in water.

Loosejaw fish

There are at least 42 recorded families of bony fish that have bioluminescent properties. One of them is the Photostomias guernei, or the “loosejaw fish”. This fish has a remarkable organ that emits light on the sides of its eyes. These lights, which resemble the headlight lamps of our cars, are not constantly lit, in order to avoid waste. When hunting, the fish illuminates the way ahead with the light it produces, and it can turn these lights off when they are no longer needed. A wonderful feature of this organ is that, just like headlights, a highly reflective layer is created behind the main center of the light. The reason that the fish is able to turn the light off may be because its black velvety body is contrasted by the light color of the organ and would thus attract much unwanted attention.

Deep sea hatchetfish

Bioluminescent systems were also given to creatures in order to act as a means of camouflage. They work phenomenally for both hunting and survival in situations where blending in with the environment is paramount for catching prey or evading predators. In the depths of the underwater world, the silhouette of an animal bathing in light is an easily recognizable target. One of the best examples of this phenomenon is the deep-sea hatchetfish. The fish has been created with its eyes on top of its body and its mouth facing upwards, making it easier to hunt. It also emits bioluminescence from its abdomen to provide camouflage against more aggressive, larger fish that swim lower than itself. The color of the light emitted makes it difficult to recognize the fish from below as it perfectly matches the color intensity of the environment. In the meantime, if the sunlight that hits the sea is interrupted in any way, the fish will turn off its lights and the camouflage will continue.

Black dragonfish

Diversity in the light organs of the scaleless black dragonfish (Melanostomias bartonbeani)

This species of black dragonfish (Melanostomias bartonbeani) takes advantage of luminescence in a number of ways. An illuminated area next to the eyes is used to find prey and send signals to its mates. The black dragonfish’s chin also has an illuminated extension that dangles in the waves as bait for naive prey. In addition, a set of small organs of light arranged along its abdomen play a role in concealing its silhouette. Furthermore, light-emitting pocket-like structures surrounded by a gelatinous capsule embedded in the skin are used as alarm systems. The bioluminescent systems within this creature are immensely complex and beautiful, and when observed in detail reveal the dazzling splendor of the world that we live in.

Fish with 3 different types of illumination

The Northern Stoplight Loosejaw (Malacosteus niger) has three different types of light organs, the complex use of which cannot be possible without top engineering skills. The wide, drop-shaped, illuminated organ under its eyes emits a red light at a wavelength of 702 nm as if it knows the laws of optics under the sea. This red light is not visible to most deep-sea creatures, for it is quickly absorbed in water. Yet, with this red light this fish is able to have vision in a close proximity while remaining largely undetected. This is similar to infrared binoculars soldiers use for night vision without giving away their position. The loosejaw is thus a dangerous hunter that has an edge over its prey. There also exists a blue light-emitting oval section, behind the organ, that emits red light and is usually larger in males. A third light organ is round and smaller and is located between the eyes and the red-light organ.

Angler fish

The angler fish is one of the most iconic fish of the deep ocean due to its famous rod and bioluminescence. The angler fish does not actually produce its light on its own: the light is credited to bioluminescent symbiotic bacteria that inhabit the end of the rod on their forehead. This illuminated part, which resembles a worm-like bait, is very attractive to small fish. These fish are thus lured to the angler expecting a quick snack, but instead the angler swallows them whole with its massive mouth. While doing their task of helping the angler hunt small fish, the bacteria maintain a symbiotic relationship with the fish and also find an environment in which to proliferate. In this way, they form a good example of cooperation and solidarity. One may wonder: how can such a mutual agreement come into fruition between a fish and some bacteria which are deprived of a nervous system, mind, and consciousness?

One of the reasons that marine biologists are interested in light-emitting bacteria is the wide-lit regions called the “Milky Seas.” These can be observed in satellite images of Earth. Recently, satellites helped detect a bioluminescent area of roughly 5,946 sq. mi in the Indian Ocean; scientists wondered if some bioluminescent bacteria or Dinoflagellate-type flame-colored algae may be the cause of the phenomenon.

