Itsy bitsy critters in an itty bitty poo

Sometime in the early 1990s, a textbook publisher flew me to Manhattan with a bunch of other troublemaker-type bio teachers – I was the only grad student – to consult about their upcoming release. We’d read the manuscript and made our separate recommendations and for whatever reason, the publisher had the budget and inclination to have us all get together and power-talk. This was intended to be a text that distinguished itself from the encyclopedic, boring, and rather conceptually-fossilized standard ones. That aim is tricky for a publisher – they have to appeal to academic instructors’ characteristic agonized blend of wanting to be both up-to-date and not too weird. Therefore the editor wanted our take on some of the most obvious breaks between what all the texts said and what the scientists wearily taught via saying “the text isn’t really correct here,” which in the early 1990s, had piled up pretty high.

One of their concerns was the 5-Kingdom model of living diversity: good ol’ Monera, Protista, Fungi, Animalia, and Plantae, illustrated above, as some readers may recall. No one was teaching this in the classrooms any more except for those who droned straight from the same book every year and wouldn’t be ordering anything new anyway. The author wanted this text to reflect what scientific thought was actually doing, to abandon Monera and treat its former members as two fully-different Kingdoms, Archaeobacteria and Eubacteria. The editors asked us, “Well? Five Kingdoms or six?”

“Six,” we all said simultaneously, and that would be that, except that we weren’t done. Divvying up the prokaryotes was easy and obvious compared to what on earth should be done with that unbelievable grab-bag, Protista. Here’s the thing: if you apply the same cellular comparison-and-diversity logic that defined the other four Kingdoms, and which properly applied had just now split one of them into two to our mutual acclaim, then the critters currently dubbed Protista would yield ten – no, twentymaybe more full-on Kingdoms. Yes, you read that right. The biological diversity of Protista turns all the rest of known life, our proud little three multicellular Kingdoms included, into footnotes.

Serves them right for bringing in a bunch of glittery-eyed mavericks for consultation. For 20+ years ago, that was going a little far for the publisher to feel comfortable with, to say the least, but we knew what was coming. The “Kingdoms” naming convention was doomed. The biggest distinction, prokaryotic/eukaryotic, needed a real name – it would arrive soon, Domain – and Protista as a term was going to have to be patted on the head and sent to that old taxonomic scrap heap in the sky. That latter remains a work in progress, but it is now in the same state that Monera was at that meeting. No biologist takes it seriously; we still have to “un-teach” it every time, gritting our teeth.

To learn Protista back then and maybe still now, depending on the class, here’s what you would have seen & memorized, along with a pack of details for each:

Their features would also strike you as curiously arbitrary and hard to learn systematically, compared to the other groups. The structures emphasized per group don’t track to homological associations and understandable evolutionary changes. Some of them are so bizarre they seem purely alien, like the diatoms manufacturing glass from sand to make their cell walls, or the way paramecia divide up their chromosomes during reproduction, which has nothing to do with meiosis at all. Making people memorize “this one has a flagellum!” just wasn’t cutting it.

Linnaeus’ original classification included two supergroups, or Kingdoms, Plantae and Animalia. The former was soon sensibly divided into Plantae and Fungi, for three Kingdoms. In the mid-19th century, people realized the environment was literally crawling with microbes and the whole concept of Kingdoms had to be scaled smaller to add them. Protists were named as a group by Ernst Haeckel, and they merited special attention because people immediately spotted that these pond creepy-crawlies are suspiciously similar to the cells in bodies, only not stuck together, and you can count this with the discovery of the ovum in the major observational components that led to cell theory. In the 1890s, discovering malaria to be caused by Plasmodium falciparum elevated protist biology into serious, globally-significant business, just as the plague’s little agent Yersinia pestis did for bacteria.

Here’s what we were teaching a little while later, say around 2000. When you break it down by cells, the six-Kingdom level of classification doesn’t seem too bad.

  • The Prokarya Domain includes all the prokaryotes
    • Archaeobacteria: sulfur metabolism (weirdos)
    • Eubacteria: glucose metabolism (this is the biggie, all the bacteria & blue-green algae)
  • The Eukarya Domain includes all the eukaryotes
    • Protista (includes a multitude of cell types and clustering)
    • Fungi (multi-cellular) – chitinous cell walls, can’t photosynthesize
    • Animalia (multi-cellular) – no cell walls, can’t photosynthesize
    • Plantae (multi-cellular) – cellulose cell walls, photosynthesizes

You can see the problem, though, right? The multicellular Kingdoms don’t form a single group that diverged from a common ancestor with Protista, but rather three fairly independent bunches, each corresponding to a single protistan group in terms of cell types (not shown). To the casual, i.e. sensible observer, it would seem as if these three should be subsets of Protista, just like the other protist groups , not great big Kingdoms. Or if that’s too much to swallow (what? Animals? Us, not a Kingdom? Shock, coronary, no, never), then the rest of Protista’s diversity oughtta be upgraded to a bunch of Kingdoms, as they definitely rate it based on the criteria of cell type and function (also shock, what, protists, as good as us?).

