Let there be Light !... Bioluminescence part 2

The roles that bioluminescence plays in the lives of organisms today is fascinating. How did this trait evolve? This is a complex question, because bioluminescence is believed to have evolved around 50 different times in different species of animals.
So how do living creatures produce light? Well, the actual question that needs to be asked is how do living creatures produce visible light.

To fully work out the evolutionary roots of bioluminescence, we must look into the very earliest stages in the evolution of life as we know it.

Those roots begin, more than 2,500 million years ago. Back when bacteria and ancient life forms called archaea ruled the earth.  Some of the bacteria had found a way to use the energy of sunlight to make food. Using this reaction, known as photosynthesis, these bacteria managed to spread and proliferate. However, as a waste product, they produced a molecule called oxygen.
Whilst we all know and love oxygen, it is actually a remarkably reactive compound. Back before there was oxygen, you would have a lot of difficulty , say striking a match , despite the fact that most of the atmosphere contains methane. The thing that makes oxygen reactive is that as a molecule is its stability, or lack thereof. To sum up, without delving two deeply into the chemistry, each of the oxygens in a molecule have an unpaired electron. Since electrons traditionally like to be in a pair, these extra electrons will often try to bond with electrons on other molecules, such as methane.

 The methane atmosphere of early earth burned away as the oxygen built up, converting the methane to carbon dioxide. Vast deposits of iron began to rust as a result of reacting to oxygen. These reactions initially acted as "sinks" for the excess oxygen, and prevented its build up within the atmosphere. At around 2,500 million years ago, these sinks finally were exhausted. Oxygen began to build up in the atmosphere, and in the sea. This highly reactive compound corroded and changed almost everything it came into contact with. Organisms had to develop new ways to detoxify this compound or die out. This was probably the most destructive extinction that life has ever seen, and the closest it has come to being completely wiped from the earth

The organisms that survived did so because they managed to produce antioxidant compounds.

 One of the compounds that evolved was Flavin Mononucleotide. This molecule can shuttle excess hydrogen ions around a cell, which can neutralise the effects of oxygen by converting it to water.

Flavin mononucleotide can produce light when it is oxidised . Bioluminescence first occurred as a by-product of these antioxidant reactions.

It is also believed that bioluminescence can also act as an intracellular signal to help prevent DNA damage.

There are enzymes known as photolyases which act to repair DNA after damage by ultraviolet light. These can be activated by blue light, which coincidentally is generated by the bioluminescence reactions of Flavin mononucleotide.
As these bacteria proliferated, they eventually formed relationships with the multicellular organisms that were also evolving.  It is unknown exactly what sort of relationships they started out with, although it is believed that they were initially parasitic. Eventually, these relationships became mutualistic, with organisms often developing specialist organs for housing bioluminescent bacteria.

Many bioluminescent organisms we see today are reliant on symbiotic bacteria.However, not all creatures that emit light use bacteria to produce it. One of the most famous organisms doesn't use bacteria at all, and had developed bioluminescence through a quite different route.

The firefly is known for its dramatic sexual displays of luminescence. It did not start off like that. It is believed that its ancestor was a unassuming beetle that defended itself through being distasteful and poisonous.It did this by producing complex compounds and toxic compounds. One of the hazards of accumulating these compounds is that they have to be made safe for the organism producing them. And thus, this beetle needed to develop antioxidant reactions.
To do this, it produced a compound known as D-luciferin. This compound acts as an antioxidant, and can counteract the effects of excess free radicals building up within a cell. It also spontaneously produces photons of visible light when it decays.
So this highly poisonous beetle began to glow in the dark. And because of this, predators would associate luminescence with this little poisonous beetle. So the beetles evolved to be brighter, to spread the message of their toxicity further. More predaotrs got the message, and the bugs survived. The progeny of these beetles evolved into a diversity of bioluminescent organisms, including fireflies.

Great though fireflies and bacteria are at producing luminescence, it did take them a long time to evolve it.
Some organisms hijack bacterial bioluminescence through forming direct sympbiotic relationships with bacteria.
However, there is another way that organisms can become bioluminescent without having to evolve it themselves, or form relationships with bacteria.
 There are marine copepods that have evolved to produce a compound called coelentarazine. This compound naturally decays to produce bioluminescence. Predators who consumed these creatures and found a way to metabolize coelentarizine so that they themselves can become bioluminescent. This way, they simply need to eat copepods in order to become luminescent.

Summary
In researching this post, I was surprised by the amazing variety of different mechanisms for bioluminescence that there are out there.  Considering that bioluminescence is believed to have evolved independently around 40 times, I've barely scratched the surface with this post.
I've attempted to give a few examples that illustrate some of the underlying trends in the development of bioluminescence. Many creatures that are bioluminescent can become so through partnerships with micro-organisms, through feeding on bioluminescent organisms, or through co-opting antioxidant reactions to produce bioluminescence.
Whilst there is a massive diversity I haven't talked about, they all seem to have evolved along the same lines. But scientists still haven't pieced the whole picture together, and we are still in the dark about much of the evolutionary history of bioluminescence.
What is interesting is how the roots of bioluminescence are so intimately tied into our evolution. The same antioxidant reactions which enabled bioluminescence were the same ones which also gave single celled organisms the ability to become multicellular, and in turn the ability to form into more complex life forms. Life forms like us.
At the beginning of this article, I made a note that what makes bioluminescent organisms special is that they can emit visible light. This distinction is important,  because those antioxidant reactions are present in all life forms. These reactions are weakly bioluminescent, and as a result, we all emit small numbers of photons. We just can't see them. You could say that to some extent,  we are all luminous beings.

References
Branham, M. (2003). The origin of photic behavior and the evolution of sexual communication in fireflies (Coleoptera: Lampyridae) Cladistics, 19 (1), 1-22 DOI: 10.1016/S0748-3007(02)00131-7

Dubuisson M, Marchand C, & Rees JF (2004). Fire fly luciferin as antioxidant and light emitter: the evolution of insect bioluminescence. Luminescence : the journal of biological and chemical luminescence, 19 (6), 339-44 PMID: 15558801

Timmins GS, Jackson SK, & Swartz HM (2001). The evolution of bioluminescent oxygen consumption as an ancient oxygen detoxification mechanism. Journal of molecular evolution, 52 (4), 321-32 PMID: 11343128
Kozakiewicz J, Gajewska M, Lyzeń R, Czyz A, & Wegrzyn G (2005). Bioluminescence-mediated stimulation of photoreactivation in bacteria. FEMS microbiology letters, 250 (1), 105-10 PMID: 16040205

Kobayashi M, Kikuchi D, & Okamura H (2009). Imaging of ultraweak spontaneous photon emission from human body displaying diurnal rhythm. PloS one, 4 (7) PMID: 19606225