Bioluminescence

©Paul o’Dowd, 2013

Bioluminescence

 In many environments, various organisms emit a ghostly green, blue, yellow or even red radiance.

 On the reef and in the rainforest, bioluminescent displays are an important feature of the nocturnal landscape.

 The spooky emanations may appear as points of light, blinking or otherwise, dotting the rainforest floor.

 It may look like inexplicable patches of moonlight under the rainforest canopy on a moonless night.

 It may appear as flashing pin-points of brilliance, carving punctuated tracks through the gaps in the vegetation.

 Some generators of this living light will flock into large groups that shimmer with random scintillations which occasionally become synchronized, causing pulses of light to course through the collective.

 Sometimes, simply moving through certain environments can result in vivid blue emissions which leave persistent glowing records of your passage.

 In each of these cases, the light is being emitted by an amazing chemical reaction which appears to have evolved independently in a number of very different organisms.

 Some important ideas in chemistry are very useful at this point.

 For a chemical reaction to occur there needs to be enough energy available to drive the process.

 Some reactions happen easily, like acid eating limestone, just drop it in and it’ll be white froth in seconds. Other reactions need a push, like scrubbing poisons from your car exhaust, which requires heat and a controlled environment and a catalyst.

 Catalysts help reactions to occur by holding the reactants in exactly the state they need to be in, in order to react.

 Enzymes are biological catalysts.

 Organic pigments called “luciferins” can, under certain conditions, react with oxygen to produce light.

 These conditions are not easily arranged for inside living tissues because this reaction requires lots of energy to kick it off.

 Enzymes, collectively referred to as “luciferase”, catalyze the reaction, lowering the energy required for the process and bringing it within the energy budget available to cells.

 Various approaches to bioluminescence include the addition of other chemicals like ATP to help energize the reaction or modify the colour of the light it produces, but luciferin, luciferase and oxygen are the basis of the reaction.

 Bioluminescence serves many functions in nature.

 Fireflies flash their lights as signals to mates and rivals.

 They can also form large tree-bound swarms that become semi-synchronized, and in such a state the light may serve as a means of coordinating the group for social or reproductive purposes.

 Flashlight fish do something very similar. They swim in dense schools which display a bright scintillating flicker across the school.

 As the fish approach other animals they begin to coordinate their flashes and gradually fall into perfect pulsing synchrony. As the school passes, the pattern falls apart and the random scintillations once again come to dominate the display.

 This behaviour probably serves to keep the school together on their nocturnal meanderings and probably has a defensive function by either dazzling, confusing or intimidating would-be predators.

 It might also help to illuminate prey or even light the way.

 Various deep sea fish use their light production skills to directly illuminate their world for finding food and for hazard detection and avoidance.

 Recently, red bioluminescence was discovered in a number of deep sea fish including anglerfish and dragonfish.

 Most fish do not see the colour red. Their eyes are not equipped with the hardware to detect light of that wavelength.

 The fish with red lanterns are also equipped with eyes sensitive to red light.

 The ability to produce and perceive red light provides these fish with a band of illumination that none of their prey, or their own predators, can perceive. This represents a stealth vision system on par with any radar or night goggles the military might devise.

 Just as stealthy is the emission of light as a means of camouflage.

 When viewed from below, objects in the ocean appear as clear silhouettes against the even illumination of the surface.

 A carefully tuned emission of light from the lower surface of many fish enables them to blend into the luminous background of the surface, making them nearly invisible when viewed from below.

 The sudden appearance of bright light can perturb many small predators. This may be due to the fear of higher order predators noticing the action and popping by.

 Many small marine creatures and a good number of forest invertebrates, appear to produce light for this reason, highlighting to anyone watching, a spot in the landscape where something is going on.

 Glow worms in the rainforest are in fact larval fireflies which are themselves, not flies but beetles. They produce a steady, or slowly pulsing, bead of light in the leaf litter.

 Many predators of insect larvae seek their prey amongst the dark environment of the forest floor. They seek out dark places and have little love of the light.

 An animal with an aversion to light is described as “negatively phototactic”.

 The glow worm may be employing a repulsive defense against the dark loving predators of the rainforest leaf litter habitat.

 On a similar note, and still within the rainforest, fungi are amongst the best known bioluminescent organisms.

 Different parts of a fungus may glow.

 In some cases the mushroom produces sharp pinpoints of relatively bright light.

