Feature Article - September 2010
by Do-While Jones


This month we shine light on the problems that bioluminescence causes for the theory of evolution.

In last month’s email column we stumbled on an interesting article simply because it had a reference to cladistics in its footnotes. We mentioned it in passing, but didn’t discuss it in detail because we didn’t have room for it in that newsletter. It had to do with sea creatures that glow in the dark, and the problems they pose for evolutionary biologists. Here’s the abstract of that article.

From bacteria to fish, a remarkable variety of marine life depends on bioluminescence (the chemical generation of light) for finding food, attracting mates, and evading predators. Disparate biochemical systems and diverse phylogenetic distribution patterns of light-emitting organisms highlight the ecological benefits of bioluminescence, with biochemical and genetic analyses providing new insights into the mechanisms of its evolution. The origins and functions of some bioluminescent systems, however, remain obscure. Here, I review recent advances in understanding bioluminescence in the ocean and highlight future research efforts that will unite molecular details with ecological and evolutionary relationships. 1

In plain English, it says there is a “remarkable variety” of sea creatures that use chemical means to produce their own light which apparently don’t have a close common ancestor. The evolutionary process that must (in his mind) have produced all these creatures “remains obscure.” But he is convinced that future research will answer all his questions.

Remarkable Variety

In the standard biological classification system, living things are grouped by kingdom, phylum, class, order, family, genus, and species. That is, similar species are grouped into genera. One genus contains many species. Since there are more than 700 different genera that contain luminous species, there must be more than 700 different species of living things that glow in the dark.

The vast majority of bioluminescent organisms reside in the ocean; of the more than 700 genera known to contain luminous species, some 80% are marine. These occupy a diverse range of habitats, from polar to tropical and from surface waters to the sea floor. The ecological importance of bioluminescence in the ocean is manifest in the dominance of light emitters in open waters; luminescent fish (e.g., mycophids and hatchetfish) and crustaceans (e.g., copepods, krill, and decapods) dominate in terms of biomass, whereas bacteria and dinoflagellates dominate in terms of abundance. Its import is also evident in the large number of organisms that retain functional eyes to detect bioluminescence at depths where sunlight never penetrates and in the remarkable degree of diversity and evolutionary convergence among light-emitting organisms.

Bioluminescent species are found in most of the major marine phyla from bacteria to fish. As a phylum, comb jellies have the highest proportion of bioluminescent species, whereas other phyla such as diatoms and arrow worms have none or few luminescent representatives. 2


Whenever apparently unrelated species have similar characteristics, evolutionists claim it is the result of “evolutionary convergence,” which is simply their way of saying, “The devil (the environment) made me do it.” In this case, living in the depths of the ocean forced many unrelated species to evolve the ability to produce their own light.

There is no real evidence that evolutionary convergence actually happens. Evolutionists just assume it must happen because, well, uh, it must have happened.

Cladistics is a method for classifying things based on shared characteristics. Bioluminescence is a significant shared characteristic which could reasonably be used as a classifying criterion. But, since that would lump bacteria, fish, and fireflies together, it isn’t used. It just doesn’t fit the standard evolutionary scheme of things.

Lost Traits

Sometimes, when distantly related species share a characteristic not found in more closely related species, evolutionists use another fairy tale to explain the problem away. They assume that a common ancestor had the trait, but some of the descendants lost the trait for one reason or another.

Since some bacteria can produce light, and since just about everything supposedly evolved from bacteria, one might assume that practically every living thing initially inherited the ability to glow in the dark, but later lost it for some reason. Evolutionists don’t claim this, however, because there are so many different ways in which living things produce light.

Understanding what function bioluminescence serves in a particular organism provides insight into what selection pressures imposed by the environment and by intergroup competition may have favored the evolution of bioluminescence in one group over another. Wide diversity among light-emitting chemistries has long confounded efforts to trace evolutionary origins. 3

Specifically, there are at least two different processes by which living things produce light.

