Saturday, March 13, 2010

Holocene extincion pt. 1


An extinction in biology is the end of an organism or group of taxa. Taxonomy, the hierarchy of biological classification, divides all life into eight major taxonomic ranks (taxa), which are (in descending order) domain – kingdom – phylym – class – order – family – genus – species. An example of this would be the species Homo sapiens. A full taxonomy will follow.

<- British paleontologist Richard Owen and the skeleton of a South Island Giant Moa, (Dinornis giganteus) a fligthless bird once native to New Zeeland. Little does Richard know, this species was slain to extinction just 600 years ago, by maori warriors.


A domain or Superkingdom (alias Superregnum, also: Empire) is the highest taxonomic rank of organisms. All life is divided into three Domains: Archae, Bacteria and Eukarya. Of these three, the first two can be summarized as single-celled micro-organisms commonly lacking a cell nucleus. Neither the recently discovered Archae (formerly a sub-division of Bacteria known as Archaebacteria) or the familiar Bacteria constitute complicated multicellular organisms. That is their Empires branch into strange Kingdoms like the Euryarcheota, and not for example Plantae, or Animalia. To get a general idea of what these guys are up to, have a glance at the Archae Haloquadratum walsbyi, of the afore-mentioned Euryarcheota Kingdom. Forming strange geometrical shapes and then floating in the water or more notoriously, freeriding on more complicated multi-cellular organisms.
Haloquadratum walsbyi under an electron microscope. ->

It is of note that there is no domain called Virus, since the virus is a self-replicating contagious agent, a combination of organic molecules, rather than life. Scientists have wittily summarized this condition as pseudo-life. Problem is, viruses are not a combination of, nor do they ever constitute a cell. Which as far as taxonomy is concerned, is a fundamental requirement for life. Thus an entire alternative taxonomy has been established, based on factors like “host organism”, further illustrating that all life, even pseudo-life, needs cells to exist – the virus then exist on account of someone else's cells.

It is of no note and little consequence to the Holocene extinction that viruses are not the only borderline life on planet Earth. There are also viroids, prions and satellites, all of which are even smaller and less lifelike than viruses.

Before the discovery of the Archae, Bacteria and Archae were grouped together as Prokaryotes. As opposed to Eukaryotes, the Domain to which the Kingdom of Animalia, and thus the species Homo sapiens belongs. This division was based on the Prokaryotes (etymology: “before the nucleus”) not having a cell nucleus and the Eukaryotes (“true nucleus”) indeed having one. Things were simpler back then. Prokaryotes were the ancient proto-life, swarming bacteria, horror of the microbiological level, while Eukaryotes were the juicy bits that make up plants and animals. Although the confusing genetical adventure that is Archae is not at all relevant to the Holocene extinction, I suggest we still divide the Prokayotes into Archae and Bacteria, for modernity's sake.
It is, after all, what they do in America.


And because we have decided to go down this route, we get The Six Kingdoms: Animalia, Plantae, Fungi, Protista, Archae and Bacteria. The Domain of Eukaryotes divides into Animalia, Plantae, Fungi and Protista (Protista being a kind Eukaryote counterpart to Bacteria – they do not form complicated multi-cellular organisms, instead opting to get in on as single-celled algae, slime molds, and amoeba – while at the same time remaining decidedly Eukaryote. Meaning they are generally more normal than Prokaryotes.) The rest of the three Eukaryote Kingdoms – Animalia, Plantae and Fungi – we are already familiar with.

For Bacteria and Archae, Kingdoms are the same as Domains. So yestinia pestis, the bacteria responsible for the bubonic plague gets classified as: Domain – bacteria; Kingdom – bacteria. As a side-note I would like to say that apparently this is not always the case since some biologists want things to be more complicated, and have thus devised the Kingdom of eubacteria. ZA/UM does not look kindly upon this development.

