In the language of topology, the branch of mathematics concerned with shapes and surfaces, the form of a ring doughnut is a torus.  Topologically an animal is a torus, with the digestive tract the equivalent of the hole in the doughnut.

Which means that the gastrointestinal system is technically outside the body (hence egestion rather than excretion is the correct term for elimination of digesta).

Food moves through the human gut at the rate of about 0.25 m h^-1 (which means, in the very interesting words of Peter Cook, that it’s never really fresh.)  I guess it’s about the same for a cow or an elephant (the latter’s digestive tract is, as you would expect scale-wise, a mighty 19 m long).

Before the era of X-rays, CT scanners, safe invasive surgery and the like, faeces was medically important as just about the only way of finding out about the state of one’s innards.  And it’s fascinating stuff – no, really, it is, believe me.

For researchers on plant pigments, the typical colour of faeces has a relevant story to tell.  Because it is the consequence of the degradation of haem (USA: heme), a molecule structurally related to chlorophyll.

Haem is broken down in the body by haem oxygenase, an enzyme with many functions beyond its simple catalytic role.  Before it was found out how the tetrapyrrole ring of chlorophyll was opened up, the mechanism of haem oxygenase was a possible model.

In fact chlorophyll and haem catabolism turned out to be fundamentally different.  Without going into too much detail, the haem ring is opened by oxidation and the elimination of one of the carbon atoms as CO – amazing, considering carbon monoxide is such a potent inhibitor of haemoglobin function.  The central metal (Fe) atom also plays a part in the reaction.  In chlorophyll breakdown no carbon is eliminated, and the central Mg is not a participant.

The product of haem oxygenase is the straight-chain tetrapyrrole biliverdin.  This is converted by a reductase to bilirubin which is expelled into the digestive tract and gives faeces its red-brown colour.

Although awareness of blood understandably makes haem almost symbolic of animal physiology, plants make haem too and they also have haem oxygenase.  One function of this enzyme is to make the photoreceptor phytochrome.  This molecule (which flip-flops between two configurations, P_R and P_FR) is central to the plant’s capacity to measure daylength, perceive light quality and sense the proximity of other plants.

Of course, the digestive systems of herbivores and ominivores will also contain chlorophyll from the plants that went in the front end.  What happens to this pigment on its way through the gut?

Normally it passes through pretty harmlessly, perhaps undergoing some modifications on the way such as loss of the phytol side-chain and removal of Mg.  The typical olive-green colour of a fresh cowpat suggests there’s a lot of phaeo material there.

In some circumstances, however, chlorophyll derivatives penetrate the gut barrier into the bloodstream and in rare cases this can turn serious.

Dietary chlorophyll getting to the skin can be bad for albino animals, because the light absorbed by the pigment will trigger free radical formation which in turn can cause unpleasant skin lesions.

Occasionally shellfish that feed on plankton can accumulate high levels of pyro-derivatives of chlorophyll.  This explains why, in Japan, it is said that excessive consumption of abalone may cause your ears to fall off!  The reason is that these pigments accumulate in the skin and the light striking the top of the head can cause such severe lesions that the junction with the ear is eaten away.

On a global scale the fate of an awful lot of chlorophyll is to pass through an animal.  In some ecosystems as much as 70% of plant biomass is disposed of this way.  This has interesting ecological and economic implications.

Consider the silkworm, which is traditionally fed on mulberry leaves.  Silkworm faeces are a concentrated source of chlorophyll (I’ve never seen this in real life, but I imagine the dark deposits in the picture are the droppings).  Until intensive silk production moved over to artificial diets, chlorophyll was a valuable by-product of the industry, supplying much of the world’s needs for chlorophyll as a food colour, breath freshener and surgical adhesive.

A large proportion of global chlorophyll is found in the oceans.  A rain of chlorophyll has been constantly falling to the ocean bed throughout geological time.  Much of it has been through the guts of animals in the food chain.

Many planktonic animals are transparent and, when they are stuffed with planktonic chlorophylls, they have to adopt special measures to avoid the fate of albinos or Japanese ears.  In some species the wall of the gut is dark-coloured, making it opaque.

Others, such as the brine shrimp Calanus, avoid the light by undertaking a daily vertical migration in the water-column.  If you shine a light on these creatures after they have fed, you can make the unfortunate beasts pop.

The geological ocean chlorophyll rain is thought to be the origin of the distinctive porphyrins found in crude oils and bitumens.  These appear to be chlorophyll derivatives in which the central Mg atom has been replaced by vanadium or nickel during fossilisation.

Incidentally, Thomas Gold is one scientist who famously dissents from this mainstream view of how oil formed.  I don’t have an opinion on the rights and wrongs of his case, but it’s quite interesting to read his story.  Inevitably the creationists have got hold of this, but I don’t want to go there either.  Read and make your own mind up.

Moving back to less controversial subjects, ingested chlorophyll in the marine environment also plays a role in the bioluminescence of certain planktonic and krill species.  In dinoflagellates and euphausids, tetrapyrroles evidently derived from chlorophylls by ring-opening are substrates for the light-emitting enzyme luciferase.

So the superficially unsavoury subject of guts and faeces turns out to lead in many unexpected directions, including global energy sources, creationism and the beauty of photobiology.

Urine, like dung, reports on what goes on in the body.  In particular, it represents the excess nitrogen from dietary and metabolic sources.  As described here, when animals (and people) respire amino acids rather than building them into new proteins, ammonia is released and excreted.

Ammonia is the odour of affluence. People of the disadvantaged nations struggle to obtain calories and have to consume (and egest) large amounts of fibrous nutrient-poor bulk to meet even basic needs. By contrast, the appetite of the rich countries for energy is so avid and indiscriminate that people, animals and crops are plundering proteins for carbon skeletons and inundating the environment with inorganic nitrogen.

Which is why a sensitive nose can evaluate economic circumstances: to put it bluntly, poor countries smell of faeces, affluent countries of urine.

Aspects of this story are mentioned here:

H Thomas, C M Smart (1993) Crops that stay green. Annals of Applied Biology 123: 193-219