 In others, the microscopic threads, or mycelium, of the fungus, produce dim and diffuse patches of light that look like moonlight striking the rotting humus through which the mycelium grows.

 In the case of the mushroom, it is a reproductive organ and it has spores to distribute.

 Conscripting the use of flying creatures that are generally positively phototactic, is a great way to spread these spores.

 In the case of the mycelium, it has nothing to distribute, but it is edible.

 Creatures who eat fungus must seek it where it grows; in dark, wet places. They are usually repelled by light.

 When a negatively phototactic, fungus feeding, leaf litter critter finds itself in a place full of edible fungus but lit like a stadium, they may think twice about sticking around for long enough to do any real damage.  

 Bioluminescence attracts, repels, illuminates and obscures. It also inspires art, with fantasy landscapes glowing, and science with powerful lighting technologies already on the market.

 The next time you’re on a night dive, spare a thought for the pedigree of the light stick you’ve tied to your tank and its direct relationship to the light you see in the creatures all around you.

Iridescence.

Iridescence

  Colour can be generated in a couple of ways. We are very familiar with colours produced by pigments or dies.
 Some insects and birds, compact disks, oil slicks and other things however, produce their bright, pure colour through the process of iridescence.
  A pigment absorbs light in most parts of the spectrum and reflects a small range of wavelengths to give the impression of the pigmented surface being ‘coloured’.
  Clothing, hair, paint, plant tissue and skin colours are all pigment based effects. It is a chemical effect, in fact the colour of something can tell you a lot about its chemical make-up. Hemoglobin makes blood red, carotene, from carrots is yellow-orange, and melanin gives you your tan and hair colour. The effect relies on electrons in the pigment molecules behaving in certain ways to achieve the result of absorbing particular wavelengths of light and reflecting others.
  Iridescence is a very different process. It relies on some of the weirder, quantum aspects of light to achieve the effect of making a surface seem to reflect bright light of a very pure colour. It relies on the microscopic, three dimensional structure of the iridescent surface and as a result it is sometimes called structural colour.
  Light can be thought of as traveling as a wave. Waves can be thought of as fluctuations of a particular value over time or space. As such, if you can cause a couple of waves to overlap and interact you can get some interesting things to happen.
  Wave peaks are ‘high’ energy values and wave troughs are ‘low’ energy values. The wavelength is the distance between the wave peaks. If waves of a particular wavelength can be lined up with each other, the peaks and troughs can be superimposed in different ways to either amplify or cancel the waveform. This is known as interference. Amplification of a wave is constructive interference and cancellation of a wave is destructive interference.
  Iridescent surfaces use microscopic, layered, reflective structures to superimpose multiple waves of light over each other as they are reflected. The exact dimensions of the layered reflectors determine which wavelengths of light are constructively or destructively interfered with.
 The important thing to realize is that all of the light is reflected by the reflector arrays on an iridescent surface, it’s just that after reflection, on their way back to your eyes, the waves themselves work together to either amplify or cancel each other. Light really is extremely weird stuff.

On the wings of a butterfly like a Ulysses, or on the surfaces of various other creatures with similarly vivid colour displays, are arrays of these layered reflectors which the animals use to generate spectacular iridescence effects. The exact reflector structure varies between species but the theory behind the effect is the same.

Some have precisely perforated layers of chitin stacked one above the other and held apart by columns that keep the layers separate by an exact multiple of the desired colours’ wavelength. The perforations let some light reach the lower layers where it is reflected back up through the stack to rejoin the rest of the reflection and cause the interference.  
Ulysses Butterfly wing scales are covered by arrays of what look like microscopic library shelves. In cross-section these arrays looks like pine trees, each successively lower shelf is longer than the one above it. From above, the distance between the shelves is an exact multiple of the wavelength of the bright blue light you see from that angle. All other colours cancel as their wavelengths are not exact fractions of the array dimensions.
  However, as you move to a more oblique viewing angle, the relative spacing of the reflector arrays change for light bouncing off at that angle. The iridescence effect shifts to purple as that wavelength becomes an exact fraction of the reflector array at that angle, and blue joins the other colours in being cancelled.