Alarming jellyfish

The luminescence of some marine life serves as an alarm or distress siren. A remarkable example of this is the Atolla jellyfish (Atolla wyvillei), an elegant inhabitant of deep waters. This jellyfish produces blue lights that are spread in circles in the water when it is attacked. Thanks to these lights, it tries to draw the attention of larger and stronger animals than the initial attacker in order to escape from harm’s way.

As can be observed in some species that we are familiar with, such as fireflies, the bioluminescence feature that is full of wisdom granted to some living beings is a thought-provoking biological miracle which does not only make us ponder where they got these abilities from but also reveals how so many intricate patterns are found in nature.

References

• Steven H.D. Haddock, Mark A. Moline and James F. Case. 2010. Bioluminescence in the Sea, Article in Annual Review of Marine Science, DOI:10.1146/annurev-marine-120308-081028 Source: PubMed.
• Edith A. Widder. 2001. Harbor Branch Oceanographic Institution, Fort Pierce, Florida, Marine Bioluminescence, Bioscience Explained, vol 1, no 1, pp. 1-9.
• Edith A. Widder. 2010. “Bioluminescence in the Ocean: Origins of Biological, Chemical, and Ecological Diversity,” Science, vol. 328, pp. 704-708.
• www.wired.com/2012/01/glow-little-spewing-shrimp-glow/ March 28, 2018.
• en.wikipedia.org/wiki/Malacosteus_niger / April 1, 2018.
• Harold, A. 2015. Malacosteus niger. The IUCN Red List of Threatened Species 2015: e.T190149A21909439. http://dx.doi.org/10.2305/IUCN.UK.2015-4.RLTS.T190149A21909439.en.
• https://www.iucnredlist.org/species/190149/21909439

Each creation is a work of art. All animals and plants, as well as every human being, are unique and priceless. And those who appreciate their value are like antique dealers as in the passage above. I recently had the chance to listen to such an “antique dealer,” Joanna Aizenberg of Bell Laboratories/Lucent Technologies, and witnessing the appreciation of the valuables she presented to us helped me better understand Said Nursi. Both the valuable object she was talking about and her appreciation of it were equally inspiring for me, and this is the reason why I have decided to share this story with you. Without any further ado, here is the story of a sponge species called the Venus’ Flower Basket and its “eternally” incarcerated residents: a pair of shrimp. Now, you must find what is hiding behind all this; after all, it is the eyes that look but the heart that perceives.

Venus’ Flower Baskets (Figure 1a) are vase-like sponges that grow upright on the sea floor of the Pacific Ocean, mostly around Japan. They have a very sophisticated mesh structure which caused medieval Europeans to assume they were glasswork made in China. In Japan they are called Kairou-Douketsu (together for eternity) and given as wedding gifts, since they generally house a pair of mated shrimp which are trapped in their cavity. As you have probably already understood, our story is about the engineering secrets of these sponges and their relationship with their guests.

The design

The skeleton of the Venus’ Flower Basket is made of silica, which is a very brittle material (remember the glass windows that you broke with your football when you were a kid; they were made with silica). How can these amazing creatures withstand the pressure and the currents present at the sea floor or the disturbance caused by two shrimp? The secret lies in the hierarchical construction of their cylindrical cage-like structure. As can be seen in Figure 1b, their skeleton is made up of beams that run perpendicular and parallel to the axis of the sponge, which forms a rectangular grid. This grid is further supported by beams that run diagonally in both directions. Finally, this whole structure is reinforced by ridges that spiral around. But these are just the macroscopic hierarchical levels of the construction. Now let’s start from the very first level of this hierarchy and try to understand how each level adds to the stability of the sponge.

