Diagrams that make me cry, part LargeNumber

I was calmly blogging about real content, of course procrastinating simultaneously by writing pieces of stuff for work, as well as planning on possibly contemplating actually doing the readings for tomorrow's paleontology class. In the intro chapter titled "Fossils and Evolution", we get shown the following figure as The Taxonomic System, with a mention in passing the there have been some minor adjustments in the past, such as Three Domains, etc. Of course, such trivial taxonomic nitpicking is apparently of no use to paleontology students, so we'll use the horribly outdated Whittaker 1963 classification which should never be seen outside history of science lectures...

Aaaaaaaaaaah! Gotta love the 3:2 vertebrate:invert ratio too. Apparently bryophytes and 'pteridophytes' don't actually exist either. My own kingdom makes me weep. Also, for personal sanity, ignore the "Protoctista". That's just Margulis trying to feel special. And somehow succeeding outside her own field. (Levin 1999 Ancient Invertebrates and Their Living Relatives. Prentice Hall, NJ)

'Oh but the textbook's from 1999, cut 'em some slack with the volatile ever-changing taxonomy mess!' If they had used the Woese tree, which I have other personal issues with, I'd be fine with it. Of course, Woese tree in 2010 is a bit irritating, but I can still live with that. But...what truly adds insult to the injury, and rubs various salts even deeper into the bleeding wounds of my inner soul – THAT FUCKING PIE CHART!

"Proportions of members of each kingdom living today"

Hang on, gonna go break some furniture with energetic *headdesk* maneuvers. And my forehead with epic *facepalming*. BRB.

...ok, back. Lab benches are quite sturdy, it turns out. I'll just let Star Trek and internet memes take care of this:

Source: The Internets. All of them.

And they teach this as an uncontroversial, neutral fact. When, in fact, reality looks more like this:

Proportions of total marine biomass and abundance occupied by the only noticeable taxonomic groupings. Also, anyone who replaces "eukaryotes" with "protists" must be pretty freaking awesome. And/or actually understand biodiversity. (Suttle 2007 Nature Rev Microbiol)

I don't mean to bash the textbook itself. Aside from the little taxonomical issue there, the rest of the book seems quite interesting and perhaps a great source for paleontology (not being of that field, I have little idea). It just bothers me when something so cheap and simple to fix is left ignored and perpetrated on and on as students fail to learn any better, and teach what the learned, and further students learn that, and so on, ad infinitum, until we're left wondering why modern anthropology graduates seem to think evolutionary biology progressed little since Darwin's time. It's kind of annoying. And detrimental to efficient progress in all relevant fields. Not even asking for a new section in the book; just fix what's already there!


Ok, my blogging spirit is back now. Time to write up actual posts, relying on the creative writing juices (if any) unlocked by the power of RANT.

Taxonomic tidbit: parabasalids and strippers

Sometimes the taxonomist's character lies concealed in the etymology of a new taxon name:

"The arrangement of the long cilia, clothing the body, reminded him of the nymphs in a recent spectacular drama, in which they appeared with their nakedness barely concealed by long cords suspended from the shoulders, and this arrangement has suggested the name applied to the parasite." Leidy 1877 Proc Acad Nat Sci Philadelphia (h/t PJK)

So yes, Trichonympha (third from left in the blog header), reminded some proper Victorian scientist of his latest stripper experience. And this is why it sometimes pays to read the original taxonomic descriptions.

Also, apparently it wasn't too weird for the author to refer to himself in third person back then...

Adorable apusomonads

Behold, purveyors of tiny soil flagellates: today, Santa brings you not one, but two whole species of Apusomonas. In fact, both described species of this, poor neglected genus. That's right, I've seen 'em all*, and after this post, you will too.

*I'm sure there's plenty more out there who've yet to encounter the microscope. Or be paid any attention to if seen. In fact, these may in fact be new species for all I know. They do fit their respective described ones quite nicely though, I think.