Speaking of ZA/UM, it is our intent to bring our readership the utmost level of elitism in any field of human endeavor, ever striving towards an intimidatingly snobist image, and thus it is my duty to inform you that the entire concept of division into taxa is in fact a misleading idea from the 19th century, one that has very little to do with the actual branching of the tree of life. The complexity of which does not lend itself well to hierarchical constructions such as the taxonomic system. One is left with the impression that taxonomy is a remnant of pre-darwinist notions of ascending order. From worms to to God, so to say. (Also, note the feudal images of Kingdoms and Empires.) The only reason we will continue down this path is because the alternative is Bringing Out The Yggdrasill. You do not want me to Bring Out The Yggdrasill, because in doing so we would leave the safe confines of taxonomy for the head-spinning wilderness of its rival – cladistics. A clade, you see, is what we call an individual branch on the tree of life.

However, let it be noted that ZA/UM is big up for cladistics. In fact Jüri Saks spends his free time surfing the tree of life for those few species of Actinobacteria he has not yet rendered into psychographic images.

<-The Yggdrasill, a highly resolved, automatically created tree of life based on completely sequenced genomes.

Meanwhile, at you backwater hick-town taxonomy conference, Homo sapiens is: Domain – Eukaryote; Kingdom – Animalia. Animals are both eukaryotic and organisms meaning almost all of them have multi-cellularity composed into organs. These organs are layed out within a fixed body plan – than is, metamorphosis aside, their physical presence remains within certain frames until they expire. They are also motile, moving spontaneously and independently. Last but not least, animals ingest other organisms for sustenance instead of creating their own food in the fashion of say bacteria.

Animals appeared during the Cambrian explosion, 530 million years ago. And so they are a rather recent development in the circa 4500 million year history of the planet. Why evolution suddenly accelerated, replacing stationary colonies of loosely related cells called Ediacara biota – imagine a blob on the sea floor – with maginificent Waptia, Marella, Opabinia, remains as enigmatic as when Charles Darwin first considered the Cambrian explosion as a major counter-argument to his theories.


Homo sapiens belongs to the Chordate sub-phylym Vertebrate. Phylym is a loose taxonomical rank, no generally accepted definition exists. It is where we leave the biochemical level of the Domains and the somewhat metaphysical plane of Kingdoms, beginning, for the first time, to actually describe our freshly established animal in terms of appearance. For which the scientific term would be “body plan”.

Setting aside the various plant, fungi, and bacterial Phyla (yes, that is the plural of Phylym) I give you the golden greats of nature, the most famous fundamental layouts of animal organisms: Molluscs, Sponges, Cnidaria (medusae, polyps and other radially symmetrical aquatic organisms) Flatworms, Roundworms, Annelids (earthworms, leaches and the like), Echinoderms (starfish and sea cucumbers) Anthropods, (Invertibrates with exosceletons to wich the Class of Insects belongs) and finally Chordates.

To put it bluntly, Chordates are built around flexible rods. Whereas Molluscs for example are free-flowing muscles, Chordates have a rod in the center, known as the notochord, with organs built around it. All Chordates have a notochord present in their embryonal state – Jack and Jill included. However, only one sub-phylym of Chordates developes this into an inflexible spinal column. This Sub-Phylym is of course the Vertebrates. Other Chordate Sub-Phyla include the Urochordata, which means Jack and Jill share a phylym with Bluebell tunicates.

Bulebell tunicates -> just one of the many aquatic Animal species that attempts to look like a Plant, although it's almost a Vertebrate.

Very intelligent people will now want to add Craniata (basically Chordates in possession of a cranium or a skull, which by the way succeedes the spinal column) as a Sub-Phylym between Chordata and Vertebrata. Further horrifying Jack and Jill with a shared ancestry with the hagfish. Other, even more intelligent people, will then point out that Craniata is more of a clade than a Sub-Phylym. The cladists will then perform a fist-pump.


Because eight ranks is quite a lot, I like to mentally split them in two between Phylym and Class. The first three – Domain, Kingdom and Phylym – are the Lovecraftian ranks. This is where life seems alien, ancient, a questionable experiment in complexity. Chaos reigns, here be monsters, cosmic horror. Even familiar elements like the spinal chord present the viewer with unpleasant surprises, belonging in some proto-form to the Sea Lilly as well as oneself.

<- Chaos reigns beautiful: Salmonella enterica, the bacterial cause of the Salmonelellosis disease

Beginning with Class, the overwhelming creativeness of nature gets narrowed down into more acceptable forms. These are the five Familiar ranks – Class, Order, Family, Genus and Species. (Notice the absence of the word “phyla” - surely most awful of the ranks.)

