SHELL MIDDENS: CaCO3 + CO2 + H2O → Ca (HCO3)2

This past weekend, I was exploring the western edge of central Vancouver Island, home to the Pacheedaht First Nation. Their traditional unceded territory is wonderous.  

The beaches are covered with bits of fir, cedar and arbutus worn smooth by the awesome west coast waves! I can see why they have made a home here for millennia. 

Those of you who live near the sea understand the compulsion to collect driftwood, unusual stones, fossils—and shells. They add a little something to our homes and gardens. 

With a strong love of natural objects, my own home boasts several stunning abalone shells conscripted into service as both spice dish, soap dish and the place I both store and display beautiful bits from nature.

As well as beautiful debris, shells also played an embalming role as they collect in shell middens from coastal communities. Having food “packaging” accumulate in vast heaps around towns and villages is hardly a modern phenomenon.

Many First Nations sites were inhabited continually for centuries. The discarded shells and scraps of bone from their food formed enormous mounds, called middens. Left over time, these unwanted dinner scraps transform through a quiet process of preservation.

Time and pressure leach the calcium carbonate, CaCO3, from the surrounding marine shells and help “embalm” bone and antler artifacts that would otherwise decay. Useful this, as antler makes for a fine sewing tool when worked into a needle. Much of what we know around the modification of natural objects into tools comes from this preservation.

Comox Beach, Kʼómoks First Nation / Photo: Kat Frank 

Calcium carbonate is a chemical compound that shares the typical properties of other carbonates. CaCO3 is common in rocks and shells and is a useful antacid for those of you with touchy stomachs. 

In prepping fossil specimens embedded in limestone, it is useful to know that it reacts with stronger acids, releasing carbon dioxide: CaCO3(s) + 2HCl(aq) → CaCl2(aq) + CO2(g) + H2O(l)

For those of you wildly interested in the properties of CaCO3, may also find it interesting to note that calcium carbonate also releases carbon dioxide on when heated to greater than 840°C, to form calcium oxide or quicklime, reaction enthalpy 178 kJ / mole: CaCO3 → CaO + CO2.

Calcium carbonate reacts with water saturated with carbon dioxide to form the soluble calcium bicarbonate. Bone already contains calcium carbonate, as well as calcium phosphate, Ca2, but it is also made of protein, cells and living tissue.

Decaying bone acts as a sort of natural sponge that wicks in the calcium carbonate displaced from the shells. As protein decays inside the bone, it is replaced by the incoming calcium carbonate, making makes the bone harder and more durable.

The shells, beautiful in their own right, make the surrounding soil more alkaline, helping to preserve the bone and turning the dinner scraps into exquisite scientific specimens for future generations.

The lovely photo from Comox showing the many shells on the beach is by my beautiful cousin Kat Frank of the Kʼómoks First Nation—an amazing human being and, as you can see, a great photographer!

AMYLASE: YOU ARE WHAT YOU EAT

The old adage, you are what you eat, might be best amended to you are what you can digest. 

For all the mammals, you and I included, we need the amylase gene (AMY). It codes for a starch-digesting enzyme needed to break down the vegetation we eat. 

Humans, dogs and mice have record numbers of the amylase gene. The AMY gene copy number increases in mammal populations where starch-based foods are more abundant. Think toast and jam versus raw chicken.

A good example of this is seen when we compare wolves living in the wild to dogs from agricultural societies. Dogs split off the lineage from wolves around 30,000–40,000 years ago. 

Domesticated dogs have extra copies of amylase and other genes involved in starch digestion that contribute to an increased ability to thrive on a starch-rich diet, allowing Fido to make the most of those table scraps. Similar to humans, some dog breeds produce amylase in their saliva, a clear marker of a high starch diet. So do mice, rats, and pigs, as expected as they live in concert with humans. Curiously, so do some New World monkeys, boars, deer mice, woodrats, and giant African pouched rats. 

More like cats and less like other omnivores, dogs can only produce bile acid with taurine and they cannot produce vitamin D, which they obtain from animal flesh. Also, more like cats, dogs require arginine to maintain their nitrogen balance. These nutritional requirements place dogs halfway between carnivores and omnivores.

The amount of AMY and starch in the diet varies among subspecies, and sometimes even amongst geographically distinct populations of the same species. I was at a talk recently given by Alaskan wolf researchers who shared that two individual packs of wolves separated by less than a kilometre ate vastly different diets. This had me thinking about what we eat and it is mostly driven by what is on offer. 

Diet impacts our genetics and this, in turn, allows the fittest to eat, digest and survive. While wolves win the carnivore contest, they will still eat opportunistically and that includes vegetation when other food is scarce. Would they evolve similar levels of AMY as humans, dogs and mice? Maybe if their diets evolved to be similar. Likely. The choice would be that or starvation.

The evolution of amylase in other domesticated or human commensal mammals remains an alluring area of inquiry.

Reference: 

Amylase in Dietary Food Preferences in Mammals: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6516957/

BIOLUMINESCENCE: CHEMICAL POETRY

Light in the oceans? It is chemistry, my friends. 