The basic building block of the Venus’ Flower Baskets is a fiber composed of silica nano-spheres (Figures 1i and 2a) that grows around an organic filament (the black dots at the center of the circles in Figure 1f). Though this fiber is not very stress tolerant, due to the size of the spheres from which it is made, in the next level of hierarchy it is toughened by alternating organic and silica sheets that form a concentric lamellar (fine, alternating layers of different materials) fiber structure. The thickness of each layer in the fiber decreases from 1.5 (: 1/1000 mm) at the center to 0.2 towards the periphery (Figures 1f, 1g and 2b). Hence any crack that is initiated at the periphery is halted at the organic interlayers and while the thinner outer layers lessen the depth of crack propagation, the thicker inner layers enhance mechanical rigidity (in addition to their mechanical stability, these silica fibers are endowed with optical properties which are superior to man-made fibers, which will be discussed later on in the article).

Figure 1. Structural analysis of the mineralized skeletal system of Euplectella sp. (a) Photograph of the entire skeleton, showing cylindrical glass cage. Scale bar, 1 cm. (b) Fragment of the cage structure showing the square-grid lattice of vertical and horizontal struts with diagonal elements arranged in a chessboard manner. Orthogonal ridges on the cylinder surface are indicated by arrows. Scale bar, 5 mm. (c) Scanning electron micrograph (SEM) showing that each strut (enclosed by a bracket) is composed of bundled multiple spicules (the arrow indicates the long axis of the skeletal lattice). Scale bar, 100 mm. (d) SEM of a fractured and partially HF-etched (25) single beam revealing its ceramic fiber-composite structure. Scale bar, 20 mm. (e) SEM of the HF-etched (25) junction area showing that the lattice is cemented with laminated silica layers. Scale bar, 25 mm. (f) Contrast-enhanced SEM image of a cross section through one of the spicular struts, revealing that they are composed of a wide range of different-sized spicules surrounded by a laminated silica matrix. Scale bar, 10 mm. (g) SEM of a cross section through a typical spicule in a strut, showing its characteristic laminated architecture. Scale bar, 5 mm. (h) SEM of a fractured spicule, revealing an organic interlayer. Scale bar, 1 mm. (i) Bleaching of biosilica surface revealing its consolidated nanoparticulate nature (25). Scale bar, 500 nm. Figure and captions from ref. 2.

Fibers of different diameters reinforced this way are then bundled loosely in a silica matrix (Figure 1d and 1f). The different diameter of the fibers in the bundle and the weak lateral bonding between them are essential for increasing the strength of the bundle against crack propagation. At the next level of hierarchy, these bundles are used as building blocks of the cylindrical cage of the sponge, being arranged horizontally and vertically into a square grid. This grid in turn is reinforced by diagonal bundles that run in both directions along every second square lattice. The minimum number of pin-jointed struts (i.e. ones that are free to rotate at the joints) per node needed in order to form a rigid two-dimensional grid has been shown to be six; this is the number present in the skeleton of the Venus’ Flower Basket. In fact, if the diagonal bundles were to run along every square lattice, the number of struts per node would be 8, which would be redundant for the stability in the skeleton.

At the early stages of the growth of the Venus’ Flower Basket the struts are not connected at the nodes. However as the sponge gets older the struts are joined by a silica cement which itself also has a lamellar structure (Figure 1e). Hence, while the younger sponges are flexible, the older ones are stiff; this also has important implications for the symbiotic relation that the sponge has with its guests, the shrimp. (This issue will be discussed in detail when the lifecycle of the shrimp is examined.) While the resulting grid is stable in two dimensions, in three dimensions it may still suffer from exterior effects, such as ovalization. This problem however is solved at the next level of hierarchy by the helical ridges that surround the grid (Figure 1b). The absence of the ridges at the base of the skeleton of the sponge where the cage diameter is small, and their increased density further up the cage where the diameter is much greater is proposed as evidence supporting this argument. Finally, this whole cage structure must be anchored to the sea floor in a way that will withstand the bending stresses caused by the currents. This is managed through the use of the fibers that have been discussed earlier; they are used as connectors between the base of the sponge that is anchored to the sea floor and the vertical struts of the skeleton, resulting in a flexible connection that enables the cage to swing freely in the currents (Figure 1a).