In bacteria, two simple substrates [a reduced flavin mononucleotide (FMNH2) and a long-chain aliphatic aldehyde (RCHO)] are oxidized by molecular oxygen and luciferase. The aldehyde is consumed during the reaction but is continuously synthesized by the bacteria, resulting in a persistent glow. Alternatively, the chemical structure of dinoflagellate luciferin bears a striking similarity to chlorophyll (Fig. 2), which suggests that it originated in photosynthetic species. Although the biosynthetic pathway of luciferin is unknown in dinoflagellates, a dietary dependence on dinoflagellate luciferin has been suggested in krill. Ostracod luciferin is an imidazopyrazinone synthesized from three amino acids (Trp-Ile-Arg) as is coelenterazine (Phe-Tyr-Tyr) (Fig. 2), but in both cases the details of biosynthesis are unknown. In the case of coelenterazine, its manner of biosynthesis has recently become of particular interest with the discovery that coelenterates require it as a dietary source. Although there is some circumstantial evidence for its synthesis in crustaceans, such a linkage remains to be confirmed. In some bioluminescent systems, accessory proteins serve as secondary emitters, which shift the color of the bioluminescent emission to longer wavelengths. 4

Why Glow?

Evolutionists run into trouble when they search for meaning in a meaningless process. They are stuck in a dilemma. On the one hand, they insist that there is no meaning to life. It is all just the result of a purposeless, random process. But, on the other hand, they can’t help wondering why it happened that way. So, they try to come up with explanations for how things happened unintentionally.

… bioluminescence can aid animal survival in at least three critical ways: (i) It can serve as an aid in locating food, either by means of built-in headlights or by the use of glowing lures. (ii) It can be used to attract a mate by means of species-specific spatial or temporal patterns of light emission. (iii) It can function as a defense against predators. The last is probably the most common use and takes many forms. 5

There is no argument that bioluminescence is useful. The argument is whether or not usefulness makes things happen by chance.

How Did it Happen?

After coming to the conclusion that bioluminescence must have happened because it is beneficial, the next obvious step is to ponder how it could have happened by chance.

What Are Evolutionary Processes That Lead to Bioluminescence?

Based on the number of light-producing chemistries across the monophyletic lineages, bioluminescence is estimated to have evolved independently at least 40 times. Remarkably, not only is there evidence of independent origins within taxa (e.g., ostracods have two known chemistries: coelenterazine and vargulin) but even within individual species (e.g., the deep-sea anglerfish, Linophryne coronata, has two different light-emitting systems in adult females: bacterial luminescence in the dorsal lure and an intrinsic, unidentified chemistry in the chin barbel) (Fig. 3A).

Most hypotheses put forth to explain the evolution of luminescent systems fall into two basic categories related to selection acting on either substrates or enzymes. 6

Widder’s article contains detailed technical explanations of both hypotheses, which we will kindly spare you.

Hijacked Classification

The biological classification system was originally devised to facilitate scientific study of living things. Now things get reclassified willy-nilly in an attempt to bolster whatever evolutionists believe today.

In bioluminescent bacteria, the question of evolutionary origins has recently gained new focus with the reclassification of members of the Vibrio fischeri species group as a new genus, Aliivibrio. The taxonomy of luminescent bacteria has been revised often in efforts to better define evolutionary relationships and origins. 7

I Believe—Help My Unbelief!

We can summarize the article as follows: There are lots of apparently unrelated creatures which can produce their own light. Light benefits these creatures in a variety of ways. The benefits are so great that bioluminescence must have evolved 40 different times. Nobody knows how it happened, but it must have happened because evolution must be true. In Widder’s words,

Although it was once thought that such complex and tightly coupled associations must have coevolved, recent phylogenetic analyses of bacteria isolated from two squid families and seven teleost families revealed deep divergences among the hosts that are not reflected in the symbionts, pointing to evolutionarily independent origins of these symbioses. 8

The many examples of evolutionary convergence related to bioluminescence are a testament to the survival value of the trait, whereas its abundance and ubiquity in the ocean attests to its importance in marine ecosystems. 9

Widder is convinced that bioluminescence must have evolved by chance many times because it is so useful for survival. But whenever evolutionists use phrases like, “origins remain obscure”, “linkage remains to be confirmed”, “confounded efforts to trace evolutionary origins”, “question of evolutionary origins”, “estimated to have evolved independently”, and “must have coevolved”, they are simply saying that the observable facts don’t fit the theory. They believe in evolution despite the scientific evidence, not because of it.

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1 Widder, Science, 7 May 2010, “Bioluminescence in the Ocean: Origins of Biological, Chemical, and Ecological Diversity”, pp. 704 - 708, https://www.science.org/doi/10.1126/science.1174269
2 ibid.
3 ibid.
4 ibid.
5 ibid.
6 ibid.
7 ibid.
8 ibid.
9 ibid.