In the inky blackness of the deep sea, more than 90% of the animals are luminescent. It is quite a startling number but makes good sense when you think of the edge bioluminescence provides. 

The ability to generate light helps umpteen animals find mates, attracts prey and avoid predation. Handy stuff, light. 

What you know about light above the surface does not hold true for the light you see as bioluminescence. Its energy and luminosity come from a chemical reaction. 

In a luminescent reaction, two types of chemicals — luciferin and luciferase — combine together. Together, they produce cold light — light that generates less than 20% thermal radiation or heat. 

The light you see is produced by a compound called Luciferin. It is the shiny, showy bit in this chemical show. Luciferase acts as an enzyme, the substance that acts as a catalyst controlling the rate of chemical reactions, allowing the luciferin to release energy as it is oxidized. The colour of the light depends on the chemical structures of the chemicals. There are more than a dozen known chemical luminescent systems, meaning that bioluminescence evolved independently in different groups of organisms.

Coelenterazine is the type of luciferin we find in shrimp, fish and jellyfish. Dinoflagellates and krill share another class of unique luciferins, while ostracods or firefleas and some fish have a completely different luciferin. 

The luciferase found in dinoflagellates is related to the green chemical chlorophyll found in plants. Bioluminescent dinoflagellates are a type of plankton — teensy marine organisms that make the seaways shimmer like the Milky Way as you swim through them. 

Their twinkling lights are brief, each containing about 100 million photons that shine for a tenth of a second. While each individual flicker is here and gone in the wink of an eye, en masse they are awe-inspiring. I have spent many wondrous evenings scuba diving amongst these glittering denizens off our shores. 

Cotylorhiza Tuberculata Jellyfish

In this close up of a Cotylorhiza Tuberculata Jellyfish, you can see the luminosity of her blue and white tentacles. The occurrence of identical luciferins for different types of organisms may suggest a dietary source for some groups strengthening the adage, you are what you eat, or perhaps you glow how you eat. 

Bacteria and fireflies have unique luminescent chemistries. Fireflies light up when oxygen combines with calcium, adenosine triphosphate (ATP) and luciferin in the presence of luciferase. 

For bacteria, the world stage of luminosity is quite small — and a bit gormless. Just how much light they emit and when is a free-for-all. Not so for the rest of our bioluminescent friends who have very precise control over when they shine and just how bright. 

Bioluminescence comes in a variety of colours, from blue through red. The colour is based on the chemistry, which involves a substrate molecule called luciferin, the source of energy that goes into light, and an enzyme called luciferase or photoprotein. 

Most of this lighting up of our world happens on land or in saltwater. There are almost no bioluminescent organisms native to freshwater.

In terrestrial plants and animals — fireflies, beetles and fungi like this Ghost Fungus, Omphalotus nidiformis, a gilled basidiomycete mushroom — we commonly find green, yellow, and sometimes red. 

In the ocean, bioluminescence is mostly blue-green or green. You would think that blues and green would not show up all that well in our seas but, surprisingly, they do. While sound travels better through saltwater than air, it is the reverse for light. 

Various colours of light do not transmit equally through saltwater. Once we move deeper than the top layer of the ocean warmed by the sun and brimming with nutrients, the epipelagic zone, and move deeper through the mesopelagic, deeper and deeper still to the bathypelagic, frigid abyssalpelagic and finally the deep trenches of the icy pressure and all but inhospitable hadalpelagic, less and less light — until no light — gets through.

It is the twilight of the mesopelagic, 200 - 1000 metres below the surface, that is the sweet spot for most of our bioluminescent friends. Here, only very faint sunlight gets through. The water pressure is higher than at the surface but still lacks the crushing intensity of the lower zones. It is here that bioluminescence becomes a real advantage — good real estate and the showmanship of light pays gold.

We know that the deeper you go in our oceans, less and less sunlight gets through, so if the purpose of bioluminescence is to provide a signal that is noticed by prey, potential mates and predators alike, it is important that the light moves through the seawater, and not be absorbed or scattered — and this plays out in the colours evolved to be seen here. 

If you have spent any time underwater, you will know that blue-green light transmits best through seawater. The deeper you go, the colours fade. Gone are the reds and yellows until everything looks brown or blue-green. Because of this, it is no surprise that blue-green is the most common colouring of bioluminescence in our oceans. 

There are some exceptions to the blue-green/green colour rule — minuscule planktonic polychaete worms, Tomopteris helgolandica, emit yellow light, and deep-sea fish Malacosteus niger in the family Stomiidae, the barbeled dragonfishes, produce both red and blue. 

Malacosteus niger's unique adaptation of producing red bioluminescence is only found in two other deep-sea dwelling creatures, Aristostomias and Pachystomias. 

This rare form of bioluminescence can reach up to 700 nm in the deep-sea and cannot be perceived by green and blue bioluminescent organisms — granting M. niger a considerable advantage while hunting at depth.

The red light may function as an invisible searchlight of sorts because most animals in the ocean cannot see red light, while the eyes of M. niger are red-sensitive. It is much easier to find and eat something that cannot see you, particularly if it is lit up like a tasty red holiday snack.

Reference: https://latzlab.ucsd.edu/bioluminescence/