The Familiar ranks start with Classes. Classes include Insects (of the Anthoropod phylym) Arachnids (of a sub-phylum of the Anthoropods called Chelicerata, establishing again that although spiders, crabs, scorpions and other Arachnids are indeed Invertibrates, they are not Insects) and, of interest to us, the five classes of Vertibrates: Fish, Amphibians, Reptiles, Birds and Mammals. One might notice having a spinal colum makes one both aesthetically pleasing and able to dominate other Phyla in your local food chain. The latter is because the sceleton is the optimal mechanism for both carrying body mass on land and allowing that mass to move at great speed. Why the Diplodocus is an awe-inspiring masterpiece of bone and the Amur tiger an orange-striped demon, while the seapig is an abomination of nature, has something to do with repulsion and psychology.

Diplodocus carnegii skeleton on temprorary display in Berlin Hauptbahnhoff -> For a full side-view of the 53 metre back-bone of the longest animal to ever have existed, conduct your own search. Photos of it are dimensionally incompatible with blogspot tools - that is how long it is. And no, I am not kidding, I tried for 2 hours.

In one way or another, the super-predator slots for the last 230 million years have been taken up by vertebrate ranks. Even a catastrophic meteorite impact wiping out 95% of life on the planet couldn't help the ill-equipped Crustacians back on top. This is all-too-familiar territory, but yes, it was the mammals who took over.

In addition to milk glands on the females, all mammals have neocortexes. These are situated in the mammal's head as part of its brain and in the long run have allowed one mammalian species to send an artificial object with pictures of itself engraved on a gold plate, out of our solar system. Giving a clear signal to any extraterrestrial life, that this is the metal we would like to be presented with, in exchange for protection.

Concerning sub-classes of mammals, Homo sapiens belongs to the Theria, that is we give birth to our young without using a shelled egg. Further classification places humans as Eutherians – placental mammals – while Metatherians – the marsupials – would have been another way to go about it.


A bit deeper into the Familiar ranks, Order is where we are no longer reminded of life's eldritch abominations. In fact, things get so close to home, Mother Nature begins to display a sense of humor. As illustrated by her invention of ischial callosities, for example.

Aside from the Order of Primates, an example of another Order of the mammalian Class would be the Carnivores. Or the Chiroptera, also known as Bats. Also of note: the Lepidoptera (butterflies and moths) and Diptera (flies and mosquitos) of the Class of Holometabolistic insects. By now one also gets the sense that taxonomic terms are not at all unimpressive.

The Order of Primates (latin for “prime”, “first rank”) consists of assorted small dudes (lemurs, lorisids, galagos and tarsiers) along with monkeys and apes. The small dudes being the earlier branch of Prosimans, while monkeys along with apes constitute the latter Simians. This has nothing to do with the taxonomic classification of Homo sapiens, though, as these are not Sub-Orders of the Order of Primates. Instead I believe Prosimian and Simian are cladistic terms, and here – possibly not for the first time – I might be wrong.

Instead, Homo sapiens belongs to the Sub-Order of Primates known as Haplorrhini, or dry-nosed primates. Aside from other more confusing biological jargon, this means us apes and monkeys (and surprisingly tarsiers) have a wider range of facial expressions.

<- Check out the wide range of facial expressions on the Lesser Spectral Tarsier. Other traits include: upper lip, dry nose, psionic capacity.

Molecular clock studies suggest that primates might have existed as long as 85 million years ago. This means we survived the Cretaceous-Tertiary Extinction Event, the magna carta in this part of town. This event I have already alluded to, in conjunction to the rise of mammals.


Perhaps this would be a good time to disclose that there never seem to be any “hard rules” a taxonomist “needs to follow” in establishing the Class or Family or even Order of any given Species, as it's generally accepted that a Family is what a taxonomist wants it to be. Much like art is what the artist does.

So an example of a Family is as close as you can get to its definition. Ursidae, Felidae and Canidae - the three Families of the Order of Carnivores - will have to suffice for now. But do believe me, we will go into further detail on this some time later.

The Family of Hominidae of the Order of Primates consists of: chimpanzees, gorillaz, humans and orangutans. Hominids, also known as “great apes” thereafter lose the orangutans and form the sub-family of hominae. Orangutans go to their own lonely little sub-family called Ponginae, the five other genera of which have long since become extinct. Seeing as of the two species of the orangutan genus, one is endangered and the other is critically endangered, I do not predict a future of space conquest for this group of animals.