As a conclusion, it can be said that “The resultant structure might be regarded as a textbook sample in mechanical engineering, because the seven hierarchical levels in the sponge skeleton represent major fundamental construction strategies, such as laminated structures, fiber-reinforced composites, bundled beams, and diagonally reinforced square-grid cells to name a few.”

Now let’s concentrate more on the fibers (or spicules) that anchor the cage to the sea floor. These anchorage spicules (a term used for describing the skeletal structures of sponges which comes from the Latin word speculum, meaning the head of a spear or arrow)* are 5-15 cm in length and 40-70 um in diameter. In the above discussion we have briefly discussed the cross-sectional structure of these fibers that gives them their flexible, but resistant nature. Here we will focus on the optical properties of these spicules. But before doing so, let’s briefly explain how optical fibers work.

Optical fibers are silica fibers of a 5 to 80 um diameter that are coated with a cladding layer; light waves can travel in these for long distances by constantly bouncing off the cladding. The reason for this is the refractive index difference between the silica core and the cladding layer. Refractive index (n) is a measure of the ability of a medium to change the phase velocity of light and cause the light waves to bend while leaving one medium and entering another (refraction); in the case of fiber optics, leaving the core and entering the cladding. However, if the refractive index of the second medium is lower than that of the initial one, the incident light waves that have an incidence angle higher than a critical value or critical angle can be reflected back to the first medium and this is what happens in fiber optics (See red ray in figure 2). If the core diameter is small (5-10 um), light rays can propagate only through a single path in the fiber (which runs parallel to the fiber axis), hence these type of fibers are called single-mode fibers (See Figure 2a). If the core diameter is larger however, (60-80 um) several paths are accessible, and more paths will have incidence angles that are greater than the critical angle, hence they are called multi-mode (See Figure 2b).

Now with this information in mind, let’s have a look at the characteristics of the anchoring spicules of the Venus’ Flower Basket. First of all, as mentioned in the previous discussion, the lamellar structure of these spicules prevents crack propagation, which is the main failure mode of commercial silica fibers. This lamellar structure, however, also determines the dependence of the optical behavior of the spicules on the environment in which they are embedded. For instance if the spicules are embedded in an epoxide medium with a refractive index of 1.57, the spicule as a whole would not be able to act as an optical fiber, due to the smaller refractive index of the cladding. However, since the core region of the spicules has a slightly higher refractive index than that of the cladding, the core acts as a single mode fiber in such an environment (see Figure 2a). In sea water-the spicules’ native environment-which has a refractive index of 1.33, the whole spicule acts as a multimode fiber, since the refractive index difference between the core and the cladding is much smaller than that between the cladding and the surrounding sea water.

Another advantage of these spicules over man-made fibers is their formation/production parameters, which are ambient temperature and pressure; these enable the introduction of impurities into the silica. Though at first it may not sound as if impurities are a positive characteristic, these impurities are very important for increasing the refractive index of silica and act as dopants (impurity elements added to a semiconductor lattices in low concentrations in order to alter the optical/electrical properties of the semiconductor). The core section of the spicules, for instance, shows increased sodium concentration, which is the cause of the higher refractive index of this section. Such dopant introduction in the silica during the fabrication process, however, is not possible in the case of man-made fibers, due to the very high processing temperatures.