Apusomonas is a member of the Apusomonads, a group that includes Apusomonas, Amastigomonas, then Thecamonas, etc (as of Cavalier-Smith & Chao 2010 Protist) and, according to David Patterson (presumably) at Micro*scope, Etceterix etcetera (noticed by Opisthokont). Apusomonads seem to lean towards branching as sister to opisthokonts. They make their living by nibbling on bacteria, which they crawl over and ingest at their posterior ventral surface. Apusomonads are fascinating from both morphological and evolutionary perspectives, and perhaps if you prod Opisthokont persistently enough, he'll eventually dust off his blog and give these adorable creatures their deserved publicity.

For now, enjoy their strange and amusing mode of motility. By the way, the flagellar basal bodies are located at the kink in the proboscis, not within the cell body proper as in normal eukaryotes. Considering there's a strong tendency for the flagellar basal bodies to be fairly closely associated with nucleus among normal, non ass-tailed (opisthokont) eukaryotes, this is quite odd.

A.proboscidea Type species. First described in 1922.

A.australiensis
Differs from A.proboscidea in having a bit of a kink on the left side of its body. (it's crawling on the coverglass here, so it's upside down/ventral side up). Seems to have only been reported in Australia thus far. Now we know it lives in North America too (or some sort of new species, but I doubt it).

A.proboscidea (left) and A.australiensis (right) from their respective Micro*scope pages:

Want to find your own? Grab some soil, put in a dish and fill with some water. Let it stand for a couple of days, and the apusomonads should crawl out of their cysts. I placed coverslips on the surface, which tends to attract benthic-y crawly things. After about 3 days, the coverslips were transferred to the slide, and there was about one apusomonad per cover slip (n=2, heh). Careful though: they're pretty small – around 10µm. A.australiensis is slightly bigger, at least of my two specimens. Good luck!

Anoxic microforay Part II: Everything looks like Bodo

To the untrained eye, all tiny heteroflagellates look the same. To the slightly trained eye, all tiny heteroflagellates look like Bodo.

Anyway, here's a continuation of the smelly marine anoxic sludge microforay I should've finished over a month ago. Taking a break from the much too long Sunday Protist post...

There were lots of bodonids (kinetoplastids, see phylogeny in this post). A lot. Plenty of other excavates around too.

They tend to move about by twisting around their anterior-posterior axis with the anterior flagellum sticking in front, the posterior often wrapping around the body as it trails behind.

Free-living bodonids are quite common and diverse. Also quite understudied, as they don't cause disease. This makes them kind of annoying, as there's so many of them and so little to say. They do have interesting mitochondrial genomes, constituting the kinetoplasts, the group's namesake.

This next thing is another excavate. It reminds me of Carpediemonas (a basal fornicate, near diplomonads et al.), but I'm not entirely sure.

Chilomastix-y thing? Can't tell if there's supposed to be more flagella there...

Unidentifiable mess, but there appears to be a peculiar ridge or line of vesicles or something:

Presumably another bodonid. Wasn't moving quite like the others though...

Trigonomonas or something like it. Hard to catch the bugger in its distinctive pose.

Heteroloboseans! They showed some dramatic eruptive pseudopodial motion; will put up a video once I figure out how to. Though I can't currently rule out their being amoebozoans with eruptive pseudopodia (there are some). The human eye isn't particularly great at distinguishing apart amoeboid things.

Another interesting excavate with a very obvious oral groove. It apparently noticed being noticed, and immediately swam away into a pile of debris, and sneered at me from there. That bastard. The second image shows it from its side. Hard to ID anyway... perhaps some Enteromonad-y thing? Hard to tell how many flagella this one has...

A few more shots of that weird flagellate I mentioned earlier. I think it has four flagella now. Who knows how many tomorrow shall bring...

A heterotrophic euglenid, perhaps Petalomonas sp; it feels its way around with its thick anterior flagellum as it crawls around. The posterior flagellum remains inside the flagellar pocket. The cytostome is also visible inside the cell as the wedge-looking thing.

*shrug* Could be some cercozoany thing. Or maybe not.

Bacterial jungle the above critters seem to thrive in:

Next installment: Misc. non-excavate stuff.

Oh, on the topic of excavates, a jakobid from a freshwater (pond) sample. At least I think it is – looks like Reclinomonas americana. Do they form small stalked colonies like that?