Genus and Species make up the last two ranks. These two and always in that order – first Genus then Species – composit the scientific name of the Species. The Genus Homo is estimated to be about 2.5 million years old, with all other species of the Genus extinct.
24.000 years ago Homo neanderthalensis did not make it into the Neolithic revolution, 12.000 years ago Homo floresiensis almost did, becoming the first and last species of the Genus Homo to have vanished during the Holocene extinction.


There is a useful analogy for understanding the scale and timeline of the processes that have led to the advent of Homo sapiens. It is called the “geological clock” and it requires you to imagine the 4550 million year history of the Earth (I tend do not use billions because it's easy to lose grasp of them) as a standard 12-hour clock face. Right now, it's 12 o´ clock in the noon, the sun is shining.

At midnight the Earth was formed, about a minute later (4527 Ma) the Moon came along. At 01:45 the period known as Late Heavy Bombardment came to an end and almost simultanously Prokaryotes appeared. For almost as long as any other form of life has existed on this planet, Prokaryotes have been the only form. Eukaryotes come along as late as 06:30.

Meanwhile, at 03:00 Prokaryotes have started photosynthesis as a new way of gaining energy. Previously these ancient bacteria just floated in the water, alowing sulphur and corpses of other bacteria to seep in through their membranes. At exactly 06:00 and not coincidentally just a little before the appearance of the Eukaryotes, these photosynthesizing Bacteria and Archae have created the greatest natural catastrophy in the history of the planet. Combining elements of CO2 required for photosynthesis into O2, its waste product, they have created a cosmically rare, extremely flammable and volotile gas called Oxygen. Because photosynthesis has been going on for well over a 1000 million years, now a significant part of the atmosphere has been turned into this deadly gas.

It is more than plausable that these new challenges give rise to the Eukaryotes, as well as to multi-cellular life, one and a half hours after the Eukaryotes, at 08:00. (Notice that it's evening already and the first two Eukaryotes have just now come together in sweet harmony.)
At 09:50, Multicellular life produces the first Animals. These are Ediacara biota, the afore-mentioned enigmatic blobs. Little is known about the Ediacara. They were stationary, and apparantly quite large, and at approximately 10:05 they dissappeared in an unprecedented upsurge of speciation (development of species) known as the Cambrian explosion. It is during this period that Earth's first true predators appeared. In addition to its natural weapons, a predator functions on the premise of being faster (more mobile) than its prey, or compared to the Ediacara - capable of movement to begin with. Movement requires energy and the main source of this energy in the case of complicated life-forms is a result of the ecological catastrophy brought into being by early Prokaryote bacteria - Oxygen. It is during the Cambrian explosion that life begins to harness this volotile gas, turning Oxygen into prevously unimaginable reserves of energy. In other words: breathing. Think of it as having an internal combustion reactor. It is no surprise radical speciation coincides with the advent of aerobial organisms.
Waptia fieldensis -> just one of the many Cambrian predator fossils preserved in the Burgess shale, in Canada. The Burgess shale is the world's most celebrated fossil field, the Mecca of anthropologists

Five minutes later, at 10:10 plants are the first life to claim Earth's unexplored land-masses as their domain. Although Animals - in the form of of the Anthropod Phylym - are already present on land, it's another five minutes later that their Kingdom develops an optimal body-plan for moving in this new environment. At 10:15 the Chordate Phylym, and soon after, its Sub-Phylym the Vertebrates, take over from the slow-moving Anthropods. Giant land Anthropod fossiles dissappear from geological records, hunted to extinction.

Soon after the Tetrapoda (four-legged) Super-Class develops under the Vertebrate Phylym. At 11:20 this Super-Class branches into the Class of Amniotes, Tetrapod Vertebrates with terrestrially adapted eggs. It is from this common ancestor that both Reptiles and Mammals (first Reptiles, then Mammals) are to descend in the following minutes.