The various teaching devices to define these three were showing themselves to be ineffective at this level too. “Plant cells have cell walls!” well OK, so do the protists associated with them (the green algae), and the exact same kind. “Fungal cells have cell walls, only made of chitin!” yeah OK, so do the protists associated with them (slime molds), and the exact same kind.” Lots of protists photosynthesize in a dizzying assortment of ways. And as for multicellularity, suspiciously single/colonial cell activities lurk within the nominally multicellular Kingdoms (sponges in Animalia, e.g., and yeasts in Fungi … or our very own immune cells, and sperm cells, for that matter) and there are suspiciously tissue-organized groups in Protista (e.g. brown algae), all blowing raspberries loud and clear.

So what’s wrong with calling Protista a thing? Naming is supposed to reflect phylogeny, both coming and going. The first means a group (“clade”) needs to be justified by a common origin; the second means that you can’t pull out some piece nested in there and call it an equivalent group; you have to subdivide it instead.

Let’s check it out, coming and going. The first concerns the origin question. Establishing the endosymbiotic relationship with mitochondria is no joke – did it happen once, or more than once? Was the nuclear/outer membranes structure formed by making the inner one, or the outer one? Or different ways at different times? And how about the origin of linear, paired chromosomes from the ancestral single, circular one?

These probably didn’t occur all at once, but current thinking is that the whole sequence of events, in whatever order, happened only once, such that Eukarya does in fact constitute an evolutionary group. Closer looks at protists might call it into question or demand significant subdivision, but that’s where we are at the moment, so OK. Both of the following diagrams properly treat the “base” as unresolved to reflect the open question.

or similarly if not identical,


Now for the “going,” or diversification. As a minor point, lookit all those names in each color-group, in either diagram. They represent insanely different ways for cells to be organized, to propagate, and to interact with the environment, beyond the wildest dreams of science fiction authors. This is practically a whole universe of life which, educationally speaking, has been relegated to “uh, this one has a flagellum” for way too long. The real questions blow open serious doors about what a body is, how endosymbiotic mitochondria really are, and what chromosomes as structures really do.

But the pattern regarding the three most-familiar Kingdoms’ placement is what matters to my current point. Clearly “multicellular” is a subset of small-p protistan variables. and when you examine where it shows up in this arrangement … then whoa – Houston, we have a problem, and its name is paraphyly.

The simple problem is that you can’t just pick twigs and elevate them into bigger-named groups because you like them, irrespective of evolutionary historical groups. Specifically, that it makes a hash of what to do with everything else. The first phylogeny above shows this perfectly: calling all the yellow-tagged groups a single evolutionary thing is obviously pure ass. Paraphyly is given a name in order that it be something taxonomists do not do.

With that in mind, fortunately, now all that nervous parsing of “semi-colonial, colonial, semi-tissue, real tissue” across the respective protist-animal, protist-fungal, and protist-plant boundaries can be relaxed – there isn”t a real boundary in any of them. It also means admitting that the only reason we privilege animals, plants, and (later) fungi with Kingdom status is because we can see them without technological assistance. Which is if you’ll excuse the expression a piss-poor excuse for scientific induction. You might as well call constellations “star clusters” on that basis.

Why is this perfectly sensible issue so slow to change? Bumping five Kingdoms to six wasn’t so tough.

True, all scientific education is slowed by institutional inertia, especially for basic texts. The publishers don’t want to spook the profs with weird & unfamiliar or to imply “you’re doing it wrong,” and the departments and profs regrettably let the texts lead their curricula a bit too often, or resist doing the work of revising their long-standing syllabi for classes serving as many as a thousand students at once. Add to that the significant delaying factor imposed by the Texas schoolboard, a primary textbook client in the U.S. textbook industry, regarding anything to do with evolution from about 1990 through 2010.

But the real culprit in this case is human exceptionalism. Distinguishing one prokaryote group from another is fine, no skin off our nose. Mess with groups that reduce the one we’re in from special-case status naming, and every hind foot in the room curls its toes.

This is no minor quibble. The same trick has dogged taxonomy throughout its history specifically where we’re concerned. The discipline has mistakenly privileged “Hominidae” as its own family within Primates to make Homo falsely stand out, “Reptilia” as a vertebrate order to make Mammalia falsely stand out, “Invertebrata” as an animal group to make Vertebrata falsely stand out, and now, “Animalia” as a Kingdom to make animals (us) stand out, and in each case, encountered disproportionate resistance to standard, intellectually non-controversial, data-driven correction. (meaning: there is no such thing as a hominid, a reptile, or an invertebrate – yup, still a troublemaker)

Oh hell, now I have to detour … remember, read this thing as nested V’s, shorthand for enclosed boxes.

See? If you name a group Reptilia, it has to include [snakes + crocs + birds] or [turtles + snakes + crocs + birds] or it might as well be synonymous with Amniota and include [mammals + turtles + snakes + crocs + birds]. It simply cannot exclude birds to include only [turtles + snakes + crocs] and reflect evolutionary history.

Same for Protista: if you want to retain it as a Kingdom name, then it might as well be synonymous with Domain Prokarya, and Animalia, Fungi, and Plantae have to remain within it and be downgraded to a lower level than Kingdom. Or similarly, the big color-groups get to be the Kingdoms, and similarly, those “special” three get downgraded. Or if you want to keep the three as Kingdoms, then all those other little names get to be Kingdoms too. All else is blither.

Textbooks are coming along, at last, presenting phylogenies full of teaching moments. But the names are still lagging, until we admit it: we’re protists who practice multicellular behavior. We and the others who do it aren’t one unified group, nor are the ones who don’t.

Next: Why matters


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