Most iridescence in animals is at the blue end of the spectrum, with green, blue and purple iridescence being most common. The red end colours have long wavelengths, so the structures needed to play with those colours would need to be much larger in scale, they could pose problems like getting particles trapped in the larger arrays. The arrays would also be more prone to damage through abrasion and impacts.
  Most iridescence effects are probably used for the obvious advertising functions that antlers, squawks and Lamborghinis serve in other organisms. “I’M GORGEOUS, AND I’M OVER HERE, BABY!!!”
 Giant Clams though, use iridescence for something else entirely.

These animals do not have eyes. They have eyespots which detect light and dark but nothing that can form an image of their environment. Rings of dazzling iridescent tissue often surround the eyespots. It now appears that the iridescent tissue is used by the clam to extract some directional information from the local light field. As a potential threat approaches a clam, the light bouncing off the subject will interact differently with the iridescent tissue depending on its angle and be detectable to the clam as a subtle shift in colour, indicating the direction from which the light came. Try it using a DVD. Notice how the colours wheel about dramatically with only small movements of the disk. That’s iridescence

Recently it was noticed that the black sections of Some butterfly wings are blacker than they have any right to be if pigment was being used to produce the black. No pigment known is able to achieve perfect black and Ulysses Black is very close to perfect black.
Scientists looked into it and discovered that the Ulysses butterfly has developed structural colour devices that achieve an almost complete cancellation of the entire visible spectrum!!! That’s a first, and it has generated quite some excitement in a number of fields where the blackening of surfaces is important. Astronomers want it to reduce light contamination in telescope barrels and the military naturally want to put it to good use in stealth applications so that they can kill more people more effectively.
Leave it to Homo sapiens to name a creature a symbol of peace and then use it to develop weapons of war.

Rainforest Architechure

Rainforest Architecture.


The structure of a tropical rainforest is what many people would consider a bit upside down. While the deep-rooted trees of temperate forests are free-standing, and often ancient, behemoths, tropical rainforest trees are not as massive or old. They have roots only at the surface and they are supported mainly by their crowns.

A healthy tropical rainforest possesses a highly ordered and organised architecture.
Enough trees have reached a sufficient height to form a “canopy” of interlocking tree crowns bound together by vines.
The canopy forms a skin over the rainforest ecosystem and it regulates many of the conditions within the forest.
The canopy provides almost complete shade to the forest floor. In the absence of light, plants don’t do much growing and this subdues the plants below the canopy. Thus, the understory is dominated by a relatively open forest floor, studded with an even spread of younger plants and trees of all ages which are not so much growing as much as waiting for an opportunity to grow.
When rainforest reaches this mature and stable state it is called “Primary Rainforest”.
“Virgin Rainforest” has never been logged or otherwise modified by humans and will be dominated by primary rainforest with patches of thicker vegetation dotted throughout.

Walking through primary rainforest is easy. It is not the impenetrable “jungle” that many of us expect. In fact the term “jungle” comes from the Hindi word for messy or chaotic. It entered our language during the Raj when British colonial administrators in India heard the locals referring to the thick vegetation around their facilities as “jungle”. When they returned to England and regaled their society friends over dinner with their “Adventures in the Jungles of India”, and the name just stuck.
Had more of the colonial thugs from Old Blighty taken more breaks from counting loot on the cushy cots on the verandas of their pukka bungalows, they may have learned something. If they’d gotten out of their pyjamas and into their khaki, then jumped in a dinghy to venture into the primary forest further away from the base, they would not have heard the term “jungle” again until they got back to the thickets on the edges of their clearings. Hindi words italicized.

If the canopy is breached, the undergrowth rapidly thickens in the extra light. This thickened understory is referred to as “Secondary Growth”.  Secondary growth is found anywhere the canopy is breached, in gaps both man-made and natural. Healthy primary forest will be studded with secondary growth thickets in places where canopy gaps have formed naturally. These natural thickets are islands of important habitat for many plants and animals.

  A rainforest that is dominated by secondary growth is not a mature forest. Densely vegetated rainforests are often that way due to logging or other forest damaging practices. Many tours claim to be accessing “Virgin Rainforest” while taking people to impenetrable secondary growth areas which have been heavily logged. This is obvious to anyone who knows these facts about rainforest architecture.