In addition to this, the spicules have crown-like caps at their base and thorn-like structures throughout their middle section. While the crown-like termini most probably are used to anchor the sponge to the ocean floor, it has also been shown that the waveguiding efficiency of the spicules increases when the illumination comes through the end that has the crown-like structure. Hence, it has been proposed that this structure may be acting as a light harvesting lens. The thorn-like structures, on the other hand, share the lamellar construction of the spicule body, and the light guided through the body branches out to these spines and emerges at the tip. Since sea water comes into contact with the tip at an almost perpendicular angle to the guided light, the coupling is pretty efficient. Hence the combination of crown-like ends and thorn-like structures forms optical networks that collect and distribute light. However, at the depths inhabited by the Venus’ Flower Baskets there is no accessible light source. If one accepts the fact that there is no waste in nature-whether one believes in “creation” or “evolution”-the existence of such an advanced network-like structure as a part of a sponge-the most primitive animal-is at least thought-provoking. In the case of sponges that dwell in shallower waters with similar spicules, it has been postulated that such spicules gather and provide sunlight for the sponge’s endosymbiotic algae. However, at the depths at which the Venus’ Flower Baskets live, direct sunlight is not available. However it has been suggested that if light sources, such as bioluminescent microorganisms (bioluminescence is the production and emission of light by a living organism as the result of a chemical reaction during which chemical energy is converted to light energy) or chemiluminescence (emission of light as the result of a chemical reaction) exist, their light may be efficiently distributed by the sponge and act as an attractant for juvenile shrimp that are searching for a host. But for now these suggestions are just speculation and merit further investigation.

Before concluding this section, we should also note that, as a natural outcome of their construction/composition, these spicules do not have as great a transparency as their industrial counterparts and light cannot be transferred over long distances with them. However, it seems this is not a problem for the Venus’ Flower Basket as, apparently, they just need fibers of 5-15 cm to survive and it is the scientists who need to figure out a way to incorporate the traits of the Venus’ Flower Basket into industrial fibers.

The love

As mentioned in the introduction, the Venus Flower Basket hosts a pair of mated shrimp. These belong to the family of Spongicolidae, the Spongicala japonica. These shrimp, which can be as “big” as 9 mm in length, spend most of their lives in their host sponge. Though studies about them are limited, it is believed that before permanently being entrapped in their host, the shrimp have two free- living periods. The first one is just after hatching when they are small enough to exit through the mesh of the sponge. During this period they exit and re-enter their cages and live in a group with their parents and other juveniles. Studies suggest that the females generally stay with their parents until sexual maturity, whereas the males tend to leave their original host and live a solitary life until they reach a length of about 4 mm.

The second free-living period comes at the time of sexual maturity, when it is believed that the male and female mate outside and then invade a host, or the female searches for a host that is already occupied by a solitary male. During this stage, the shrimp have a body length of 3.5 to 6.5 mm which is bigger than the mesh size of the host sponges. Though this seems puzzling, it is thought that the mated shrimp enter the sponge in its flexible stage-when it may be easier to penetrate through the mesh-and get trapped there “forever” as the sponge grows older and stiffer. In fact this theory is supported by the finding that several flexible sponge specimens host solitary and young mated shrimp, whereas in the stiff specimens only very few solitary and young mated shrimp have been observed.

References

1. “Biological glass fibers: Correlation between optical and structural properties.” J. Aizenberg, V. C. Sundar, A. D. Yablon, J. C. Weaver, and G. Chen, Proc. Nat. Ac. Sci. 101 3358 (2004).

2. “Skeleton of Euplectella sp.: Structural hierarchy from the nanoscale to the macroscale.” J. Aizenberg, J. C. Weaver, M. S. Thanawala, V. C. Sundar, D. E. Morse, P. Fratzl, Science, 309 275 (2005).

3. “Fibre-optical features of a glass sponge – Some superior technological secrets have come to light from a deep-sea organism.” V. C. Sundar, A. D. Yablon, J. L. Grazul, M. Ilan, J. Aizenberg, Nature 424 899 (2003).

4. “Skeletal growth of the deep-sea hexactinellid sponge Euplectella oweni, and host election by the symbiotic shrimp Spongicola japonica” (Crustacea: Decapoda: Spongicolidae). T. Saito, I. Uchida and M. Takeda J. Zool., Lond. 258 521 (2002)

5. “Pair formation in Spongicola japonica (Crustacea: Stenopodidea: Spongicolidae), a shrimp associated with deep-sea hexactinellid sponges.” T. Saito, I. Uchida and M. Takeda J. Mar. Biol. Ass. U.K. 81 789 (2001).

Note

*. Also defined as, one of the minute calcareous or siliceous bodies that support the tissue of various invertebrates (Merriam-Webster’s English dictionary)