At 11:25, a mere 35 minutes ago, the Reptile Super-Order of Dinosaurs is the first of the Amniotes to take over. They fill all existing super-predator slots, covering the entire ecosphere, just to vanish during the Crataceous-Tertiary Extinction Event. This is approximately 5 minutes ago. They leave behind a flock of birds and a hand-full of reptiles. None of which is of the Super-Order of Dinosaurs - that's done with, will never return, good-bye.

During the freshly ended reign of Dinosaurs, small Mammals have been devoloping in the background. Among this Class of Mammals is the Order of the Primates. Although during the last remaining 5 minutes no specific Order of The Class of Mammals goes nearly as unchallenged as the Dinosaur Super-Order, something is about to happen to a tiny Family in the Primate Order. That Family is the Homonidae, and that something takes place no more than 2.5 million years ago, a mere millisecond. It is its Genus - Homo. To the paleonthologist, there are stone tools in the sediment already. An instant later, 200.000 years ago, the Homo Sapiens speciates.

<- The geological spiral, a rival of the geological clock. Although infinitely more confusing, the spiral has been known to look rather handsome.


12.000 years ago "Würm", the last Ice Age ends, Homo Sapiens begins the Neolithic revolution, turning from hunter-gatherers into Civilizations.

Another turning is the Pleistocene into the Holocene. This is a turning of geological epochs. Lodged between these two, is the Quarternary Extinction Event. (The Quarternary being the current geological period. It is divided into the epochs of Pleistocene and Holocene.) The Quarternary Extinction Event sparks off the Holocene Extinction, and is thus believed to be a part of it.

The advent of Civilization is not a coincidence to the Holocene extinction, it is the root of it, the Holocene extinction is an anthropogenic extinction. It is also an ungoing extinction and has been so for the last 12.000 years.

It is a result of an unprecedented devolopment in ecological relations - the total domination of a single species. A bat of a lash ago, after the next major revolution - the Industrial revolution - Homo Sapiens has effectively left the food-chain.


This series of articles will take a closer look at the species that are already lost, beginning with the ones who disappeared before the dawn of history, in the Quarternary Extinction event (colloquially named "Pleistocene megafauna"). And although stricktly speaking, these are all "late extinctions", we will then move on to even even later extinctions. These are the ones taking place in the last 2000 years.

We will mostly be looking at large mammals and birds. That is because large and specialized species are always the first to go. And in doing so - in addition to merely describing an extinct species - we will now hopefully understand the significance of its taxonomy. The significance of an extinct Species of the Genus Homo - Homo Floresiensis - or the radical decline of the Carnivore Order of the Class Mammal.

This will be a journey of epochal proportions. And in its undertaking, we will show little pity to the Animal Kingdom, we will feel no guilt. Because the Animal Kingdom does not deserve either, it is guiltless and without pity. Disrespect, as well as reverance, falls on the death years of the Animal Kingdom, it respects nothing, admires no one.

All these things - pity, guilt, disrespect or reverance, your sense of loss - are its demise. At their first appearance, the one thing the Animal Kingdom ever needed is lost. The Animal Kingdom does not need you to conserve it, it needs you to fear it.




  1. Mine putsi kui suur ja ilus see on! Kindlasti suurem kui elu, võib-olla ka suurem kui Anarhia aga ma pole kindel.

    Autoril muide ununes kindlasti asjakohane Wall of text tag.

  2. Eepiline! Robert, sa oled GEENIUS!

  3. Tunnen end valgustatuna.

  4. Tänud komplimentide eest, aga üks küsimus: kas keegi päriselt läbi ka luges?

    Peab lugema, muidu ei saa uut väljasurnud inimliiki, lennuvõimetut Kuuba hiidöökulli, skimitar-kassi ja kabjalist lihasööjat, kelle lähim sugulane oli sinivaal.

  5. It's a secret banner and I'm seeing it!

  6. I totally read it. I'm quite sure some others did as well, they just ain't got those typin' kinds of hands.

  7. WOW! Bravissimo!

    PS - Teie blogist on taas saamas kõva asi. Palun (palun!) tehkem nüüd nii, et siia otsa ei potsata mingi põrgu radadele sattunud tsirkulaarintervjuu vaid hoopis veel palju kõva asja väärilisi artikleid.

  8. Fascinating article if you want my opinion.

  9. This is one of the best articles I ever read.

    Good job.

  10. Thanks, much appreciated. It wasn't exactly a breeze to write, you know.