  In most rainforests, there has been so much voracious vegetation growing in the soil for so long, that every last molecule of nutrient has been stripped from the dirt and turned into living tissue. In the absence of nutrients deeper down, the roots of the rainforest compete for resources at the surface as the leaf litter decomposes.For the past many millions of years, the forest has recycled, in the leaf litter and in the first few feet of soil, the nutrients it originally acquired from much deeper down.
 Rainforest root systems form a dense mat of interlocking roots just below the surface. The root mat of the rainforest is exceptionally shallow, generally reaching no more than a meter below the surface, even on truly massive trees.The roots of the rainforest plants and trees are highly interconnected both directly and via a vast fungal network which penetrates the root cells and physically connects almost every plant in the rainforest. This network is capable of sending nutrients and chemical signals throughout the forest.
The signals include information about pests, leading to leaf defence activation prior to pest arrival.
Information about disease threats, leading to the ramping up of immune response before the direct detection of the disease. Information about resource depletion, prompting as yet unaffected plants to create stores of the resource that other plants report a local shortage of.
The science that is revealing this capacity for information networks to arise in ecosystems is very convincing. Under conditions of predation or infection and for many reasons beyond defense, plants have been found to communicate through the soil and through the emission of chemical signals into the air which other plants receive, act upon and re-emit, passing the message down the line
In terms of defense, upon exposure to substances which identify a threat, like caterpillar spit, the plant begins synthesizing chemicals which waft away to be detected by neighboring plants. The canopy and roots carry signals that activate plant defenses in sites distant from the point of the original transmission.
These chemical messages are specific to particular threats and elicit appropriate, threat specific responses in the plants that receive the messages.
The agents of the outbreak encounter much more resistance in subsequent plants because they are now actively anticipating a threat and have bolstered their defenses.
This is not unlike the function of an immune system working with the nervous system to monitor and defend the body.

In the absence of deep roots, the canopy becomes the rainforest’s main agent of architectural stability. It is elastic and self regenerating, enabling it to withstand severe physical stress without losing its structural integrity and to mend itself if it is damaged. Think cyclones.
The canopy is an intricately interconnected fabric of living tree crowns bound together by vines.
It is highly homeostatic. The canopy is a sensitive regulator of the internal balance of temperature and humidity within the forest.
Under varying conditions of temperature and humidity the canopy trees may adjust leaf aspect, alter transpiration rates or even emit substances into the air to modify the weather.
The canopy is literally the “skin” of the forest.
The canopy provides physical stability to the trees in the same way that a very crowded bus is easier to ride than if you were standing alone. If you are jammed in tight on all sides then there’s no direction in which you could lean far enough to lose balance and fall over. As long as a tree is part of the canopy structure it will be able to survive cyclones despite the fact of its insubstantial roots.
This function is as architectural as is your own skeleton's function.

By the time a tree reaches three or four hundred years old, it will be a very well established member of the canopy community. Any further growth, begins to remove the tree from the canopy, at which point the tree becomes known as an “emergent”.

 Emergents are giants who lose exposed limbs to storms, exposing the tree’s heartwood.
The heartwood is invaded by termites and beetles who inoculate it with fungus and bacteria.
The resultant wood-rot creates hollows and vital habitat for many animals.
If a rainforest tree gets to 700 years old it is very lucky.  Emergents eventually get so big that they lose the support of the canopy and will ultimately be toppled by a tropical storms, ripping a gaping hole in the skin of the rainforest.

Throughout the rainforest there are many plants which maintain a low background presence.
If the canopy is breached, these plants explode in size and number. Many are rapid growing climbers which quickly seal the open forest edges. This has the effect of insulating the forest’s delicate internal climatic balance from the atmospheric conditions outside the canopy. This is highly analogous to the function provided by scar tissue.

In the clearing, surrounded by the thickening walls of vines and young rainforest trees, plants which have been waiting as dormant saplings for many years, explode in growth in response to the sunlight and huge compost dump caused by the fallen tree. Everything in the gap will grow at a prodigious rate until the canopy closes over again. Small gaps will be quickly closed by established trees spreading into the space available. Big gaps are slowly closed by the vegetation within them replacing the fallen trees.
Until the gap closes, the thicket will host a large array of thicket specialists who rely on these dense patches of forest for their existence. The high activity around thickets attracts animals who deposit seeds and nutrients from the intact forest, reminiscent of stem cells migrating into badly damaged body parts to restore the full range of function to the regenerating tissue.

The analogies between a rainforest and an organism are not trivial. In many ways a rainforest ecosystem behaves as an organism in its own right. The features we see as being in common between systems on different scales are reflections of deeper realities in nature that connect us in ways we're only beginning to fathom.